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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
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diff --git a/resources/project/SM-7XD5VEsEA2ReW_Gcx0KdVR4E/A3BkjYsewYZv3b_c9MKlO0lijG4p.xml b/resources/project/SM-7XD5VEsEA2ReW_Gcx0KdVR4E/A3BkjYsewYZv3b_c9MKlO0lijG4p.xml
new file mode 100644
index 000000000..48f06a319
--- /dev/null
+++ b/resources/project/SM-7XD5VEsEA2ReW_Gcx0KdVR4E/A3BkjYsewYZv3b_c9MKlO0lijG4p.xml
@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="saveMtpActivationAndExcitationData.m" type="File"/>
\ No newline at end of file
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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
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\ No newline at end of file
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/resources/project/gK_nb01P4_6XSSogizZJn5zmzQQ/m4YW3kyFKhaw2jhfe5pX4koVSF0p.xml b/resources/project/gK_nb01P4_6XSSogizZJn5zmzQQ/m4YW3kyFKhaw2jhfe5pX4koVSF0p.xml
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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="motToTrc" type="File"/>
\ No newline at end of file
diff --git a/resources/project/gK_nb01P4_6XSSogizZJn5zmzQQ/rjqiBcq-Lf6PHOzurJu8wmXPRLcp.xml b/resources/project/gK_nb01P4_6XSSogizZJn5zmzQQ/rjqiBcq-Lf6PHOzurJu8wmXPRLcp.xml
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+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<Info location="MuscleCalculations" type="File"/>
\ No newline at end of file
diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/9ULi2Alw-JmXjkCxz2ppBf5D2nUd.xml b/resources/project/m4YW3kyFKhaw2jhfe5pX4koVSF0/Ge7ijHD-QOCX1Vh_15TrHFqSGPQd.xml
similarity index 100%
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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="makeTimeSeriesTableVec3.m" type="File"/>
\ No newline at end of file
diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/9orjn84dnpAKkkuchjb6ZXb4lYod.xml b/resources/project/m4YW3kyFKhaw2jhfe5pX4koVSF0/IGJLBsn5zyrwrJ0Ri0i1Ko7r_xkd.xml
similarity index 100%
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@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="getCoordinateFromName.m" type="File"/>
\ No newline at end of file
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similarity index 100%
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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similarity index 100%
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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@@ -0,0 +1,2 @@
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diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/T3r09B-NxK1oaHW6j-rPgd2Qj6Ud.xml b/resources/project/m4YW3kyFKhaw2jhfe5pX4koVSF0/hH_1Yj64xFVM9hFUXve2TuYwxLcd.xml
similarity index 100%
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@@ -0,0 +1,2 @@
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diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/WtpDLoJHlDx008KY8cwkBcD2AT8d.xml b/resources/project/o2cKHtbeLCI5dGNR0Lwpzdptr4s/-IEsxSr0pUR0RE2Q2b5wpQX0KkEd.xml
similarity index 100%
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@@ -0,0 +1,2 @@
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\ No newline at end of file
diff --git a/resources/project/gK_nb01P4_6XSSogizZJn5zmzQQ/_2w7KV6EHc1SMHPJ5sv5BJ_TE_4d.xml b/resources/project/o2cKHtbeLCI5dGNR0Lwpzdptr4s/2XppXtEHR0PCZWWNfUwQdRTKlDcd.xml
similarity index 100%
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@@ -0,0 +1,2 @@
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diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/XbzuDmDFV-LdTDKCBgtbIoNIeDAd.xml b/resources/project/o2cKHtbeLCI5dGNR0Lwpzdptr4s/3DhOOe0Tl7hipLJtC66oxocIr9cd.xml
similarity index 100%
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@@ -0,0 +1,2 @@
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+<Info location="makeGpopsValuesAsStruct.m" type="File"/>
\ No newline at end of file
diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/aN6B9nVEXMPwk5nipy2pReqfe9kd.xml b/resources/project/o2cKHtbeLCI5dGNR0Lwpzdptr4s/AxKLxQn_Q5ExtyTFauEpYntfsssd.xml
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@@ -0,0 +1,2 @@
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\ No newline at end of file
diff --git a/resources/project/dYvx6wp33Ts8hX1S_rzdiQ3NP4A/dKRagt73aqMStWRIRrbSi8CTiWEd.xml b/resources/project/o2cKHtbeLCI5dGNR0Lwpzdptr4s/IDetplA4BCvExeTDnnCPfg2MhBwd.xml
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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similarity index 100%
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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similarity index 100%
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@@ -0,0 +1,2 @@
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\ No newline at end of file
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\ No newline at end of file
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similarity index 100%
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index 000000000..7a6326b99
--- /dev/null
+++ b/resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/scEHrBcR_4DaGlInftNFgaoYFTMd.xml
@@ -0,0 +1,6 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info>
+    <Category UUID="FileClassCategory">
+        <Label UUID="design"/>
+    </Category>
+</Info>
\ No newline at end of file
diff --git a/resources/project/_2w7KV6EHc1SMHPJ5sv5BJ_TE_4/8N6cWgm0bCQbFtUjwVpJKMr3DlEp.xml b/resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/scEHrBcR_4DaGlInftNFgaoYFTMp.xml
similarity index 100%
rename from resources/project/_2w7KV6EHc1SMHPJ5sv5BJ_TE_4/8N6cWgm0bCQbFtUjwVpJKMr3DlEp.xml
rename to resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/scEHrBcR_4DaGlInftNFgaoYFTMp.xml
diff --git a/resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/ux2HJV4G7O8gtSZERsaoTt6GWQkd.xml b/resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/ux2HJV4G7O8gtSZERsaoTt6GWQkd.xml
new file mode 100644
index 000000000..a75f7a81b
--- /dev/null
+++ b/resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/ux2HJV4G7O8gtSZERsaoTt6GWQkd.xml
@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info/>
\ No newline at end of file
diff --git a/resources/project/_2w7KV6EHc1SMHPJ5sv5BJ_TE_4/pDfDXpP-F2Cd6B91DGM44psBFJwp.xml b/resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/ux2HJV4G7O8gtSZERsaoTt6GWQkp.xml
similarity index 100%
rename from resources/project/_2w7KV6EHc1SMHPJ5sv5BJ_TE_4/pDfDXpP-F2Cd6B91DGM44psBFJwp.xml
rename to resources/project/tkAoR0wDeR9bDqF10NY7YqXFvL4/ux2HJV4G7O8gtSZERsaoTt6GWQkp.xml
diff --git a/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/GNyWdCWXwy_FnEw-XS9bcAQnRkId.xml b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/GNyWdCWXwy_FnEw-XS9bcAQnRkId.xml
new file mode 100644
index 000000000..7a6326b99
--- /dev/null
+++ b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/GNyWdCWXwy_FnEw-XS9bcAQnRkId.xml
@@ -0,0 +1,6 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info>
+    <Category UUID="FileClassCategory">
+        <Label UUID="design"/>
+    </Category>
+</Info>
\ No newline at end of file
diff --git a/resources/project/pDfDXpP-F2Cd6B91DGM44psBFJw/l8FwG4TnKj8gyMwHPAtYvu1WQGUp.xml b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/GNyWdCWXwy_FnEw-XS9bcAQnRkIp.xml
similarity index 100%
rename from resources/project/pDfDXpP-F2Cd6B91DGM44psBFJw/l8FwG4TnKj8gyMwHPAtYvu1WQGUp.xml
rename to resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/GNyWdCWXwy_FnEw-XS9bcAQnRkIp.xml
diff --git a/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/STP0mSEMvKb0C99CAKfVG-FjFdUd.xml b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/STP0mSEMvKb0C99CAKfVG-FjFdUd.xml
new file mode 100644
index 000000000..a75f7a81b
--- /dev/null
+++ b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/STP0mSEMvKb0C99CAKfVG-FjFdUd.xml
@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info/>
\ No newline at end of file
diff --git a/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/STP0mSEMvKb0C99CAKfVG-FjFdUp.xml b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/STP0mSEMvKb0C99CAKfVG-FjFdUp.xml
new file mode 100644
index 000000000..842de6ab3
--- /dev/null
+++ b/resources/project/ux2HJV4G7O8gtSZERsaoTt6GWQk/STP0mSEMvKb0C99CAKfVG-FjFdUp.xml
@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="1" type="DIR_SIGNIFIER"/>
\ No newline at end of file
diff --git a/resources/project/y98yrTc3pwfcIzBAdQ_9LFtWOBI/LUTCgzJ-pVvvop9t9kpRDPo21OQp.xml b/resources/project/y98yrTc3pwfcIzBAdQ_9LFtWOBI/LUTCgzJ-pVvvop9t9kpRDPo21OQp.xml
index d2e13e4a9..a0fe9a8cb 100644
--- a/resources/project/y98yrTc3pwfcIzBAdQ_9LFtWOBI/LUTCgzJ-pVvvop9t9kpRDPo21OQp.xml
+++ b/resources/project/y98yrTc3pwfcIzBAdQ_9LFtWOBI/LUTCgzJ-pVvvop9t9kpRDPo21OQp.xml
@@ -1,2 +1,2 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<Info location="getSynergyGroups.m" type="File"/>
\ No newline at end of file
+<Info location="parseSynergyGroups.m" type="File"/>
\ No newline at end of file
diff --git a/src/DesignOptimization/calcDesignOptimizationDiscreteObjective.m b/src/DesignOptimization/calcDesignOptimizationDiscreteObjective.m
deleted file mode 100644
index c801b9acb..000000000
--- a/src/DesignOptimization/calcDesignOptimizationDiscreteObjective.m
+++ /dev/null
@@ -1,37 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the discrete objectives for design optimization.
-%
-% (struct, struct, struct) -> (Number)
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function discrete = calcDesignOptimizationDiscreteObjective(values, ...
-    modeledValues, auxdata)
-
-[costTermCalculations, allowedTypes] = ...
-    generateCostTermStruct("discrete", "DesignOptimization");
-discrete = calcTreatmentOptimizationCost( ...
-    costTermCalculations, allowedTypes, values, modeledValues, auxdata);
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/calcDesignOptimizationDynamicsConstraint.m b/src/DesignOptimization/calcDesignOptimizationDynamicsConstraint.m
deleted file mode 100644
index eca7b3af8..000000000
--- a/src/DesignOptimization/calcDesignOptimizationDynamicsConstraint.m
+++ /dev/null
@@ -1,36 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the dynamic constraint for design optimization.
-%
-% (struct, struct) -> (2D matrix)
-% Returns the dynamic constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function dynamics = calcDesignOptimizationDynamicsConstraint(values, ...
-    params)
-
-dynamics = (params.maxTime - params.minTime) * ...
-    ([values.stateVelocities values.stateAccelerations ...
-    values.controlJerks]) ./ (params.maxState - params.minState);
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/calcDesignOptimizationIntegrand.m b/src/DesignOptimization/calcDesignOptimizationIntegrand.m
deleted file mode 100644
index 8774f7f18..000000000
--- a/src/DesignOptimization/calcDesignOptimizationIntegrand.m
+++ /dev/null
@@ -1,38 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the integrand for design optimization.
-%
-% (struct, struct, struct) -> (2D matrix)
-% Returns scaled integrand
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function integrand = calcDesignOptimizationIntegrand(values, ...
-    modeledValues, auxdata)
-[costTermCalculations, allowedTypes] = ...
-    generateCostTermStruct("continuous", "DesignOptimization");
-integrand = calcTreatmentOptimizationCost( ...
-    costTermCalculations, allowedTypes, values, modeledValues, auxdata);
-integrand = integrand ./ (auxdata.maxIntegral - auxdata.minIntegral);
-integrand = integrand .^ 2;
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/calcDesignOptimizationPathConstraint.m b/src/DesignOptimization/calcDesignOptimizationPathConstraint.m
deleted file mode 100644
index ebb2b7e23..000000000
--- a/src/DesignOptimization/calcDesignOptimizationPathConstraint.m
+++ /dev/null
@@ -1,71 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the path constraint for design optimization.
-%
-% (struct, struct, struct) -> (2D matrix)
-% Returns path constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function path = calcDesignOptimizationPathConstraint(values, modeledValues, ...
-    params)
-path = [];
-for i = 1:length(params.path)
-    constraintTerm = params.path{i};
-    if constraintTerm.isEnabled
-        switch constraintTerm.type
-            case "root_segment_residual_load"
-                path = cat(2, path, ...
-                    calcRootSegmentResidualsPathConstraints(...
-                    constraintTerm.load, ...
-                    params.inverseDynamicMomentLabels, ...
-                    modeledValues.inverseDynamicMoments));
-            case "muscle_model_moment_consistency"
-                path = cat(2, path, ...
-                    calcMuscleActuatedMomentsPathConstraints(params, ...
-                    modeledValues, constraintTerm.load));
-            case "torque_model_moment_consistency"
-                path = cat(2, path, ...
-                    calcTorqueActuatedMomentsPathConstraints(params, ...
-                    modeledValues, values.controlTorques, constraintTerm.load));   
-            case "limit_muscle_activation"
-                path = cat(2, path, ...
-                    calcMuscleActivationsPathConstraint(params, ...
-                    modeledValues, constraintTerm.muscle));
-            case "limit_normalized_fiber_length"
-                path = cat(2, path, ...
-                    calcNormalizedFiberLengthPathConstraint(params, ...
-                    modeledValues, constraintTerm.muscle));
-            case "external_control_muscle_moment_consistency"
-                path = cat(2, path, ...
-                    calcMuscleActuatedMomentsWithExternalAidPathConstraints( ...
-                    params, modeledValues, values.externalTorqueControls, ...
-                    constraintTerm.coordinate));
-            otherwise
-                throw(MException('', ['Constraint term type ' ...
-                    constraintTerm.type ' does not exist for this tool.']))    
-        end
-    end
-end
-path = scaleToBounds(path, params.maxPath, params.minPath);
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/calcDesignOptimizationTerminalConstraint.m b/src/DesignOptimization/calcDesignOptimizationTerminalConstraint.m
deleted file mode 100644
index c496a23db..000000000
--- a/src/DesignOptimization/calcDesignOptimizationTerminalConstraint.m
+++ /dev/null
@@ -1,90 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the terminal constraint for design optimization
-%
-% (struct, struct, struct) -> (Array of number)
-% Returns terminal constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function event = calcDesignOptimizationTerminalConstraint(values, ...
-    modeledValues, params)
-
-event = [];
-for i = 1:length(params.terminal)
-    constraintTerm = params.terminal{i};
-    if constraintTerm.isEnabled
-        switch constraintTerm.type
-            case "state_position_periodicity"
-                event = cat(2, event, ...
-                    calcStatePositionPeriodicity(values.statePositions, ...
-                    params.coordinateNames, ...
-                    constraintTerm.coordinate));
-            case "state_velocity_periodicity"
-                event = cat(2, event, ...
-                    calcStateVelocityPeriodicity(values.stateVelocities, ...
-                    params.coordinateNames, ...
-                    constraintTerm.coordinate));
-            case "root_segment_residual_load_periodicity"
-                event = cat(2, event, ...
-                    calcRootSegmentResidualsPeriodicity(... 
-                    modeledValues.inverseDynamicMoments, ...
-                    params.inverseDynamicMomentLabels, ...
-                    constraintTerm.load));    
-            case "external_force_periodicity"
-                event = cat(2, event, ...
-                    calcExternalForcesPeriodicity(... 
-                    modeledValues.groundReactionsLab.forces, ...
-                    params.contactSurfaces, ...
-                    constraintTerm.force));  
-            case "external_moment_periodicity"
-                event = cat(2, event, ...
-                    calcExternalMomentsPeriodicity(... 
-                    modeledValues.groundReactionsLab.moments, ...
-                    params.contactSurfaces, ...
-                    constraintTerm.moment));  
-            case "final_state_position"
-                event = cat(2, event, ...
-                    calcFinalStatePosition(values.statePositions, ...
-                    params.coordinateNames, ...
-                    constraintTerm));  
-            case "final_state_velocity"
-                event = cat(2, event, ...
-                    calcFinalStateVelocity(values.stateVelocities, ...
-                    params.coordinateNames, ...
-                    constraintTerm)); 
-            case "final_point_position"
-                event = cat(2, event, ...
-                    calcFinalPointPosition(params, values, ...
-                    constraintTerm));      
-            case "final_point_velocity"
-                event = cat(2, event, ...
-                    calcFinalPointVelocity(params, values, ...
-                    constraintTerm));
-            otherwise
-                throw(MException('', ['Constraint term type ' ...
-                    constraintTerm.type ' does not exist for this tool.']))    
-        end
-    end
-end
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/computeDesignOptimizationEndpointFunction.m b/src/DesignOptimization/computeDesignOptimizationEndpointFunction.m
deleted file mode 100644
index b8f1210df..000000000
--- a/src/DesignOptimization/computeDesignOptimizationEndpointFunction.m
+++ /dev/null
@@ -1,68 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function computes the terminal constraint (if any), discrete 
-% objective (if any), and total cost function objective for design
-% optimization.
-% 
-% (struct) -> (struct)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function output = computeDesignOptimizationEndpointFunction(inputs)
-
-inputs.phase.state = [inputs.phase.initialstate; inputs.phase.finalstate];
-inputs.phase.time = [inputs.phase.initialtime; inputs.phase.finaltime];
-inputs.phase.control = ones(size(inputs.phase.time,1), ...
-    length(inputs.auxdata.minControl));
-phase = inputs.phase;
-if isfield(inputs, "parameter")
-    phase.parameter = inputs.parameter;
-end
-values = getDesignOptimizationValueStruct(phase, inputs.auxdata);
-inputs = updateSystemFromUserDefinedFunctions(inputs, values);
-modeledValues = calcTorqueBasedModeledValues(values, inputs.auxdata);
-
-if ~isempty(inputs.auxdata.terminal)
-    output.eventgroup.event = calcDesignOptimizationTerminalConstraint( ...
-        values, modeledValues, inputs.auxdata);
-end
-discrete = calcDesignOptimizationDiscreteObjective(values, ...
-    modeledValues, inputs.auxdata);
-% discrete = computeStaticParameterCost(inputs);
-output.objective = calcDesignOptimizationObjective(discrete, ...
-    inputs.phase.integral, values.time(end), inputs.auxdata);
-end
-
-function cost = computeStaticParameterCost(inputs)
-costTerms = inputs.auxdata.costTerms;
-cost = 0;
-for i = 1:length(costTerms)
-    costTerm = costTerms{i};
-    if strcmp(costTerm.type, "user_defined") && ...
-            strcmp(costTerm.cost_term_type, "discrete")
-        func = str2func(costTerm.function_name);
-        cost = cost + func(inputs);
-    end
-end
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/computeDesignOptimizationMainFunction.m b/src/DesignOptimization/computeDesignOptimizationMainFunction.m
deleted file mode 100644
index e4366c65c..000000000
--- a/src/DesignOptimization/computeDesignOptimizationMainFunction.m
+++ /dev/null
@@ -1,89 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function sets up GPOPS-II to run Design Optimization.
-% 
-% (struct) -> (struct, struct)
-% Assigns optimal control settings and runs Design Optimization 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function output = computeDesignOptimizationMainFunction(inputs, params)
-guess = setupCommonOptimalControlInitialGuess(inputs);
-bounds = setupProblemBounds(inputs, params, guess);
-guess = addUserDefinedTermsToGuess(guess, inputs);
-setup = setupCommonOptimalControlSolverSettings(inputs, ...
-    bounds, guess, params, ...
-    @computeDesignOptimizationContinuousFunction, ...
-    @computeDesignOptimizationEndpointFunction);
-checkInitialGuess(guess, inputs, ...
-    @computeDesignOptimizationContinuousFunction);
-solution = gpops2(setup);
-solution = solution.result.solution;
-solution.auxdata = inputs;
-if isfield(solution, 'parameter')
-    solution.phase.parameter = [solution.parameter];
-end
-output = computeDesignOptimizationContinuousFunction(solution);
-output.solution = solution;
-end
-
-function bounds = setupProblemBounds(inputs, params, guess)
-bounds = setupCommonOptimalControlBounds(inputs, params);
-% setup parameter bounds
-if strcmp(inputs.controllerType, 'synergy_driven')
-    if inputs.optimizeSynergyVectors
-        bounds.parameter.lower = -0.5 * ones(1, length(inputs.minParameter));
-        bounds.parameter.upper = 0.5 * ones(1, length(inputs.minParameter));
-    end
-end
-for i = 1:length(inputs.userDefinedVariables)
-    variable = inputs.userDefinedVariables{i};
-    if ~isfield(bounds, "parameter") || ...
-            ~isfield(bounds.parameter, "lower")
-        bounds.parameter.lower = [-0.5];
-        bounds.parameter.upper = [0.5];
-    else
-        bounds.parameter.lower = [bounds.parameter.lower, ...
-            -0.5];
-        bounds.parameter.upper = [bounds.parameter.upper, ...
-            0.5];
-    end
-end
-if isfield(inputs, "finalTimeRange")
-    bounds.phase.finaltime.lower = guess.phase.time(end) - (0.5 - guess.phase.time(end));
-    bounds.phase.finaltime.upper = 0.5;
-end
-end
-function guess = addUserDefinedTermsToGuess(guess, inputs)
-for i = 1:length(inputs.userDefinedVariables)
-    variable = inputs.userDefinedVariables{i};
-    if ~isfield(guess, "parameter") 
-        guess.parameter = [];
-    end
-    guess.parameter = [guess.parameter, ...
-        scaleToBounds( ...
-        variable.initial_values, ...
-        variable.upper_bounds, ...
-        variable.lower_bounds)];
-end
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/getDesignOptimizationValueStruct.m b/src/DesignOptimization/getDesignOptimizationValueStruct.m
deleted file mode 100644
index dfab7f79a..000000000
--- a/src/DesignOptimization/getDesignOptimizationValueStruct.m
+++ /dev/null
@@ -1,83 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses and scales the design variables specific to
-% Design Optimization. If the model is synergy driven, synergy weights are
-% properly calculated if they are fixed or being optimized. If the model
-% has user defined parameters, they are parsed and scaled. Lastly, if
-% the model has external torque actuators, they are parsed and
-% scaled.
-%
-% (struct, struct) -> (struct)
-% Design variables specific to Design Optimization are parsed and scaled
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function values = getDesignOptimizationValueStruct(inputs, params)
-values = getTreatmentOptimizationValueStruct(inputs, params);
-
-numParameters = 0;
-if strcmp(params.controllerType, 'synergy_driven')
-    if params.optimizeSynergyVectors
-        values.synergyWeights = scaleToOriginal(inputs.parameter(1, ...
-            1 : params.numSynergyWeights), ...
-            params.maxParameter, params.minParameter);
-        values.synergyWeights = getSynergyWeightsFromGroups(...
-            values.synergyWeights, params);
-        numParameters = params.numSynergyWeights;
-    else
-        values.synergyWeights = getSynergyWeightsFromGroups(...
-            params.synergyWeightsGuess, params);
-    end
-    if params.splineSynergyActivations.dim > 1
-        values.controlSynergyActivations = ...
-            fnval(params.splineSynergyActivations, values.time)';
-    else
-        values.controlSynergyActivations = ...
-            fnval(params.splineSynergyActivations, values.time);
-    end
-    if params.enableExternalTorqueControl
-        controls = scaleToOriginal(inputs.control, ones(size( ...
-            inputs.control, 1), 1) .* params.maxControl, ...
-            ones(size(inputs.control, 1), 1) .* params.minControl);
-        values.externalTorqueControls = controls(:, params.numCoordinates + ...
-            params.numSynergies + 1 : end);
-    end
-else 
-    if isfield(params, "enableExternalTorqueControl") && ...
-            params.enableExternalTorqueControl
-        controls = scaleToOriginal(inputs.control, ones(size( ...
-            inputs.control, 1), 1) .* params.maxControl, ...
-            ones(size(inputs.control, 1), 1) .* params.minControl);
-        values.externalTorqueControls = controls(:, params.numCoordinates + ...
-            params.numTorqueControls + 1 : end);
-    end
-end
-if isfield(params, 'userDefinedVariables')
-    for i = 1:length(params.userDefinedVariables)
-        values.(params.userDefinedVariables{i}.type)(i) = scaleToOriginal( ...
-            inputs.parameter(1, i + numParameters), ...
-            params.userDefinedVariables{i}.upper_bounds, ...
-            params.userDefinedVariables{i}.lower_bounds);
-    end
-end
-end
\ No newline at end of file
diff --git a/src/DesignOptimization/parseDesignOptimizationSettingsTree.m b/src/DesignOptimization/parseDesignOptimizationSettingsTree.m
deleted file mode 100644
index 5fccf93a2..000000000
--- a/src/DesignOptimization/parseDesignOptimizationSettingsTree.m
+++ /dev/null
@@ -1,127 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses the settings tree resulting from xml2struct of the
-% Design Optimizatoin settings XML file.
-%
-% (struct) -> (struct, struct)
-% returns the input values for Design Optimization
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function [inputs, params] = ...
-    parseDesignOptimizationSettingsTree(settingsTree)
-inputs = getInputs(settingsTree);
-params = getParams(settingsTree);
-inputs = modifyModelForces(inputs);
-inputs = updateMuscleModelProperties(inputs);
-end
-
-function inputs = getInputs(tree)
-import org.opensim.modeling.Storage
-inputs = getTreatmentOptimizationInputs(tree);
-inputs = getDesignVariableBounds(tree, inputs);
-if strcmpi(inputs.controllerType, 'synergy_driven')
-inputs.synergyWeights = parseTreatmentOptimizationStandard(...
-    {getTextFromField(getFieldByName(tree, 'synergy_vectors_file'))});
-end
-inputs.systemFns = parseSpaceSeparatedList(tree, "model_functions");
-parameterTree = getFieldByNameOrError(tree, "RCNLParameterTermSet");
-if isstruct(parameterTree) && isfield(parameterTree, "RCNLParameterTerm")
-    inputs.userDefinedVariables = parseRcnlCostTermSet( ...
-        parameterTree.RCNLParameterTerm);
-else
-    inputs.userDefinedVariables = {};
-end
-end
-
-function inputs = getDesignVariableBounds(tree, inputs)
-designVariableTree = getFieldByNameOrError(tree, ...
-    'RCNLDesignVariableBoundsTerms');
-jointPositionsMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_positions_multiple');
-if(isstruct(jointPositionsMultiple))
-    inputs.statePositionsMultiple = getDoubleFromField(jointPositionsMultiple);
-end
-jointVelocitiesMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_velocities_multiple');
-if(isstruct(jointVelocitiesMultiple))
-    inputs.stateVelocitiesMultiple = getDoubleFromField(jointVelocitiesMultiple);
-end
-jointAccelerationsMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_accelerations_multiple');
-if(isstruct(jointAccelerationsMultiple))
-    inputs.stateAccelerationsMultiple = ...
-        getDoubleFromField(jointAccelerationsMultiple);
-end
-jointJerkMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_jerks_multiple');
-if(isstruct(jointJerkMultiple))
-    inputs.controlJerksMultiple = getDoubleFromField(jointJerkMultiple);
-end
-if strcmp(inputs.controllerType, 'synergy_driven')
-maxControlSynergyActivations = getFieldByNameOrError(designVariableTree, ...
-    'synergy_activations_max');
-if(isstruct(maxControlSynergyActivations))
-    inputs.maxControlSynergyActivations = ...
-        getDoubleFromField(maxControlSynergyActivations);
-end
-if inputs.optimizeSynergyVectors
-    maxParameterSynergyWeights = getFieldByNameOrError(designVariableTree, ...
-        'synergy_weights_max');
-    if(isstruct(maxParameterSynergyWeights))
-        inputs.maxParameterSynergyWeights = ...
-            getDoubleFromField(maxParameterSynergyWeights);
-    end
-end
-else 
-maxControlTorques = getFieldByName(designVariableTree, ...
-    'torque_controls_multiple');
-if(isstruct(maxControlTorques))
-    inputs.maxControlTorquesMultiple = getDoubleFromField(maxControlTorques);
-else
-    inputs.maxControlTorquesMultiple = 1;
-end
-end
-finalTimeRange = getFieldByName(designVariableTree, ...
-    'final_time_range');
-if(isstruct(finalTimeRange))
-    inputs.finalTimeRange = getDoubleFromField(finalTimeRange);
-end
-inputs.enableExternalTorqueControl = getBooleanLogicFromField( ...
-    getFieldByName(tree, "enable_external_torque_controls"));
-if inputs.enableExternalTorqueControl
-    inputs.externalControlTorqueNames = parseSpaceSeparatedList(tree, ...
-        "external_control_coordinate_list");
-    inputs.numExternalTorqueControls = ...
-        length(inputs.externalControlTorqueNames);
-    inputs.maxExternalTorqueControls = getDoubleFromField( ...
-        getFieldByNameOrError(designVariableTree, ...
-        'external_torque_control_multiple'));
-end
-inputs.toolName = "DesignOptimization";
-end
-
-function params = getParams(tree)
-params.solverSettings = getOptimalControlSolverSettings(...
-    getTextFromField(getFieldByName(tree, 'optimal_control_settings_file')));
-end
\ No newline at end of file
diff --git a/src/GroundContactPersonalization/Analysis/plotGcpFootKinematicsFromFiles.m b/src/GroundContactPersonalization/Analysis/plotGcpFootKinematicsFromFiles.m
index ea26c61cc..570f9c616 100644
--- a/src/GroundContactPersonalization/Analysis/plotGcpFootKinematicsFromFiles.m
+++ b/src/GroundContactPersonalization/Analysis/plotGcpFootKinematicsFromFiles.m
@@ -45,8 +45,10 @@ function plotGcpFootKinematicsFromFiles(experimentalKinematicsFileName, ...
 time = findTimeColumn(Storage(experimentalKinematicsFileName));
 
 figure(plotNumber)
+t = tiledlayout(2, 4, ...
+    TileSpacing='compact', Padding='compact');
 for i = 1:7
-    subplot(2, 4, i)
+    nexttile(i)
     % Rotational coordinate data are converted to degrees. 
     if i <= 4
         experimental = rad2deg(experimentalKinematics(i, :));
diff --git a/src/GroundContactPersonalization/Analysis/plotGcpGroundReactionsFromFiles.m b/src/GroundContactPersonalization/Analysis/plotGcpGroundReactionsFromFiles.m
index 964c8e768..581437505 100644
--- a/src/GroundContactPersonalization/Analysis/plotGcpGroundReactionsFromFiles.m
+++ b/src/GroundContactPersonalization/Analysis/plotGcpGroundReactionsFromFiles.m
@@ -47,8 +47,10 @@ function plotGcpGroundReactionsFromFiles( ...
 time = findTimeColumn(Storage(experimentalGroundReactionsFileName));
 
 figure(plotNumber)
+t = tiledlayout(2, 3, ...
+    TileSpacing='compact', Padding='compact');
 for i = 1:6
-    subplot(2, 3, i);
+    nexttile(i)
     experimental = experimentalGroundReactions(i, :);
     model = modeledGroundReactions(i, :);
     plot(time, experimental, "red", "LineWidth", 2)
diff --git a/src/GroundContactPersonalization/GroundContactPersonalization.m b/src/GroundContactPersonalization/GroundContactPersonalization.m
index a3478b9dd..15ab377a6 100644
--- a/src/GroundContactPersonalization/GroundContactPersonalization.m
+++ b/src/GroundContactPersonalization/GroundContactPersonalization.m
@@ -59,6 +59,7 @@
     replaceMomentsAboutMidfootSuperior(surface, inputs)
     replacedMoments = ...
         zeros(size(surface.experimentalGroundReactionMoments));
+    momentCenter = zeros(size(surface.midfootSuperiorPosition));
     for i = 1:size(replacedMoments, 2)
         newCenter = surface.midfootSuperiorPosition(:, i);
         newCenter(2) = inputs.restingSpringLength;
@@ -66,6 +67,6 @@
             surface.experimentalGroundReactionMoments(:, i) + ...
             cross((surface.electricalCenter(:, i) - newCenter), ...
             surface.experimentalGroundReactionForces(:, i));
-        momentCenter = repmat(newCenter, 1, 101);
+        momentCenter(:, i) = newCenter;
     end
 end
diff --git a/src/GroundContactPersonalization/Optimizations/ModelCalculation/calcModeledVerticalGroundReactionForce.m b/src/GroundContactPersonalization/Optimizations/ModelCalculation/calcModeledVerticalGroundReactionForce.m
index 53993f83a..40b66a368 100644
--- a/src/GroundContactPersonalization/Optimizations/ModelCalculation/calcModeledVerticalGroundReactionForce.m
+++ b/src/GroundContactPersonalization/Optimizations/ModelCalculation/calcModeledVerticalGroundReactionForce.m
@@ -49,17 +49,15 @@
     ymax = 1e-2;
     Kval = springConstants(i);
     height = height - springRestingLength;
+    if height > 0.354237930036971
+        height = 0.354237930036971;
+    end
     numFrames = length(height);
     v = ones(numFrames, 1)' .* ((Kval + klow) ./ (Kval - klow));
     s = ones(numFrames, 1)' .* ((Kval - klow) ./ 2);
     constant = -s .* (v .* ymax - c .* log(cosh((ymax + h) ./ c)));
     freglyVerticalGrf = -s .* (v .* height - c .* ...
         log(cosh((height + h) ./ c))) - constant;
-    % Account for potential errors in force model
-    freglyVerticalGrf(isnan(freglyVerticalGrf)) = ...
-        min(min(freglyVerticalGrf));
-    freglyVerticalGrf(isinf(freglyVerticalGrf)) = ...
-        min(min(freglyVerticalGrf));
     springForces(2, i) = freglyVerticalGrf * (1 + dampingFactor * ...
         verticalVelocity);
     modeledVerticalGrf = modeledVerticalGrf + springForces(2, i);
diff --git a/src/GroundContactPersonalization/Saving/saveGroundContactPersonalizationResults.m b/src/GroundContactPersonalization/Saving/saveGroundContactPersonalizationResults.m
index b7007b3a8..74cf69966 100644
--- a/src/GroundContactPersonalization/Saving/saveGroundContactPersonalizationResults.m
+++ b/src/GroundContactPersonalization/Saving/saveGroundContactPersonalizationResults.m
@@ -41,5 +41,7 @@ function saveGroundContactPersonalizationResults(inputs, params, ...
 writeOptimizedGroundReactionsToSto(inputs, params, resultsDirectory, name);
 writeGroundContactPersonalizationOsimxFile(inputs, resultsDirectory, ...
     osimxFileName);
+writeCombinedOptimizedGroundReactionsToSto(inputs, params, resultsDirectory);
+writeFullBodyKinematicsFromGcp(inputs, params, resultsDirectory);
 end
 
diff --git a/src/GroundContactPersonalization/Saving/writeCombinedOptimizedGroundReactionsToSto.m b/src/GroundContactPersonalization/Saving/writeCombinedOptimizedGroundReactionsToSto.m
new file mode 100644
index 000000000..c46b97127
--- /dev/null
+++ b/src/GroundContactPersonalization/Saving/writeCombinedOptimizedGroundReactionsToSto.m
@@ -0,0 +1,80 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+%
+%
+% (struct, string, string) -> (None)
+% Write modeled foot kinematics to an OpenSim Storage file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond, Spencer Williams                          %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function writeCombinedOptimizedGroundReactionsToSto(inputs, params, ...
+    resultsDirectory)
+for foot = 1:length(inputs.surfaces)
+    models.("model_" + foot) = Model(inputs.surfaces{foot}.model);
+end
+[~,name,ext] = fileparts(inputs.grfFileName);
+outfile = strcat(name, ext);
+
+timePoints = inputs.surfaces{1}.time;
+data = zeros(length(timePoints), 9 * length(inputs.surfaces));
+columnLabels = string([]);
+for foot = 1:length(inputs.surfaces)
+    if any(size(timePoints) ~= size(inputs.surfaces{foot}.time)) || ...
+            any(timePoints ~= inputs.surfaces{foot}.time)
+        return;
+    end
+end
+if ~exist(fullfile(resultsDirectory, "GRFData"), "dir")
+    mkdir(fullfile(resultsDirectory, "GRFData"))
+end
+for foot = 1:length(inputs.surfaces)
+    for i = 1:3
+        columnLabels(end + 1) = convertCharsToStrings( ...
+            inputs.surfaces{foot}.forceColumns(i, :));
+    end
+    for i = 1:3
+        columnLabels(end + 1) = convertCharsToStrings( ...
+            inputs.surfaces{foot}.momentColumns(i, :));
+    end
+    for i = 1:3
+        columnLabels(end + 1) = convertCharsToStrings( ...
+            inputs.surfaces{foot}.electricalCenterColumns(i, :));
+    end
+    [modeledJointPositions, modeledJointVelocities] = ...
+        calcGCPJointKinematics(inputs.surfaces{foot} ...
+        .experimentalJointPositions, inputs.surfaces{foot} ...
+        .jointKinematicsBSplines, inputs.surfaces{foot}.bSplineCoefficients);
+    modeledValues = calcGCPModeledValues(inputs, inputs, ...
+        modeledJointPositions, modeledJointVelocities, params, ...
+        length(params.tasks), foot, models);
+    center = inputs.surfaces{foot}.midfootSuperiorPosition;
+    center(2, :) = inputs.restingSpringLength;
+    data(:, (foot - 1) * 9 + 1 : foot * 9) = [modeledValues.anteriorGrf' modeledValues.verticalGrf' ...
+        modeledValues.lateralGrf' modeledValues.xGrfMoment' ...
+        modeledValues.yGrfMoment' modeledValues.zGrfMoment' center'];
+    data = lowpassFilter(inputs.surfaces{1}.time, data, 2, 6, 0);
+end
+writeToSto(columnLabels, timePoints, data, ...
+    fullfile(resultsDirectory, "GRFData", outfile));
+end
+
diff --git a/src/GroundContactPersonalization/Saving/writeFullBodyKinematicsFromGcp.m b/src/GroundContactPersonalization/Saving/writeFullBodyKinematicsFromGcp.m
new file mode 100644
index 000000000..77e093e55
--- /dev/null
+++ b/src/GroundContactPersonalization/Saving/writeFullBodyKinematicsFromGcp.m
@@ -0,0 +1,157 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% Saves a ground contact .osimx model and experimental and modeled
+% kinematics and ground reactions for each foot.
+%
+% (struct, struct, string) -> (None)
+% Save Ground Contact Personalization kinematics results.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond, Spencer Williams                          %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function writeFullBodyKinematicsFromGcp(inputs, params, resultsDirectory)
+timePoints = inputs.surfaces{1}.time;
+for foot = 1:length(inputs.surfaces)
+    if any(size(timePoints) ~= size(inputs.surfaces{foot}.time)) || ...
+            any(timePoints ~= inputs.surfaces{foot}.time)
+        return;
+    end
+end
+for foot = 1:length(inputs.surfaces)
+    models.("model_" + foot) = Model(inputs.surfaces{foot}.model);
+end
+footMarkerNames = string([]);
+for foot = 1:length(inputs.surfaces)
+    [modeledJointPositions, modeledJointVelocities] = ...
+        calcGCPJointKinematics(inputs.surfaces{foot} ...
+        .experimentalJointPositions, inputs.surfaces{foot} ...
+        .jointKinematicsBSplines, inputs.surfaces{foot}.bSplineCoefficients);
+    modeledValues = calcGCPModeledValues(inputs, inputs, ...
+        modeledJointPositions, modeledJointVelocities, params, ...
+        length(params.tasks), foot, models);
+
+    % footMarkerPositions = zeros(length(timePoints), 9 * 3 * length(inputs.surfaces));
+    footMarkerNames(end + 1) = inputs.surfaces{foot}.markerNames.toe;
+    footMarkerNames(end + 1) = inputs.surfaces{foot}.markerNames.medial;
+    footMarkerNames(end + 1) = inputs.surfaces{foot}.markerNames.lateral;
+    footMarkerNames(end + 1) = inputs.surfaces{foot}.markerNames.heel;
+    footMarkerNames(end + 1) = inputs.surfaces{foot}.markerNames.midfootSuperior;
+
+    footMarkerData.(footMarkerNames(end - 4)) = modeledValues.markerPositions.toe;
+    footMarkerData.(footMarkerNames(end - 3)) = modeledValues.markerPositions.medial;
+    footMarkerData.(footMarkerNames(end - 2)) = modeledValues.markerPositions.lateral;
+    footMarkerData.(footMarkerNames(end - 1)) = modeledValues.markerPositions.heel;
+    footMarkerData.(footMarkerNames(end)) = modeledValues.markerPositions.midfootSuperior;
+
+end
+
+% make ikdata
+
+trcFromMotParams.trcFileName = "preGcp.trc";
+trcFromMotParams.dataRate = .00001;
+TrcFromMot(inputs.bodyModel, inputs.motionFileName, trcFromMotParams)
+
+% load trc file
+timeSeriesTable = TimeSeriesTableVec3(trcFromMotParams.trcFileName);
+columnNames = timeSeriesTable.getColumnLabels();
+strings = {};
+for i=0:columnNames.size()-1
+    strings{end+1} = columnNames.get(i);
+end
+markerNames = string(strings);
+
+% put foot marker data inside trc file
+for i = 1:length(footMarkerNames)
+    column = timeSeriesTable.updDependentColumn(footMarkerNames(i));
+    for j = 1:length(inputs.surfaces{1}.time)
+        temp = footMarkerData.(footMarkerNames(i))(:, j);
+        column.set(i-1, org.opensim.modeling.Vec3(temp(1), temp(2), temp(3)));
+    end
+end
+
+for i = 1:length(timePoints)
+    timeSeriesTable.setIndependentValueAtIndex(i - 1, timePoints(i));
+end
+
+% save trc file
+trcFileName = "postGcp.trc";
+trcFileAdapter = org.opensim.modeling.TRCFileAdapter();
+trcFileAdapter.write(timeSeriesTable, trcFileName);
+
+import org.opensim.modeling.TimeSeriesTableVec3
+import org.opensim.modeling.SetMarkerWeights
+import org.opensim.modeling.MarkerWeight
+timeSeriesTable = TimeSeriesTableVec3(trcFileName);
+strings = {};
+columnNames = timeSeriesTable.getColumnLabels();
+for i=0:columnNames.size()-1
+    strings{end+1} = columnNames.get(i);
+end
+markerNames = string(strings);
+markerWeightSet = SetMarkerWeights();
+for i=1:length(markerNames)
+    if any(ismember(fieldnames(footMarkerData), markerNames(i)))
+        markerWeightSet.cloneAndAppend(MarkerWeight(markerNames(i), 1000.0));
+    else
+        markerWeightSet.cloneAndAppend(MarkerWeight(markerNames(i), 1.0));
+    end
+end
+try
+    markersReference = org.opensim.modeling.MarkersReference(trcFileName, markerWeightSet);
+catch
+    markersReference = org.opensim.modeling.MarkersReference(trcFileName);
+    markersReference.setMarkerWeightSet(markerWeightSet);
+end
+timeSeriesTable = libpointer;
+[model, state] = Model(inputs.bodyModel);
+ikSolver = org.opensim.modeling.InverseKinematicsSolver(model, markersReference, ...
+    org.opensim.modeling.SimTKArrayCoordinateReference());
+ikSolver.setAccuracy(1e-6);
+
+% make new kinematics *run ik solver*
+
+kinematicsReporter = org.opensim.modeling.Kinematics(model);
+kinematicsReporter.setInDegrees(false); 
+state.setTime(timePoints(1));
+ikSolver.assemble(state);
+kinematicsReporter.begin(state);
+for i = 1:length(timePoints)
+    state.setTime(timePoints(i));
+    ikSolver.track(state);
+    kinematicsReporter.step(state, i);
+end
+[~,name,ext] = fileparts(inputs.motionFileName);
+outfile = strcat(name, ext);
+if ~exist(fullfile(resultsDirectory, "IKData"), "dir")
+    mkdir(fullfile(resultsDirectory, "IKData"))
+end
+kinematicsReporter.getPositionStorage().print( ...
+    fullfile(resultsDirectory, "IKData", outfile));
+[columnNames, time, data] = parseMotToComponents(model, ...
+    org.opensim.modeling.Storage(fullfile(resultsDirectory, "IKData", outfile)));
+data = lowpassFilter(time, data', 4, 6, 0);
+writeToSto(columnNames, timePoints, data, ...
+    fullfile(resultsDirectory, "IKData", outfile));
+delete postGcp.trc
+delete preGcp.trc
+end
+
diff --git a/src/GroundContactPersonalization/Saving/writeGroundContactPersonalizationOsimxFile.m b/src/GroundContactPersonalization/Saving/writeGroundContactPersonalizationOsimxFile.m
index 86c9db2b3..f5d8277d0 100644
--- a/src/GroundContactPersonalization/Saving/writeGroundContactPersonalizationOsimxFile.m
+++ b/src/GroundContactPersonalization/Saving/writeGroundContactPersonalizationOsimxFile.m
@@ -33,7 +33,7 @@ function writeGroundContactPersonalizationOsimxFile(inputs, ...
 model = Model(modelFileName);
 
 if isfile(osimxFileName)
-    osimx = parseOsimxFile(inputs.inputOsimxFile);
+    osimx = parseOsimxFile(inputs.inputOsimxFile, model);
     [~, name, ~] = fileparts(inputs.inputOsimxFile);
     outfile = fullfile(resultsDirectory, strcat(name, "_gcp.xml"));
 else
@@ -61,9 +61,8 @@ function writeGroundContactPersonalizationOsimxFile(inputs, ...
     newSurface.momentColumns = string(inputs.surfaces{foot}.momentColumns)';
     newSurface.electricalCenterColumns = string(inputs.surfaces{foot} ...
         .electricalCenterColumns)';
-    newSurface.toesCoordinateName = inputs.surfaces{foot} ...
-        .toesCoordinateName;
-    newSurface.toesJointName = inputs.surfaces{foot}.toesJointName;
+    newSurface.hindfootBodyName = inputs.surfaces{foot} ...
+        .hindfootBodyName;
     newSurface.toeMarker = inputs.surfaces{foot}.markerNames.toe;
     newSurface.medialMarker = inputs.surfaces{foot}.markerNames.medial;
     newSurface.lateralMarker = inputs.surfaces{foot}.markerNames.lateral;
diff --git a/src/GroundContactPersonalization/parseGroundContactPersonalizationSettingsTree.m b/src/GroundContactPersonalization/parseGroundContactPersonalizationSettingsTree.m
index 96974cdae..91f1a8763 100644
--- a/src/GroundContactPersonalization/parseGroundContactPersonalizationSettingsTree.m
+++ b/src/GroundContactPersonalization/parseGroundContactPersonalizationSettingsTree.m
@@ -1,7 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % Parses XML settings for Ground contact personalization to determine
-% intial inputs and parameters for optimization. 
+% intial inputs and parameters for optimization.
 %
 % (struct) -> (struct, struct, string)
 % Returns the input values for Ground Contact Personalization.
@@ -53,13 +53,13 @@
     getFieldByNameOrAlternate(tree, 'latching_velocity', '0.05')));
 inputs.gridWidth = str2double(getTextFromField( ...
     getFieldByNameOrAlternate(tree, 'grid_width', '5')));
-if isempty(inputs.gridWidth) || isnan(inputs.gridWidth) 
-    inputs.gridWidth = 5; 
+if isempty(inputs.gridWidth) || isnan(inputs.gridWidth)
+    inputs.gridWidth = 5;
 end
 inputs.gridHeight = str2double(getTextFromField( ...
     getFieldByNameOrAlternate(tree, 'grid_height', '15')));
 if isempty(inputs.gridHeight) || isnan(inputs.gridHeight)
-    inputs.gridHeight = 15; 
+    inputs.gridHeight = 15;
 end
 if(~isempty(inputDirectory))
     try
@@ -86,7 +86,7 @@
 
 % (struct, struct) -> (struct)
 % Gets inputs specific to each foot, such as experimental kinematics and
-% ground reactions and foot marker names. 
+% ground reactions and foot marker names.
 function output = getContactSurfaces(inputs, tree)
 contactSurfaces = getFieldByNameOrError(tree, 'GCPContactSurfaceSet') ...
     .GCPContactSurface;
@@ -112,7 +112,7 @@
 
 % (Model, string, struct) -> (struct)
 % Determines the first and last included time point based on the input
-% kinematics motion file and start and end times given for the foot. 
+% kinematics motion file and start and end times given for the foot.
 function task = getMotionTime(bodyModel, motionFile, task)
 import org.opensim.modeling.Storage
 [~, ikTime, ~] = parseMotToComponents(...
@@ -124,7 +124,7 @@
 
 % (Model, string, struct) -> (struct)
 % Parses ground reaction data from a file. This will throw an exception if
-% any needed column is missing. 
+% any needed column is missing.
 function task = getGroundReactions(bodyModel, grfFile, task)
 import org.opensim.modeling.Storage
 [grfColumnNames, grfTime, grfData] = parseMotToComponents(...
@@ -160,47 +160,51 @@
 
 % (struct, struct, struct) -> (struct)
 % Gets foot-specific options directly included in XML file, including
-% names of markers and ground reaction columns. 
+% names of markers and ground reaction columns.
 function task = getFootData(tree)
-    task.isLeftFoot = strcmpi('true', ...
-        getFieldByNameOrError(tree, 'is_left_foot').Text);
-    task.toesCoordinateName = getFieldByNameOrError(tree, ...
-        'toe_coordinate').Text;
-    task.markerNames.toe = getFieldByNameOrError(tree, ...
-        'toe_marker').Text;
-    task.markerNames.medial = getFieldByNameOrError(tree, ...
-        'medial_marker').Text;
-    task.markerNames.lateral = getFieldByNameOrError(tree, ...
-        'lateral_marker').Text;
-    task.markerNames.heel = getFieldByNameOrError(tree, ...
-        'heel_marker').Text;
-    task.markerNames.midfootSuperior = getFieldByNameOrError(tree, ...
-        'midfoot_superior_marker').Text;
-    task.startTime = str2double(getFieldByNameOrError(tree, ...
-        'start_time').Text);
-    task.endTime = str2double(getFieldByNameOrError(tree, ...
-        'end_time').Text);
-    task.beltSpeed = str2double(getFieldByNameOrError(tree, ...
-        'belt_speed').Text);
-    task.forceColumns = cell2mat(split(getFieldByNameOrError(tree, ...
-        'force_columns').Text));
-    task.momentColumns = cell2mat(split(getFieldByNameOrError(tree, ...
-        'moment_columns').Text));
-    task.electricalCenterColumns = cell2mat(split( ...
-        getFieldByNameOrError(tree, 'electrical_center_columns').Text));
+task.isLeftFoot = strcmpi('true', ...
+    getFieldByNameOrError(tree, 'is_left_foot').Text);
+hindfootBodyName = getFieldByName(tree, "hindfoot_body");
+if ~isstruct(hindfootBodyName)
+    throw(MException('', "<toes_coordinate> is replaced by <hindfoot_body> in the GCP settings file."))
+else
+    task.hindfootBodyName = hindfootBodyName.Text;
+end
+task.markerNames.toe = getFieldByNameOrError(tree, ...
+    'toe_marker').Text;
+task.markerNames.medial = getFieldByNameOrError(tree, ...
+    'medial_marker').Text;
+task.markerNames.lateral = getFieldByNameOrError(tree, ...
+    'lateral_marker').Text;
+task.markerNames.heel = getFieldByNameOrError(tree, ...
+    'heel_marker').Text;
+task.markerNames.midfootSuperior = getFieldByNameOrError(tree, ...
+    'midfoot_superior_marker').Text;
+task.startTime = str2double(getFieldByNameOrError(tree, ...
+    'start_time').Text);
+task.endTime = str2double(getFieldByNameOrError(tree, ...
+    'end_time').Text);
+task.beltSpeed = str2double(getFieldByNameOrError(tree, ...
+    'belt_speed').Text);
+task.forceColumns = cell2mat(split(getFieldByNameOrError(tree, ...
+    'force_columns').Text));
+task.momentColumns = cell2mat(split(getFieldByNameOrError(tree, ...
+    'moment_columns').Text));
+task.electricalCenterColumns = cell2mat(split( ...
+    getFieldByNameOrError(tree, 'electrical_center_columns').Text));
 end
 
 % (Array of double, Array of double) -> (None)
 % Confirms that the time points from ground reaction and kinematics data
-% match in length and value. 
+% match in length and value.
 function verifyTime(grfTime, ikTime)
-    if size(ikTime) ~= size(grfTime)
-        throw(MException('', ['IK and GRF time columns have ' ...
-            'different lengths']))
-    end
-    if any(abs(ikTime - grfTime) > 0.005)
-        throw(MException('', 'IK and GRF time points are not equal'))
-    end
+if size(ikTime) ~= size(grfTime)
+    throw(MException('', ['IK and GRF time columns have ' ...
+        'different lengths']))
+end
+if any(abs(ikTime - grfTime) > 0.005)
+    throw(MException('', 'IK and GRF time points are not equal'))
+end
 end
 
 % Parses initial values.
@@ -244,6 +248,7 @@ function verifyTime(grfTime, ikTime)
 
 % Gets cost terms and design variables included in each task.
 function output = getOptimizationTasks(tree)
+output = {};
 tasks = getFieldByNameOrError(tree, 'GCPTaskList');
 counter = 1;
 gcpTasks = orderByIndex(tasks.GCPTask);
diff --git a/src/GroundContactPersonalization/prepareGroundContactPersonalizationInputs.m b/src/GroundContactPersonalization/prepareGroundContactPersonalizationInputs.m
index 109be671f..6358a7f9b 100644
--- a/src/GroundContactPersonalization/prepareGroundContactPersonalizationInputs.m
+++ b/src/GroundContactPersonalization/prepareGroundContactPersonalizationInputs.m
@@ -57,9 +57,20 @@
 % Prepares optimization values specific to a foot.
 function surface = prepareInputsForFoot(surface, inputs, ...
     meanMarkerLocations, surfaceNumber)
-surface.toesJointName = char(Model(inputs.bodyModel ...
-    ).getCoordinateSet().get(surface.toesCoordinateName).getJoint( ...
-    ).getName());
+model = Model(inputs.bodyModel);
+joints = getBodyJointNames(model, surface.hindfootBodyName);
+assert(length(joints) == 2, "GCP supports two segment foot models only");
+for i = 1 : length(joints)
+    [parent, ~] = getJointBodyNames(model, joints(i));
+    if strcmp(parent, surface.hindfootBodyName)
+        surface.toesJointName = joints(i);
+        break
+    end
+end
+assert(model.getJointSet().get(surface.toesJointName) ...
+    .numCoordinates() == 1, "GCP toes joint must be a pin joint");
+surface.toesCoordinateName = model.getJointSet() ...
+    .get(surface.toesJointName).getCoordinate().getName().toCharArray()';
 [surface.hindfootBodyName, surface.toesBodyName] = ...
     getJointBodyNames(Model(inputs.bodyModel), surface.toesJointName);
 surface.coordinatesOfInterest = findGCPFreeCoordinates(...
diff --git a/src/JointModelPersonalization/JointModelPersonalization.m b/src/JointModelPersonalization/JointModelPersonalization.m
index 90e10b173..53c55b1c3 100644
--- a/src/JointModelPersonalization/JointModelPersonalization.m
+++ b/src/JointModelPersonalization/JointModelPersonalization.m
@@ -34,16 +34,20 @@
 outputModel = Model(inputs.model);
 for i=1:length(inputs.tasks)
     functions = makeFunctions(inputs.tasks{i}.parameters, ...
-        inputs.tasks{i}.scaling, inputs.tasks{i}.markers);
-    params.markerNames = getMarkersOnJoints(outputModel, ...
+        inputs.tasks{i}.scaling, inputs.tasks{i}.markers, ...
+        inputs.tasks{i}.anatomicalMarkers);
+    params.markerNames = getMarkersInTask(outputModel, ...
         inputs.tasks{i});
     taskParams = mergeStructs(inputs.tasks{i}, params);
-    optimizedValues = computeKinematicCalibration(inputs.model, ...
+    outputModelFileName = saveTempOutputModel(inputs.modelFileName, ...
+        outputModel);
+    optimizedValues = computeKinematicCalibration(outputModelFileName, ...
         inputs.tasks{i}.markerFile, functions, inputs.desiredError, ...
         taskParams);
-    outputModel = adjustModelFromOptimizerOutput(outputModel, ...
-        functions, optimizedValues);
+    outputModel = adjustModelFromOptimizerOutput( ...
+        Model(outputModelFileName), functions, optimizedValues);
 end
+delete(outputModelFileName);
 end
 
 % (struct) -> (None)
@@ -97,14 +101,23 @@ function verifyParam(params, fieldName, fn, message)
 end
 end
 
-function functions = makeFunctions(parameters, scaling, markers)
+function outputModelFileName = saveTempOutputModel(modelFileName, ...
+    outputModel)
+[~,name,ext] = fileparts(modelFileName);
+outputModelFileName = name + "_jmp_temp" + ext;
+outputModel.print(outputModelFileName);
+end
+
+function functions = makeFunctions(...
+    parameters, scaling, markers, anatomicalMarkers)
 functions = {};
 for i=1:length(parameters)
     p = parameters{i};
     functions{i} = makeJointFunction(p{1}, p{2}, p{3}, p{4});
 end
 for i=1:length(scaling)
-    functions{end + 1} = makeScalingFunction(scaling(i));
+    functions{end + 1} = makeScalingFunction( ...
+        scaling(i), anatomicalMarkers);
 end
 for i=1:length(markers)
     marker = markers{i};
@@ -122,8 +135,12 @@ function verifyParam(params, fieldName, fn, message)
 end
 end
 
-function markerNames = getMarkersOnJoints(model, task)
+function markerNames = getMarkersInTask(model, task)
 import org.opensim.modeling.*
+if isfield(task, "markerNames")
+    markerNames = task.markerNames;
+    return
+end
 parameters = task.parameters;
 bodies = task.scaling;
 markerNames = {};
diff --git a/src/JointModelPersonalization/KinematicCalibration/computeInnerOptimization.m b/src/JointModelPersonalization/KinematicCalibration/computeInnerOptimization.m
index c218362b5..1245d4354 100644
--- a/src/JointModelPersonalization/KinematicCalibration/computeInnerOptimization.m
+++ b/src/JointModelPersonalization/KinematicCalibration/computeInnerOptimization.m
@@ -37,7 +37,7 @@
 end
 modelCopy = Model(model);
 for i = 1:length(values)
-    functions{i}(values(i), modelCopy);
+    functions{i}(round(values(i), 10), modelCopy);
 end
 markersReference = makeJmpMarkerRef(modelCopy, markerFileName, params);
 error = computeInnerOptimizationHeuristic(modelCopy, markersReference, ...
diff --git a/src/JointModelPersonalization/KinematicCalibration/computeInverseKinematicsSquaredError.m b/src/JointModelPersonalization/KinematicCalibration/computeInverseKinematicsSquaredError.m
index 8d49b7b12..e05c2c058 100644
--- a/src/JointModelPersonalization/KinematicCalibration/computeInverseKinematicsSquaredError.m
+++ b/src/JointModelPersonalization/KinematicCalibration/computeInverseKinematicsSquaredError.m
@@ -31,29 +31,35 @@
 function error = computeInverseKinematicsSquaredError(model, ikSolver, ...
     markersReference, params)
 import org.opensim.modeling.*
-[state, numFrames, frequency, finishTime] = prepareFrameIterations(...
-    model, ikSolver, markersReference, params);
-markerTable = markersReference.getMarkerTable();
-times = markerTable.getIndependentColumn();
-error = [];
-frameCounter = 0;
-for i=1:numFrames %start time is set so start with recording error
-    ikSolver.track(state);
-    error = [error calculateFrameSquaredError(ikSolver)];
-    frameCounter = frameCounter + 1;
-    if(state.getTime() + 1/frequency > finishTime);break;end
-    time = times.get(markerTable.getNearestRowIndexForTime( ...
-        state.getTime() + 1/frequency - 0.00001));
-    state.setTime(double(time));
+persistent errorSize;
+try
+    [state, numFrames, frequency, finishTime] = prepareFrameIterations(...
+        model, ikSolver, markersReference, params);
+    markerTable = markersReference.getMarkerTable();
+    times = markerTable.getIndependentColumn();
+    error = [];
+    frameCounter = 0;
+    for i=1:numFrames %start time is set so start with recording error
+        ikSolver.track(state);
+        error = [error calculateFrameSquaredError(ikSolver)];
+        frameCounter = frameCounter + 1;
+        if(state.getTime() + 1/frequency > finishTime);break;end
+        time = times.get(markerTable.getNearestRowIndexForTime( ...
+            state.getTime() + 1/frequency - 0.00001));
+        state.setTime(double(time));
+    end
+    error = error / sqrt(frameCounter);
+    errorSize = size(error);
+catch
+    error = 1e2 * ones(errorSize);
 end
-error = error / sqrt(frameCounter);
 end
 
 % (Model, InverseKinematicsSolver, MarkersReference, struct) =>
 % (State, number, number, number)
 % Parses params for the IKSolver
 function [state, numFrames, frequency, finishTime] = ...
-        prepareFrameIterations(model, ikSolver, markersReference, params)
+    prepareFrameIterations(model, ikSolver, markersReference, params)
 state = initModelSystem(model);
 state.setTime(valueOrAlternate(params, 'startTime', ...
     markersReference.getValidTimeRange().get(0)));
diff --git a/src/JointModelPersonalization/KinematicCalibration/computeKinematicCalibration.m b/src/JointModelPersonalization/KinematicCalibration/computeKinematicCalibration.m
index e8ac341ab..f284ea1e1 100644
--- a/src/JointModelPersonalization/KinematicCalibration/computeKinematicCalibration.m
+++ b/src/JointModelPersonalization/KinematicCalibration/computeKinematicCalibration.m
@@ -55,9 +55,9 @@
 function [lowerBounds, upperBounds] = prepareKinematicCalibrationBounds(...
     initialValues, params)
 lowerBounds = valueOrAlternate(params, 'lowerBounds', ...
-    initialValues - 0.1); 
+    initialValues - 10); 
 upperBounds = valueOrAlternate(params, 'upperBounds', ...
-    initialValues + 0.1);
+    initialValues + 10);
 end
 
 % (struct) -> (struct)
@@ -73,7 +73,10 @@
     'stepTolerance', 1e-6);
 output.MaxFunctionEvaluations = valueOrAlternate(params, ...
     'maxFunctionEvaluations', 3e3);
+output.MaxIterations = valueOrAlternate(params, ...
+    'maxIterations', 4e6);
 output.Display = valueOrAlternate(params, ...
     'display','iter');
+output.FiniteDifferenceType = 'central';
 end
 
diff --git a/src/JointModelPersonalization/KinematicCalibration/functions/adjustBodyScaling.m b/src/JointModelPersonalization/KinematicCalibration/functions/adjustBodyScaling.m
index 5d7beef86..3b00230bf 100644
--- a/src/JointModelPersonalization/KinematicCalibration/functions/adjustBodyScaling.m
+++ b/src/JointModelPersonalization/KinematicCalibration/functions/adjustBodyScaling.m
@@ -29,12 +29,17 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function adjustBodyScaling(model, bodyName, value)
-
-markers = getMarkersFromBody(model, bodyName);
-markerLocations = {};
-for i = 1:length(markers)
-    markerLocations{i} = org.opensim.modeling.Vec3(model.getMarkerSet().get(markers{i}).get_location());
+function [body, joint, coordinate] = adjustBodyScaling(model, bodyName, value, anatomicalMarkers)
+body = bodyName;
+joint = "";
+coordinate = 0;
+if ~anatomicalMarkers
+    markers = getMarkersFromBody(model, bodyName);
+    markerLocations = {};
+    for i = 1:length(markers)
+        markerLocations{i} = org.opensim.modeling.Vec3( ...
+            model.getMarkerSet().get(markers{i}).get_location());
+    end
 end
 
 state = initializeState(model);
@@ -48,8 +53,10 @@ function adjustBodyScaling(model, bodyName, value)
 scaleSet.cloneAndAppend(scale);
 model.scale(state, scaleSet, true, -1.0);
 
-for i = 1:length(markers)
-    model.getMarkerSet().get(markers{i}).set_location(markerLocations{i});
+if ~anatomicalMarkers
+    for i = 1:length(markers)
+        model.getMarkerSet().get(markers{i}).set_location(markerLocations{i});
+    end
 end
 end
 
diff --git a/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildOrientation.m b/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildOrientation.m
index e0ecc2575..543373a50 100644
--- a/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildOrientation.m
+++ b/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildOrientation.m
@@ -28,7 +28,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function adjustChildOrientation(model, jointName, coordinateNum, value)
+function [body, joint, coordinate] = adjustChildOrientation(model, jointName, coordinateNum, value)
+body = "child_orientation";
+joint = jointName;
+coordinate = coordinateNum;
 import org.opensim.modeling.*
 frame = model.getJointSet().get(jointName).getChildFrame();
 offsetFrame = PhysicalOffsetFrame.safeDownCast(frame);
diff --git a/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildTranslation.m b/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildTranslation.m
index 365c39ed7..5a95305c2 100644
--- a/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildTranslation.m
+++ b/src/JointModelPersonalization/KinematicCalibration/functions/adjustChildTranslation.m
@@ -28,7 +28,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function adjustChildTranslation(model, jointName, coordinateNum, value)
+function [body, joint, coordinate] = adjustChildTranslation(model, jointName, coordinateNum, value)
+body = "child_translation";
+joint = jointName;
+coordinate = coordinateNum;
 import org.opensim.modeling.*
 frame = model.getJointSet().get(jointName).getChildFrame();
 offsetFrame = PhysicalOffsetFrame.safeDownCast(frame);
diff --git a/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentOrientation.m b/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentOrientation.m
index 3b9792047..26b384da7 100644
--- a/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentOrientation.m
+++ b/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentOrientation.m
@@ -28,7 +28,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function adjustParentOrientation(model, jointName, coordinateNum, value)
+function [body, joint, coordinate] = adjustParentOrientation(model, jointName, coordinateNum, value)
+body = "parent_orientation";
+joint = jointName;
+coordinate = coordinateNum;
 import org.opensim.modeling.*
 frame = model.getJointSet().get(jointName).getParentFrame();
 offsetFrame = PhysicalOffsetFrame.safeDownCast(frame);
diff --git a/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentTranslation.m b/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentTranslation.m
index b983a49d1..7f51b0eee 100644
--- a/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentTranslation.m
+++ b/src/JointModelPersonalization/KinematicCalibration/functions/adjustParentTranslation.m
@@ -28,7 +28,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function adjustParentTranslation(model, jointName, coordinateNum, value)
+function [body, joint, coordinate] = adjustParentTranslation(model, jointName, coordinateNum, value)
+body = "parent_translation";
+joint = jointName;
+coordinate = coordinateNum;
 import org.opensim.modeling.*
 frame = model.getJointSet().get(jointName).getParentFrame();
 offsetFrame = PhysicalOffsetFrame.safeDownCast(frame);
diff --git a/src/JointModelPersonalization/KinematicCalibration/functions/makeScalingFunction.m b/src/JointModelPersonalization/KinematicCalibration/functions/makeScalingFunction.m
index 3308cca4b..374b2016c 100644
--- a/src/JointModelPersonalization/KinematicCalibration/functions/makeScalingFunction.m
+++ b/src/JointModelPersonalization/KinematicCalibration/functions/makeScalingFunction.m
@@ -28,6 +28,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function fn = makeScalingFunction(bodyName)
-fn = @(value, model) adjustBodyScaling(model, bodyName, value);
+function fn = makeScalingFunction(bodyName, anatomicalMarkers)
+fn = @(value, model) adjustBodyScaling( ...
+    model, bodyName, value, anatomicalMarkers);
 end
diff --git a/src/JointModelPersonalization/adjustModelFromOptimizerOutput.m b/src/JointModelPersonalization/adjustModelFromOptimizerOutput.m
index 60312a51a..435bfdf40 100644
--- a/src/JointModelPersonalization/adjustModelFromOptimizerOutput.m
+++ b/src/JointModelPersonalization/adjustModelFromOptimizerOutput.m
@@ -32,6 +32,6 @@
     values)
 outputModel = Model(model);
 for i = 1:length(values)
-    functions{i}(values(i), outputModel);
+    functions{i}(round(values(i), 10), outputModel);
 end
 end
\ No newline at end of file
diff --git a/src/JointModelPersonalization/parseJointModelPersonalizationSettingsTree.m b/src/JointModelPersonalization/parseJointModelPersonalizationSettingsTree.m
index f0c9199f2..1182ff936 100644
--- a/src/JointModelPersonalization/parseJointModelPersonalizationSettingsTree.m
+++ b/src/JointModelPersonalization/parseJointModelPersonalizationSettingsTree.m
@@ -55,7 +55,7 @@
 end
 
 function inputs = getInputs(tree)
-inputs.model = parseModel(tree);
+inputs = parseModel(tree, struct());
 model = Model(inputs.model);
 inputs.tasks = getTasks(model, tree);
 inputs.desiredError = ...
@@ -80,22 +80,37 @@
 end
 
 function output = getTask(model, tree)
-output.markerFile = tree.marker_file_name.Text;
+output.markerFile = parseElementTextByName(tree, "marker_file_name");
+output.anatomicalMarkers = getBooleanLogicFromField( ...
+    getFieldByName(tree, "anatomical_markers"));
 timeRange = getFieldByName(tree, 'time_range');
 if(isstruct(timeRange))
     timeRange = strsplit(timeRange.Text, ' ');
     output.startTime = str2double(timeRange{1});
     output.finishTime = str2double(timeRange{2});
 end
+
+try
+    markerNames = parseSpaceSeparatedList(tree, "marker_names");
+    if ~isempty(markerNames)
+        output.markerNames = markerNames;
+    end
+catch; end
+try
+    freeMarkers = parseSpaceSeparatedList(tree, "free_markers");
+catch
+    freeMarkers = [];
+end
+
 output.parameters = {};
 if(isstruct(getFieldByName(tree, "JMPJointSet")))
     output.parameters = getJointParameters(tree.JMPJointSet);
 end
 output.scaling = [];
 output.markers = [];
-if(isstruct(getFieldByName(tree, "JMPBodySet")))
+if isstruct(getFieldByName(tree, "JMPBodySet")) || ~isempty(freeMarkers)
     [output.scaling, output.markers] = ...
-        getBodyParameters(tree.JMPBodySet, model);
+        getBodyParameters(tree.JMPBodySet, model, freeMarkers);
 end
 translationBounds = getFieldByName(tree, 'translation_bounds');
 if(isstruct(translationBounds))
@@ -170,7 +185,7 @@
 end
 
 function [scaling, markers] = getBodyParameters( ...
-    bodySetTree, model)
+    bodySetTree, model, freeMarkers)
 if isfield(bodySetTree, "JMPBody")
     bodyTree = bodySetTree.JMPBody;
     scaling = getScalingBodies(bodyTree);
@@ -179,6 +194,7 @@
     scaling = string([]);
     markers = {};
 end
+markers = addFreeMarkers(markers, freeMarkers);
 end
 
 function inputs = getScalingBodies(bodyTree)
@@ -224,6 +240,21 @@
         end
     end
 end
+
+end
+
+function markers = addFreeMarkers(markers, freeMarkers)
+for i = 1:length(freeMarkers)
+    axesToBeAdded = ["x", "y", "z"];
+    for j = 1:length(markers)
+        if markers{j}(1) == freeMarkers(i) && any(ismember(axesToBeAdded, markers{j}(2)))
+            axesToBeAdded = axesToBeAdded(~ismember(axesToBeAdded, markers{j}(2)));
+        end
+    end
+    for j = 1:length(axesToBeAdded)
+        markers{end+1} = [freeMarkers(i), axesToBeAdded(j)];
+    end
+end
 end
 
 function output = getInitialValues(model, parameters, scaling, markers)
diff --git a/src/MuscleTendonLengthInitialization/CostComputations/calcNormalizedFiberLengthMeanSimilarityCost.m b/src/MuscleTendonLengthInitialization/CostComputations/calcNormalizedFiberLengthMeanSimilarityCost.m
index a24ecd428..1c93ed5af 100644
--- a/src/MuscleTendonLengthInitialization/CostComputations/calcNormalizedFiberLengthMeanSimilarityCost.m
+++ b/src/MuscleTendonLengthInitialization/CostComputations/calcNormalizedFiberLengthMeanSimilarityCost.m
@@ -26,20 +26,21 @@
 % ----------------------------------------------------------------------- %
 
 function cost = calcNormalizedFiberLengthMeanSimilarityCost( ...
-    modeledValues, experimentalData, costTerm)
+    modeledValues, inputs, costTerm)
 errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
 maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.1);
 Ind = 1;
-for i = 1:length(experimentalData.normalizedFiberLengthGroups)
+lowestIndex = min(cell2mat(inputs.normalizedFiberLengthGroups)) - 1;
+for i = 1:length(inputs.normalizedFiberLengthGroups)
 normalizedFiberLengthSimilarity = ...
     abs(modeledValues.normalizedFiberLength(:, ...
-    experimentalData.normalizedFiberLengthGroups{i}, :) - ...
+    inputs.normalizedFiberLengthGroups{i} - lowestIndex, :) - ...
     mean(modeledValues.normalizedFiberLength(:, ...
-    experimentalData.normalizedFiberLengthGroups{i}, :),  2));
+    inputs.normalizedFiberLengthGroups{i} - lowestIndex, :),  2));
 normalizedFiberLengthSimilarityCost(Ind : Ind + ...
-    size(experimentalData.normalizedFiberLengthGroups{i}, 2) - 1) = ...
+    size(inputs.normalizedFiberLengthGroups{i}, 2) - 1) = ...
     log(sum(exp(500 * (normalizedFiberLengthSimilarity)), [1 3])) / 500;
-Ind = Ind + size(experimentalData.normalizedFiberLengthGroups{i}, 2);
+Ind = Ind + size(inputs.normalizedFiberLengthGroups{i}, 2);
 end
 
 cost = calcDeviationCostArray(...
diff --git a/src/MuscleTendonLengthInitialization/MuscleTendonLengthInitialization.m b/src/MuscleTendonLengthInitialization/MuscleTendonLengthInitialization.m
index a063cafd7..4f6e6ef3d 100644
--- a/src/MuscleTendonLengthInitialization/MuscleTendonLengthInitialization.m
+++ b/src/MuscleTendonLengthInitialization/MuscleTendonLengthInitialization.m
@@ -73,7 +73,7 @@
 % setup optimizer options struct to pass to fmincon
 function output = makeOptimizerOptions(params)
 output = optimset('UseParallel', true);
-output.MaxIter = valueOrAlternate(params, 'maxIterations', 10000);
+output.MaxIter = valueOrAlternate(params, 'maxIterations', 100);
 output.MaxFunEvals = valueOrAlternate(params, ...
     'maxFunctionEvaluations', 100000000);
 output.Display = 'iter';
diff --git a/src/MuscleTendonLengthInitialization/calcMuscleTendonLengthInitializationModeledValues.m b/src/MuscleTendonLengthInitialization/calcMuscleTendonLengthInitializationModeledValues.m
index 3a77c65c5..d863249f0 100644
--- a/src/MuscleTendonLengthInitialization/calcMuscleTendonLengthInitializationModeledValues.m
+++ b/src/MuscleTendonLengthInitialization/calcMuscleTendonLengthInitializationModeledValues.m
@@ -51,5 +51,4 @@
         experimentalData, modeledValues.maxIsometricForce, ...
         modeledValues.passiveNormalizedFiberLength);
 end
-end
-
+end
\ No newline at end of file
diff --git a/src/MuscleTendonLengthInitialization/getMaxIsometricForce.m b/src/MuscleTendonLengthInitialization/getMaxIsometricForce.m
index 7cf05a2bc..86cec8a8d 100644
--- a/src/MuscleTendonLengthInitialization/getMaxIsometricForce.m
+++ b/src/MuscleTendonLengthInitialization/getMaxIsometricForce.m
@@ -30,7 +30,6 @@
 
 scaledOptimalFiberLength = experimentalData.optimalFiberLength .* ...
     values.optimalFiberLengthScaleFactors;
-
 if experimentalData.optimizeIsometricMaxForce
     scaledMaximumMuscleStress = experimentalData.maximumMuscleStress .* ...
         values.maximumMuscleStressScaleFactor;
@@ -40,4 +39,4 @@
 else 
     maxIsometricForce = experimentalData.maxIsometricForce;
 end
-end
+end
\ No newline at end of file
diff --git a/src/MuscleTendonLengthInitialization/parseMuscleTendonLengthInitializationSettingsTree.m b/src/MuscleTendonLengthInitialization/parseMuscleTendonLengthInitializationSettingsTree.m
index 778ee2595..dfac6b826 100644
--- a/src/MuscleTendonLengthInitialization/parseMuscleTendonLengthInitializationSettingsTree.m
+++ b/src/MuscleTendonLengthInitialization/parseMuscleTendonLengthInitializationSettingsTree.m
@@ -35,6 +35,7 @@
     inputs = getInputs(settingsTree);
     inputs = getMtpModelInputs(inputs);
     inputs = getMuscleVolume(inputs);
+    inputs = rmfield(inputs, "model");
 else
     inputs = false;
 end
@@ -52,6 +53,7 @@
 function inputs = getPassiveData(tree, inputs)
 import org.opensim.modeling.Storage
 passiveInputDirectory = getFieldByName(tree, 'passive_data_input_directory').Text;
+inputs.passiveInputDirectory = passiveInputDirectory;
 inputs.passiveMomentDataExists = 0;
 if (~isempty(passiveInputDirectory))
     if isfolder(passiveInputDirectory)
@@ -69,20 +71,26 @@
             passiveInputDirectory, "MAData"), inputs.passivePrefixes);
         [inputs.passiveMuscleTendonLength, ...
         inputs.passiveMuscleTendonLengthColumnNames] = ...
-            parseFileFromDirectories(passiveDirectories, "Length.sto", ...
+            parseFileFromDirectories(passiveDirectories, "_Length.sto", ...
             Model(inputs.model));
         if ~(sum(ismember(inputs.muscleNames, ...
                 inputs.passiveMuscleTendonLengthColumnNames)) == ...
                 length(inputs.muscleNames))
             throw(MException('', 'Muscle names in passive data do not match muscle names from coordinates.'))
         end
-        inputs.passiveMomentArms = ...
+        [inputs.passiveMomentArms, inputs.passiveMomentArmCoordinates] = ...
             parseMomentArms(passiveDirectories, inputs.model);
         includedIndices = ismember( ...
             inputs.passiveMuscleTendonLengthColumnNames, inputs.muscleNames);
         inputs.passiveMuscleTendonLengthColumnNames = inputs.passiveMuscleTendonLengthColumnNames(includedIndices);
-        inputs.passiveMomentArms = inputs.passiveMomentArms(:, :, includedIndices, :);
-
+        [~, ~, momentCoordinateIndices] = intersect(inputs.coordinateNames, ...
+            inputs.passiveMomentArmCoordinates, 'stable');
+        if isempty(momentCoordinateIndices)
+            [~, ~, momentCoordinateIndices] = intersect(inputs.coordinateNames, ...
+            strcat(inputs.passiveMomentArmCoordinates,"_moment"), 'stable');
+        end
+        inputs.passiveMomentArms = inputs.passiveMomentArms(:, momentCoordinateIndices, includedIndices, :);
+        
         inputs.passiveMuscleTendonLength = inputs.passiveMuscleTendonLength(:, includedIndices, :);
         inputs.passiveMomentDataExists = 1;
     end
@@ -143,10 +151,12 @@
     normalizedFiberLengthGroupNames, inputs.model);
 inputs.numMuscleGroups = numel(inputs.normalizedFiberLengthGroups);
 numMuscles = length(inputs.muscleNames);
+lowestIndex = min(cell2mat(inputs.normalizedFiberLengthGroups));
 for i = 1 : inputs.numMuscleGroups
     for j = 1 : numel(inputs.normalizedFiberLengthGroups{i})
         inputs.groupedMaxNormalizedFiberLength(...
-            inputs.normalizedFiberLengthGroups{i}(j)) = i;
+            inputs.normalizedFiberLengthGroups{i}(j) ...
+            - lowestIndex + 1) = i;
     end
 end
 inputs.numMusclesIndividual = 0;
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcStepLengthAsymmetry.m b/src/MuscleTendonPersonalization/Analysis/extractMtpDataFromSto.m
similarity index 57%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcStepLengthAsymmetry.m
rename to src/MuscleTendonPersonalization/Analysis/extractMtpDataFromSto.m
index 50bbb3328..5b4a26b7f 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcStepLengthAsymmetry.m
+++ b/src/MuscleTendonPersonalization/Analysis/extractMtpDataFromSto.m
@@ -1,11 +1,13 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates step length asymmetry. Step length asymmetry is
-% calculated as the ratio between step lengths, therefore a step length
-% asymmetry of 1 represent symmetry. 
-%
-% (struct, struct) -> (Number)
+% This function reads all .sto files in resultsDirectory and converts them
+% to a 3D array. Dimensions 1 & 2 represent rows and columns from a single 
+% file, and dimension 3 holds different files. Returns a row vector
+% containing column headings read from the .sto file, and a 3D array
+% containing data from all files in resultsDirectory.
 %
+% (string) -> (array), (array)
+% Extracts data from .sto file.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -15,7 +17,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Robert Salati                                                %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -29,21 +31,24 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function stepLengthAsymmetry = calcStepLengthAsymmetry(modeledValues, ...
-    params)
-
-for i = 1:length(params.contactSurfaces)
-    if i == 1
-        stepLength(i) = calcStepLength(modeledValues. ...
-                groundReactionsLab.forces{i}(:,2), ...
-            [modeledValues.bodyLocations.parent{i}(:, 1) ...
-            modeledValues.bodyLocations.parent{i+1}(:, 1)]);
+function [columnNames, data] = extractMtpDataFromSto(resultsDirectory)
+    import org.opensim.modeling.Storage
+    if exist(resultsDirectory, "dir")
+        dataDir = dir(resultsDirectory);
+        dataFiles = {dataDir(3:end).name};
     else
-        stepLength(i) = calcStepLength(modeledValues. ...
-                groundReactionsLab.forces{i}(:,2), ...
-            [modeledValues.bodyLocations.parent{i}(:, 1) ...
-            modeledValues.bodyLocations.parent{i-1}(:, 1)]);
+        fprintf("%s not found\n", resultsDirectory);
+        columnNames = [];
+        data = [];
+        return
+    end
+    data = cell(1, numel(dataFiles));
+    for i = 1:numel(dataFiles)
+        dataStorage = Storage(fullfile(fullfile(resultsDirectory, dataFiles{i})));
+        columnNames = getStorageColumnNames(dataStorage);
+        data{i} = storageToDoubleMatrix(dataStorage)';
     end
-end
-stepLengthAsymmetry = stepLength(1) / stepLength(2);
+    trialSize = size(data{1});
+    numTrials = numel(data);
+    data = reshape(cell2mat(data), trialSize(1), trialSize(2), numTrials);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingJointJerkIntegrand.m b/src/MuscleTendonPersonalization/Analysis/plotMeanAndStd.m
similarity index 74%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingJointJerkIntegrand.m
rename to src/MuscleTendonPersonalization/Analysis/plotMeanAndStd.m
index 0fc708907..44e8ed751 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingJointJerkIntegrand.m
+++ b/src/MuscleTendonPersonalization/Analysis/plotMeanAndStd.m
@@ -1,9 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function minimizes the joint jerk for the specified coordinate.
+% This function takes a mean and standard deviation and plots the mean with
+% a solid line and shades +/- 1 standard deviation from the mean. 
 %
-% (2D matrix, struct, Array of string) -> (Array of number)
-% 
+% (Array), (Array), (Array), (String) -> (None)
+% Plot passive moment curves from file.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Robert Salati                                                %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -26,11 +27,9 @@
 % implied. See the License for the specific language governing            %
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
-
-function cost = calcMinimizingJointJerkIntegrand(jointJerks, params, ...
-    coordinateName)
-
-indx = find(strcmp(convertCharsToStrings(params.coordinateNames), ...
-    coordinateName));
-cost = calcMinimizingCostArrayTerm(jointJerks(:, indx));
+function plotMeanAndStd(mean, std, time, color)
+    plot(time, mean, color, linewidth=2)
+    FillRegion = [(mean+std); flipud(mean-std)];
+    fill([time, fliplr(time)]', FillRegion, color, FaceAlpha=0.2, ...
+        EdgeColor='none', HandleVisibility='off')
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcStepTimeAsymmetry.m b/src/MuscleTendonPersonalization/Analysis/plotMtpHillTypeMuscleParams.m
similarity index 55%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcStepTimeAsymmetry.m
rename to src/MuscleTendonPersonalization/Analysis/plotMtpHillTypeMuscleParams.m
index 5172e4e39..3d423b813 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcStepTimeAsymmetry.m
+++ b/src/MuscleTendonPersonalization/Analysis/plotMtpHillTypeMuscleParams.m
@@ -1,11 +1,11 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates step time asymmetry. Step time asymmetry is
-% calculated as the ratio between single support times, therefore a step 
-% time asymmetry of 1 represent symmetry. 
-%
-% (struct, struct, struct) -> (Number)
+% This function reads .sto files created by
+% saveMuscleTendonPersonalizationResults.m containing optimized Hill-type
+% muscle-tendon model parameters and creates a bar plot of them.
 %
+% (string) -> (None)
+% Plot Hill-Type Muscle-Tendon model parameters from file.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -15,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,20 +28,34 @@
 % implied. See the License for the specific language governing            %
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
+function plotMtpHillTypeMuscleParams(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+[muscleNames, params] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "muscleModelParameters"));
+muscleNames = strrep(muscleNames, '_', ' ');
+figure(Name = strcat(resultsDirectory, " Muscle Model Parameters"), ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
 
-function stepTimeAsymmetry = calcStepTimeAsymmetry(values, ...
-    modeledValues, params)
+paramLabels = ["Activation Time Constant", ...
+    "Activation Nonlinearity", ...
+    "Electromechanical Time Delay", ...
+    "EMG Scaling Factor", ...
+    "Optimal Fiber Length Scaling Factor", ...
+    "Tendon Slack Length Scaling Factor"];
+t = tiledlayout(1, 6, ...
+    TileSpacing='Compact', Padding='Compact');
+for i = 1 : numel(paramLabels)
+    nexttile(i)
+    barh(1:numel(muscleNames), params(i,:))
 
-for i = 1:length(params.contactSurfaces)
+    title(textwrap(paramLabels(i), 20), FontSize=12)
     if i == 1
-        singleSupportTime(i) = calcSingleSupportTime( ...
-            modeledValues.groundReactionsLab.forces{i + 1}(:, 2), ...
-            values.time);
+        yticks(1:numel(muscleNames))
+        yticklabels(muscleNames)
     else
-        singleSupportTime(i) = calcSingleSupportTime( ...
-            modeledValues.groundReactionsLab.forces{i - 1}(:, 2), ...
-            values.time);
+        yticks([])
+        yticklabels([])
     end
 end
-stepTimeAsymmetry = singleSupportTime(1) / singleSupportTime(2);
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Analysis/plotMtpJointMoments.m b/src/MuscleTendonPersonalization/Analysis/plotMtpJointMoments.m
new file mode 100644
index 000000000..07ae559d0
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Analysis/plotMtpJointMoments.m
@@ -0,0 +1,110 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files created by
+% saveMuscleTendonPersonalizationResults.m containing inverse dynamics
+% joint moments and model joint moments and creates plots of them.
+%
+% (string) -> (None)
+% Plot joint moment curves from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotMtpJointMoments(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+% Include max allowable error, and rmse
+figureHeight = 1;
+
+[jointLabels, idMoments] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "inverseDynamicsJointMoments"));
+
+[~, modelMoments] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "modelJointMoments"));
+
+if exist(fullfile(analysisDirectory, "modelJointMomentsSynx"), "dir")
+    [~, modelMomentsSynx] = extractMtpDataFromSto( ...
+        fullfile(analysisDirectory, "modelJointMomentsSynx"));
+    figureHeight = figureHeight + 1;
+else
+    modelMomentsSynx = [];
+end
+
+jointLabels = strrep(jointLabels, '_', ' ');
+meanIdMoments = mean(idMoments, 3);
+stdIdMoments = std(idMoments, [], 3);
+meanMoments = mean(modelMoments, 3);
+stdMoments = std(modelMoments, [], 3);
+meanMomentsSynx = mean(modelMomentsSynx, 3);
+stdMomentsSynx = std(modelMomentsSynx, [], 3);
+maxMoment = max([ ...
+    max(meanIdMoments, [], "all"), ...
+    max(meanMoments, [], "all"), ...
+    max(meanMomentsSynx, [], "all")]);
+minMoment = min([ ...
+    min(meanIdMoments, [], "all"), ...
+    min(meanMoments, [], "all"), ...
+    min(meanMomentsSynx, [], "all")]);
+
+figure(Name = strcat(resultsDirectory, " Joint Moments"), ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+time = 1:1:size(meanIdMoments,1);
+figureWidth = numel(jointLabels);
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+for i=1:numel(jointLabels)
+    if ~isempty(meanMoments)
+        nexttile(i);
+        hold on
+        plotMeanAndStd(meanMoments(:,i), stdMoments(:,i), time, 'r-')
+        plotMeanAndStd(meanIdMoments(:,i), stdIdMoments(:,i), time, 'b-')
+        hold off
+        set(gca, fontsize=11)
+        rmse = rms(meanMoments(:,i) - meanIdMoments(:,i));
+        mae = mean(abs(meanMoments(:,i) - meanIdMoments(:,i)));
+        title(sprintf("%s \n RMSE: %.4f, MAE: %.4f", ...
+            jointLabels(i), rmse, mae), fontsize=12)
+        axis([time(1) time(end) minMoment, maxMoment])
+        if i == 1
+            legend("Mean Moment No Synx", "Mean Inverse Dynamics Moment")
+            ylabel("Joint Moment [Nm]")
+        end
+    end
+    if ~isempty(meanMomentsSynx)
+        nexttile(i+figureWidth);
+        hold on
+        plotMeanAndStd(meanMomentsSynx(:,i), stdMomentsSynx(:,i), time, 'r-')
+        plotMeanAndStd(meanIdMoments(:,i), stdIdMoments(:,i), time, 'b-')
+        hold off
+        set(gca, fontsize=11)
+        rmse = rms(meanMomentsSynx(:,i) - meanIdMoments(:,i));
+        mae = mean(abs(meanMomentsSynx(:,i) - meanIdMoments(:,i)));
+        title(sprintf("%s \n RMSE: %.4f, MAE: %.4f", ...
+            jointLabels(i), rmse, mae), fontsize=12)
+        axis([time(1) time(end) minMoment, maxMoment])
+        if i == 1
+            legend("Mean Moment Synx", "Mean Inverse Dynamics Moment")
+            ylabel("Joint Moment [Nm]")
+        end
+    end
+    xlabel("Time Points")
+end
+end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Analysis/plotMtpMuscleExcitationsAndActivations.m b/src/MuscleTendonPersonalization/Analysis/plotMtpMuscleExcitationsAndActivations.m
new file mode 100644
index 000000000..3b26717bc
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Analysis/plotMtpMuscleExcitationsAndActivations.m
@@ -0,0 +1,104 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files created by
+% saveMuscleTendonPersonalizationResults.m containing muscle excitations
+% and activations and creates plots of them.
+%
+% (string) -> (None)
+% Plot muscle activations and excitations from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function plotMtpMuscleExcitationsAndActivations(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+[muscleNames, excitations] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "muscleExcitations"));
+
+[~, activations] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "muscleActivations"));
+
+if exist(fullfile(analysisDirectory, "muscleExcitationsSynx"), "dir")
+    [~, excitationsSynx] = extractMtpDataFromSto( ...
+        fullfile(analysisDirectory, "muscleExcitationsSynx"));
+else
+    excitationsSynx = [];
+end
+
+if exist(fullfile(analysisDirectory, "muscleActivationsSynx"), "dir")
+    [~, activationsSynx] = extractMtpDataFromSto( ...
+        fullfile(analysisDirectory, "muscleActivationsSynx"));
+else
+    activationsSynx = [];
+end
+muscleNames = strrep(muscleNames, '_', ' ');
+meanExcitations = mean(excitations, 3);
+stdExcitations = std(excitations,[], 3);
+meanActivations = mean(activations, 3);
+stdActivations = std(activations,[], 3);
+meanExcitationsSynx = mean(excitationsSynx, 3);
+stdExcitationsSynx = std(excitationsSynx,[], 3);
+meanActivationsSynx = mean(activationsSynx, 3);
+stdActivationsSynx = std(activationsSynx,[], 3);
+time = 1:1:size(meanExcitations,1);
+
+figureWidth = ceil(sqrt(numel(muscleNames)));
+figureHeight = ceil(numel(muscleNames)/figureWidth);
+figure(Name = strcat(resultsDirectory, " Muscle Excitations and Activations"), ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+
+for i = 1:numel(muscleNames)
+    nexttile(i);
+    hold on
+    if ~isempty(meanExcitationsSynx)
+        plotMeanAndStd(meanExcitations(:,i), stdExcitations(:,i), time, 'b--');
+        plotMeanAndStd(meanActivations(:,i), stdActivations(:,i), time, 'r--');
+        plotMeanAndStd(meanExcitationsSynx(:,i), stdExcitationsSynx(:,i), time, 'b-');
+        plotMeanAndStd(meanActivationsSynx(:,i), stdActivationsSynx(:,i), time, 'r-');
+    else
+        plotMeanAndStd(meanExcitations(:,i), stdExcitations(:,i), time, 'b-');
+        plotMeanAndStd(meanActivations(:,i), stdActivations(:,i), time, 'r-');
+    end
+    set(gca, fontsize=11)
+    axis([time(1) time(end) 0 1])
+    if (max(meanExcitations(:, i)) == 0)
+        title(strcat(muscleNames(i), " *"), FontSize=12);
+    else
+        title(muscleNames(i), FontSize=12);
+    end
+    if i == 1
+        legend ('Excitation (No SynX)', ...
+            'Activation (No SynX)', ...
+            'Excitation (With SynX)', ...
+            'Activation (With SynX)');
+    end
+    if mod(i,figureWidth) == 1
+        ylabel("Magnitude")
+    end
+    if i>numel(muscleNames)-figureWidth
+        xlabel("Time Points")
+    end
+end
+end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Analysis/plotMtpNormalizedFiberLengths.m b/src/MuscleTendonPersonalization/Analysis/plotMtpNormalizedFiberLengths.m
new file mode 100644
index 000000000..b89c10d94
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Analysis/plotMtpNormalizedFiberLengths.m
@@ -0,0 +1,69 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files created by
+% saveMuscleTendonPersonalizationResults.m containing normalized fiber
+% lengths and creates plots of them.
+%
+% (string) -> (None)
+% Plot normalized fiber lengths from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotMtpNormalizedFiberLengths(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+[muscleNames, normalizedFiberLengths] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "normalizedFiberLengths"));
+muscleNames = strrep(muscleNames, '_', ' ');
+meanFiberLengths = mean(normalizedFiberLengths, 3);
+stdFiberLengths = std(normalizedFiberLengths, [], 3);
+time = 1:1:size(meanFiberLengths,1);
+passiveLower = ones(size(time))*0.7;
+passiveUpper = ones(size(time));
+
+figureWidth = ceil(sqrt(numel(muscleNames)));
+figureHeight = ceil(numel(muscleNames)/figureWidth);
+figure(Name = strcat(resultsDirectory, " Normalized Fiber Lengths"), ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+
+for i=1:numel(muscleNames)
+    nexttile(i);
+    hold on
+    plotMeanAndStd(meanFiberLengths(:,i), stdFiberLengths(:,i), time, 'b-')
+    plot(time, passiveUpper, 'r--', LineWidth=2);
+    plot(time, passiveLower, 'r--', LineWidth=2);
+    hold off
+    set(gca, fontsize=11)
+    axis([time(1) time(end) 0 1.5])
+    title(muscleNames(i), FontSize=12);
+    if mod(i,figureWidth) == 1
+        ylabel(textwrap("Normalized Fiber Length",10), FontSize=12)
+    end
+    if i>numel(muscleNames)-figureWidth
+        xlabel("Time Points")
+    end
+end
+
+end
+
diff --git a/src/MuscleTendonPersonalization/Analysis/plotMtpPassiveForceCurves.m b/src/MuscleTendonPersonalization/Analysis/plotMtpPassiveForceCurves.m
new file mode 100644
index 000000000..43b2f62b8
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Analysis/plotMtpPassiveForceCurves.m
@@ -0,0 +1,66 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files created by
+% saveMuscleTendonPersonalizationResults.m containing passive force curves 
+% and creates plots of them.
+%   
+% (string) -> (None)
+% Plot passive force curves from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotMtpPassiveForceCurves(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+
+[muscleNames, modelForce] = extractMtpDataFromSto(...
+    fullfile(analysisDirectory, "passiveForcesModel"));
+
+muscleNames = strrep(muscleNames, '_', ' ');
+meanModelForce = mean(modelForce, 3);
+stdModelForce = std(modelForce, [], 3);
+maxForce = max(meanModelForce,[], 'all');
+numWindows = ceil(sqrt(numel(muscleNames)));
+
+figureWidth = ceil(sqrt(numel(muscleNames)));
+figureHeight = ceil(numel(muscleNames)/figureWidth);
+figure(Name = strcat(resultsDirectory, " Passive Force Curves"), ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+time = 1:1:size(meanModelForce,1);
+for i = 1:numel(muscleNames)
+    nexttile(i)
+    hold on
+    plotMeanAndStd(meanModelForce(:,i), stdModelForce(:,i), time, 'b-');
+    hold off
+    set(gca, fontsize=11)
+    axis([time(1) time(end) 0 maxForce])
+    title(muscleNames(i), FontSize=12);
+    if mod(i,figureWidth) == 1
+        ylabel("Force [N]")
+    end
+    if i>numel(muscleNames)-figureWidth
+        xlabel("Time Points")
+    end
+end
+
diff --git a/src/MuscleTendonPersonalization/Analysis/plotMtpPassiveMomentCurves.m b/src/MuscleTendonPersonalization/Analysis/plotMtpPassiveMomentCurves.m
new file mode 100644
index 000000000..fa58eea62
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Analysis/plotMtpPassiveMomentCurves.m
@@ -0,0 +1,78 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files created by
+% saveMuscleTendonPersonalizationResults.m containing passive moment data 
+% and creates plots of experimental and modeled passive moment curves.
+%
+% (string) -> (None)
+% Plot passive moment curves from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function plotMtpPassiveMomentCurves(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+[momentNames, passiveMomentsExperimental] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "passiveJointMomentsExperimental"));
+[~, passiveMomentsModel] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "passiveJointMomentsModeled"));
+momentNames = strrep(momentNames, '_', ' ');
+meanMomentsExperimental = mean(passiveMomentsExperimental, 3);
+stdMomentsExperimental = std(passiveMomentsExperimental, [], 3);
+meanMomentsModel = mean(passiveMomentsModel, 3);
+stdMomentsModel = std(passiveMomentsModel, [], 3);
+maxMoment = max([max(meanMomentsExperimental, [], 'all'), ...
+    max(meanMomentsModel, [], 'all')]);
+minMoment = min([min(meanMomentsExperimental, [], 'all'), ...
+    min(meanMomentsModel, [], 'all')]);
+time = 1:1:size(meanMomentsModel,1);
+
+figureWidth = ceil(sqrt(numel(momentNames)));
+figureHeight = ceil(numel(momentNames)/figureWidth);
+
+figure(Name = strcat(resultsDirectory, " Passive Moment Curves"), ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+
+for i = 1:numel(momentNames)
+    nexttile(i);
+    hold on
+    plotMeanAndStd(meanMomentsExperimental(:,i), stdMomentsExperimental(:,i), ...
+        time, 'k-')
+    plotMeanAndStd(meanMomentsModel(:,i), stdMomentsModel(:,i), time, 'r-')
+    hold off
+    set(gca, fontsize=11)
+    rmse = rms(passiveMomentsExperimental(:,i) - passiveMomentsModel(:,i));
+    title(sprintf("%s \n RMSE: %.4f", ...
+        momentNames(i), rmse), FontSize=12)
+    axis([time(1) time(end) minMoment maxMoment])
+    if i == 1
+        legend("Experimental", "Model")
+    end
+    if mod(i,figureWidth) == 1
+        ylabel("Moment [Nm]")
+    end
+end
+end
+
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrailingLimb.m b/src/MuscleTendonPersonalization/Analysis/printMtpJointMomentMatchingError.m
similarity index 52%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrailingLimb.m
rename to src/MuscleTendonPersonalization/Analysis/printMtpJointMomentMatchingError.m
index 4d8074ba4..9c5e198ad 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrailingLimb.m
+++ b/src/MuscleTendonPersonalization/Analysis/printMtpJointMomentMatchingError.m
@@ -1,13 +1,11 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the trailing limb angle. The trailing limb angle
-% is the angle between OpenSim's vertical axis and a vector created between
-% the greater trochanter and the fifth metatarsal head. The location of the
-% greater trochanter and the fifth metatarsal is required. The name of the
-% bodies that each location is in reference to must also be assigned.  
-%
-% (struct, struct, 2D matrix, struct) -> (Array of number)
+% This function reads .sto files created by 
+% saveMuscleTendonPersonalizationResults.m containing model and 
+% experimental joint moments and outputs RMSE error via print command. 
 %
+% (string) -> (None)
+% Print joint moment matching error from file.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -17,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -31,25 +29,27 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function trailingLimbAngle = calcTrailingLimb(costTerm, values, ...
-    normalForce, params)
-
-fifthMetarsalLocation = calcBodyLocation(values, str2num( ...
-    costTerm.toe_point), costTerm.toe_body, params);
-greaterTrochanterLocation = calcBodyLocation(values, str2num( ...
-    costTerm.femur_point), costTerm.femur_body, params);
-
-normalForce(normalForce<0) = 0;
-slope = diff(normalForce);
-toeOffEvent = getToeOffEvent(slope);
-
-if ~isempty(toeOffEvent)
-    trailingLimbVector = fifthMetarsalLocation(toeOffEvent, :) - ...
-        greaterTrochanterLocation(toeOffEvent, :);
-    trailingLimbUnitVector = trailingLimbVector/norm(trailingLimbVector);
-    dotProduct = dot(trailingLimbUnitVector, [0 -1 0]);
-    trailingLimbAngle = acosd(dotProduct);
-else 
-    trailingLimbAngle = 0;
+function printMtpJointMomentMatchingError(resultsDirectory)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+[jointMomentLabels, muscleJointMoments] = extractMtpDataFromSto( ...
+    fullfile(resultsDirectory, "modelMoments"));
+[~, inverseDynamicsMoments] = extractMtpDataFromSto( ...
+    fullfile(analysisDirectory, "inverseDynamicsJointMoments"));
+jointMomentsRmse = zeros(size(jointMomentLabels));
+jointMomentsMae = zeros(size(jointMomentLabels));
+for i = 1 : size(muscleJointMoments, 2)
+    jointMomentsRmse(i) = sqrt(sum((muscleJointMoments(:, i) - ...
+        inverseDynamicsMoments(:, i)) .^ 2, 'all') / ...
+        (numel(inverseDynamicsMoments(:, 1)) - 1));
+    jointMomentsMae(i) = sum(abs(muscleJointMoments(:, i) - ...
+        inverseDynamicsMoments(:, i)) / ...
+        numel(inverseDynamicsMoments(:, 1)), 'all');
+end
+fprintf(['The root mean sqrt (RMS) errors between model-predicted ' ...
+    'and inverse dynamic moments are: \n' ]);
+fprintf(['\n ' num2str(jointMomentsRmse) ' \n']);
+fprintf(['The mean absolute errors (MAEs) between model-predicted ' ...
+    'and inverse dynamic moments are: \n' ]);
+fprintf(['\n ' num2str(jointMomentsMae) ' \n']);
 end
-end
\ No newline at end of file
+
diff --git a/src/MuscleTendonPersonalization/Analysis/readMomentArmsForPlotting.m b/src/MuscleTendonPersonalization/Analysis/readMomentArmsForPlotting.m
new file mode 100644
index 000000000..db81f74c8
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Analysis/readMomentArmsForPlotting.m
@@ -0,0 +1,31 @@
+function momentArms = readMomentArmsForPlotting(precalInputs)
+    momentArmDirectory = fullfile(precalInputs.passiveInputDirectory, "MAData");
+    momentCoordinates = precalInputs.coordinateNames;
+    momentArms = zeros(12, 6, 86, 101);
+    momentArmFolders = dir(momentArmDirectory);
+    momentArmFolders = momentArmFolders(3:end);
+    coordinateNames = "MomentArm_"+precalInputs.coordinateNames+".sto";
+    for i=1:numel(momentArmFolders)
+        momentArmFiles = dir(fullfile(momentArmFolders(i).folder, momentArmFolders(i).name));
+        momentArmFiles = momentArmFiles(3:end);
+        k = 1;
+        for j = 1:numel(momentArmFiles)
+            if contains(momentArmFiles(j).name, coordinateNames)
+                data = storageToDoubleMatrix(fullfile(momentArmFiles(j).folder, momentArmFiles(j).name));
+                momentArms(i, k, :, :) = data;
+                k = k + 1;
+            end
+        end
+    end
+    includedIndices = ismember( ...
+            precalInputs.passiveMuscleTendonLengthColumnNames, precalInputs.muscleNames);
+    momentArms = momentArms(:, :, includedIndices, :);
+    temp = momentArms;
+    momentArms(:,5,:,:) = temp(:, 1, :, :);
+    momentArms(:,2,:,:) = temp(:, 2, :, :);
+    momentArms(:,1,:,:) = temp(:, 3, :, :);
+    momentArms(:,3,:,:) = temp(:, 4, :, :);
+    momentArms(:,4,:,:) = temp(:, 5, :, :);
+    momentArms(:,6,:,:) = temp(:, 6, :, :);
+end
+
diff --git a/src/MuscleTendonPersonalization/reportMuscleTendonPersonalizationResults.m b/src/MuscleTendonPersonalization/Analysis/reportMuscleTendonPersonalizationResults.m
similarity index 72%
rename from src/MuscleTendonPersonalization/reportMuscleTendonPersonalizationResults.m
rename to src/MuscleTendonPersonalization/Analysis/reportMuscleTendonPersonalizationResults.m
index 48926ecab..a38cba0bf 100644
--- a/src/MuscleTendonPersonalization/reportMuscleTendonPersonalizationResults.m
+++ b/src/MuscleTendonPersonalization/Analysis/reportMuscleTendonPersonalizationResults.m
@@ -32,12 +32,185 @@
 function reportMuscleTendonPersonalizationResults(optimizedParams, ...
     mtpInputs, precalInputs)
 if nargin < 3; precalInputs = []; end
-[finalValues, results, resultsSynx, resultsSynxNoResiduals] = ...
-    getValuesToReport(mtpInputs, precalInputs, optimizedParams);
 if ~isempty(precalInputs)
     plotMuscleTendonLengthInitializationResults(precalInputs, mtpInputs)
 end
+if isfield(mtpInputs, "synergyExtrapolation")
+    reportSynX(optimizedParams, mtpInputs, precalInputs)
+else
+    reportNoSynX(optimizedParams, mtpInputs, precalInputs)
+end
+end
+
+function reportNoSynX(optimizedParams, mtpInputs, precalInputs)
+[finalValues, results] = ...
+    getValuesToReportNoSynX(mtpInputs, precalInputs, optimizedParams);
+printJointMomentMatchingError(results.muscleJointMoments, ...
+    mtpInputs.inverseDynamicsMoments);
+makeExcitationAndActivationPlotsNoSynX(results, mtpInputs);
+makeModelParameterPlotsNoSynX(finalValues, mtpInputs)
+makeTaskSpecificMomentMatchingPlotsNoSynX(...
+    permute(results.muscleJointMoments, [3 1 2]), ...
+    permute(mtpInputs.inverseDynamicsMoments, [3 1 2]), ...
+    mtpInputs.coordinateNames)
+% makeTaskSpecificNormalizedFiberLengthsPlots( ...
+%     permute(resultsSynx.normalizedFiberLength, [3 1 2]), ...
+%     mtpInputs, mtpInputs.synergyExtrapolation)
+end
+
+function [finalValues, results] = getValuesToReportNoSynX(mtpInputs, ...
+    precalInputs, optimizedParams)
+finalValues = makeMtpValuesAsStruct([], optimizedParams, zeros(1, 7), mtpInputs);
+results = calcMtpModeledValues(finalValues, mtpInputs, struct());
+results.time = mtpInputs.emgTime(:, mtpInputs.numPaddingFrames + 1 : ...
+    end - mtpInputs.numPaddingFrames);
+results.muscleExcitations = results.muscleExcitations(:, :, ...
+    mtpInputs.numPaddingFrames + 1 : end - mtpInputs.numPaddingFrames);
+if ~isempty(precalInputs)
+finalOptimalFiberLength = ...
+    finalValues.optimalFiberLengthScaleFactors .* mtpInputs.optimalFiberLength;
+finalValues.optimalFiberLengthScaleFactors = ...
+    finalOptimalFiberLength ./ precalInputs.optimalFiberLength;
+finalTendonSlackLength = ...
+    finalValues.tendonSlackLengthScaleFactors .* mtpInputs.tendonSlackLength;
+finalValues.tendonSlackLengthScaleFactors = ...
+    finalTendonSlackLength ./ precalInputs.tendonSlackLength;
+end
+end
+
+function makeExcitationAndActivationPlotsNoSynX(results, ...
+    experimentalData)
+
+muscleLabels = experimentalData.muscleNames;
+
+muscleExcitations = results.muscleExcitations(:, :, :);
+muscleActivations = results.muscleActivations(:, :, :);
+meanMuscleExcitation = permute(mean(muscleExcitations, 1), [3 2 1]);
+stdMuscleExcitation = permute(std(muscleExcitations, [], 1), [3 2 1]);
+meanMuscleActivation = permute(mean(muscleActivations, 1), [3 2 1]);
+stdMuscleActivation = permute(std(muscleActivations, [], 1), [3 2 1]);
 
+t = 1 : size(meanMuscleExcitation, 1);
+nplot = ceil(sqrt(numel(muscleLabels)));
+for j = 1 : numel(muscleLabels)
+    subplot(nplot,nplot,j);
+    plot(meanMuscleExcitation(:, j), 'b-', 'LineWidth', 2); hold on
+    fill([t'; flipud(t')], ...
+    [meanMuscleExcitation(:, j) - stdMuscleExcitation(:, j); ...
+    flipud(meanMuscleExcitation(:, j) + stdMuscleExcitation(:, j))], ...
+    'b', 'linestyle', 'None', 'FaceAlpha', 0.5);
+    hold on
+    plot(meanMuscleActivation(:, j), 'r-', 'LineWidth', 2); hold on
+    fill([t'; flipud(t')], ...
+    [meanMuscleActivation(:, j) - stdMuscleActivation(:, j); ...
+    flipud(meanMuscleActivation(:, j) + stdMuscleActivation(:, j))], ...
+    'r', 'linestyle', 'None', 'FaceAlpha', 0.5);
+    axis([1 size(meanMuscleExcitation, 1) 0 1])
+    title(muscleLabels{j});
+    if j == 1
+        legend ('Excitation(without residual)', '', ...
+            'Activation(without residual)', '');
+    end
+end
+set(gca, 'FontSize', 12)
+end
+
+function makeModelParameterPlotsNoSynX(finalValues, experimentalData)
+
+muscleLabels = experimentalData.muscleNames;
+
+In_width = 0.145; % witdth of each subplot
+figure('name', 'Model Parameters', 'units', 'normalized', ...
+    'outerposition', [0 0 1 1]);
+for subplotElement = 1 : 6
+    subplotTight(1, 6, subplotElement, [0.04, 0.001]);
+    switch subplotElement 
+        case 1 %activationTimeConstant
+            bar(1 : numel(muscleLabels), finalValues.activationTimeConstants, ...
+                'barwidth', 0.8, 'Horizontal', 'on', 'FaceAlpha', 0.6); 
+            hold on;
+            title('Activation Time Constant (cs)')
+            pos_in = get(gca, 'Position');
+            pos_in(3) = In_width;
+            pos_in(1) = pos_in(1) + 0.05;
+            set(gca, 'YTick', 1 : numel(muscleLabels), 'yTickLabel', ...
+                muscleLabels, 'Fontsize', 11, 'Position', pos_in);
+        case 2 %activationNonlinearity
+            bar(finalValues.activationNonlinearityConstants, 'Horizontal', 'on', ...
+                'barwidth', 0.8, 'FaceAlpha', 0.6);
+            title('Activation Nonlinearity')
+            pos_in(1) = pos_in(1) + pos_in(3) + 0.015;
+            set(gca, 'YTick', [], 'yTickLabel', [], 'Position', pos_in, ...
+                'Fontsize', 11);
+        case 3 %timeDelay
+            bar(finalValues.electromechanicalDelays, 'Horizontal', 'on', 'barwidth', 0.8, ...
+                'FaceAlpha', 0.6);
+            title('Electromechanical Time Delay (ds)')
+            pos_in(1) = pos_in(1) + pos_in(3) + 0.015;
+            set(gca, 'YTick', [], 'yTickLabel', [],'Position', pos_in, ...
+                'Fontsize', 11);
+        case 4 % emgScalingFactor
+            bar(finalValues.emgScaleFactors, 'Horizontal', 'on', 'barwidth', 0.8, ...
+                'FaceAlpha', 0.6);
+            title('Emg Scaling Factor')
+            pos_in(1) = pos_in(1) + pos_in(3) + 0.015;
+            set(gca, 'YTick', [], 'yTickLabel', [],'Position', pos_in, ...
+                'Fontsize', 11);
+        case 5 %muscleOptimalLength
+            bar(finalValues.optimalFiberLengthScaleFactors, 'Horizontal', 'on', 'barwidth', ...
+                0.8, 'FaceAlpha', 0.6);
+            title('Optimal Fiber Length Scaling Factor')
+            pos_in(1) = pos_in(1) + pos_in(3) + 0.015;
+            set(gca, 'YTick', [], 'yTickLabel', [],'Position', pos_in, ...
+                'Fontsize', 11);
+        case 6 %tendonSlackLength            
+            bar(finalValues.tendonSlackLengthScaleFactors, 'Horizontal', 'on', 'barwidth', ...
+                0.8, 'FaceAlpha', 0.6);
+            title('Tendon Slack Length Scaling Factor')
+            pos_in(1) = pos_in(1) + pos_in(3) + 0.015;
+            set(gca, 'YTick', [], 'yTickLabel', [],'Position', pos_in, ...
+                'Fontsize', 11);
+    end
+end
+end
+
+function makeTaskSpecificMomentMatchingPlotsNoSynX(jointMoments, ...
+    inverseDynamicsMoments, coordinates)
+
+figure('name', ['Joint moments']);
+meanJointMoments = squeeze(mean(jointMoments, 2));
+stdJointMoments = squeeze(std(jointMoments, [], 2));
+meaninverseDynamicsMoments = squeeze(mean(inverseDynamicsMoments, 2));
+stdinverseDynamicsMoments = squeeze(std(inverseDynamicsMoments, [], 2));
+t = 1 : size(jointMoments,1);
+for j = 1:size(jointMoments,3)
+subplot(2, size(jointMoments, 3), j);
+plot(-meanJointMoments(:, j), 'r', 'LineWidth', 2); hold on
+fill([t'; flipud(t')], ...
+    [-meanJointMoments(:,j) - stdJointMoments(:,j); ...
+    flipud(-meanJointMoments(:, j) + stdJointMoments(:, j))], ...
+    'r', 'linestyle', 'None', 'FaceAlpha', 0.5);
+subplot(2, size(jointMoments, 3), j); 
+plot(-meaninverseDynamicsMoments(:, j), 'k', 'LineWidth', 2);
+fill([t'; flipud(t')], ...
+    [-meaninverseDynamicsMoments(:, j) - stdinverseDynamicsMoments(:, j); ...
+    flipud(-meaninverseDynamicsMoments(:, j) + stdinverseDynamicsMoments(:, j))], ...
+    'k', 'linestyle', 'None', 'FaceAlpha', 0.5);
+title({[strrep(coordinates{j}, '_', ' ') ],'Moment (N-m)'});
+xlabel('Time Frames'); axis([0 100 -80 120]);
+if j == 1; ylabel('Moment (N-m)');
+elseif j == numel(coordinates)
+    lgd = legend("");
+    lgd.Orientation ='horizontal';
+    lgd.NumColumns = 2;
+end
+set(gca, 'FontSize', 12)
+end
+end
+
+function reportSynX(optimizedParams, mtpInputs, precalInputs)
+[finalValues, results, resultsSynx, resultsSynxNoResiduals] = ...
+    getValuesToReport(mtpInputs, precalInputs, optimizedParams);
 printJointMomentMatchingError(resultsSynx.muscleJointMoments, ...
     mtpInputs.inverseDynamicsMoments);
 makeExcitationAndActivationPlots(results, resultsSynx, mtpInputs, ...
@@ -53,10 +226,11 @@ function reportMuscleTendonPersonalizationResults(optimizedParams, ...
     permute(resultsSynx.normalizedFiberLength, [3 1 2]), ...
     mtpInputs, mtpInputs.synergyExtrapolation)
 end
+
 function [finalValues, results, resultsSynx, resultsSynxNoResiduals] = ...
     getValuesToReport(mtpInputs, precalInputs, optimizedParams)
 
-finalValues = makeMtpValuesAsStruct([], optimizedParams, zeros(1, 7));
+finalValues = makeMtpValuesAsStruct([], optimizedParams, zeros(1, 7), mtpInputs);
 resultsSynx = calcMtpSynXModeledValues(finalValues, mtpInputs, struct());
 finalValues.synergyWeights(mtpInputs.numberOfExtrapolationWeights + 1 : end) = 0;
 resultsSynxNoResiduals = calcMtpSynXModeledValues(finalValues, mtpInputs, struct());
@@ -68,20 +242,21 @@ function reportMuscleTendonPersonalizationResults(optimizedParams, ...
 resultsSynx.muscleExcitations = resultsSynx.muscleExcitations(:, :, ...
     mtpInputs.numPaddingFrames + 1 : end - mtpInputs.numPaddingFrames);
 if ~isempty(precalInputs)
-finalOptimalFiberLength = ...
-    finalValues.optimalFiberLengthScaleFactors .* mtpInputs.optimalFiberLength;
-finalValues.optimalFiberLengthScaleFactors = ...
-    finalOptimalFiberLength ./ precalInputs.optimalFiberLength;
-finalTendonSlackLength = ...
-    finalValues.tendonSlackLengthScaleFactors .* mtpInputs.tendonSlackLength;
-finalValues.tendonSlackLengthScaleFactors = ...
-    finalTendonSlackLength ./ precalInputs.tendonSlackLength;
+% finalOptimalFiberLength = ...
+%     finalValues.optimalFiberLengthScaleFactors .* mtpInputs.optimalFiberLength;
+% finalValues.optimalFiberLengthScaleFactors = ...
+%     finalOptimalFiberLength ./ precalInputs.optimalFiberLength;
+% finalTendonSlackLength = ...
+%     finalValues.tendonSlackLengthScaleFactors .* mtpInputs.tendonSlackLength;
+% finalValues.tendonSlackLengthScaleFactors = ...
+%     finalTendonSlackLength ./ precalInputs.tendonSlackLength;
 end
 end
 function plotMuscleTendonLengthInitializationResults(precalInputs, mtpInputs)
 
 tempValues.optimalFiberLengthScaleFactors = ...
     mtpInputs.optimalFiberLength ./ precalInputs.optimalFiberLength;
+mtpInputs.optimalFiberLength
 tempValues.tendonSlackLengthScaleFactors = ...
     mtpInputs.tendonSlackLength ./ precalInputs.tendonSlackLength;
 precalInputs.maxIsometricForce = mtpInputs.maxIsometricForce;
@@ -164,6 +339,7 @@ function printJointMomentMatchingError(muscleJointMoments, inverseDynamicsMoment
     'and inverse dynamic moments are: \n' ]);
 fprintf(['\n ' num2str(jointMomentsMae) ' \n']);
 end
+
 function makeExcitationAndActivationPlots(results, resultsSynx, ...
     experimentalData, synergyParameters)
 
@@ -182,6 +358,7 @@ function makeExcitationAndActivationPlots(results, resultsSynx, ...
     muscleLabels)
 end
 end
+
 function plotMuscleExcitationsAndActivations(muscleExcitations, ...
     muscleExcitationsSynx, muscleActivations, muscleActivationsSynx, ...
     muscleLabels)
@@ -326,6 +503,7 @@ function makeModelParameterPlots(finalValues, experimentalData, synergyParameter
 
 if nargout == 1;vargout=h; end
 end
+
 function makeTaskSpecificMomentMatchingPlots(jointMoments, jointMomentsSynx, ...
     inverseDynamicsMoments, coordinates, synergyParameters)
 
@@ -342,6 +520,7 @@ function makeTaskSpecificMomentMatchingPlots(jointMoments, jointMomentsSynx, ...
     {'','Predicted (with residual excitations)','','Inverse dynamics'});
 end
 end
+
 function plotJointMoments(jointMoments, inverseDynamicsMoments, taskName, ...
     coordinates, subplotIndex, legendName)
 
@@ -374,6 +553,7 @@ function plotJointMoments(jointMoments, inverseDynamicsMoments, taskName, ...
 set(gca, 'FontSize', 12)
 end
 end
+
 function makeTaskSpecificNormalizedFiberLengthsPlots(...
     normalizedFiberLengths, experimentalData, synergyParameters)
 
diff --git a/src/MuscleTendonPersonalization/MuscleTendonPersonalization.m b/src/MuscleTendonPersonalization/MuscleTendonPersonalization.m
index 31ddaa28a..56b0d33d0 100644
--- a/src/MuscleTendonPersonalization/MuscleTendonPersonalization.m
+++ b/src/MuscleTendonPersonalization/MuscleTendonPersonalization.m
@@ -49,17 +49,24 @@
 for i=1:length(inputs.tasks)
     [taskValues, taskLowerBounds, taskUpperBounds] = makeTaskValues( ...
         primaryValues, inputs.tasks{i}, lowerBounds, upperBounds);
-    taskParams = makeTaskParams( ...
-        inputs.tasks{i}, ...
-        params, ...
-        inputs.synergyExtrapolation);
-    [A, b] = getLinearInequalityConstraints(inputs.synergyExtrapolation, ...
-        6 * length(inputs.muscleNames), inputs.extrapolationCommands, ...
-        permute(inputs.emgData, [3 1 2]));
-%     optimizedValues = taskValues;
-    optimizedValues = computeMuscleTendonRoundOptimization(taskValues, ...
-        primaryValues, inputs.tasks{i}.isIncluded, taskLowerBounds, ...
-        taskUpperBounds, inputs, taskParams, optimizerOptions, A, b);
+    taskParams = makeTaskParams(params);
+    if isfield(inputs, "synergyExtrapolation")
+        taskParams.costTerms = ...
+            [inputs.tasks{i}.costTerms,  inputs.synergyExtrapolation.costTerms];
+        [A, b] = getLinearInequalityConstraints(inputs.synergyExtrapolation, ...
+            6 * length(inputs.muscleNames), inputs.extrapolationCommands, ...
+            permute(inputs.emgData, [3 1 2]));
+%                 optimizedValues = taskValues;
+        optimizedValues = computeMuscleTendonRoundOptimization(taskValues, ...
+            primaryValues, inputs.tasks{i}.isIncluded, taskLowerBounds, ...
+            taskUpperBounds, inputs, taskParams, optimizerOptions, A, b);
+    else
+        taskParams.costTerms = inputs.tasks{i}.costTerms;
+%         optimizedValues = taskValues;
+        optimizedValues = computeMuscleTendonRoundOptimization(taskValues, ...
+            primaryValues, inputs.tasks{i}.isIncluded, taskLowerBounds, ...
+            taskUpperBounds, inputs, taskParams, optimizerOptions, [], []);
+    end
     primaryValues = updateDesignVariables(primaryValues, ...
         optimizedValues, inputs.tasks{i}.isIncluded);
 end
@@ -75,7 +82,7 @@ function verifyInputs(inputs)
 for i=1:length(inputs.tasks)
     try verifyNumeric(inputs.tasks{i}.isIncluded);
     catch; throw(MException('',strcat('invalid isIncluded boolean', ...
-        'array for task ', num2str(i))));
+            'array for task ', num2str(i))));
     end
 end
 end
@@ -103,14 +110,22 @@ function verifyParams(params)
 values{4} = repmat(0.5, 1, numMuscles); % EMG scale factors
 values{5} = repmat(1, 1, numMuscles); % optimal fiber length scale factor
 values{6} = repmat(1, 1, numMuscles); % tendon slack length scale factor
-values{7} = repmat(0, 1, inputs.numberOfExtrapolationWeights + ...
-    inputs.numberOfResidualWeights); % synergy commands
+if isfield(inputs, "synergyExtrapolation")
+    values{7} = repmat(0, 1, inputs.numberOfExtrapolationWeights + ...
+        inputs.numberOfResidualWeights); % synergy commands
+end
 end
 
 function inputs = finalizeInputs(inputs, primaryValues, params)
-values = makeMtpValuesAsStruct(struct(), primaryValues, zeros(1, 7));
+values = makeMtpValuesAsStruct(struct(), primaryValues, zeros(1, 7), inputs);
 modeledValues = calcMtpModeledValues(values, inputs, params);
 inputs = mergeStructs(inputs, modeledValues);
+inputs = rmfield(inputs, "model");
+if ~isfield(inputs, "synergyExtrapolation")
+    for i = 1:length(inputs.tasks)
+        inputs.tasks{i}.isIncluded(7) = 0;
+    end
+end
 end
 
 % (struct, struct) -> (6 x numEnabledMuscles matrix of number)
@@ -125,8 +140,10 @@ function verifyParams(params)
     lowerBounds{4} = repmat(0.05, 1, numMuscles); % EMG scale factors
     lowerBounds{5} = repmat(0.6, 1, numMuscles); % optimal fiber length scale factor
     lowerBounds{6} = repmat(0.6, 1, numMuscles); % tendon slack length scale factor
-    lowerBounds{7} = repmat(-100, 1, inputs.numberOfExtrapolationWeights + ...
-        inputs.numberOfResidualWeights); % synergy commands
+    if isfield(inputs, "synergyExtrapolation")
+        lowerBounds{7} = repmat(-100, 1, inputs.numberOfExtrapolationWeights + ...
+            inputs.numberOfResidualWeights); % synergy commands
+    end
 end
 end
 
@@ -142,8 +159,10 @@ function verifyParams(params)
     upperBounds{4} = repmat(1, 1, numMuscles); % EMG scale factors
     upperBounds{5} = repmat(1.4, 1, numMuscles); % optimal fiber length scale factor
     upperBounds{6} = repmat(1.4, 1, numMuscles); % tendon slack length scale factor
-    upperBounds{7} = repmat(100, 1, inputs.numberOfExtrapolationWeights + ...
-        inputs.numberOfResidualWeights); % synergy commands    
+    if isfield(inputs, "synergyExtrapolation")
+        upperBounds{7} = repmat(100, 1, inputs.numberOfExtrapolationWeights + ...
+            inputs.numberOfResidualWeights); % synergy commands
+    end
 end
 end
 
@@ -162,6 +181,8 @@ function verifyParams(params)
 output.Display = 'iter';
 output.Hessian = 'lbfgs';
 output.GradObj = 'off';
+output.DiffMaxChange = 10;
+output.DiffMinChange = 1e-5;
 end
 
 % (struct, struct) -> (Array of number)
@@ -172,19 +193,18 @@ function verifyParams(params)
 taskLowerBounds = [];
 taskUpperBounds = [];
 for i = 1:length(taskInputs.isIncluded)
-   if(taskInputs.isIncluded(i))
-       taskValues = [taskValues primaryValues{i}];
-       taskLowerBounds = [taskLowerBounds lowerBounds{i}];
-       taskUpperBounds = [taskUpperBounds upperBounds{i}];
-   end
+    if(taskInputs.isIncluded(i))
+        taskValues = [taskValues primaryValues{i}];
+        taskLowerBounds = [taskLowerBounds lowerBounds{i}];
+        taskUpperBounds = [taskUpperBounds upperBounds{i}];
+    end
 end
 end
 
 % (struct, struct) -> (struct)
 % prepare optimizer parameters for the given task
-function taskParams = makeTaskParams(taskInputs, params, synergyExtrapolation)
+function taskParams = makeTaskParams(params)
 taskParams = params;
-taskParams.costTerms = [taskInputs.costTerms, synergyExtrapolation.costTerms];
 if(~isfield(params, 'maxIterations'))
     taskParams.maxIterations = 2e3;
 end
diff --git a/src/MuscleTendonPersonalization/MuscleTendonPersonalizationTool.m b/src/MuscleTendonPersonalization/MuscleTendonPersonalizationTool.m
index 9e843563d..9a72cfd22 100644
--- a/src/MuscleTendonPersonalization/MuscleTendonPersonalizationTool.m
+++ b/src/MuscleTendonPersonalization/MuscleTendonPersonalizationTool.m
@@ -42,23 +42,17 @@ function MuscleTendonPersonalizationTool(settingsFileName)
 else
     precalInputs = struct('optimizeIsometricMaxForce', false);
 end
-
 optimizedParams = MuscleTendonPersonalization(inputs, params);
 if params.performMuscleTendonLengthInitialization
-    reportMuscleTendonPersonalizationResults(optimizedParams, ...
-        inputs, precalInputs);
+    [finalValues, resultsStruct, modeledValues] = ...
+        getMtpResultsToSave(inputs, params, optimizedParams, precalInputs);
+    saveMuscleTendonPersonalizationResults(inputs, finalValues, modeledValues, ...
+        resultsStruct, resultsDirectory, precalInputs);
 else
-    reportMuscleTendonPersonalizationResults(optimizedParams, inputs);
-end
-finalValues = makeMtpValuesAsStruct([], optimizedParams, zeros(1, 7));
-if precalInputs.optimizeIsometricMaxForce
-    finalValues.maxIsometricForce = inputs.maxIsometricForce;
-end
-results = calcMtpSynXModeledValues(finalValues, inputs, params);
-
-results.time = inputs.emgTime(:, inputs.numPaddingFrames + 1 : ...
-    end - inputs.numPaddingFrames);
-saveMuscleTendonPersonalizationResults(inputs.model, ...
-    inputs.osimxFileName, inputs.prefixes, inputs.coordinateNames, ...
-    finalValues, results, resultsDirectory, inputs.muscleTendonColumnNames);
+    [finalValues, resultsStruct, modeledValues] = ...
+        getMtpResultsToSave(inputs, params, optimizedParams);
+    saveMuscleTendonPersonalizationResults(inputs, finalValues, modeledValues, ...
+        resultsStruct, resultsDirectory);
 end
+printMtpJointMomentMatchingError(resultsDirectory);
+end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Optimization/CostComputations/calcDifferencesInEmgGroups.m b/src/MuscleTendonPersonalization/Optimization/CostComputations/calcDifferencesInEmgGroups.m
index 997660790..475a262f4 100644
--- a/src/MuscleTendonPersonalization/Optimization/CostComputations/calcDifferencesInEmgGroups.m
+++ b/src/MuscleTendonPersonalization/Optimization/CostComputations/calcDifferencesInEmgGroups.m
@@ -31,10 +31,11 @@
 function deviationsEMGScale = calcDifferencesInEmgGroups( ...
     emgScale, activationGroups)
 
+lowestIndex = min(cell2mat(activationGroups)) - 1;
 Ind = 1;
 for i = 1:length(activationGroups)
     deviationsEMGScale(:, Ind:Ind + size(activationGroups{i}, 2) - 1) = ...
-        calcMeanDifference2D(emgScale(activationGroups{i}));
+        calcMeanDifference2D(emgScale(activationGroups{i} - lowestIndex));
     Ind = Ind + size(activationGroups{i}, 2);
 end
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Optimization/CostComputations/calcMuscleTendonNonLinearConstraints.m b/src/MuscleTendonPersonalization/Optimization/CostComputations/calcMuscleTendonNonLinearConstraints.m
index f364e7474..8c28fef96 100644
--- a/src/MuscleTendonPersonalization/Optimization/CostComputations/calcMuscleTendonNonLinearConstraints.m
+++ b/src/MuscleTendonPersonalization/Optimization/CostComputations/calcMuscleTendonNonLinearConstraints.m
@@ -25,12 +25,12 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function [c,ceq] = calcMuscleTendonNonLinearConstraints(values, ...
-    primaryValues, isIncluded, experimentalData, params)
+function [c, ceq] = calcMuscleTendonNonLinearConstraints(values, ...
+    primaryValues, isIncluded, inputs, params)
 
 ceq = [];
-values = makeMtpValuesAsStruct(values, primaryValues, isIncluded);
-modeledValues = calcMtpModeledValues(values, experimentalData, struct());
+values = makeMtpValuesAsStruct(values, primaryValues, isIncluded, inputs);
+modeledValues = calcMtpModeledValues(values, inputs, struct());
 softmaxlmtildaCon = log(sum(exp(500 * ...
     (modeledValues.normalizedFiberLength - 1.3)), [1 3])) / 500; % max lmtilda less than 1.5
 softminlmtildaCon = log(sum(exp(500 * (0.3 - ...
diff --git a/src/MuscleTendonPersonalization/Optimization/CostTerms/calcNormalizedFiberLengthGroupedSimilarityCost.m b/src/MuscleTendonPersonalization/Optimization/CostTerms/calcNormalizedFiberLengthGroupedSimilarityCost.m
index 635acdbae..660eb14d1 100644
--- a/src/MuscleTendonPersonalization/Optimization/CostTerms/calcNormalizedFiberLengthGroupedSimilarityCost.m
+++ b/src/MuscleTendonPersonalization/Optimization/CostTerms/calcNormalizedFiberLengthGroupedSimilarityCost.m
@@ -26,16 +26,19 @@
 % ----------------------------------------------------------------------- %
 
 function cost = calcNormalizedFiberLengthGroupedSimilarityCost( ...
-    modeledValues, experimentalData, costTerm)
+    modeledValues, inputs, costTerm)
 errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
-maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.05);
+maximumAllowableError = valueOrAlternate(costTerm, ...
+    "maxAllowableError", 0.05);
+lowestIndex = min(cell2mat(inputs.normalizedFiberLengthGroups)) - 1;
 index = 1;
-for i = 1:length(experimentalData.normalizedFiberLengthGroups)
-    muscleGroup = experimentalData.normalizedFiberLengthGroups{i};
+for i = 1:length(inputs.normalizedFiberLengthGroups)
+    muscleGroup = inputs.normalizedFiberLengthGroups{i} ...
+        - lowestIndex;
     normalizedFiberLengthMagnitudeDeviation(:, index : index + size(...
         muscleGroup, 2) - 1) = calcMeanDeviations( ...
         modeledValues.normalizedFiberLength(:, muscleGroup, :), ...
-        experimentalData.normalizedFiberLength(:, muscleGroup, :));
+        inputs.normalizedFiberLength(:, muscleGroup, :));
     normalizedFiberLengthShapeDeviation(:, index : index + size(...
         muscleGroup, 2) - 1, :) = calcMeanShapeDeviations( ...
         modeledValues.normalizedFiberLength(:, muscleGroup, :));
diff --git a/src/MuscleTendonPersonalization/Optimization/CostTerms/calcSynergyExtrapolationMuscleActivationCost.m b/src/MuscleTendonPersonalization/Optimization/CostTerms/calcSynergyExtrapolationMuscleActivationCost.m
index 94d884fc2..e10ee7c15 100644
--- a/src/MuscleTendonPersonalization/Optimization/CostTerms/calcSynergyExtrapolationMuscleActivationCost.m
+++ b/src/MuscleTendonPersonalization/Optimization/CostTerms/calcSynergyExtrapolationMuscleActivationCost.m
@@ -26,11 +26,12 @@
 % ----------------------------------------------------------------------- %
 
 function cost = calcSynergyExtrapolationMuscleActivationCost( ...
-    modeledValues, experimentalData, costTerm)
+    modeledValues, inputs, costTerm)
 errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
 maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.3);
+lowestIndex = min(cell2mat(inputs.normalizedFiberLengthGroups)) - 1;
 cost = calcDeviationCostTerm(...
     modeledValues.muscleActivations(:, ...
-    [experimentalData.synergyExtrapolation.missingEmgChannelGroups{:}], ...
-    :), errorCenter, maximumAllowableError);
+    reshape(cell2mat(inputs.synergyExtrapolation.missingEmgChannelGroups), 1, []) ...
+    - lowestIndex, :), errorCenter, maximumAllowableError);
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m b/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m
index 7ec645d8d..bb2442549 100644
--- a/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m
+++ b/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m
@@ -26,20 +26,23 @@
 % ----------------------------------------------------------------------- %
 
 function totalCost = calcMtpCost(values, synxModeledValues, modeledValues, ...
-    experimentalData, params)
+    inputs, params)
 totalCost = 0;
 for i = 1 : length(params.costTerms)
     costTerm = params.costTerms{i};
     if costTerm.isEnabled
+        cost = 0;
         switch costTerm.type
             case "measured_inverse_dynamics_joint_moment"
-                cost = calcSynergyExtrapolationMomentTrackingCost( ...
-                    synxModeledValues, ...
-                    experimentalData, ...
-                    costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcSynergyExtrapolationMomentTrackingCost( ...
+                        synxModeledValues, ...
+                        inputs, ...
+                        costTerm);
+                end
             case "inverse_dynamics_joint_moment"
                 cost = calcMomentTrackingCost(modeledValues, ...
-                    experimentalData, costTerm);
+                    inputs, costTerm);
             case "activation_time_constant"
                 cost = calcActivationTimeConstantDeviationCost(values, ...
                     costTerm);
@@ -48,35 +51,55 @@
                     costTerm);
             case "optimal_muscle_fiber_length"
                 cost = calcOptimalFiberLengthDeviationCost(values, ...
-                    experimentalData, costTerm);
+                    inputs, costTerm);
             case "tendon_slack_length"
                 cost = calcTendonSlackLengthDeviationCost(values, ...
-                    experimentalData, costTerm);
+                    inputs, costTerm);
             case "emg_scale_factor"
                 cost = calcEmgScaleFactorDevationCost(values, costTerm);
             case "normalized_muscle_fiber_length"
-                cost = calcNormalizedFiberLengthDeviationCost( ...
-                    synxModeledValues, experimentalData, costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcNormalizedFiberLengthDeviationCost( ...
+                        synxModeledValues, inputs, costTerm);
+                else
+                    cost = calcNormalizedFiberLengthDeviationCost( ...
+                        modeledValues, inputs, costTerm);
+                end
             case "passive_muscle_force"
-                cost = calcPassiveForceCost(synxModeledValues, costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcPassiveForceCost(synxModeledValues, costTerm);
+                else
+                    cost = calcPassiveForceCost(modeledValues, costTerm);
+                end
             case "grouped_normalized_muscle_fiber_length"
-                cost = calcNormalizedFiberLengthGroupedSimilarityCost( ...
-                    synxModeledValues, experimentalData, costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcNormalizedFiberLengthGroupedSimilarityCost( ...
+                        synxModeledValues, inputs, costTerm);
+                else
+                    cost = calcNormalizedFiberLengthGroupedSimilarityCost( ...
+                        modeledValues, inputs, costTerm);
+                end
             case "grouped_emg_scale_factor"
                 cost = calcEmgScaleFactorGroupedSimilarityCost(values, ...
-                    experimentalData, costTerm);
+                    inputs, costTerm);
             case "grouped_electromechanical_delay"
                 cost = calcElectromechanicalDelayGroupedSimilarityCost( ...
-                    values, experimentalData, costTerm);
+                    values, inputs, costTerm);
             case "extrapolated_muscle_activation"
-                cost = calcSynergyExtrapolationMuscleActivationCost( ...
-                    synxModeledValues, experimentalData, costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcSynergyExtrapolationMuscleActivationCost( ...
+                        synxModeledValues, inputs, costTerm);
+                end
             case "residual_muscle_activation"
-                cost = calcResidualMuscleActivationCost( ...
-                    synxModeledValues, modeledValues, experimentalData, costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcResidualMuscleActivationCost( ...
+                        synxModeledValues, modeledValues, inputs, costTerm);
+                end
             case "muscle_excitation_penalty"
-                cost = calcMuscleExcitationPenaltyCost( ...
-                    synxModeledValues, experimentalData, costTerm);
+                if isfield(inputs, "synergyExtrapolation")
+                    cost = calcMuscleExcitationPenaltyCost( ...
+                        synxModeledValues, inputs, costTerm);
+                end
             otherwise
                 throw(MException('', 'Cost term %s is not valid for MTP', ...
                     costTerm.type))
diff --git a/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonCostFunction.m b/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonCostFunction.m
index fafd73598..96950f18f 100644
--- a/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonCostFunction.m
+++ b/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonCostFunction.m
@@ -26,10 +26,16 @@
 % ----------------------------------------------------------------------- %
 
 function cost = computeMuscleTendonCostFunction(secondaryValues, ...
-    primaryValues, isIncluded, experimentalData, params)
-values = makeMtpValuesAsStruct(secondaryValues, primaryValues, isIncluded);
-synxModeledValues = calcMtpSynXModeledValues(values, experimentalData, params);
-modeledValues = calcMtpModeledValues(values, experimentalData, params);
-cost = calcMtpCost(values, synxModeledValues, modeledValues, ...
-    experimentalData, params);
+    primaryValues, isIncluded, inputs, params)
+values = makeMtpValuesAsStruct(secondaryValues, primaryValues, ...
+    isIncluded, inputs);
+modeledValues = calcMtpModeledValues(values, inputs, params);
+if isfield(inputs, "synergyExtrapolation")
+    synxModeledValues = calcMtpSynXModeledValues(values, inputs, params);
+    cost = calcMtpCost(values, synxModeledValues, modeledValues, ...
+        inputs, params);
+else
+    cost = calcMtpCost(values, struct(), modeledValues, ...
+        inputs, params);
+end
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonRoundOptimization.m b/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonRoundOptimization.m
index dc21cec9d..72de0f1b9 100644
--- a/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonRoundOptimization.m
+++ b/src/MuscleTendonPersonalization/Optimization/computeMuscleTendonRoundOptimization.m
@@ -30,11 +30,11 @@
 
 function optimizedValues = computeMuscleTendonRoundOptimization( ...
     initialValues, primaryValues, isIncluded, lowerBounds, upperBounds, ...
-    experimentalData, params, optimizerOptions, A, b)
+    inputs, params, optimizerOptions, A, b)
 
 optimizedValues = fmincon(@(values)computeMuscleTendonCostFunction( ...
-    values, primaryValues, isIncluded, experimentalData, params), ...
+    values, primaryValues, isIncluded, inputs, params), ...
     initialValues, A, b, [], [], lowerBounds, upperBounds, ...
     @(values)calcMuscleTendonNonLinearConstraints(values, primaryValues, ...
-    isIncluded, experimentalData, params), optimizerOptions);
+    isIncluded, inputs, params), optimizerOptions);
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Optimization/makeMtpValuesAsStruct.m b/src/MuscleTendonPersonalization/Optimization/makeMtpValuesAsStruct.m
index c22ec5ae4..beb43b5e5 100644
--- a/src/MuscleTendonPersonalization/Optimization/makeMtpValuesAsStruct.m
+++ b/src/MuscleTendonPersonalization/Optimization/makeMtpValuesAsStruct.m
@@ -26,7 +26,8 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function values = makeMtpValuesAsStruct(secondaryValues, primaryValues, isIncluded)
+function values = makeMtpValuesAsStruct(secondaryValues, primaryValues, ...
+    isIncluded, inputs)
 valuesHelper.secondaryValues = secondaryValues;
 valuesHelper.primaryValues = primaryValues;
 valuesHelper.isIncluded = isIncluded;
@@ -36,7 +37,9 @@
 values.emgScaleFactors = findCorrectMtpValues(4, valuesHelper);
 values.optimalFiberLengthScaleFactors = findCorrectMtpValues(5, valuesHelper);
 values.tendonSlackLengthScaleFactors = findCorrectMtpValues(6, valuesHelper);
-values.synergyWeights = findCorrectMtpValues(7, valuesHelper);
+if isfield(inputs, "synergyExtrapolation")
+    values.synergyWeights = findCorrectMtpValues(7, valuesHelper);
+end
 end
 
 function output = findCorrectMtpValues(index, valuesStruct)
diff --git a/src/MuscleTendonPersonalization/Optimization/updateDesignVariables.m b/src/MuscleTendonPersonalization/Optimization/updateDesignVariables.m
index a76e4db89..7de0c7c80 100644
--- a/src/MuscleTendonPersonalization/Optimization/updateDesignVariables.m
+++ b/src/MuscleTendonPersonalization/Optimization/updateDesignVariables.m
@@ -39,7 +39,9 @@
             primaryValues, isIncluded, i);
         newPrimaryValues{i} = secondaryValues(startIndex:endIndex);
     else
-        newPrimaryValues{i} = primaryValues{i};
+        if i ~= 7
+            newPrimaryValues{i} = primaryValues{i};
+        end
     end
 end
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Saving/getMtpResultsToSave.m b/src/MuscleTendonPersonalization/Saving/getMtpResultsToSave.m
new file mode 100644
index 000000000..49e8a7eb4
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Saving/getMtpResultsToSave.m
@@ -0,0 +1,79 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function takes MTP inputs and optimized muscle parameters and
+% calculates normalized fiber length, passive force, passive moment, muscle
+% activation, and muscle excitation curves to be later saved.
+%
+% (struct), (struct), (cell), (struct) -> (struct), (struct), (struct)
+% Calculates relevant MTP curves
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Di Ao, Marleny Vega, Robert Salati                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function [finalValues, resultsStruct, modeledValues] = ...
+    getMtpResultsToSave(mtpInputs, params, optimizedParams, precalInputs)
+finalValues = makeMtpValuesAsStruct([], optimizedParams, zeros(1, 7), mtpInputs);
+if nargin < 4
+    modeledValues = [];
+    precalInputs = [];
+else
+    updatedMaxIsometricForce = precalInputs.optimizeIsometricMaxForce;
+    tempValues.optimalFiberLengthScaleFactors = ...
+        mtpInputs.optimalFiberLength ./ precalInputs.optimalFiberLength;
+    tempValues.tendonSlackLengthScaleFactors = ...
+        mtpInputs.tendonSlackLength ./ precalInputs.tendonSlackLength;
+    precalInputs.maxIsometricForce = mtpInputs.maxIsometricForce;
+    precalInputs.optimizeIsometricMaxForce = 0;
+    modeledValues = calcMuscleTendonLengthInitializationModeledValues(tempValues, precalInputs);
+    if updatedMaxIsometricForce
+        finalValues.maxIsometricForce = mtpInputs.maxIsometricForce;
+    end
+end
+
+results = calcMtpModeledValues(finalValues, mtpInputs, struct());
+results.time = mtpInputs.emgTime(:, mtpInputs.numPaddingFrames + 1 : ...
+    end - mtpInputs.numPaddingFrames);
+results.muscleExcitations = results.muscleExcitations(:, :, ...
+    mtpInputs.numPaddingFrames + 1 : end - mtpInputs.numPaddingFrames);
+if isfield(mtpInputs, "synergyExtrapolation")
+    resultsSynx = calcMtpSynXModeledValues(finalValues, mtpInputs, params);
+    resultsSynx.time = mtpInputs.emgTime(:, mtpInputs.numPaddingFrames + 1 : ...
+        end - mtpInputs.numPaddingFrames);
+    resultsSynx.muscleExcitations = resultsSynx.muscleExcitations(:, :, ...
+        mtpInputs.numPaddingFrames + 1 : end - mtpInputs.numPaddingFrames);
+    finalValues.synergyWeights(mtpInputs.numberOfExtrapolationWeights + 1 : end) = 0;
+    resultsStruct = struct("results", results, ...
+        "resultsSynx", resultsSynx);
+else
+    resultsStruct = struct("results", results);
+end
+if ~isempty(precalInputs)
+finalOptimalFiberLength = ...
+    finalValues.optimalFiberLengthScaleFactors .* mtpInputs.optimalFiberLength;
+finalValues.optimalFiberLengthScaleFactors = ...
+    finalOptimalFiberLength ./ precalInputs.optimalFiberLength;
+finalTendonSlackLength = ...
+    finalValues.tendonSlackLengthScaleFactors .* mtpInputs.tendonSlackLength;
+finalValues.tendonSlackLengthScaleFactors = ...
+    finalTendonSlackLength ./ precalInputs.tendonSlackLength;
+end
+end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Saving/saveMtpActivationAndExcitationData.m b/src/MuscleTendonPersonalization/Saving/saveMtpActivationAndExcitationData.m
new file mode 100644
index 000000000..4bb6a4288
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Saving/saveMtpActivationAndExcitationData.m
@@ -0,0 +1,69 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function saves muscle exctiations and activations with and without
+% SynX to their appropriate .sto files in a directory specified by
+% resultsDirectory.
+%
+% (struct, struct, struct, string) -> (None)
+% Saves muscle activation and excitation data to .sto file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function saveMtpActivationAndExcitationData(mtpInputs, resultsStruct, ...
+    resultsDirectory)
+writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsStruct.results.muscleExcitations, ...
+    resultsStruct.results.time, ...
+    fullfile(resultsDirectory, "muscleExcitations"), ...
+    "_muscleExcitations.sto")
+writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsStruct.results.muscleActivations, ...
+    resultsStruct.results.time, ...
+    fullfile(resultsDirectory, "muscleActivations"), ...
+    "_muscleActivations.sto")
+if isfield(mtpInputs, "synergyExtrapolation")
+    writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+        resultsStruct.resultsSynx.muscleExcitations, ...
+        resultsStruct.resultsSynx.time, ...
+        fullfile(resultsDirectory, "muscleExcitationsSynx"), ...
+        "_muscleExcitationsSynx.sto")
+    
+    writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+        resultsStruct.resultsSynx.muscleActivations, ...
+        resultsStruct.resultsSynx.time, ...
+        fullfile(resultsDirectory, "muscleActivationsSynx"), ...
+        "_muscleActivationsSynx.sto")
+
+    writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+        resultsStruct.resultsSynx.muscleActivations, ...
+        resultsStruct.resultsSynx.time, ...
+        fullfile(resultsDirectory, "..", "muscleActivations"), ...
+        "_muscleActivations.sto")
+else
+    writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+        resultsStruct.results.muscleActivations, ...
+        resultsStruct.results.time, ...
+        fullfile(resultsDirectory, "..", "muscleActivations"), ...
+        "_muscleActivations.sto")
+end
+end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Saving/saveMtpJointMomentData.m b/src/MuscleTendonPersonalization/Saving/saveMtpJointMomentData.m
new file mode 100644
index 000000000..166518b78
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Saving/saveMtpJointMomentData.m
@@ -0,0 +1,65 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function saves experimental joint moment data, and modeled joint
+% moment data without SynX, with SynX, and with SynX with no residuals to
+% their appropriate .sto files in a directory specified by 
+% resultsDirectory.
+%
+% (struct, struct, struct, struct, struct, string) -> (None)
+% Saves joint moment data to .sto files.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function saveMtpJointMomentData(mtpInputs, resultsStruct, resultsDirectory)
+writeMtpDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+    resultsStruct.results.muscleJointMoments, ...
+    resultsStruct.results.time, ...
+    fullfile(resultsDirectory, "\modelJointMoments"), ...
+    "_modelJointMoments.sto")
+
+writeMtpDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+    mtpInputs.inverseDynamicsMoments, ...
+    mtpInputs.time, ...
+    fullfile(resultsDirectory, "\inverseDynamicsJointMoments"), ...
+    "_inverseDynamicsJointMoments.sto")
+
+if isfield(mtpInputs, "synergyExtrapolation")
+    writeMtpDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+        resultsStruct.resultsSynx.muscleJointMoments, ...
+        resultsStruct.resultsSynx.time, ...
+        fullfile(resultsDirectory, "\modelJointMomentsSynx"), ...
+        "_modelJointMomentsSynx.sto")
+
+    writeMtpDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+        resultsStruct.resultsSynx.muscleJointMoments, ...
+        resultsStruct.resultsSynx.time, ...
+        fullfile(resultsDirectory, "..", "modelMoments"), ...
+        "_modelMoments.sto");
+else
+    writeMtpDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+        resultsStruct.results.muscleJointMoments, ...
+        resultsStruct.results.time, ...
+        fullfile(resultsDirectory, "..", "modelMoments"), ...
+        "_modelMoments.sto");
+end
+end
\ No newline at end of file
diff --git a/src/VerificationOptimization/computeVerificationOptimizationContinuousFunction.m b/src/MuscleTendonPersonalization/Saving/saveMtpMuscleModelParameters.m
similarity index 57%
rename from src/VerificationOptimization/computeVerificationOptimizationContinuousFunction.m
rename to src/MuscleTendonPersonalization/Saving/saveMtpMuscleModelParameters.m
index 614800536..9a851e162 100644
--- a/src/VerificationOptimization/computeVerificationOptimizationContinuousFunction.m
+++ b/src/MuscleTendonPersonalization/Saving/saveMtpMuscleModelParameters.m
@@ -1,10 +1,15 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function computes the dynamic constraints, path constraints (if any)
-% and cost function terms (if any) for verification optimization.
-% 
-% (struct) -> (struct)
+% This function saves optimized Hill-type muscle-tendon model parameters
+% output by MTP to a .sto file in a directory specified by
+% resultsDirectory. Each row in the .sto file corresponds to a parameter.
+% In order from top to bottom, these are: activation time constants, 
+% activation nonlinearity constants, electromechanical delays, emg scale
+% factors, optimal fiber length scale factors, tendon slack length scale
+% factors. 
 %
+% (struct, struct, struct, struct, struct, string) -> (None)
+% Saves joint moment data to .sto files.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +19,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Robert Salati                                                %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,16 +33,17 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function modeledValues = computeVerificationOptimizationContinuousFunction(inputs)
-
-values = getVerificationOptimizationValueStruct(inputs.phase, inputs.auxdata);
-modeledValues = calcTorqueBasedModeledValues(values, inputs.auxdata);
-modeledValues = calcSynergyBasedModeledValues(values, inputs.auxdata, modeledValues);
-modeledValues.dynamics = calcVerificationOptimizationDynamicsConstraint(values, inputs.auxdata);
-path = calcVerificationOptimizationPathConstraint(values, modeledValues, inputs.auxdata);
-if ~isempty(path)
-    modeledValues.path = path;
+function saveMtpMuscleModelParameters(mtpInputs, finalValues, resultsDirectory)
+if ~exist(resultsDirectory, "dir")
+    mkdir(resultsDirectory);
 end
-modeledValues.integrand = calcVerificationOptimizationIntegrand(values, ...
-    modeledValues, inputs.auxdata);
+columnLabels = mtpInputs.muscleNames;
+dataPoints = [finalValues.activationTimeConstants;
+    finalValues.activationNonlinearityConstants;
+    finalValues.electromechanicalDelays;
+    finalValues.emgScaleFactors;
+    finalValues.optimalFiberLengthScaleFactors;
+    finalValues.tendonSlackLengthScaleFactors];
+writeToSto(columnLabels, 1:1:size(dataPoints,1), dataPoints, ...
+    fullfile(resultsDirectory, "muscleModelParameters.sto"));
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Saving/saveMtpPassiveForceData.m b/src/MuscleTendonPersonalization/Saving/saveMtpPassiveForceData.m
new file mode 100644
index 000000000..f7d97c6a1
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Saving/saveMtpPassiveForceData.m
@@ -0,0 +1,39 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function saves experimental passive force data, modeled passive 
+% force data without SynX, with SynX, and with SynX with no residuals to
+% their appropriate .sto files in a directory specified by
+% resultsDirectory.
+%
+% (struct, struct, struct, struct, struct, string) -> (None)
+% Saves passive force data to .sto files.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function saveMtpPassiveForceData(mtpInputs, resultsStruct, ...
+    resultsDirectory)
+writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsStruct.results.passiveForce, resultsStruct.results.time, ...
+    strcat(resultsDirectory, "\passiveForcesModel"), ...
+    "_passiveForcesModel.sto");
+end
diff --git a/src/VerificationOptimization/calcVerificationOptimizationPathConstraint.m b/src/MuscleTendonPersonalization/Saving/saveMtpPassiveMomentData.m
similarity index 50%
rename from src/VerificationOptimization/calcVerificationOptimizationPathConstraint.m
rename to src/MuscleTendonPersonalization/Saving/saveMtpPassiveMomentData.m
index fe37276f0..afaa65c52 100644
--- a/src/VerificationOptimization/calcVerificationOptimizationPathConstraint.m
+++ b/src/MuscleTendonPersonalization/Saving/saveMtpPassiveMomentData.m
@@ -1,10 +1,11 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the path constraint for verification 
-% optimization.
+% This function formats experimental and modeled passive moment data and
+% saves them to appropriate .sto files in a directory specified by
+% resultsDirectory.
 %
-% (struct, struct, struct) -> (2D matrix)
-% Returns path constraint
+% (struct, struct, string) -> (None)
+% Saves passive moment data to .sto file.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Robert Salati                                                %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,32 +29,26 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function path = calcVerificationOptimizationPathConstraint(values, modeledValues, ...
-    params)
-path = [];
-for i = 1:length(params.path)
-    constraintTerm = params.path{i};
-    if constraintTerm.isEnabled
-        switch constraintTerm.type
-            case "root_segment_residual_load"
-                path = cat(2, path, ...
-                    calcRootSegmentResidualsPathConstraints(...
-                    constraintTerm.load, ...
-                    params.inverseDynamicMomentLabels, ...
-                    modeledValues.inverseDynamicMoments));
-            case "muscle_model_moment_consistency"
-                path = cat(2, path, ...
-                    calcMuscleActuatedMomentsPathConstraints(params, ...
-                    modeledValues, constraintTerm.load));
-            case "torque_model_moment_consistency"
-                path = cat(2, path, ...
-                    calcTorqueActuatedMomentsPathConstraints(params, ...
-                    modeledValues, values.controlTorques, constraintTerm.load));   
-            otherwise
-                throw(MException('', ['Constraint term type ' ...
-                    constraintTerm.type ' does not exist for this tool.']))    
-        end
-    end
-end
-path = scaleToBounds(path, params.maxPath, params.minPath);
+function saveMtpPassiveMomentData(precalInputs, modeledValues, resultsDirectory)
+modelPassiveMoments = permute(modeledValues.passiveModelMoments, [3 2 1]);
+experimentalPassiveMoments = permute(precalInputs.passiveData.inverseDynamicsMoments, [3 2 1]);
+numberOfMoments = size(modelPassiveMoments, 3);
+dataLength = size(modelPassiveMoments, 1);
+zeroIndices = experimentalPassiveMoments == 0;
+modelPassiveMoments = modelPassiveMoments(~zeroIndices);
+modelPassiveMoments = permute( ...
+    reshape(modelPassiveMoments, [dataLength, numberOfMoments, 1]), ...
+    [3 2 1]);
+experimentalPassiveMoments = experimentalPassiveMoments(~zeroIndices);
+experimentalPassiveMoments = permute( ...
+    reshape(experimentalPassiveMoments, [dataLength, numberOfMoments, 1]), ...
+    [3 2 1]);
+writeMtpDataToSto(precalInputs.passivePrefixes, precalInputs.prefixes, ...
+    experimentalPassiveMoments, 1:1:size(experimentalPassiveMoments, 3), ...
+    fullfile(resultsDirectory, "passiveJointMomentsExperimental"), ...
+    "_passiveJointMomentsExperimental.sto")
+writeMtpDataToSto(precalInputs.passivePrefixes, precalInputs.prefixes, ...
+    modelPassiveMoments, 1:1:size(modelPassiveMoments, 3), ...
+    fullfile(resultsDirectory, "passiveJointMomentsModeled"), ...
+    "_passiveJointMomentsModeled.sto")
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Saving/saveMuscleTendonOptimizationParamsOld.m b/src/MuscleTendonPersonalization/Saving/saveMuscleTendonOptimizationParamsOld.m
new file mode 100644
index 000000000..598c03238
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Saving/saveMuscleTendonOptimizationParamsOld.m
@@ -0,0 +1,217 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function saves optimization results to .sto files to be plotted by
+% the user in either MATLAB or Opensim
+%
+% (struct, struct, struct, string) -> (None)
+% Saves MTP optimization parameters to .sto files to be plotted.
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati, Di Ao, Marleny Vega                           %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function saveMuscleTendonOptimizationParams(resultsDirectory, optimizedParams, ...
+    mtpInputs, precalInputs)
+if nargin < 4
+    precalInputs = [];
+end
+[finalValues, results, resultsSynx, resultsSynxNoResiduals] = ...
+    getValuesToReport(mtpInputs, precalInputs, optimizedParams);
+if ~isempty(precalInputs)
+    modeledValues = getMuscleTendonLengthInitializationData(precalInputs, ...
+        mtpInputs);  % Modeled passive force data & params from experimental data.
+    savePassiveMomentDataToSto(precalInputs, modeledValues, resultsDirectory);
+    savePassiveForceDataToSto(mtpInputs, modeledValues, results, resultsSynx, ...
+        resultsSynxNoResiduals, resultsDirectory);
+end
+
+printJointMomentMatchingError(resultsSynx.muscleJointMoments, ...
+    mtpInputs.inverseDynamicsMoments);  % Keep this
+
+saveActivationAndExcitationDataToSto(mtpInputs, results, resultsSynx, resultsDirectory);
+
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, results.normalizedFiberLength, ...
+    strcat(resultsDirectory, "\normalizedFiberLengths"), "_normalizedFiberLengths.sto")
+
+saveJointMomentDataToSto(mtpInputs, results, resultsSynx, resultsSynxNoResiduals, ...
+    resultsDirectory);
+
+saveMuscleModelParametersToSto(mtpInputs, finalValues, fullfile(resultsDirectory, ...
+    "muscleModelParameters"));
+end
+
+function [finalValues, results, resultsSynx, resultsSynxNoResiduals] = ...
+    getValuesToReport(mtpInputs, precalInputs, optimizedParams)  % Need to downscale excitation arrays
+
+finalValues = makeMtpValuesAsStruct([], optimizedParams, zeros(1, 7));
+save('finalvalues.mat', 'finalValues')
+resultsSynx = calcMtpSynXModeledValues(finalValues, mtpInputs, struct());
+finalValues.synergyWeights(mtpInputs.numberOfExtrapolationWeights + 1 : end) = 0;
+resultsSynxNoResiduals = calcMtpSynXModeledValues(finalValues, mtpInputs, struct());
+results = calcMtpModeledValues(finalValues, mtpInputs, struct());
+results.time = mtpInputs.emgTime(:, mtpInputs.numPaddingFrames + 1 : ...
+    end - mtpInputs.numPaddingFrames);
+results.muscleExcitations = results.muscleExcitations(:, :, ...
+    mtpInputs.numPaddingFrames + 1 : end - mtpInputs.numPaddingFrames);
+resultsSynx.muscleExcitations = resultsSynx.muscleExcitations(:, :, ...
+    mtpInputs.numPaddingFrames + 1 : end - mtpInputs.numPaddingFrames);
+end
+
+function modeledValues = getMuscleTendonLengthInitializationData(...
+    precalInputs, mtpInputs)
+
+tempValues.optimalFiberLengthScaleFactors = ...
+    mtpInputs.optimalFiberLength ./ precalInputs.optimalFiberLength;
+
+tempValues.tendonSlackLengthScaleFactors = ...
+    mtpInputs.tendonSlackLength ./ precalInputs.tendonSlackLength;
+
+precalInputs.maxIsometricForce = mtpInputs.maxIsometricForce;
+
+precalInputs.optimizeIsometricMaxForce = 0;
+
+modeledValues = calcMuscleTendonLengthInitializationModeledValues(tempValues, precalInputs);
+end
+
+function savePassiveMomentDataToSto(precalInputs, modeledValues, resultsDirectory)
+% Passive moments need processing first.
+modelPassiveMoments = permute(modeledValues.passiveModelMoments, [3 1 2]);
+sizeTemp = size(modelPassiveMoments,1);
+experimentalPassiveMoments = permute(precalInputs.passiveData.inverseDynamicsMoments, [3 1 2]);
+
+columnsWithAllZeros = all(experimentalPassiveMoments == 0, 1);
+
+experimentalPassiveMoments = experimentalPassiveMoments(repmat(~columnsWithAllZeros, ...
+    size(experimentalPassiveMoments, 1), 1, 1));
+
+modelPassiveMoments = modelPassiveMoments(repmat(~columnsWithAllZeros, ...
+    size(modelPassiveMoments, 1), 1, 1));
+
+experimentalPassiveMoments = ...
+    reshape(experimentalPassiveMoments, sizeTemp, []);
+experimentalPassiveMoments = ...
+    reshape(experimentalPassiveMoments', 1, 12, 101); % Want a better way to do this
+modelPassiveMoments = ...
+    reshape(modelPassiveMoments, sizeTemp, []);
+modelPassiveMoments = ...
+    reshape(modelPassiveMoments', 1, 12, 101); % Want a better way to do this
+saveAnalysisDataToSto(precalInputs.passivePrefixes, precalInputs.prefixes, ...
+    experimentalPassiveMoments, fullfile(resultsDirectory, ...
+    "passiveJointMomentsExperimental"), "_passiveJointMomentsExperimental.sto")
+saveAnalysisDataToSto(precalInputs.passivePrefixes, precalInputs.prefixes, ...
+    modelPassiveMoments, fullfile(resultsDirectory, ...
+    "passiveJointMomentsModeled"), "_passiveJointMomentsModeled.sto")
+end
+
+function savePassiveForceDataToSto(mtpInputs, modeledValues, results, resultsSynx, ...
+    resultsSynxNoResiduals, resultsDirectory)
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    modeledValues.passiveForce, strcat(resultsDirectory, ...
+    "\passiveForcesExperimental"), "_passiveForcesExperimental.sto");
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    results.passiveForce, strcat(resultsDirectory, ...
+    "\passiveForcesModel"), "_passiveForcesModel.sto");
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsSynx.passiveForce, strcat(resultsDirectory, ...
+    "\passiveForcesModelSynx"), "_passiveForcesModelSynx.sto");
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsSynxNoResiduals.passiveForce, strcat(resultsDirectory, ...
+    "\passiveForcesModelSynxNoResiduals"), "_passiveForcesModelSynxNoResiduals.sto");
+end
+
+function printJointMomentMatchingError(muscleJointMoments, inverseDynamicsMoments)  % Good
+
+for i = 1 : size(muscleJointMoments, 2)
+    jointMomentsRmse(i) = sqrt(sum((muscleJointMoments(:, i, :) - ...
+        inverseDynamicsMoments(:, i, :)) .^ 2, 'all') / ...
+        (numel(inverseDynamicsMoments(:, 1, :)) - 1));
+    jointMomentsMae(i) = sum(abs(muscleJointMoments(:, i, :) - ...
+        inverseDynamicsMoments(:, i, :)) / ...
+        numel(inverseDynamicsMoments(:, 1, :)), 'all');
+end
+fprintf(['The root mean sqrt (RMS) errors between model-predicted ' ...
+    'and inverse dynamic moments are: \n' ]);
+fprintf(['\n ' num2str(jointMomentsRmse) ' \n']);
+fprintf(['The mean absolute errors (MAEs) between model-predicted ' ...
+    'and inverse dynamic moments are: \n' ]);
+fprintf(['\n ' num2str(jointMomentsMae) ' \n']);
+end
+
+function saveActivationAndExcitationDataToSto(mtpInputs, results, ...
+    resultsSynx, resultsDirectory)
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    results.muscleExcitations, strcat(resultsDirectory, ...
+    "\muscleExcitations"), "_muscleExcitations.sto")
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsSynx.muscleExcitations, strcat(resultsDirectory, ...
+    "\muscleExcitationsSynx"), "_muscleExcitationsSynx.sto")
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    results.muscleActivations, strcat(resultsDirectory, ...
+    "\muscleActivations"), "_muscleActivations.sto")
+saveAnalysisDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsSynx.muscleActivations, strcat(resultsDirectory, ...
+    "\muscleActivationsSynx"), "_muscleActivationsSynx.sto")
+
+end
+
+function saveJointMomentDataToSto(mtpInputs, results, resultsSynx, ...
+    resultsSynxNoResiduals, resultsDirectory)
+saveAnalysisDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+    results.muscleJointMoments, strcat(resultsDirectory, ...
+    "\modelJointMomentsNoSynx"), "_modelJointMomentsNoSynx.sto")
+saveAnalysisDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+    resultsSynx.muscleJointMoments, strcat(resultsDirectory, ...
+    "\modelJointMomentsSynx"), "_modelJointMomentsSynx.sto")
+saveAnalysisDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+    resultsSynxNoResiduals.muscleJointMoments, strcat(resultsDirectory, ...
+    "\modelJointMomentsSynxNoResiduals"), "_modelJointMomentsSynxNoResiduals.sto")
+saveAnalysisDataToSto(mtpInputs.coordinateNames, mtpInputs.prefixes, ...
+    mtpInputs.inverseDynamicsMoments, strcat(resultsDirectory, ...
+    "\inverseDynamicsJointMoments"), "_inverseDynamicsJointMoments.sto")
+end
+
+function saveMuscleModelParametersToSto(mtpInputs, finalValues, resultsDirectory)
+if ~exist(resultsDirectory, "dir")
+    mkdir(resultsDirectory);
+end
+columnLabels = mtpInputs.muscleNames;
+% columnLabels = ["Activation Time Constant", "Activation Nonlinearity", ...
+%     "Electromechanical Time Delay", "EMG Scaling Factor", ...
+%     "Optimal Fiber Length Scaling Factor", "Tendon Slack Length Scaling Factor"];
+
+dataPoints = [finalValues.activationTimeConstants;
+    finalValues.activationNonlinearityConstants;
+    finalValues.electromechanicalDelays;
+    finalValues.emgScaleFactors;
+    finalValues.optimalFiberLengthScaleFactors;
+    finalValues.tendonSlackLengthScaleFactors];
+
+writeToSto(columnLabels, 1:1:size(dataPoints,1), dataPoints, ...
+    fullfile(resultsDirectory, "muscleModelParameters.sto"));
+end
+
+function saveAnalysisDataToSto(columnLabels, taskNames, data, directory, fileName)
+if ~exist(directory, "dir")
+    mkdir(directory);
+end
+for i = 1 : size(data,1)
+    writeToSto(columnLabels, 1:1:length(data(i,:,:)), ...
+        permute(data(i,:,:), [3 2 1]), strcat(directory, "\", taskNames(i), fileName))
+end
+end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Saving/saveMuscleTendonPersonalizationResults.m b/src/MuscleTendonPersonalization/Saving/saveMuscleTendonPersonalizationResults.m
new file mode 100644
index 000000000..8a7ef12f3
--- /dev/null
+++ b/src/MuscleTendonPersonalization/Saving/saveMuscleTendonPersonalizationResults.m
@@ -0,0 +1,62 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+% 
+% This function takes the input, finalValues, result structs and writes to
+% the appropriate .osimx muscle model, .sto joint moments, .sto muscle 
+% activations & excitations, .sto Hill-Type muscle-tendon model parameter, 
+% .sto passive forces, and .sto passive moment files. The model is included 
+% in instances where the results are relative to the original model, which 
+% is used for reference.
+%
+% (struct, struct, struct, struct, string, struct) -> (None)
+% Saves results in the struct to the given filenames
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond, Robert Salati               %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function saveMuscleTendonPersonalizationResults(mtpInputs, finalValues, ...
+    modeledValues, resultsStruct, resultsDirectory, precalInputs)
+analysisDirectory = fullfile(resultsDirectory, "Analysis");
+if exist(analysisDirectory, "dir")
+    rmdir(analysisDirectory, 's')
+end
+if nargin < 6
+    precalInputs = [];
+end
+
+if ~isempty(precalInputs)
+    saveMtpPassiveMomentData(precalInputs, modeledValues, analysisDirectory);
+end
+saveMtpPassiveForceData(mtpInputs, resultsStruct, analysisDirectory);
+saveMtpActivationAndExcitationData(mtpInputs, resultsStruct, analysisDirectory);
+writeMtpDataToSto(mtpInputs.muscleNames, mtpInputs.prefixes, ...
+    resultsStruct.results.normalizedFiberLength, ...
+    resultsStruct.results.time, ...
+    fullfile(analysisDirectory, "normalizedFiberLengths"), ...
+    "_normalizedFiberLengths.sto")
+saveMtpJointMomentData(mtpInputs, resultsStruct, analysisDirectory);
+saveMtpMuscleModelParameters(mtpInputs, finalValues, ...
+    fullfile(analysisDirectory, "muscleModelParameters"));
+model = Model(mtpInputs.model);
+muscleNames = getMusclesFromCoordinates(model, mtpInputs.coordinateNames);
+writeMuscleTendonPersonalizationOsimxFile(mtpInputs.modelFileName, ...
+    mtpInputs.osimxFileName, finalValues, muscleNames, resultsDirectory);
+end
\ No newline at end of file
diff --git a/src/DesignOptimization/calcDesignOptimizationObjective.m b/src/MuscleTendonPersonalization/Saving/writeMtpDataToSto.m
similarity index 69%
rename from src/DesignOptimization/calcDesignOptimizationObjective.m
rename to src/MuscleTendonPersonalization/Saving/writeMtpDataToSto.m
index 977e809cf..513c8fd84 100644
--- a/src/DesignOptimization/calcDesignOptimizationObjective.m
+++ b/src/MuscleTendonPersonalization/Saving/writeMtpDataToSto.m
@@ -1,10 +1,12 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the cost function objective for design 
-% optimization.
+% This function formats and saves MTP data to a .sto file. It splits data
+% by gait cycle and saves each gait cycle to a separate file with the
+% appropriate prefix. If the output directory does not already exist, it is
+% created.
 %
-% (Number, Array of number, Number, struct) -> (Number)
-% Returns objective
+% (array), (cell), (array), (string), (string) -> (none)
+% Saves MTP data to a .sto file.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +16,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Robert Salati                                                %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,14 +29,14 @@
 % implied. See the License for the specific language governing            %
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
-
-function objective = calcDesignOptimizationObjective(discrete, ...
-    continuous, finalTime, inputs)
-continuousObjective = sum(continuous) / length(continuous);
-if isfield(inputs, "finalTimeRange")
-    continuousObjective = continuousObjective / finalTime;
+function writeMtpDataToSto(columnLabels, taskNames, data, time, ...
+    directory, fileName)
+if ~exist(directory, "dir")
+    mkdir(directory);
+end
+for i = 1 : size(data,1)
+    writeToSto(columnLabels, time(i, :), ...
+        permute(data(i,:,:), [3 2 1]), ...
+        strcat(directory, "\", taskNames(i), fileName))
 end
-discreteObjective = sum(discrete) / length(discrete);
-if isnan(discreteObjective); discreteObjective = 0; end
-objective = continuousObjective + discreteObjective;
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/SynergyExtrapolation/calcMuscleExcitationsSynX.m b/src/MuscleTendonPersonalization/SynergyExtrapolation/calcMuscleExcitationsSynX.m
index eae6b2404..e6ab86266 100644
--- a/src/MuscleTendonPersonalization/SynergyExtrapolation/calcMuscleExcitationsSynX.m
+++ b/src/MuscleTendonPersonalization/SynergyExtrapolation/calcMuscleExcitationsSynX.m
@@ -70,7 +70,8 @@
     experimentalData.numberOfExtrapolationWeights + 1 : end));
 % Insert unmeasured muscle excitations from SynX
 emgData = updateEmgSignals(params.missingEmgChannelGroups, ...
-    experimentalData.emgDataExpanded, unmeasuredEmgSignals);
+    experimentalData.emgDataExpanded, unmeasuredEmgSignals, ...
+    experimentalData.normalizedFiberLengthGroups);
 % muscleExcitations are scaled processed Emg signals
 emgData = emgData .* emgScalingFactor;
 % Distribute residual excitations
@@ -153,11 +154,12 @@
 end
 
 function emgData = updateEmgSignals(missingEmgChannelGroups, emgData, ...
-    unmeasuredEmgSignals)
+    unmeasuredEmgSignals, normalizedFiberLengthGroups)
 
+lowestIndex = min(cell2mat(normalizedFiberLengthGroups)) - 1;
 for i = 1 : size(missingEmgChannelGroups, 2)
     for j = 1 : size(missingEmgChannelGroups{i}, 2)
-        emgData(:, missingEmgChannelGroups{i}(1, j), :) = ...
+        emgData(:, missingEmgChannelGroups{i}(1, j) - lowestIndex, :) = ...
             unmeasuredEmgSignals(:, i, :);
     end
 end
diff --git a/src/MuscleTendonPersonalization/SynergyExtrapolation/getLinearInequalityConstraints.m b/src/MuscleTendonPersonalization/SynergyExtrapolation/getLinearInequalityConstraints.m
index 67f50956e..07c3f56f7 100644
--- a/src/MuscleTendonPersonalization/SynergyExtrapolation/getLinearInequalityConstraints.m
+++ b/src/MuscleTendonPersonalization/SynergyExtrapolation/getLinearInequalityConstraints.m
@@ -121,7 +121,7 @@
 function aMatrixSynergy = updateHalfMatrixA(emgData, aMatrix,...
     numberOfSynergies, missingEmgChannelGroups, thirdMatrixDimension, ...
     matrixFactorizationFactor)
-
+aMatrixSynergy = [];
 for i = 1:size(missingEmgChannelGroups,2)
     aMatrixSynergy((i - 1) * size(emgData, 1) * size(emgData, 2) + 1 : ...
         i * size(emgData, 1) * size(emgData, 2), (i - 1) * ( ...
diff --git a/src/MuscleTendonPersonalization/SynergyExtrapolation/getSynergyCommands.m b/src/MuscleTendonPersonalization/SynergyExtrapolation/getSynergyCommands.m
index 48ecdb469..974950d8a 100644
--- a/src/MuscleTendonPersonalization/SynergyExtrapolation/getSynergyCommands.m
+++ b/src/MuscleTendonPersonalization/SynergyExtrapolation/getSynergyCommands.m
@@ -98,7 +98,7 @@
 
 function pcaCommands = getPcaCommands(normalizedEMG, numberOfSynergies, ...
     categorizationOfTrials)
-
+pcaCommands = {};
 for i = 1 : length(categorizationOfTrials)
     [~, principleComponents] = pca(reshape(permute(normalizedEMG(:, :, ...
         categorizationOfTrials{i}), [1 3 2]), size(normalizedEMG, 1) * ...
diff --git a/src/MuscleTendonPersonalization/parseMuscleTendonPersonalizationSettingsTree.m b/src/MuscleTendonPersonalization/parseMuscleTendonPersonalizationSettingsTree.m
index aa91bfa21..7e093bd23 100644
--- a/src/MuscleTendonPersonalization/parseMuscleTendonPersonalizationSettingsTree.m
+++ b/src/MuscleTendonPersonalization/parseMuscleTendonPersonalizationSettingsTree.m
@@ -33,13 +33,15 @@
 inputs = getInputs(settingsTree);
 params = getParams(settingsTree);
 inputs = getMtpModelInputs(inputs);
-inputs = mergeStructs(getSynergyExtrapolationInputs(...
-    inputs.model, ...
-    inputs.synergyExtrapolation, ...
-    inputs.emgDataColumnNames, ...
-    inputs.emgData, ...
-    inputs.muscleNames), ...
-    inputs);
+if isfield(inputs, "synergyExtrapolation")
+    inputs = mergeStructs(getSynergyExtrapolationInputs(...
+        inputs.model, ...
+        inputs.synergyExtrapolation, ...
+        inputs.emgDataColumnNames, ...
+        inputs.emgData, ...
+        inputs.muscleNames), ...
+        inputs);
+end
 resultsDirectory = getFieldByName(settingsTree, 'results_directory').Text;
 if(isempty(resultsDirectory))
     resultsDirectory = pwd;
@@ -51,10 +53,14 @@
 dataDirectory = getFieldByNameOrError(tree, 'data_directory').Text;
 inputs = parseEmgData(tree, inputs, dataDirectory);
 inputs.tasks = getTasks(tree);
-inputs.synergyExtrapolation = getSynergyExtrapolationParameters(tree, ...
-    inputs.model);
-inputs.synergyExtrapolation = getTrialIndexes( ...
-    inputs.synergyExtrapolation, size(inputs.emgData, 1), inputs.prefixes);
+if strcmpi(getTextFromField(getFieldByNameOrAlternate( ...
+        getFieldByNameOrError(tree, "MTPSynergyExtrapolation"), ...
+        'is_enabled', 'false')), 'true')
+    inputs.synergyExtrapolation = getSynergyExtrapolationParameters(tree, ...
+        inputs.model);
+    inputs.synergyExtrapolation = getTrialIndexes( ...
+        inputs.synergyExtrapolation, size(inputs.emgData, 1), inputs.prefixes);
+end
 inputs = reorderPreprocessedDataByMuscleNames(inputs, inputs.muscleNames);
 if ~isfield(inputs, "emgSplines")
     inputs.emgSplines = makeEmgSplines(inputs.emgTime, ...
@@ -156,7 +162,7 @@
 end
 
 function inputs = getSynergyExtrapolationInputs(model, ...
-     synergyExtrapolation, emgDataColumnNames, emgData, muscleNames)
+    synergyExtrapolation, emgDataColumnNames, emgData, muscleNames)
 model = Model(model);
 groupToName = getMuscleNameByGroupStruct(model, ...
     emgDataColumnNames);
diff --git a/src/MuscleTendonPersonalization/saveMuscleTendonPersonalizationResults.m b/src/MuscleTendonPersonalization/saveMuscleTendonPersonalizationResults.m
deleted file mode 100644
index ed9954558..000000000
--- a/src/MuscleTendonPersonalization/saveMuscleTendonPersonalizationResults.m
+++ /dev/null
@@ -1,61 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function takes the result struct and writes the values to the
-% appropriate .osimx muscle model, .mot muscle moment, and .sto muscle
-% activation files. The model is included in instances where the results
-% are relative to the original model, which is used for reference.
-%
-% (Model, struct, string, string, string) -> (None)
-% Saves results in the struct to the given filenames
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function saveMuscleTendonPersonalizationResults(modelFileName, ...
-    osimxFileName, prefixes, coordinateNames, finalValues, results, ...
-    resultsDirectory, muscleColumnNames)
-
-model = Model(modelFileName);
-% muscleColumnNames = getEnabledMusclesInOrder(model);
-if ~exist(resultsDirectory, "dir")
-    mkdir(resultsDirectory);
-end
-if ~exist(fullfile(resultsDirectory, "muscleActivations"), "dir")
-    mkdir(fullfile(resultsDirectory, "muscleActivations"));
-end
-if ~exist(fullfile(resultsDirectory, "modelMoments"), "dir")
-    mkdir(fullfile(resultsDirectory, "modelMoments"));
-end
-for i = 1:size(results.muscleActivations, 1)
-    % Need to figure out how to print out individuals file names for each trial
-    writeToSto(muscleColumnNames, results.time(i, :), ...
-        squeeze(results.muscleActivations(i, :, :))', fullfile(resultsDirectory, ...
-        "muscleActivations", strcat(prefixes(i), "_muscleActivations", ".sto")));
-    writeToSto(coordinateNames, results.time(i, :), ...
-        squeeze(results.muscleJointMoments(i, :, :))', fullfile(resultsDirectory, ...
-        "modelMoments", strcat(prefixes(i), "_modelMoments", ".sto")));
-end
-muscleNames = getMusclesFromCoordinates(model, coordinateNames);
-writeMuscleTendonPersonalizationOsimxFile(modelFileName, osimxFileName, ...
-    finalValues, muscleNames, resultsDirectory);
-end
-
diff --git a/src/NeuralControlPersonalization/Analysis/plotMomentMatchingResults.m b/src/NeuralControlPersonalization/Analysis/plotMomentMatchingResults.m
index d301d2b05..05dfbdb30 100644
--- a/src/NeuralControlPersonalization/Analysis/plotMomentMatchingResults.m
+++ b/src/NeuralControlPersonalization/Analysis/plotMomentMatchingResults.m
@@ -49,24 +49,32 @@ function plotMomentMatchingResults(experimentalMomentsFile, ...
 [modeledColumns, modeledTime, modeledMoments] = parseMotToComponents( ...
     org.opensim.modeling.Model(), Storage(modeledMomentsFile));
 
-includedColumns = ismember(experimentalColumns, modeledColumns);
+includedColumns = logical(ismember(experimentalColumns, modeledColumns) ...
+    + ismember(experimentalColumns + "_moment", modeledColumns));
 experimentalMoments = experimentalMoments(includedColumns, :);
 experimentalColumns = experimentalColumns(includedColumns);
 
 subplotNumber = 1;
 hasLegend = false;
-figure(figureNumber)
+% figure(figureNumber)
 figureIndex = 1;
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='compact', Padding='compact');
 for i = 1:length(experimentalColumns)
     if i > figureSize * figureIndex
         figureIndex = figureIndex + 1;
         figure(figureNumber + figureIndex - 1)
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='compact', Padding='compact');
         subplotNumber = 1;
         hasLegend = false;
     end
-    subplot(figureHeight, figureWidth, subplotNumber)
-    plot(experimentalTime, experimentalMoments(i, :), 'LineWidth', 2)
+    nexttile(subplotNumber)
+    plot(modeledTime, experimentalMoments(i, :), 'LineWidth', 2)
     modeledIndex = find(experimentalColumns(i) == modeledColumns);
+    if isempty(modeledIndex)
+        modeledIndex = find(experimentalColumns(i) + "_moment" == modeledColumns);
+    end
     if ~isempty(modeledIndex)
         hold on
         plot(modeledTime, modeledMoments(modeledIndex, :), 'LineWidth', 2);
diff --git a/src/NeuralControlPersonalization/Analysis/plotNcpActivationRmsAndVaf.m b/src/NeuralControlPersonalization/Analysis/plotNcpActivationRmsAndVaf.m
new file mode 100644
index 000000000..f2e871867
--- /dev/null
+++ b/src/NeuralControlPersonalization/Analysis/plotNcpActivationRmsAndVaf.m
@@ -0,0 +1,75 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% Plot total VAF and RMS error for invdividual NCP muscle activations
+% compared to tracked activations. RMS error is used for individual muscles
+% instead of VAF because it better describes the fit of smaller
+% activations. 
+%
+% (string, string, string) -> (None)
+% Plot total VAF and RMS error for NCP muscle activations.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Spencer Williams                                             %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function plotNcpActivationRmsAndVaf(weightsFile, commandsFile, ...
+    mtpActivationsFile)
+import org.opensim.modeling.Storage
+weightsStorage = Storage(weightsFile);
+ncpMuscleNames = getStorageColumnNames(weightsStorage);
+synergyWeights = storageToDoubleMatrix(weightsStorage);
+commandsStorage = Storage(commandsFile);
+synergyCommands = storageToDoubleMatrix(commandsStorage);
+ncpActivations = synergyWeights * synergyCommands;
+
+mtpStorage = Storage(mtpActivationsFile);
+mtpMuscleNames = getStorageColumnNames(mtpStorage);
+mtpActivations = storageToDoubleMatrix(mtpStorage);
+
+[sharedMuscleNames, ncpIndices, mtpIndices] = ...
+    intersect(ncpMuscleNames, mtpMuscleNames);
+ncpSubset = ncpActivations(ncpIndices, :);
+mtpSubset = mtpActivations(mtpIndices, :);
+
+rmsError = zeros(1, length(sharedMuscleNames));
+for i = 1 : length(sharedMuscleNames)
+    rmsError(i) = rms(mtpSubset(i, :) - ncpSubset(i, :));
+end
+totalVaf = calcPercentVaf(reshape(mtpSubset, 1, []), ...
+    reshape(ncpSubset, 1, []));
+[worstError, worstMuscleIndex] = max(rmsError);
+worstMuscleName = sharedMuscleNames(worstMuscleIndex);
+
+boxplot(rmsError)
+title("RMS error for muscles with tracked activations", ...
+    "Total VAF: " + sprintf('\\bf{%.2f}%%\\rm', totalVaf) + newline + ...
+    "Worst individual muscle: " + strrep(worstMuscleName, '_', '\_') + ...
+    sprintf(" (RMSE: %.3f)", worstError))
+ylabel("RMSE")
+set(gca, 'XTick', [])
+end
+
+function percentVaf = calcPercentVaf(experimental, reconstructed)
+sr = sum((experimental - reconstructed) .^ 2);
+st = sum(experimental .^ 2);
+
+percentVaf = (1 - sr/st) * 100;
+end
diff --git a/src/NeuralControlPersonalization/Analysis/plotNeuralControlPersonalizationActivations.m b/src/NeuralControlPersonalization/Analysis/plotNeuralControlPersonalizationActivations.m
index 4a4b070f0..63adafcf3 100644
--- a/src/NeuralControlPersonalization/Analysis/plotNeuralControlPersonalizationActivations.m
+++ b/src/NeuralControlPersonalization/Analysis/plotNeuralControlPersonalizationActivations.m
@@ -59,15 +59,19 @@ function plotNeuralControlPersonalizationActivations(weightsFile, ...
 figureNumber = 1;
 subplotNumber = 1;
 hasLegend = false;
-figure(1)
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+% figure(1)
 for i = 1:size(muscleActivations, 1)
     if i > figureSize * figureNumber
         figureNumber = figureNumber + 1;
         figure(figureNumber)
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
         subplotNumber = 1;
         hasLegend = false;
     end
-    subplot(figureHeight, figureWidth, subplotNumber)
+    nexttile(subplotNumber)
     plot(time, muscleActivations(i, :), 'LineWidth', 2)
     mtpIndex = find(muscleNames(i) == mtpMuscleNames);
     if ~isempty(mtpIndex)
diff --git a/src/NeuralControlPersonalization/NeuralControlPersonalizationTool.m b/src/NeuralControlPersonalization/NeuralControlPersonalizationTool.m
index 83d807c45..dfecfb3d4 100644
--- a/src/NeuralControlPersonalization/NeuralControlPersonalizationTool.m
+++ b/src/NeuralControlPersonalization/NeuralControlPersonalizationTool.m
@@ -47,17 +47,19 @@ function NeuralControlPersonalizationTool(settingsFileName)
     optimizedValues, inputs, params);
 [synergyWeights, synergyCommands] = normalizeSynergiesByMaximumWeight(...
     synergyWeights, synergyCommands);
-combinedActivations = combineFinalActivations(inputs, synergyWeights, ...
-    synergyCommands);
-muscleJointMoments = calcFinalMuscleJointMoments(inputs, ...
+[combinedActivations, ncpActivations] = combineFinalActivations(inputs, ...
+    synergyWeights, synergyCommands);
+combinedMuscleJointMoments = calcFinalMuscleJointMoments(inputs, ...
     combinedActivations);
+ncpMuscleJointMoments = calcFinalMuscleJointMoments(inputs, ...
+    ncpActivations);
 saveNeuralControlPersonalizationResults(synergyWeights, ...
-    synergyCommands, combinedActivations, muscleJointMoments, inputs, ...
-    resultsDirectory, precalInputs);
+    synergyCommands, combinedActivations, combinedMuscleJointMoments, ...
+    ncpMuscleJointMoments, inputs, resultsDirectory, precalInputs);
 end
 
-function combinedActivations = combineFinalActivations(inputs, ...
-    synergyWeights, synergyCommands)
+function [combinedActivations, synergyActivations] = ...
+    combineFinalActivations(inputs, synergyWeights, synergyCommands)
 synergyActivations = zeros(inputs.numTrials, inputs.numMuscles, ...
     inputs.numPoints);
 for i = 1:inputs.numTrials
diff --git a/src/NeuralControlPersonalization/Optimization/CostComputations/calcMomentTrackingCost.m b/src/NeuralControlPersonalization/Optimization/CostComputations/calcMomentTrackingCost.m
deleted file mode 100644
index c02c9aff6..000000000
--- a/src/NeuralControlPersonalization/Optimization/CostComputations/calcMomentTrackingCost.m
+++ /dev/null
@@ -1,11 +0,0 @@
-function cost = calcMomentTrackingCost(modeledValues, ...
-    experimentalData, params)
-costWeight = valueOrAlternate(params, "momentTrackingCostWeight", 1);
-errorCenter = valueOrAlternate(params, "momentTrackingErrorCenter", 0);
-maximumAllowableError = valueOrAlternate(params, ...
-    "momentTrackingMaximumAllowableError", 2);
-cost = costWeight * calcTrackingCostTerm( ...
-    modeledValues.muscleJointMoments, ...
-    experimentalData.muscleJointMoments, errorCenter, ...
-    maximumAllowableError);
-end
\ No newline at end of file
diff --git a/src/NeuralControlPersonalization/parseNeuralControlPersonalizationSettingsTree.m b/src/NeuralControlPersonalization/parseNeuralControlPersonalizationSettingsTree.m
index 62337e9d9..d7833e3a2 100644
--- a/src/NeuralControlPersonalization/parseNeuralControlPersonalizationSettingsTree.m
+++ b/src/NeuralControlPersonalization/parseNeuralControlPersonalizationSettingsTree.m
@@ -37,11 +37,12 @@
 if(isempty(resultsDirectory))
     resultsDirectory = pwd;
 end
+inputs = rmfield(inputs, "model");
 end
 
 function inputs = getInputs(tree)
 inputs = parseMtpNcpSharedInputs(tree);
-inputs.synergyGroups = getSynergyGroups(tree, Model(inputs.model));
+inputs.synergyGroups = parseSynergyGroups(tree, inputs.model);
 inputs = matchMuscleNamesFromCoordinatesAndSynergyGroups(inputs);
 inputs = reorderPreprocessedDataByMuscleNames(inputs, inputs.muscleNames);
 [inputs.maxIsometricForce, inputs.optimalFiberLength, ...
@@ -71,7 +72,7 @@
 % if ~isstruct(osimxFileName) || isempty(osimxFileName.Text)
 %     throw(MException('', 'An input .osimx file is required if using data from MTP.'))
 % end
-inputs.mtpMuscleData = parseOsimxFile(osimxFileName.Text);
+inputs.mtpMuscleData = parseOsimxFile(osimxFileName.Text, inputs.model);
 % Remove activations of muscles from coordinates not included
 includedSubset = ismember(inputs.mtpActivationsColumnNames, ...
     inputs.muscleTendonColumnNames);
@@ -100,7 +101,6 @@
 end
 
 function params = getParams(tree, model, inputs)
-model = Model(model);
 params = struct();
 params.activationGroupNames = parseSpaceSeparatedList(tree, ...
     'activation_muscle_groups');
@@ -132,29 +132,6 @@
     '1e6')));
 end
 
-function groups = getSynergyGroups(tree, model)
-synergySetTree = getFieldByNameOrError(tree, "RCNLSynergySet");
-groupsTree = getFieldByNameOrError(synergySetTree, "RCNLSynergy");
-groups = {};
-for i=1:length(groupsTree)
-    if(length(groupsTree) == 1)
-        group = groupsTree;
-    else
-        group = groupsTree{i};
-    end
-    groups{i}.numSynergies = ...
-        str2double(group.num_synergies.Text);
-    groupMembers = model.getForceSet().getGroup( ...
-        group.muscle_group_name.Text).getMembers();
-    muscleNames = string([]);
-    for j=0:groupMembers.getSize() - 1
-        muscleNames(end + 1) = groupMembers.get(j);
-    end
-    groups{i}.muscleNames = muscleNames;
-    groups{i}.muscleGroupName = group.muscle_group_name.Text;
-end
-end
-
 function [optimalFiberLengthScaleFactors, ...
     tendonSlackLengthScaleFactors, maxIsometricForce] = ...
     getMtpDataInputs(inputs)
diff --git a/src/NeuralControlPersonalization/saveNeuralControlPersonalizationResults.m b/src/NeuralControlPersonalization/saveNeuralControlPersonalizationResults.m
index bd3f33f26..3a31364ad 100644
--- a/src/NeuralControlPersonalization/saveNeuralControlPersonalizationResults.m
+++ b/src/NeuralControlPersonalization/saveNeuralControlPersonalizationResults.m
@@ -1,12 +1,9 @@
 function saveNeuralControlPersonalizationResults(synergyWeights, ...
-    synergyCommands, activations, moments, inputs, resultsDirectory, ...
+    synergyCommands, activations, combinedMoments, ncpMoments, inputs, resultsDirectory, ...
     precalInputs)
 if ~exist(resultsDirectory, "dir")
     mkdir(resultsDirectory);
 end
-if ~exist(fullfile(resultsDirectory, "combinedMuscleActivations"))
-    mkdir(fullfile(resultsDirectory, "combinedMuscleActivations"))
-end
 if ~exist(fullfile(resultsDirectory, "modelMoments"))
     mkdir(fullfile(resultsDirectory, "modelMoments"))
 end
@@ -16,8 +13,13 @@ function saveNeuralControlPersonalizationResults(synergyWeights, ...
     synergyWeights, ...
     fullfile(resultsDirectory, "synergyWeights.sto"));
 commandColumns = [];
-for i = 1 : size(synergyWeights, 1)
-    commandColumns = [commandColumns convertCharsToStrings(num2str(i))];
+for j = 1 : length(inputs.synergyGroups)
+    for i = 1 : inputs.synergyGroups{j}.numSynergies
+        commandColumns = [commandColumns ...
+            convertCharsToStrings( ...
+            inputs.synergyGroups{j}.muscleGroupName) + ...
+            "_" + convertCharsToStrings(num2str(i))];
+    end
 end
 for i = 1 : size(synergyCommands, 1)
     writeToSto( ...
@@ -36,13 +38,11 @@ function saveNeuralControlPersonalizationResults(synergyWeights, ...
         tempActivations, ...
         fullfile( ...
         resultsDirectory, ...
-        "combinedMuscleActivations", ...
         inputs.prefixes(i) + "_combinedActivations.sto" ...
         ) ...
         )
-    tempMoments = permute(moments(i, :, :), [3 1 2]);
     momentColumns = inputs.coordinateNames;
-    model = Model(inputs.model);
+    model = Model(inputs.modelFileName);
     for j = 1:length(momentColumns)
         if strcmpi(model.getCoordinateSet.get(momentColumns(j)).getMotionType.toString.toCharArray', 'Rotational')
             momentColumns(j) = momentColumns(j) + "_moment";
@@ -53,16 +53,25 @@ function saveNeuralControlPersonalizationResults(synergyWeights, ...
     writeToSto( ...
         momentColumns, ...
         inputs.time(i, :), ...
-        tempMoments, ...
+        permute(combinedMoments(i, :, :), [3 1 2]), ...
         fullfile( ...
         resultsDirectory, ...
         "modelMoments", ...
-        inputs.prefixes(i) + "_modeledMoments.sto" ...
+        inputs.prefixes(i) + "_modeledMomentsMtpNcpCombined.sto" ...
+        ) ...
+        )
+    writeToSto( ...
+        momentColumns, ...
+        inputs.time(i, :), ...
+        permute(ncpMoments(i, :, :), [3 1 2]), ...
+        fullfile( ...
+        resultsDirectory, ...
+        "modelMoments", ...
+        inputs.prefixes(i) + "_modeledMomentsNcp.sto" ...
         ) ...
         )
 end
-if isstruct(precalInputs)
-    writeNeuralControlPersonalizationOsimxFile(inputs, ...
-        resultsDirectory, precalInputs)
-end
+writeNeuralControlPersonalizationOsimxFile(inputs, ...
+    resultsDirectory, precalInputs)
+
 end
diff --git a/src/Preprocessing/createMuscleTendonVelocity.m b/src/Preprocessing/createMuscleTendonVelocity.m
index 10cf27158..c0f01d8a0 100644
--- a/src/Preprocessing/createMuscleTendonVelocity.m
+++ b/src/Preprocessing/createMuscleTendonVelocity.m
@@ -33,20 +33,15 @@ function createMuscleTendonVelocity(muscleTendonLengthFileName, ...
 storage = org.opensim.modeling.Storage(muscleTendonLengthFileName);
 lengthData = storageToDoubleMatrix(storage);
 time = findTimeColumn(storage);
-isLongFile = length(time) > 200;
+columnNames = getStorageColumnNames(storage);
 
-if isLongFile
-    numNodes = splFitWithCutoff(time(1:200), lengthData(:, 1:200), ...
-        cutoffFrequency, 4);
-    numNodes = numNodes * length(time) / 200;
-else
-    numNodes = splFitWithCutoff(time, lengthData, cutoffFrequency, 4);
-end
-velocityData = calcBSplineDerivative(time, lengthData, 4, numNodes);
+lengthData = lowpassFilter(time, lengthData', 4, cutoffFrequency, 0);
+splineSet = makeGcvSplineSet(time, lengthData, columnNames);
+velocityData = evaluateGcvSplines(splineSet, columnNames, time, 1)';
 
 [filepath, name, ext] = fileparts(muscleTendonLengthFileName);
 name = strrep(name, "_Length", "");
-writeToSto(getStorageColumnNames(storage), time, velocityData', ...
+writeToSto(columnNames, time, velocityData', ...
     fullfile(filepath, strcat(name, "_Velocity", ext)));
 
 end
diff --git a/src/Preprocessing/sectionDataFiles.m b/src/Preprocessing/sectionDataFiles.m
index 505efb316..8dcedc983 100644
--- a/src/Preprocessing/sectionDataFiles.m
+++ b/src/Preprocessing/sectionDataFiles.m
@@ -33,17 +33,21 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function sectionDataFiles(fileNames, timePairs, numRows, prefix)
+function sectionDataFiles(fileNames, timePairs, numRows, prefix, ...
+    filesToFilter, cutoffFrequency)
 import org.opensim.modeling.Storage
 for i=1:length(fileNames)
     storage = Storage(fileNames(i));
     data = storageToDoubleMatrix(storage);
     time = findTimeColumn(storage);
+    if filesToFilter(i)
+        data = lowpassFilter(time, data', 4, cutoffFrequency, 0);
+    end
     columnNames = getStorageColumnNames(storage);
     for j=1:size(timePairs, 1)
         [filepath, name, ext] = fileparts(fileNames(i));
         [newData, newTime] = cutData(data, time, timePairs(j,1), ...
-            timePairs(j,2), numRows);
+            timePairs(j,2), numRows, columnNames);
         newFileName = insertAfter(name, prefix, "_" + num2str(j));
         writeToSto(columnNames, newTime, newData', fullfile(filepath, ...
             newFileName + ext));
@@ -52,8 +56,9 @@ function sectionDataFiles(fileNames, timePairs, numRows, prefix)
 end
 
 function [newData, newTime] = cutData(data, time, startTime, endTime, ...
-    numRows)
+    numRows, columnNames)
 newTime = linspace(startTime, endTime, numRows);
-newData = spline(time, data, newTime);
+splineSet = makeGcvSplineSet(time, data, columnNames);
+newData = evaluateGcvSplines(splineSet, columnNames, newTime)';
 end
 
diff --git a/src/Preprocessing/splitIntoTrials.m b/src/Preprocessing/splitIntoTrials.m
index c54f3d7ea..d56512523 100644
--- a/src/Preprocessing/splitIntoTrials.m
+++ b/src/Preprocessing/splitIntoTrials.m
@@ -54,6 +54,8 @@ function splitIntoTrials(timePairs, inputSettings, outputSettings)
     'trial');
 outputDir = getFieldByNameOrAlternate(outputSettings, ...
     'resultsDirectory', 'preprocessed');
+cutoffFrequency = valueOrAlternate(inputSettings, 'cutoffFrequency', 6);
+rowsPerTrial = valueOrAlternate(inputSettings, 'rowsPerTrial', 101);
 
 model = Model(model);
 ikOutputDir = 'IKData';
@@ -90,16 +92,20 @@ function splitIntoTrials(timePairs, inputSettings, outputSettings)
     preprocessDataFile(emgFileName, outputDir, emgOutputDir, trialName)
 end
 
-filesToSection = makeFilesToSection(outputDir, ikOutputDir, ...
-    idOutputDir, maOutputDir, grfOutputDir, trialName, coordinates, ...
-    included);
-sectionDataFiles(filesToSection, timePairs, 101, trialName);
+[filesToSection, filesToFilter] = makeFilesToSection(outputDir, ...
+    ikOutputDir, idOutputDir, maOutputDir, grfOutputDir, trialName, ...
+    coordinates, included);
+sectionDataFiles(filesToSection, timePairs, rowsPerTrial, trialName, ...
+    filesToFilter, cutoffFrequency);
 
-numBufferRows = calcNumPaddingFrames(timePairs);
-paddedTimePairs = addBufferToTimePairs(timePairs, numBufferRows);
+% numBufferRows = calcNumPaddingFrames(timePairs, rowsPerTrial);
+numBufferRows = 19;
+paddedTimePairs = addBufferToTimePairs(timePairs, numBufferRows, ...
+    rowsPerTrial);
 sectionDataFiles( ...
     [fullfile(outputDir, emgOutputDir, trialName + ".sto")], ...
-    paddedTimePairs, (2 * numBufferRows) + 101, trialName)
+    paddedTimePairs, (2 * numBufferRows) + rowsPerTrial, trialName, ...
+    false, cutoffFrequency);
 for i=1:length(filesToSection)
     delete(filesToSection(i));
 end
@@ -167,34 +173,40 @@ function preprocessMuscleAnalysisData(outputDir, muscleAnalysisDirectory, ...
 end
 end
 
-function filesToSection = makeFilesToSection(outputDir, ikOutputDir, ...
-    idOutputDir, maOutputDir, grfOutputDir, trialName, coordinates, ...
-    included)
-filesToSection = [];
+function [filesToSection, filesToFilter] = makeFilesToSection( ...
+    outputDir, ikOutputDir, idOutputDir, maOutputDir, grfOutputDir, ...
+    trialName, coordinates, included)
+filesToSection = string([]);
+filesToFilter = [];
 if included.ma
     filesToSection = [ ...
         fullfile(outputDir, maOutputDir, trialName + ...
         "_Length.sto"), ...
         fullfile(outputDir, maOutputDir, trialName + ...
         "_Velocity.sto")];
+    filesToFilter = [true, false];
 end
 if included.ik
     filesToSection(end+1) = ...
         fullfile(outputDir, ikOutputDir, trialName + ".sto");
+    filesToFilter(end+1) = true;
 end
 if included.id
     filesToSection(end+1) = ...
         fullfile(outputDir, idOutputDir, trialName + ".sto");
+    filesToFilter(end+1) = true;
 end
 if included.grf
     filesToSection(end+1) = fullfile(outputDir, grfOutputDir, ...
         trialName + ".sto");
+    filesToFilter(end+1) = false;
 end
 for i=1:length(coordinates)
     if isfile(fullfile(outputDir, maOutputDir, ...
             trialName + "_MomentArm_" + coordinates(i) + ".sto"))
         filesToSection(end+1) = fullfile(outputDir, maOutputDir, ...
             trialName + "_MomentArm_" + coordinates(i) + ".sto");
+        filesToFilter(end+1) = true;
     end
 end
 end
@@ -232,8 +244,8 @@ function throwCantFindMAFileException(fileName)
 throw(MException('', "Cannot find Muscle Analysis file for " + fileName));
 end
 
-function numFramesBuffer = calcNumPaddingFrames(timePairs)
-normalizedNumDataPoints = 101;
+function numFramesBuffer = calcNumPaddingFrames(timePairs, ...
+    normalizedNumDataPoints)
 shortestTrialLength = timePairs(1,2) - timePairs(1,1);
 for i=2:size(timePairs, 1)
     if(timePairs(i,2) - timePairs(i,1) < shortestTrialLength)
@@ -244,8 +256,8 @@ function throwCantFindMAFileException(fileName)
 numFramesBuffer = ceil(0.2 / timePerFrame);
 end
 
-function newTimePairs = addBufferToTimePairs(timePairs, numBufferRows)
-rowsPerTrial = 101;
+function newTimePairs = addBufferToTimePairs(timePairs, numBufferRows, ...
+    rowsPerTrial)
 for i=1:size(timePairs, 1)
     trialTime = timePairs(i,2) - timePairs(i,1);
     timePairs(i,1) = timePairs(i,1) - (numBufferRows / ...
diff --git a/src/SurrogateModelCreation/SurrogateModelCreation.m b/src/SurrogateModelCreation/SurrogateModelCreation.m
index 48034c28a..171c2a0f3 100644
--- a/src/SurrogateModelCreation/SurrogateModelCreation.m
+++ b/src/SurrogateModelCreation/SurrogateModelCreation.m
@@ -11,7 +11,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Spencer Williams                               %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -25,7 +25,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function SurrogateModelCreation(inputs)
+function surrogateMuscles = SurrogateModelCreation(inputs)
 
 inputs = getData(inputs);
 
@@ -34,55 +34,59 @@ function SurrogateModelCreation(inputs)
         inputs.experimentalJointAngles] = performLhsSampling(inputs);
 end
 inputs = getMuscleSpecificSurrogateModelData(inputs);
-[inputs.polynomialExpressionMuscleTendonLengths, ...
-    inputs.polynomialExpressionMuscleTendonVelocities, ...
-    inputs.polynomialExpressionMomentArms, inputs.coefficients] = ...
-    createSurrogateModel(inputs.muscleSpecificJointAngles, ...
-    inputs.muscleTendonLengths, inputs.muscleSpecificMomentArms,  ...
-    inputs.polynomialDegree);
-
-saveSurrogateModel(inputs);
-reportSurrogateModel(inputs);
+surrogateMuscles = createSurrogateModel( ...
+    inputs.muscleSpecificJointAngles, inputs.muscleTendonLengths, ...
+    inputs.muscleSpecificMomentArms,  inputs.polynomialDegree);
+
+if valueOrAlternate(inputs, 'plotResults', false)
+    inputs.surrogateMuscles = surrogateMuscles;
+    reportSurrogateModel(inputs);
+end
 end
 
 function inputs = getData(inputs)
 
-tree.trial_prefixes = inputs.trialPrefixes;
+tree.trial_prefixes.Text = inputs.trialName;
 prefixes = findPrefixes(tree.trial_prefixes, inputs.dataDirectory);
-inputs.muscleNames = getMusclesFromCoordinates(inputs.model, ...
-    inputs.surrogateModelCoordinateNames);
+if ~isfield(inputs, 'muscleNames')
+    inputs.muscleNames = getMusclesFromCoordinates(inputs.model, ...
+        inputs.surrogateModelCoordinateNames);
+end
 inputs.numMuscles = length(inputs.muscleNames);
 
-inverseKinematicsFileNames = findFileListFromPrefixList(fullfile( ...
-    inputs.dataDirectory, "IKData"), prefixes);
-[inputs.experimentalJointAngles, inputs.coordinateNames] = ...
-    parseInverseKinematicsFile(inverseKinematicsFileNames, inputs.model);
-inputs.experimentalJointAngles =  ...
-    reshape(permute(inputs.experimentalJointAngles, [1 3 2]), [], ...
-    length(inputs.coordinateNames));
 
-directories = findFirstLevelSubDirectoriesFromPrefixes(fullfile( ...
-    inputs.dataDirectory, "MAData"), prefixes);
+[inputs.experimentalJointAngles, inputs.coordinateNames, experimentalTime] = ...
+    parseTrialData(fullfile(inputs.dataDirectory, "IKData"), inputs.trialName, inputs.model);
+% inputs.experimentalJointAngles =  ...
+%     reshape(permute(inputs.experimentalJointAngles, [1 3 2]), [], ...
+%     length(inputs.coordinateNames));
+inputs.experimentalJointVelocities = calcBSplineDerivative( ...
+    experimentalTime, inputs.experimentalJointAngles, 5, 20);
+
+directory = fullfile(inputs.dataDirectory, "MAData", inputs.trialName);
 [inputs.muscleTendonLengths, inputs.muscleTendonColumnNames] = ...
-    parseFileFromDirectories(directories, "Length.sto", Model(inputs.model));
+    parseFileFromDirectories(directory, "Length.sto", inputs.model);
+% inputs.muscleNames = findMusclesFromSynergyGroups(inputs);
+% inputs.surrogateModelCoordinateNames = findSurrogateModelCoordinates( ...
+%     inputs, directories);
 inputs.muscleTendonLengths = findSpecificMusclesInData( ...
     inputs.muscleTendonLengths, inputs.muscleTendonColumnNames, ...
     inputs.muscleNames);
 inputs.muscleTendonLengths = reshape(permute(inputs.muscleTendonLengths, ...
     [1 3 2]), [], length(inputs.muscleNames));
 [inputs.muscleTendonVelocities, muscleTendonColumnNames] = ...
-    parseFileFromDirectories(directories, "Velocity.sto", Model(inputs.model));
+    parseFileFromDirectories(directory, "Velocity.sto", Model(inputs.model));
 inputs.muscleTendonVelocities = findSpecificMusclesInData( ...
     inputs.muscleTendonVelocities, muscleTendonColumnNames, ...
     inputs.muscleNames);
 inputs.muscleTendonVelocities = reshape(permute(inputs.muscleTendonVelocities, ...
     [1 3 2]), [], length(inputs.muscleNames));
-inputs.momentArms = parseSelectMomentArms(directories, ...
+inputs.momentArms = parseSelectMomentArms(directory, ...
     inputs.surrogateModelCoordinateNames, inputs.muscleNames);
 inputs.momentArms = reshape(permute(inputs.momentArms, [1 4 2 3]), [], ...
     length(inputs.surrogateModelCoordinateNames), length(inputs.muscleNames));
 
-if(isempty(inputs.resultsDirectory))
+if(~isfield(inputs, "resultsDirectory") || isempty(inputs.resultsDirectory))
     inputs.resultsDirectory = pwd;
 end
 end
@@ -102,6 +106,33 @@ function SurrogateModelCreation(inputs)
 end
 end
 
+function coordinates = findSurrogateModelCoordinates(inputs, ...
+    directories)
+coordinates = string([]);
+includedMuscles = ismember(inputs.muscleTendonColumnNames, ...
+    inputs.muscleNames);
+[data, fullCoordinates] = parseMomentArms(directories, ...
+    Model(inputs.model));
+for i = 1 : length(fullCoordinates)
+    if any(any(any(data(:, i, includedMuscles, :) > inputs.epsilon)))
+        coordinates(end+1) = fullCoordinates(i);
+    end
+end
+end
+
+function muscleNames = findMusclesFromSynergyGroups(inputs)
+muscleNames = string([]);
+model = Model(inputs.model);
+for i = 1 : length(inputs.synergyGroups)
+    group = model.getForceSet.getGroup( ...
+        inputs.synergyGroups{i}.muscleGroupName).getMembers();
+    for j = 0 : group.getSize() - 1
+        muscleNames(end+1) = convertCharsToStrings( ...
+            group.get(j).getName.toCharArray');
+    end
+end
+end
+
 function [muscleTendonLengths, momentArms, ...
     experimentalJointAngles] = performLhsSampling(inputs)
 
diff --git a/src/SurrogateModelCreation/SurrogateModelPreviewTool.m b/src/SurrogateModelCreation/SurrogateModelPreviewTool.m
new file mode 100644
index 000000000..44e3e0cdc
--- /dev/null
+++ b/src/SurrogateModelCreation/SurrogateModelPreviewTool.m
@@ -0,0 +1,52 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function takes a properly formatted XML file and fits surrogate
+% muscle geometry to validate the surrogate muscle model settings. 
+%
+% (string) -> (None)
+% Create and plot surrogate model from Treatment Optimization settings file
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Spencer Williams                                             %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function SurrogateModelPreviewTool(settingsFileName)
+settingsTree = xml2struct(settingsFileName);
+toolFields = fieldnames(settingsTree.NMSMPipelineDocument);
+switch toolFields{1} 
+    case 'TrackingOptimizationTool'
+        verifyVersion(settingsTree, "TrackingOptimizationTool");
+        [inputs, params] = parseTrackingOptimizationSettingsTree(settingsTree);
+    case 'VerificationOptimizationTool'
+        verifyVersion(settingsTree, "VerificationOptimizationTool");
+        [inputs, params] = parseVerificationOptimizationSettingsTree(settingsTree);
+    case 'DesignOptimizationTool'
+        verifyVersion(settingsTree, "DesignOptimizationTool");
+        [inputs, params] = parseDesignOptimizationSettingsTree(settingsTree);
+    otherwise
+        MException('Incorrect Settings File', ...
+            "Invalid settings file type. Valid types include " + ...
+            "TrackingOptimizationTool, VerificationOptimizationTool," + ...
+            " and DesignOptimizationTool.")
+end
+inputs.plotResults = true;
+SurrogateModelCreation(inputs);
+end
diff --git a/src/SurrogateModelCreation/calcSurrogateModel.m b/src/SurrogateModelCreation/calcSurrogateModel.m
index 3b639573d..46ea12847 100644
--- a/src/SurrogateModelCreation/calcSurrogateModel.m
+++ b/src/SurrogateModelCreation/calcSurrogateModel.m
@@ -23,7 +23,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Spencer Williams                               %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -38,25 +38,20 @@
 % -----------------------------------------------------------------------
 
 function [newMuscleTendonLengths, newMomentArms, ...
-    newMuscleTendonVelocities] = calcSurrogateModel(params, jointAngles, ...
+    newMuscleTendonVelocities] = calcSurrogateModel(inputs, jointAngles, ...
     jointVelocities)
 
 newMomentArms = zeros(size(jointAngles{1}, 1), ...
-    length(params.coordinateNames), size(jointAngles, 2));
+    length(inputs.coordinateNames), size(jointAngles, 2));
 for i = 1 : size(jointAngles, 2)
-    % Get A matrix
-    matrix = PatientSpecificSurrogateModel(jointAngles{i}, jointVelocities{i}, i);
-    % Caculate new muscle tendon lengths and moment arms
-    vector = matrix * params.coefficients{i};
-    newMuscleTendonLengths(:, i) = vector(1 : size(jointAngles{i}, 1));
-    newMuscleTendonVelocities(:, i) = vector(1 + ...
-        size(jointAngles{i}, 1) : size(jointAngles{i}, 1) * 2);
-    index = 2;
-    for j = 1 : length(params.coordinateNames)
-        for k = 1 : length(params.surrogateModelLabels{i})
-            if strcmp(params.coordinateNames(j), params.surrogateModelLabels{i}(k))
-                newMomentArms(:, j, i) = vector(size(jointAngles{i}, 1) * ...
-                    index + 1 : size(jointAngles{i}, 1) * (index + 1));
+    [newMuscleTendonLengths(:, i), newMuscleTendonVelocities(:, i), ...
+        momentArms] = inputs.surrogateMuscles{i}(jointAngles{i}, ...
+        jointVelocities{i});
+    index = 1;
+    for j = 1 : length(inputs.coordinateNames)
+        for k = 1 : length(inputs.surrogateModelLabels{i})
+            if strcmp(inputs.coordinateNames(j), inputs.surrogateModelLabels{i}{k})
+                newMomentArms(:, j, i) = momentArms(:, index);
                 index = index + 1;
             end
         end
diff --git a/src/SurrogateModelCreation/createSurrogateModel.m b/src/SurrogateModelCreation/createSurrogateModel.m
index 7715d4d8c..ffb82b194 100644
--- a/src/SurrogateModelCreation/createSurrogateModel.m
+++ b/src/SurrogateModelCreation/createSurrogateModel.m
@@ -24,7 +24,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Spencer Williams                               %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -36,20 +36,27 @@
 % WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
 % implied. See the License for the specific language governing            %
 % permissions and limitations under the License.                          %
-% -----------------------------------------------------------------------
-
-function [polynomialExpressionMuscleTendonLengths, ...
-    polynomialExpressionMuscleTendonVelocities, ...
-    polynomialExpressionMomentArms, coefficients] = ...
-    createSurrogateModel(jointAngles, muscleTendonLengths, ...
-    momentArms, polynomialDegree)
+% ----------------------------------------------------------------------- %
 
+function surrogateMuscles = createSurrogateModel(jointAngles, ...
+    muscleTendonLengths, momentArms, polynomialDegree)
+surrogateMuscles = cell(1, size(muscleTendonLengths, 2));
 % Create surorogate model for all muscles
 for i = 1 : size(muscleTendonLengths, 2)
-[polynomialExpressionMuscleTendonLengths{i}, ... 
-    polynomialExpressionMuscleTendonVelocities{i}, ...
-    polynomialExpressionMomentArms{i}, coefficients{i}] = ...
+[polynomialExpressionMuscleTendonLengths, ... 
+    polynomialExpressionMuscleTendonVelocities, ...
+    polynomialExpressionMomentArms, coefficients] = ...
     createMuscleSpecificSurrogateModel(jointAngles{i}, ...
     muscleTendonLengths(:, i), momentArms{i}, polynomialDegree);
+
+polynomialMuscleTendonLengths = matlabFunction(polynomialExpressionMuscleTendonLengths);
+polynomialMuscleTendonVelocities = matlabFunction(polynomialExpressionMuscleTendonVelocities);
+polynomialMomentArms = matlabFunction(polynomialExpressionMomentArms);
+
+surrogateMuscles{i} = @(jointAngles, jointVelocities)evaluateSurrogate( ...
+    jointAngles, jointVelocities, ...
+    polynomialMuscleTendonLengths, ...
+    polynomialMuscleTendonVelocities, ...
+    polynomialMomentArms, coefficients);
+end
 end
-end
\ No newline at end of file
diff --git a/src/SurrogateModelCreation/evaluateSurrogate.m b/src/SurrogateModelCreation/evaluateSurrogate.m
new file mode 100644
index 000000000..cd2073b96
--- /dev/null
+++ b/src/SurrogateModelCreation/evaluateSurrogate.m
@@ -0,0 +1,56 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function evaluates a surrogate model using polynomials and
+% coefficents. This function is only intended to be used as a saved
+% function handle, with one handle saved for each surrogate muscle. The
+% polynomials and coefficients belonging to each muscle are stored in the
+% handle. 
+%
+% (2D Array of double, 2D Array of double, Array of symbol, 
+% Array of symbol, 2D Array of symbol, 2D Array of double) -> 
+% (Array of double, Array of double, 2D Array of double)
+%
+% Evaluates the surrogate model for a single muscle. 
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Spencer Williams                                             %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function [muscleTendonLength, muscleTendonVelocity, momentArms] = ...
+    evaluateSurrogate(jointAngles, jointVelocities, ...
+    polynomialExpressionMuscleTendonLength, ...
+    polynomialExpressionMuscleTendonVelocity, ...
+    polynomialExpressionMomentArms, coefficients)
+
+muscleTendonLength = zeros(size(jointAngles, 1), 1);
+muscleTendonVelocity = zeros(size(jointAngles, 1), 1);
+momentArms = zeros(size(jointAngles)).';
+
+for i = 1 : size(jointAngles, 1)
+    positionArgs = num2cell(jointAngles(i, :));
+    velocityArgs = [positionArgs num2cell(jointVelocities(i, :))];
+    muscleTendonLength(i) = polynomialExpressionMuscleTendonLength(positionArgs{:}) * coefficients;
+    muscleTendonVelocity(i) = polynomialExpressionMuscleTendonVelocity(velocityArgs{:}) * coefficients;
+    momentArms(:, i) = polynomialExpressionMomentArms(positionArgs{:}) * coefficients;
+end
+
+momentArms = momentArms.';
+end
diff --git a/src/SurrogateModelCreation/getMuscleSpecificSurrogateModelData.m b/src/SurrogateModelCreation/getMuscleSpecificSurrogateModelData.m
index b98f76d9d..215d67e7f 100644
--- a/src/SurrogateModelCreation/getMuscleSpecificSurrogateModelData.m
+++ b/src/SurrogateModelCreation/getMuscleSpecificSurrogateModelData.m
@@ -11,7 +11,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Spencer Williams                               %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -32,9 +32,9 @@
     for j = 1:length(inputs.coordinateNames)
         for k = 1:length(inputs.surrogateModelCoordinateNames)
             if strcmp(inputs.coordinateNames(j), inputs.surrogateModelCoordinateNames(k))
-                if range(inputs.momentArms(:,k,i)) > inputs.epsilon
+                if max(abs(inputs.momentArms(:,k,i))) > inputs.epsilon
                     inputs.surrogateModelLabels{i}(counter) = ...
-                        inputs.coordinateNames(j);
+                        {convertStringsToChars(inputs.coordinateNames(j))};
                     inputs.muscleSpecificJointAngles{i}(:,counter) = ...
                         inputs.experimentalJointAngles(:,j);
                     inputs.muscleSpecificMomentArms{i}(:,counter) = ...
diff --git a/src/SurrogateModelCreation/getPolynomialExpressions.m b/src/SurrogateModelCreation/getPolynomialExpressions.m
index 34e542a1e..4a9b01d3f 100644
--- a/src/SurrogateModelCreation/getPolynomialExpressions.m
+++ b/src/SurrogateModelCreation/getPolynomialExpressions.m
@@ -54,21 +54,37 @@
     children(expand(polynomialExpressionMuscleTendonLength));
 polynomialExpressionMuscleTendonLength = ...
     cat(2, polynomialExpressionMuscleTendonLength{:});
+% Remove all coefficients
+for i = 1 : size(polynomialExpressionMuscleTendonLength, 2)
+    polynomialExpressionMuscleTendonLength(i) = ...
+        polynomialExpressionMuscleTendonLength(i) / ...
+        coeffs(polynomialExpressionMuscleTendonLength(i)); 
+end
 % Differentiate muscle tendon length w.r.t. time
 for i = 1 : size(jointAngles, 2)
     for j = 1 : size(polynomialExpressionMuscleTendonLength, 2)
         syms(sprintf('theta%d(t)', i))
         theta_t(i) = symfun(eval(sprintf('theta%d(t)', i)), t);
-        tempPolynomialExpressionMuscleTendonVelocity = subs(polynomialExpressionMuscleTendonLength(1, j), theta(i), theta_t(i));
-        tempPolynomialExpressionMuscleTendonVelocity = diff(tempPolynomialExpressionMuscleTendonVelocity, t);
-        tempPolynomialExpressionMuscleTendonVelocity = subs(tempPolynomialExpressionMuscleTendonVelocity, diff(theta_t(i), t), thetaDot(i));
-        polynomialExpressionMuscleTendonVelocity(i, j) = subs(tempPolynomialExpressionMuscleTendonVelocity, theta_t(i), theta(i));
+        tempPolynomialExpressionMuscleTendonVelocity = ...
+            subs(polynomialExpressionMuscleTendonLength(1, j), ...
+            theta(i), theta_t(i));
+        tempPolynomialExpressionMuscleTendonVelocity = ...
+            diff(tempPolynomialExpressionMuscleTendonVelocity, t);
+        tempPolynomialExpressionMuscleTendonVelocity = ...
+            subs(tempPolynomialExpressionMuscleTendonVelocity, ...
+            diff(theta_t(i), t), thetaDot(i));
+        polynomialExpressionMuscleTendonVelocity(i, j) = ...
+            subs(tempPolynomialExpressionMuscleTendonVelocity, ...
+            theta_t(i), theta(i));
     end
 end
-polynomialExpressionMuscleTendonVelocities = polynomialExpressionMuscleTendonVelocity(1, :);
-for i = 1 : size(jointAngles, 2)
+polynomialExpressionMuscleTendonVelocities = ...
+    polynomialExpressionMuscleTendonVelocity(1, :);
+for i = 2 : size(jointAngles, 2)
     for j = 1 : size(polynomialExpressionMuscleTendonLength, 2)
-        polynomialExpressionMuscleTendonVelocities(1, j) = polynomialExpressionMuscleTendonVelocity(i, j) + polynomialExpressionMuscleTendonVelocities(1, j);
+        polynomialExpressionMuscleTendonVelocities(1, j) = ...
+            polynomialExpressionMuscleTendonVelocity(i, j) + ...
+            polynomialExpressionMuscleTendonVelocities(1, j);
     end
 end
 % Differentiate -muscle tendon length w.r.t. associated joint angle
diff --git a/src/SurrogateModelCreation/printSurrogateModel.m b/src/SurrogateModelCreation/printSurrogateModel.m
deleted file mode 100644
index 7348b323e..000000000
--- a/src/SurrogateModelCreation/printSurrogateModel.m
+++ /dev/null
@@ -1,88 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% () -> ()
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function printSurrogateModel(numMuscles, ...
-    polynomialExpressionMuscleTendonLengths, ...
-    polynomialExpressionMuscleTendonVelocities, ...
-    polynomialExpressionMomentArms, jointAngles, resultsDirectory)
-
-fid = fopen(fullfile(resultsDirectory, 'PatientSpecificSurrogateModel.m'), 'wt');
-fprintf(fid, 'function [matrix] = PatientSpecificSurrogateModel(jointAngles, jointVelocities, numMuscles)\n');
-fprintf(fid, 'onesCol = ones(size(jointAngles, 1), 1);\n');
-fprintf(fid, 'zeroCol = zeros(size(jointAngles, 1), 1);\n');
-fprintf(fid, 'switch numMuscles\n');
-for i=1:numMuscles
-    fprintf(fid, ['    case ' num2str(i) '\n']);
-    for j=1:size(jointAngles{i}, 2)
-        fprintf(fid, ['        theta' num2str(j) ' = jointAngles(:, ' num2str(j) ');\n']);
-    end
-    for j=1:size(jointAngles{i}, 2)
-        fprintf(fid, ['        thetaDot' num2str(j) ' = jointVelocities(:, ' num2str(j) ');\n']);
-    end
-    fprintf(fid, '        muscleTendonLengths = [');
-    for j=1:size(polynomialExpressionMuscleTendonLengths{i}, 2)
-        if polynomialExpressionMuscleTendonLengths{i}(1,j) == 1
-            fprintf(fid, ' onesCol,');
-        else
-            fprintf(fid, [' ' strrep(strrep(char(polynomialExpressionMuscleTendonLengths{i}(1,j)),'*','.*'),'^','.^') ',']);
-        end
-    end
-    fprintf(fid, '];\n');
-    fprintf(fid, '        muscleTendonVelocities = [');
-    for j=1:size(polynomialExpressionMuscleTendonVelocities{i}, 2)
-        if polynomialExpressionMuscleTendonVelocities{i}(1,j) == 1
-            fprintf(fid, ' onesCol,');
-        elseif polynomialExpressionMuscleTendonVelocities{i}(1,j) == 0
-            fprintf(fid, ' zeroCol,'); 
-        else
-            fprintf(fid, [' ' strrep(strrep(char(polynomialExpressionMuscleTendonVelocities{i}(1,j)),'*','.*'),'^','.^') ',']);
-        end
-    end
-    fprintf(fid, '];\n');
-    for k=1:size(polynomialExpressionMomentArms{i},1)
-        fprintf(fid, ['        momentArms' num2str(k) ' = [']);
-        for j=1:size(polynomialExpressionMomentArms{i},2)
-            if polynomialExpressionMomentArms{i}(k,j) == 0
-                fprintf(fid, ' zeroCol,');     
-            elseif polynomialExpressionMomentArms{i}(k,j) / coeffs(polynomialExpressionMomentArms{i}(k,j)) == 1
-                fprintf(fid, [char(polynomialExpressionMomentArms{i}(k,j)) '*onesCol,']);
-            else
-                fprintf(fid, [' ' strrep(strrep(char(polynomialExpressionMomentArms{i}(k,j)),'*','.*'),'^','.^') ',']);
-            end
-        end
-        fprintf(fid, '];\n');
-    end
-    fprintf(fid, '        matrix = [muscleTendonLengths; muscleTendonVelocities;');
-    for k=1:size(polynomialExpressionMomentArms{i}, 1)
-        fprintf(fid, ['momentArms' num2str(k) '; ']);
-    end
-    fprintf(fid, '];\n');
-end
-fprintf(fid, 'end\n');
-fprintf(fid, 'end\n');
-fclose(fid);
-end
\ No newline at end of file
diff --git a/src/SurrogateModelCreation/reportSurrogateModel.m b/src/SurrogateModelCreation/reportSurrogateModel.m
index e8e9243d3..34856db83 100644
--- a/src/SurrogateModelCreation/reportSurrogateModel.m
+++ b/src/SurrogateModelCreation/reportSurrogateModel.m
@@ -27,14 +27,14 @@
 
 function reportSurrogateModel(inputs)
 
-[newMuscleTendonLengths, newMomentArms] = ...
+[newMuscleTendonLengths, newMomentArms, newMuscleTendonVelocities] = ...
     calcSurrogateModel(inputs, inputs.muscleSpecificJointAngles, ...
-    inputs.muscleSpecificJointAngles);
+    inputs.muscleSpecificJointVelocities);
 plotSurrogateModelFitting(inputs, newMuscleTendonLengths, ...
-    newMomentArms);
+    newMomentArms, newMuscleTendonVelocities);
 end
 function plotSurrogateModelFitting(inputs, newMuscleTendonLengths, ...
-    newMomentArms)
+    newMomentArms, newMuscleTendonVelocities)
 
 nplots = ceil(sqrt(inputs.numMuscles));
 % Plot muscle tendon lengths
@@ -55,6 +55,25 @@ function plotSurrogateModelFitting(inputs, newMuscleTendonLengths, ...
 end
 end
 
+nplots = ceil(sqrt(inputs.numMuscles));
+% Plot muscle tendon velocities
+figure('name', 'Muscle Tendon Velocities')
+for i = 1 : inputs.numMuscles
+subplot(nplots, nplots, i)
+plotData(inputs.muscleTendonVelocities(:, i), newMuscleTendonVelocities(:, i), ...
+    inputs.muscleNames{i})
+axis([1 size(inputs.muscleTendonVelocities, 1) min(inputs.muscleTendonVelocities,  [], ...
+    'all') max(inputs.muscleTendonVelocities,  [], 'all')])
+if i > inputs.numMuscles - nplots; xlabel('Data Points'); 
+else xticklabels(''); end
+if ismember(i, 1 : nplots : inputs.numMuscles)
+    ylabel({'Muscle','Tendon Velocities'});
+else yticklabels(''); end
+if i == inputs.numMuscles
+    legend('Original', 'Predicted'); 
+end
+end
+
 % Plot moment arms
 for j = 1 : length(inputs.surrogateModelCoordinateNames)
 figure('name', 'Moment Arms')
diff --git a/src/SurrogateModelCreation/saveSurrogateModel.m b/src/SurrogateModelCreation/saveSurrogateModel.m
deleted file mode 100644
index ca616143b..000000000
--- a/src/SurrogateModelCreation/saveSurrogateModel.m
+++ /dev/null
@@ -1,37 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% () -> ()
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function saveSurrogateModel(inputs)
-
-printSurrogateModel(inputs.numMuscles, ...
-    inputs.polynomialExpressionMuscleTendonLengths, ...
-    inputs.polynomialExpressionMuscleTendonVelocities, ...
-    inputs.polynomialExpressionMomentArms, ...
-    inputs.muscleSpecificJointAngles, inputs.resultsDirectory);
-coefficients = inputs.coefficients;
-save("coefficients.mat", "coefficients")
-end
\ No newline at end of file
diff --git a/src/SurrogateModelCreation/surrogate.m b/src/SurrogateModelCreation/surrogate.m
deleted file mode 100644
index ea6e0c1bf..000000000
--- a/src/SurrogateModelCreation/surrogate.m
+++ /dev/null
@@ -1,55 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% The following script can be used to create a surrogate model of the
-% muscle tendon lengths, moment arms, and muscle tendon velocities
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-%% Required Values
-inputSettings.model = 'preprocessed\exampleModel.osim';
-inputSettings.dataDirectory = 'preprocessed';
-inputSettings.epsilon = 1e-4;
-inputSettings.polynomialDegree = 5;
-% Indicate 'true' or 'false' for performing latin hyper cube sampling 
-inputSettings.performLatinHyperCubeSampling = 'false';
-% Indicate the coordinates that should be used in the surrogate model
-inputSettings.surrogateModelCoordinateNames = ["hip_adduction_l", ...
-    "hip_flexion_l", "hip_rotation_l", "knee_angle_l", "ankle_angle_l", ...
-    "subtalar_angle_l", "hip_adduction_r", "hip_flexion_r", ...
-    "hip_rotation_r", "knee_angle_r", "ankle_angle_r", "subtalar_angle_r"];
-
-% If performLatinHyperCubeSampling is set to true, set the range multiplier
-% and the number of points used for latin hyper cube sampling, otherwise,
-% leave blank
-inputSettings.lhsRangeMultiplier = [];
-inputSettings.lhsNumPoints = [];
-
-%% *Optional* Values
-% The trial prefix is the prefix of each output file, identifying the
-% motion such as 'gait' or 'squat' or 'step_up'.
-inputSettings.trialPrefixes = ["gait_1", "gait_2", "gait_3"];
-% Results directory, if blank, results are printed to current directory
-inputSettings.resultsDirectory = [];
-
-%% Create surrogate model
-SurrogateModelCreation(inputSettings);
\ No newline at end of file
diff --git a/src/TrackingOptimization/calcTorqueBasedModeledValues.m b/src/TrackingOptimization/calcTorqueBasedModeledValues.m
deleted file mode 100644
index 2976ee9de..000000000
--- a/src/TrackingOptimization/calcTorqueBasedModeledValues.m
+++ /dev/null
@@ -1,117 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the position and velocities of the spring
-% locations and corresponding ground reaction forces and moments if
-% contact surfaces are present. This function also calculates inverse
-% dynamic moments.
-%
-% (struct, struct) -> (struct)
-% returns body locations, ground reactions, and inverse dynamic moments
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function modeledValues = calcTorqueBasedModeledValues(values, params)
-appliedLoads = [zeros(length(values.time), params.numTotalMuscles)];
-if ~isempty(params.contactSurfaces)
-    clear pointKinematics
-    [springPositions, springVelocities] = getSpringLocations( ...
-        values.time, values.statePositions, values.stateVelocities, params);
-    modeledValues.bodyLocations = getBodyLocations(values.time, ....
-        values.statePositions, values.stateVelocities, params);
-    groundReactions = calcFootGroundReactions(springPositions, ...
-        springVelocities, params, modeledValues.bodyLocations);
-    groundReactionsBody = tranferGroundReactionMoments( ...
-        modeledValues.bodyLocations, groundReactions, params);
-    modeledValues.groundReactionsLab = calcGroundReactionsLab(groundReactions);
-    appliedLoads = [appliedLoads groundReactionsBody];
-end
-modeledValues.inverseDynamicMoments = inverseDynamics(values.time, ...
-    values.statePositions, values.stateVelocities, ...
-    values.stateAccelerations, params.coordinateNames, appliedLoads, ...
-    params.mexModel);
-end
-
-function [springPositions, springVelocities] = getSpringLocations(time, ....
-    statePositions, stateVelocities, params)
-
-for i = 1:length(params.contactSurfaces)
-    [springPositions.parent{i}, springVelocities.parent{i}] = ...
-        pointKinematics(time, statePositions, stateVelocities, ...
-        params.contactSurfaces{i}.parentSpringPointsOnBody, ...
-        params.contactSurfaces{i}.parentBody * ones(1, ...
-        size(params.contactSurfaces{i}.parentSpringPointsOnBody, 1)), ...
-        params.mexModel, params.coordinateNames);
-    [springPositions.child{i}, springVelocities.child{i}] = ...
-        pointKinematics(time, statePositions, stateVelocities, ...
-        params.contactSurfaces{i}.childSpringPointsOnBody, ...
-        params.contactSurfaces{i}.childBody * ones(1, ...
-        size(params.contactSurfaces{i}.childSpringPointsOnBody, 1)), ...
-        params.mexModel, params.coordinateNames);
-end
-end
-
-function bodyLocations = getBodyLocations(time, statePositions, ...
-    stateVelocities, params)
-
-for i = 1:length(params.contactSurfaces)
-    bodyLocations.midfootSuperior{i} = pointKinematics(time, ...
-        statePositions, stateVelocities, ...
-        params.contactSurfaces{i}.midfootSuperiorPointOnBody, ...
-        params.contactSurfaces{i}.midfootSuperiorBody, ...
-        params.mexModel, params.coordinateNames);
-    bodyLocations.midfootSuperior{i}(:, 2) = 0;
-    bodyLocations.parent{i} = pointKinematics(time, statePositions, ...
-        stateVelocities, [0 0 0], params.contactSurfaces{i}.parentBody, ...
-        params.mexModel, params.coordinateNames);
-    bodyLocations.child{i} = pointKinematics(time, statePositions, ...
-        stateVelocities, [0 0 0], params.contactSurfaces{i}.childBody, ...
-        params.mexModel, params.coordinateNames);
-end
-end
-
-function groundReactionsBody = tranferGroundReactionMoments( ...
-    bodyLocations, groundReactions, params)
-
-groundReactionsBody = [];
-for i = 1:length(params.contactSurfaces)
-    parentMoment = transferMoments(bodyLocations.midfootSuperior{i}, ...
-        bodyLocations.parent{i}, groundReactions.parentMoments{i}, ...
-        groundReactions.parentForces{i});
-    childMoment = transferMoments(bodyLocations.midfootSuperior{i}, ...
-        bodyLocations.child{i}, groundReactions.childMoments{i}, ...
-        groundReactions.childForces{i});
-    groundReactionsBody = [groundReactionsBody ...
-        groundReactions.parentForces{i} groundReactions.childForces{i} ...
-        parentMoment childMoment];
-end
-end
-
-function groundReactionsInLab = calcGroundReactionsLab(groundReactions)
-
-for i = 1:length(groundReactions.parentForces)
-    groundReactionsInLab.forces{i} = ...
-        groundReactions.parentForces{i} + groundReactions.childForces{i};
-    groundReactionsInLab.moments{i} = ...
-        groundReactions.parentMoments{i} + groundReactions.childMoments{i};
-end
-end
\ No newline at end of file
diff --git a/src/TrackingOptimization/calcTrackingOptimizationDynamicsConstraint.m b/src/TrackingOptimization/calcTrackingOptimizationDynamicsConstraint.m
deleted file mode 100644
index d44c31709..000000000
--- a/src/TrackingOptimization/calcTrackingOptimizationDynamicsConstraint.m
+++ /dev/null
@@ -1,36 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the dynamic constraint for tracking optimization.
-%
-% (struct, struct) -> (2D matrix)
-% Returns the dynamic constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function dynamics = calcTrackingOptimizationDynamicsConstraint(values, ...
-    params)
-
-dynamics = (params.maxTime - params.minTime) * ...
-    ([values.stateVelocities values.stateAccelerations ...
-    values.controlJerks]) ./ (params.maxState - params.minState);
-end
\ No newline at end of file
diff --git a/src/TrackingOptimization/calcTrackingOptimizationPathConstraint.m b/src/TrackingOptimization/calcTrackingOptimizationPathConstraint.m
deleted file mode 100644
index b6796f09c..000000000
--- a/src/TrackingOptimization/calcTrackingOptimizationPathConstraint.m
+++ /dev/null
@@ -1,58 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the path constraint for tracking optimization.
-%
-% (struct, struct, struct) -> (2D matrix)
-% Returns path constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function path = calcTrackingOptimizationPathConstraint(values, modeledValues, ...
-    params)
-path = [];
-for i = 1:length(params.path)
-    constraintTerm = params.path{i};
-    if constraintTerm.isEnabled
-        switch constraintTerm.type
-            case "root_segment_residual_load"
-                path = cat(2, path, ...
-                    calcRootSegmentResidualsPathConstraints(...
-                    constraintTerm.load, ...
-                    params.inverseDynamicMomentLabels, ...
-                    modeledValues.inverseDynamicMoments));
-            case "muscle_model_moment_consistency"
-                path = cat(2, path, ...
-                    calcMuscleActuatedMomentsPathConstraints(params, ...
-                    modeledValues, constraintTerm.load));
-            case "torque_model_moment_consistency"
-                path = cat(2, path, ...
-                    calcTorqueActuatedMomentsPathConstraints(params, ...
-                    modeledValues, values.controlTorques, constraintTerm.load));   
-            otherwise
-                throw(MException('', ['Constraint term type ' ...
-                    constraintTerm.type ' does not exist for this tool.']))    
-        end
-    end
-end
-path = scaleToBounds(path, params.maxPath, params.minPath);
-end
\ No newline at end of file
diff --git a/src/TrackingOptimization/calcTrackingOptimizationTerminalConstraint.m b/src/TrackingOptimization/calcTrackingOptimizationTerminalConstraint.m
deleted file mode 100644
index 5ca95148a..000000000
--- a/src/TrackingOptimization/calcTrackingOptimizationTerminalConstraint.m
+++ /dev/null
@@ -1,87 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the terminal constraint for tracking
-% optimization
-%
-% (struct, struct, struct) -> (Array of number)
-% Returns terminal constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function event = calcTrackingOptimizationTerminalConstraint(inputs, params)
-
-inputs.phase.state = [inputs.phase.initialstate; inputs.phase.finalstate];
-inputs.phase.time = [inputs.phase.initialtime; inputs.phase.finaltime];
-inputs.phase.control = ones(size(inputs.phase.time,1),length(params.minControl));
-if inputs.auxdata.optimizeSynergyVectors
-    inputs.phase.parameter = inputs.parameter;
-end
-values = getTrackingOptimizationValueStruct(inputs.phase, params);
-modeledValues = calcTorqueBasedModeledValues(values, params);
-
-event = [];
-for i = 1:length(params.terminal)
-    constraintTerm = params.terminal{i};
-    if constraintTerm.isEnabled
-        switch constraintTerm.type
-            case "state_position_periodicity"
-                event = cat(2, event, ...
-                    calcStatePositionPeriodicity(values.statePositions, ...
-                    params.coordinateNames, ...
-                    constraintTerm.coordinate));
-            case "state_velocity_periodicity"
-                event = cat(2, event, ...
-                    calcStateVelocityPeriodicity(values.stateVelocities, ...
-                    params.coordinateNames, ...
-                    constraintTerm.coordinate));
-            case "root_segment_residual_load_periodicity"
-                event = cat(2, event, ...
-                    calcRootSegmentResidualsPeriodicity(... 
-                    modeledValues.inverseDynamicMoments, ...
-                    params.inverseDynamicMomentLabels, ...
-                    constraintTerm.load));    
-            case "external_force_tracking_periodicity"
-                event = cat(2, event, ...
-                    calcExternalForcesPeriodicity(... 
-                    modeledValues.groundReactionsLab.forces, ...
-                    params.contactSurfaces, ...
-                    constraintTerm.force));  
-            case "external_moment_tracking_periodicity"
-                event = cat(2, event, ...
-                    calcExternalMomentsPeriodicity(... 
-                    modeledValues.groundReactionsLab.moments, ...
-                    params.contactSurfaces, ...
-                    constraintTerm.moment));  
-            case "synergy_weight_sum"
-                event = cat(2, event, ...
-                    calcSynergyWeightsSum(... 
-                    values.synergyWeights, ...
-                    params.synergyGroups, ...
-                    constraintTerm.synergy_group)); 
-            otherwise
-                throw(MException('', ['Constraint term type ' ...
-                    constraintTerm.type ' does not exist for this tool.']))    
-        end
-    end
-end
-end
\ No newline at end of file
diff --git a/src/TrackingOptimization/computeTrackingOptimizationEndpointFunction.m b/src/TrackingOptimization/computeTrackingOptimizationEndpointFunction.m
deleted file mode 100644
index 75dc6cc77..000000000
--- a/src/TrackingOptimization/computeTrackingOptimizationEndpointFunction.m
+++ /dev/null
@@ -1,39 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function computes the terminal constraint (if any) and total cost 
-% function objective for tracking optimization.
-% 
-% (struct) -> (struct)
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function output = computeTrackingOptimizationEndpointFunction(inputs)
-if ~isempty(inputs.auxdata.terminal)
-    event = calcTrackingOptimizationTerminalConstraint( ...
-        inputs, inputs.auxdata);
-    if ~isempty(event)
-        output.eventgroup.event = event;
-    end
-end
-output.objective = calcTrackingOptimizationObjective(inputs.phase.integral);
-end
\ No newline at end of file
diff --git a/src/TrackingOptimization/parseTrackingOptimizationSettingsTree.m b/src/TrackingOptimization/parseTrackingOptimizationSettingsTree.m
deleted file mode 100644
index 69de76a0b..000000000
--- a/src/TrackingOptimization/parseTrackingOptimizationSettingsTree.m
+++ /dev/null
@@ -1,89 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses the settings tree resulting from xml2struct of the
-% Tracking Optimizatoin settings XML file.
-%
-% (struct) -> (struct, struct)
-% returns the input values for Tracking Optimization
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function [inputs, params, resultsDirectory] = ...
-    parseTrackingOptimizationSettingsTree(settingsTree)
-inputs = getTreatmentOptimizationInputs(settingsTree);
-inputs = getDesignVariableBounds(settingsTree, inputs);
-params = getParams(settingsTree);
-inputs = modifyModelForces(inputs);
-end
-
-function inputs = getDesignVariableBounds(tree, inputs)
-designVariableTree = getFieldByNameOrError(tree, ...
-    'RCNLDesignVariableBoundsTerms');
-jointPositionsMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_positions_multiple');
-if(isstruct(jointPositionsMultiple))
-    inputs.statePositionsMultiple = getDoubleFromField(jointPositionsMultiple);
-end
-jointVelocitiesMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_velocities_multiple');
-if(isstruct(jointVelocitiesMultiple))
-    inputs.stateVelocitiesMultiple = getDoubleFromField(jointVelocitiesMultiple);
-end
-jointAccelerationsMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_accelerations_multiple');
-if(isstruct(jointAccelerationsMultiple))
-    inputs.stateAccelerationsMultiple = ...
-        getDoubleFromField(jointAccelerationsMultiple);
-end
-jointJerkMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_jerks_multiple');
-if(isstruct(jointJerkMultiple))
-    inputs.controlJerksMultiple = getDoubleFromField(jointJerkMultiple);
-end
-if strcmp(inputs.controllerType, 'synergy_driven')
-maxControlSynergyActivations = getFieldByNameOrError(designVariableTree, ...
-    'synergy_activations_max');
-if(isstruct(maxControlSynergyActivations))
-    inputs.maxControlSynergyActivations = ...
-        getDoubleFromField(maxControlSynergyActivations);
-end
-maxParameterSynergyWeights = getFieldByNameOrError(designVariableTree, ...
-    'synergy_weights_max');
-if(isstruct(maxParameterSynergyWeights))
-    inputs.maxParameterSynergyWeights = ...
-        getDoubleFromField(maxParameterSynergyWeights);
-end
-else 
-maxControlTorques = getFieldByNameOrError(designVariableTree, ...
-    'torque_controls_max');
-if(isstruct(maxControlTorques))
-    inputs.maxControlTorquesMultiple = getDoubleFromField(maxControlTorques);
-end
-end
-inputs.toolName = "TrackingOptimization";
-end
-
-function params = getParams(tree)
-params.solverSettings = getOptimalControlSolverSettings(...
-    getTextFromField(getFieldByName(tree, 'optimal_control_settings_file')));
-end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationGroundReactions.m b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationGroundReactions.m
new file mode 100644
index 000000000..671c1c748
--- /dev/null
+++ b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationGroundReactions.m
@@ -0,0 +1,145 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files for experimental and model ground
+% reactions and plots them. There is an option to plot multiple model files
+% by passing in a list of model file names.
+%
+% There are 2 optional arguments for figure width and figure height. If no
+% optional arguments are given, the figure size is automatically adjusted
+% to fit all data on one plot. Giving just figure width and no figure
+% height will set figure height to a default value and extra figures will
+% be created as needed. If both figure width and figure height are given,
+% the figure size will be fixed and extra figures will be created as
+% needed.
+%
+% (string) (List of strings) (int), (int) -> (None)
+% Plot experimental and model ground reactions from file
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotTreatmentOptimizationGroundReactions(experimentalFile, ...
+    modelFiles, figureWidth, figureHeight)
+
+import org.opensim.modeling.Storage
+experimentalStorage = Storage(experimentalFile);
+experimentalLabels = getStorageColumnNames(experimentalStorage);
+experimentalData = storageToDoubleMatrix(experimentalStorage)';
+experimentalTime = findTimeColumn(experimentalStorage);
+if experimentalTime(1) ~= 0
+    experimentalTime = experimentalTime - experimentalTime(1);
+end
+for j = 1 : numel(modelFiles)
+    modelStorage = Storage(modelFiles(j));
+    modelData{j} = storageToDoubleMatrix(modelStorage)';
+    modelLabels{j} = getStorageColumnNames(modelStorage);
+    modelTime{j} = findTimeColumn(modelStorage);
+end
+
+experimentalMomentIndices = contains(experimentalLabels, ["_m", "M"]);
+experimentalForceIndices = contains(experimentalLabels, ["_v", "F"]);
+experimentalIncludedIndices = experimentalMomentIndices | experimentalForceIndices;
+experimentalData = experimentalData(:, experimentalIncludedIndices);
+experimentalLabels = experimentalLabels(experimentalIncludedIndices);
+experimentalForcePlate1 = contains(experimentalLabels, "1");
+for j = 1 : numel(modelFiles)
+    modelMomentIndices = contains(modelLabels{j}, "_m");
+    modelForceIndices = contains(modelLabels{j}, "_v");
+    modelIncludedIndices = modelMomentIndices | modelForceIndices;
+    modelData{j} = modelData{j}(:, modelIncludedIndices);
+    modelLabels{j} = modelLabels{j}(modelIncludedIndices);
+    modelForcePlate1 = contains(modelLabels{j}, "1");
+    if experimentalForcePlate1 ~= modelForcePlate1
+        temp = modelData{j};
+        modelData{j}(:, ~experimentalForcePlate1) = ...
+            modelData{j}(:, experimentalForcePlate1);
+        modelData{j}(:, experimentalForcePlate1) = ...
+            temp(:, ~experimentalForcePlate1);
+    end
+end
+
+% Spline experimental time to the same time points as the model.
+experimentalSpline = makeGcvSplineSet(experimentalTime, ...
+    experimentalData, experimentalLabels);
+resampledExperimental = {};
+for i = 1 : numel(modelFiles)
+    resampledExperimental{i} = evaluateGcvSplines(experimentalSpline, ...
+        experimentalLabels, modelTime{i});
+end
+if nargin < 3
+    figureWidth = 3;
+end
+if nargin < 4
+    figureHeight = 2;
+end
+figureSize = figureWidth * figureHeight;
+figure(Name = "Treatment Optimization Ground Reactions", ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+subplotNumber = 1;
+figureNumber = 1;
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='compact', Padding='compact');
+xlabel(t, "Time [s]")
+ylabel(t, "Ground Reaction")
+for i=1:numel(experimentalLabels)
+    if i > figureSize * figureNumber
+        figureNumber = figureNumber + 1;
+        figure(Name="Treatment Optimization Ground Reactions", ...
+            Units='normalized', ...
+            Position=[0.05 0.05 0.9 0.85])
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
+        xlabel(t, "Time [s]")
+        ylabel(t, "Ground Reaction")
+        subplotNumber = 1;
+    end
+    nexttile(subplotNumber);
+    hold on
+    plot(experimentalTime, experimentalData(:, i), LineWidth=2);
+    for j = 1 : numel(modelFiles)
+        plot(modelTime{j}, modelData{j}(:, i), LineWidth=2);
+    end
+    hold off
+    titleString = [sprintf("%s", strrep(experimentalLabels(i), "_", " "))];
+    for j = 1 : numel(modelFiles)
+        rmse = rms(resampledExperimental{j}(:, i) - modelData{j}(:, i));
+        titleString(j+1) = sprintf("RMSE %d: %.4f", j, rmse);
+    end
+    title(titleString)
+    if subplotNumber==1
+        splitFileName = split(experimentalFile, ["/", "\"]);
+        for k = 1 : numel(splitFileName)
+            if ~strcmp(splitFileName(k), "..")
+                legendValues = sprintf("%s (T)", ...
+                    strrep(splitFileName(k), "_", " "));
+                break
+            end
+        end
+        for j = 1 : numel(modelFiles)
+            splitFileName = split(modelFiles(j), ["/", "\"]);
+            legendValues(j+1) = sprintf("%s (%d)", splitFileName(1), j);
+        end
+        legend(legendValues)
+    end
+    xlim("tight")
+    subplotNumber = subplotNumber + 1;
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointAngles.m b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointAngles.m
new file mode 100644
index 000000000..04c833481
--- /dev/null
+++ b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointAngles.m
@@ -0,0 +1,151 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files for experimental and model joint angles
+% and plots them. There is an option to plot multiple model files by
+% passing in a list of model file names.
+%
+% There are 2 optional arguments for figure width and figure height. If no
+% optional arguments are given, the figure size is automatically adjusted
+% to fit all data on one plot. Giving just figure width and no figure
+% height will set figure height to a default value and extra figures will
+% be created as needed. If both figure width and figure height are given,
+% the figure size will be fixed and extra figures will be created as
+% needed.
+%
+% (string) (List of strings) (int), (int) -> (None)
+% Plot experimental and model joint angles from file
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotTreatmentOptimizationJointAngles(modelFileName, ...
+    experimentalFile, modelFiles, figureWidth, figureHeight)
+
+import org.opensim.modeling.Storage
+model = Model(modelFileName);
+experimentalStorage = Storage(experimentalFile);
+labels = getStorageColumnNames(experimentalStorage);
+experimentalData = storageToDoubleMatrix(experimentalStorage)';
+experimentalData = experimentalData .* 180/pi;
+experimentalTime = findTimeColumn(experimentalStorage);
+if experimentalTime(1) ~= 0
+    experimentalTime = experimentalTime - experimentalTime(1);
+end
+modelData = {};
+for i=1:numel(modelFiles)
+    modelStorage = Storage(modelFiles(i));
+    modelData{i} = storageToDoubleMatrix(modelStorage)' .* 180/pi;
+    modelTime{i} = findTimeColumn(modelStorage);
+end
+
+% Spline experimental time to the same time points as the model.
+experimentalSpline = makeGcvSplineSet(experimentalTime, ...
+    experimentalData, labels);
+resampledExperimental = {};
+for i = 1 : numel(modelFiles)
+    resampledExperimental{i}= evaluateGcvSplines(experimentalSpline, ...
+        labels, modelTime{i});
+end
+if nargin < 4
+    figureWidth = ceil(sqrt(numel(labels)));
+    figureHeight = ceil(numel(labels)/figureWidth);
+elseif nargin < 5
+    figureHeight = ceil(sqrt(numel(labels)));
+end
+figureSize = figureWidth * figureHeight;
+figure(Name = "Treatment Optimization Joint Angles", ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+subplotNumber = 1;
+figureNumber = 1;
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='compact', Padding='compact');
+xlabel(t, "Time [s]")
+ylabel(t, "Joint Angle [deg]")
+for i=1:numel(labels)
+    if model.getCoordinateSet().get(labels(i)).getMotionType() ...
+            .toString().toCharArray()' ~= "Rotational"
+        experimentalData(:, i) = experimentalData(:, i) * pi/180;
+        for j = 1 : numel(modelFiles)
+            modelData{j}(:, i) = modelData{j}(:, i) * pi/180;
+        end
+    end
+    if i > figureSize * figureNumber
+        figureNumber = figureNumber + 1;
+        figure(Name="Treatment Optimization Joint Angles", ...
+            Units='normalized', ...
+            Position=[0.05 0.05 0.9 0.85])
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
+        xlabel(t, "Time [s]")
+        ylabel(t, "Joint Angle [deg]")
+        subplotNumber = 1;
+    end
+    nexttile(subplotNumber);
+    hold on
+        plot(experimentalTime, experimentalData(:, i), LineWidth=2);
+        for j = 1 : numel(modelFiles)
+            plot(modelTime{j}, modelData{j}(:, i), LineWidth=2);
+        end
+    hold off
+    titleString = [sprintf("%s", strrep(labels(i), "_", " "))];
+    for j = 1 : numel(modelFiles)
+        rmse = rms(resampledExperimental{j}(:, i) - modelData{j}(:, i));
+        titleString(j+1) = sprintf("RMSE %d: %.4f", j, rmse);
+    end
+    title(titleString)
+    if subplotNumber==1
+        splitFileName = split(experimentalFile, ["/", "\"]);
+        for k = 1 : numel(splitFileName)
+            if ~strcmp(splitFileName(k), "..")
+                legendValues = sprintf("%s (T)", ...
+                    strrep(splitFileName(k), "_", " "));
+                break
+            end
+        end
+        for j = 1 : numel(modelFiles)
+            splitFileName = split(modelFiles(j), ["/", "\"]);
+            legendValues(j+1) = sprintf("%s (%d)", splitFileName(1), j);
+        end
+        legend(legendValues)
+    end
+    xlim("tight")
+    maxData = [];
+    minData = [];
+    for j = 1 : numel(modelFiles)
+        maxData(j) = max(modelData{j}(:, i), [], "all");
+        minData(j) = min(modelData{j}(:, i), [], "all");
+    end
+    maxData(j+1) = max(experimentalData(:, i), [], "all");
+    minData(j+1) = min(experimentalData(:, i), [], "all");
+    yLimitUpper = max(maxData);
+    yLimitLower = min(minData);
+    if model.getCoordinateSet().get(labels(i)).getMotionType() ...
+            .toString().toCharArray()' == "Rotational"
+        minimum = 10;
+    else
+        minimum = 0.1;
+    end
+    if yLimitUpper - yLimitLower < minimum
+        ylim([(yLimitUpper+yLimitLower)/2-minimum, (yLimitUpper+yLimitLower)/2+minimum])
+    end
+    subplotNumber = subplotNumber + 1;
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointLoads.m b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointLoads.m
new file mode 100644
index 000000000..20601b24a
--- /dev/null
+++ b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointLoads.m
@@ -0,0 +1,142 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files for experimental and model joint loads
+% and plots them. There is an option to plot multiple model files by
+% passing in a list of model file names.
+%
+% There are 2 optional arguments for figure width and figure height. If no
+% optional arguments are given, the figure size is automatically adjusted
+% to fit all data on one plot. Giving just figure width and no figure
+% height will set figure height to a default value and extra figures will
+% be created as needed. If both figure width and figure height are given,
+% the figure size will be fixed and extra figures will be created as
+% needed.
+%
+% (string) (List of strings) (int), (int) -> (None)
+% Plot experimental and model joint loads from file
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotTreatmentOptimizationJointLoads(experimentalFile, ...
+    modelFiles, figureWidth, figureHeight)
+
+import org.opensim.modeling.Storage
+experimentalStorage = Storage(experimentalFile);
+labels = getStorageColumnNames(experimentalStorage);
+experimentalData = storageToDoubleMatrix(experimentalStorage)';
+experimentalTime = findTimeColumn(experimentalStorage);
+if experimentalTime(1) ~= 0
+    experimentalTime = experimentalTime - experimentalTime(1);
+end
+for i=1:numel(modelFiles)
+    modelStorage = Storage(modelFiles(i));
+    modelData{i} = storageToDoubleMatrix(modelStorage)';
+    modelTime{i} = findTimeColumn(modelStorage);
+end
+
+% Spline experimental time to the same time points as the model.
+experimentalSpline = makeGcvSplineSet(experimentalTime, ...
+    experimentalData, labels);
+for i = 1 : numel(modelFiles)
+    resampledExperimental{i}= evaluateGcvSplines(experimentalSpline, ...
+        labels, modelTime{i});
+end
+if nargin < 3
+    figureWidth = ceil(sqrt(numel(labels)));
+    figureHeight = ceil(numel(labels)/figureWidth);
+elseif nargin < 4
+    figureHeight = ceil(sqrt(numel(labels)));
+end
+figureSize = figureWidth * figureHeight;
+figure(Name = "Treatment Optimization Joint Loads", ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+subplotNumber = 1;
+figureNumber = 1;
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='compact', Padding='compact');
+xlabel(t, "Time [s]")
+ylabel(t, "Joint Loads")
+for i=1:numel(labels)
+    if i > figureSize * figureNumber
+        figureNumber = figureNumber + 1;
+        figure(Name="Treatment Optimization Joint Loads", ...
+            Units='normalized', ...
+            Position=[0.05 0.05 0.9 0.85])
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
+        xlabel(t, "Time [s]")
+        ylabel(t, "Joint Loads")
+        subplotNumber = 1;
+    end
+    nexttile(subplotNumber);
+    hold on
+    plot(experimentalTime, experimentalData(:, i), LineWidth=2);
+    for j = 1 : numel(modelFiles)
+        plot(modelTime{j}, modelData{j}(:, i), LineWidth=2);
+    end
+    hold off
+    if contains(labels(i), "moment")
+        titleString = [sprintf("%s [Nm]", strrep(labels(i), "_", " "))];
+    elseif contains(labels(i), "force")
+        titleString = [sprintf("%s [N]", strrep(labels(i), "_", " "))];
+    else
+        titleString = [sprintf("%s", strrep(labels(i), "_", " "))];
+    end
+    for j = 1 : numel(modelFiles)
+        rmse = rms(resampledExperimental{j}(:, i) - modelData{j}(:, i));
+        titleString(j+1) = sprintf("RMSE %d: %.4f", j, rmse);
+    end
+    title(titleString)
+    if subplotNumber==1
+        splitFileName = split(experimentalFile, ["/", "\"]);
+        for k = 1 : numel(splitFileName)
+            if ~strcmp(splitFileName(k), "..")
+                legendValues = sprintf("%s (T)", ...
+                    strrep(splitFileName(k), "_", " "));
+                break
+            end
+        end
+        for j = 1 : numel(modelFiles)
+            splitFileName = split(modelFiles(j), ["/", "\"]);
+            legendValues(j+1) = sprintf("%s (%d)", splitFileName(1), j);
+        end
+        legend(legendValues)
+    end
+    xlim("tight")
+    maxData = [];
+    minData = [];
+    for j = 1 : numel(modelFiles)
+        maxData(j) = max(modelData{j}(1:end-1, i), [], "all");
+        minData(j) = min(modelData{j}(1:end-1, i), [], "all");
+    end
+    maxData(j+1) = max(experimentalData(1:end-1, i), [], "all");
+    minData(j+1) = min(experimentalData(1:end-1, i), [], "all");
+    yLimitUpper = max(maxData);
+    yLimitLower = min(minData);
+    if yLimitUpper - yLimitLower < 10
+        ylim([(yLimitUpper+yLimitLower)/2-10, (yLimitUpper+yLimitLower)/2+10])
+    else
+        ylim([yLimitLower, yLimitUpper]);
+    end
+    subplotNumber = subplotNumber + 1;
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationMuscleActivations.m b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationMuscleActivations.m
new file mode 100644
index 000000000..1187b41fd
--- /dev/null
+++ b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationMuscleActivations.m
@@ -0,0 +1,124 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads .sto files for experimental and model muscle
+% activations and plots them. There is an option to plot multiple model
+% files by passing in a list of model file names.
+%
+% There are 2 optional arguments for figure width and figure height. If no
+% optional arguments are given, the figure size is automatically adjusted
+% to fit all data on one plot. Giving just figure width and no figure
+% height will set figure height to a default value and extra figures will
+% be created as needed. If both figure width and figure height are given,
+% the figure size will be fixed and extra figures will be created as
+% needed.
+%
+% (string) (List of strings) (int), (int) -> (None)
+% Plot experimental and model activations from file
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotTreatmentOptimizationMuscleActivations(experimentalFile, ...
+    modelFiles, figureWidth, figureHeight)
+
+import org.opensim.modeling.Storage
+experimentalStorage = Storage(experimentalFile);
+labels = getStorageColumnNames(experimentalStorage);
+experimentalData = storageToDoubleMatrix(experimentalStorage)';
+experimentalTime = findTimeColumn(experimentalStorage);
+if experimentalTime(1) ~= 0
+    experimentalTime = experimentalTime - experimentalTime(1);
+end
+for i=1:numel(modelFiles)
+    modelStorage = Storage(modelFiles(i));
+    modelData{i} = storageToDoubleMatrix(modelStorage)';
+    modelLabels{i} = getStorageColumnNames(modelStorage);
+    modelTime{i} = findTimeColumn(modelStorage);
+end
+
+% Spline experimental time to the same time points as the model.
+experimentalSpline = makeGcvSplineSet(experimentalTime, ...
+    experimentalData, labels);
+resampledExperimental = {};
+for i = 1 : numel(modelFiles)
+    resampledExperimental{i}= evaluateGcvSplines(experimentalSpline, ...
+        labels, modelTime{i});
+end
+if nargin < 3
+    figureWidth = ceil(sqrt(numel(labels)));
+    figureHeight = ceil(numel(labels)/figureWidth);
+elseif nargin < 4
+    figureHeight = ceil(sqrt(numel(labels)));
+end
+figureSize = figureWidth * figureHeight;
+figure(Name = "Treatment Optimization Muscle Activations", ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+subplotNumber = 1;
+figureNumber = 1;
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='compact', Padding='compact');
+xlabel(t, "Time [s]")
+ylabel(t, "Muscle Activations")
+for i=1:numel(labels)
+    if i > figureSize * figureNumber
+        figureNumber = figureNumber + 1;
+        figure(Name="Treatment Optimization Muscle Activations", ...
+            Units='normalized', ...
+            Position=[0.05 0.05 0.9 0.85])
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
+        xlabel(t, "Time [s]")
+        ylabel(t, "Muscle Activations")
+        subplotNumber = 1;
+    end
+    nexttile(subplotNumber);
+    hold on
+    plot(experimentalTime, experimentalData(:, i), LineWidth=2);
+    for j = 1 : numel(modelFiles)
+        plot(modelTime{j}, modelData{j}(:, i), LineWidth=2);
+    end
+    hold off
+    titleString = [sprintf("%s", strrep(labels(i), "_", " "))];
+    for j = 1 : numel(modelFiles)
+        rmse = rms(resampledExperimental{j}(:, i) - modelData{j}(:, i));
+        titleString(j+1) = sprintf("RMSE %d: %.4f", j, rmse);
+    end
+    title(titleString)
+    if subplotNumber==1
+        splitFileName = split(experimentalFile, ["/", "\"]);
+        for k = 1 : numel(splitFileName)
+            if ~strcmp(splitFileName(k), "..")
+                legendValues = sprintf("%s (T)", ...
+                    strrep(splitFileName(k), "_", " "));
+                break
+            end
+        end
+        for j = 1 : numel(modelFiles)
+            splitFileName = split(modelFiles(j), ["/", "\"]);
+            legendValues(j+1) = sprintf("%s (%d)", splitFileName(1), j);
+        end
+        legend(legendValues)
+    end
+    xlim("tight")
+    ylim([0, 1])
+    subplotNumber = subplotNumber + 1;
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationSynergyControls.m b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationSynergyControls.m
new file mode 100644
index 000000000..4589fc6ca
--- /dev/null
+++ b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationSynergyControls.m
@@ -0,0 +1,86 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads one .sto file for treatment optimization synergy
+% controls and plots it.
+%
+% There are 2 optional arguments for figure width and figure height. If no
+% optional arguments are given, the figure size is automatically adjusted
+% to fit all data on one plot. Giving just figure width and no figure
+% height will set figure height to a default value and extra figures will
+% be created as needed. If both figure width and figure height are given,
+% the figure size will be fixed and extra figures will be created as
+% needed.
+%
+% (string) -> (None)
+% Plot joint moment curves from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotTreatmentOptimizationSynergyControls(controlsFile, ...
+    figureWidth, figureHeight)
+
+import org.opensim.modeling.Storage
+controlsStorage = Storage(controlsFile);
+labels = getStorageColumnNames(controlsStorage);
+controls = storageToDoubleMatrix(controlsStorage)';
+time = findTimeColumn(controlsStorage);
+if time(1) ~= 0
+    time = time - time(1);
+end
+if nargin < 2
+    figureWidth = ceil(sqrt(numel(labels)));
+    figureHeight = ceil(numel(labels)/figureWidth);
+elseif nargin < 3
+    figureHeight = ceil(sqrt(numel(labels)));
+end
+figureSize = figureWidth * figureHeight;
+figure(Name="Treatment Optimization Synergy Controls", ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+xlabel(t, "Time [s]")
+ylabel(t, "Synergy Controls")
+subplotNumber = 1;
+figureNumber = 1;
+for i=1:numel(labels)
+    if i > figureSize * figureNumber
+        figureNumber = figureNumber + 1;
+        figure(Name="Treatment Optimization Synergy Controls", ...
+            Units='normalized', ...
+            Position=[0.05 0.05 0.9 0.85])
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
+        xlabel(t, "Time [s]")
+        ylabel(t, "Synergy Controls")
+        subplotNumber = 1;
+    end
+    nexttile(subplotNumber);
+    hold on
+    plot(time, controls(:, i), LineWidth=2);
+    hold off
+    title(strrep(labels(i), "_", " "));
+    xlim("tight")
+    subplotNumber = subplotNumber + 1;
+end
+end
+
diff --git a/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationTorqueControls.m b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationTorqueControls.m
new file mode 100644
index 000000000..264c8ca9c
--- /dev/null
+++ b/src/TreatmentOptimization/Analysis/plotTreatmentOptimizationTorqueControls.m
@@ -0,0 +1,86 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads one .sto file for treatment optimization torque
+% controls and plots it.
+%
+% There are 2 optional arguments for figure width and figure height. If no
+% optional arguments are given, the figure size is automatically adjusted
+% to fit all data on one plot. Giving just figure width and no figure
+% height will set figure height to a default value and extra figures will
+% be created as needed. If both figure width and figure height are given,
+% the figure size will be fixed and extra figures will be created as
+% needed.
+%
+% (string) -> (None)
+% Plot joint moment curves from file.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Robert Salati                                                %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+function plotTreatmentOptimizationTorqueControls(controlsFile, ...
+    figureWidth, figureHeight)
+
+import org.opensim.modeling.Storage
+controlsStorage = Storage(controlsFile);
+labels = getStorageColumnNames(controlsStorage);
+controls = storageToDoubleMatrix(controlsStorage)';
+time = findTimeColumn(controlsStorage);
+if time(1) ~= 0
+    time = time - time(1);
+end
+if nargin < 2
+    figureWidth = ceil(sqrt(numel(labels)));
+    figureHeight = ceil(numel(labels)/figureWidth);
+elseif nargin < 3
+    figureHeight = ceil(sqrt(numel(labels)));
+end
+figureSize = figureWidth * figureHeight;
+figure(Name="Treatment Optimization Torque Controls", ...
+    Units='normalized', ...
+    Position=[0.05 0.05 0.9 0.85])
+subplotNumber = 1;
+figureNumber = 1;
+t = tiledlayout(figureHeight, figureWidth, ...
+    TileSpacing='Compact', Padding='Compact');
+xlabel(t, "Time [s]")
+ylabel(t, "Torque Controls [Nm]")
+for i=1:numel(labels)
+    if i > figureSize * figureNumber
+        figureNumber = figureNumber + 1;
+        figure(Name="Treatment Optimization Torque Controls", ...
+            Units='normalized', ...
+            Position=[0.05 0.05 0.9 0.85])
+        t = tiledlayout(figureHeight, figureWidth, ...
+            TileSpacing='Compact', Padding='Compact');
+        xlabel(t, "Time [s]")
+        ylabel(t, "Torque Controls [Nm]")
+        subplotNumber = 1;
+    end
+    nexttile(subplotNumber);
+    hold on
+    plot(time, controls(:, i), LineWidth=2);
+    hold off
+    title(strrep(labels(i), "_", " "));
+    xlim("tight")
+    subplotNumber = subplotNumber + 1;
+end
+end
+
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/adjustMaxIsometricForce.m b/src/TreatmentOptimization/BuiltInParameters/adjustMaxIsometricForce.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/adjustMaxIsometricForce.m
rename to src/TreatmentOptimization/BuiltInParameters/adjustMaxIsometricForce.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/adjustModelMaxIsometricForce.m b/src/TreatmentOptimization/BuiltInParameters/adjustModelMaxIsometricForce.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/adjustModelMaxIsometricForce.m
rename to src/TreatmentOptimization/BuiltInParameters/adjustModelMaxIsometricForce.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/adjustModelOptimalFiberLength.m b/src/TreatmentOptimization/BuiltInParameters/adjustModelOptimalFiberLength.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/adjustModelOptimalFiberLength.m
rename to src/TreatmentOptimization/BuiltInParameters/adjustModelOptimalFiberLength.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/adjustModelTendonSlackLength.m b/src/TreatmentOptimization/BuiltInParameters/adjustModelTendonSlackLength.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/adjustModelTendonSlackLength.m
rename to src/TreatmentOptimization/BuiltInParameters/adjustModelTendonSlackLength.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/adjustOptimalFiberLength.m b/src/TreatmentOptimization/BuiltInParameters/adjustOptimalFiberLength.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/adjustOptimalFiberLength.m
rename to src/TreatmentOptimization/BuiltInParameters/adjustOptimalFiberLength.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/adjustTendonSlackLength.m b/src/TreatmentOptimization/BuiltInParameters/adjustTendonSlackLength.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/adjustTendonSlackLength.m
rename to src/TreatmentOptimization/BuiltInParameters/adjustTendonSlackLength.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/applyBeltSpeedParameter.m b/src/TreatmentOptimization/BuiltInParameters/applyBeltSpeedParameter.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/applyBeltSpeedParameter.m
rename to src/TreatmentOptimization/BuiltInParameters/applyBeltSpeedParameter.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/applyMaxIsometricForceParameter.m b/src/TreatmentOptimization/BuiltInParameters/applyMaxIsometricForceParameter.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/applyMaxIsometricForceParameter.m
rename to src/TreatmentOptimization/BuiltInParameters/applyMaxIsometricForceParameter.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/applyOptimalFiberLengthParameter.m b/src/TreatmentOptimization/BuiltInParameters/applyOptimalFiberLengthParameter.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/applyOptimalFiberLengthParameter.m
rename to src/TreatmentOptimization/BuiltInParameters/applyOptimalFiberLengthParameter.m
diff --git a/src/core/TreatmentOptimization/BuiltInParameters/applyTendonSlackLengthParameter.m b/src/TreatmentOptimization/BuiltInParameters/applyTendonSlackLengthParameter.m
similarity index 100%
rename from src/core/TreatmentOptimization/BuiltInParameters/applyTendonSlackLengthParameter.m
rename to src/TreatmentOptimization/BuiltInParameters/applyTendonSlackLengthParameter.m
diff --git a/src/DesignOptimization/DesignOptimizationTool.m b/src/TreatmentOptimization/DesignOptimization/DesignOptimizationTool.m
similarity index 90%
rename from src/DesignOptimization/DesignOptimizationTool.m
rename to src/TreatmentOptimization/DesignOptimization/DesignOptimizationTool.m
index a9f20347e..744dab4ab 100644
--- a/src/DesignOptimization/DesignOptimizationTool.m
+++ b/src/TreatmentOptimization/DesignOptimization/DesignOptimizationTool.m
@@ -33,7 +33,10 @@ function DesignOptimizationTool(settingsFileName)
 settingsTree = xml2struct(settingsFileName);
 verifyVersion(settingsTree, "DesignOptimizationTool");
 [inputs, params] = parseDesignOptimizationSettingsTree(settingsTree);
-[outputs, inputs] = DesignOptimization(inputs, params);
-reportTreatmentOptimizationResults(outputs, inputs);
+inputs = normalizeSynergyData(inputs);
+inputs = setupMuscleSynergies(inputs);
+inputs = setupTorqueControls(inputs);
+inputs = makeTreatmentOptimizationInputs(inputs, params);
+[inputs, outputs] = solveOptimalControlProblem(inputs, params);
 saveDesignOptimizationResults(outputs, inputs);
 end
diff --git a/src/TreatmentOptimization/DesignOptimization/parseDesignOptimizationSettingsTree.m b/src/TreatmentOptimization/DesignOptimization/parseDesignOptimizationSettingsTree.m
new file mode 100644
index 000000000..00a2592c4
--- /dev/null
+++ b/src/TreatmentOptimization/DesignOptimization/parseDesignOptimizationSettingsTree.m
@@ -0,0 +1,84 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function parses the settings tree resulting from xml2struct of the
+% Design Optimizatoin settings XML file.
+%
+% (struct) -> (struct, struct)
+% returns the input values for Design Optimization
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function [inputs, params] = ...
+    parseDesignOptimizationSettingsTree(settingsTree)
+inputs = parseTreatmentOptimizationInputs(settingsTree);
+inputs = parseDesignSettings(settingsTree, inputs);
+inputs = parseUserDefinedFunctions(settingsTree, inputs);
+params = parseTreatmentOptimizationParams(settingsTree);
+end
+
+function inputs = parseUserDefinedFunctions(tree, inputs)
+import org.opensim.modeling.Storage
+if isstruct(getFieldByName(tree, "model_functions"))
+    systemFns = parseSpaceSeparatedList(tree, "model_functions");
+    if ~isempty(systemFns)
+        inputs.systemFns = systemFns;
+    end
+end
+parameterTree = getFieldByName(tree, "RCNLParameterTermSet");
+if isstruct(parameterTree) && isfield(parameterTree, "RCNLParameterTerm")
+    inputs.userDefinedVariables = parseRcnlCostTermSet( ...
+        parameterTree.RCNLParameterTerm);
+    for i = 1:length(inputs.userDefinedVariables)
+        inputs.userDefinedVariables{i}.initial_values = ...
+            stringToSpaceSeparatedList(inputs.userDefinedVariables{i}.initial_values);
+        inputs.userDefinedVariables{i}.upper_bounds = ...
+            stringToSpaceSeparatedList(inputs.userDefinedVariables{i}.upper_bounds);
+        inputs.userDefinedVariables{i}.lower_bounds = ...
+            stringToSpaceSeparatedList(inputs.userDefinedVariables{i}.lower_bounds);
+    end
+else
+    inputs.userDefinedVariables = {};
+end
+end
+
+function output = stringToSpaceSeparatedList(string)
+if isnumeric(string)
+    output = string;
+    return;
+end
+string = strtrim(string);
+output = strsplit(string, ' ');
+output = str2double(output);
+end
+
+function inputs = parseDesignSettings(tree, inputs)
+try
+finalTimeRange = parseSpaceSeparatedList(tree, ...
+    'final_time_range');
+if(~isempty(finalTimeRange))
+    inputs.finalTimeRange = str2double(finalTimeRange);
+end
+catch
+end
+end
+
diff --git a/src/DesignOptimization/reportingGaitSpecificMeasurements.m b/src/TreatmentOptimization/DesignOptimization/reportingGaitSpecificMeasurements.m
similarity index 100%
rename from src/DesignOptimization/reportingGaitSpecificMeasurements.m
rename to src/TreatmentOptimization/DesignOptimization/reportingGaitSpecificMeasurements.m
diff --git a/src/DesignOptimization/saveDesignOptimizationResults.m b/src/TreatmentOptimization/DesignOptimization/saveDesignOptimizationResults.m
similarity index 61%
rename from src/DesignOptimization/saveDesignOptimizationResults.m
rename to src/TreatmentOptimization/DesignOptimization/saveDesignOptimizationResults.m
index 2cc6b6bf1..ac16976be 100644
--- a/src/DesignOptimization/saveDesignOptimizationResults.m
+++ b/src/TreatmentOptimization/DesignOptimization/saveDesignOptimizationResults.m
@@ -1,6 +1,6 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function saves and prints the unscaled results from 
+% This function saves and prints the unscaled results from
 % Design Optimization. An osim model may also be printed if model specific
 % values were optimized
 %
@@ -30,13 +30,36 @@
 % ----------------------------------------------------------------------- %
 
 function saveDesignOptimizationResults(solution, inputs)
-values = getDesignOptimizationValueStruct(solution.solution.phase, inputs);
-saveCommonOptimalControlResults(solution, inputs, values)
+values = makeGpopsValuesAsStruct(solution.solution.phase, inputs);
+saveTreatmentOptimizationResults(solution, inputs, values)
 if isfield(inputs, "systemFns")
-    values = getDesignOptimizationValueStruct(solution.solution.phase, inputs);
     inputs.auxdata = inputs;
     inputs = updateSystemFromUserDefinedFunctions(inputs, values);
     model = Model(inputs.auxdata.model);
     model.print(strrep(inputs.mexModel, '_inactiveMuscles.osim', 'DesignOpt.osim'));
 end
+printUserDefinedVariablesToXml(solution, inputs);
+end
+
+function printUserDefinedVariablesToXml(solution, inputs)
+if isfield(inputs, 'userDefinedVariables')
+    counter = 1;
+    for i = 1:length(inputs.userDefinedVariables)
+        numParameters = length(inputs.userDefinedVariables{i}.initial_values);
+        parameterResults = scaleToOriginal( ...
+            solution.solution.phase.parameter( ...
+            counter : counter + numParameters - 1), ...
+            inputs.userDefinedVariables{i}.upper_bounds, ...
+            inputs.userDefinedVariables{i}.lower_bounds);
+        counter = counter + numParameters;
+        valuesStr = num2str(parameterResults(1));
+        for j = 2:length(parameterResults)
+            valuesStr = strcat(valuesStr, " ", num2str(parameterResults(j)));
+        end
+        parameters.NMSMPipelineDocument.RCNLParameters{i}.RCNLParameterSet.type = inputs.userDefinedVariables{i}.type;
+        parameters.NMSMPipelineDocument.RCNLParameters{i}.RCNLParameterSet.values = convertStringsToChars(valuesStr);
+        struct2xml(parameters, fullfile(inputs.resultsDirectory, ...
+            strcat(inputs.trialName, "_parameterSolution.xml")));
+    end
+end
 end
\ No newline at end of file
diff --git a/src/DesignOptimization/updateSystemFromUserDefinedFunctions.m b/src/TreatmentOptimization/DesignOptimization/updateSystemFromUserDefinedFunctions.m
similarity index 90%
rename from src/DesignOptimization/updateSystemFromUserDefinedFunctions.m
rename to src/TreatmentOptimization/DesignOptimization/updateSystemFromUserDefinedFunctions.m
index 3649e31d5..0c623f955 100644
--- a/src/DesignOptimization/updateSystemFromUserDefinedFunctions.m
+++ b/src/TreatmentOptimization/DesignOptimization/updateSystemFromUserDefinedFunctions.m
@@ -29,8 +29,10 @@
 % ----------------------------------------------------------------------- %
 
 function inputs = updateSystemFromUserDefinedFunctions(inputs, values)
-for i = 1:length(inputs.auxdata.systemFns)
-    func = str2func(inputs.auxdata.systemFns(i));
-    inputs = func(inputs, values);
+if getFieldByName(inputs.auxdata, "systemFns")
+    for i = 1:length(inputs.auxdata.systemFns)
+        func = str2func(inputs.auxdata.systemFns(i));
+        inputs = func(inputs, values);
+    end
 end
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingPropulsiveForceIntegrand.m b/src/TreatmentOptimization/DiscreteTerms/calcGoalRelativeWalkingSpeedDiscrete.m
similarity index 73%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingPropulsiveForceIntegrand.m
rename to src/TreatmentOptimization/DiscreteTerms/calcGoalRelativeWalkingSpeedDiscrete.m
index 54a6f8e74..c85033cc7 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingPropulsiveForceIntegrand.m
+++ b/src/TreatmentOptimization/DiscreteTerms/calcGoalRelativeWalkingSpeedDiscrete.m
@@ -1,9 +1,11 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function maximizes the propulsive force for the specified foot. 
-%
-% (struct, struct, struct) -> (Array of number)
+% This function returns a discrete cost for matching a goal walking speed.
+% This speed is defined relative to the ground. For example, with a subject
+% walking at 0.6 m/s on a treadmill, a goal of 0.2 m/s will seek a solution
+% with the subject walking at 0.8 m/s. 
 %
+% (struct, struct, struct) -> (double)
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Spencer Williams                                             %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,14 +29,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMaximizingPropulsiveForceIntegrand(modeledValues, ...
-    params, costTerm)
+function cost = calcGoalRelativeWalkingSpeedDiscrete(values, ...
+    modeledValues, inputs, costTerm)
+
+rawCost = modeledValues.massCenterVelocity;
 
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        propulsiveForce = getPropulsiveForce( ...
-            modeledValues.groundReactionsLab.forces{i}(:,1));
-    end
+cost = ((rawCost - costTerm.errorCenter) ./ costTerm.maxAllowableError) .^ 2;
 end
-cost = calcMaximizingCostArrayTerm(propulsiveForce);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/DiscreteTerms/calcTrackingSynergyVectorsDiscrete.m b/src/TreatmentOptimization/DiscreteTerms/calcTrackingSynergyVectorsDiscrete.m
similarity index 93%
rename from src/core/TreatmentOptimization/DiscreteTerms/calcTrackingSynergyVectorsDiscrete.m
rename to src/TreatmentOptimization/DiscreteTerms/calcTrackingSynergyVectorsDiscrete.m
index c2abeb7c2..4f3929673 100644
--- a/src/core/TreatmentOptimization/DiscreteTerms/calcTrackingSynergyVectorsDiscrete.m
+++ b/src/TreatmentOptimization/DiscreteTerms/calcTrackingSynergyVectorsDiscrete.m
@@ -31,11 +31,10 @@
 function cost = calcTrackingSynergyVectorsDiscrete(synergyWeights, ...
     params, costTerm)
 
-origSynergyWeights = getSynergyWeightsFromGroups(...
-            params.synergyWeightsGuess, params);
+origSynergyWeights = params.initialSynergyWeights;
 origSynergyWeights(origSynergyWeights==0) = [];
 synergyWeights(synergyWeights==0) = [];
 cost = calcTrackingCostArrayTerm(synergyWeights, ...
     origSynergyWeights, 1:size(synergyWeights, 2));
-cost = cost(:) / costTerm.maxAllowableError;
+cost = cost(:);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandComputations/calcMaximizingCostArrayTerm.m b/src/TreatmentOptimization/IntegrandComputations/calcMaximizingCostArrayTerm.m
similarity index 100%
rename from src/core/TreatmentOptimization/IntegrandComputations/calcMaximizingCostArrayTerm.m
rename to src/TreatmentOptimization/IntegrandComputations/calcMaximizingCostArrayTerm.m
diff --git a/src/core/TreatmentOptimization/IntegrandComputations/calcMinimizingCostArrayTerm.m b/src/TreatmentOptimization/IntegrandComputations/calcMinimizingCostArrayTerm.m
similarity index 100%
rename from src/core/TreatmentOptimization/IntegrandComputations/calcMinimizingCostArrayTerm.m
rename to src/TreatmentOptimization/IntegrandComputations/calcMinimizingCostArrayTerm.m
diff --git a/src/core/TreatmentOptimization/IntegrandComputations/calcTrackingCostArrayTerm.m b/src/TreatmentOptimization/IntegrandComputations/calcTrackingCostArrayTerm.m
similarity index 100%
rename from src/core/TreatmentOptimization/IntegrandComputations/calcTrackingCostArrayTerm.m
rename to src/TreatmentOptimization/IntegrandComputations/calcTrackingCostArrayTerm.m
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcSingleSupportTime.m b/src/TreatmentOptimization/IntegrandTerms/calcBrakingImpulseGoalIntegrand.m
similarity index 64%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcSingleSupportTime.m
rename to src/TreatmentOptimization/IntegrandTerms/calcBrakingImpulseGoalIntegrand.m
index d0a98b91c..1de0b1f36 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcSingleSupportTime.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcBrakingImpulseGoalIntegrand.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the single support time for the specified foot 
-% for one gait cycle. 
-%
-% (Array of number, Array of number) -> (Number)
+% This function calculates the error in braking impulse for the side 
+% defined in the cost term. Only the braking impulse (negative) is
+% included in the output. 
 %
+% (struct, Array of double, struct, struct) -> (Array of double)
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Spencer Williams                                             %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,29 +28,20 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function singleSupportTime = calcSingleSupportTime(normalForce, time)
-
-normalForce = normalForce - 30; % Noise buffer
-normalForce(normalForce<0) = 0;
-slope = diff(normalForce);
-
-heelStrikeEvent = getHeelStrikeEvent(slope);
-toeOffEvent = getToeOffEvent(slope);
-
-if isempty(heelStrikeEvent)
-    if normalForce(1) == 0
-        heelStrikeEvent = 1;
+function cost = calcBrakingImpulseGoalIntegrand(modeledValues, ...
+    time, inputs, costTerm)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", false);
+braking = [];
+for i = 1:length(inputs.contactSurfaces)
+    if inputs.contactSurfaces{i}.isLeftFoot == strcmpi(costTerm.side, "left")
+        braking = -modeledValues.groundReactionsLab.forces{i}(:,1);
     end
 end
-
-singleSupportTime = [];
-if toeOffEvent < heelStrikeEvent
-    singleSupportTime = time(heelStrikeEvent) - time(toeOffEvent);
-end
-if toeOffEvent > heelStrikeEvent
-    singleSupportTime = (time(end) - time(toeOffEvent)) + time(heelStrikeEvent);
+assert(~isempty(braking), "Unable to find braking force.")
+cost = real(sqrt((braking - costTerm.errorCenter) / ...
+    costTerm.maxAllowableError));
+if normalizeByFinalTime
+    cost = cost / time(end);
 end
-if isempty(singleSupportTime)
-    singleSupportTime = 0;
 end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcGoalBeltSpeedDiscrete.m b/src/TreatmentOptimization/IntegrandTerms/calcGoalBeltSpeedDiscrete.m
similarity index 100%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcGoalBeltSpeedDiscrete.m
rename to src/TreatmentOptimization/IntegrandTerms/calcGoalBeltSpeedDiscrete.m
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcJointEnergyAbsorptionGoalIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcJointEnergyAbsorptionGoalIntegrand.m
new file mode 100644
index 000000000..f3113c385
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcJointEnergyAbsorptionGoalIntegrand.m
@@ -0,0 +1,54 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the joint power error for the specified
+% coordinate and absorption goal. Only negative power (absorbed energy) is
+% included in the output. 
+%
+% (2D matrix, 2D matrix, struct, Array of string) -> (Array of number)
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Spencer Williams, Marleny Vega                               %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcJointEnergyAbsorptionGoalIntegrand(costTerm, ...
+    jointVelocity, time, jointMoment, params, loadName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+loadName = erase(loadName, '_moment');
+loadName = erase(loadName, '_force');
+indx = find(strcmp(convertCharsToStrings(params.coordinateNames), ...
+    loadName));
+momentLabelsNoSuffix = erase(params.inverseDynamicsMomentLabels, '_moment');
+momentLabelsNoSuffix = erase(momentLabelsNoSuffix, '_force');
+includedJointMomentCols = ismember(momentLabelsNoSuffix, ...
+    convertCharsToStrings(params.coordinateNames));
+if isequal(mexext, 'mexw64')
+    jointMoment = jointMoment(:, includedJointMomentCols);
+end
+jointPower = jointMoment(:, indx) .* jointVelocity(:, indx);
+
+cost = real(sqrt((-jointPower - costTerm.errorCenter) / ...
+    costTerm.maxAllowableError));
+
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcJointEnergyGenerationGoalIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcJointEnergyGenerationGoalIntegrand.m
new file mode 100644
index 000000000..9d1089504
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcJointEnergyGenerationGoalIntegrand.m
@@ -0,0 +1,54 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the joint power error for the specified
+% coordinate and generation goal. Only positive power (generated energy) is
+% included in the output. 
+%
+% (2D matrix, 2D matrix, struct, Array of string) -> (Array of number)
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Spencer Williams, Marleny Vega                               %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcJointEnergyGenerationGoalIntegrand(costTerm, ...
+    jointVelocity, time, jointMoment, params, loadName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+loadName = erase(loadName, '_moment');
+loadName = erase(loadName, '_force');
+indx = find(strcmp(convertCharsToStrings(params.coordinateNames), ...
+    loadName));
+momentLabelsNoSuffix = erase(params.inverseDynamicsMomentLabels, '_moment');
+momentLabelsNoSuffix = erase(momentLabelsNoSuffix, '_force');
+includedJointMomentCols = ismember(momentLabelsNoSuffix, ...
+    convertCharsToStrings(params.coordinateNames));
+if isequal(mexext, 'mexw64')
+    jointMoment = jointMoment(:, includedJointMomentCols);
+end
+jointPower = jointMoment(:, indx) .* jointVelocity(:, indx);
+
+cost = real(sqrt((jointPower - costTerm.errorCenter) / ...
+    costTerm.maxAllowableError));
+
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMassCenterVelocity.m b/src/TreatmentOptimization/IntegrandTerms/calcMassCenterVelocity.m
similarity index 100%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMassCenterVelocity.m
rename to src/TreatmentOptimization/IntegrandTerms/calcMassCenterVelocity.m
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcStrideLength.m b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingAngularMomentumIntegrand.m
similarity index 68%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcStrideLength.m
rename to src/TreatmentOptimization/IntegrandTerms/calcMinimizingAngularMomentumIntegrand.m
index c40aa054c..8558b64f5 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcStrideLength.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingAngularMomentumIntegrand.m
@@ -1,9 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates stride length.
-%
-% (struct, struct) -> (number)
+% This function minimizes the whole body angular momentum for the specified
+% axis.
 %
+% (2D matrix, struct, Array of string) -> (Array of number)
+% 
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Spencer Williams                                             %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,20 +28,20 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function strideLength = calcStrideLength(modeledValues, params)
+function cost = calcMinimizingAngularMomentumIntegrand( ...
+    modeledValues, time, costTerm)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+
+assert(isfield(costTerm, 'axis'), "Angular momentum minimization " + ...
+    "requires an 'axis' field in the cost term settings.")
+
+index = find(strcmpi(costTerm.axis, ["x" "y" "z"]));
+assert(~isempty(index), "Angular momentum axis must be X, Y, or Z, " + ...
+    "but '" + costTerm.axis + "' was given.");
 
-for i = 1:length(params.contactSurfaces)
-    if i == 1
-        stepLength(i) = calcStepLength(modeledValues. ...
-                groundReactionsLab.forces{i}(:,2), ...
-            [modeledValues.bodyLocations.parent{i}(:, 1) ...
-            modeledValues.bodyLocations.parent{i+1}(:, 1)]);
-    else
-        stepLength(i) = calcStepLength(modeledValues. ...
-                groundReactionsLab.forces{i}(:,2), ...
-            [modeledValues.bodyLocations.parent{i}(:, 1) ...
-            modeledValues.bodyLocations.parent{i-1}(:, 1)]);
-    end
+cost = modeledValues.angularMomentum(:, index);
+if normalizeByFinalTime
+    cost = cost / time(end);
 end
-strideLength = sum(stepLength);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingExternalTorqueControl.m b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingExternalTorqueControl.m
similarity index 88%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingExternalTorqueControl.m
rename to src/TreatmentOptimization/IntegrandTerms/calcMinimizingExternalTorqueControl.m
index 2b5ccb068..db74dc3b8 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingExternalTorqueControl.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingExternalTorqueControl.m
@@ -28,10 +28,14 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingExternalTorqueControl(...
-    externalTorqueControl, params, coordinate)
-
+function cost = calcMinimizingExternalTorqueControl(costTerm, ...
+    externalTorqueControl, time, params, coordinate)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
 indx = find(strcmp(convertCharsToStrings( ...
     params.externalControlTorqueNames), coordinate));
 cost = calcMinimizingCostArrayTerm(externalTorqueControl(:, indx));
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingCoordinateIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingInverseDynamicLoadsIntegrand.m
similarity index 77%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrackingCoordinateIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcMinimizingInverseDynamicLoadsIntegrand.m
index 7c3049d32..fcb44945f 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingCoordinateIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingInverseDynamicLoadsIntegrand.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the difference between the experimental and
-% predicted joint angles for the specified coordinate. 
+% predicted inverse dynamic moments for the specified coordinate.
 %
 % (struct, Array of number, 2D matrix, Array of string) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -28,17 +28,14 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcTrackingCoordinateIntegrand(auxdata, time, ...
-    statePositions, coordinateName)
-
-indx = find(strcmp(convertCharsToStrings(auxdata.coordinateNames), ...
-    coordinateName));
-if auxdata.splineJointAngles.dim > 1
-    experimentalJointAngles = fnval(auxdata.splineJointAngles, time)';
-else
-    experimentalJointAngles = fnval(auxdata.splineJointAngles, time);
+function cost = calcMinimizingInverseDynamicLoadsIntegrand(costTerm, ...
+    inputs, time, inverseDynamicsMoments, loadName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+indx = find(strcmp(inputs.inverseDynamicsMomentLabels, loadName));
+cost = calcTrackingCostArrayTerm(zeros(size(inverseDynamicsMoments)), ...
+    inverseDynamicsMoments, indx);
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
 end
-
-cost = calcTrackingCostArrayTerm(experimentalJointAngles, ...
-    statePositions, indx);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingJointPowerIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingJointPowerIntegrand.m
similarity index 86%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingJointPowerIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcMinimizingJointPowerIntegrand.m
index 39673ae16..4feb0fed3 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingJointPowerIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingJointPowerIntegrand.m
@@ -1,7 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates and minimizes the joint power for the specified
-% coordinate. 
+% coordinate.
 %
 % (2D matrix, 2D matrix, struct, Array of string) -> (Array of number)
 
@@ -27,14 +27,15 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingJointPowerIntegrand(jointVelocity, ...
-    jointMoment, params, loadName)
-
+function cost = calcMinimizingJointPowerIntegrand(costTerm, ...
+    jointVelocity, time, jointMoment, params, loadName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
 loadName = erase(loadName, '_moment');
 loadName = erase(loadName, '_force');
 indx = find(strcmp(convertCharsToStrings(params.coordinateNames), ...
     loadName));
-momentLabelsNoSuffix = erase(params.inverseDynamicMomentLabels, '_moment');
+momentLabelsNoSuffix = erase(params.inverseDynamicsMomentLabels, '_moment');
 momentLabelsNoSuffix = erase(momentLabelsNoSuffix, '_force');
 includedJointMomentCols = ismember(momentLabelsNoSuffix, ...
     convertCharsToStrings(params.coordinateNames));
@@ -43,4 +44,7 @@
 end
 jointPower = jointMoment(:, indx) .* jointVelocity(:, indx);
 cost = calcMinimizingCostArrayTerm(jointPower);
-end
\ No newline at end of file
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMuscleActivationIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingMuscleActivationIntegrand.m
similarity index 89%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMuscleActivationIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcMinimizingMuscleActivationIntegrand.m
index 0cccf99a1..aa8b74e5c 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMuscleActivationIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcMinimizingMuscleActivationIntegrand.m
@@ -27,10 +27,14 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingMuscleActivationIntegrand(...
+function cost = calcMinimizingMuscleActivationIntegrand(costTerm, time, ...
     muscleActivations, params, muscleName)
-
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
 indx = find(strcmp(convertCharsToStrings(params.muscleNames), ...
     muscleName));
 cost = calcMinimizingCostArrayTerm(muscleActivations(:, indx));
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/getTerminalConstraintTerms.m b/src/TreatmentOptimization/IntegrandTerms/calcPropulsiveImpulseGoalIntegrand.m
similarity index 65%
rename from src/core/TreatmentOptimization/getTerminalConstraintTerms.m
rename to src/TreatmentOptimization/IntegrandTerms/calcPropulsiveImpulseGoalIntegrand.m
index 8f532ae19..8f6cc4b9b 100644
--- a/src/core/TreatmentOptimization/getTerminalConstraintTerms.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcPropulsiveImpulseGoalIntegrand.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% Parses XML settings for a RCNLTerminalConstraintTerms, adding all fields 
-% included in the xml block.  
+% This function calculates the error in propulsive impulse for the side 
+% defined in the cost term. Only the positive impulse (propulsive) is
+% included in the output. 
 %
-% (struct) -> (struct)
-% Parses settings from a RCNLTerminalConstraintTerms.
+% (struct, Array of double, struct, struct) -> (Array of double)
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
+% Author(s): Spencer Williams                                             %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,17 +28,20 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function terminal = getTerminalConstraintTerms(tree)
-terminalConstraintTermsTree = getFieldByName(tree, ...
-    'RCNLTerminalConstraintTerms');
-if(isstruct(terminalConstraintTermsTree))
-    terminalConstraints = getFieldByName(terminalConstraintTermsTree, ...
-        "RCNLConstraintTerm");
-    if isstruct(terminalConstraints) || iscell(terminalConstraints)
-        terminal = parseRcnlConstraintTermSet(terminalConstraints);
-    else        
-        terminal = {};
+function cost = calcPropulsiveImpulseGoalIntegrand(modeledValues, ...
+    time, inputs, costTerm)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", false);
+propulsiveForce = [];
+for i = 1:length(inputs.contactSurfaces)
+    if inputs.contactSurfaces{i}.isLeftFoot == strcmpi(costTerm.side, "left")
+        propulsiveForce = modeledValues.groundReactionsLab.forces{i}(:,1);
     end
-else
-    terminal = {};
-end
\ No newline at end of file
+end
+assert(~isempty(propulsiveForce), "Unable to find propulsive force.")
+cost = real(sqrt((propulsiveForce - costTerm.errorCenter) / ...
+    costTerm.maxAllowableError));
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
diff --git a/src/DesignOptimization/computeDesignOptimizationContinuousFunction.m b/src/TreatmentOptimization/IntegrandTerms/calcRelativeMetabolicCostPerDistanceGoalDiscrete.m
similarity index 59%
rename from src/DesignOptimization/computeDesignOptimizationContinuousFunction.m
rename to src/TreatmentOptimization/IntegrandTerms/calcRelativeMetabolicCostPerDistanceGoalDiscrete.m
index f1588cf52..c669f8c3d 100644
--- a/src/DesignOptimization/computeDesignOptimizationContinuousFunction.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcRelativeMetabolicCostPerDistanceGoalDiscrete.m
@@ -1,10 +1,9 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function computes the dynamic constraints, path constraints (if any)
-% and cost function terms (if any) for design optimization.
-% 
-% (struct) -> (struct)
+% This function returns an integrand cost for metabolic cost normalized by
+% distance. 
 %
+% (struct, struct, struct, struct) -> (Array of double)
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +13,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Spencer Williams, Claire V. Hammond                          %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,19 +27,24 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function modeledValues = computeDesignOptimizationContinuousFunction(inputs)
+function cost = calcRelativeMetabolicCostPerDistanceGoalDiscrete( ...
+    modeledValues, values, inputs, costTerm)
 
-values = getDesignOptimizationValueStruct(inputs.phase, inputs.auxdata);
-inputs = updateSystemFromUserDefinedFunctions(inputs, values);
-modeledValues = calcTorqueBasedModeledValues(values, inputs.auxdata);
-modeledValues = calcSynergyBasedModeledValues(values, inputs.auxdata, ...
-    modeledValues);
-modeledValues.dynamics = calcDesignOptimizationDynamicsConstraint(values, ...
-    inputs.auxdata);
-if ~isempty(inputs.auxdata.path)
-    modeledValues.path = calcDesignOptimizationPathConstraint(values, ...
-        modeledValues, inputs.auxdata);
+beltSpeed = 0;
+if ~isempty(inputs.contactSurfaces)
+    for i = 1 : length(inputs.contactSurfaces)
+        beltSpeed = beltSpeed + inputs.contactSurfaces{i}.beltSpeed;
+    end
+    beltSpeed = beltSpeed / length(inputs.contactSurfaces);
+end
+
+currentMetabolicCost = modeledValues.metabolicCost / values.time(end) ...
+    / (modeledValues.massCenterVelocity + beltSpeed);
+normalizedInitialMetabolicCost = inputs.initialMetabolicCost / ...
+    inputs.experimentalTime(end) / (inputs.initialMassCenterVelocity + beltSpeed);
+
+rawCost = (currentMetabolicCost - normalizedInitialMetabolicCost) / ...
+    normalizedInitialMetabolicCost;
+assert(~any(isnan(rawCost)), "Relative metabolic cost is infinity, is the initial metabolic cost 0?")
+cost = ((rawCost - costTerm.errorCenter) ./ costTerm.maxAllowableError) .^ 2;
 end
-modeledValues.integrand = calcDesignOptimizationIntegrand(values, ...
-    modeledValues, inputs.auxdata);
-end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcRelativeMetabolicCostPerTimeGoalDiscrete.m b/src/TreatmentOptimization/IntegrandTerms/calcRelativeMetabolicCostPerTimeGoalDiscrete.m
new file mode 100644
index 000000000..5f0b91dfe
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcRelativeMetabolicCostPerTimeGoalDiscrete.m
@@ -0,0 +1,39 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function returns an integrand cost for metabolic cost normalized by
+% time. 
+%
+% (struct, struct, struct, struct) -> (Array of double)
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Spencer Williams, Claire V. Hammond                          %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcRelativeMetabolicCostPerTimeGoalDiscrete( ...
+    modeledValues, values, inputs, costTerm)
+currentMetabolicCost = modeledValues.metabolicCost / values.time(end);
+normalizedInitialMetabolicCost = inputs.initialMetabolicCost / ...
+    inputs.experimentalTime(end);
+rawCost = (currentMetabolicCost - normalizedInitialMetabolicCost) / ...
+    normalizedInitialMetabolicCost;
+assert(~any(isnan(rawCost)), "Relative metabolic cost is infinity, is the initial metabolic cost 0?")
+cost = ((rawCost - costTerm.errorCenter) ./ costTerm.maxAllowableError) .^ 2;
+end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingControllerIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingControllerIntegrand.m
similarity index 58%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrackingControllerIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcTrackingControllerIntegrand.m
index 8f22e433a..7bcad1929 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingControllerIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingControllerIntegrand.m
@@ -30,30 +30,46 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcTrackingControllerIntegrand(auxdata, values, time, ...
-    controllerName)
-
-switch auxdata.controllerType
-    case 'synergy_driven'
-        indx = find(strcmp(convertCharsToStrings( ...
-            auxdata.synergyLabels), controllerName));
-        synergyActivations = ...
-            fnval(auxdata.splineSynergyActivations, time)';
-        cost = calcTrackingCostArrayTerm(synergyActivations, ...
-            values.controlSynergyActivations, indx);
-    case 'torque_driven'
-        indx1 = find(strcmp(convertCharsToStrings( ...
-            auxdata.inverseDynamicMomentLabels), controllerName));
-        indx2 = find(strcmp(convertCharsToStrings( ...
-            strcat(auxdata.controlTorqueNames, '_moment')), ...
-            controllerName));
-        if auxdata.splineJointMoments.dim > 1
-            experimentalJointMoments = ...
-                fnval(auxdata.splineJointMoments, time)';
+function cost = calcTrackingControllerIntegrand(costTerm, inputs, ...
+    values, time, controllerName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+if strcmp(inputs.controllerType, 'synergy')
+    indx = find(strcmp(convertCharsToStrings( ...
+        inputs.synergyLabels), controllerName));
+    if ~isempty(indx)
+        if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+            max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+            synergyActivations = inputs.splinedSynergyActivations;
         else
-            experimentalJointMoments = ...
-                fnval(auxdata.splineJointMoments, time);
+            synergyActivations = ...
+                evaluateGcvSplines(inputs.splineSynergyActivations, ...
+                inputs.synergyLabels, time);
         end
-        cost = experimentalJointMoments(:, indx1) - ...
-            values.controlTorques(:, indx2);
-end
\ No newline at end of file
+        cost = calcTrackingCostArrayTerm(synergyActivations, ...
+            values.controlSynergyActivations, indx);
+        return
+    end
+end
+indx1 = find(strcmp(convertCharsToStrings( ...
+    strcat(inputs.torqueLabels, '_moment')), controllerName));
+indx2 = find(strcmp(convertCharsToStrings( ...
+    strcat(inputs.torqueControllerCoordinateNames, '_moment')), ...
+    controllerName));
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalJointMoments = inputs.splinedTorqueControls;
+else
+    experimentalJointMoments = ...
+        evaluateGcvSplines(inputs.splineTorqueControls, ...
+        inputs.torqueLabels, time);
+end
+cost = experimentalJointMoments(:, indx1) - ...
+    values.torqueControls(:, indx2);
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcTrackingCoordinateIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingCoordinateIntegrand.m
new file mode 100644
index 000000000..a9b00eca6
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingCoordinateIntegrand.m
@@ -0,0 +1,58 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the difference between the experimental and
+% predicted joint angles for the specified coordinate.
+%
+% (struct, Array of number, 2D matrix, Array of string) -> (Array of number)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega                                                 %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcTrackingCoordinateIntegrand(costTerm, inputs, time, ...
+    positions, coordinateName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+indx = find(strcmp(convertCharsToStrings(inputs.coordinateNames), ...
+    coordinateName));
+if isempty(indx)
+    throw(MException('CostTermError:CoordinateNotInState', ...
+        strcat("Coordinate ", coordinateName, " is not in the ", ...
+        "<states_coordinate_list>")))
+end
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalJointAngles = inputs.splinedJointAngles;
+else
+    experimentalJointAngles = evaluateGcvSplines( ...
+        inputs.splineJointAngles, inputs.coordinateNames, time);
+end
+cost = calcTrackingCostArrayTerm(experimentalJointAngles, ...
+    positions, indx);
+
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingExternalForcesIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingExternalForcesIntegrand.m
similarity index 72%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrackingExternalForcesIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcTrackingExternalForcesIntegrand.m
index 377a5d0ae..7dfabfb47 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingExternalForcesIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingExternalForcesIntegrand.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the difference between the experimental and
-% predicted ground reaction forces for the specified force. 
+% predicted ground reaction forces for the specified force.
 %
 % (struct, 2D matrix, Array of number, Array of string) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -28,20 +28,24 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcTrackingExternalForcesIntegrand(params, ...
+function cost = calcTrackingExternalForcesIntegrand(costTerm, inputs, ...
     groundReactionsForces, time, forceName)
-
-for i = 1:length(params.contactSurfaces)
-    indx = find(strcmp(convertCharsToStrings(params.contactSurfaces{i}. ...
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+for i = 1:length(inputs.contactSurfaces)
+    indx = find(strcmp(convertCharsToStrings(inputs.contactSurfaces{i}. ...
         forceColumns), forceName));
     if ~isempty(indx)
-        if params.splineExperimentalGroundReactionForces{i}.dim > 1
-            experimentalGroundReactions = ...
-                fnval(params.splineExperimentalGroundReactionForces{i}, ...
-                time)';
+        if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+            experimentalGroundReactions = inputs.splinedGroundReactionForces{i};
         else
             experimentalGroundReactions = ...
-                fnval(params.splineExperimentalGroundReactionForces{i}, ...
+                evaluateGcvSplines( ...
+                inputs.splineExperimentalGroundReactionForces{i}, 0:2, ...
                 time);
         end
         cost = calcTrackingCostArrayTerm(...
@@ -49,4 +53,7 @@
             indx);
     end
 end
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingExternalMomentsIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingExternalMomentsIntegrand.m
similarity index 72%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrackingExternalMomentsIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcTrackingExternalMomentsIntegrand.m
index b903723a4..dbae7bc38 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingExternalMomentsIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingExternalMomentsIntegrand.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the difference between the experimental and
-% predicted ground reaction moments for the specified moment. 
+% predicted ground reaction moments for the specified moment.
 %
 % (struct, 2D matrix, Array of number, Array of string) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -28,20 +28,24 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcTrackingExternalMomentsIntegrand(params, ...
+function cost = calcTrackingExternalMomentsIntegrand(costTerm, inputs, ...
     groundReactionMoments, time, loadName)
-
-for i = 1:length(params.contactSurfaces)
-    indx = find(strcmp(convertCharsToStrings(params.contactSurfaces{i}. ...
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+for i = 1:length(inputs.contactSurfaces)
+    indx = find(strcmp(convertCharsToStrings(inputs.contactSurfaces{i}. ...
         momentColumns), loadName));
     if ~isempty(indx)
-        if params.splineExperimentalGroundReactionMoments{i}.dim > 1
-            experimentalGroundReactions = ...
-                fnval(params.splineExperimentalGroundReactionMoments{i}, ...
-                time)';
+        if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+            experimentalGroundReactions = inputs.splinedGroundReactionMoments{i};
         else
             experimentalGroundReactions = ...
-                fnval(params.splineExperimentalGroundReactionMoments{i}, ...
+                evaluateGcvSplines( ...
+                inputs.splineExperimentalGroundReactionMoments{i}, 0:2, ...
                 time);
         end
         cost = calcTrackingCostArrayTerm(...
@@ -49,4 +53,7 @@
             indx);
     end
 end
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicLoadsIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicLoadsIntegrand.m
similarity index 64%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicLoadsIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicLoadsIntegrand.m
index 9fb687f49..9d0e9a675 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicLoadsIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicLoadsIntegrand.m
@@ -28,26 +28,30 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcTrackingInverseDynamicLoadsIntegrand(params, time, ...
-    inverseDynamicMoments, loadName)
-
-loadName = erase(loadName, '_moment');
-loadName = erase(loadName, '_force');
-indx = find(strcmp(convertCharsToStrings(params.coordinateNames), ...
-    loadName));
-
-if params.splineJointMoments.dim > 1
-    experimentalJointMoments = fnval(params.splineJointMoments, time)';
+function cost = calcTrackingInverseDynamicLoadsIntegrand(costTerm, ...
+    inputs, time, inverseDynamicsMoments, loadName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+indx = find(strcmp(inputs.inverseDynamicsMomentLabels, loadName));
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalJointMoments = inputs.splinedJointMoments;
 else
-    experimentalJointMoments = fnval(params.splineJointMoments, time);
+    experimentalJointMoments = evaluateGcvSplines( ...
+        inputs.splineJointMoments, inputs.inverseDynamicsMomentLabels, time);
 end
-
-momentLabelsNoSuffix = erase(params.inverseDynamicMomentLabels, '_moment');
-momentLabelsNoSuffix = erase(momentLabelsNoSuffix, '_force');
-includedJointMomentCols = ismember(momentLabelsNoSuffix, convertCharsToStrings(params.coordinateNames));
-if size(inverseDynamicMoments, 2) ~= size(experimentalJointMoments, 2)
+if size(inverseDynamicsMoments, 2) ~= size(experimentalJointMoments, 2)
+    momentLabelsNoSuffix = erase(inputs.inverseDynamicsMomentLabels, '_moment');
+    momentLabelsNoSuffix = erase(momentLabelsNoSuffix, '_force');
+    includedJointMomentCols = ismember(momentLabelsNoSuffix, convertCharsToStrings(inputs.coordinateNames));
     experimentalJointMoments = experimentalJointMoments(:, includedJointMomentCols);
 end
 cost = calcTrackingCostArrayTerm(experimentalJointMoments, ...
-    inverseDynamicMoments, indx);
-end
\ No newline at end of file
+    inverseDynamicsMoments, indx);
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicSlopeIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicSlopeIntegrand.m
new file mode 100644
index 000000000..a3c3c7dda
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingInverseDynamicSlopeIntegrand.m
@@ -0,0 +1,63 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the difference between the slope of experimental 
+% and predicted inverse dynamic moments for the specified coordinate.
+%
+% (struct, Array of number, 2D matrix, Array of string) -> (Array of number)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Spencer Williams                               %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcTrackingInverseDynamicSlopeIntegrand(costTerm, ...
+    inputs, time, inverseDynamicsMoments, loadName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+indx = find(strcmp(inputs.inverseDynamicsMomentLabels, loadName));
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalJointMoments = inputs.splinedJointMoments;
+else
+    experimentalJointMoments = evaluateGcvSplines( ...
+        inputs.splineJointMoments, inputs.inverseDynamicsMomentLabels, time);
+end
+if size(inverseDynamicsMoments, 2) ~= size(experimentalJointMoments, 2)
+    momentLabelsNoSuffix = erase(inputs.inverseDynamicsMomentLabels, '_moment');
+    momentLabelsNoSuffix = erase(momentLabelsNoSuffix, '_force');
+    includedJointMomentCols = ismember(momentLabelsNoSuffix, convertCharsToStrings(inputs.coordinateNames));
+    experimentalJointMoments = experimentalJointMoments(:, includedJointMomentCols);
+end
+
+timeDiff = diff(time);
+experimentalDiff = diff(experimentalJointMoments, 1) ./ timeDiff;
+experimentalDiff(end + 1, :) = 0;
+modeledDiff = diff(inverseDynamicsMoments, 1) ./ timeDiff;
+modeledDiff(end + 1, :) = 0;
+
+cost = calcTrackingCostArrayTerm(experimentalDiff, modeledDiff, indx);
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcTrackingMarkerPosition.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingMarkerPosition.m
new file mode 100644
index 000000000..61ec0bb63
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingMarkerPosition.m
@@ -0,0 +1,64 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the error in marker tracking
+%
+% (struct, Array of number, 2D matrix, Array of string) -> (Array of number)
+% returns the distance between the experimental and calculated markers.
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcTrackingMarkerPosition(costTerm, time, ...
+    markerPositions, inputs)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+indx = find(strcmp(convertCharsToStrings(inputs.trackedMarkerNames), ...
+    costTerm.marker));
+if isempty(indx)
+    throw(MException('CostTermError:MarkerDoesNotExist', ...
+        strcat("Marker ", costTerm.marker, " is not in the ", ...
+        "list of tracked markers")))
+end
+assert(length(indx) == 1, "Marker " + costTerm.marker + ...
+    " must only have one tracking cost term.")
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalMarkerPositions = inputs.splinedMarkerPositions{indx};
+else
+    experimentalMarkerPositions = ...
+        evaluateGcvSplines(inputs.splineMarkerPositions{indx}, ...
+        0:2, time);
+end
+cost = calcTrackingCostArrayTerm(experimentalMarkerPositions, ...
+    markerPositions, indx);
+cost = cost + calcTrackingCostArrayTerm(experimentalMarkerPositions, ...
+    markerPositions, indx + 1);
+cost = cost + calcTrackingCostArrayTerm(experimentalMarkerPositions, ...
+    markerPositions, indx + 2);
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
+
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingMuscleActivationIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingMuscleActivationIntegrand.m
similarity index 70%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcTrackingMuscleActivationIntegrand.m
rename to src/TreatmentOptimization/IntegrandTerms/calcTrackingMuscleActivationIntegrand.m
index 392789b9c..e041a7448 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcTrackingMuscleActivationIntegrand.m
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingMuscleActivationIntegrand.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the difference between the experimental and
-% predicted muscle activations for the specified muscle. 
+% predicted muscle activations for the specified muscle.
 %
 % (2D matrix, Array of number, struct, Array of string) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -28,21 +28,25 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcTrackingMuscleActivationIntegrand(muscleActivations, ...
-    time, params, muscleName)
-
-indx = find(strcmp(convertCharsToStrings(params.muscleNames), ...
+function cost = calcTrackingMuscleActivationIntegrand(costTerm, ...
+    muscleActivations, time, inputs, muscleName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+indx = find(strcmp(convertCharsToStrings(inputs.muscleNames), ...
     muscleName));
-
-if params.splineMuscleActivations.dim > 1
-    experimentalMuscleActivations = ...
-        fnval(params.splineMuscleActivations, time)';
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalMuscleActivations = inputs.splinedMuscleActivations;
 else
-    experimentalMuscleActivations = ...
-        fnval(params.splineMuscleActivations, time);
+    experimentalMuscleActivations = evaluateGcvSplines( ...
+        inputs.splineMuscleActivations, inputs.muscleNames, time);
 end
-
-experimentalMuscleActivations = fnval(params.splineMuscleActivations, time)';
 cost = calcTrackingCostArrayTerm(experimentalMuscleActivations, ...
     muscleActivations, indx);
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
 end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/IntegrandTerms/calcTrackingSpeedIntegrand.m b/src/TreatmentOptimization/IntegrandTerms/calcTrackingSpeedIntegrand.m
new file mode 100644
index 000000000..cad63cb18
--- /dev/null
+++ b/src/TreatmentOptimization/IntegrandTerms/calcTrackingSpeedIntegrand.m
@@ -0,0 +1,59 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the difference between the experimental and
+% predicted joint angles for the specified coordinate.
+%
+% (struct, Array of number, 2D matrix, Array of string) -> (Array of number)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega                                                 %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function cost = calcTrackingSpeedIntegrand(costTerm, inputs, time, ...
+    velocities, coordinateName)
+normalizeByFinalTime = valueOrAlternate(costTerm, ...
+    "normalize_by_final_time", true);
+if normalizeByFinalTime
+    time = time * inputs.experimentalTime(end) / time(end);
+end
+indx = find(strcmp(convertCharsToStrings(inputs.coordinateNames), ...
+    coordinateName));
+if isempty(indx)
+    throw(MException('CostTermError:CoordinateNotInState', ...
+        strcat("Coordinate ", coordinateName, " is not in the ", ...
+        "<states_coordinate_list>")))
+end
+if all(size(time) == size(inputs.collocationTimeOriginal)) && ...
+        max(abs(time - inputs.collocationTimeOriginal)) < 1e-6
+    experimentalJointVelocities = inputs.splinedJointSpeeds;
+else
+    experimentalJointVelocities = evaluateGcvSplines( ...
+        inputs.splineJointAngles, inputs.coordinateNames, time, 1);
+end
+
+cost = calcTrackingCostArrayTerm(experimentalJointVelocities, ...
+    velocities, indx);
+
+if normalizeByFinalTime
+    cost = cost / time(end);
+end
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGpopsInitialGuess.m b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGpopsInitialGuess.m
new file mode 100644
index 000000000..1a6638e38
--- /dev/null
+++ b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGpopsInitialGuess.m
@@ -0,0 +1,150 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function sets up the common initial guess for an optimal control
+% problem and is used by Tracking Optimization, Verification Optimization,
+% and Design Optimization
+%
+% (struct) -> (struct)
+% return a set of setup values common to all optimal control problems
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function guess = setupGpopsInitialGuess(inputs)
+guess = struct();
+guess = setupInitialStatesGuess(inputs, guess);
+guess = setupInitialControlsGuess(inputs, guess);
+guess = setupInitialParametersGuess(inputs, guess);
+guess.phase.integral = scaleToBounds(1e1, inputs.continuousMaxAllowableError, ...
+    zeros(size(inputs.continuousMaxAllowableError)));
+if valueOrAlternate(inputs, 'calculateMetabolicCost', false)
+    guess.phase.integral(:, end + 1) = 1;
+end
+end
+
+function guess = setupInitialStatesGuess(inputs, guess)
+if isfield(inputs, "initialStates")
+    states = subsetInitialStatesDataByCoordinates( ...
+        inputs.initialStates, ...
+        inputs.initialStatesLabels, ...
+        inputs.statesCoordinateNames);
+    guess.phase.state = scaleToBounds(states, ...
+        inputs.maxState, inputs.minState);
+    guess.phase.time = scaleToBounds(inputs.initialTime, inputs.maxTime, ...
+        inputs.minTime);
+else
+    stateJointAngles = subsetDataByCoordinates( ...
+        inputs.experimentalJointAngles, ...
+        inputs.coordinateNames, ...
+        inputs.statesCoordinateNames);
+    stateJointVelocities = subsetDataByCoordinates( ...
+        inputs.experimentalJointVelocities, ...
+        inputs.coordinateNames, ...
+        inputs.statesCoordinateNames);
+    % stateJointAccelerations = subsetDataByCoordinates( ...
+    %     inputs.experimentalJointAccelerations, ...
+    %     inputs.coordinateNames, ...
+    %     inputs.statesCoordinateNames);
+    guess.phase.state = scaleToBounds([ ...
+        stateJointAngles, ...
+        stateJointVelocities, ...
+        % stateJointAccelerations, ...
+        ], inputs.maxState, ...
+        inputs.minState);
+    guess.phase.time = scaleToBounds(inputs.experimentalTime, inputs.maxTime, ...
+        inputs.minTime);
+end
+end
+
+function guess = setupInitialControlsGuess(inputs, guess)
+if isfield(inputs, "initialAccelerations")
+    controls = inputs.initialAccelerations;
+else
+    stateJointAccelerations = subsetDataByCoordinates( ...
+        inputs.experimentalJointAccelerations, ...
+        inputs.coordinateNames, ...
+        inputs.statesCoordinateNames);
+
+    controls = stateJointAccelerations;
+end
+if strcmp(inputs.controllerType, "synergy")
+    if isfield(inputs, "initialSynergyControls")
+        controls = [controls, inputs.initialSynergyControls];
+    else
+        throw(MException("NoInitialSynergyControls", ...
+            strcat("initial synergy controls required for synergy", ...
+            " driven, have you run NCP?")));
+    end
+end
+if isfield(inputs, "initialTorqueControls")
+    controls = [controls, inputs.initialTorqueControls];
+else
+    if ~isempty(valueOrAlternate(inputs, "torqueControllerCoordinateNames", []))
+        stateTorqueControls = subsetDataByCoordinates( ...
+            inputs.experimentalJointMoments, ...
+            erase(erase(inputs.inverseDynamicsMomentLabels, '_moment'), '_force'), ...
+            inputs.torqueControllerCoordinateNames);
+        controls = [controls, stateTorqueControls];
+    end
+end
+guess.phase.control = scaleToBounds(controls, inputs.maxControl, ...
+    inputs.minControl);
+end
+
+function guess = setupInitialParametersGuess(inputs, guess)
+if valueOrAlternate(inputs, "optimizeSynergyVectors", false)
+    guess.parameter = [];
+    for i = 1 : length(inputs.synergyGroups)
+        for j = 1 : length(inputs.synergyGroups{i}.muscleNames)
+            index = find(ismember(inputs.synergyWeightsLabels, ...
+                inputs.synergyGroups{i}.muscleNames{j}));
+            guess.parameter(end + 1) = inputs.synergyWeights(i, index);
+        end
+    end
+end
+if strcmp(inputs.toolName, "DesignOptimization")
+    for i = 1:length(inputs.userDefinedVariables)
+        if ~isfield(guess, "parameter")
+            guess.parameter = [];
+        end
+        guess.parameter = [guess.parameter, ...
+            inputs.userDefinedVariables{i}.initial_values];
+    end
+end
+if isfield(guess, "parameter")
+    guess.parameter = scaleToBounds(guess.parameter, inputs.maxParameter, ...
+        inputs.minParameter);
+    guess.phase.parameter = guess.parameter;
+end
+end
+
+function output = subsetInitialStatesDataByCoordinates(data, ...
+    coordinateNames, subsetOfCoordinateNames)
+includedSubset = ismember(coordinateNames, subsetOfCoordinateNames);
+numCoordinates = length(includedSubset) / 2;
+for i = 1:numCoordinates
+    if includedSubset(i)
+        includedSubset(i + numCoordinates) = true;
+    end
+end
+output = data(:, includedSubset);
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlSolverSettings.m b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGpopsSettings.m
similarity index 56%
rename from src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlSolverSettings.m
rename to src/TreatmentOptimization/OptimalControlSetupFunctions/setupGpopsSettings.m
index 6f2798ed3..4445aaf64 100644
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlSolverSettings.m
+++ b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGpopsSettings.m
@@ -30,40 +30,39 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function setup = setupCommonOptimalControlSolverSettings(inputs, ...
+function setup = setupGpopsSettings(inputs, ...
     bounds, guess, params, continuousFunction, endpointFunction)
-setup.name = params.solverSettings.optimizationFileName;
+setup.name = inputs.gpops.optimizationFileName;
 setup.functions.continuous = continuousFunction;
-auxdata.ContinuousFunc = setup.functions.continuous;
 setup.functions.endpoint = endpointFunction;
 setup.auxdata = inputs;
 setup.bounds = bounds;
 setup.guess = guess;
-setup.derivatives.supplier = params.solverSettings.derivativeSupplier;
-setup.derivatives.derivativelevel = params.solverSettings.derivativeLevel;
-setup.derivatives.dependencies = params.solverSettings.derivativeDependencies;
-setup.derivatives.stepsize1 = params.solverSettings.stepSize;
-setup.scales.method = params.solverSettings.scaleMethods;
-setup.method = params.solverSettings.method;
-setup.mesh.method = params.solverSettings.meshMethod;
-setup.mesh.tolerance = params.solverSettings.meshTolerance;
-setup.mesh.maxiterations = params.solverSettings.meshMaxIterations;
-setup.mesh.colpointsmin = params.solverSettings.meshColpointsMin;
-setup.mesh.colpointsmax = params.solverSettings.meshColpointsMax;
-setup.mesh.splitmult = params.solverSettings.meshSplitMult;
-setup.mesh.curveRatio = params.solverSettings.meshCurveRatio;
-setup.mesh.R = params.solverSettings.meshR;
-setup.mesh.sigma = params.solverSettings.meshSigma;
-N = params.solverSettings.numCollocationPoints;
-P = params.solverSettings.numIntervals;
+setup.derivatives.supplier = inputs.gpops.derivativeSupplier;
+setup.derivatives.derivativelevel = inputs.gpops.derivativeLevel;
+setup.derivatives.dependencies = inputs.gpops.derivativeDependencies;
+setup.derivatives.stepsize1 = inputs.gpops.stepSize;
+setup.scales.method = inputs.gpops.scaleMethods;
+setup.method = inputs.gpops.method;
+setup.mesh.method = inputs.gpops.meshMethod;
+setup.mesh.tolerance = inputs.gpops.meshTolerance;
+setup.mesh.maxiterations = inputs.gpops.meshMaxIterations;
+setup.mesh.colpointsmin = inputs.gpops.meshColpointsMin;
+setup.mesh.colpointsmax = inputs.gpops.meshColpointsMax;
+setup.mesh.splitmult = inputs.gpops.meshSplitMult;
+setup.mesh.curveRatio = inputs.gpops.meshCurveRatio;
+setup.mesh.R = inputs.gpops.meshR;
+setup.mesh.sigma = inputs.gpops.meshSigma;
+N = inputs.gpops.numCollocationPoints;
+P = inputs.gpops.numIntervals;
 setup.mesh.phase.colpoints = P * ones(1, N);
 setup.mesh.phase.fraction = ones(1, N) / N;
-setup.nlp.solver = params.solverSettings.solverType;
-setup.nlp.ipoptoptions.linear_solver = params.solverSettings.linearSolverType;
-setup.nlp.ipoptoptions.tolerance = params.solverSettings.solverTolerance;
-setup.nlp.ipoptoptions.maxiterations = params.solverSettings.maxIterations;
-setup.nlp.snoptoptions.linear_solver = params.solverSettings.linearSolverType;
-setup.nlp.snoptoptions.tolerance = params.solverSettings.solverTolerance;
-setup.nlp.snoptoptions.maxiterations = params.solverSettings.maxIterations;
-setup.displaylevel = params.solverSettings.displayLevel;
+setup.nlp.solver = inputs.gpops.solverType;
+setup.nlp.ipoptoptions.linear_solver = inputs.gpops.linearSolverType;
+setup.nlp.ipoptoptions.tolerance = inputs.gpops.solverTolerance;
+setup.nlp.ipoptoptions.maxiterations = inputs.gpops.maxIterations;
+setup.nlp.snoptoptions.linear_solver = inputs.gpops.linearSolverType;
+setup.nlp.snoptoptions.tolerance = inputs.gpops.solverTolerance;
+setup.nlp.snoptoptions.maxiterations = inputs.gpops.maxIterations;
+setup.displaylevel = inputs.gpops.displayLevel;
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupGroundContact.m b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGroundContact.m
similarity index 92%
rename from src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupGroundContact.m
rename to src/TreatmentOptimization/OptimalControlSetupFunctions/setupGroundContact.m
index 098aefc94..dcaaf4123 100644
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupGroundContact.m
+++ b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupGroundContact.m
@@ -34,13 +34,13 @@
     midfootSuperiorLocation = pointKinematics(inputs.experimentalTime, ...
         inputs.experimentalJointAngles, inputs.experimentalJointVelocities, ...
         inputs.contactSurfaces{i}.midfootSuperiorPointOnBody, ...
-        inputs.contactSurfaces{i}.midfootSuperiorBody, inputs.mexModel, ...
-        inputs.coordinateNames);
-    midfootSuperiorLocation(:, 2) = 0;
+        inputs.contactSurfaces{i}.midfootSuperiorBody, ...
+        inputs.modelFileName, inputs.coordinateNames);
+    midfootSuperiorLocation(:, 2) = inputs.contactSurfaces{i}.restingSpringLength;
     inputs.contactSurfaces{i}.experimentalGroundReactionMoments = ...
         transferMoments(inputs.contactSurfaces{i}.electricalCenter, ...
         midfootSuperiorLocation, ...
         inputs.contactSurfaces{i}.experimentalGroundReactionMoments, ...
         inputs.contactSurfaces{i}.experimentalGroundReactionForces);
 end
-end
\ No newline at end of file
+end
diff --git a/src/VerificationOptimization/computeVerificationOptimizationEndpointFunction.m b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupMuscleSynergies.m
similarity index 74%
rename from src/VerificationOptimization/computeVerificationOptimizationEndpointFunction.m
rename to src/TreatmentOptimization/OptimalControlSetupFunctions/setupMuscleSynergies.m
index 7820b6e96..677f1c11b 100644
--- a/src/VerificationOptimization/computeVerificationOptimizationEndpointFunction.m
+++ b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupMuscleSynergies.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function computes the terminal constraint (if any), and total cost 
-% function objective for verification optimization.
-% 
-% (struct) -> (struct)
+% This function stores the initial synergy activations as a spline for use
+% in cost terms for Treatment Optimization
 %
+% (string) -> (None)
+% Spline input synergy activations
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,12 +28,11 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function output = computeVerificationOptimizationEndpointFunction(inputs)
-if ~isempty(inputs.auxdata.terminal)
-    output.eventgroup.event = ...
-        calcVerificationOptimizationTerminalConstraint(inputs, ...
-        inputs.auxdata);
+function inputs = setupMuscleSynergies(inputs)
+if strcmp(inputs.controllerType, 'synergy')
+    inputs.splineSynergyActivations = makeGcvSplineSet( ...
+        inputs.initialTime, inputs.initialSynergyControls', ...
+        inputs.initialSynergyControlsLabels);
+    inputs.synergyLabels = inputs.initialSynergyControlsLabels;
 end
-output.objective = ...
-    calcVerificationOptimizationObjective(inputs.phase.integral);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingBreakingForceIntegrand.m b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupTorqueControls.m
similarity index 73%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingBreakingForceIntegrand.m
rename to src/TreatmentOptimization/OptimalControlSetupFunctions/setupTorqueControls.m
index a77b5524c..265298d4f 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingBreakingForceIntegrand.m
+++ b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupTorqueControls.m
@@ -1,9 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function minimizes the breaking force for the specified foot. 
-%
-% (struct, struct, struct) -> (Array of number)
+% This function stores the initial control torques as a spline for use
+% in cost terms for Treatment Optimization
 %
+% (string) -> (None)
+% Spline input control torques
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,14 +28,11 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingBreakingForceIntegrand(modeledValues, ...
-    params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        breakingForce = getBreakingForce( ...
-            modeledValues.groundReactionsLab.forces{i}(:,1));
-    end
+function inputs = setupTorqueControls(inputs)
+if isfield(inputs, "torqueControllerCoordinateNames") && ...
+        ~isempty(inputs.torqueControllerCoordinateNames)
+inputs.splineTorqueControls = makeGcvSplineSet(inputs.initialTime, ...
+    inputs.initialTorqueControls', inputs.initialTorqueControlsLabels);
+inputs.torqueLabels = inputs.initialTorqueControlsLabels;
 end
-cost = calcMinimizingCostArrayTerm(breakingForce);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlBounds.m b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupTreatmentOptimizationBounds.m
similarity index 69%
rename from src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlBounds.m
rename to src/TreatmentOptimization/OptimalControlSetupFunctions/setupTreatmentOptimizationBounds.m
index c24af6d92..7fbefdfe6 100644
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlBounds.m
+++ b/src/TreatmentOptimization/OptimalControlSetupFunctions/setupTreatmentOptimizationBounds.m
@@ -29,12 +29,16 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function bounds = setupCommonOptimalControlBounds(inputs, params)
+function bounds = setupTreatmentOptimizationBounds(inputs, params)
 % setup time bounds
 bounds.phase.initialtime.lower = -0.5;
 bounds.phase.initialtime.upper = -0.5;
 bounds.phase.finaltime.lower = 0.5;
 bounds.phase.finaltime.upper = 0.5;
+if isfield(inputs, "finalTimeRange")
+    bounds.phase.finaltime.lower = scaleToBounds( ...
+        inputs.finalTimeRange(1), inputs.maxTime, inputs.minTime);
+end
 % setup state bounds
 bounds.phase.initialstate.lower = -0.5 * ones(1, length(inputs.minState));
 bounds.phase.initialstate.upper = 0.5 * ones(1, length(inputs.minState));
@@ -49,8 +53,9 @@
 bounds.phase.control.lower = -0.5 * ones(1, length(inputs.minControl));
 bounds.phase.control.upper = 0.5 * ones(1, length(inputs.minControl));
 % setup integral bounds
-bounds.phase.integral.lower = zeros(1, length(inputs.minIntegral));
-bounds.phase.integral.upper = params.solverSettings.integralBound * ones(1, length(inputs.minIntegral));
+bounds.phase.integral.lower = zeros(1, length(inputs.continuousMaxAllowableError));
+bounds.phase.integral.upper = inputs.gpops.integralBound * ...
+    ones(1, length(inputs.continuousMaxAllowableError));
 % setup terminal constraint bounds
 if ~isempty(inputs.minTerminal)
     bounds.eventgroup.lower = inputs.minTerminal;
@@ -58,5 +63,27 @@
 if ~isempty(inputs.maxTerminal)
     bounds.eventgroup.upper = inputs.maxTerminal;
 end
+if strcmp(inputs.controllerType, 'synergy')
+    if inputs.optimizeSynergyVectors
+        bounds.parameter.lower = -0.5 * ones(1, length(inputs.minParameter));
+        bounds.parameter.upper = 0.5 * ones(1, length(inputs.minParameter));
+    end
+end
+if strcmp(inputs.toolName, "DesignOptimization")
+    for i = 1:length(inputs.userDefinedVariables)
+        lower = -0.5 * ones(1, length(inputs.userDefinedVariables{i}.initial_values));
+        upper = 0.5 * ones(1, length(inputs.userDefinedVariables{i}.initial_values));
+        if ~isfield(bounds, "parameter") || ...
+                ~isfield(bounds.parameter, "lower")
+            bounds.parameter.lower = lower;
+            bounds.parameter.upper = upper;
+        else
+            bounds.parameter.lower = [bounds.parameter.lower, ...
+                lower];
+            bounds.parameter.upper = [bounds.parameter.upper, ...
+                upper];
+        end
+    end
+end
 end
 
diff --git a/src/TreatmentOptimization/PathTerms/calcKineticPathConstraint.m b/src/TreatmentOptimization/PathTerms/calcKineticPathConstraint.m
new file mode 100644
index 000000000..f5eca5d1d
--- /dev/null
+++ b/src/TreatmentOptimization/PathTerms/calcKineticPathConstraint.m
@@ -0,0 +1,66 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the difference between the inverse dynamic
+% moments and the sum of the torque and synergy controller produced moments
+% for the specified coordinate.
+%
+% (struct, struct, string) -> (number)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function pathTerm = calcKineticPathConstraint(inputs, ...
+    modeledValues, torqueControls, loadName)
+inverseDynamicsIndex = find(strcmp(convertCharsToStrings(inputs.inverseDynamicsMomentLabels), ...
+    loadName));
+if strcmpi(inputs.controllerType, "synergy")
+    coordinateNameIndex = find(strcmp(convertCharsToStrings(inputs.coordinateNames), ...
+        replace(replace(loadName, '_moment', ''), '_force', '')));
+    synergyIndex = find(inputs.surrogateModelIndex == coordinateNameIndex);
+else
+    synergyIndex = [];
+end
+torqueIndex = find(strcmp(strcat(inputs.torqueControllerCoordinateNames, ...
+    '_moment'), loadName));
+if isempty(torqueIndex)
+    torqueIndex = find(strcmp(strcat(inputs.torqueControllerCoordinateNames, ...
+        '_force'), loadName));
+end
+if isempty(synergyIndex)
+    synergyLoad = 0;
+else
+    synergyLoad = modeledValues.muscleJointMoments(:, synergyIndex);
+end
+if isempty(torqueIndex)
+    torqueLoad = 0;
+else
+    torqueLoad = torqueControls(:, torqueIndex);
+end
+if length(synergyLoad) == 1 && length(torqueLoad) == 1 && ...
+        torqueLoad == 0 && synergyLoad == 0
+    throw(MException('', "kinetic path constraint load is not a" + ...
+        " synergy driven or torque driven coordinate"))
+end
+pathTerm = modeledValues.inverseDynamicsMoments(:, inverseDynamicsIndex) - ...
+    (synergyLoad + torqueLoad);
+end
diff --git a/src/core/TreatmentOptimization/PathTerms/calcMuscleActivationsPathConstraint.m b/src/TreatmentOptimization/PathTerms/calcMuscleActivationsPathConstraint.m
similarity index 100%
rename from src/core/TreatmentOptimization/PathTerms/calcMuscleActivationsPathConstraint.m
rename to src/TreatmentOptimization/PathTerms/calcMuscleActivationsPathConstraint.m
diff --git a/src/core/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsPathConstraints.m b/src/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsPathConstraints.m
similarity index 87%
rename from src/core/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsPathConstraints.m
rename to src/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsPathConstraints.m
index 396b5ec15..b12e66b84 100644
--- a/src/core/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsPathConstraints.m
+++ b/src/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsPathConstraints.m
@@ -1,9 +1,9 @@
 % This function is part of the NMSM Pipeline, see file for full license.
-% 
+%
 % This function calculates the difference between the inverse dynamic
-% moments and the muscle produced moments for the specified coordinate. 
+% moments and the muscle produced moments for the specified coordinate.
 % Applicable only if the model is synergy driven.
-% 
+%
 % (struct, struct, Array of string) -> (Array of number)
 %
 
@@ -29,12 +29,12 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function pathTerm = calcMuscleActuatedMomentsPathConstraints(params, ...
+function pathTerm = calcMuscleActuatedMomentsPathConstraints(inputs, ...
     modeledValues, loadName)
-indx1 = find(strcmp(convertCharsToStrings(params.inverseDynamicMomentLabels), ...
+indx1 = find(strcmp(convertCharsToStrings(inputs.inverseDynamicsMomentLabels), ...
     loadName));
-indx2 = find(strcmp(strcat(params.surrogateModelCoordinateNames, ...
+indx2 = find(strcmp(strcat(inputs.surrogateModelCoordinateNames, ...
     '_moment'), loadName));
-pathTerm = modeledValues.inverseDynamicMoments(:, indx1) - ...
+pathTerm = modeledValues.inverseDynamicsMoments(:, indx1) - ...
     modeledValues.muscleJointMoments(:, indx2);
-end
\ No newline at end of file
+end
diff --git a/src/core/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsWithExternalAidPathConstraints.m b/src/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsWithExternalAidPathConstraints.m
similarity index 90%
rename from src/core/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsWithExternalAidPathConstraints.m
rename to src/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsWithExternalAidPathConstraints.m
index 438b7962d..2ffcd8562 100644
--- a/src/core/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsWithExternalAidPathConstraints.m
+++ b/src/TreatmentOptimization/PathTerms/calcMuscleActuatedMomentsWithExternalAidPathConstraints.m
@@ -1,12 +1,12 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the difference between the inverse dynamic
-% moments and the muscle produced moments with the aid of an external 
+% moments and the muscle produced moments with the aid of an external
 % torque controller for the specified coordinate. Applicable only if the
 % model is synergy driven and if an external torque controller is present.
 %
 % (struct, struct, 2D matrix, Array of string) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -32,16 +32,16 @@
 
 function pathTerm = ...
     calcMuscleActuatedMomentsWithExternalAidPathConstraints(params, ...
-    modeledValues, externalControlTorques, coordinate)
+    modeledValues, externalTorqueControls, coordinate)
 
-indx1 = find(strcmp(convertCharsToStrings(params.inverseDynamicMomentLabels), ...
+indx1 = find(strcmp(convertCharsToStrings(params.inverseDynamicsMomentLabels), ...
     [coordinate '_moment']));
 indx2 = find(strcmp(params.surrogateModelCoordinateNames, ...
      coordinate));
 indx3 = find(strcmp(params.externalControlTorqueNames, ...
      coordinate));
 
-pathTerm = modeledValues.inverseDynamicMoments(:, indx1) - ...
+pathTerm = modeledValues.inverseDynamicsMoments(:, indx1) - ...
     (modeledValues.muscleJointMoments(:, indx2) + ...
-    externalControlTorques(:, indx3));
-end
\ No newline at end of file
+    externalTorqueControls(:, indx3));
+end
diff --git a/src/core/TreatmentOptimization/PathTerms/calcNormalizedFiberLengthPathConstraint.m b/src/TreatmentOptimization/PathTerms/calcNormalizedFiberLengthPathConstraint.m
similarity index 100%
rename from src/core/TreatmentOptimization/PathTerms/calcNormalizedFiberLengthPathConstraint.m
rename to src/TreatmentOptimization/PathTerms/calcNormalizedFiberLengthPathConstraint.m
diff --git a/src/core/TreatmentOptimization/PathTerms/calcRootSegmentResidualsPathConstraints.m b/src/TreatmentOptimization/PathTerms/calcRootSegmentResidualsPathConstraints.m
similarity index 90%
rename from src/core/TreatmentOptimization/PathTerms/calcRootSegmentResidualsPathConstraints.m
rename to src/TreatmentOptimization/PathTerms/calcRootSegmentResidualsPathConstraints.m
index 084180cfe..01b5840e9 100644
--- a/src/core/TreatmentOptimization/PathTerms/calcRootSegmentResidualsPathConstraints.m
+++ b/src/TreatmentOptimization/PathTerms/calcRootSegmentResidualsPathConstraints.m
@@ -4,7 +4,7 @@
 % specified by the user for the specified root semgment loads.
 %
 % (Array of string, Cell, 2D matrix) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -29,9 +29,7 @@
 % ----------------------------------------------------------------------- %
 
 function pathTerm = calcRootSegmentResidualsPathConstraints(loadName, ...
-    inverseDynamicMomentLabels, inverseDynamicMoments)
-
-indx = find(strcmp(convertCharsToStrings(inverseDynamicMomentLabels), ...
-    loadName));
-pathTerm = inverseDynamicMoments(:, indx);
-end
\ No newline at end of file
+    inverseDynamicsMomentLabels, inverseDynamicsMoments)
+pathTerm = inverseDynamicsMoments(:, ...
+    find(strcmp(inverseDynamicsMomentLabels, loadName)));
+end
diff --git a/src/core/TreatmentOptimization/PathTerms/calcTorqueActuatedMomentsPathConstraints.m b/src/TreatmentOptimization/PathTerms/calcTorqueActuatedMomentsPathConstraints.m
similarity index 83%
rename from src/core/TreatmentOptimization/PathTerms/calcTorqueActuatedMomentsPathConstraints.m
rename to src/TreatmentOptimization/PathTerms/calcTorqueActuatedMomentsPathConstraints.m
index 8f05a4972..2a66bc3a2 100644
--- a/src/core/TreatmentOptimization/PathTerms/calcTorqueActuatedMomentsPathConstraints.m
+++ b/src/TreatmentOptimization/PathTerms/calcTorqueActuatedMomentsPathConstraints.m
@@ -5,7 +5,7 @@
 % Applicable only if the model is torque driven.
 %
 % (struct, struct, 2D matrix, Array of string) -> (Array of number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -29,14 +29,14 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function pathTerm = calcTorqueActuatedMomentsPathConstraints(params, ...
-    modeledValues, controlTorques, loadName)
+function pathTerm = calcTorqueActuatedMomentsPathConstraints(inputs, ...
+    modeledValues, torqueControls, loadName)
 
 loadName = erase(loadName, '_moment');
 loadName = erase(loadName, '_force');
-indx1 = find(cellfun(@isequal, params.coordinateNames, ...
-    repmat({loadName}, 1, length(params.coordinateNames))));
-indx2 = find(strcmp(params.controlTorqueNames, loadName));
-pathTerm = modeledValues.inverseDynamicMoments(:, indx1) - ...
-    controlTorques(:, indx2);
-end
\ No newline at end of file
+indx1 = find(cellfun(@isequal, inputs.coordinateNames, ...
+    repmat({loadName}, 1, length(inputs.coordinateNames))));
+indx2 = find(strcmp(inputs.torqueControllerCoordinateNames, loadName));
+pathTerm = modeledValues.inverseDynamicsMoments(:, indx1) - ...
+    torqueControls(:, indx2);
+end
diff --git a/src/core/TreatmentOptimization/SetupBounds/getIntegralBounds.m b/src/TreatmentOptimization/SetupBounds/makeMaxAllowableError.m
similarity index 63%
rename from src/core/TreatmentOptimization/SetupBounds/getIntegralBounds.m
rename to src/TreatmentOptimization/SetupBounds/makeMaxAllowableError.m
index a7d046336..e0d4ac2e2 100644
--- a/src/core/TreatmentOptimization/SetupBounds/getIntegralBounds.m
+++ b/src/TreatmentOptimization/SetupBounds/makeMaxAllowableError.m
@@ -28,30 +28,42 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = getIntegralBounds(inputs)
-[~, continuousAllowedTypes] = generateCostTermStruct("continuous", inputs.toolName);
-[~, discreteAllowedTypes] = generateCostTermStruct("discrete", inputs.toolName);
+function [continuousMaxAllowableError, discreteMaxAllowableError] = ...
+    makeMaxAllowableError(toolName, costTerms)
+[~, continuousAllowedTypes] = generateCostTermStruct("continuous", toolName);
+[~, discreteAllowedTypes] = generateCostTermStruct("discrete", toolName);
 
-inputs.maxIntegral = [];
-inputs.minIntegral = [];
-for i = 1:length(inputs.costTerms)
-    costTerm = inputs.costTerms{i};
+continuousMaxAllowableError = [];
+discreteMaxAllowableError = [];
+for i = 1:length(costTerms)
+    costTerm = costTerms{i};
     if costTerm.isEnabled
         if any(ismember(costTerm.type, continuousAllowedTypes)) && ...
                 ~strcmp(costTerm.type, "user_defined")
-            inputs.maxIntegral = cat(2, inputs.maxIntegral, ...
-                costTerm.maxAllowableError);
+            continuousMaxAllowableError = cat(2, ...
+                continuousMaxAllowableError, costTerm.maxAllowableError);
         elseif strcmp(costTerm.type, "user_defined")
             if strcmp(costTerm.cost_term_type, "continuous")
-                inputs.maxIntegral = cat(2, inputs.maxIntegral, ...
+                continuousMaxAllowableError = cat(2, ...
+                    continuousMaxAllowableError, ...
                     costTerm.maxAllowableError);
+            elseif strcmp(costTerm.cost_term_type, "discrete")
+                discreteMaxAllowableError = cat(2, ...
+                    discreteMaxAllowableError, ...
+                    costTerm.maxAllowableError);
+            else
+                throw(MException('', "User-defined cost terms must " + ...
+                    "be specified as either discrete or continuous " + ...
+                    "in the cost_term_type field."))
             end
-        elseif any(ismember(costTerm.type, continuousAllowedTypes)) && ...
-                    any(ismember(costTerm.type, discreteAllowedTypes))
+        elseif any(ismember(costTerm.type, discreteAllowedTypes))
+            discreteMaxAllowableError = cat(2, ...
+                discreteMaxAllowableError, costTerm.maxAllowableError);
+        elseif ~any(ismember(costTerm.type, continuousAllowedTypes)) || ...
+                    ~any(ismember(costTerm.type, discreteAllowedTypes))
             throw(MException('', ['Cost term type ' costTerm.type ...
                 ' does not exist for this tool.']))
         end
     end
 end
-inputs.minIntegral = zeros(1, length(inputs.maxIntegral));
-end
\ No newline at end of file
+end
diff --git a/src/TreatmentOptimization/SetupBounds/makeOptimalControlBounds.m b/src/TreatmentOptimization/SetupBounds/makeOptimalControlBounds.m
new file mode 100644
index 000000000..4e6769ff2
--- /dev/null
+++ b/src/TreatmentOptimization/SetupBounds/makeOptimalControlBounds.m
@@ -0,0 +1,145 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This functions computes the maximum and minimum values for all design
+% variables. The maximum and minimum values for most design variables are
+% based on the multiples value selected by the user times the range of data.
+% For example, if the angle B has a range of -5 to +5, and state position
+% multiple is 1, the maximum value of angle B is 15 and the minimum value
+% of angle B is -15.
+%
+% (struct) -> (struct)
+% Computes max and min design variable bounds
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function inputs = makeOptimalControlBounds(inputs)
+inputs = makeStateBounds(inputs);
+inputs = makeControlBounds(inputs);
+end
+
+function inputs = makeStateBounds(inputs)
+if isfield(inputs, "finalTimeRange")
+    inputs.maxTime = inputs.finalTimeRange(2);
+else
+    inputs.maxTime = max(inputs.experimentalTime);
+end
+inputs.minTime = min(inputs.experimentalTime);
+
+stateJointAngles = subsetDataByCoordinates( ...
+    inputs.experimentalJointAngles, ...
+    inputs.coordinateNames, ...
+    inputs.statesCoordinateNames);
+stateJointVelocities = subsetDataByCoordinates( ...
+    inputs.experimentalJointVelocities, ...
+    inputs.coordinateNames, ...
+    inputs.statesCoordinateNames);
+% stateJointAccelerations = subsetDataByCoordinates( ...
+%     inputs.experimentalJointAccelerations, ...
+%     inputs.coordinateNames, ...
+%     inputs.statesCoordinateNames);
+
+maxStatePositions = max(stateJointAngles) + ...
+    inputs.jointPositionsMultiple * range(stateJointAngles);
+minStatePositions = min(stateJointAngles) - ...
+    inputs.jointPositionsMultiple * range(stateJointAngles);
+maxStateVelocities = max(stateJointVelocities) + ...
+    inputs.jointVelocitiesMultiple * range(stateJointVelocities);
+minStateVelocities = min(stateJointVelocities) - ...
+    inputs.jointVelocitiesMultiple * range(stateJointVelocities);
+
+inputs.maxState = [ ...
+    maxStatePositions, ...
+    maxStateVelocities, ...
+    % maxStateAccelerations, ...
+    ];
+inputs.minState = [ ...
+    minStatePositions, ...
+    minStateVelocities, ...
+    % minStateAccelerations, ...
+    ];
+end
+
+function inputs = makeControlBounds(inputs)
+
+stateJointAccelerations = subsetDataByCoordinates( ...
+    inputs.experimentalJointAccelerations, ...
+    inputs.coordinateNames, ...
+    inputs.statesCoordinateNames);
+
+inputs.maxControl = max(stateJointAccelerations) + ...
+    inputs.jointAccelerationsMultiple * range(stateJointAccelerations);
+inputs.minControl = min(stateJointAccelerations) - ...
+    inputs.jointAccelerationsMultiple * range(stateJointAccelerations);
+
+if strcmp(inputs.controllerType, 'synergy')
+    maxControlSynergyActivations = inputs.maxControlSynergyActivations * ...
+        ones(1, inputs.numSynergies);
+    inputs.maxControl = [inputs.maxControl maxControlSynergyActivations];
+    inputs.minControl = [inputs.minControl zeros(1, inputs.numSynergies)];
+
+    if inputs.optimizeSynergyVectors
+        numParameters = 0;
+        for i = 1 : length(inputs.synergyGroups)
+            numParameters = numParameters + ...
+                inputs.synergyGroups{i}.numSynergies * ...
+                length(inputs.synergyGroups{i}.muscleNames);
+        end
+        inputs.maxParameter = ones(1, numParameters);
+        inputs.minParameter = zeros(1, numParameters);
+    end
+end
+if strcmp(inputs.toolName, "DesignOptimization")
+    if ~isfield(inputs, "maxParameter")
+        inputs.maxParameter = [];
+        inputs.minParameter = [];
+    end
+    for i = 1:length(inputs.userDefinedVariables)
+        inputs.maxParameter = [inputs.maxParameter ...
+            inputs.userDefinedVariables{i}.upper_bounds];
+        inputs.minParameter = [inputs.minParameter ...
+            inputs.userDefinedVariables{i}.lower_bounds];
+    end
+end
+if isfield(inputs, "torqueControllerCoordinateNames")
+    maxTorqueControls = [];
+    minTorqueControls = [];
+    for i = 1:length(inputs.torqueControllerCoordinateNames)
+        indx = find(strcmp(convertCharsToStrings( ...
+            inputs.inverseDynamicsMomentLabels), ...
+            strcat(inputs.torqueControllerCoordinateNames(i), '_moment')));
+        if isempty(indx)
+            indx = find(strcmp(convertCharsToStrings( ...
+                inputs.inverseDynamicsMomentLabels), ...
+                strcat(inputs.torqueControllerCoordinateNames(i), '_force')));
+        end
+        maxTorqueControls(i) = max(inputs.experimentalJointMoments(:, ...
+            indx)) + inputs.maxTorqueControlsMultiple * ...
+            range(inputs.experimentalJointMoments(:, indx));
+        minTorqueControls(i) = min(inputs.experimentalJointMoments(:, ...
+            indx)) - inputs.maxTorqueControlsMultiple * ...
+            range(inputs.experimentalJointMoments(:, indx));
+    end
+    inputs.maxControl = [inputs.maxControl maxTorqueControls];
+    inputs.minControl = [inputs.minControl minTorqueControls];
+end
+end
diff --git a/src/core/TreatmentOptimization/SetupBounds/getPathConstraintBounds.m b/src/TreatmentOptimization/SetupBounds/makePathConstraintBounds.m
similarity index 96%
rename from src/core/TreatmentOptimization/SetupBounds/getPathConstraintBounds.m
rename to src/TreatmentOptimization/SetupBounds/makePathConstraintBounds.m
index cda10fc8f..3a0d966b7 100644
--- a/src/core/TreatmentOptimization/SetupBounds/getPathConstraintBounds.m
+++ b/src/TreatmentOptimization/SetupBounds/makePathConstraintBounds.m
@@ -1,7 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function gathers the maximum and minimum bounds for all path
-% constraint terms. 
+% constraint terms.
 %
 % (struct) -> (struct)
 % Computes max and min path bounds
@@ -28,7 +28,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = getPathConstraintBounds(inputs)
+function inputs = makePathConstraintBounds(inputs)
 inputs.maxPath = [];
 inputs.minPath = [];
 for i = 1:length(inputs.path)
@@ -40,4 +40,4 @@
             constraintTerm.minError);
     end
 end
-end
\ No newline at end of file
+end
diff --git a/src/core/TreatmentOptimization/SetupBounds/getTerminalConstraintBounds.m b/src/TreatmentOptimization/SetupBounds/makeTerminalConstraintBounds.m
similarity index 97%
rename from src/core/TreatmentOptimization/SetupBounds/getTerminalConstraintBounds.m
rename to src/TreatmentOptimization/SetupBounds/makeTerminalConstraintBounds.m
index 4317d4fa3..cd4dad8c8 100644
--- a/src/core/TreatmentOptimization/SetupBounds/getTerminalConstraintBounds.m
+++ b/src/TreatmentOptimization/SetupBounds/makeTerminalConstraintBounds.m
@@ -1,7 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function gathers the maximum and minimum bounds for all terminal
-% constraint terms. 
+% constraint terms.
 %
 % (struct) -> (struct)
 % Computes max and min terminal bounds
@@ -28,7 +28,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = getTerminalConstraintBounds(inputs)
+function inputs = makeTerminalConstraintBounds(inputs)
 inputs.maxTerminal = [];
 inputs.minTerminal = [];
 for i = 1:length(inputs.terminal)
@@ -54,4 +54,4 @@
         end
     end
 end
-end
\ No newline at end of file
+end
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcExternalForcesPeriodicity.m b/src/TreatmentOptimization/TerminalTerms/calcExternalForcesPeriodicity.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcExternalForcesPeriodicity.m
rename to src/TreatmentOptimization/TerminalTerms/calcExternalForcesPeriodicity.m
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcExternalMomentsPeriodicity.m b/src/TreatmentOptimization/TerminalTerms/calcExternalMomentsPeriodicity.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcExternalMomentsPeriodicity.m
rename to src/TreatmentOptimization/TerminalTerms/calcExternalMomentsPeriodicity.m
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcFinalPointPosition.m b/src/TreatmentOptimization/TerminalTerms/calcFinalPointPosition.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcFinalPointPosition.m
rename to src/TreatmentOptimization/TerminalTerms/calcFinalPointPosition.m
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcFinalPointVelocity.m b/src/TreatmentOptimization/TerminalTerms/calcFinalPointVelocity.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcFinalPointVelocity.m
rename to src/TreatmentOptimization/TerminalTerms/calcFinalPointVelocity.m
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcFinalStatePosition.m b/src/TreatmentOptimization/TerminalTerms/calcFinalStatePosition.m
similarity index 91%
rename from src/core/TreatmentOptimization/TerminalTerms/calcFinalStatePosition.m
rename to src/TreatmentOptimization/TerminalTerms/calcFinalStatePosition.m
index d212e50d9..78be6acdb 100644
--- a/src/core/TreatmentOptimization/TerminalTerms/calcFinalStatePosition.m
+++ b/src/TreatmentOptimization/TerminalTerms/calcFinalStatePosition.m
@@ -32,5 +32,10 @@
     statePositions, coordinateNames, constraintTerm)
 indx = find(strcmp(convertCharsToStrings(coordinateNames), ...
     constraintTerm.coordinate));
+if isempty(indx)
+    throw(MException('ConstraintTermError:CoordinateNotInState', ...
+        strcat("Coordinate ", constraintTerm.coordinate, " is not in the ", ...
+        "<states_coordinate_list>")))
+end
 finalStatePosition = statePositions(end, indx) - constraintTerm.target_error;
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcFinalStateVelocity.m b/src/TreatmentOptimization/TerminalTerms/calcFinalStateVelocity.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcFinalStateVelocity.m
rename to src/TreatmentOptimization/TerminalTerms/calcFinalStateVelocity.m
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingTrailingLimbAngleIntegrand.m b/src/TreatmentOptimization/TerminalTerms/calcInitialStatePosition.m
similarity index 70%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingTrailingLimbAngleIntegrand.m
rename to src/TreatmentOptimization/TerminalTerms/calcInitialStatePosition.m
index f4c7ac140..41efc4048 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingTrailingLimbAngleIntegrand.m
+++ b/src/TreatmentOptimization/TerminalTerms/calcInitialStatePosition.m
@@ -1,9 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function maximizes the trailing limb for the specified foot. 
-%
-% (struct, struct, struct, struct) -> (Array of number)
+% This function calculates the difference between the initial state 
+% position and current state position for the specified coordinate. 
 %
+% (2D matrix, Cell, struct) -> (Number)
+% 
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -27,17 +28,15 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMaximizingTrailingLimbAngleIntegrand(values, ...
-    modeledValues, params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        normalForce = ...
-            modeledValues.groundReactionsLab.forces{i}(:, 2) - 20;
-    end
+function initialStatePosition = calcInitialStatePosition( ...
+    statePositions, coordinateNames, auxdata, constraintTerm)
+indx = find(strcmp(convertCharsToStrings(coordinateNames), ...
+    constraintTerm.coordinate));
+if isempty(indx)
+    throw(MException('ConstraintTermError:CoordinateNotInState', ...
+        strcat("Coordinate ", constraintTerm.coordinate, " is not in the ", ...
+        "<states_coordinate_list>")))
 end
-trailingLimbAngle = calcTrailingLimb(costTerm, values, ...
-    normalForce, params);
-cost = calcMaximizingCostArrayTerm(trailingLimbAngle * ...
-    ones(length(values.time), 1));
+initialStatePosition = statePositions(1, indx) - ...
+    auxdata.initialStatePositions(1, indx);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcRootSegmentResidualsPeriodicity.m b/src/TreatmentOptimization/TerminalTerms/calcRootSegmentResidualsPeriodicity.m
similarity index 87%
rename from src/core/TreatmentOptimization/TerminalTerms/calcRootSegmentResidualsPeriodicity.m
rename to src/TreatmentOptimization/TerminalTerms/calcRootSegmentResidualsPeriodicity.m
index 27dbc3d4e..6eb2140ae 100644
--- a/src/core/TreatmentOptimization/TerminalTerms/calcRootSegmentResidualsPeriodicity.m
+++ b/src/TreatmentOptimization/TerminalTerms/calcRootSegmentResidualsPeriodicity.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the difference between the starting and final
-% inverse dynamic moment for the specified coordinate. 
+% inverse dynamic moment for the specified coordinate.
 %
 % (2D matrix, Cell, Array of string) -> (Number)
-% 
+%
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -29,8 +29,8 @@
 % ----------------------------------------------------------------------- %
 
 function rootSegmentResidualsPeriodicity = calcRootSegmentResidualsPeriodicity( ...
-    inverseDynamicMoments, inverseDynamicMomentLabels, loadNames)
-indx = find(strcmp(convertCharsToStrings(inverseDynamicMomentLabels), ...
+    inverseDynamicsMoments, inverseDynamicsMomentLabels, loadNames)
+indx = find(strcmp(convertCharsToStrings(inverseDynamicsMomentLabels), ...
     loadNames));
-rootSegmentResidualsPeriodicity = diff(inverseDynamicMoments(:, indx));
-end
\ No newline at end of file
+rootSegmentResidualsPeriodicity = diff(inverseDynamicsMoments(:, indx));
+end
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcStatePositionPeriodicity.m b/src/TreatmentOptimization/TerminalTerms/calcStatePositionPeriodicity.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcStatePositionPeriodicity.m
rename to src/TreatmentOptimization/TerminalTerms/calcStatePositionPeriodicity.m
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcStateVelocityPeriodicity.m b/src/TreatmentOptimization/TerminalTerms/calcStateVelocityPeriodicity.m
similarity index 100%
rename from src/core/TreatmentOptimization/TerminalTerms/calcStateVelocityPeriodicity.m
rename to src/TreatmentOptimization/TerminalTerms/calcStateVelocityPeriodicity.m
diff --git a/src/core/TreatmentOptimization/TerminalTerms/calcSynergyWeightsSum.m b/src/TreatmentOptimization/TerminalTerms/calcSynergyWeightsSum.m
similarity index 74%
rename from src/core/TreatmentOptimization/TerminalTerms/calcSynergyWeightsSum.m
rename to src/TreatmentOptimization/TerminalTerms/calcSynergyWeightsSum.m
index ffba690bc..780da5f39 100644
--- a/src/core/TreatmentOptimization/TerminalTerms/calcSynergyWeightsSum.m
+++ b/src/TreatmentOptimization/TerminalTerms/calcSynergyWeightsSum.m
@@ -13,7 +13,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -30,22 +30,17 @@
 function synergyWeightsSum = calcSynergyWeightsSum(synergyWeights, ...
     synergyGroups, synergyGroupName)
 
-numSynergiesIndex(1) = 0;
-numMusclesIndex(1) = 0;
+counter = 1;
 for i = 1 : length(synergyGroups)
-    temp = find(strcmp(convertCharsToStrings(synergyGroups{i}.muscleGroupName), ...
-        synergyGroupName));
-    if ~isempty(temp)
-        indx = i;
+    if strcmp(synergyGroups{i}.muscleGroupName, synergyGroupName)
+        break;
     end
+    counter = counter + synergyGroups{i}.numSynergies;
 end
-for j = 1 : indx
-    numSynergiesIndex(end+1) = numSynergiesIndex(end) + ...
-        synergyGroups{j}.numSynergies;
-    numMusclesIndex(end+1) = numMusclesIndex(end) + ...
-        size(synergyGroups{j}.muscleNames, 2);
+
+numSynergies = synergyGroups{i}.numSynergies;
+synergyWeightsSum = zeros(numSynergies, 1);
+for j = counter : counter + numSynergies - 1
+    synergyWeightsSum(j - counter + 1) = sum(synergyWeights(j, :));
 end
-synergyWeightsSum = sum(synergyWeights(1 + numSynergiesIndex(end-1): ...
-    numSynergiesIndex(end), 1 + numMusclesIndex(end-1) : ...
-    numMusclesIndex(end)), 2)';
 end
\ No newline at end of file
diff --git a/src/TrackingOptimization/TrackingOptimizationTool.m b/src/TreatmentOptimization/TrackingOptimization/TrackingOptimizationTool.m
similarity index 90%
rename from src/TrackingOptimization/TrackingOptimizationTool.m
rename to src/TreatmentOptimization/TrackingOptimization/TrackingOptimizationTool.m
index 885dcd756..862ab3c89 100644
--- a/src/TrackingOptimization/TrackingOptimizationTool.m
+++ b/src/TreatmentOptimization/TrackingOptimization/TrackingOptimizationTool.m
@@ -15,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -33,7 +33,8 @@ function TrackingOptimizationTool(settingsFileName)
 settingsTree = xml2struct(settingsFileName);
 verifyVersion(settingsTree, "TrackingOptimizationTool");
 [inputs, params] = parseTrackingOptimizationSettingsTree(settingsTree);
-[outputs, inputs] = TrackingOptimization(inputs, params);
-reportTreatmentOptimizationResults(outputs, inputs);
+%inputs = normalizeSynergyData(inputs);
+inputs = makeTreatmentOptimizationInputs(inputs, params);
+[inputs, outputs] = solveOptimalControlProblem(inputs, params);
 saveTrackingOptimizationResults(outputs, inputs);
 end
diff --git a/src/TrackingOptimization/calcFootGroundReactions.m b/src/TreatmentOptimization/TrackingOptimization/calcFootGroundReactions.m
similarity index 100%
rename from src/TrackingOptimization/calcFootGroundReactions.m
rename to src/TreatmentOptimization/TrackingOptimization/calcFootGroundReactions.m
diff --git a/src/TrackingOptimization/calcSynergyBasedModeledValues.m b/src/TreatmentOptimization/TrackingOptimization/calcSynergyBasedModeledValues.m
similarity index 67%
rename from src/TrackingOptimization/calcSynergyBasedModeledValues.m
rename to src/TreatmentOptimization/TrackingOptimization/calcSynergyBasedModeledValues.m
index d5b33778e..c77095150 100644
--- a/src/TrackingOptimization/calcSynergyBasedModeledValues.m
+++ b/src/TreatmentOptimization/TrackingOptimization/calcSynergyBasedModeledValues.m
@@ -18,7 +18,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -32,39 +32,44 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function modeledValues = calcSynergyBasedModeledValues(values, params, ...
-    modeledValues)
-if strcmp(params.controllerType, 'synergy_driven')
-    [jointAngles, jointVelocities] = getMuscleActuatedDOFs(values, params);
-    [params.muscleTendonLength, params.momentArms, ...
-        params.muscleTendonVelocity] = calcSurrogateModel(params, ...
+function modeledValues = calcSynergyBasedModeledValues(values, inputs)
+if strcmp(inputs.controllerType, 'synergy')
+    [jointAngles, jointVelocities] = getMuscleActuatedDOFs(values, inputs);
+    [inputs.muscleTendonLength, inputs.momentArms, ...
+        inputs.muscleTendonVelocity] = calcSurrogateModel(inputs, ...
         jointAngles, jointVelocities);
+    inputs.muscleTendonLength = permute(inputs.muscleTendonLength, [3 2 1]);
+    inputs.muscleTendonVelocity = permute(inputs.muscleTendonVelocity, [3 2 1]);
+    inputs.momentArms = permute(inputs.momentArms, [4 2 3 1]);
     [modeledValues.normalizedFiberLength, modeledValues.normalizedFiberVelocity] = ...
-        calcNormalizedMuscleFiberLengthsAndVelocities(params, ...
-        ones(1, params.numMuscles), ones(1, params.numMuscles));
+        calcNormalizedMuscleFiberLengthsAndVelocities(inputs, ...
+        ones(1, inputs.numMuscles), ones(1, inputs.numMuscles));
     modeledValues.muscleActivations = calcMuscleActivationFromSynergies(values);
-    muscleJointMoments = calcMuscleJointMoments(params, ...
+    muscleJointMoments = calcMuscleJointMoments(inputs, ...
         modeledValues.muscleActivations, modeledValues.normalizedFiberLength, ...
         modeledValues.normalizedFiberVelocity);
-    modeledValues.muscleJointMoments = muscleJointMoments(:, ...
-        params.surrogateModelIndex);
+    modeledValues.muscleJointMoments = permute(muscleJointMoments, [3 2 1]);
     modeledValues.muscleJointMoments = modeledValues.muscleJointMoments(:, ...
-        params.dofsActuatedIndex);
+        inputs.surrogateModelIndex);
+    modeledValues.muscleActivations = permute(modeledValues.muscleActivations, [3 2 1]);
+else
+    modeledValues.muscleActivations = [];
 end
 end
 
 function muscleActivations = calcMuscleActivationFromSynergies(values)
 muscleActivations = values.controlSynergyActivations * values.synergyWeights;
+muscleActivations = permute(muscleActivations, [3 2 1]);
 end
 
-function [jointAngles, jointVelocities] = getMuscleActuatedDOFs(values, params)
-for i = 1:params.numMuscles
+function [jointAngles, jointVelocities] = getMuscleActuatedDOFs(values, inputs)
+for i = 1 : inputs.numMuscles
     counter = 1;
-    for j = 1:length(params.coordinateNames)
-        for k = 1:length(params.surrogateModelLabels{i})
-            if strcmp(params.coordinateNames(j), params.surrogateModelLabels{i}{k})
-                jointAngles{i}(:,counter) = values.statePositions(:,j);
-                jointVelocities{i}(:,counter) = values.stateVelocities(:,j);
+    for j = 1:length(inputs.coordinateNames)
+        for k = 1:length(inputs.surrogateModelLabels{i})
+            if strcmp(inputs.coordinateNames(j), inputs.surrogateModelLabels{i}{k})
+                jointAngles{i}(:, counter) = values.positions(:, j);
+                jointVelocities{i}(:, counter) = values.velocities(:, j);
                 counter = counter + 1;
             end
         end
diff --git a/src/TreatmentOptimization/TrackingOptimization/calcTorqueBasedModeledValues.m b/src/TreatmentOptimization/TrackingOptimization/calcTorqueBasedModeledValues.m
new file mode 100644
index 000000000..32faa975c
--- /dev/null
+++ b/src/TreatmentOptimization/TrackingOptimization/calcTorqueBasedModeledValues.m
@@ -0,0 +1,155 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function calculates the position and velocities of the spring
+% locations and corresponding ground reaction forces and moments if
+% contact surfaces are present. This function also calculates inverse
+% dynamic moments.
+%
+% (struct, struct) -> (struct)
+% returns body locations, ground reactions, and inverse dynamic moments
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function modeledValues = calcTorqueBasedModeledValues(values, inputs, ...
+    modeledValues)
+[appliedLoads, modeledValues] = setupAppliedLoads(values, inputs, ...
+    modeledValues);
+modeledValues.markerPositions = calcTrackedMarkerPositions(values, inputs);
+[modeledValues.inverseDynamicsMoments, modeledValues.angularMomentum, ....
+    modeledValues.metabolicCost, massCenterPositons] = ...
+    inverseDynamics(values.time, ...
+    values.positions, values.velocities, ...
+    values.accelerations, inputs.coordinateNames, appliedLoads, ...
+    inputs.mexModel, modeledValues.muscleActivations, ...
+    sum(valueOrAlternate(inputs, 'calculateAngularMomentum', false)), ...
+    sum(valueOrAlternate(inputs, 'calculateMetabolicCost', false)));
+modeledValues.massCenterVelocity = (massCenterPositons(2) - ...
+    massCenterPositons(1)) / values.time(end);
+end
+
+function [appliedLoads, modeledValues] = setupAppliedLoads(values, ...
+    inputs, modeledValues)
+appliedLoads = [];
+numCoordinateLoads = inputs.model.getForceSet().getSize() - ...
+    inputs.model.getForceSet().getMuscles().getSize() - ...
+    (12 * length(inputs.contactSurfaces));
+coordinateLoads = zeros(length(values.time), numCoordinateLoads);
+appliedLoads = [zeros(length(values.time), ...
+    inputs.model.getForceSet().getMuscles().getSize()) ...
+    coordinateLoads];
+if ~isempty(inputs.contactSurfaces)
+    clear pointKinematics
+    [springPositions, springVelocities] = getSpringLocations( ...
+        values.time, values.positions, values.velocities, inputs);
+    modeledValues.bodyLocations = getBodyLocations(values.time, ....
+        values.positions, values.velocities, inputs);
+    groundReactions = calcFootGroundReactions(springPositions, ...
+        springVelocities, inputs, modeledValues.bodyLocations);
+    % modeledValues.bodyLocations.child = modeledValues.bodyLocations.parent;
+    groundReactionsBody = tranferGroundReactionMoments( ...
+        modeledValues.bodyLocations, groundReactions, inputs);
+    modeledValues.groundReactionsLab = calcGroundReactionsLab(groundReactions);
+    appliedLoads = [appliedLoads groundReactionsBody];
+end
+end
+
+function [springPositions, springVelocities] = getSpringLocations(time, ....
+    positions, velocities, inputs)
+
+for i = 1:length(inputs.contactSurfaces)
+    [springPositions.parent{i}, springVelocities.parent{i}] = ...
+        pointKinematics(time, positions, velocities, ...
+        inputs.contactSurfaces{i}.parentSpringPointsOnBody, ...
+        inputs.contactSurfaces{i}.parentBody * ones(1, ...
+        size(inputs.contactSurfaces{i}.parentSpringPointsOnBody, 1)), ...
+        inputs.mexModel, inputs.coordinateNames);
+    [springPositions.child{i}, springVelocities.child{i}] = ...
+        pointKinematics(time, positions, velocities, ...
+        inputs.contactSurfaces{i}.childSpringPointsOnBody, ...
+        inputs.contactSurfaces{i}.childBody * ones(1, ...
+        size(inputs.contactSurfaces{i}.childSpringPointsOnBody, 1)), ...
+        inputs.mexModel, inputs.coordinateNames);
+end
+end
+
+function bodyLocations = getBodyLocations(time, positions, ...
+    velocities, inputs)
+
+for i = 1:length(inputs.contactSurfaces)
+    bodyLocations.midfootSuperior{i} = pointKinematics(time, ...
+        positions, velocities, ...
+        inputs.contactSurfaces{i}.midfootSuperiorPointOnBody, ...
+        inputs.contactSurfaces{i}.midfootSuperiorBody, ...
+        inputs.mexModel, inputs.coordinateNames);
+    bodyLocations.midfootSuperior{i}(:, 2) = ...
+        inputs.contactSurfaces{i}.restingSpringLength;
+    bodyLocations.parent{i} = pointKinematics(time, positions, ...
+        velocities, [0 0 0], inputs.contactSurfaces{i}.parentBody, ...
+        inputs.mexModel, inputs.coordinateNames);
+    bodyLocations.child{i} = pointKinematics(time, positions, ...
+        velocities, [0 0 0], inputs.contactSurfaces{i}.childBody, ...
+        inputs.mexModel, inputs.coordinateNames);
+end
+end
+
+function groundReactionsBody = tranferGroundReactionMoments( ...
+    bodyLocations, groundReactions, params)
+
+groundReactionsBody = [];
+for i = 1:length(params.contactSurfaces)
+    parentMoment = transferMoments(bodyLocations.midfootSuperior{i}, ...
+        bodyLocations.parent{i}, groundReactions.parentMoments{i}, ...
+        groundReactions.parentForces{i});
+    childMoment = transferMoments(bodyLocations.midfootSuperior{i}, ...
+        bodyLocations.child{i}, groundReactions.childMoments{i}, ...
+        groundReactions.childForces{i});
+    % parentMoment = parentMoment + childMoment;
+    % childMoment(:) = 0;
+    groundReactionsBody = [groundReactionsBody, ...
+        groundReactions.parentForces{i}, groundReactions.childForces{i}, ...
+        ... zeros(size(groundReactions.childForces{i})) ...
+        parentMoment, childMoment];
+end
+end
+
+function groundReactionsInLab = calcGroundReactionsLab(groundReactions)
+
+for i = 1:length(groundReactions.parentForces)
+    groundReactionsInLab.forces{i} = ...
+        groundReactions.parentForces{i} + groundReactions.childForces{i};
+    groundReactionsInLab.moments{i} = ...
+        groundReactions.parentMoments{i} + groundReactions.childMoments{i};
+end
+end
+
+function markerPositions = calcTrackedMarkerPositions(values, inputs)
+markerPositions = [];
+if isfield(inputs, 'trackedMarkerNames') ...
+        && ~isempty(inputs.trackedMarkerNames)
+    clear pointKinematics
+    markerPositions = pointKinematics(values.time, values.positions, ...
+        values.velocities, inputs.trackedMarkerLocations, ...
+        inputs.trackedMarkerBodyIndices, inputs.mexModel, ...
+        inputs.coordinateNames);
+end
+end
diff --git a/src/TrackingOptimization/TrackingOptimization.m b/src/TreatmentOptimization/TrackingOptimization/parseTrackingOptimizationSettingsTree.m
similarity index 78%
rename from src/TrackingOptimization/TrackingOptimization.m
rename to src/TreatmentOptimization/TrackingOptimization/parseTrackingOptimizationSettingsTree.m
index 3521a8da6..71fb268f8 100644
--- a/src/TrackingOptimization/TrackingOptimization.m
+++ b/src/TreatmentOptimization/TrackingOptimization/parseTrackingOptimizationSettingsTree.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function sets up the input variables and mex files (or parallel 
-% matlab function) for the main function of tracking optimization.
+% This function parses the settings tree resulting from xml2struct of the
+% Tracking Optimizatoin settings XML file.
 %
-% (struct, struct) -> (struct, struct)
-% Inputs for the main function are setup
+% (struct) -> (struct, struct)
+% returns the input values for Tracking Optimization
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -28,8 +28,9 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function [output, inputs] = TrackingOptimization(inputs, params)
-inputs = makeTreatmentOptimizationInputs(inputs, params);
-initializeMexOrMatlabParallelFunctions(inputs.mexModel);
-output = computeTrackingOptimizationMainFunction(inputs, params);
+function [inputs, params] = ...
+    parseTrackingOptimizationSettingsTree(settingsTree)
+inputs = parseTreatmentOptimizationInputs(settingsTree);
+params = parseTreatmentOptimizationParams(settingsTree);
 end
+
diff --git a/src/TrackingOptimization/saveTrackingOptimizationResults.m b/src/TreatmentOptimization/TrackingOptimization/saveTrackingOptimizationResults.m
similarity index 76%
rename from src/TrackingOptimization/saveTrackingOptimizationResults.m
rename to src/TreatmentOptimization/TrackingOptimization/saveTrackingOptimizationResults.m
index 5850ee81c..b64192e6b 100644
--- a/src/TrackingOptimization/saveTrackingOptimizationResults.m
+++ b/src/TreatmentOptimization/TrackingOptimization/saveTrackingOptimizationResults.m
@@ -29,14 +29,6 @@
 % ----------------------------------------------------------------------- %
 
 function saveTrackingOptimizationResults(solution, inputs)
-values = getTrackingOptimizationValueStruct(solution.solution.phase, inputs);
-saveCommonOptimalControlResults(solution, inputs, values);
-if strcmp(inputs.controllerType, 'synergy_driven')
-    writeToSto(inputs.muscleLabels, linspace(1, inputs.numSynergies, ...
-        inputs.numSynergies), [values.synergyWeights], ...
-        fullfile(inputs.resultsDirectory, "parameterSolution.sto"));
-    writeToSto(inputs.muscleLabels, values.time, ...
-        solution.muscleActivations, ...
-        fullfile(inputs.resultsDirectory, "optimal", "muscleActivations.sto"));
+values = makeGpopsValuesAsStruct(solution.solution.phase, inputs);
+saveTreatmentOptimizationResults(solution, inputs, values);
 end
-end
\ No newline at end of file
diff --git a/src/VerificationOptimization/VerificationOptimizationTool.m b/src/TreatmentOptimization/VerificationOptimization/VerificationOptimizationTool.m
similarity index 90%
rename from src/VerificationOptimization/VerificationOptimizationTool.m
rename to src/TreatmentOptimization/VerificationOptimization/VerificationOptimizationTool.m
index 55fe31f62..c43e67280 100644
--- a/src/VerificationOptimization/VerificationOptimizationTool.m
+++ b/src/TreatmentOptimization/VerificationOptimization/VerificationOptimizationTool.m
@@ -33,7 +33,10 @@ function VerificationOptimizationTool(settingsFileName)
 settingsTree = xml2struct(settingsFileName);
 verifyVersion(settingsTree, "VerificationOptimizationTool");
 [inputs, params] = parseVerificationOptimizationSettingsTree(settingsTree);
-[outputs, inputs] = VerificationOptimization(inputs, params);
-reportTreatmentOptimizationResults(outputs, inputs);
+inputs = normalizeSynergyData(inputs);
+inputs = setupMuscleSynergies(inputs);
+inputs = setupTorqueControls(inputs);
+inputs = makeTreatmentOptimizationInputs(inputs, params);
+[inputs, outputs] = solveOptimalControlProblem(inputs, params);
 saveVerificationOptimizationResults(outputs, inputs);
 end
diff --git a/src/VerificationOptimization/getVerificationOptimizationValueStruct.m b/src/TreatmentOptimization/VerificationOptimization/parseVerificationOptimizationSettingsTree.m
similarity index 70%
rename from src/VerificationOptimization/getVerificationOptimizationValueStruct.m
rename to src/TreatmentOptimization/VerificationOptimization/parseVerificationOptimizationSettingsTree.m
index f3709571a..82dad5a83 100644
--- a/src/VerificationOptimization/getVerificationOptimizationValueStruct.m
+++ b/src/TreatmentOptimization/VerificationOptimization/parseVerificationOptimizationSettingsTree.m
@@ -1,11 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function parses and scales the design variables specific to
-% Verification Optimization. If the model is synergy driven, synergy 
-% weights are properly calculated and fixed.
+% This function parses the settings tree resulting from xml2struct of the
+% Verification Optimizatoin settings XML file.
 %
-% (struct, struct) -> (struct)
-% Design variables specific to Verification Optimization are parsed and scaled
+% (struct) -> (struct, struct)
+% returns the input values for Verification Optimization
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -29,10 +28,15 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function values = getVerificationOptimizationValueStruct(inputs, params)
-values = getTreatmentOptimizationValueStruct(inputs, params);
-if strcmp(params.controllerType, 'synergy_driven')
-    values.synergyWeights = getSynergyWeightsFromGroups(...
-        params.synergyWeightsGuess, params);
+function [inputs, params] = ...
+    parseVerificationOptimizationSettingsTree(settingsTree)
+inputs = parseTreatmentOptimizationInputs(settingsTree);
+if isfield(inputs, "optimizeSynergyVectors") && ...
+        inputs.optimizeSynergyVectors
+    throw(MException('VerificationOptimizationTool:parseVerificationOptimizationSettingsTree', ...
+        'Verification Optimization does not support synergy vector optimization.'));
 end
+params = parseTreatmentOptimizationParams(settingsTree);
 end
+
+
diff --git a/src/VerificationOptimization/saveVerificationOptimizationResults.m b/src/TreatmentOptimization/VerificationOptimization/saveVerificationOptimizationResults.m
similarity index 94%
rename from src/VerificationOptimization/saveVerificationOptimizationResults.m
rename to src/TreatmentOptimization/VerificationOptimization/saveVerificationOptimizationResults.m
index eb8daf0be..147a911ca 100644
--- a/src/VerificationOptimization/saveVerificationOptimizationResults.m
+++ b/src/TreatmentOptimization/VerificationOptimization/saveVerificationOptimizationResults.m
@@ -28,7 +28,7 @@
 % ----------------------------------------------------------------------- %
 
 function saveVerificationOptimizationResults(solution, inputs)
-values = getVerificationOptimizationValueStruct( ...
+values = makeGpopsValuesAsStruct( ...
     solution.solution.phase, inputs);
-saveCommonOptimalControlResults(solution, inputs, values)
+saveTreatmentOptimizationResults(solution, inputs, values)
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/addContactSurfaceActuators.m b/src/TreatmentOptimization/addContactSurfaceActuators.m
similarity index 72%
rename from src/core/TreatmentOptimization/addContactSurfaceActuators.m
rename to src/TreatmentOptimization/addContactSurfaceActuators.m
index fab90bec1..17b9df83e 100644
--- a/src/core/TreatmentOptimization/addContactSurfaceActuators.m
+++ b/src/TreatmentOptimization/addContactSurfaceActuators.m
@@ -32,18 +32,18 @@
 function model = addContactSurfaceActuators(inputs, model)
 import org.opensim.modeling.Vec3
 for i = 1:length(inputs.contactSurfaces)
-addPointActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(1, 0, 0));
-addPointActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 1, 0));
-addPointActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 0, 1));
-addPointActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(1, 0, 0));
-addPointActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 1, 0));
-addPointActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 0, 1));
-addTorqueActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(1, 0, 0));
-addTorqueActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 1, 0));
-addTorqueActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 0, 1));
-addTorqueActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(1, 0, 0));
-addTorqueActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 1, 0));
-addTorqueActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 0, 1));
+    addPointActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(1, 0, 0));
+    addPointActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 1, 0));
+    addPointActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 0, 1));
+    addPointActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(1, 0, 0));
+    addPointActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 1, 0));
+    addPointActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 0, 1));
+    addTorqueActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(1, 0, 0));
+    addTorqueActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 1, 0));
+    addTorqueActuator(model, string(inputs.contactSurfaces{i}.parentBodyName), Vec3(0, 0, 1));
+    addTorqueActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(1, 0, 0));
+    addTorqueActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 1, 0));
+    addTorqueActuator(model, string(inputs.contactSurfaces{i}.childBodyName), Vec3(0, 0, 1));
 end
 end
 function addPointActuator(model, bodyName, direction)
diff --git a/src/VerificationOptimization/calcVerificationOptimizationDynamicsConstraint.m b/src/TreatmentOptimization/calcDynamicConstraint.m
similarity index 86%
rename from src/VerificationOptimization/calcVerificationOptimizationDynamicsConstraint.m
rename to src/TreatmentOptimization/calcDynamicConstraint.m
index 6427cf5f5..f7bcf164b 100644
--- a/src/VerificationOptimization/calcVerificationOptimizationDynamicsConstraint.m
+++ b/src/TreatmentOptimization/calcDynamicConstraint.m
@@ -1,6 +1,6 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the dynamic constraint for verification
+% This function calculates the dynamic constraint for treatment
 % optimization.
 %
 % (struct, struct) -> (2D matrix)
@@ -28,10 +28,9 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function dynamics = calcVerificationOptimizationDynamicsConstraint(values, ...
+function dynamics = calcDynamicConstraint(values, ...
     params)
 
 dynamics = (params.maxTime - params.minTime) * ...
-    ([values.stateVelocities values.stateAccelerations ...
-    values.controlJerks]) ./ (params.maxState - params.minState);
-end
\ No newline at end of file
+    ([values.stateVelocities values.controlAccelerations]) ./ (params.maxState - params.minState);
+end
diff --git a/src/core/TreatmentOptimization/calcTreatmentOptimizationCost.m b/src/TreatmentOptimization/calcTreatmentOptimizationCost.m
similarity index 94%
rename from src/core/TreatmentOptimization/calcTreatmentOptimizationCost.m
rename to src/TreatmentOptimization/calcTreatmentOptimizationCost.m
index 6463a0b56..00d291069 100644
--- a/src/core/TreatmentOptimization/calcTreatmentOptimizationCost.m
+++ b/src/TreatmentOptimization/calcTreatmentOptimizationCost.m
@@ -40,9 +40,9 @@
             cost = cat(2, ...
                 cost,  ...
                 fn(values, modeledValues, auxdata, costTerm));
-%         else
-%             throw(MException('', ['Cost term type ' costTerm.type ...
-%                 ' does not exist for this tool.']))
+%          else
+%              throw(MException('', ['Cost term type ' costTerm.type ...
+%                  ' does not exist for this tool.']))
         end
     end
 end
diff --git a/src/core/TreatmentOptimization/checkInitialGuess.m b/src/TreatmentOptimization/checkInitialGuess.m
similarity index 82%
rename from src/core/TreatmentOptimization/checkInitialGuess.m
rename to src/TreatmentOptimization/checkInitialGuess.m
index 89b714ab1..a2c2c18f8 100644
--- a/src/core/TreatmentOptimization/checkInitialGuess.m
+++ b/src/TreatmentOptimization/checkInitialGuess.m
@@ -30,12 +30,20 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function checkInitialGuess(guess, inputs, continuousFunction)
+function inputs = checkInitialGuess(guess, inputs, continuousFunction)
 initialGuess = guess;
 initialGuess.auxdata = inputs;
+values = makeGpopsValuesAsStruct(guess.phase, inputs);
+inputs.initialStatePositions = values.statePositions;
 if isfield(initialGuess,'parameter')
     initialGuess.phase.parameter = initialGuess.parameter;
 end
 output = continuousFunction(initialGuess);
 output.solution = initialGuess;
-end
\ No newline at end of file
+if length(output.metabolicCost) == length(inputs.experimentalTime)
+cumulativeMetabolicCost = trapz(inputs.experimentalTime, ...
+    output.metabolicCost);
+inputs.initialMetabolicCost = cumulativeMetabolicCost;
+inputs.initialMassCenterVelocity = output.massCenterVelocity;
+end
+end
diff --git a/src/core/TreatmentOptimization/disableModelMuscles.m b/src/TreatmentOptimization/disableModelMuscles.m
similarity index 83%
rename from src/core/TreatmentOptimization/disableModelMuscles.m
rename to src/TreatmentOptimization/disableModelMuscles.m
index df39b7064..a03de3844 100644
--- a/src/core/TreatmentOptimization/disableModelMuscles.m
+++ b/src/TreatmentOptimization/disableModelMuscles.m
@@ -27,11 +27,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function [model, inputs] = disableModelMuscles(inputs, model)
-import org.opensim.modeling.Model
-inputs.numTotalMuscles = model.getForceSet().getMuscles().getSize();
-for i = 0:model.getForceSet().getMuscles().getSize()-1
-    if model.getForceSet().getMuscles().get(i).get_appliesForce()
-        model.getForceSet().getMuscles().get(i).set_appliesForce(0);
+function model = disableModelMuscles(model)
+    for i = 0:model.getForceSet().getMuscles().getSize()-1
+        if model.getForceSet().getMuscles().get(i).get_appliesForce()
+            model.getForceSet().getMuscles().get(i).set_appliesForce(0);
+        end
     end
 end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/generateConstraintTermStruct.m b/src/TreatmentOptimization/generateConstraintTermStruct.m
new file mode 100644
index 000000000..056ba228b
--- /dev/null
+++ b/src/TreatmentOptimization/generateConstraintTermStruct.m
@@ -0,0 +1,295 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function returns all of the constraint term calculation methods
+% Tools use this function for the discrete and continuous constraint
+% calculations.
+%
+% inputs:
+% constraintTermType - one of ["path", "terminal"]
+% controllerType - one of ["torque", "synergy"]
+% toolName - one of ["TrackingOptimization", "TreatmentOptimization", ...
+%   "DesignOptimization"]
+%
+% (string, string) -> (struct of function handles, Array of string)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function [constraintTermCalculations, allowedTypes] = ...
+    generateConstraintTermStruct(constraintTermType, controllerType, ...
+    toolName)
+allowedTypes = getAllowedTypes(constraintTermType, controllerType, ...
+    toolName);
+constraintTermCalculations = ...
+    getConstraintTermCalculations();
+end
+
+function allowedTypes = getAllowedTypes(constraintTermType, ...
+    controllerType, toolName)
+allowedTypes = [];
+if strcmp(controllerType, "torque")
+    switch toolName
+        case "TrackingOptimization"
+            if strcmp(constraintTermType, "path")
+                allowedTypes = [ ...
+                    "root_segment_residual_load", ...
+                    "torque_model_moment_consistency", ...
+                    "kinetic_consistency", ...
+                    ];
+            end
+            if strcmp(constraintTermType, "terminal")
+                allowedTypes = [ ...
+                    "state_position_periodicity", ...
+                    "state_velocity_periodicity", ...
+                    "root_segment_residual_load_periodicity", ...
+                    "external_force_periodicity", ...
+                    "external_moment_periodicity", ...
+                    ];
+            end
+        case "VerificationOptimization"
+            if strcmp(constraintTermType, "path")
+                allowedTypes = [ ...
+                    "root_segment_residual_load", ...
+                    "torque_model_moment_consistency", ...
+                    "kinetic_consistency", ...
+                    ];
+            end
+            if strcmp(constraintTermType, "terminal")
+                allowedTypes = [ ...
+                    "state_position_periodicity", ...
+                    "state_velocity_periodicity", ...
+                    "root_segment_residual_load_periodicity", ...
+                    "external_force_periodicity", ...
+                    "external_moment_periodicity", ...
+                    ];
+            end
+        case "DesignOptimization"
+            if strcmp(constraintTermType, "path")
+                allowedTypes = [ ...
+                    "root_segment_residual_load", ...
+                    "torque_model_moment_consistency", ...
+                    "kinetic_consistency", ...
+                    "limit_normalized_fiber_length", ...
+                    ];
+            end
+            if strcmp(constraintTermType, "terminal")
+                allowedTypes = [ ...
+                    "state_position_periodicity", ...
+                    "state_velocity_periodicity", ...
+                    "root_segment_residual_load_periodicity", ...
+                    "external_force_periodicity", ...
+                    "external_moment_periodicity", ...
+                    "initial_state_position_tracking", ...
+                    "final_state_position", ...
+                    "final_state_velocity", ...
+                    "final_point_position", ...
+                    "final_point_velocity", ...
+                    ];
+            end
+    end
+end
+if strcmp(controllerType, "synergy")
+    switch toolName
+        case "TrackingOptimization"
+            if strcmp(constraintTermType, "path")
+                allowedTypes = [ ...
+                    "root_segment_residual_load", ...
+                    "muscle_model_moment_consistency", ...
+                    "kinetic_consistency", ...
+                    ];
+            end
+            if strcmp(constraintTermType, "terminal")
+                allowedTypes = [ ...
+                    "state_position_periodicity", ...
+                    "state_velocity_periodicity", ...
+                    "root_segment_residual_load_periodicity", ...
+                    "external_force_periodicity", ...
+                    "external_moment_periodicity", ...
+                    "synergy_weight_sum", ...
+                    ];
+            end
+        case "VerificationOptimization"
+            if strcmp(constraintTermType, "path")
+                allowedTypes = [ ...
+                    "root_segment_residual_load", ...
+                    "muscle_model_moment_consistency", ...
+                    "kinetic_consistency", ...
+                    ];
+            end
+            if strcmp(constraintTermType, "terminal")
+                allowedTypes = [ ...
+                    "state_position_periodicity", ...
+                    "state_velocity_periodicity", ...
+                    "root_segment_residual_load_periodicity", ...
+                    "external_force_periodicity", ...
+                    "external_moment_periodicity", ...
+                    ];
+            end
+        case "DesignOptimization"
+            if strcmp(constraintTermType, "path")
+                allowedTypes = [ ...
+                    "root_segment_residual_load", ...
+                    "muscle_model_moment_consistency", ...
+                    "kinetic_consistency", ...
+                    "limit_muscle_activation", ...
+                    "limit_normalized_fiber_length", ...
+                    "external_control_muscle_moment_consistency", ...
+                    ];
+            end
+            if strcmp(constraintTermType, "terminal")
+                allowedTypes = [ ...
+                    "state_position_periodicity", ...
+                    "state_velocity_periodicity", ...
+                    "root_segment_residual_load_periodicity", ...
+                    "external_force_periodicity", ...
+                    "external_moment_periodicity", ...
+                    "synergy_weight_sum", ...
+                    "initial_state_position_tracking", ...
+                    "final_state_position", ...
+                    "final_state_velocity", ...
+                    "final_point_position", ...
+                    "final_point_velocity", ...
+                    ];
+            end
+    end
+end
+end
+
+function constraintTermCalculations = getConstraintTermCalculations()
+
+constraintTermCalculations.root_segment_residual_load = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcRootSegmentResidualsPathConstraints( ...
+    constraintTerm.load, ...
+    auxdata.inverseDynamicsMomentLabels, ...
+    modeledValues.inverseDynamicsMoments ...
+    );
+
+constraintTermCalculations.muscle_model_moment_consistency = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcMuscleActuatedMomentsPathConstraints( ...
+    auxdata, ...
+    modeledValues, ...
+    constraintTerm.load ...
+    );
+
+constraintTermCalculations.torque_model_moment_consistency = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcTorqueActuatedMomentsPathConstraints( ...
+    auxdata, ...
+    modeledValues, ...
+    values.torqueControls, ...
+    constraintTerm.load ...
+    );
+
+constraintTermCalculations.kinetic_consistency = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcKineticPathConstraint( ...
+    auxdata, ...
+    modeledValues, ...
+    values.torqueControls, ...
+    constraintTerm.load ...
+    );
+
+constraintTermCalculations.limit_muscle_activation = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcMuscleActivationsPathConstraint( ...
+    auxdata, ...
+    modeledValues, ...
+    constraintTerm.muscle);
+
+constraintTermCalculations.limit_normalized_fiber_length = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcNormalizedFiberLengthPathConstraint( ...
+    auxdata, ...
+    modeledValues, ...
+    constraintTerm.muscle ...
+    );
+
+constraintTermCalculations.external_control_muscle_moment_consistency = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcMuscleActuatedMomentsWithExternalAidPathConstraints( ...
+    auxdata, ...
+    modeledValues, ...
+    values.externalTorqueControls, ...
+    contraintTerm.coordinate ...
+    );
+
+constraintTermCalculations.state_position_periodicity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcStatePositionPeriodicity( ...
+    values.statePositions, ...
+    auxdata.statesCoordinateNames, ...
+    constraintTerm.coordinate ...
+    );
+
+constraintTermCalculations.state_velocity_periodicity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcStateVelocityPeriodicity( ...
+    values.stateVelocities, ...
+    auxdata.statesCoordinateNames, ...
+    constraintTerm.coordinate ...
+    );
+
+constraintTermCalculations.root_segment_residual_load_periodicity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcRootSegmentResidualsPeriodicity(...
+    modeledValues.inverseDynamicsMoments, ...
+    auxdata.inverseDynamicsMomentLabels, ...
+    constraintTerm.load);
+
+constraintTermCalculations.external_force_periodicity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcExternalForcesPeriodicity(...
+    modeledValues.groundReactionsLab.forces, ...
+    auxdata.contactSurfaces, ...
+    constraintTerm.force);
+
+constraintTermCalculations.external_moment_periodicity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcExternalMomentsPeriodicity(...
+    modeledValues.groundReactionsLab.moments, ...
+    auxdata.contactSurfaces, ...
+    constraintTerm.moment);
+
+constraintTermCalculations.initial_state_position_tracking = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcInitialStatePosition( ...
+    values.statePositions, ...
+    auxdata.statesCoordinateNames, ...
+    auxdata, ...
+    constraintTerm);
+
+constraintTermCalculations.final_state_position = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcFinalStatePosition( ...
+    values.statePositions, ...
+    auxdata.statesCoordinateNames, ...
+    constraintTerm);
+
+constraintTermCalculations.final_state_velocity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcFinalStateVelocity(values.stateVelocities, ...
+    auxdata.coordinateNames, ...
+    constraintTerm);
+
+constraintTermCalculations.final_point_position = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcFinalPointPosition(auxdata, values, ...
+    constraintTerm);
+
+constraintTermCalculations.final_point_velocity = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcFinalPointVelocity(auxdata, values, ...
+    constraintTerm);
+
+constraintTermCalculations.synergy_weight_sum = @(values, modeledValues, auxdata, constraintTerm) ...
+    calcSynergyWeightsSum(...
+    values.synergyWeights, ...
+    auxdata.synergyGroups, ...
+    constraintTerm.synergy_group);
+
+end
diff --git a/src/core/TreatmentOptimization/generateCostTermStruct.m b/src/TreatmentOptimization/generateCostTermStruct.m
similarity index 61%
rename from src/core/TreatmentOptimization/generateCostTermStruct.m
rename to src/TreatmentOptimization/generateCostTermStruct.m
index 8e00962c7..0c40de2c8 100644
--- a/src/core/TreatmentOptimization/generateCostTermStruct.m
+++ b/src/TreatmentOptimization/generateCostTermStruct.m
@@ -45,45 +45,43 @@
     switch toolName
         case "TrackingOptimization"
             allowedTypes = [ ...
-                "coordinate_tracking", ...
+                "generalized_coordinate_tracking", ...
+                "generalized_speed_tracking", ...
+                "marker_position_tracking", ...
                 "inverse_dynamics_load_tracking", ...
+                "inverse_dynamics_load_minimization", ...
+                "inverse_dynamics_slope_tracking", ...
+                "kinetic_inconsistency_minimization", ...
                 "external_force_tracking", ...
                 "external_moment_tracking", ...
                 "muscle_activation_tracking", ...
-                "joint_jerk_minimization", ...
                 ];
         case "VerificationOptimization"
             allowedTypes = [ ...
-                "coordinate_tracking", ...
+                "generalized_coordinate_tracking", ...
+                "generalized_speed_tracking", ...
+                "marker_position_tracking", ...
                 "controller_tracking", ...
-                "joint_jerk_minimization", ...
             ];
         case "DesignOptimization"
             allowedTypes = [ ...
-                "coordinate_tracking", ...
+                "generalized_coordinate_tracking", ...
+                "generalized_speed_tracking", ...
+                "marker_position_tracking", ...
+                "inverse_dynamics_load_tracking", ...
+                "inverse_dynamics_slope_tracking", ...
+                "external_force_tracking", ...
+                "external_moment_tracking", ...
+                "muscle_activation_tracking", ...
                 "controller_tracking", ...
-                "joint_jerk_minimization", ...
-                "metabolic_cost_minimization" ...
-                "propulsive_force_maximization" ...
-                "propulsive_force_minimization" ...
-                "breaking_force_maximization" ...
-                "breaking_force_minimization" ...
-                "step_length_maximization" ... 
-                "step_length_asymmetry_minimization" ...
-                "single_support_time_maximization" ...
-                "single_support_time_goal" ...
-                "step_time_asymmetry_minimization" ...
                 "joint_power_minimization" ...
-                "trailing_limb_angle_minimization" ...
-                "trailing_limb_angle_maximization" ...
+                "joint_energy_generation_goal" ...
+                "joint_energy_absorption_goal" ...
+                "propulsive_impulse_goal" ...
+                "braking_impulse_goal" ...
                 "muscle_activation_minimization" ...
-                "muscle_activation_maximization" ...
-                "center_mass_velocity_x_minimization" ...
-                "center_mass_velocity_y_minimization" ...
-                "center_mass_velocity_z_minimization" ...
-                "kinematic_symmetry" ...
-                "walking_speed_goal" ...
                 "external_torque_control_minimization" ...
+                "angular_momentum_minimization" ...
                 "user_defined", ...
                 ];
         otherwise
@@ -103,10 +101,13 @@
             allowedTypes = [ ...
                 "synergy_vector_tracking" ...
                 "belt_speed_goal" ...
+                "relative_walking_speed_goal" ...
+                "relative_metabolic_cost_per_time" ...
+                "relative_metabolic_cost_per_distance" ...
                 "user_defined" ...
                 ];
         otherwise
-            throw(MException('', ['Tool name' toolName 'is not valid']))
+            throw(MException('', ['Tool name ' toolName ' is not valid']))
     end
 else
     throw(MException('', ['Cost term type ' costTermType ...
@@ -116,45 +117,71 @@
 
 function costTermCalculations = getCostTermCalculations(costTermType)
 
-costTermCalculations.coordinate_tracking = @(values, modeledValues, auxdata, costTerm) ...
+costTermCalculations.generalized_coordinate_tracking = @(values, modeledValues, auxdata, costTerm) ...
     calcTrackingCoordinateIntegrand( ...
+    costTerm, ...
+    auxdata, ...
+    values.time, ...
+    values.positions, ...
+    costTerm.coordinate ...
+    );
+
+costTermCalculations.generalized_speed_tracking = @(values, modeledValues, auxdata, costTerm) ...
+    calcTrackingSpeedIntegrand( ...
+    costTerm, ...
     auxdata, ...
     values.time, ...
-    values.statePositions, ...
+    values.velocities, ...
     costTerm.coordinate ...
     );
 
+costTermCalculations.marker_position_tracking = @(values, modeledValues, auxdata, costTerm) ...
+    calcTrackingMarkerPosition( ...
+    costTerm, ...
+    values.time, ...
+    modeledValues.markerPositions, ...
+    auxdata ...
+    );
+
 costTermCalculations.controller_tracking = @(values, modeledValues, auxdata, costTerm) ...
     calcTrackingControllerIntegrand( ...
+    costTerm, ...
     auxdata, ...
     values, ...
     values.time, ...
     costTerm.controller ...
     );
 
-costTermCalculations.joint_jerk_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingJointJerkIntegrand( ...
-    values.controlJerks, ...
+costTermCalculations.inverse_dynamics_load_tracking = @(values, modeledValues, auxdata, costTerm) ...
+    calcTrackingInverseDynamicLoadsIntegrand( ...
+    costTerm, ...
     auxdata, ...
-    costTerm.coordinate ...
+    values.time, ...
+    modeledValues.inverseDynamicsMoments, ...
+    costTerm.load ...
     );
 
-costTermCalculations.metabolic_cost_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingMetabolicCost( ...
-    values, ...
-    modeledValues, ...
-    auxdata);
+costTermCalculations.inverse_dynamics_load_minimization = @(values, modeledValues, auxdata, costTerm) ...
+    calcMinimizingInverseDynamicLoadsIntegrand( ...
+    costTerm, ...
+    auxdata, ...
+    values.time, ...
+    modeledValues.inverseDynamicsMoments, ...
+    costTerm.load ...
+    );
 
-costTermCalculations.inverse_dynamics_load_tracking = @(values, modeledValues, auxdata, costTerm) ...
-    calcTrackingInverseDynamicLoadsIntegrand( ...
+costTermCalculations.inverse_dynamics_slope_tracking = @(values, modeledValues, auxdata, costTerm) ...
+    calcTrackingInverseDynamicSlopeIntegrand( ...
+    costTerm, ...
     auxdata, ...
     values.time, ...
-    modeledValues.inverseDynamicMoments, ...
+    modeledValues.inverseDynamicsMoments, ...
     costTerm.load ...
     );
 
 costTermCalculations.external_force_tracking = @(values, modeledValues, auxdata, costTerm) ...
     calcTrackingExternalForcesIntegrand( ...
+    costTerm, ...
     auxdata, ...
     modeledValues.groundReactionsLab.forces, ...
     values.time, ...
@@ -162,6 +189,7 @@
 
 costTermCalculations.external_moment_tracking = @(values, modeledValues, auxdata, costTerm) ...
     calcTrackingExternalMomentsIntegrand( ...
+    costTerm, ...
     auxdata, ...
     modeledValues.groundReactionsLab.moments, ...
     values.time, ...
@@ -169,143 +197,95 @@
 
 costTermCalculations.muscle_activation_tracking = @(values, modeledValues, auxdata, costTerm) ...
     calcTrackingMuscleActivationIntegrand( ...
+    costTerm, ...
     modeledValues.muscleActivations, ...
     values.time, ...
     auxdata, ...
     costTerm.muscle);
 
-costTermCalculations.propulsive_force_maximization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMaximizingPropulsiveForceIntegrand( ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-costTermCalculations.propulsive_force_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingPropulsiveForceIntegrand( ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-costTermCalculations.breaking_force_maximization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMaximizingBreakingForceIntegrand( ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-costTermCalculations.breaking_force_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingBreakingForceIntegrand( ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-costTermCalculations.step_length_maximization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMaximizingStepLengthIntegrand( ...
-    values, ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-costTermCalculations.step_length_asymmetry_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcStepLengthAsymmetryIntegrand( ...
-    values, ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-costTermCalculations.single_support_time_maximization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMaximizingSingleSupportTimeIntegrand( ...
-    values, ...
-    modeledValues, ...
-    auxdata, ...
-    costTerm);
-
-
-costTermCalculations.single_support_time_goal = @(values, modeledValues, auxdata, costTerm) ...
-    calcGoalSingleSupportTimeIntegrand( ...
-    values, ...
-    modeledValues, ...
+costTermCalculations.joint_power_minimization = @(values, modeledValues, auxdata, costTerm) ...
+    calcMinimizingJointPowerIntegrand( ...
+    costTerm, ...
+    values.velocities, ...
+    values.time, ...
+    modeledValues.inverseDynamicsMoments, ...
     auxdata, ...
-    costTerm);
+    costTerm.load ...
+    );
 
-costTermCalculations.step_time_asymmetry_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcStepTimeAsymmetryIntegrand( ...
-    values, ...
-    modeledValues, ...
+costTermCalculations.joint_energy_generation_goal = @(values, modeledValues, auxdata, costTerm) ...
+    calcJointEnergyGenerationGoalIntegrand( ...
+    costTerm, ...
+    values.velocities, ...
+    values.time, ...
+    modeledValues.inverseDynamicsMoments, ...
     auxdata, ...
-    costTerm);
+    costTerm.load ...
+    );
 
-costTermCalculations.joint_power_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingJointPowerIntegrand( ...
-    values.stateVelocities, ...
-    modeledValues.inverseDynamicMoments, ...
+costTermCalculations.joint_energy_absorption_goal = @(values, modeledValues, auxdata, costTerm) ...
+    calcJointEnergyAbsorptionGoalIntegrand( ...
+    costTerm, ...
+    values.velocities, ...
+    values.time, ...
+    modeledValues.inverseDynamicsMoments, ...
     auxdata, ...
     costTerm.load ...
     );
 
-costTermCalculations.trailing_limb_angle_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingTrailingLimbAngleIntegrand( ...
-    values, ...
+costTermCalculations.propulsive_impulse_goal = @(values, modeledValues, auxdata, costTerm) ...
+    calcJointEnergyAbsorptionGoalIntegrand( ...
     modeledValues, ...
+    values.time, ...
     auxdata, ...
     costTerm ...
     );
 
-costTermCalculations.trailing_limb_angle_maximization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMaximizingTrailingLimbAngleIntegrand( ...
-    values, ...
+costTermCalculations.braking_impulse_goal = @(values, modeledValues, auxdata, costTerm) ...
+    calcJointEnergyAbsorptionGoalIntegrand( ...
     modeledValues, ...
+    values.time, ...
     auxdata, ...
     costTerm ...
     );
 
 costTermCalculations.muscle_activation_minimization = @(values, modeledValues, auxdata, costTerm) ...
     calcMinimizingMuscleActivationIntegrand( ...
+    costTerm, ...
+    values.time, ...
     modeledValues.muscleActivations, ...
     auxdata, ...
     costTerm.muscle ...
     );
 
-costTermCalculations.muscle_activation_maximization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMaximizingMuscleActivationIntegrand( ...
-    modeledValues.muscleActivations, ...
+costTermCalculations.external_torque_control_minimization = @(values, modeledValues, auxdata, costTerm) ...
+    calcMinimizingExternalTorqueControl( ...
+    costTerm, ...
+    values.externalTorqueControls, ...
+    values.time, ...
     auxdata, ...
-    costTerm.muscle ...
-    );
-
-costTermCalculations.center_mass_velocity_x_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingMassCenterVelocityXIntegrand( ...
-    values, ...
-    auxdata);
+    costTerm.coordinate);
 
-costTermCalculations.center_mass_velocity_y_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingMassCenterVelocityYIntegrand( ...
-    values, ...
-    auxdata);
+costTermCalculations.angular_momentum_minimization = @(values, modeledValues, auxdata, costTerm) ...
+    calcMinimizingAngularMomentumIntegrand( ...
+    modeledValues, ...
+    values.time, ...
+    costTerm);
 
-costTermCalculations.center_mass_velocity_z_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingMassCenterVelocityZIntegrand( ...
+costTermCalculations.relative_metabolic_cost_per_time = @(values, modeledValues, auxdata, costTerm) ...
+    calcRelativeMetabolicCostPerTimeGoalDiscrete( ...
+    modeledValues, ...
     values, ...
-    auxdata);
-
-costTermCalculations.kinematic_symmetry = @(values, modeledValues, auxdata, costTerm) ...
-    calcKinematicSymmetryIntegrand( ...
-    values.statePositions, ...
     auxdata, ...
     costTerm);
 
-costTermCalculations.walking_speed_goal = @(values, modeledValues, auxdata, costTerm) ...
-    calcGoalWalkingSpeedIntegrand( ...
-    values, ...
+costTermCalculations.relative_metabolic_cost_per_distance = @(values, modeledValues, auxdata, costTerm) ...
+    calcRelativeMetabolicCostPerDistanceGoalDiscrete( ...
     modeledValues, ...
+    values, ...
     auxdata, ...
     costTerm);
 
-costTermCalculations.external_torque_control_minimization = @(values, modeledValues, auxdata, costTerm) ...
-    calcMinimizingExternalTorqueControl( ...
-    values.externalTorqueControls, ...
-    auxdata, ...
-    costTerm.coordinate);
-    
 costTermCalculations.synergy_vector_tracking = @(values, modeledValues, auxdata, costTerm) ...
     calcTrackingSynergyVectorsDiscrete( ...
     values.synergyWeights, ...
@@ -318,6 +298,13 @@
     auxdata, ...
     costTerm);
 
+costTermCalculations.relative_walking_speed_goal = @(values, modeledValues, auxdata, costTerm) ...
+    calcGoalRelativeWalkingSpeedDiscrete( ...
+    values, ...
+    modeledValues, ...
+    auxdata, ...
+    costTerm);
+
 costTermCalculations.user_defined = @(values, modeledValues, auxdata, costTerm) ...
     userDefinedFunction(values, ...
     modeledValues, ...
diff --git a/src/core/TreatmentOptimization/getCorrectStates.m b/src/TreatmentOptimization/getCorrectStates.m
similarity index 100%
rename from src/core/TreatmentOptimization/getCorrectStates.m
rename to src/TreatmentOptimization/getCorrectStates.m
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingSingleSupportTimeIntegrand.m b/src/TreatmentOptimization/gpops/calcGpopsConstraint.m
similarity index 63%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingSingleSupportTimeIntegrand.m
rename to src/TreatmentOptimization/gpops/calcGpopsConstraint.m
index 9d8089cff..217ba5a34 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingSingleSupportTimeIntegrand.m
+++ b/src/TreatmentOptimization/gpops/calcGpopsConstraint.m
@@ -1,8 +1,8 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function maximizes the single support time for the specified foot.
+% This function computes path constraints (if any) for a gpops2 problem
 %
-% (struct, struct, struct, struct) -> (Array of number)
+% (struct) -> (struct)
 %
 
 % ----------------------------------------------------------------------- %
@@ -13,7 +13,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,22 +27,24 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMaximizingSingleSupportTimeIntegrand(values, ...
-    modeledValues, params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        if i == 1
-            singleSupportTime = calcSingleSupportTime( ...
-                modeledValues.groundReactionsLab.forces{i + 1}(:, 2), ...
-                values.time);
+function constraint = calcGpopsConstraint(constraints, ...
+    constraintTermCalculations, allowedTypes, values, modeledValues, ...
+    inputs)
+constraint = [];
+for i = 1:length(constraints)
+    constraintTerm = constraints{i};
+    if constraintTerm.isEnabled
+        if isfield(constraintTermCalculations, constraintTerm.type) && ...
+                any(ismember(allowedTypes, constraintTerm.type))
+            fn = constraintTermCalculations.(constraintTerm.type);
+            constraint = cat(2, constraint, ...
+                fn(values, modeledValues, inputs, constraintTerm));
         else
-            singleSupportTime = calcSingleSupportTime( ...
-                modeledValues.groundReactionsLab.forces{i - 1}(:, 2), ...
-                values.time);
+%             throw(MException('ConstraintTerms:IllegalTerm', ...
+%                 strcat("Constraint term ",  constraintTerm.type, ...
+%                 " is not allowed for this tool")))
         end
     end
 end
-cost = calcMaximizingCostArrayTerm(singleSupportTime * ...
-    ones(length(values.time), 1));
-end
\ No newline at end of file
+end
+
diff --git a/src/TrackingOptimization/calcTrackingOptimizationIntegrand.m b/src/TreatmentOptimization/gpops/calcGpopsIntegrand.m
similarity index 83%
rename from src/TrackingOptimization/calcTrackingOptimizationIntegrand.m
rename to src/TreatmentOptimization/gpops/calcGpopsIntegrand.m
index a25d721c4..6798d4bf1 100644
--- a/src/TrackingOptimization/calcTrackingOptimizationIntegrand.m
+++ b/src/TreatmentOptimization/gpops/calcGpopsIntegrand.m
@@ -1,6 +1,6 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the integrand for tracking optimization.
+% This function calculates the integrand for gpops.
 %
 % (struct, struct, struct) -> (2D matrix)
 % Returns scaled integrand
@@ -27,12 +27,12 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function integrand = calcTrackingOptimizationIntegrand(values, ...
-    modeledValues, auxdata)
+function integrand = calcGpopsIntegrand(values, modeledValues, inputs)
 [costTermCalculations, allowedTypes] = ...
-    generateCostTermStruct("continuous", "TrackingOptimization");
+    generateCostTermStruct("continuous", inputs.toolName);
 integrand = calcTreatmentOptimizationCost( ...
-    costTermCalculations, allowedTypes, values, modeledValues, auxdata);
-integrand = integrand ./ (auxdata.maxIntegral - auxdata.minIntegral);
+    costTermCalculations, allowedTypes, values, modeledValues, inputs);
+integrand = integrand ./ inputs.continuousMaxAllowableError;
 integrand = integrand .^ 2;
-end
\ No newline at end of file
+end
+
diff --git a/src/TrackingOptimization/computeTrackingOptimizationContinuousFunction.m b/src/TreatmentOptimization/gpops/computeGpopsContinuousFunction.m
similarity index 54%
rename from src/TrackingOptimization/computeTrackingOptimizationContinuousFunction.m
rename to src/TreatmentOptimization/gpops/computeGpopsContinuousFunction.m
index b6bd7c732..cf13f25a8 100644
--- a/src/TrackingOptimization/computeTrackingOptimizationContinuousFunction.m
+++ b/src/TreatmentOptimization/gpops/computeGpopsContinuousFunction.m
@@ -1,8 +1,8 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function computes the dynamic constraints, path constraints (if any)
-% and cost function terms (if any) for tracking optimization.
-% 
+% and cost function terms (if any) for gpops2.
+%
 % (struct) -> (struct)
 %
 
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,14 +28,30 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function modeledValues = computeTrackingOptimizationContinuousFunction(inputs)
-values = getTrackingOptimizationValueStruct(inputs.phase, inputs.auxdata);
-modeledValues = calcTorqueBasedModeledValues(values, inputs.auxdata);
-modeledValues = calcSynergyBasedModeledValues(values, inputs.auxdata, modeledValues);
-modeledValues.dynamics = calcTrackingOptimizationDynamicsConstraint(values, inputs.auxdata);
-path = calcTrackingOptimizationPathConstraint(values, modeledValues, inputs.auxdata);
-if ~isempty(path)
-    modeledValues.path = path;
+function modeledValues = computeGpopsContinuousFunction(setup)
+values = makeGpopsValuesAsStruct(setup.phase, setup.auxdata);
+if strcmp(setup.auxdata.toolName, "DesignOptimization")
+    setup = updateSystemFromUserDefinedFunctions(setup, values);
+end
+modeledValues = calcSynergyBasedModeledValues(values, setup.auxdata);
+modeledValues = calcTorqueBasedModeledValues(values, setup.auxdata, ...
+    modeledValues);
+modeledValues.dynamics = calcDynamicConstraint(values, setup.auxdata);
+if any(cellfun(@(x) x.isEnabled == 1, setup.auxdata.path))
+    [constraintTermCalculations, allowedTypes] = ...
+        generateConstraintTermStruct("path", ...
+        setup.auxdata.controllerType, setup.auxdata.toolName);
+    modeledValues.path = calcGpopsConstraint( ...
+        setup.auxdata.path, constraintTermCalculations, allowedTypes, ...
+        values, modeledValues, setup.auxdata);
+    modeledValues.path = scaleToBounds( ...
+        modeledValues.path, setup.auxdata.maxPath, setup.auxdata.minPath);
+end
+modeledValues.integrand = calcGpopsIntegrand(values, modeledValues, setup.auxdata);
+if valueOrAlternate(setup.auxdata, 'calculateMetabolicCost', false)
+    modeledValues.integrand(:, end+1) = modeledValues.metabolicCost;
+end
+if isempty(modeledValues.integrand)
+    modeledValues = rmfield(modeledValues, "integrand");
+end
 end
-modeledValues.integrand = calcTrackingOptimizationIntegrand(values, modeledValues, inputs.auxdata);
-end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/gpops/computeGpopsEndpointFunction.m b/src/TreatmentOptimization/gpops/computeGpopsEndpointFunction.m
new file mode 100644
index 000000000..745676e3a
--- /dev/null
+++ b/src/TreatmentOptimization/gpops/computeGpopsEndpointFunction.m
@@ -0,0 +1,90 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function computes the terminal constraint (if any), and total cost
+% function objective for gpops treatment optimization.
+%
+% (struct) -> (struct)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function output = computeGpopsEndpointFunction(setup)
+if any(cellfun(@(x) x.isEnabled == 1, setup.auxdata.terminal)) || strcmp(setup.auxdata.toolName, "DesignOptimization")
+    setup.phase.state = [setup.phase.initialstate; setup.phase.finalstate];
+    setup.phase.time = [setup.phase.initialtime; setup.phase.finaltime];
+    setup.phase.control = ones(size(setup.phase.time,1),length(setup.auxdata.minControl));
+    if isfield(setup, "parameter")
+        setup.phase.parameter = setup.parameter;
+    end
+    values = makeGpopsValuesAsStruct(setup.phase, setup.auxdata);
+    if strcmp(setup.auxdata.toolName, "DesignOptimization")
+        setup = updateSystemFromUserDefinedFunctions(setup, values);
+    end
+    modeledValues = calcSynergyBasedModeledValues(values, setup.auxdata);
+    modeledValues = calcTorqueBasedModeledValues(values, setup.auxdata, ...
+        modeledValues);
+    if valueOrAlternate(setup.auxdata, 'calculateMetabolicCost', false)
+        modeledValues.metabolicCost = setup.phase.integral(end);
+    end
+    if valueOrAlternate(setup.auxdata, 'calculateRelativeSpeed', false)
+        
+    end
+end
+
+if any(cellfun(@(x) x.isEnabled == 1, setup.auxdata.terminal))
+    [constraintTermCalculations, allowedTypes] = ...
+        generateConstraintTermStruct("terminal", ...
+        setup.auxdata.controllerType, setup.auxdata.toolName);
+    event = ...
+        calcGpopsConstraint(setup.auxdata.terminal, ...
+        constraintTermCalculations, allowedTypes, values, ...
+        modeledValues, setup.auxdata);
+    if ~isempty(event)
+        output.eventgroup.event = event;
+    end
+end
+
+if strcmp(setup.auxdata.toolName, "DesignOptimization")
+    [costTermCalculations, allowedTypes] = ...
+        generateCostTermStruct("discrete", "DesignOptimization");
+    discrete = calcTreatmentOptimizationCost( ...
+        costTermCalculations, allowedTypes, values, modeledValues, setup.auxdata);
+    discreteObjective = sum(discrete) / length(discrete);
+    if isnan(discreteObjective); discreteObjective = 0; end
+else
+    discreteObjective = 0;
+end
+
+if isfield(setup.phase, "integral") && ~any(isnan(setup.phase.integral)) && ~isempty(setup.phase.integral)
+    if valueOrAlternate(setup.auxdata, 'calculateMetabolicCost', false)
+        integral = setup.phase.integral(1:end-1);
+    else
+        integral = setup.phase.integral;
+    end
+    continuousObjective = sum(integral) / length(integral);
+else
+    continuousObjective = 0;
+end
+
+output.objective = continuousObjective + discreteObjective;
+end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingBreakingForceIntegrand.m b/src/TreatmentOptimization/gpops/convertFromGpopsOutputs.m
similarity index 72%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingBreakingForceIntegrand.m
rename to src/TreatmentOptimization/gpops/convertFromGpopsOutputs.m
index 561829a9c..6886b6356 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingBreakingForceIntegrand.m
+++ b/src/TreatmentOptimization/gpops/convertFromGpopsOutputs.m
@@ -1,8 +1,5 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function maximizes the breaking force for the specified foot. 
-%
-% (struct, struct, struct) -> (Array of number)
 %
 
 % ----------------------------------------------------------------------- %
@@ -13,7 +10,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,14 +24,21 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMaximizingBreakingForceIntegrand(modeledValues, ...
-    params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        breakingForce = getBreakingForce( ...
-            modeledValues.groundReactionsLab.forces{i}(:,1));
+function output = convertFromGpopsOutputs(solution, ...
+    inputs, params)
+solution = solution.result.solution;
+solution.auxdata = inputs;
+if isfield(inputs, "optimizeSynergyVectors") && ...
+        inputs.optimizeSynergyVectors
+    solution.phase.parameter = [solution.parameter];
+else
+    if strcmp(inputs.toolName, "DesignOptimization")
+        if isfield(solution, 'parameter')
+            solution.phase.parameter = [solution.parameter];
+        end
     end
 end
-cost = calcMaximizingCostArrayTerm(breakingForce);
-end
\ No newline at end of file
+output = computeGpopsContinuousFunction(solution);
+output.solution = solution;
+end
+
diff --git a/src/TreatmentOptimization/gpops/convertToGpopsInputs.m b/src/TreatmentOptimization/gpops/convertToGpopsInputs.m
new file mode 100644
index 000000000..4c747aa15
--- /dev/null
+++ b/src/TreatmentOptimization/gpops/convertToGpopsInputs.m
@@ -0,0 +1,43 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function [setup, inputs] = convertToGpopsInputs(inputs, params)
+bounds = setupTreatmentOptimizationBounds(inputs, params);
+guess = setupGpopsInitialGuess(inputs);
+setup = setupGpopsSettings(inputs, ...
+    bounds, guess, params, ...
+    @computeGpopsContinuousFunction, ...
+    @computeGpopsEndpointFunction);
+setup = preSplineGpopsInputs(setup);
+inputs = checkInitialGuess(guess, setup.auxdata, ...
+    @computeGpopsContinuousFunction);
+if valueOrAlternate(inputs, 'calculateMetabolicCost', false)
+setup.bounds.phase.integral.lower(end + 1) = 0;
+setup.bounds.phase.integral.upper(end + 1) = (inputs.gpops.integralBound + 1) * ... 
+    max(inputs.initialMetabolicCost);
+setup.guess.phase.integral(end) = inputs.initialMetabolicCost;
+end
+end
diff --git a/src/TreatmentOptimization/gpops/makeGpopsValuesAsStruct.m b/src/TreatmentOptimization/gpops/makeGpopsValuesAsStruct.m
new file mode 100644
index 000000000..e7c52f906
--- /dev/null
+++ b/src/TreatmentOptimization/gpops/makeGpopsValuesAsStruct.m
@@ -0,0 +1,156 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function takes the raw values from gpops and turns them into a
+% struct that can be interacted with more easily during calculations
+%
+% (struct, struct) -> (struct)
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function values = makeGpopsValuesAsStruct(phase, inputs)
+values.time = scaleToOriginal(phase.time, inputs.maxTime, ...
+    inputs.minTime);
+state = scaleToOriginal(phase.state, ones(size(phase.state, 1), 1) .* ...
+    inputs.maxState, ones(size(phase.state, 1), 1) .* inputs.minState);
+control = scaleToOriginal(phase.control, ones(size(phase.control, 1), 1) .* ...
+    inputs.maxControl, ones(size(phase.control, 1), 1) .* inputs.minControl);
+values.statePositions = getCorrectStates( ...
+    state, 1, length(inputs.statesCoordinateNames));
+values.stateVelocities = getCorrectStates( ...
+    state, 2, length(inputs.statesCoordinateNames));
+% values.stateAccelerations = getCorrectStates( ...
+%     state, 3, length(inputs.statesCoordinateNames));
+values.controlAccelerations = control(:, 1 : length(inputs.statesCoordinateNames));
+% [values.positions, values.velocities, values.accelerations] = recombineFullState(values, inputs);
+[values.positions, values.velocities] = recombineFullState(values, inputs);
+values.accelerations = recombineFullAccelerations(values, inputs);
+if strcmp(inputs.controllerType, 'synergy')
+    values.controlSynergyActivations = control(:, ...
+        length(inputs.statesCoordinateNames) + 1 : ...
+        length(inputs.statesCoordinateNames) + inputs.numSynergies);
+end
+values.torqueControls = control(:, ...
+    length(inputs.statesCoordinateNames) + 1 + inputs.numSynergies : ...
+    length(inputs.statesCoordinateNames) + inputs.numSynergies + ...
+    length(inputs.torqueControllerCoordinateNames));
+
+if strcmp(inputs.toolName, "TrackingOptimization")
+    if strcmp(inputs.controllerType, 'synergy')
+        values.synergyWeights = inputs.synergyWeights;
+        if inputs.optimizeSynergyVectors
+            parameters = scaleToOriginal(phase.parameter(1,:), ...
+                inputs.maxParameter, inputs.minParameter);
+            counter = 1;
+            for i = 1 : length(inputs.synergyGroups)
+                for j = 1 : length(inputs.synergyGroups{i}.muscleNames)
+                    index = find(ismember(inputs.synergyWeightsLabels, ...
+                        inputs.synergyGroups{i}.muscleNames{j}));
+                    values.synergyWeights(i, index) = ...
+                        parameters(counter);
+                    counter = counter + 1;
+                end
+            end
+        end
+    end
+end
+if strcmp(inputs.toolName, "VerificationOptimization")
+    if strcmp(inputs.controllerType, 'synergy')
+        values.synergyWeights = inputs.synergyWeights;
+    end
+end
+if strcmp(inputs.toolName, "DesignOptimization")
+    counter = 1;
+    if strcmp(inputs.controllerType, 'synergy')
+        values.synergyWeights = inputs.synergyWeights;
+        if inputs.optimizeSynergyVectors
+            parameters = scaleToOriginal(phase.parameter(1,:), ...
+                inputs.maxParameter, inputs.minParameter);
+            for i = 1 : length(inputs.synergyGroups)
+                for j = 1 : length(inputs.synergyGroups{i}.muscleNames)
+                    index = find(ismember(inputs.synergyWeightsLabels, ...
+                        inputs.synergyGroups{i}.muscleNames{j}));
+                    values.synergyWeights(i, index) = ...
+                        parameters(counter);
+                    counter = counter + 1;
+                end
+            end
+        end
+    end
+    if isfield(inputs, 'userDefinedVariables') && ...
+            ~isempty(inputs.userDefinedVariables)
+        parameters = scaleToOriginal(phase.parameter(1,:), ...
+            inputs.maxParameter, inputs.minParameter);
+        for i = 1:length(inputs.userDefinedVariables)
+            values.parameters.(inputs.userDefinedVariables{i}.type) ...
+                = parameters(counter : counter + ...
+                length(inputs.userDefinedVariables{i}.initial_values) - 1);
+            counter = counter + ...
+                length(inputs.userDefinedVariables{i}.initial_values);
+        end
+    end
+end
+end
+
+% function [positions, velocities, accelerations] = recombineFullState( ...
+%     values, inputs)
+function [positions, velocities] = recombineFullState( ...
+    values, inputs)
+if size(values.time) == size(inputs.collocationTimeOriginal)
+    positions = inputs.splinedJointAngles;
+    velocities = inputs.splinedJointSpeeds;
+    accelerations = inputs.splinedJointAccelerations;
+else
+    positions = evaluateGcvSplines(inputs.splineJointAngles, ...
+        inputs.coordinateNames, values.time);
+    velocities = evaluateGcvSplines(inputs.splineJointAngles, ...
+        inputs.coordinateNames, values.time, 1);
+    % accelerations = evaluateGcvSplines(inputs.splineJointAngles, ...
+    %     inputs.coordinateNames, values.time, 2);
+end
+for i = 1:length(inputs.coordinateNames)
+    index = find(ismember( ...
+        inputs.statesCoordinateNames, inputs.coordinateNames{i}));
+    if ~isempty(index)
+        positions(:, i) = values.statePositions(:, index);
+        velocities(:, i) = values.stateVelocities(:, index);
+        % accelerations(:, i) = values.stateAccelerations(:, index);
+    end
+end
+end
+
+function accelerations = recombineFullAccelerations(values, inputs)
+if size(values.time) == size(inputs.collocationTimeOriginal)
+    accelerations = inputs.splinedJointAccelerations;
+else
+    accelerations = evaluateGcvSplines(inputs.splineJointAngles, ...
+        inputs.coordinateNames, values.time, 2);
+end
+for i = 1:length(inputs.coordinateNames)
+    index = find(ismember( ...
+        inputs.statesCoordinateNames, inputs.coordinateNames{i}));
+    if ~isempty(index)
+        accelerations(:, i) = values.controlAccelerations(:, index);
+    end
+end
+end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/gpops/preSplineGpopsInputs.m b/src/TreatmentOptimization/gpops/preSplineGpopsInputs.m
new file mode 100644
index 000000000..06041359e
--- /dev/null
+++ b/src/TreatmentOptimization/gpops/preSplineGpopsInputs.m
@@ -0,0 +1,126 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+%
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function splinedSetup = preSplineGpopsInputs(setup)
+tempSetup = makeMinimalSetup(setup);
+collocationPointTimes = findCollocationPointsForSetup(tempSetup);
+splinedSetup = applyPreSpline(setup, collocationPointTimes);
+end
+
+function collocationPointTimes = findCollocationPointsForSetup(tempSetup)
+output = gpops2(tempSetup);
+collocationPointTimes = output.result.solution.phase.timeRadau;
+end
+
+function setup = applyPreSpline(setup, collocationPointTimes)
+setup.auxdata.collocationTimeBound = collocationPointTimes;
+time = scaleToOriginal(collocationPointTimes, setup.auxdata.maxTime, ...
+    setup.auxdata.minTime);
+setup.auxdata.collocationTimeOriginal = time;
+
+setup.auxdata.splinedJointAngles = evaluateGcvSplines(setup.auxdata.splineJointAngles, ...
+    setup.auxdata.coordinateNames, time, 0);
+setup.auxdata.splinedJointSpeeds = evaluateGcvSplines(setup.auxdata.splineJointAngles, ...
+    setup.auxdata.coordinateNames, time, 1);
+setup.auxdata.splinedJointAccelerations = evaluateGcvSplines(setup.auxdata.splineJointAngles, ...
+    setup.auxdata.coordinateNames, time, 2);
+setup.auxdata.splinedJointMoments = evaluateGcvSplines(setup.auxdata.splineJointMoments, ...
+    setup.auxdata.inverseDynamicsMomentLabels, time, 0);
+if strcmp(setup.auxdata.controllerType, 'synergy') && ...
+        isfield(setup.auxdata, 'splineSynergyActivations')
+    setup.auxdata.splinedSynergyActivations = evaluateGcvSplines( ...
+        setup.auxdata.splineSynergyActivations, ...
+        setup.auxdata.synergyLabels, time, 0);
+end
+if strcmp(setup.auxdata.controllerType, 'synergy') && ...
+        isfield(setup.auxdata, 'splineMuscleActivations')
+    setup.auxdata.splinedMuscleActivations = evaluateGcvSplines( ...
+        setup.auxdata.splineMuscleActivations, setup.auxdata.muscleLabels, time, 0);
+end
+if isfield(setup.auxdata, 'torqueControllerCoordinateNames') && ...
+        ~isempty(setup.auxdata.torqueControllerCoordinateNames)
+    if isfield(setup.auxdata, "splineTorqueControls")
+        setup.auxdata.splinedTorqueControls = evaluateGcvSplines( ...
+            setup.auxdata.splineTorqueControls, setup.auxdata.torqueLabels, time, 0);
+    end
+end
+if isfield(setup.auxdata, "splineMarkerPositions")
+    for i = 1:length(setup.auxdata.splineMarkerPositions)
+        setup.auxdata.splinedMarkerPositions{i} = evaluateGcvSplines( ...
+            setup.auxdata.splineMarkerPositions{i}, 0:2, time, 0);
+    end
+end
+for i = 1:length(setup.auxdata.contactSurfaces)
+    setup.auxdata.splinedGroundReactionForces{i} = evaluateGcvSplines( ...
+        setup.auxdata.splineExperimentalGroundReactionForces{i}, 0:2, time, 0);
+    setup.auxdata.splinedGroundReactionMoments{i} = evaluateGcvSplines( ...
+        setup.auxdata.splineExperimentalGroundReactionMoments{i}, 0:2, time, 0);
+end
+end
+
+function tempSetup = makeMinimalSetup(setup)
+tempSetup.name = 'Test';
+tempSetup.functions.continuous = @continuous;
+tempSetup.functions.endpoint = @endpoint;
+
+tempSetup.guess.phase.time = setup.guess.phase.time;
+
+tempSetup.guess.phase.state = zeros(size(tempSetup.guess.phase.time));
+tempSetup.guess.phase.control = zeros(size(tempSetup.guess.phase.time));
+tempSetup.guess.phase.integral = 0;
+
+tempSetup.bounds.phase.initialtime.lower = tempSetup.guess.phase.time(1);
+tempSetup.bounds.phase.initialtime.upper = tempSetup.guess.phase.time(1);
+tempSetup.bounds.phase.finaltime.lower = tempSetup.guess.phase.time(end);
+tempSetup.bounds.phase.finaltime.upper = tempSetup.guess.phase.time(end);
+tempSetup.bounds.phase.initialstate.lower = -1;
+tempSetup.bounds.phase.initialstate.upper = 1;
+tempSetup.bounds.phase.state.lower = -1;
+tempSetup.bounds.phase.state.upper = 1;
+tempSetup.bounds.phase.finalstate.lower = -1;
+tempSetup.bounds.phase.finalstate.upper = 1;
+tempSetup.bounds.phase.control.lower = -1;
+tempSetup.bounds.phase.control.upper = 1;
+tempSetup.bounds.phase.integral.lower = -1;
+tempSetup.bounds.phase.integral.upper = 1;
+tempSetup.derivatives.derivativelevel= 'first';
+tempSetup.nlp.ipoptoptions.maxiterations = 1;
+tempSetup.scales.method = 'none';
+
+tempSetup.mesh.phase.colpoints = setup.mesh.phase.colpoints;
+tempSetup.mesh.phase.fraction = setup.mesh.phase.fraction;
+tempSetup.mesh.maxiterations = 0;
+tempSetup.displaylevel = 0;
+end
+
+function output = continuous(input)
+output.dynamics = zeros(size(input.phase.time));
+output.integrand = zeros(size(input.phase.time));
+end
+
+function output = endpoint(input)
+output.objective = input.phase.integral;
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/getSplines.m b/src/TreatmentOptimization/makeExperimentalDataSplines.m
similarity index 77%
rename from src/core/TreatmentOptimization/getSplines.m
rename to src/TreatmentOptimization/makeExperimentalDataSplines.m
index 26200073c..49aef1065 100644
--- a/src/core/TreatmentOptimization/getSplines.m
+++ b/src/TreatmentOptimization/makeExperimentalDataSplines.m
@@ -1,7 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
 % This function calculates the splines for all experimental data. These
-% splines are evaluated at the collocation points to allow tracking of 
+% splines are evaluated at the collocation points to allow tracking of
 % these quanitites during treatment optimization
 %
 % (struct) -> (struct)
@@ -15,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -29,21 +29,21 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = getSplines(inputs)
-inputs.splineJointAngles = spaps(inputs.experimentalTime, ...
-    inputs.experimentalJointAngles', 0.0000001);
-inputs.splineJointMoments = spaps(inputs.experimentalTime, ...
-    inputs.experimentalJointMoments', 0.0000001);
-if strcmp(inputs.controllerType, 'synergy_driven')
-inputs.splineMuscleActivations = spaps(inputs.experimentalTime, ...
-    inputs.experimentalMuscleActivations', 0.0000001);
+function inputs = makeExperimentalDataSplines(inputs)
+inputs.splineJointMoments = makeGcvSplineSet(inputs.experimentalTime, ...
+    inputs.experimentalJointMoments, ...
+    inputs.inverseDynamicsMomentLabels);
+if strcmp(inputs.controllerType, 'synergy')
+    inputs.splineMuscleActivations = makeGcvSplineSet( ...
+        inputs.experimentalTime, inputs.experimentalMuscleActivations, ...
+        inputs.muscleLabels);
 end
 for i = 1:length(inputs.contactSurfaces)
     inputs.splineExperimentalGroundReactionForces{i} = ...
-        spaps(inputs.experimentalTime, ...
-        inputs.contactSurfaces{i}.experimentalGroundReactionForces', 0.0000001);
+        makeGcvSplineSet(inputs.experimentalTime, ...
+        inputs.contactSurfaces{i}.experimentalGroundReactionForces, string(0:2));
     inputs.splineExperimentalGroundReactionMoments{i} = ...
-        spaps(inputs.experimentalTime, ...
-        inputs.contactSurfaces{i}.experimentalGroundReactionMoments', 0.0000001);
+        makeGcvSplineSet(inputs.experimentalTime, ...
+        inputs.contactSurfaces{i}.experimentalGroundReactionMoments, string(0:2));
+end
 end
-end
\ No newline at end of file
diff --git a/src/TreatmentOptimization/makeMarkerTracking.m b/src/TreatmentOptimization/makeMarkerTracking.m
new file mode 100644
index 000000000..89cc013c4
--- /dev/null
+++ b/src/TreatmentOptimization/makeMarkerTracking.m
@@ -0,0 +1,66 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function parses the settings tree resulting from xml2struct from the
+% settings XML file common to all treatment optimizatin modules (trackning,
+% verification, and design optimization).
+%
+% (struct) -> (struct, struct)
+% returns the input values for all treatment optimization modules
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function inputs = makeMarkerTracking(inputs)
+names = string([]);
+locations = [];
+bodies = [];
+for i = 1:length(inputs.costTerms)
+    costTerm = inputs.costTerms{i};
+    if strcmp(costTerm.type, "marker_position_tracking")
+        names(end + 1) = convertCharsToStrings(inputs.model.getMarkerSet().get( ...
+            costTerm.marker).getName().toCharArray()');
+        locations = cat(1, locations, ...
+            Vec3ToArray(inputs.model.getMarkerSet().get(...
+            costTerm.marker).get_location()));
+        bodies(end + 1) = inputs.model.getBodySet().getIndex( ...
+            getMarkerBodyName(inputs.model, costTerm.marker));
+    end
+end
+inputs.trackedMarkerNames = names;
+inputs.trackedMarkerLocations = locations;
+inputs.trackedMarkerBodyIndices = bodies;
+if ~isempty(inputs.trackedMarkerNames)
+    inputs.experimentalMarkerPositions = pointKinematics( ...
+        inputs.experimentalTime, inputs.experimentalJointAngles, ...
+        inputs.experimentalJointVelocities, inputs.trackedMarkerLocations, ...
+        inputs.trackedMarkerBodyIndices, inputs.mexModel, ...
+        inputs.coordinateNames);
+    for i = 1:size(inputs.experimentalMarkerPositions, 3)
+        experimentalMarkerPositions = ...
+            reshape(inputs.experimentalMarkerPositions(:, :, i), ...
+            size(inputs.experimentalMarkerPositions, 1), []);
+        inputs.splineMarkerPositions{i} = makeGcvSplineSet(inputs.experimentalTime, ...
+            experimentalMarkerPositions, ["x", "y", "z"]);
+    end
+end
+end
+
diff --git a/src/core/TreatmentOptimization/getStateDerivatives.m b/src/TreatmentOptimization/makeStateDerivatives.m
similarity index 78%
rename from src/core/TreatmentOptimization/getStateDerivatives.m
rename to src/TreatmentOptimization/makeStateDerivatives.m
index 697897800..689655b84 100644
--- a/src/core/TreatmentOptimization/getStateDerivatives.m
+++ b/src/TreatmentOptimization/makeStateDerivatives.m
@@ -28,14 +28,13 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = getStateDerivatives(inputs)
-points = length(inputs.experimentalTime);
-interval = inputs.experimentalTime(2) - inputs.experimentalTime(1);
-[N, Np, Npp] = BSplineMatrices(5, 10, points, interval);
-Nodes = N\inputs.experimentalJointAngles;
-inputs.experimentalJointVelocities = Np * Nodes;
-inputs.experimentalJointAccelerations = Npp * Nodes;
-inputs.experimentalJointJerks = calcBSplineDerivative( ...
-    inputs.experimentalTime, inputs.experimentalJointAccelerations, ...
-    2, 10);
+function inputs = makeStateDerivatives(inputs, params)
+inputs.splineJointAngles = makeGcvSplineSet(inputs.experimentalTime, ...
+    inputs.experimentalJointAngles', inputs.coordinateNames);
+inputs.experimentalJointVelocities = evaluateGcvSplines( ...
+    inputs.splineJointAngles, inputs.coordinateNames, ...
+    inputs.experimentalTime, 1);
+inputs.experimentalJointAccelerations = evaluateGcvSplines( ...
+    inputs.splineJointAngles, inputs.coordinateNames, ...
+    inputs.experimentalTime, 2);
 end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingPropulsiveForceIntegrand.m b/src/TreatmentOptimization/makeSurrogateModel.m
similarity index 73%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingPropulsiveForceIntegrand.m
rename to src/TreatmentOptimization/makeSurrogateModel.m
index 65659a815..49cc3bf55 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingPropulsiveForceIntegrand.m
+++ b/src/TreatmentOptimization/makeSurrogateModel.m
@@ -1,9 +1,9 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function minimizes the propulsive force for the specified foot. 
-%
-% (struct, struct, struct) -> (Array of number)
+% This function prepares the inputs for the all treatment optimization
+% modules (tracking, verification, and design optimization.
 %
+% (struct, struct) -> (struct)
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +13,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,14 +27,14 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingPropulsiveForceIntegrand(modeledValues, ...
-    params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        propulsiveForce = getPropulsiveForce(...
-            modeledValues.groundReactionsLab.forces{i}(:,1));
+function inputs = makeSurrogateModel(inputs)
+if strcmp(inputs.controllerType, 'synergy')
+    for i = 1 : length(inputs.coordinateNames)
+        for j = 1 : length(inputs.surrogateModelCoordinateNames)
+            if strcmp(inputs.coordinateNames(i), inputs.surrogateModelCoordinateNames(j))
+                inputs.surrogateModelIndex(j) = i;
+            end
+        end
     end
 end
-cost = calcMinimizingCostArrayTerm(propulsiveForce);
-end
\ No newline at end of file
+end
diff --git a/src/DesignOptimization/DesignOptimization.m b/src/TreatmentOptimization/makeTreatmentOptimizationInputs.m
similarity index 57%
rename from src/DesignOptimization/DesignOptimization.m
rename to src/TreatmentOptimization/makeTreatmentOptimizationInputs.m
index df507bcaa..ab9bb71da 100644
--- a/src/DesignOptimization/DesignOptimization.m
+++ b/src/TreatmentOptimization/makeTreatmentOptimizationInputs.m
@@ -1,10 +1,9 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function sets up the input variables and mex files (or parallel 
-% matlab function) for the main function of design optimization
+% This function prepares the inputs for the all treatment optimization
+% modules (tracking, verification, and design optimization.
 %
-% (struct, struct) -> (struct, struct)
-% Inputs for the main function are setup
+% (struct, struct) -> (struct)
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -28,28 +27,33 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function [output, inputs] = DesignOptimization(inputs, params)
-inputs = makeTreatmentOptimizationInputs(inputs, params);
+function inputs = makeTreatmentOptimizationInputs(inputs, params)
+inputs = makeStateDerivatives(inputs, params);
+inputs.contactSurfaces = prepareGroundContactSurfaces( ...
+    inputs.modelFileName, inputs.contactSurfaces);
+inputs = modifyModelForces(inputs);
 initializeMexOrMatlabParallelFunctions(inputs.mexModel);
-if strcmp(inputs.controllerType, 'synergy_driven')
-    inputs = setupMuscleSynergies(inputs);
-end
-if inputs.enableExternalTorqueControl
-    inputs = setupExternalTorqueControls(inputs);
-end
-output = computeDesignOptimizationMainFunction(inputs, params);
-end
-function inputs = setupMuscleSynergies(inputs)
-inputs.splineSynergyActivations = spaps(inputs.initialGuess.time, ...
-    inputs.initialGuess.control(:, inputs.numCoordinates + 1 : ...
-    inputs.numCoordinates + inputs.numSynergies)', 0.0000001);
-inputs.synergyLabels = inputs.initialGuess.controlLabels(:, ...
-    inputs.numCoordinates + 1 : inputs.numCoordinates + inputs.numSynergies);
+inputs = setupGroundContact(inputs);
+inputs = makeExperimentalDataSplines(inputs);
+inputs = makeSurrogateModel(inputs);
+[inputs.continuousMaxAllowableError, inputs.discreteMaxAllowableError] ...
+    = makeMaxAllowableError(inputs.toolName, inputs.costTerms);
+inputs = makeMarkerTracking(inputs);
+inputs = makePathConstraintBounds(inputs);
+inputs = makeTerminalConstraintBounds(inputs);
+inputs = makeOptimalControlBounds(inputs);
+
+if strcmpi(inputs.controllerType, "synergy")
+    if inputs.loadSurrogate && isfile("surrogateMuscles.mat")
+        inputs.surrogateMuscles = load("surrogateMuscles.mat") ...
+            .surrogateMuscles;
+    else
+        inputs.surrogateMuscles = SurrogateModelCreation(inputs);
+    end
+    if inputs.saveSurrogate
+        surrogateMuscles = inputs.surrogateMuscles;
+        save("surrogateMuscles.mat", "surrogateMuscles");
+    end
 end
-function inputs = setupExternalTorqueControls(inputs)
-if size(inputs.initialGuess.control, 2) ~= length(inputs.maxControl)
-    inputs.initialGuess.control = [inputs.initialGuess.control ...
-        zeros(size(inputs.initialGuess.control, 1), ...
-        inputs.numExternalTorqueControls)];
 end
-end
\ No newline at end of file
+
diff --git a/src/core/TreatmentOptimization/modifyModelForces.m b/src/TreatmentOptimization/modifyModelForces.m
similarity index 74%
rename from src/core/TreatmentOptimization/modifyModelForces.m
rename to src/TreatmentOptimization/modifyModelForces.m
index 01082b6a6..602d87f42 100644
--- a/src/core/TreatmentOptimization/modifyModelForces.m
+++ b/src/TreatmentOptimization/modifyModelForces.m
@@ -15,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -30,11 +30,20 @@
 % ----------------------------------------------------------------------- %
 
 function inputs = modifyModelForces(inputs)
-if ~isa(inputs.model, 'org.opensim.modeling.Model')
-    model = Model(inputs.model);
+model = disableModelMuscles(inputs.model);
+if valueOrAlternate(inputs, 'calculateMetabolicCost', false)
+    probe = org.opensim.modeling.Bhargava2004MuscleMetabolicsProbe( ...
+        true, true, true, false, true);
+    model.addProbe(probe);
+    probe.setOperation("value");
+    probe.set_report_total_metabolics_only(true);
+    probe.setName("metabolics");
+    for i = 1:length(inputs.muscleNames)
+        probe.addMuscle(inputs.muscleNames(i), 0.5, 40, 133, 74, 111);
+    end
 end
-[model, inputs] = disableModelMuscles(inputs, model);
 model = addContactSurfaceActuators(inputs, model);
-inputs.mexModel = strcat(strrep(inputs.model,'.osim',''), '_inactiveMuscles.osim');
+inputs.mexModel = strcat(strrep(inputs.modelFileName,'.osim',''), '_inactiveMuscles.osim');
 model.print(inputs.mexModel);
+inputs.model = Model(inputs.mexModel);
 end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkStateGuess.m b/src/TreatmentOptimization/normalizeSynergyData.m
similarity index 71%
rename from src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkStateGuess.m
rename to src/TreatmentOptimization/normalizeSynergyData.m
index 987783638..e3ad6d933 100644
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkStateGuess.m
+++ b/src/TreatmentOptimization/normalizeSynergyData.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function checks that the initial guess states file is in the correct
-% order
+% This function ensures the synergy weights are normalized to sum to one
+% and the synergy commands are scaled in proportion
 %
 % (struct) -> (struct)
-%
+% scale synergy weights and commands for sum of weights to equal one
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,16 +28,15 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = checkStateGuess(inputs)
-if isfield(inputs.initialGuess, 'state')
-    for i = 1 : inputs.numCoordinates
-        for j = 1 : length(inputs.initialGuess.stateLabels)
-            if strcmpi(inputs.coordinateNames(i), inputs.initialGuess.stateLabels(j))
-                stateIndex(i) = j;
-            end
-        end 
+function inputs = normalizeSynergyData(inputs)
+if strcmp(inputs.controllerType, "synergy")
+    for i = 1:size(inputs.synergyWeights, 1)
+        total = sum(inputs.synergyWeights(i, :));
+        inputs.synergyWeights(i, :) = ...
+            inputs.synergyWeights(i, :) / total;
+        inputs.initialSynergyControls(:, i) = ...
+            inputs.initialSynergyControls(:, i) * total;
     end
-    inputs.initialGuess.state = inputs.initialGuess.state(:, [stateIndex ...
-    stateIndex + inputs.numCoordinates stateIndex + inputs.numCoordinates * 2]);
 end
-end
\ No newline at end of file
+end
+
diff --git a/src/core/TreatmentOptimization/prepareGroundContactSurfaces.m b/src/TreatmentOptimization/parseGroundContactSurfaces.m
similarity index 65%
rename from src/core/TreatmentOptimization/prepareGroundContactSurfaces.m
rename to src/TreatmentOptimization/parseGroundContactSurfaces.m
index be84b8ca3..495238d73 100644
--- a/src/core/TreatmentOptimization/prepareGroundContactSurfaces.m
+++ b/src/TreatmentOptimization/parseGroundContactSurfaces.m
@@ -25,7 +25,19 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function output = prepareGroundContactSurfaces(osimModel, contactSurfaces, grfFileName)
+function contactSurfaces = parseGroundContactSurfaces(inputs)
+contactSurfacesField = getFieldByName(inputs.osimx, "contactSurface");
+if (isstruct(contactSurfacesField) || iscell(contactSurfacesField)) && ...
+        isfield(inputs, "grfFileName")
+    contactSurfaces = prepareGroundContactSurfaces(inputs.model, ...
+        contactSurfacesField, inputs.grfFileName);
+else
+    contactSurfaces = {};
+end
+end
+
+function output = prepareGroundContactSurfaces(osimModel, ...
+    contactSurfaces, grfFileName)
 import org.opensim.modeling.Model
 osimModel = Model(osimModel);
 osimModel.finalizeConnections();
@@ -48,28 +60,39 @@
         grfFileName, output{i});
 end
 end
-function output = getParentChildSprings(osimModel, contactSurfaces)
-output = contactSurfaces;
-output.parentSpringPointsOnBody = [];
-output.parentSpringConstants = [];
-output.childSpringPointsOnBody = [];
-output.childSpringConstants = [];
-[output.parentBodyName, output.childBodyName] = ...
-    getJointBodyNames(osimModel, contactSurfaces.toesJointName);
-for j = 1:length(contactSurfaces.springs)
-    if strcmp(contactSurfaces.springs{j}.parentBody, output.parentBodyName)
-        output.parentSpringPointsOnBody(end+1, :) = ...
-            contactSurfaces.springs{j}.location;
-        output.parentSpringConstants(end+1) = ...
-            contactSurfaces.springs{j}.springConstant;
-    elseif strcmp(contactSurfaces.springs{j}.parentBody, output.childBodyName)
-        output.childSpringPointsOnBody(end+1, :) = ...
-            contactSurfaces.springs{j}.location;
-        output.childSpringConstants(end+1) = ...
-            contactSurfaces.springs{j}.springConstant;
+
+function contactSurface = getParentChildSprings(osimModel, contactSurface)
+contactSurface.parentSpringPointsOnBody = [];
+contactSurface.parentSpringConstants = [];
+contactSurface.childSpringPointsOnBody = [];
+contactSurface.childSpringConstants = [];
+joints = getBodyJointNames(osimModel, contactSurface.hindfootBodyName);
+assert(length(joints) == 2, ...
+    "Treatment Optimization supports two segment foot models only");
+for i = 1 : length(joints)
+    [parent, ~] = getJointBodyNames(osimModel, joints(i));
+    if strcmp(parent, contactSurface.hindfootBodyName)
+        contactSurface.toesJointName = joints(i);
+        break
+    end
+end
+[contactSurface.parentBodyName, contactSurface.childBodyName] = ...
+    getJointBodyNames(osimModel, contactSurface.toesJointName);
+for j = 1:length(contactSurface.springs)
+    if strcmp(contactSurface.springs{j}.parentBody, contactSurface.parentBodyName)
+        contactSurface.parentSpringPointsOnBody(end+1, :) = ...
+            contactSurface.springs{j}.location;
+        contactSurface.parentSpringConstants(end+1) = ...
+            contactSurface.springs{j}.springConstant;
+    elseif strcmp(contactSurface.springs{j}.parentBody, contactSurface.childBodyName)
+        contactSurface.childSpringPointsOnBody(end+1, :) = ...
+            contactSurface.springs{j}.location;
+        contactSurface.childSpringConstants(end+1) = ...
+            contactSurface.springs{j}.springConstant;
     end
 end
 end
+
 function output = parseGroundReactionDataWithoutTime(model, grfFile, output)
 import org.opensim.modeling.Storage
 [grfColumnNames, ~, grfData] = parseMotToComponents(model, Storage(grfFile));
diff --git a/src/TreatmentOptimization/prepareGroundContactSurfaces.m b/src/TreatmentOptimization/prepareGroundContactSurfaces.m
new file mode 100644
index 000000000..5f318e7e5
--- /dev/null
+++ b/src/TreatmentOptimization/prepareGroundContactSurfaces.m
@@ -0,0 +1,78 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+%
+% (struct) -> (struct)
+% Prepares the ground contact surface parameters and springs
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega                                                 %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function contactSurfaces = prepareGroundContactSurfaces(osimModel, ...
+    contactSurfaces)
+import org.opensim.modeling.Model
+osimModel = Model(osimModel);
+osimModel.finalizeConnections();
+
+for i=1:length(contactSurfaces)
+    contactSurfaces{i} = getParentChildSprings(osimModel, contactSurfaces{i});
+    contactSurfaces{i}.midfootSuperiorPointOnBody = Vec3ToArray(osimModel ...
+        .getMarkerSet.get(contactSurfaces{i}.midfootSuperiorMarker).get_location());
+    contactSurfaces{i}.midfootSuperiorBody = osimModel.getBodySet.getIndex( ...
+        osimModel.getMarkerSet.get(contactSurfaces{i}.midfootSuperiorMarker). ...
+        getParentFrame().getName());
+    contactSurfaces{i}.childBody = osimModel.getBodySet.getIndex(contactSurfaces{i}.childBodyName);
+    contactSurfaces{i}.parentBody = osimModel.getBodySet. ...
+        getIndex(contactSurfaces{i}.parentBodyName);
+end
+end
+
+function contactSurface = getParentChildSprings(osimModel, contactSurface)
+contactSurface.parentSpringPointsOnBody = [];
+contactSurface.parentSpringConstants = [];
+contactSurface.childSpringPointsOnBody = [];
+contactSurface.childSpringConstants = [];
+joints = getBodyJointNames(osimModel, contactSurface.hindfootBodyName);
+assert(length(joints) == 2, ...
+    "Treatment Optimization supports two segment foot models only");
+for i = 1 : length(joints)
+    [parent, ~] = getJointBodyNames(osimModel, joints(i));
+    if strcmp(parent, contactSurface.hindfootBodyName)
+        contactSurface.toesJointName = joints(i);
+        break
+    end
+end
+[contactSurface.parentBodyName, contactSurface.childBodyName] = ...
+    getJointBodyNames(osimModel, contactSurface.toesJointName);
+for j = 1:length(contactSurface.springs)
+    if strcmp(contactSurface.springs{j}.parentBody, contactSurface.parentBodyName)
+        contactSurface.parentSpringPointsOnBody(end+1, :) = ...
+            contactSurface.springs{j}.location;
+        contactSurface.parentSpringConstants(end+1) = ...
+            contactSurface.springs{j}.springConstant;
+    elseif strcmp(contactSurface.springs{j}.parentBody, contactSurface.childBodyName)
+        contactSurface.childSpringPointsOnBody(end+1, :) = ...
+            contactSurface.springs{j}.location;
+        contactSurface.childSpringConstants(end+1) = ...
+            contactSurface.springs{j}.springConstant;
+    end
+end
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/reportTreatmentOptimizationResults.m b/src/TreatmentOptimization/reportTreatmentOptimizationResults.m
similarity index 55%
rename from src/core/TreatmentOptimization/reportTreatmentOptimizationResults.m
rename to src/TreatmentOptimization/reportTreatmentOptimizationResults.m
index f51169e41..91ef81a37 100644
--- a/src/core/TreatmentOptimization/reportTreatmentOptimizationResults.m
+++ b/src/TreatmentOptimization/reportTreatmentOptimizationResults.m
@@ -28,55 +28,44 @@
 % ----------------------------------------------------------------------- %
 
 function reportTreatmentOptimizationResults(solution, inputs)
-if isfield(inputs, 'userDefinedVariables')
-    for i = 1:length(inputs.userDefinedVariables)
-        parameterResults = scaleToOriginal( ...
-            solution.solution.phase.parameter(i, 1), ...
-            inputs.userDefinedVariables{i}.upper_bounds, ...
-            inputs.userDefinedVariables{i}.lower_bounds)
+values = makeGpopsValuesAsStruct(solution.solution.phase, inputs);
+if strcmp(inputs.controllerType, 'synergy')
+    % plot Muscle Activations
+    plotMuscleActivations(solution.muscleActivations, values.time, ...
+        inputs.experimentalMuscleActivations, inputs.experimentalTime, ...
+        inputs.muscleLabels);
+    % plot synergy activations
+    synergyTitles = {};
+    for i = 1 : inputs.numSynergies
+        synergyTitles{end + 1} = strcat('synergy activation', num2str(i));
     end
+    plotResultsWithOutComparison(values.controlSynergyActivations, values.time, ...
+        synergyTitles, ["Synergy" "Activations"]);
 end
-values = getTreatmentOptimizationValueStruct(solution.solution.phase, inputs);
-if strcmp(inputs.controllerType, 'synergy_driven')
-% plot Muscle Activations
-plotMuscleActivations(solution.muscleActivations, values.time, ...
-    inputs.experimentalMuscleActivations, inputs.experimentalTime, ...
-    inputs.muscleLabels);
-% plot synergy activations
-synergyTitles = {};
-for i = 1 : inputs.numSynergies
-    synergyTitles{end + 1} = strcat('synergy activation', num2str(i));
-end
-plotResultsWithOutComparison(values.controlSynergyActivations, values.time, ...
-    synergyTitles, ["Synergy" "Activations"]);
-else 
 % plot torque controls
-plotResultsWithOutComparison(values.controlTorques, values.time, ...
-    inputs.controlTorqueNames, ["Torque" "Controls"]);
-end
-% plot external torque controls
-if isfield(inputs, 'enableExternalTorqueControl')
-    if inputs.enableExternalTorqueControl
-        plotResultsWithOutComparison(values.externalTorqueControls, values.time, ...
-            inputs.externalControlTorqueNames, ["External" "Torque Controls"]);
-    end
+if isfield(inputs, 'torqueControllerCoordinateNames') && ...
+        ~isempty(inputs.torqueControllerCoordinateNames)
+    plotResultsWithOutComparison(values.torqueControls, values.time, ...
+        inputs.torqueControllerCoordinateNames, ["Torque" "Controls"]);
 end
+jointAngles = subsetDataByCoordinates(inputs.experimentalJointAngles, ...
+    inputs.coordinateNames, inputs.statesCoordinateNames);
 % plot joint angles
 plotResultsWithComparison(values.statePositions, values.time, ...
-    inputs.experimentalJointAngles, inputs.experimentalTime, ...
-    strcat(inputs.coordinateNames, ' [rad]'), ["Joint" "Angles [rad]"]);
+    jointAngles, inputs.experimentalTime, ...
+    strcat(inputs.statesCoordinateNames, ' [rad]'), ["Joint" "Angles [rad]"]);
 % plot joint moments
-plotResultsWithComparison(solution.inverseDynamicMoments, values.time, ...
+plotResultsWithComparison(solution.inverseDynamicsMoments, values.time, ...
     inputs.experimentalJointMoments, inputs.experimentalTime, ...
-    strcat(inputs.inverseDynamicMomentLabels, ' [Nm]'), ["Joint" "Moments"]);
+    strcat(inputs.inverseDynamicsMomentLabels, ' [Nm]'), ["Joint" "Moments"]);
 % plot ground reactions
 for i = 1:length(inputs.contactSurfaces)
-plotResultsWithComparison(solution.groundReactionsLab.forces{i}, values.time, ...
-    inputs.contactSurfaces{i}.experimentalGroundReactionForces, inputs.experimentalTime, ...
-    ["GRFx", "GRFy", "GRFz"], ["Ground" "Reaction Forces"]);
-plotResultsWithComparison(solution.groundReactionsLab.moments{i}, values.time, ...
-    inputs.contactSurfaces{i}.experimentalGroundReactionMoments, inputs.experimentalTime, ...
-    ["GRTx", "GRTy", "GRTz"], ["Ground" "Reaction Moments"]);
+    plotResultsWithComparison(solution.groundReactionsLab.forces{i}, values.time, ...
+        inputs.contactSurfaces{i}.experimentalGroundReactionForces, inputs.experimentalTime, ...
+        ["GRFx", "GRFy", "GRFz"], ["Ground" "Reaction Forces"]);
+    plotResultsWithComparison(solution.groundReactionsLab.moments{i}, values.time, ...
+        inputs.contactSurfaces{i}.experimentalGroundReactionMoments, inputs.experimentalTime, ...
+        ["GRTx", "GRTy", "GRTz"], ["Ground" "Reaction Moments"]);
 end
 
 % if strcmp(inputs.toolName, 'DesignOptimization')
@@ -92,13 +81,13 @@ function plotMuscleActivations(muscleActivations, time, ...
 figure('name', 'Muscle Activations')
 nplots = ceil(sqrt(size(muscleActivations, 2)));
 for i = 1 : size(muscleActivations,2)
-subplot(nplots, nplots, i)
-plot(time, muscleActivations(:, i)); hold on
-plot(experimentalTime, experimentalMuscleActivations(:, i), 'r')
-axis([0 1 0 experimentalTime(end)])
-title(muscleLabels(i))
-figureXLabels(numel(muscleLabels), nplots, i, "Time")
-figureYLabels(numel(muscleLabels), nplots, i, ["Muscle" "Activation"])
+    subplot(nplots, nplots, i)
+    plot(time, muscleActivations(:, i)); hold on
+    plot(experimentalTime, experimentalMuscleActivations(:, i), 'r')
+    axis([0 experimentalTime(end) 0 1])
+    title(muscleLabels(i))
+    figureXLabels(numel(muscleLabels), nplots, i, "Time")
+    figureYLabels(numel(muscleLabels), nplots, i, ["Muscle" "Activation"])
 end
 end
 function plotResultsWithComparison(solutionData, solutionTime, ...
@@ -107,12 +96,12 @@ function plotResultsWithComparison(solutionData, solutionTime, ...
 figure('name', strjoin(figureTitle))
 nplots = ceil(sqrt(numel(labels)));
 for i = 1 : size(solutionData,2)
-subplot(nplots, nplots, i)
-plot(solutionTime, solutionData(:, i)); hold on
-plot(experimentalTime, experimentalData(:, i), 'r')
-xlim([0 experimentalTime(end)])
-title(strrep(labels(i), "_", " "))
-figureXLabels(numel(labels), nplots, i, "Time")
+    subplot(nplots, nplots, i)
+    plot(solutionTime, solutionData(:, i)); hold on
+    plot(experimentalTime, experimentalData(:, i), 'r')
+    xlim([0 experimentalTime(end)])
+    title(strrep(labels(i), "_", " "))
+    figureXLabels(numel(labels), nplots, i, "Time")
 end
 end
 function plotResultsWithOutComparison(solutionData, solutionTime, ...
@@ -120,11 +109,11 @@ function plotResultsWithOutComparison(solutionData, solutionTime, ...
 
 figure('name', strjoin(figureTitle))
 for i = 1 : size(solutionData,2)
-subplot(numel(labels), 1, i)
-plot(solutionTime, solutionData(:, i)); hold on
-xlim([0 solutionTime(end)])
-title(labels(i))
-figureXLabels(numel(labels), 1, i, "Time")
+    subplot(numel(labels), 1, i)
+    plot(solutionTime, solutionData(:, i)); hold on
+    xlim([0 solutionTime(end)])
+    title(labels(i))
+    figureXLabels(numel(labels), 1, i, "Time")
 end
 end
 function figureXLabels(numTotalPlots, numColumnPlots, plotIndex, xLabel)
diff --git a/src/TreatmentOptimization/saveTreatmentOptimizationResults.m b/src/TreatmentOptimization/saveTreatmentOptimizationResults.m
new file mode 100644
index 000000000..d6e5222af
--- /dev/null
+++ b/src/TreatmentOptimization/saveTreatmentOptimizationResults.m
@@ -0,0 +1,168 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function saves and prints the unscaled results from all
+% treatment optimization modules (tracking, verification, and design
+% optimization.
+%
+% (struct, struct) -> (None)
+% Prints treatment optimization results
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond, Marleny Vega                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function saveTreatmentOptimizationResults(solution, inputs, values)
+if ~exist(inputs.resultsDirectory, 'dir')
+    mkdir(inputs.resultsDirectory)
+end
+
+saveInverseKinematicsResults(inputs, values, inputs.resultsDirectory);
+saveInverseDynamicsResults(solution, inputs, values, inputs.resultsDirectory);
+saveGroundReactionResults(solution, inputs, values, inputs.resultsDirectory);
+saveExperimentalGroundReactions(inputs, inputs.resultsDirectory);
+
+stateLabels = inputs.statesCoordinateNames;
+for i = 1 : length(inputs.statesCoordinateNames)
+    stateLabels{end + 1} = strcat(inputs.statesCoordinateNames{i}, '_u');
+end
+% for i = 1 : length(inputs.statesCoordinateNames)
+%     stateLabels{end + 1} = strcat(inputs.statesCoordinateNames{i}, '_dudt');
+% end
+[time, data] = splineToEvenlySpaced(values.time, [values.statePositions ...
+    values.stateVelocities], length(inputs.experimentalTime));
+writeToSto(stateLabels, time, data, ...
+    fullfile(inputs.resultsDirectory, strcat(inputs.trialName, "_states.sto")));
+[time, accelerations] = splineToEvenlySpaced(values.time, ...
+    values.controlAccelerations, length(inputs.experimentalTime));
+writeToSto(inputs.statesCoordinateNames, time, accelerations, ...
+    fullfile(inputs.resultsDirectory, strcat(inputs.trialName, "_accelerations.sto")));
+if strcmp(inputs.controllerType, 'synergy')
+    controlLabels = {};
+    for i = 1 : length(inputs.osimx.synergyGroups)
+        for j = 1 : inputs.osimx.synergyGroups{i}.numSynergies
+            controlLabels{end + 1} = convertStringsToChars( ...
+                strcat(inputs.osimx.synergyGroups{i}.muscleGroupName, ...
+                "_", num2str(j)));
+        end
+    end
+    [time, controls] = splineToEvenlySpaced(values.time, ...
+        values.controlSynergyActivations, length(inputs.experimentalTime));
+    writeToSto(controlLabels, time, controls, ...
+        fullfile(inputs.resultsDirectory, ...
+        strcat(inputs.trialName, "_synergyCommands.sto")));
+end
+if ~isempty(valueOrAlternate(inputs, "torqueControllerCoordinateNames", []))
+    controlLabels = {};
+    for i = 1 : length(inputs.torqueControllerCoordinateNames)
+        controlLabels{end + 1} = inputs.torqueControllerCoordinateNames{i};
+    end
+    [time, controls] = splineToEvenlySpaced(values.time, values.torqueControls, ...
+        length(inputs.experimentalTime));
+    writeToSto(controlLabels, time, controls, ...
+        fullfile(inputs.resultsDirectory, ...
+        strcat(inputs.trialName, "_torqueControls.sto")));
+end
+if strcmp(inputs.controllerType, 'synergy')
+    writeToSto(inputs.muscleLabels, linspace(1, inputs.numSynergies, ...
+        inputs.numSynergies), [values.synergyWeights], ...
+        fullfile(inputs.resultsDirectory, "synergyWeights.sto"));
+    [time, activations] = splineToEvenlySpaced(values.time, ...
+        solution.muscleActivations, length(inputs.experimentalTime));
+    writeToSto(inputs.muscleLabels, time, ...
+        activations, fullfile(inputs.resultsDirectory, ...
+        strcat(inputs.trialName, "_combinedActivations.sto")));
+end
+delete(inputs.mexModel);
+end
+
+function saveInverseKinematicsResults(inputs, values, outputDirectory)
+if ~exist(fullfile(outputDirectory, "IKData"), "dir")
+    mkdir(fullfile(outputDirectory, "IKData"))
+end
+[time, positions] = splineToEvenlySpaced(values.time, ...
+    values.positions, length(inputs.experimentalTime));
+writeToSto(inputs.coordinateNames, time, positions, ...
+    fullfile(outputDirectory, "IKData", strcat(inputs.trialName, ".sto")));
+end
+
+function saveInverseDynamicsResults(solution, inputs, values, outputDirectory)
+if ~exist(fullfile(outputDirectory, "IDData"), "dir")
+    mkdir(fullfile(outputDirectory, "IDData"))
+end
+[time, moments] = splineToEvenlySpaced(values.time, ...
+    solution.inverseDynamicsMoments, length(inputs.experimentalTime));
+writeToSto(inputs.inverseDynamicsMomentLabels, time, ...
+    moments, fullfile(outputDirectory, "IDData", ...
+    strcat(inputs.trialName, ".sto")));
+end
+
+function saveGroundReactionResults(solution, inputs, values, outputDirectory)
+groundContactLabels = [];
+groundContactData = [];
+for i = 1:length(inputs.contactSurfaces)
+    groundContactLabels = cat(2, groundContactLabels, ...
+        [inputs.contactSurfaces{i}.forceColumns, ...
+        inputs.contactSurfaces{i}.momentColumns, ...
+        inputs.contactSurfaces{i}.electricalCenterColumns]);
+    midfootSuperiorLocation = pointKinematics(values.time, ...
+        values.positions, values.velocities, ...
+        inputs.contactSurfaces{i}.midfootSuperiorPointOnBody, ...
+        inputs.contactSurfaces{i}.midfootSuperiorBody, inputs.modelFileName, ...
+        inputs.coordinateNames);
+    midfootSuperiorLocation(:, 2) = inputs.contactSurfaces{i}.restingSpringLength;
+    groundContactData = [groundContactData, ...
+        solution.groundReactionsLab.forces{i}, ...
+        solution.groundReactionsLab.moments{i}, ...
+        midfootSuperiorLocation];
+end
+if ~isempty(groundContactData)
+    if ~exist(fullfile(outputDirectory, "GRFData"), "dir")
+        mkdir(fullfile(outputDirectory, "GRFData"))
+    end
+    [time, splinedGroundContactData] = splineToEvenlySpaced(values.time, ...
+        groundContactData, length(inputs.experimentalTime));
+    writeToSto(groundContactLabels, time, splinedGroundContactData, ...
+    fullfile(inputs.resultsDirectory, "GRFData", ...
+        strcat(inputs.trialName, ".sto")));
+end
+end
+
+function saveExperimentalGroundReactions(inputs, resultsDirectory)
+if isempty(inputs.contactSurfaces)
+    return
+end
+columnLabels = strings(1, 9*numel(inputs.contactSurfaces));
+dataToSave = zeros(size(inputs.experimentalTime, 1), numel(columnLabels));
+for surface = 1 : numel(inputs.contactSurfaces)
+    contactSurface = inputs.contactSurfaces{surface};
+    columnLabels((surface-1)*9+1:surface*9) = ...
+        [contactSurface.forceColumns', ...
+        contactSurface.momentColumns', ...
+        contactSurface.electricalCenterColumns'];
+    dataToSave(:, (surface-1)*9+1:surface*9) = ...
+        [contactSurface.experimentalGroundReactionForces, ...
+        contactSurface.experimentalGroundReactionMoments, ...
+        contactSurface.electricalCenter];    
+end
+writeToSto(columnLabels, inputs.experimentalTime, dataToSave, ...
+    fullfile(resultsDirectory, ...
+        strcat(inputs.trialName, "_replacedExperimentalGroundReactions.sto")));
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/scaleToBounds.m b/src/TreatmentOptimization/scaleToBounds.m
similarity index 100%
rename from src/core/TreatmentOptimization/scaleToBounds.m
rename to src/TreatmentOptimization/scaleToBounds.m
diff --git a/src/core/TreatmentOptimization/scaleToOriginal.m b/src/TreatmentOptimization/scaleToOriginal.m
similarity index 100%
rename from src/core/TreatmentOptimization/scaleToOriginal.m
rename to src/TreatmentOptimization/scaleToOriginal.m
diff --git a/src/VerificationOptimization/calcVerificationOptimizationObjective.m b/src/TreatmentOptimization/solveOptimalControlProblem.m
similarity index 80%
rename from src/VerificationOptimization/calcVerificationOptimizationObjective.m
rename to src/TreatmentOptimization/solveOptimalControlProblem.m
index f12b2aa69..e04561826 100644
--- a/src/VerificationOptimization/calcVerificationOptimizationObjective.m
+++ b/src/TreatmentOptimization/solveOptimalControlProblem.m
@@ -1,10 +1,6 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the cost function objective for verification 
-% optimization.
 %
-% (Number, Array of number, Number, struct) -> (Number)
-% Returns objective
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +10,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,7 +24,11 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function objective = calcVerificationOptimizationObjective(integral)
-continuousObjective = sum(integral) / length(integral);
-objective = continuousObjective;
-end
\ No newline at end of file
+function [inputs, output] = solveOptimalControlProblem(inputs, params)
+[setup, inputs] = convertToGpopsInputs(inputs, params);
+setup.auxdata = inputs;
+solution = gpops2(setup);
+inputs = setup.auxdata;
+output = convertFromGpopsOutputs(solution, ...
+    inputs, params);
+end
diff --git a/src/TreatmentOptimization/splineToEvenlySpaced.m b/src/TreatmentOptimization/splineToEvenlySpaced.m
new file mode 100644
index 000000000..e904415af
--- /dev/null
+++ b/src/TreatmentOptimization/splineToEvenlySpaced.m
@@ -0,0 +1,40 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% makeStateDerivatives() requires evenly spaced points for the b-spline
+% derivatives. This function should be used to make the points evenly
+% spaced via splining
+%
+% (struct, struct) -> (None)
+% Splines results to make them evenly spaced
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function [newTime, newData] = splineToEvenlySpaced(time, data, ...
+    numPoints)
+gcvSplineSet = makeGcvSplineSet(time(1 : end - 1), ...
+    data(1 : end - 1, :), string(1:size(data, 2)));
+newTime = linspace(time(1), time(end), numPoints);
+newData = evaluateGcvSplines( gcvSplineSet, string(1:size(data, 2)), ...
+    newTime, 0);
+end
+
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingTrailingLimbAngleIntegrand.m b/src/TreatmentOptimization/subsetDataByCoordinates.m
similarity index 66%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingTrailingLimbAngleIntegrand.m
rename to src/TreatmentOptimization/subsetDataByCoordinates.m
index ea2b804f8..29a9e9366 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingTrailingLimbAngleIntegrand.m
+++ b/src/TreatmentOptimization/subsetDataByCoordinates.m
@@ -1,9 +1,12 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function minimizes the trailing limb for the specified foot. 
-%
-% (struct, struct, struct, struct) -> (Array of number)
+% This convenience function simply returns the subset of values that are
+% included in the second coordinate list from the first. This is ordered
+% assuming Treatment Optimization ordering, not Model Personalization
+% ordering.
 %
+% (matrix, array of string, array of string) -> (matrix)
+% return a set of setup values common to all optimal control problems
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +16,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,17 +30,15 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingTrailingLimbAngleIntegrand(values, ...
-    modeledValues, params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        normalForce = ...
-            modeledValues.groundReactionsLab.forces{i}(:, 2) - 20;
-    end
+function output = subsetDataByCoordinates(data, coordinateNames, ...
+    subsetOfCoordinateNames)
+includedSubset = [];
+for i = 1 : length(subsetOfCoordinateNames)
+    temp = find(coordinateNames == subsetOfCoordinateNames(i));
+    assert(~isempty(temp), subsetOfCoordinateNames(i) + ...
+        " is not a coordinate in the IK data");
+    includedSubset(end + 1) = temp;
 end
-trailingLimbAngle = calcTrailingLimb(costTerm, values, ...
-    normalForce, params);
-cost = calcMinimizingCostArrayTerm(trailingLimbAngle * ...
-    ones(length(values.time), 1));
-end
\ No newline at end of file
+output = data(:, includedSubset);
+end
+
diff --git a/src/core/TreatmentOptimization/transferMoments.m b/src/TreatmentOptimization/transferMoments.m
similarity index 100%
rename from src/core/TreatmentOptimization/transferMoments.m
rename to src/TreatmentOptimization/transferMoments.m
diff --git a/src/VerificationOptimization/calcVerificationOptimizationIntegrand.m b/src/VerificationOptimization/calcVerificationOptimizationIntegrand.m
deleted file mode 100644
index d8128427b..000000000
--- a/src/VerificationOptimization/calcVerificationOptimizationIntegrand.m
+++ /dev/null
@@ -1,38 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the integrand for verification optimization.
-%
-% (struct, struct, struct) -> (2D matrix)
-% Returns scaled integrand
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function integrand = calcVerificationOptimizationIntegrand(values, ...
-    modeledValues, auxdata)
-[costTermCalculations, allowedTypes] = ...
-    generateCostTermStruct("continuous", "VerificationOptimization");
-integrand = calcTreatmentOptimizationCost( ...
-    costTermCalculations, allowedTypes, values, modeledValues, auxdata);
-integrand = integrand ./ (auxdata.maxIntegral - auxdata.minIntegral);
-integrand = integrand .^ 2;
-end
\ No newline at end of file
diff --git a/src/VerificationOptimization/calcVerificationOptimizationTerminalConstraint.m b/src/VerificationOptimization/calcVerificationOptimizationTerminalConstraint.m
deleted file mode 100644
index bc82b7b81..000000000
--- a/src/VerificationOptimization/calcVerificationOptimizationTerminalConstraint.m
+++ /dev/null
@@ -1,78 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the terminal constraint for verification
-% optimization
-%
-% (struct, struct, struct) -> (Array of number)
-% Returns terminal constraint
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function event = calcVerificationOptimizationTerminalConstraint(inputs, params)
-
-inputs.phase.state = [inputs.phase.initialstate; inputs.phase.finalstate];
-inputs.phase.time = [inputs.phase.initialtime; inputs.phase.finaltime];
-inputs.phase.control = ones(size(inputs.phase.time,1),length(params.minControl));
-values = getVerificationOptimizationValueStruct(inputs.phase, params);
-modeledValues = calcTorqueBasedModeledValues(values, params);
-
-event = [];
-for i = 1:length(params.terminal)
-    constraintTerm = params.terminal{i};
-    if constraintTerm.isEnabled
-        switch constraintTerm.type
-            case "state_position_periodicity"
-                event = cat(2, event, ...
-                    calcStatePositionPeriodicity(values.statePositions, ...
-                    params.coordinateNames, ...
-                    constraintTerm.coordinate));
-            case "state_velocity_periodicity"
-                event = cat(2, event, ...
-                    calcStateVelocityPeriodicity(values.stateVelocities, ...
-                    params.coordinateNames, ...
-                    constraintTerm.coordinate));
-            case "root_segment_residual_load_periodicity"
-                event = cat(2, event, ...
-                    calcRootSegmentResidualsPeriodicity(... 
-                    modeledValues.inverseDynamicMoments, ...
-                    params.inverseDynamicMomentLabels, ...
-                    constraintTerm.load));    
-            case "external_force_periodicity"
-                event = cat(2, event, ...
-                    calcExternalForcesPeriodicity(... 
-                    modeledValues.groundReactionsLab.forces, ...
-                    params.contactSurfaces, ...
-                    constraintTerm.force));  
-            case "external_moment_periodicity"
-                event = cat(2, event, ...
-                    calcExternalMomentsPeriodicity(... 
-                    modeledValues.groundReactionsLab.moments, ...
-                    params.contactSurfaces, ...
-                    constraintTerm.moment));  
-            otherwise
-                throw(MException('', ['Constraint term type ' ...
-                    constraintTerm.type ' does not exist for this tool.']))    
-        end
-    end
-end
-end
\ No newline at end of file
diff --git a/src/VerificationOptimization/computeVerificationOptimizationMainFunction.m b/src/VerificationOptimization/computeVerificationOptimizationMainFunction.m
deleted file mode 100644
index ec4b76e32..000000000
--- a/src/VerificationOptimization/computeVerificationOptimizationMainFunction.m
+++ /dev/null
@@ -1,48 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function sets up GPOPS-II to run Verification Optimization.
-% 
-% (struct) -> (struct, struct)
-% Assigns optimal control settings and runs Verification Optimization 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function output = computeVerificationOptimizationMainFunction(inputs, params)
-bounds = setupProblemBounds(inputs, params);
-guess = setupCommonOptimalControlInitialGuess(inputs);
-setup = setupCommonOptimalControlSolverSettings(inputs, ...
-    bounds, guess, params, ...
-    @computeVerificationOptimizationContinuousFunction, ...
-    @computeVerificationOptimizationEndpointFunction);
-checkInitialGuess(guess, inputs, ...
-    @computeVerificationOptimizationContinuousFunction);
-solution = gpops2(setup);
-solution = solution.result.solution;
-solution.auxdata = inputs;
-output = computeVerificationOptimizationContinuousFunction(solution);
-output.solution = solution;
-end
-
-function bounds = setupProblemBounds(inputs, params)
-bounds = setupCommonOptimalControlBounds(inputs, params);
-end
diff --git a/src/VerificationOptimization/parseVerificationOptimizationSettingsTree.m b/src/VerificationOptimization/parseVerificationOptimizationSettingsTree.m
deleted file mode 100644
index df0bbbd49..000000000
--- a/src/VerificationOptimization/parseVerificationOptimizationSettingsTree.m
+++ /dev/null
@@ -1,92 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses the settings tree resulting from xml2struct of the
-% Verification Optimizatoin settings XML file.
-%
-% (struct) -> (struct, struct)
-% returns the input values for Verification Optimization
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function [inputs, params] = ...
-    parseVerificationOptimizationSettingsTree(settingsTree)
-inputs = getInputs(settingsTree);
-params = getParams(settingsTree);
-inputs = modifyModelForces(inputs);
-end
-
-function inputs = getInputs(tree)
-import org.opensim.modeling.Storage
-inputs = getTreatmentOptimizationInputs(tree);
-inputs = getDesignVariableBounds(tree, inputs);
-if strcmpi(inputs.controllerType, 'synergy_driven')
-inputs.synergyWeights = parseTreatmentOptimizationStandard(...
-    {getTextFromField(getFieldByName(tree, 'synergy_vectors_file'))});
-end
-end
-
-function inputs = getDesignVariableBounds(tree, inputs)
-designVariableTree = getFieldByNameOrError(tree, ...
-    'RCNLDesignVariableBoundsTerms');
-jointPositionsMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_positions_multiple');
-if(isstruct(jointPositionsMultiple))
-    inputs.statePositionsMultiple = getDoubleFromField(jointPositionsMultiple);
-end
-jointVelocitiesMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_velocities_multiple');
-if(isstruct(jointVelocitiesMultiple))
-    inputs.stateVelocitiesMultiple = getDoubleFromField(jointVelocitiesMultiple);
-end
-jointAccelerationsMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_accelerations_multiple');
-if(isstruct(jointAccelerationsMultiple))
-    inputs.stateAccelerationsMultiple = ...
-        getDoubleFromField(jointAccelerationsMultiple);
-end
-jointJerkMultiple = getFieldByNameOrError(designVariableTree, ...
-    'joint_jerks_multiple');
-if(isstruct(jointJerkMultiple))
-    inputs.controlJerksMultiple = getDoubleFromField(jointJerkMultiple);
-end
-if strcmp(inputs.controllerType, 'synergy_driven')
-maxControlSynergyActivations = getFieldByNameOrError(designVariableTree, ...
-    'synergy_activations_max');
-if(isstruct(maxControlSynergyActivations))
-    inputs.maxControlSynergyActivations = ...
-        getDoubleFromField(maxControlSynergyActivations);
-end
-else 
-maxControlTorques = getFieldByNameOrError(designVariableTree, ...
-    'torque_controls_max');
-if(isstruct(maxControlTorques))
-    inputs.maxControlTorquesMultiple = getDoubleFromField(maxControlTorques);
-end
-end
-inputs.toolName = "VerificationOptimization";
-end
-
-function params = getParams(tree)
-params.solverSettings = getOptimalControlSolverSettings(...
-    getTextFromField(getFieldByName(tree, 'optimal_control_settings_file')));
-end
\ No newline at end of file
diff --git a/src/core/BSpline/CutoffFrequencyToNumberOfNodes/lowpassFilter.m b/src/core/BSpline/CutoffFrequencyToNumberOfNodes/lowpassFilter.m
index 85129cfab..67f9fbfd3 100644
--- a/src/core/BSpline/CutoffFrequencyToNumberOfNodes/lowpassFilter.m
+++ b/src/core/BSpline/CutoffFrequencyToNumberOfNodes/lowpassFilter.m
@@ -29,41 +29,36 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function dataOut = lowpassFilter(timeIn,dataIn,order,fCutoff,plotFlag)
-
-% Pad front and back of data with complete data set to eliminate
-% filter transients at the start and end
-% This step assumes the data are periodic
-npts = length(dataIn);
-dt = timeIn(2,1)-timeIn(1,1);
-dataInLong = [dataIn(1:npts-1,1); dataIn; dataIn(2:npts,1)];
-
-% dataMirrored = zeros(npts-1,1);
-% for i = 1:npts-1
-%     dataMirrored(i,1) = dataIn(npts-i,1);
-% end
-% dataInLong = [dataMirrored; dataIn; dataMirrored];
-% dataInLong = [dataIn(1,1)*ones(npts-1,1); dataIn; dataIn(npts,1)*ones(npts-1,1)]; % Old choice
-% dataInLong = [dataIn(npts,1)*ones(npts-1,1); dataIn; dataIn(1,1)*ones(npts-1,1)];
+function yFilt = lowpassFilter(t,y,order,fCutoff,plotFlag)
+% Perform zero phase-lag lowpass Butterworth filter on input data
 
 % Set up filter inputs
+dt = t(2)-t(1);
 fSample = 1/dt; % Sampling frequency in Hz
 normCutoff = fCutoff/(fSample/2);
 
-% Create butterworth filer
+% Create butterworth filter
 [b,a] = butter(order,normCutoff);
 
-% Use filtfilt to perform zero phase-lag filtering
-dataOutLong = filtfilt(b,a,dataInLong);
-dataOut = dataOutLong(npts:2*npts-1);
+% Demean input data to minimize edge effects
+yMean = mean(y);
+yDemeaned = y-yMean;
+
+% Use filtfilt to perform zero phase-lag filtering on demeaned data
+yFiltDemeaned = filtfilt(b,a,yDemeaned);
+
+% Add mean value back into filtered data
+yFilt = yFiltDemeaned+yMean;
 
 % Plot original and filtered data if desired
 if plotFlag
-    plot(timeIn,dataIn,'k-')
+    plot(t,y,'k-')
     hold on
-    plot(timeIn,dataOut,'b-')
+    plot(t,yFilt,'b-')
     xlabel('time')
     ylabel('data')
     pause
     close all
+end
+
 end
\ No newline at end of file
diff --git a/src/TrackingOptimization/computeTrackingOptimizationMainFunction.m b/src/core/GCVSpline/evaluateGcvSplines.m
similarity index 52%
rename from src/TrackingOptimization/computeTrackingOptimizationMainFunction.m
rename to src/core/GCVSpline/evaluateGcvSplines.m
index ba06489af..9ae498e2e 100644
--- a/src/TrackingOptimization/computeTrackingOptimizationMainFunction.m
+++ b/src/core/GCVSpline/evaluateGcvSplines.m
@@ -1,9 +1,14 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function sets up GPOPS-II to run Tracking Optimization.
+% Evaluates a GCV spline for its fitted values or a derivative at a set of
+% time points. The spline to evaluate is chosen by the given column label,
+% which can be provided as either an integer (the raw index in the spline
+% set) or a string defining a column label that should exist in the spline
+% set. The derivative level is given as an integer (0 for position, 1 for
+% velocity, 2 for acceleration, etc.).
 %
-% (struct) -> (struct, struct)
-% Assigns optimal control settings and runs Tracking Optimization
+% (GCVSplineSet, string OR int, Array of double, int) -> (Array of double)
+% Evaluate GCV spline values or derivatives at a set of time points.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +18,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Spencer Williams                                             %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,32 +32,34 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function output = computeTrackingOptimizationMainFunction(inputs, params)
-bounds = setupProblemBounds(inputs, params);
-guess = setupCommonOptimalControlInitialGuess(inputs);
-setup = setupCommonOptimalControlSolverSettings(inputs, ...
-    bounds, guess, params, ...
-    @computeTrackingOptimizationContinuousFunction, ...
-    @computeTrackingOptimizationEndpointFunction);
-checkInitialGuess(guess, inputs, ...
-    @computeTrackingOptimizationContinuousFunction);
-solution = gpops2(setup);
-solution = solution.result.solution;
-solution.auxdata = inputs;
-if inputs.optimizeSynergyVectors
-    solution.phase.parameter = solution.parameter;
+function values = evaluateGcvSplines(splineSet, columnLabels, time, ...
+    derivative)
+values = zeros(length(time), length(columnLabels));
+
+if iscell(columnLabels)
+    columnLabels = string(columnLabels);
+end
+if isstring(columnLabels) || ischar(columnLabels)
+    for i = 1 : length(columnLabels)
+        columnLabels(i) = splineSet.getIndex(columnLabels(i));
+        assert(str2double(columnLabels(i)) > -1, "The specified coordinate is not included in" + ...
+            " the spline set.")
+    end
+    columnLabels = str2double(columnLabels);
 end
-output = computeTrackingOptimizationContinuousFunction(solution);
-output.solution = solution;
+
+if nargin < 4
+    derivative = 0;
 end
 
-function bounds = setupProblemBounds(inputs, params)
-bounds = setupCommonOptimalControlBounds(inputs, params);
-% setup parameter bounds
-if strcmp(inputs.controllerType, 'synergy_driven')
-    if inputs.optimizeSynergyVectors
-        bounds.parameter.lower = -0.5 * ones(1, length(inputs.minParameter));
-        bounds.parameter.upper = 0.5 * ones(1, length(inputs.minParameter));
+% if isequal(mexext, 'mexw64')
+%     values = evaluateGcvSplinesMexWindows(splineSet, columnLabels, time, ...
+%         derivative);
+% else
+for i = 1 : length(columnLabels)
+    for j = 1 : length(time)
+        values(j, i) = splineSet.evaluate(columnLabels(i), derivative, time(j));
     end
 end
+% end
 end
diff --git a/src/VerificationOptimization/VerificationOptimization.m b/src/core/GCVSpline/makeGcvSplineSet.m
similarity index 57%
rename from src/VerificationOptimization/VerificationOptimization.m
rename to src/core/GCVSpline/makeGcvSplineSet.m
index cbfbd3989..1cc9643c3 100644
--- a/src/VerificationOptimization/VerificationOptimization.m
+++ b/src/core/GCVSpline/makeGcvSplineSet.m
@@ -1,10 +1,15 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function sets up the input variables and mex files (or parallel 
-% matlab function) for the main function verification optimization.
+% Fit data with a GCVSplineSet, a set of GCV splines defined by the OpenSim
+% API. The arguments represent a time column, data to fit, column labels,
+% the degree of splines to fit, and a smoothing parameter. The first three
+% arguments are required, and the last two are optional, defaulting to
+% degree 5 and no smoothing. 
 %
-% (struct, struct) -> (struct, struct)
-% Inputs for the main function are setup
+% (Array of double, 2D Array of double, Array of string, int, double) -> 
+% (GCVSplineSet)
+%
+% Fit data with a set of GCV splines.
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +19,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
+% Author(s): Spencer Williams                                             %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,17 +33,27 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function [output, inputs] = VerificationOptimization(inputs, params)
-inputs = makeTreatmentOptimizationInputs(inputs, params);
-initializeMexOrMatlabParallelFunctions(inputs.mexModel);
-if strcmp(inputs.controllerType, 'synergy_driven')
-    inputs = setupMuscleSynergies(inputs);
+function splineSet = makeGcvSplineSet(time, data, columnLabels, degree)
+import org.opensim.modeling.*
+
+if length(time) ~= size(data, 1)
+    data = data';
 end
-output = computeVerificationOptimizationMainFunction(inputs, params);
+assert(length(time) == size(data, 1), "Length of time column must" + ...
+    " equal number of frames of data to spline-fit.")
+assert(length(columnLabels)==size(data, 2), "Number of column labels" + ...
+    " must match number of data columns to spline-fit.")
+
+timeVec = StdVectorDouble(time);
+matrix = Matrix.createFromMat(data);
+labels = StdVectorString(columnLabels);
+table = TimeSeriesTable(timeVec, matrix, labels);
+
+if nargin < 4
+    degree = 5;
+elseif isempty(degree)
+    degree = 5;
 end
 
-function inputs = setupMuscleSynergies(inputs)
-inputs.splineSynergyActivations = spaps(inputs.initialGuess.time, ...
-    inputs.initialGuess.control(:, inputs.numCoordinates + 1:end)', 0.0000001);
-inputs.synergyLabels = inputs.initialGuess.controlLabels(:, inputs.numCoordinates + 1:end);
+splineSet = GCVSplineSet(table, labels, degree);
 end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcGoalSingleSupportTimeIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcGoalSingleSupportTimeIntegrand.m
deleted file mode 100644
index 6c7ed2674..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcGoalSingleSupportTimeIntegrand.m
+++ /dev/null
@@ -1,52 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function tracks the difference between the predicted single spport
-% phase and the error center for the specified foot. On average, single 
-% support phase is around 0.37 to 0.39 of the gait cycle. 
-%
-% (struct, struct, struct, struct) -> (Array of number)
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcGoalSingleSupportTimeIntegrand(values, ...
-    modeledValues, params, costTerm)
-
-errorCenter = valueOrAlternate(costTerm, "error_center", 0.38);
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        if i == 1
-            singleSupportTime = calcSingleSupportTime( ...
-                modeledValues.groundReactionsLab.forces{i + 1}(:, 2), ...
-                values.time);
-        else
-            singleSupportTime = calcSingleSupportTime( ...
-                modeledValues.groundReactionsLab.forces{i - 1}(:, 2), ...
-                values.time);
-        end
-    end
-end
-percentSingleSupportTime = singleSupportTime / values.time(end);
-cost = calcTrackingCostArrayTerm(percentSingleSupportTime * ...
-    ones(length(values.time), 1), errorCenter * ...
-    ones(length(values.time), 1), 1);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcGoalWalkingSpeedIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcGoalWalkingSpeedIntegrand.m
deleted file mode 100644
index b46467729..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcGoalWalkingSpeedIntegrand.m
+++ /dev/null
@@ -1,41 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the difference between the walking speed and the
-% error center specified by the user. On average, normal walking speed is 
-% around 1.2 to 1.4 meters per second. 
-%
-% (struct, struct, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcGoalWalkingSpeedIntegrand(modeledValues,...
-    params, costTerm)
-
-errorCenter = valueOrAlternate(costTerm, "errorCenter", 1.3);
-strideLength = calcStrideLength(values, modeledValues,...
-    params);
-speed = strideLength / values.time(end);
-cost = calcTrackingCostArrayTerm(speed * ones(length(values.time), 1), ...
-    errorCenter * ones(length(values.time), 1), 1);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcKinematicSymmetryIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcKinematicSymmetryIntegrand.m
deleted file mode 100644
index 9da220a19..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcKinematicSymmetryIntegrand.m
+++ /dev/null
@@ -1,49 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates kinematic symmetry, or the difference between 
-% two joint angles. Kinematic symmetry is calculated as the difference 
-% between one joint angle and the second joint angle with a 50% phase
-% shift. To use this term, an even number is encouraged for the
-% <setup_mesh_phase_intervals> tag in the optimal control settings.
-% Additionally, two coordinate names are required to calculate the
-% difference. 
-%
-% (2D matrix, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcKinematicSymmetryIntegrand(statePositions, auxdata, ...
-    costTerm)
-
-halfWayFrame = size(statePositions, 1)/2;
-
-indx1 = find(strcmp(convertCharsToStrings(auxdata.coordinateNames), ...
-    costTerm.coordinate1));
-indx2 = find(strcmp(convertCharsToStrings(auxdata.coordinateNames), ...
-    costTerm.coordinate2));
-
-cost = calcTrackingCostArrayTerm(statePositions(:,indx1), ...
-    [statePositions(1 + round(halfWayFrame):end, indx2); ...
-    statePositions(1:round(halfWayFrame), indx2)], 1);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingStepLengthIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingStepLengthIntegrand.m
deleted file mode 100644
index a3b5ef3d7..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingStepLengthIntegrand.m
+++ /dev/null
@@ -1,50 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function maximizes the step length for the specified foot.
-%
-% (struct, struct, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcMaximizingStepLengthIntegrand(values, modeledValues,...
-    params, costTerm)
-
-for i = 1:length(params.contactSurfaces)
-    if params.contactSurfaces{i}.isLeftFoot == costTerm.is_left_foot
-        if i == 1
-            stepLength = calcStepLength(modeledValues. ...
-                groundReactionsLab.forces{i}(:, 2), ...
-                [modeledValues.bodyLocations.parent{i}(:, 1) ...
-                modeledValues.bodyLocations.parent{i+1}(:, 1)]);
-        else
-            stepLength = calcStepLength(modeledValues. ...
-                groundReactionsLab.forces{i}(:,2), ...
-                [modeledValues.bodyLocations.parent{i}(:, 1) ...
-                modeledValues.bodyLocations.parent{i-1}(:, 1)]);
-        end
-    end
-end
-cost = calcMaximizingCostArrayTerm(stepLength * ...
-    ones(length(values.time), 1));
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityYIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityYIntegrand.m
deleted file mode 100644
index 3438a0a38..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityYIntegrand.m
+++ /dev/null
@@ -1,35 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function minimizes the center of mass velocity in the y direction.
-%
-% (struct, struct) -> (Array of number)
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcMinimizingMassCenterVelocityYIntegrand(values, params)
-
-massCenterVelocity = calcMassCenterVelocity(values, params.model, ...
-    params.coordinateNames);
-cost = calcMinimizingCostArrayTerm(massCenterVelocity(:, 2));
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityZIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityZIntegrand.m
deleted file mode 100644
index 25afe9742..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityZIntegrand.m
+++ /dev/null
@@ -1,35 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-% 
-% This function minimizes the center of mass velocity in the z direction.
-%
-% (struct, struct) -> (Array of number)
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcMinimizingMassCenterVelocityZIntegrand(values, params)
-
-massCenterVelocity = calcMassCenterVelocity(values, params.model, ...
-    params.coordinateNames);
-cost = calcMinimizingCostArrayTerm(massCenterVelocity(:, 3));
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcStepLengthAsymmetryIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcStepLengthAsymmetryIntegrand.m
deleted file mode 100644
index 95eb8f2f5..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcStepLengthAsymmetryIntegrand.m
+++ /dev/null
@@ -1,41 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function tracks the difference between the predicted step length 
-% asymmetry and the error center specified. An error center of "1" would
-% encourage step legth symmetry. 
-%
-% (struct, struct, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcStepLengthAsymmetryIntegrand(values, modeledValues,...
-    params, costTerm)
-
-errorCenter = valueOrAlternate(costTerm, "errorCenter", 1);
-stepLengthAsymmetry = calcStepLengthAsymmetry(modeledValues,...
-    params, costTerm.reference_body);
-cost = calcTrackingCostArrayTerm(stepLengthAsymmetry * ...
-    ones(length(values.time), 1), errorCenter * ...
-    ones(length(values.time), 1), 1);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcStepTimeAsymmetryIntegrand.m b/src/core/TreatmentOptimization/IntegrandTerms/calcStepTimeAsymmetryIntegrand.m
deleted file mode 100644
index eac8181e9..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcStepTimeAsymmetryIntegrand.m
+++ /dev/null
@@ -1,41 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function tracks the difference between the predicted step time
-% asymmetry and the error center specified. An error center of "1" would
-% encourage step time symmetry. 
-%
-% (struct, struct, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function cost = calcStepTimeAsymmetryIntegrand(values, ...
-    modeledValues, params, costTerm)
-
-errorCenter = valueOrAlternate(costTerm, "errorCenter", 1);
-stepTimeAsymmetry = calcStepTimeAsymmetry(values, ...
-    modeledValues, params);
-cost = calcTrackingCostArrayTerm(stepTimeAsymmetry * ...
-    ones(length(values.time), 1), errorCenter * ...
-    ones(length(values.time), 1), 1);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/getBreakingForce.m b/src/core/TreatmentOptimization/IntegrandTerms/getBreakingForce.m
deleted file mode 100644
index 9c90c97be..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/getBreakingForce.m
+++ /dev/null
@@ -1,36 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function zeros out the positive portions of the anterior-posterior 
-% force to obtain the breaking force. 
-%
-% (struct, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function breakingForce = getBreakingForce(anteroPosteriorForce)
-
-anteroPosteriorForce = anteroPosteriorForce + 10; % Noise buffer
-anteroPosteriorForce(anteroPosteriorForce>=0) = 0;
-breakingForce = anteroPosteriorForce;
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/getHeelStrikeEvent.m b/src/core/TreatmentOptimization/IntegrandTerms/getHeelStrikeEvent.m
deleted file mode 100644
index 315916c31..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/getHeelStrikeEvent.m
+++ /dev/null
@@ -1,42 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function identifies the heel strike event by detecting changes in
-% slope of the normal force. To avoid erroneous detection of a heel strike
-% event, the slope of the normal force must be positive for at least 10% of
-% the time. Detects only one heel strike (use for only one gait cycle). 
-%
-% (Array of number) -> (Number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function heelStrikeEvent = getHeelStrikeEvent(slope)
-
-timePadding = round(length(slope) * 0.10);
-heelStrikeEvent = [];
-for i = 2 : length(slope) - timePadding
-    if slope(i - 1) == 0 && all(slope(i : i + timePadding) > 0)
-        heelStrikeEvent = i;
-    end
-end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/getPropulsiveForce.m b/src/core/TreatmentOptimization/IntegrandTerms/getPropulsiveForce.m
deleted file mode 100644
index 2c6dae23f..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/getPropulsiveForce.m
+++ /dev/null
@@ -1,36 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function zeros out the negative portions of the anterior-posterior 
-% force to obtain the propulive force. 
-%
-% (struct, struct, struct) -> (Array of number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function propulsiveForce = getPropulsiveForce(anteroPosteriorForce)
-
-anteroPosteriorForce = anteroPosteriorForce - 10; % Noise buffer
-anteroPosteriorForce(anteroPosteriorForce<=0) = 0;
-propulsiveForce = anteroPosteriorForce;
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/getToeOffEvent.m b/src/core/TreatmentOptimization/IntegrandTerms/getToeOffEvent.m
deleted file mode 100644
index 6d61940fb..000000000
--- a/src/core/TreatmentOptimization/IntegrandTerms/getToeOffEvent.m
+++ /dev/null
@@ -1,42 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function identifies the toe off event by detecting changes in
-% slope of the normal force. To avoid erroneous detection of a toe off
-% event, the slope of the normal force must be negative for at least 10% of
-% the time. Detects only one toe off event (use for only one gait cycle). 
-%
-% (Array of number) -> (Number)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function toeOffEvent = getToeOffEvent(slope)
-
-timePadding = round(length(slope) * 0.10) + 1;
-toeOffEvent = [];
-for i = 1 + timePadding : length(slope)
-    if slope(i) == 0 && all(slope(i - timePadding : i - 1) < 0)
-        toeOffEvent = i;
-    end
-end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMexWindows.mexw64 b/src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMexWindows.mexw64
deleted file mode 100644
index 61228f3ae..000000000
Binary files a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMexWindows.mexw64 and /dev/null differ
diff --git a/src/core/TreatmentOptimization/OpenSimMex/pointKinematicsMexWindows.mexw64 b/src/core/TreatmentOptimization/OpenSimMex/pointKinematicsMexWindows.mexw64
deleted file mode 100644
index b8ca6b73f..000000000
Binary files a/src/core/TreatmentOptimization/OpenSimMex/pointKinematicsMexWindows.mexw64 and /dev/null differ
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkParameterGuess.m b/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkParameterGuess.m
deleted file mode 100644
index f7e38d727..000000000
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkParameterGuess.m
+++ /dev/null
@@ -1,95 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function checks that the initial guess parameters file is in the 
-% correct order
-%
-% (struct) -> (struct)
-%
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function inputs = checkParameterGuess(inputs)
-if isfield(inputs.initialGuess, 'parameter') || isfield(inputs,"synergyWeights") 
-    if isfield(inputs.initialGuess, 'parameter')
-        inputs.synergyWeightsGuess = inputs.initialGuess.parameter;
-    elseif isfield(inputs,"synergyWeights") 
-        inputs.synergyWeightsGuess = inputs.synergyWeights;
-    end
-
-    parameterIndex = zeros(length(inputs.synergyGroups), inputs.numMuscles);
-    for i = 1 : length(inputs.synergyGroups)
-        for j = 1 : inputs.numMuscles
-            for k = 1 : length(inputs.synergyGroups{i}.muscleNames)
-                if strcmpi(inputs.muscleNames(j), inputs.synergyGroups{i}.muscleNames(k))
-                    if i <= 1 
-                        parameterIndex(i, k) = j;
-                    else
-                        parameterIndex(i, k + length(inputs.synergyGroups{i}.muscleNames)) = j;
-                    end
-                end
-            end
-        end 
-    end
-    synergyWeightsFlattened = [];
-    numSynergiesIndex = 0;
-    for j = 1 : length(inputs.synergyGroups)
-        synergyWeightsFlattened = cat(2, synergyWeightsFlattened, ...
-            reshape(inputs.synergyWeightsGuess(1 + numSynergiesIndex: ...
-            inputs.synergyGroups{j}.numSynergies + numSynergiesIndex, ...
-            nonzeros(parameterIndex(j, :)))', 1, []));
-        numSynergiesIndex = numSynergiesIndex + inputs.synergyGroups{j}.numSynergies;
-    end
-    inputs.synergyWeightsGuess = synergyWeightsFlattened;
-end
-if strcmp(inputs.controllerType, 'synergy_driven') 
-    inputs = getMuscleSynergiesInitialGuess(inputs);
-    for i = 1 : length(inputs.coordinateNames)
-        for j = 1 : length(inputs.surrogateModelCoordinateNames)
-            if strcmp(inputs.coordinateNames(i), inputs.surrogateModelCoordinateNames(j))
-                inputs.surrogateModelIndex(j) = i;
-            end
-        end 
-    end
-    inputs.dofsActuatedIndex = [];
-    for i = 1 : length(inputs.inverseDynamicMomentLabels)
-        for j = 1 : length(inputs.surrogateModelCoordinateNames)
-            if strcmp(inputs.inverseDynamicMomentLabels(i), ...
-                    strcat(inputs.surrogateModelCoordinateNames(j), '_moment'))
-                inputs.dofsActuatedIndex(end+1) = j;
-            end
-        end 
-    end
-end
-end
-function inputs = getMuscleSynergiesInitialGuess(inputs)
-if isfield(inputs.initialGuess,"parameter") || isfield(inputs,"synergyWeights") 
-    synergyWeights = getSynergyWeightsFromGroups(inputs.synergyWeightsGuess, inputs);
-    inputs.synergyActivationsGuess = inputs.experimentalMuscleActivations / synergyWeights;    
-else
-    inputs.mtpActivationsColumnNames = inputs.muscleLabels;
-    inputs.mtpActivations = permute(inputs.experimentalMuscleActivations, [3 2 1]);
-    inputs.synergyWeightsGuess = prepareNonNegativeMatrixFactorizationInitialValues(inputs, inputs)';
-    synergyWeights = getSynergyWeightsFromGroups(inputs.synergyWeightsGuess, inputs);
-    inputs.synergyActivationsGuess = inputs.experimentalMuscleActivations / synergyWeights;
-end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/getGpopsInitialGuess.m b/src/core/TreatmentOptimization/OptimalControlSetupFunctions/getGpopsInitialGuess.m
deleted file mode 100644
index fd804d2b3..000000000
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/getGpopsInitialGuess.m
+++ /dev/null
@@ -1,53 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses and loads the initial guesses for states (if
-% specified), controls (if specified), and parameters (if specified)
-%
-% (struct) -> (struct)
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function initialGuess = getGpopsInitialGuess(tree)
-import org.opensim.modeling.Storage
-initialGuess = [];
-statesFileName = getTextFromField(getFieldByNameOrAlternate(tree, ...
-    'initial_states_file', ''));
-if ~isempty(statesFileName)
-    initialGuess.time = parseTimeColumn({statesFileName})';
-    initialGuess.stateLabels = getStorageColumnNames(Storage({statesFileName}));
-    initialGuess.state = parseTreatmentOptimizationStandard({statesFileName});
-end
-controlsFileName = getTextFromField(getFieldByNameOrAlternate(tree, ...
-    'initial_controls_file', ''));
-if ~isempty(controlsFileName)
-    initialGuess.controlLabels = getStorageColumnNames(Storage({controlsFileName}));
-    initialGuess.control = parseTreatmentOptimizationStandard({controlsFileName});
-end
-parametersFileName = getTextFromField(getFieldByNameOrAlternate(tree, ...
-    'initial_parameters_file', ''));
-if ~isempty(parametersFileName)
-    initialGuess.parameterLabels = getStorageColumnNames(Storage({parametersFileName}));
-    initialGuess.parameter = parseTreatmentOptimizationStandard({parametersFileName});
-end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/getOptimalControlSolverSettings.m b/src/core/TreatmentOptimization/OptimalControlSetupFunctions/getOptimalControlSolverSettings.m
deleted file mode 100644
index 86d37a3c4..000000000
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/getOptimalControlSolverSettings.m
+++ /dev/null
@@ -1,80 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function reads the optimal control settings (GPOPS-II based) from a
-% separate XML file.  
-%
-% (struct) -> (Array of string)
-% Optimal control solver settings are loaded 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function solverSettings = getOptimalControlSolverSettings(settingsFileName)
-solverSettingsTree = xml2struct(settingsFileName);
-solverSettings.optimizationFileName = 'trackingOptimizationOutputFile.txt';
-solverSettings.derivativeSupplier = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_derivatives_supplier', 'sparseFD'));
-solverSettings.derivativeLevel = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_derivatives_level', 'first'));
-solverSettings.derivativeDependencies = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_derivatives_dependencies', 'sparse'));
-solverSettings.scaleMethods = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_scales_method', 'none'));
-solverSettings.method = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_method', 'RPM-Differentiation'));
-solverSettings.meshMethod = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_method', 'hp-PattersonRao'));
-solverSettings.meshTolerance = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_tolerance', '10e-3')));
-solverSettings.meshMaxIterations = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_max_iterations', '10')));
-solverSettings.meshColpointsMin = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_colpoints_min', '3')));
-solverSettings.meshColpointsMax = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_colpoints_max', '10')));
-solverSettings.meshSplitMult = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_splitmult', '1.2')));
-solverSettings.meshCurveRatio = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_curveratio', '2')));
-solverSettings.meshR = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_R', '1.2')));
-solverSettings.meshSigma = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_sigma', '0.5')));
-solverSettings.numCollocationPoints = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_phase_intervals', '6')));
-solverSettings.numIntervals = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_mesh_phase_colpoints_per_Interval', '10')));
-solverSettings.solverType = getTextFromField(getFieldByNameOrAlternate( ...
-    solverSettingsTree, 'setup_nlp_solver', 'ipopt'));
-solverSettings.linearSolverType = getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_nlp_linear_solver', 'ma57'));
-solverSettings.solverTolerance = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_nlp_tolerance', '1e-3')));
-solverSettings.stepSize = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_nlp_step_size', '1e-8')));
-solverSettings.maxIterations = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_nlp_max_iterations', '2e4')));
-solverSettings.displayLevel = str2double(getTextFromField( ...
-    getFieldByNameOrAlternate(solverSettingsTree, 'setup_display_level', '2')));
-solverSettings.integralBound = str2double( ...
-    parseElementTextByNameOrAlternate(solverSettingsTree, "integral_bound", "1"));
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlInitialGuess.m b/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlInitialGuess.m
deleted file mode 100644
index c3fd7153f..000000000
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/setupCommonOptimalControlInitialGuess.m
+++ /dev/null
@@ -1,81 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function sets up the common initial guess for an optimal control
-% problem and is used by Tracking Optimization, Verification Optimization,
-% and Design Optimization
-%
-% (struct) -> (struct)
-% return a set of setup values common to all optimal control problems
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Claire V. Hammond, Marleny Vega                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function guess = setupCommonOptimalControlInitialGuess(inputs)
-if isfield(inputs.initialGuess, 'state')
-    guess.phase.time = scaleToBounds(inputs.initialGuess.time, inputs.maxTime, ...
-        inputs.minTime);
-    guess.phase.state = scaleToBounds(inputs.initialGuess.state, ...
-        inputs.maxState, inputs.minState);
-else
-    guess.phase.state = scaleToBounds([inputs.experimentalJointAngles ...
-        inputs.experimentalJointVelocities ...
-        inputs.experimentalJointAccelerations], inputs.maxState, ...
-        inputs.minState);
-    guess.phase.time = scaleToBounds(inputs.experimentalTime, inputs.maxTime, ...
-        inputs.minTime);
-end
-if strcmp(inputs.controllerType, 'synergy_driven')
-    if isfield(inputs.initialGuess, 'control')
-        guess.phase.control = scaleToBounds(inputs.initialGuess.control, ...
-            inputs.maxControl, inputs.minControl);
-    else
-        guess.phase.control = scaleToBounds([inputs.experimentalJointJerks ...
-            inputs.synergyActivationsGuess], inputs.maxControl, inputs.minControl);
-    end
-    if isfield(inputs, "optimizeSynergyVectors") && ...
-            inputs.optimizeSynergyVectors
-        guess.parameter = scaleToBounds(inputs.synergyWeightsGuess, ...
-            inputs.maxParameter, inputs.minParameter);
-    end
-elseif strcmp(inputs.controllerType, 'torque_driven')
-    if isfield(inputs.initialGuess, 'control')
-        guess.phase.control = scaleToBounds(inputs.initialGuess.control, ...
-            inputs.maxControl, inputs.minControl);
-    else
-        for i = 1:length(inputs.controlTorqueNames)
-            indx = find(strcmp(convertCharsToStrings( ...
-                inputs.inverseDynamicMomentLabels), ...
-                strcat(inputs.controlTorqueNames(i), '_moment')));
-            if isempty(indx)
-                indx = find(strcmp(convertCharsToStrings( ...
-                inputs.inverseDynamicMomentLabels), ...
-                strcat(inputs.controlTorqueNames(i), '_force')));
-            end
-            controlTorquesGuess(:, i) = inputs.experimentalJointMoments(:, indx);
-        end
-        guess.phase.control = scaleToBounds([inputs.experimentalJointJerks ...
-            controlTorquesGuess], inputs.maxControl, inputs.minControl);
-    end
-end
-guess.phase.integral = scaleToBounds(1e1, inputs.maxIntegral, ...
-    inputs.minIntegral);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/SetupBounds/getDesignVariableInputBounds.m b/src/core/TreatmentOptimization/SetupBounds/getDesignVariableInputBounds.m
deleted file mode 100644
index 8f4f2c143..000000000
--- a/src/core/TreatmentOptimization/SetupBounds/getDesignVariableInputBounds.m
+++ /dev/null
@@ -1,112 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This functions computes the maximum and minimum values for all design
-% variables. The maximum and minimum values for most design variables are
-% based on the multiples value selected by the user times the range of data.
-% For example, if the angle B has a range of -5 to +5, and state position
-% multiple is 1, the maximum value of angle B is 15 and the minimum value
-% of angle B is -15. 
-%
-% (struct) -> (struct)
-% Computes max and min design variable bounds
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function inputs = getDesignVariableInputBounds(inputs)
-if isfield(inputs, "finalTimeRange")
-    inputs.maxTime = max(inputs.experimentalTime) + inputs.finalTimeRange;
-else
-    inputs.maxTime = max(inputs.experimentalTime);
-end
-inputs.minTime = min(inputs.experimentalTime);
-
-maxStatePositions = max(inputs.experimentalJointAngles) + ...
-    inputs.statePositionsMultiple * range(inputs.experimentalJointAngles);
-minStatePositions = min(inputs.experimentalJointAngles) - ...
-    inputs.statePositionsMultiple * range(inputs.experimentalJointAngles);
-maxStateVelocities = max(inputs.experimentalJointVelocities) + ...
-    inputs.stateVelocitiesMultiple * range(inputs.experimentalJointVelocities);
-minStateVelocities = min(inputs.experimentalJointVelocities) - ...
-    inputs.stateVelocitiesMultiple * range(inputs.experimentalJointVelocities);
-maxStateAccelerations = max(inputs.experimentalJointAccelerations) + ...
-    inputs.stateAccelerationsMultiple * range(inputs.experimentalJointAccelerations);
-minStateAccelerations = min(inputs.experimentalJointAccelerations) - ...
-    inputs.stateAccelerationsMultiple * range(inputs.experimentalJointAccelerations);
-
-inputs.maxState = [maxStatePositions maxStateVelocities maxStateAccelerations];
-inputs.minState = [minStatePositions minStateVelocities minStateAccelerations];
-
-maxControlJerks = max(inputs.experimentalJointJerks) + ...
-    inputs.controlJerksMultiple * range(inputs.experimentalJointJerks);
-minControlJerks = min(inputs.experimentalJointJerks) - ...
-    inputs.controlJerksMultiple * range(inputs.experimentalJointJerks);
-
-if strcmp(inputs.controllerType, 'synergy_driven') 
-    maxControlSynergyActivations = inputs.maxControlSynergyActivations * ...
-        ones(1, inputs.numSynergies);
-    inputs.maxControl = [maxControlJerks maxControlSynergyActivations];
-    inputs.minControl = [minControlJerks zeros(1, inputs.numSynergies)];
-    
-    if inputs.optimizeSynergyVectors
-    inputs.maxParameter = inputs.maxParameterSynergyWeights * ...
-        ones(1, inputs.numSynergyWeights);
-    inputs.minParameter = zeros(1, inputs.numSynergyWeights);
-    end
-elseif strcmp(inputs.controllerType, 'torque_driven') 
-    for i = 1:length(inputs.controlTorqueNames)
-        indx = find(strcmp(convertCharsToStrings( ...
-            inputs.inverseDynamicMomentLabels), ...
-            strcat(inputs.controlTorqueNames(i), '_moment')));
-        if isempty(indx)
-            indx = find(strcmp(convertCharsToStrings( ...
-                inputs.inverseDynamicMomentLabels), ...
-                strcat(inputs.controlTorqueNames(i), '_force')));
-        end
-        maxControlTorques(i) = max(inputs.experimentalJointMoments(:, ...
-            indx)) + inputs.maxControlTorquesMultiple * ...
-            range(inputs.experimentalJointMoments(:, indx));
-        minControlTorques(i) = min(inputs.experimentalJointMoments(:, ...
-            indx)) - inputs.maxControlTorquesMultiple * ...
-            range(inputs.experimentalJointMoments(:, indx));
-    end
-    inputs.maxControl = [maxControlJerks maxControlTorques];
-    inputs.minControl = [minControlJerks minControlTorques];
-end
-
-if isfield(inputs, "enableExternalTorqueControl") && ...
-        inputs.enableExternalTorqueControl 
-    for i = 1:length(inputs.externalControlTorqueNames)
-        indx = find(strcmp(convertCharsToStrings( ...
-            inputs.inverseDynamicMomentLabels), ...
-            strcat(inputs.externalControlTorqueNames(i), '_moment')));
-        maxExternalControlTorques(i) = max(inputs.experimentalJointMoments(:, ...
-            indx)) + inputs.maxExternalTorqueControls * ...
-            range(inputs.experimentalJointMoments(:, indx));
-        minExternalControlTorques(i) = min(inputs.experimentalJointMoments(:, ...
-            indx)) - inputs.maxExternalTorqueControls * ...
-            range(inputs.experimentalJointMoments(:, indx));
-    end
-    inputs.maxControl = [inputs.maxControl maxExternalControlTorques];
-    inputs.minControl = [inputs.minControl minExternalControlTorques];
-end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/calcDerivative.m b/src/core/TreatmentOptimization/calcDerivative.m
deleted file mode 100644
index ca429a890..000000000
--- a/src/core/TreatmentOptimization/calcDerivative.m
+++ /dev/null
@@ -1,47 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function calculates the first derivative of the curve provided using
-% piecewise polynomials.
-%
-% (Array of number, array of number) -> (Array of number)
-% Returns first derivative
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function [dataDerivative] = calcDerivative(time, data)
-
-fittingType = fittype('smoothingspline');
-fittingOptions = fitoptions('method', 'SmoothingSpline');
-fittedModel = fit(time, data, fittingType, fittingOptions);
-dataCoefficientStructure = fittedModel.p;
-% Calculate first derivative of smoothed curve
-dataDerivativeCoefficientStructure = dataCoefficientStructure;
-dataDerivativeCoefficientStructure.coefs(:,1) = 0;
-dataDerivativeCoefficientStructure.coefs(:,2) = ...
-    3*dataCoefficientStructure.coefs(:,1);
-dataDerivativeCoefficientStructure.coefs(:,3) = ...
-    2*dataCoefficientStructure.coefs(:,2);
-dataDerivativeCoefficientStructure.coefs(:,4) = ...
-    dataCoefficientStructure.coefs(:,3);
-dataDerivative = ppval(dataDerivativeCoefficientStructure, time);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/getTreatmentOptimizationInputs.m b/src/core/TreatmentOptimization/getTreatmentOptimizationInputs.m
deleted file mode 100644
index 6adee21f7..000000000
--- a/src/core/TreatmentOptimization/getTreatmentOptimizationInputs.m
+++ /dev/null
@@ -1,81 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses the settings tree resulting from xml2struct from the
-% settings XML file common to all treatment optimizatin modules (trackning,
-% verification, and design optimization).
-%
-% (struct) -> (struct, struct)
-% returns the input values for all treatment optimization modules
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function inputs = getTreatmentOptimizationInputs(tree)
-inputs.resultsDirectory = getTextFromField(getFieldByName(tree, ...
-    'results_directory'));
-if(isempty(inputs.resultsDirectory)); inputs.resultsDirectory = pwd; end
-inputs.controllerType = getTextFromField(getFieldByNameOrError(tree, ...
-    'type_of_controller'));
-inputs.model = parseModel(tree);
-inputs.osimx = parseOsimxFile(getTextFromField(getFieldByName(tree, ...
-    'osimx_file')));
-if strcmp(inputs.controllerType, 'synergy_driven')
-    inputs.synergyGroups = getSynergyGroups(tree, Model(inputs.model));
-    inputs.numSynergies = getNumSynergies(inputs.synergyGroups);
-    inputs.numSynergyWeights = getNumSynergyWeights(inputs.synergyGroups);
-    inputs.surrogateModelCoordinateNames = parseSpaceSeparatedList(tree, ...
-        "coordinate_list");
-    inputs.muscleNames = getMusclesFromCoordinates(inputs.model, ...
-        inputs.surrogateModelCoordinateNames);
-    inputs.numMuscles = length(inputs.muscleNames);
-    inputs.epsilon = str2double(parseElementTextByNameOrAlternate(tree, ...
-        "epsilon", "1e-4"));
-    inputs.vMaxFactor = str2double(parseElementTextByNameOrAlternate(tree, ...
-        "v_max_factor", "10"));
-    surrogateModelCoefficients = load(getTextFromField(getFieldByName(tree, ...
-        'surrogate_model_coefficients')));
-    inputs.coefficients = surrogateModelCoefficients.coefficients;
-    inputs = getModelOrOsimxInputs(inputs);
-elseif strcmp(inputs.controllerType, 'torque_driven')
-    inputs.controlTorqueNames = parseSpaceSeparatedList(tree, ...
-        "coordinate_list");
-    inputs.numTorqueControls = length(inputs.controlTorqueNames);
-end
-inputs.optimizeSynergyVectors = getBooleanLogic(...
-    parseElementTextByNameOrAlternate(tree, "optimize_synergy_vectors", 0));
-inputs = parseTreatmentOptimizationDataDirectory(tree, inputs);
-inputs.initialGuess = getGpopsInitialGuess(tree);
-% inputs.experimentalTime = inputs.experimentalTime / ...
-%     inputs.experimentalTime(end);
-inputs.costTerms = parseRcnlCostTermSet( ...
-    getFieldByNameOrError(tree, 'RCNLCostTermSet').RCNLCostTerm);
-inputs.path = getPathConstraintTerms(tree);
-inputs.terminal = getTerminalConstraintTerms(tree);
-contactSurfaces = getFieldByName(inputs.osimx, "contactSurface");
-if (isstruct(contactSurfaces) || iscell(contactSurfaces)) && ...
-        isfield(inputs, "grfFileName")
-    inputs.contactSurfaces = prepareGroundContactSurfaces(inputs.model, ...
-        contactSurfaces, inputs.grfFileName);
-else
-    inputs.contactSurfaces = {};
-end
-end
diff --git a/src/core/TreatmentOptimization/getTreatmentOptimizationValueStruct.m b/src/core/TreatmentOptimization/getTreatmentOptimizationValueStruct.m
deleted file mode 100644
index 5d526ba2d..000000000
--- a/src/core/TreatmentOptimization/getTreatmentOptimizationValueStruct.m
+++ /dev/null
@@ -1,53 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function parses and scales the design variables common to all 
-% treatment optimization modules (tracking, verification, and design 
-% optimization). Time, states, and controls are parsed and scaled back to
-% their original values.
-%
-% (struct, struct) -> (struct)
-% Design variables common to all treatment optimization modules are parsed
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function values = getTreatmentOptimizationValueStruct(inputs, params)
-
-values.time = scaleToOriginal(inputs.time, params.maxTime, ...
-    params.minTime);
-state = scaleToOriginal(inputs.state, ones(size(inputs.state, 1), 1) .* ...
-    params.maxState, ones(size(inputs.state, 1), 1) .* params.minState);
-control = scaleToOriginal(inputs.control, ones(size(inputs.control, 1), 1) .* ...
-    params.maxControl, ones(size(inputs.control, 1), 1) .* params.minControl);
-values.statePositions = getCorrectStates(state, 1, params.numCoordinates);
-values.stateVelocities = getCorrectStates(state, 2, params.numCoordinates);
-values.stateAccelerations = getCorrectStates(state, 3, params.numCoordinates);
-values.controlJerks = control(:, 1 : params.numCoordinates);
-
-if ~strcmp(params.controllerType, 'synergy_driven')
-    values.controlTorques = control(:, params.numCoordinates + 1 : ...
-    params.numCoordinates + params.numTorqueControls);
-else 
-    values.controlSynergyActivations = control(:, ...
-    params.numCoordinates + 1 : params.numCoordinates + params.numSynergies);
-end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/saveCommonOptimalControlResults.m b/src/core/TreatmentOptimization/saveCommonOptimalControlResults.m
deleted file mode 100644
index 6ca194c34..000000000
--- a/src/core/TreatmentOptimization/saveCommonOptimalControlResults.m
+++ /dev/null
@@ -1,97 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% This function saves and prints the unscaled results from all
-% treatment optimization modules (tracking, verification, and design 
-% optimization. 
-%
-% (struct, struct) -> (None)
-% Prints treatment optimization results
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Claire V. Hammond, Marleny Vega                              %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function saveCommonOptimalControlResults(solution, inputs, values)
-outputDirectory = fullfile(inputs.resultsDirectory, 'optimal');
-if ~exist(outputDirectory, 'dir')
-    mkdir(outputDirectory)
-end
-writeToSto(inputs.coordinateNames, values.time, values.statePositions, ...
-    fullfile(outputDirectory, "inverseKinematics.sto"));
-writeToSto(inputs.inverseDynamicMomentLabels, values.time, ...
-    solution.inverseDynamicMoments, fullfile(outputDirectory, ...
-    "inverseDynamics.sto"));
-groundContactLabels = [];
-groundContactData = [];
-for i = 1:length(inputs.contactSurfaces)
-    groundContactLabels = cat(2, groundContactLabels, ...
-        [inputs.contactSurfaces{i}.forceColumns, ...
-        inputs.contactSurfaces{i}.momentColumns, ...
-        inputs.contactSurfaces{i}.electricalCenterColumns]);
-    midfootSuperiorLocation = pointKinematics(values.time, ...
-        values.statePositions, values.stateVelocities, ...
-        inputs.contactSurfaces{i}.midfootSuperiorPointOnBody', ...
-        inputs.contactSurfaces{i}.midfootSuperiorBody, inputs.coordinateNames);
-    midfootSuperiorLocation(:, 2) = 0;
-    groundContactData = [groundContactData, ...
-        solution.groundReactionsLab.forces{i}, ...
-        solution.groundReactionsLab.moments{i}, ...
-        midfootSuperiorLocation];
-end
-if ~isempty(groundContactData)
-    writeToSto(groundContactLabels, values.time, ...
-        groundContactData, fullfile(outputDirectory, ...
-        "groundReactions.sto"));
-end
-stateLabels = inputs.coordinateNames;
-for i = 1 : length(inputs.coordinateNames)
-    stateLabels{end + 1} = strcat(inputs.coordinateNames{i}, '_u');
-end
-for i = 1 : length(inputs.coordinateNames)
-    stateLabels{end + 1} = strcat(inputs.coordinateNames{i}, '_dudt');
-end
-writeToSto(stateLabels, values.time, [values.statePositions ...
-    values.stateVelocities values.stateAccelerations], ...
-    fullfile(inputs.resultsDirectory, "statesSolution.sto"));
-if strcmp(inputs.controllerType, 'synergy_driven')
-    controlLabels = inputs.coordinateNames;
-    for i = 1 : inputs.numSynergies
-        controlLabels{end + 1} = strcat('synergy_activation', num2str(i));
-    end
-    if isfield(values, "controlNeuralCommands")
-        commands = values.controlNeuralCommands;
-    else
-        commands = values.controlSynergyActivations;
-    end
-    writeToSto(controlLabels, values.time, [values.controlJerks ...
-        commands], fullfile(inputs.resultsDirectory, ...
-        "controlSolution.sto"));
-elseif strcmp(inputs.controllerType, 'torque_driven')
-    controlLabels = inputs.coordinateNames;
-    for i = 1 : inputs.numTorqueControls
-        controlLabels{end + 1} = strcat('torqueControl', num2str(i));
-    end
-    writeToSto(controlLabels, values.time, [values.controlJerks ...
-        values.controlTorques], fullfile(inputs.resultsDirectory, ...
-        "controlSolution.sto"));
-end
-delete(inputs.mexModel);
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/updateMuscleModelProperties.m b/src/core/TreatmentOptimization/updateMuscleModelProperties.m
deleted file mode 100644
index 42d9fa3ca..000000000
--- a/src/core/TreatmentOptimization/updateMuscleModelProperties.m
+++ /dev/null
@@ -1,46 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% If muscles are present, this model updates the optimal fiber length, max
-% isometric force, and tendon slack length values based on changes 
-% resulting from design optimization or from updated values from the 
-% osimx file. 
-%
-% (struct) -> (struct)
-% Updated muscle model properties in the osim model
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE-2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function inputs = updateMuscleModelProperties(inputs)
-if ~isa(inputs.model, 'org.opensim.modeling.Model')
-    inputs.model = Model(inputs.model);
-end
-if strcmp(inputs.controllerType, 'synergy_driven')
-for i = 1 : inputs.numMuscles
-    inputs.model.getForceSet().getMuscles().get(inputs.muscleNames(i)). ...
-        setOptimalFiberLength(inputs.optimalFiberLength(i));
-    inputs.model.getForceSet().getMuscles().get(inputs.muscleNames(i)). ...
-        setTendonSlackLength(inputs.tendonSlackLength(i));
-    inputs.model.getForceSet().getMuscles().get(inputs.muscleNames(i)). ...
-        setMaxIsometricForce(inputs.maxIsometricForce(i));
-end
-end
\ No newline at end of file
diff --git a/src/core/mex/PointKinematics.cpp b/src/core/mex/PointKinematics.cpp
new file mode 100644
index 000000000..b11d21a11
--- /dev/null
+++ b/src/core/mex/PointKinematics.cpp
@@ -0,0 +1,139 @@
+#include "mex.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <OpenSim/OpenSim.h>
+#include <omp.h>
+
+using namespace OpenSim;
+using namespace SimTK;
+using namespace std;
+#define NTHREADS 20
+
+//______________________________________________________________________________
+
+
+static Model *osimModel[NTHREADS];
+static State *osimState[NTHREADS];
+static bool modelIsLoaded = false;
+
+void ClearMemory(void)
+{
+	for (int i = 0; i<NTHREADS; ++i)
+		delete osimModel[i];
+	modelIsLoaded = false;
+	mexPrintf("Cleared memory from opensimPointKin mex file.\n");
+}
+
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
+{
+
+	mexAtExit(ClearMemory); // exit function to clear memory allocated in heap
+
+	if (nrhs == 1) // Load model if only one right hand side argument
+	{
+		if (modelIsLoaded == true) {
+			ClearMemory();
+		}
+		string model_name = mxArrayToString(prhs[0]);
+
+		std::streambuf* oldCoutStreamBuf = std::cout.rdbuf();
+		std::ostringstream strCout;
+		std::cout.rdbuf(strCout.rdbuf());
+
+		for (int i = 0; i < NTHREADS; ++i)
+		{
+			osimModel[i] = new Model(model_name);
+			osimState[i] = &osimModel[i]->initSystem();
+		}
+
+		std::cout.rdbuf(oldCoutStreamBuf);
+		modelIsLoaded = true;
+	}
+	else if (nrhs == 6)
+	{
+		if (modelIsLoaded == false)
+		{
+			mexErrMsgTxt("!!!No OpenSim model has been loaded!!!\n");
+		}
+
+		const int numPts = mxGetM(prhs[0]); // get number of rows of time vector
+		const int numSprings = mxGetN(prhs[3]); // get number of bodies springs are located on
+		const int numLabels = mxGetN(prhs[5]);
+
+		double *time = mxGetPr(prhs[0]); // time vector
+		double *q = mxGetPr(prhs[1]); // joint angles matrix
+		double *qp = mxGetPr(prhs[2]); // joint velocities matrix
+		double *SpringMat = mxGetPr(prhs[3]); // spring locations within body
+		double *SpringBodyMat = mxGetPr(prhs[4]); // body number index for springs
+
+		OpenSim::BodySet *refBodySet[NTHREADS];
+		for (int i = 0; i<NTHREADS; ++i)
+		{
+			refBodySet[i] = &osimModel[i]->updBodySet();
+		}
+
+		mwSize dims[3];
+		dims[0] = numPts;
+		dims[1] = 3;
+		dims[2] = numSprings;
+		plhs[0] = mxCreateNumericArray(3, dims, mxDOUBLE_CLASS, mxREAL);
+		plhs[1] = mxCreateNumericArray(3, dims, mxDOUBLE_CLASS, mxREAL);
+		//plhs[0] = mxCreateDoubleMatrix(numPts * numSprings, 3, mxREAL);
+		//plhs[1] = mxCreateDoubleMatrix(numPts * numSprings, 3, mxREAL);
+		double *sp_pos = mxGetPr(plhs[0]);
+		double *sp_vel = mxGetPr(plhs[1]);
+		
+		const mxArray *cell_element_ptr;
+        char* c_array;
+        mwIndex k;
+		mwSize buflen;
+
+		#pragma omp parallel for num_threads(NTHREADS)
+		for (int i = 0; i<numPts; ++i)
+		{
+			int thread_id = omp_get_thread_num();
+
+            for (int k = 0; k < numLabels; k++){
+                cell_element_ptr = mxGetCell(prhs[5], k);
+				buflen = mxGetN(cell_element_ptr) * sizeof(mxChar) + 1;
+				c_array = (char *)mxCalloc(buflen, sizeof(char));
+				mxGetString(cell_element_ptr, c_array, buflen);
+				string c_string(c_array);
+
+				if (!osimModel[thread_id]->getCoordinateSet().get(c_array).get_locked())
+				{
+					osimModel[thread_id]->getCoordinateSet().get(c_array).setValue(*osimState[thread_id], q[k*numPts + i]);
+					osimModel[thread_id]->getCoordinateSet().get(c_array).setSpeedValue(*osimState[thread_id], qp[k*numPts + i]);
+				}
+				mxFree(c_array);
+            }
+			
+            osimModel[thread_id]->realizeVelocity(*osimState[thread_id]);
+
+			for (int j = 0; j<numSprings; j++)
+			{
+				OpenSim::Body& tempRefParentBody = refBodySet[thread_id]->get(SpringBodyMat[j]);
+				Vec3 tempLocalPos;
+				tempLocalPos.set(0, SpringMat[j * 3]);
+				tempLocalPos.set(1, SpringMat[j * 3 + 1]);
+				tempLocalPos.set(2, SpringMat[j * 3 + 2]);
+
+				Vec3 tempGlobalPos;
+				Vec3 tempGlobalVel;
+
+				osimModel[thread_id]->getSimbodyEngine().getPosition(*osimState[thread_id], tempRefParentBody, tempLocalPos, tempGlobalPos);
+				osimModel[thread_id]->getSimbodyEngine().getVelocity(*osimState[thread_id], tempRefParentBody, tempLocalPos, tempGlobalVel);
+				
+				sp_pos[i + j * numPts * 3 + numPts * 0] = tempGlobalPos(0);
+				sp_pos[i + j * numPts * 3 + numPts * 1] = tempGlobalPos(1);
+				sp_pos[i + j * numPts * 3 + numPts * 2] = tempGlobalPos(2);
+
+				sp_vel[i + j * numPts * 3 + numPts * 0] = tempGlobalVel(0);
+				sp_vel[i + j * numPts * 3 + numPts * 1] = tempGlobalVel(1);
+				sp_vel[i + j * numPts * 3 + numPts * 2] = tempGlobalVel(2);
+				
+			}
+		}
+	}
+}
\ No newline at end of file
diff --git a/src/core/mex/PointKinematicsMatlab.m b/src/core/mex/PointKinematicsMatlab.m
new file mode 100644
index 000000000..1b977216f
--- /dev/null
+++ b/src/core/mex/PointKinematicsMatlab.m
@@ -0,0 +1,47 @@
+function [SpringPos, SpringVel] = pointKinematicsMatlab(time,q,qp,SpringMat,SpringBodyMat,...
+    modelFile,IKLabels)
+
+    % Load Library
+    import org.opensim.modeling.*;
+
+    % Open a Model by name
+    osimModel = Model(modelFile);
+
+    % Initialize the system and get the initial state
+    osimState = osimModel.initSystem();
+    
+    % Get the number of coords and markers
+    numPts = size(time,1);
+    numSprings = size(SpringMat,1);
+
+    refBodySet = osimModel.getBodySet; 
+        
+    for j=1:numPts
+        osimState.setTime(time(j,1));
+        for k=1:size(IKLabels,2)
+            if ~osimModel.getCoordinateSet.get(IKLabels{k}).get_locked
+                osimModel.getCoordinateSet.get(IKLabels{k}).setValue(osimState,q(j,k));
+                osimModel.getCoordinateSet.get(IKLabels{k}).setSpeedValue(osimState,qp(j,k));
+            end
+        end
+        osimModel.realizeVelocity(osimState);
+
+        for i=1:numSprings
+            tempRefParentBody = refBodySet.get(SpringBodyMat(i));
+            tempLocalPos = Vec3(3,0);
+            tempGlobalPos = Vec3(3,0);
+            tempGlobalVel = Vec3(3,0);
+            tempLocalPos.set(0,SpringMat(i,1));
+            tempLocalPos.set(1,SpringMat(i,2));
+            tempLocalPos.set(2,SpringMat(i,3));
+
+            osimModel.getSimbodyEngine.getPosition(osimState,tempRefParentBody,tempLocalPos,tempGlobalPos);
+            osimModel.getSimbodyEngine.getVelocity(osimState,tempRefParentBody,tempLocalPos,tempGlobalVel);
+            
+            for k=0:2
+               SpringPos(j,(i-1)*3+k+1)=tempGlobalPos.get(k);
+               SpringVel(j,(i-1)*3+k+1)=tempGlobalVel.get(k);
+            end
+        end
+    end
+end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OpenSimMex/calcBodyLocation.m b/src/core/mex/calcBodyLocation.m
similarity index 100%
rename from src/core/TreatmentOptimization/OpenSimMex/calcBodyLocation.m
rename to src/core/mex/calcBodyLocation.m
diff --git a/src/core/TreatmentOptimization/OpenSimMex/calcBodyVelocity.m b/src/core/mex/calcBodyVelocity.m
similarity index 100%
rename from src/core/TreatmentOptimization/OpenSimMex/calcBodyVelocity.m
rename to src/core/mex/calcBodyVelocity.m
diff --git a/src/core/mex/compileMex.m b/src/core/mex/compileMex.m
new file mode 100644
index 000000000..ffef55e49
--- /dev/null
+++ b/src/core/mex/compileMex.m
@@ -0,0 +1,24 @@
+mex CXXFLAGS="/$CXXFLAGS -fopenmp" LDFLAGS="/$LDFLAGS -fopenmp"...
+    COMPFLAGS="/openmp $COMPFLAGS"...
+    inverseDynamicsWithExtraCalcsMexWindows.cpp...
+    -L'C:\OpenSim 4.4\sdk\lib'...
+    -L'C:\OpenSim 4.4\sdk\Simbody\lib'...
+    -L'C:\OpenSim 4.4\sdk\spdlog\lib\spdlog'...
+    -L'C:\OpenSim 4.4\sdk\spdlog\include'...
+    -L'C:\OpenSim 4.4\sdk\spdlog\include\spdlog'...
+    -losimCommon -losimSimulation...
+    -losimAnalyses -losimActuators -losimTools...
+    -lSimTKcommon -lSimTKmath...
+    -lSimTKsimbody -lliblapack...
+    -llibblas -losimJavaJNI -losimLepton...
+    -lspdlog...
+    -I'C:\OpenSim 4.4\sdk\include'...
+    -I'C:\OpenSim 4.4\sdk\include\OpenSim'...
+    -I'C:\OpenSim 4.4\sdk\Simbody\include'...
+    -I'C:\OpenSim 4.4\sdk\include\OpenSim\Simulation'...
+    -I'C:\OpenSim 4.4\sdk\spdlog\include'...
+    -I'C:\OpenSim 4.4\sdk\spdlog\include\spdlog\details'...
+    -I'C:\Program Files (x86)\Windows Kits\10\Include\10.0.22621.0\ucrt'...
+    -I'C:\OpenSim 4.4\sdk\include\OpenSim\Common'...
+    -DWIN32 -D_WINDOWS  -DNDEBUG...
+    ; 
\ No newline at end of file
diff --git a/src/core/mex/evaluateGcvSplinesMexWindows.cpp b/src/core/mex/evaluateGcvSplinesMexWindows.cpp
new file mode 100644
index 000000000..23e0a5f9f
--- /dev/null
+++ b/src/core/mex/evaluateGcvSplinesMexWindows.cpp
@@ -0,0 +1,112 @@
+// This function is part of the NMSM Pipeline, see file for full license.
+//
+// performs inverse dynamics with openMP
+
+// ----------------------------------------------------------------------- //
+// The NMSM Pipeline is a toolkit for model personalization and treatment  //
+// optimization of neuromusculoskeletal models through OpenSim. See        //
+// nmsm.rice.edu and the NOTICE file for more information. The             //
+// NMSM Pipeline is developed at Rice University and supported by the US   //
+// National Institutes of Health (R01 EB030520).                           //
+//                                                                         //
+// Copyright (c) 2021 Rice University and the Authors                      //
+// Author(s): Marleny Vega                                                 //
+//                                                                         //
+// Licensed under the Apache License, Version 2.0 (the "License");         //
+// you may not use this file except in compliance with the License.        //
+// You may obtain a copy of the License at                                 //
+// http://www.apache.org/licenses/LICENSE-2.0.                             //
+//                                                                         //
+// Unless required by applicable law or agreed to in writing, software     //
+// distributed under the License is distributed on an "AS IS" BASIS,       //
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         //
+// implied. See the License for the specific language governing            //
+// permissions and limitations under the License.                          //
+// ----------------------------------------------------------------------- //
+
+#include "mex.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <OpenSim/OpenSim.h>
+#include <GCVSplineSet.h>
+#include <string.h>
+#include <omp.h>
+#include <matrix.h>
+#include <iostream> 
+#include <vector>
+#include <io.h>
+#include <process.h>
+#include <windows.h>
+
+using namespace OpenSim;
+using namespace SimTK;
+using namespace std;
+
+//______________________________________________________________________________
+
+
+void ClearMemory(void){
+}
+
+vector<vector<double>> mexArrayToVector(const mxArray *input) {
+    const mwSize *dimension;
+    dimension = mxGetDimensions(input);
+    int rows = (int) dimension[0];
+    int columns = (int) dimension[1];
+    double *data = (double *) mxGetData(input);
+    vector<vector<double>> output(rows, vector<double>(columns));
+    for (int i = 0; i < rows; i++) {
+        for (int j = 0; j < columns; j++) {
+            memcpy(&output[i][j], data + i + j * rows, sizeof(double) );
+        }
+    }
+    return output;
+}
+
+vector<int> mexArrayToVectorInt(const mxArray *input, int numPts) {
+    int *data = (int *) mxGetData(input);
+    vector<int> output(numPts);
+    for (int i = 0; i < numPts; i++) {
+        memcpy(&output[i], data + i, sizeof(int) );
+    }
+    return output;
+}
+
+vector<double> mexArrayToVectorDouble(const mxArray *input, int numPts) {
+    double *data = (double *) mxGetData(input);
+    vector<double> output(numPts);
+    for (int i = 0; i < numPts; i++) {
+        memcpy(&output[i], data + i, sizeof(double) );
+    }
+    return output;
+}
+
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
+    mexAtExit(ClearMemory);
+    if (nrhs == 4) {
+        const int numColumns = mxGetN(prhs[1]);
+		const int numPts = mxGetN(prhs[2]);
+
+        vector<int> columns = mexArrayToVectorInt(prhs[1], numColumns);
+        vector<double> time = mexArrayToVectorDouble(prhs[2], numPts);
+
+        mexPrintf(typeid(dynamic_cast<GCVSplineSet*>(mxGetPr(prhs[0]))).name());
+
+        GCVSplineSet *splineSet = dynamic_cast<GCVSplineSet*>(mxGetPr(prhs[0]));
+
+        // int derivative = mxGetScalar(prhs[3]);
+
+        // plhs[0] = mxCreateDoubleMatrix(numPts,numColumns,mxREAL);
+		// double *values = mxGetPr(plhs[0]);
+
+        // for (int i = 0; i < numColumns; i++) {
+        //     for (int j = 0; j < numPts; j++) {
+        //         values[j + numPts * i] = splineSet->evaluate(columns[i], 0, time[j]);
+        //     }
+        // }
+
+		// columns.clear();
+		// time.clear();
+    }   
+}
\ No newline at end of file
diff --git a/src/core/mex/evaluateGcvSplinesMexWindows.mexw64 b/src/core/mex/evaluateGcvSplinesMexWindows.mexw64
new file mode 100644
index 000000000..d23d58b32
Binary files /dev/null and b/src/core/mex/evaluateGcvSplinesMexWindows.mexw64 differ
diff --git a/src/core/mex/howToMakeMex.txt b/src/core/mex/howToMakeMex.txt
new file mode 100644
index 000000000..689ea3eef
--- /dev/null
+++ b/src/core/mex/howToMakeMex.txt
@@ -0,0 +1,21 @@
+mex CXXFLAGS="/$CXXFLAGS -fopenmp" LDFLAGS="/$LDFLAGS -fopenmp"...
+    COMPFLAGS="/openmp $COMPFLAGS"...
+    inverseDynamicsMexWindows.cpp...  
+    -L'C:\OpenSim 4.4\sdk\lib'...
+    -L'C:\OpenSim 4.4\sdk\Simbody\lib'...
+    -L'C:\OpenSim 4.4\sdk\spdlog\lib\spdlog'...
+    -L'C:\OpenSim 4.4\sdk\spdlog\include'...
+    -L'C:\OpenSim 4.4\sdk\spdlog\include\spdlog'...
+    -losimCommon -losimSimulation...
+    -losimAnalyses -losimActuators -losimTools...
+    -lSimTKcommon -lSimTKmath...
+    -lSimTKsimbody -lliblapack...
+    -llibblas -losimJavaJNI -losimLepton...
+    -lspdlog...
+    -I'C:\OpenSim 4.4\sdk\include'...
+    -I'C:\OpenSim 4.4\sdk\include\OpenSim'...
+    -I'C:\OpenSim 4.4\sdk\Simbody\include'...
+    -I'C:\OpenSim 4.4\sdk\include\OpenSim\Simulation'...
+    -I'C:\OpenSim 4.4\sdk\spdlog\include'...
+    -DWIN32 -D_WINDOWS  -DNDEBUG...
+    ; 
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/OpenSimMex/initializeMexOrMatlabParallelFunctions.m b/src/core/mex/initializeMexOrMatlabParallelFunctions.m
similarity index 97%
rename from src/core/TreatmentOptimization/OpenSimMex/initializeMexOrMatlabParallelFunctions.m
rename to src/core/mex/initializeMexOrMatlabParallelFunctions.m
index 9be9ddd71..b088f68c3 100644
--- a/src/core/TreatmentOptimization/OpenSimMex/initializeMexOrMatlabParallelFunctions.m
+++ b/src/core/mex/initializeMexOrMatlabParallelFunctions.m
@@ -32,7 +32,7 @@
 function initializeMexOrMatlabParallelFunctions(modelFile)
 if isequal(mexext, 'mexw64')
     pointKinematicsMexWindows(modelFile);
-    inverseDynamicsMexWindows(modelFile);
+    inverseDynamicsWithExtraCalcsMexWindows(modelFile);
 end
 clear inverseDynamicsMatlabParallel
 clear pointKinematicsMatlabParallel
diff --git a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamics.m b/src/core/mex/inverseDynamics.m
similarity index 61%
rename from src/core/TreatmentOptimization/OpenSimMex/inverseDynamics.m
rename to src/core/mex/inverseDynamics.m
index f42c0a267..b4f5eeaa8 100644
--- a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamics.m
+++ b/src/core/mex/inverseDynamics.m
@@ -2,8 +2,10 @@
 %
 % This function uses a mex file or a matlab function with parallel workers
 % to calculate inverse dynamics moments.
-% 
-% (Array of number, 2D matrix, 2D matrix, 2D matrix, Cell, 2D matrix, 
+%
+% This assumes muscleActivations matrix is in model muscle order
+%
+% (Array of number, 2D matrix, 2D matrix, 2D matrix, Cell, 2D matrix,
 % Array of string) -> (2D matrix)
 % Returns inverse dynamic moments
 
@@ -29,16 +31,28 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inverseDynamicMoments = inverseDynamics(time, jointAngles, ...
-    jointVelocities, jointAccelerations, coordinateLabels, appliedLoads, ...
-    modelName)
-% if isequal(mexext, 'mexw64')
-%     inverseDynamicMoments = inverseDynamicsMexWindows(time, jointAngles, ...
-%         jointVelocities, jointAccelerations, coordinateLabels, ...
-%         appliedLoads);
-% else
-    inverseDynamicMoments = inverseDynamicsMatlabParallel(time, ...
-        jointAngles, jointVelocities, jointAccelerations, coordinateLabels, ...
-        appliedLoads, modelName);
-% end
-end
\ No newline at end of file
+function [inverseDynamicsMoments, angularMomentum, metabolicCost, ...
+    massCenterVelocity] = ...
+    inverseDynamics( time, jointAngles, jointVelocities, ...
+    jointAccelerations, coordinateLabels, appliedLoads, modelName, ...
+    muscleActivations, computeAngularMomentum, computeMetabolicCost)
+if isequal(mexext, 'mexw64')
+    [inverseDynamicsMoments, angularMomentum, metabolicCost, ...
+        massCenterVelocity] = ...
+        inverseDynamicsWithExtraCalcsMexWindows(time, jointAngles, ...
+        jointVelocities, jointAccelerations, coordinateLabels, ...
+        appliedLoads, muscleActivations, computeAngularMomentum, ...
+        computeMetabolicCost);
+else
+    if nargout == 1
+        inverseDynamicsMoments = inverseDynamicsMatlabParallel(time, ...
+            jointAngles, jointVelocities, jointAccelerations, ...
+            coordinateLabels, appliedLoads, modelName);
+    else
+        [inverseDynamicsMoments, angularMomentum] = ...
+            inverseDynamicsMatlabParallel(time, ...
+            jointAngles, jointVelocities, jointAccelerations, ...
+            coordinateLabels, appliedLoads, modelName);
+    end
+end
+end
diff --git a/src/core/mex/inverseDynamicsAngularMomentumMexWindows.cpp b/src/core/mex/inverseDynamicsAngularMomentumMexWindows.cpp
new file mode 100644
index 000000000..5a9cb0b4c
--- /dev/null
+++ b/src/core/mex/inverseDynamicsAngularMomentumMexWindows.cpp
@@ -0,0 +1,172 @@
+// This function is part of the NMSM Pipeline, see file for full license.
+//
+// performs inverse dynamics with openMP
+
+// ----------------------------------------------------------------------- //
+// The NMSM Pipeline is a toolkit for model personalization and treatment  //
+// optimization of neuromusculoskeletal models through OpenSim. See        //
+// nmsm.rice.edu and the NOTICE file for more information. The             //
+// NMSM Pipeline is developed at Rice University and supported by the US   //
+// National Institutes of Health (R01 EB030520).                           //
+//                                                                         //
+// Copyright (c) 2021 Rice University and the Authors                      //
+// Author(s): Marleny Vega                                                 //
+//                                                                         //
+// Licensed under the Apache License, Version 2.0 (the "License");         //
+// you may not use this file except in compliance with the License.        //
+// You may obtain a copy of the License at                                 //
+// http://www.apache.org/licenses/LICENSE-2.0.                             //
+//                                                                         //
+// Unless required by applicable law or agreed to in writing, software     //
+// distributed under the License is distributed on an "AS IS" BASIS,       //
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         //
+// implied. See the License for the specific language governing            //
+// permissions and limitations under the License.                          //
+// ----------------------------------------------------------------------- //
+
+#include "mex.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <OpenSim/OpenSim.h>
+#include <InverseDynamicsSolver.h>
+#include <string.h>
+#include <omp.h> //
+#include <matrix.h>
+#include <iostream> 
+#include <vector>
+
+using namespace OpenSim;
+using namespace SimTK;
+using namespace std;
+#define numThreads 20 //
+
+//______________________________________________________________________________
+
+static Model *osimModel[numThreads];
+static State *osimState[numThreads];
+static InverseDynamicsSolver *idSolver[numThreads];
+static bool modelIsLoaded = false;
+
+void ClearMemory(void){
+    for (int i = 0; i < numThreads; i++){
+		delete osimModel[i];
+		delete idSolver[i];
+	}
+    modelIsLoaded = false;
+    mexPrintf("Cleared memory from inverseDynamics mex file.\n");
+}
+
+vector<vector<double>> mexArrayToVector(const mxArray *input) {
+    const mwSize *dimension;
+    dimension = mxGetDimensions(input);
+    int rows = (int) dimension[0];
+    int columns = (int) dimension[1];
+    double *data = (double *) mxGetData(input);
+    vector<vector<double>> output(rows, vector<double>(columns));
+    for (int i = 0; i < rows; i++) {
+        for (int j = 0; j < columns; j++) {
+            memcpy(&output[i][j], data + i + j * rows, sizeof(double) );
+        }
+    }
+    return output;
+}
+
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
+    mexAtExit(ClearMemory);
+    if (nrhs == 1) {    
+        if (modelIsLoaded == true){
+            ClearMemory();
+        }
+        string modelName = mxArrayToString(prhs[0]);      
+        std::streambuf* oldCoutStreamBuf = std::cout.rdbuf();
+		std::ostringstream strCout;
+		std::cout.rdbuf(strCout.rdbuf());
+        for (int i = 0; i < numThreads; i++){
+			osimModel[i] = new Model(modelName); 
+			osimState[i] = &osimModel[i]->initSystem();
+			idSolver[i] = new InverseDynamicsSolver(*osimModel[i]);
+		}  
+		std::cout.rdbuf(oldCoutStreamBuf);
+        modelIsLoaded = true;
+    }
+    else if (nrhs == 6) {
+        if (modelIsLoaded == false){
+            mexErrMsgTxt("!!!No OpenSim model has been loaded!!!\n");
+        }   
+		const int numPts = mxGetM(prhs[0]);
+        const int numQs = mxGetN(prhs[1]);
+		const int numControls = mxGetN(prhs[5]);
+        const int numCoords = osimState[0]->getNQ();
+
+        double *time = mxGetPr(prhs[0]);
+        vector<vector<double>> q = mexArrayToVector(prhs[1]);
+        vector<vector<double>> qp = mexArrayToVector(prhs[2]);
+        vector<vector<double>> qpp = mexArrayToVector(prhs[3]);
+        vector<vector<double>> u = mexArrayToVector(prhs[5]);
+
+        mwIndex k;
+        mwSize numLabels, buflen;
+        numLabels = mxGetNumberOfElements(prhs[4]);
+
+        plhs[0] = mxCreateDoubleMatrix(numPts,numCoords,mxREAL);
+		double *idLoads = mxGetPr(plhs[0]);
+ 		plhs[1] = mxCreateDoubleMatrix(numPts, 3, mxREAL);
+        double* angularMomentum = mxGetPr(plhs[1]);
+
+        #pragma omp parallel for num_threads(numThreads)
+        for (int i = 0; i < numPts; ++i){
+            int thread_id = omp_get_thread_num();
+            osimState[thread_id]->setTime(time[i]);
+			
+            for (int k = 0; k < numLabels; k++){
+				const mxArray *cellElementPtr;
+                cellElementPtr = mxGetCell(prhs[4], k);
+                buflen = mxGetN(cellElementPtr)*sizeof(mxChar) + 1;
+                char* c_array;
+                c_array = (char *)  mxCalloc(buflen, sizeof(char));
+                int status = mxGetString(cellElementPtr, c_array, buflen);
+                osimModel[thread_id]->getCoordinateSet().get(c_array).setValue(*osimState[thread_id], q[i][k], false);
+                osimModel[thread_id]->getCoordinateSet().get(c_array).setSpeedValue(*osimState[thread_id], qp[i][k]);
+                mxFree(c_array);
+            }
+
+            osimModel[thread_id]->realizeVelocity(*osimState[thread_id]);
+            if (nlhs > 1) {
+                SpatialVec momentum = osimModel[thread_id]->getMatterSubsystem().calcSystemCentralMomentum(*osimState[thread_id]);
+                Vec3 angularMomentumPoint = momentum.get(0);
+                for (int j = 0; j <= 2; j++) {
+                    angularMomentum[i + numPts * j] = angularMomentumPoint.get(j);
+                }
+            }
+
+            Vector AccelsVec(numCoords, 0.0);
+            for (int j = 0; j < numCoords; j++){
+                double StateQ = osimState[thread_id]->getQ().get(j);
+                for (int k = 0; k < numQs; k++){
+                    if (abs(q[i][k] - StateQ) <= 1e-6){
+                        AccelsVec.set(j, qpp[i][k]);
+                    }
+                }
+            }
+
+            Vector newControls(numControls, 0.0);
+            for (int j = 0; j < numControls; j++){
+                newControls.set(j, u[i][j]);
+            }
+            osimModel[thread_id]->setControls(*osimState[thread_id], newControls);
+            osimModel[thread_id]->markControlsAsValid(*osimState[thread_id]);
+            osimModel[thread_id]->realizeDynamics(*osimState[thread_id]);
+            
+            Vector IDLoadsVec;
+            IDLoadsVec = idSolver[thread_id]->solve(*osimState[thread_id], AccelsVec);
+            for (int j = 0; j < numCoords; j++){
+				idLoads[i + numPts * j] = IDLoadsVec[j]; 
+			}
+        }
+		//q.clear();
+		//qp.clear();
+		//qpp.clear();
+		//u.clear();
+    }   
+}
\ No newline at end of file
diff --git a/src/core/mex/inverseDynamicsAngularMomentumMexWindows.mexw64 b/src/core/mex/inverseDynamicsAngularMomentumMexWindows.mexw64
new file mode 100644
index 000000000..3d48b22a6
Binary files /dev/null and b/src/core/mex/inverseDynamicsAngularMomentumMexWindows.mexw64 differ
diff --git a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMatlab.m b/src/core/mex/inverseDynamicsMatlab.m
similarity index 100%
rename from src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMatlab.m
rename to src/core/mex/inverseDynamicsMatlab.m
diff --git a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMatlabParallel.m b/src/core/mex/inverseDynamicsMatlabParallel.m
similarity index 70%
rename from src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMatlabParallel.m
rename to src/core/mex/inverseDynamicsMatlabParallel.m
index 5a090dfef..e72a7b2b9 100644
--- a/src/core/TreatmentOptimization/OpenSimMex/inverseDynamicsMatlabParallel.m
+++ b/src/core/mex/inverseDynamicsMatlabParallel.m
@@ -3,8 +3,8 @@
 % This function uses OpenSim's inverse dynamics solver to calculate inverse
 % dynamics moments. Parallel workers are used to speed up computational
 % time.
-% 
-% (Array of number, 2D matrix, 2D matrix, 2D matrix, Cell, 2D matrix, 
+%
+% (Array of number, 2D matrix, 2D matrix, 2D matrix, Cell, 2D matrix,
 % Array of string) -> (2D matrix)
 % Returns inverse dynamic moments
 
@@ -30,9 +30,9 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inverseDynamicMoments = inverseDynamicsMatlabParallel(time, ...
-    jointAngles, jointVelocities, jointAccelerations, coordinateLabels, ...
-    appliedLoads, modelName)
+function [inverseDynamicsMoments, angularMomentum] = ...
+    inverseDynamicsMatlabParallel(time, jointAngles, jointVelocities, ...
+    jointAccelerations, coordinateLabels, appliedLoads, modelName)
 
 % Get the number of coords and markers
 numPts = size(time,1);
@@ -40,24 +40,45 @@
 numCoords = length(coordinateLabels);
 % Split time points into parallel problems
 numWorkers = gcp().NumWorkers;
-inverseDynamicJobs = cell(1, numWorkers);
-parfor worker = 1:numWorkers
-    inverseDynamicJobs{worker} = idWorkerHelper(modelName, numPts, ...
-        numControls, numCoords, numWorkers, ...
-        time, jointAngles, jointVelocities, jointAccelerations, ...
-        coordinateLabels,appliedLoads,worker);
+inverseDynamicsJobs = cell(1, numWorkers);
+if nargout > 1
+    angularMomentumJobs = cell(1, numWorkers);
+    parfor worker = 1:numWorkers
+        [inverseDynamicsJobs{worker}, angularMomentumJobs{worker}] = ...
+            idWorkerHelper(modelName, numPts, ...
+            numControls, numCoords, numWorkers, ...
+            time, jointAngles, jointVelocities, jointAccelerations, ...
+            coordinateLabels,appliedLoads,worker);
+    end
+else
+    parfor worker = 1:numWorkers
+        inverseDynamicsJobs{worker} = idWorkerHelper(modelName, numPts, ...
+            numControls, numCoords, numWorkers, ...
+            time, jointAngles, jointVelocities, jointAccelerations, ...
+            coordinateLabels,appliedLoads,worker);
+    end
 end
-inverseDynamicMoments = inverseDynamicJobs{1};
+
+inverseDynamicsMoments = inverseDynamicsJobs{1};
 for job = 2 : numWorkers
-    inverseDynamicMoments = cat(1, inverseDynamicMoments, ...
-        inverseDynamicJobs{job});
+    inverseDynamicsMoments = cat(1, inverseDynamicsMoments, ...
+        inverseDynamicsJobs{job});
 end
+if nargout > 1
+    angularMomentum = angularMomentumJobs{1};
+    for job = 2 : numWorkers
+        angularMomentum = cat(1, angularMomentum, ...
+            angularMomentumJobs{job});
+    end
 end
-function inverseDynamicJobs = idWorkerHelper(modelName, numPts, ...
+end
+
+function [inverseDynamicsJobs, angularMomentumJobs] = ...
+    idWorkerHelper(modelName, numPts, ...
     numControls, numCoords, numWorkers, time, jointAngles, ...
     jointVelocities, jointAccelerations, coordinateLabels, appliedLoads, ...
     worker)
-    
+
 import org.opensim.modeling.*;
 persistent osimModel;
 persistent osimState;
@@ -67,7 +88,8 @@
     osimState = osimModel.initSystem();
     inverseDynamicsSolver = InverseDynamicsSolver(osimModel);
 end
-inverseDynamicJobs = [];
+inverseDynamicsJobs = [];
+angularMomentumJobs = [];
 start = round((numPts/numWorkers) * (worker-1)) + 1;
 stop = round((numPts/numWorkers) * (worker));
 for j = start : stop
@@ -82,6 +104,17 @@
         end
     end
     osimModel.realizeVelocity(osimState);
+
+    % Whole body angular momentum
+    if nargout > 1
+        momentum = osimModel.getMatterSubsystem() ...
+            .calcSystemCentralMomentum(osimState);
+        angularMomentum = momentum.get(0);
+        for i = 0 : 2
+            angularMomentumJobs(j-start + 1, i + 1) = angularMomentum.get(i);
+        end
+    end
+    
     accelsTempVec = zeros(1, osimState.getNQ());
     for i=1:osimState.getNQ
         StateQ = osimState.getQ.get(i-1);
@@ -98,7 +131,7 @@
     osimModel.setControls(osimState, newControls);
     osimModel.markControlsAsValid(osimState);
     osimModel.realizeDynamics(osimState);
-    
+
     accelsVec = Vector(osimState.getNQ, 0);
     includedQIndex = 1;
     for i=0:osimState.getNQ-1
@@ -107,10 +140,10 @@
             accelsVec.set(i, accelsTempVec(includedQIndex));
             includedQIndex = includedQIndex + 1;
 %         end
-    end    
+    end
     IDLoadsVec = inverseDynamicsSolver.solve(osimState, accelsVec);
     for i=0 : numCoords - 1
-        inverseDynamicJobs(j-start + 1, i + 1) = IDLoadsVec.get(i);
+        inverseDynamicsJobs(j-start + 1, i + 1) = IDLoadsVec.get(i);
     end
 end
-end
\ No newline at end of file
+end
diff --git a/src/core/mex/inverseDynamicsMexWindows.cpp b/src/core/mex/inverseDynamicsMexWindows.cpp
new file mode 100644
index 000000000..3f81ef92b
--- /dev/null
+++ b/src/core/mex/inverseDynamicsMexWindows.cpp
@@ -0,0 +1,158 @@
+// This function is part of the NMSM Pipeline, see file for full license.
+//
+// performs inverse dynamics with openMP
+
+// ----------------------------------------------------------------------- //
+// The NMSM Pipeline is a toolkit for model personalization and treatment  //
+// optimization of neuromusculoskeletal models through OpenSim. See        //
+// nmsm.rice.edu and the NOTICE file for more information. The             //
+// NMSM Pipeline is developed at Rice University and supported by the US   //
+// National Institutes of Health (R01 EB030520).                           //
+//                                                                         //
+// Copyright (c) 2021 Rice University and the Authors                      //
+// Author(s): Marleny Vega                                                 //
+//                                                                         //
+// Licensed under the Apache License, Version 2.0 (the "License");         //
+// you may not use this file except in compliance with the License.        //
+// You may obtain a copy of the License at                                 //
+// http://www.apache.org/licenses/LICENSE-2.0.                             //
+//                                                                         //
+// Unless required by applicable law or agreed to in writing, software     //
+// distributed under the License is distributed on an "AS IS" BASIS,       //
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         //
+// implied. See the License for the specific language governing            //
+// permissions and limitations under the License.                          //
+// ----------------------------------------------------------------------- //
+
+#include "mex.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <OpenSim/OpenSim.h>
+#include <InverseDynamicsSolver.h>
+#include <string.h>
+#include <omp.h> //
+#include <matrix.h>
+#include <iostream> 
+#include <vector>
+
+using namespace OpenSim;
+using namespace SimTK;
+using namespace std;
+#define numThreads 20 //
+
+//______________________________________________________________________________
+
+static Model *osimModel;
+static State *osimState;
+static InverseDynamicsSolver *idSolver;
+static bool modelIsLoaded = false;
+
+void ClearMemory(void){
+	delete osimModel;
+	delete idSolver;
+    modelIsLoaded = false;
+    mexPrintf("Cleared memory from inverseDynamics mex file.\n");
+}
+
+vector<vector<double>> mexArrayToVector(const mxArray *input) {
+    const mwSize *dimension;
+    dimension = mxGetDimensions(input);
+    int rows = (int) dimension[0];
+    int columns = (int) dimension[1];
+    double *data = (double *) mxGetData(input);
+    vector<vector<double>> output(rows, vector<double>(columns));
+    for (int i = 0; i < rows; i++) {
+        for (int j = 0; j < columns; j++) {
+            memcpy(&output[i][j], data + i + j * rows, sizeof(double) );
+        }
+    }
+    return output;
+}
+
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
+    mexAtExit(ClearMemory);
+    if (nrhs == 1) {    
+        if (modelIsLoaded == true){
+            ClearMemory();
+        }
+        string modelName = mxArrayToString(prhs[0]);      
+        std::streambuf* oldCoutStreamBuf = std::cout.rdbuf();
+		std::ostringstream strCout;
+		std::cout.rdbuf(strCout.rdbuf());
+			osimModel = new Model(modelName); 
+			osimState = &osimModel->initSystem();
+			idSolver = new InverseDynamicsSolver(*osimModel);
+		std::cout.rdbuf(oldCoutStreamBuf);
+        modelIsLoaded = true;
+    }
+    else if (nrhs == 6) {
+        if (modelIsLoaded == false){
+            mexErrMsgTxt("!!!No OpenSim model has been loaded!!!\n");
+        }   
+		const int numPts = mxGetM(prhs[0]);
+        const int numQs = mxGetN(prhs[1]);
+		const int numControls = mxGetN(prhs[5]);
+        const int numCoords = osimState[0].getNQ();
+
+        double *time = mxGetPr(prhs[0]);
+        vector<vector<double>> q = mexArrayToVector(prhs[1]);
+        vector<vector<double>> qp = mexArrayToVector(prhs[2]);
+        vector<vector<double>> qpp = mexArrayToVector(prhs[3]);
+        vector<vector<double>> u = mexArrayToVector(prhs[5]);
+
+        const mxArray *cellElementPtr;
+        mwIndex k;
+        mwSize numLabels, buflen;
+        numLabels = mxGetNumberOfElements(prhs[4]);
+        int status;
+
+        plhs[0] = mxCreateDoubleMatrix(numPts,numCoords,mxREAL);
+		double *idLoads = mxGetPr(plhs[0]);
+
+        for (int i = 0; i < numPts; ++i){
+            osimState->setTime(time[i]);
+
+            for (int k = 0; k < numLabels; k++){
+                cellElementPtr = mxGetCell(prhs[4], k);
+                buflen = mxGetN(cellElementPtr)*sizeof(mxChar) + 1;
+                char* c_array;
+                c_array = (char *)  mxCalloc(buflen, sizeof(char));
+                status = mxGetString(cellElementPtr, c_array, buflen);
+                osimModel->getCoordinateSet().get(c_array).setValue(*osimState, q[i][k], false);
+                osimModel->getCoordinateSet().get(c_array).setSpeedValue(*osimState, qp[i][k]);
+                mxFree(c_array);
+            }
+            osimModel->realizeVelocity(*osimState);
+
+            Vector AccelsVec(numCoords, 0.0);
+            for (int j = 0; j < numCoords; j++){
+                double StateQ = osimState->getQ().get(j);
+                for (int k = 0; k < numQs; k++){
+                    if (abs(q[i][k] - StateQ) <= 1e-6){
+                        AccelsVec.set(j, qpp[i][k]);
+                    }
+                }
+            }
+
+            Vector newControls(numControls, 0.0);
+            for (int j = 0; j < numControls; j++){
+                newControls.set(j, u[i][j]);
+            }
+            osimModel->setControls(*osimState, newControls);
+            osimModel->markControlsAsValid(*osimState);
+            osimModel->realizeDynamics(*osimState);
+            
+            Vector IDLoadsVec;
+            IDLoadsVec = idSolver->solve(*osimState, AccelsVec);
+            for (int j = 0; j < numCoords; j++){
+				idLoads[i + numPts * j] = IDLoadsVec[j]; 
+			}
+           
+        }
+		q.clear();
+		qp.clear();
+		qpp.clear();
+		u.clear();
+    }   
+}
\ No newline at end of file
diff --git a/src/core/mex/inverseDynamicsMexWindows.mexw64 b/src/core/mex/inverseDynamicsMexWindows.mexw64
new file mode 100644
index 000000000..9937d9413
Binary files /dev/null and b/src/core/mex/inverseDynamicsMexWindows.mexw64 differ
diff --git a/src/core/mex/inverseDynamicsWithExtraCalcsMexWindows.cpp b/src/core/mex/inverseDynamicsWithExtraCalcsMexWindows.cpp
new file mode 100644
index 000000000..6e464a692
--- /dev/null
+++ b/src/core/mex/inverseDynamicsWithExtraCalcsMexWindows.cpp
@@ -0,0 +1,195 @@
+// This function is part of the NMSM Pipeline, see file for full license.
+//
+// performs inverse dynamics with openMP
+
+// ----------------------------------------------------------------------- //
+// The NMSM Pipeline is a toolkit for model personalization and treatment  //
+// optimization of neuromusculoskeletal models through OpenSim. See        //
+// nmsm.rice.edu and the NOTICE file for more information. The             //
+// NMSM Pipeline is developed at Rice University and supported by the US   //
+// National Institutes of Health (R01 EB030520).                           //
+//                                                                         //
+// Copyright (c) 2021 Rice University and the Authors                      //
+// Author(s): Marleny Vega                                                 //
+//                                                                         //
+// Licensed under the Apache License, Version 2.0 (the "License");         //
+// you may not use this file except in compliance with the License.        //
+// You may obtain a copy of the License at                                 //
+// http://www.apache.org/licenses/LICENSE-2.0.                             //
+//                                                                         //
+// Unless required by applicable law or agreed to in writing, software     //
+// distributed under the License is distributed on an "AS IS" BASIS,       //
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         //
+// implied. See the License for the specific language governing            //
+// permissions and limitations under the License.                          //
+// ----------------------------------------------------------------------- //
+
+#include "mex.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <OpenSim/OpenSim.h>
+#include <InverseDynamicsSolver.h>
+#include <string.h>
+#include <omp.h> //
+#include <matrix.h>
+#include <iostream> 
+#include <vector>
+
+using namespace OpenSim;
+using namespace SimTK;
+using namespace std;
+#define numThreads 20 //
+
+//______________________________________________________________________________
+
+static Model *osimModel[numThreads];
+static State *osimState[numThreads];
+static InverseDynamicsSolver *idSolver[numThreads];
+static bool modelIsLoaded = false;
+
+void ClearMemory(void){
+    for (int i = 0; i < numThreads; i++){
+		delete osimModel[i];
+		delete idSolver[i];
+	}
+    modelIsLoaded = false;
+    mexPrintf("Cleared memory from inverseDynamics mex file.\n");
+}
+
+vector<vector<double>> mexArrayToVector(const mxArray *input) {
+    const mwSize *dimension;
+    dimension = mxGetDimensions(input);
+    int rows = (int) dimension[0];
+    int columns = (int) dimension[1];
+    double *data = (double *) mxGetData(input);
+    vector<vector<double>> output(rows, vector<double>(columns));
+    for (int i = 0; i < rows; i++) {
+        for (int j = 0; j < columns; j++) {
+            memcpy(&output[i][j], data + i + j * rows, sizeof(double) );
+        }
+    }
+    return output;
+}
+
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
+    mexAtExit(ClearMemory);
+    if (nrhs == 1) {    
+        if (modelIsLoaded == true){
+            ClearMemory();
+        }
+        string modelName = mxArrayToString(prhs[0]);      
+        std::streambuf* oldCoutStreamBuf = std::cout.rdbuf();
+		std::ostringstream strCout;
+		std::cout.rdbuf(strCout.rdbuf());
+        for (int i = 0; i < numThreads; i++){
+			osimModel[i] = new Model(modelName); 
+			osimState[i] = &osimModel[i]->initSystem();
+			idSolver[i] = new InverseDynamicsSolver(*osimModel[i]);
+		}  
+		std::cout.rdbuf(oldCoutStreamBuf);
+        modelIsLoaded = true;
+    }
+    else if (nrhs > 1) {
+        if (modelIsLoaded == false){
+            mexErrMsgTxt("!!!No OpenSim model has been loaded!!!\n");
+        }   
+		const int numPts = mxGetM(prhs[0]);
+        const int numQs = mxGetN(prhs[1]);
+		const int numControls = mxGetN(prhs[5]);
+        const int numMuscles = mxGetN(prhs[6]);
+        const int numCoords = osimState[0]->getNQ();
+
+        double *time = mxGetPr(prhs[0]);
+        vector<vector<double>> q = mexArrayToVector(prhs[1]);
+        vector<vector<double>> qp = mexArrayToVector(prhs[2]);
+        vector<vector<double>> qpp = mexArrayToVector(prhs[3]);
+        vector<vector<double>> u = mexArrayToVector(prhs[5]);
+        vector<vector<double>> muscleActivations = mexArrayToVector(prhs[6]);
+		double* computeAngularMomentum = (double *) mxGetData(prhs[7]);
+		double* computeMetabolicCost = (double *) mxGetData(prhs[8]);
+
+        mwIndex k;
+        mwSize numLabels, buflen;
+        numLabels = mxGetNumberOfElements(prhs[4]);
+
+        plhs[0] = mxCreateDoubleMatrix(numPts,numCoords,mxREAL);
+		double *idLoads = mxGetPr(plhs[0]);
+ 		plhs[1] = mxCreateDoubleMatrix(numPts, 3, mxREAL);
+        double* angularMomentum = mxGetPr(plhs[1]);
+        plhs[2] = mxCreateDoubleMatrix(numPts, 1, mxREAL);
+		double* metabolicCost = mxGetPr(plhs[2]);
+        plhs[3] = mxCreateDoubleMatrix(2, 1, mxREAL);
+        double* massCenterPositions = mxGetPr(plhs[3]);
+
+        #pragma omp parallel for num_threads(numThreads)
+        for (int i = 0; i < numPts; ++i){
+            int thread_id = omp_get_thread_num();
+            osimState[thread_id]->setTime(time[i]);
+			
+            for (int k = 0; k < numLabels; k++){
+				const mxArray *cellElementPtr;
+                cellElementPtr = mxGetCell(prhs[4], k);
+                buflen = mxGetN(cellElementPtr)*sizeof(mxChar) + 1;
+                char* c_array;
+                c_array = (char *)  mxCalloc(buflen, sizeof(char));
+                int status = mxGetString(cellElementPtr, c_array, buflen);
+                osimModel[thread_id]->getCoordinateSet().get(c_array).setValue(*osimState[thread_id], q[i][k], false);
+                osimModel[thread_id]->getCoordinateSet().get(c_array).setSpeedValue(*osimState[thread_id], qp[i][k]);
+                mxFree(c_array);
+            }
+
+            osimModel[thread_id]->realizeVelocity(*osimState[thread_id]);
+            if (*computeAngularMomentum > 0.5) {
+                SpatialVec momentum = osimModel[thread_id]->getMatterSubsystem().calcSystemCentralMomentum(*osimState[thread_id]);
+                Vec3 angularMomentumPoint = momentum.get(0);
+                for (int j = 0; j <= 2; j++) {
+                    angularMomentum[i + numPts * j] = angularMomentumPoint.get(j);
+                }
+            }
+
+            if (i == 0) {
+                massCenterPositions[0] = osimModel[thread_id]->calcMassCenterVelocity(*osimState[thread_id]).get(0);
+            } else if (i == numPts - 1) {
+                massCenterPositions[1] = osimModel[thread_id]->calcMassCenterVelocity(*osimState[thread_id]).get(0);
+            }
+
+            Vector AccelsVec(numCoords, 0.0);
+            for (int j = 0; j < numCoords; j++){
+                double StateQ = osimState[thread_id]->getQ().get(j);
+                for (int k = 0; k < numQs; k++){
+                    if (abs(q[i][k] - StateQ) <= 1e-6){
+                        AccelsVec.set(j, qpp[i][k]);
+                    }
+                }
+            }
+
+            Vector newControls(numControls, 0.0);
+            for (int j = 0; j < numControls; j++){
+                newControls.set(j, u[i][j]);
+            }
+            osimModel[thread_id]->setControls(*osimState[thread_id], newControls);
+            osimModel[thread_id]->markControlsAsValid(*osimState[thread_id]);
+            osimModel[thread_id]->realizeDynamics(*osimState[thread_id]);
+
+            Vector IDLoadsVec;
+            IDLoadsVec = idSolver[thread_id]->solve(*osimState[thread_id], AccelsVec);
+            for (int j = 0; j < numCoords; j++){
+				idLoads[i + numPts * j] = IDLoadsVec[j]; 
+			}     
+
+            if (*computeMetabolicCost > 0.5) {
+                for (int j = 0; j < numMuscles; j++) {
+                    osimModel[thread_id]->getForceSet().getMuscles().get(j).setActivation(*osimState[thread_id], muscleActivations[i][j]);
+                }
+                osimModel[thread_id]->realizeDynamics(*osimState[thread_id]);
+                osimModel[thread_id]->equilibrateMuscles(*osimState[thread_id]);
+				metabolicCost[i] = osimModel[thread_id]->getProbeSet().get(0).getProbeOutputs(*osimState[thread_id]).get(0);
+			}
+        }
+		//q.clear();
+		//qp.clear();
+		//qpp.clear();
+		//u.clear();
+    }   
+}
\ No newline at end of file
diff --git a/src/core/mex/inverseDynamicsWithExtraCalcsMexWindows.mexw64 b/src/core/mex/inverseDynamicsWithExtraCalcsMexWindows.mexw64
new file mode 100644
index 000000000..68bca8b8f
Binary files /dev/null and b/src/core/mex/inverseDynamicsWithExtraCalcsMexWindows.mexw64 differ
diff --git a/src/core/TreatmentOptimization/OpenSimMex/pointKinematics.m b/src/core/mex/pointKinematics.m
similarity index 100%
rename from src/core/TreatmentOptimization/OpenSimMex/pointKinematics.m
rename to src/core/mex/pointKinematics.m
diff --git a/src/core/TreatmentOptimization/OpenSimMex/pointKinematicsMatlabParallel.m b/src/core/mex/pointKinematicsMatlabParallel.m
similarity index 100%
rename from src/core/TreatmentOptimization/OpenSimMex/pointKinematicsMatlabParallel.m
rename to src/core/mex/pointKinematicsMatlabParallel.m
diff --git a/src/core/mex/pointKinematicsMexWindows.mexw64 b/src/core/mex/pointKinematicsMexWindows.mexw64
new file mode 100644
index 000000000..11c9a1511
Binary files /dev/null and b/src/core/mex/pointKinematicsMexWindows.mexw64 differ
diff --git a/src/core/TreatmentOptimization/OpenSimMex/setOsimStateBySingleFrame.m b/src/core/mex/setOsimStateBySingleFrame.m
similarity index 94%
rename from src/core/TreatmentOptimization/OpenSimMex/setOsimStateBySingleFrame.m
rename to src/core/mex/setOsimStateBySingleFrame.m
index 8b542af5e..17a7dc9b2 100644
--- a/src/core/TreatmentOptimization/OpenSimMex/setOsimStateBySingleFrame.m
+++ b/src/core/mex/setOsimStateBySingleFrame.m
@@ -35,9 +35,9 @@
 for k=1:size(coordinateNames,2)
     if ~osimModel.getCoordinateSet.get(coordinateNames{k}).get_locked
         osimModel.getCoordinateSet.get(coordinateNames{k}). ...
-            setValue(osimState, values.statePositions(indx, k));
+            setValue(osimState, values.positions(indx, k));
         osimModel.getCoordinateSet.get(coordinateNames{k}). ...
-            setSpeedValue(osimState, values.stateVelocities(indx, k));
+            setSpeedValue(osimState, values.velocities(indx, k));
     end
 end
 osimModel.realizeVelocity(osimState);
diff --git a/src/core/model/getMusclesFromCoordinates.m b/src/core/model/getMusclesFromCoordinates.m
index 5ef691104..29f46b2b6 100644
--- a/src/core/model/getMusclesFromCoordinates.m
+++ b/src/core/model/getMusclesFromCoordinates.m
@@ -45,7 +45,7 @@
 
 function output = isMuscleInCoordinates(model, coordinates, muscle)
 if muscle.get_appliesForce()
-    path = muscle.get_GeometryPath().getPathPointSet();
+    path = muscle.getGeometryPath().getPathPointSet();
     for j = 0 : path.getSize() - 1
         bodyCoordinates = getCoordinatesFromBodies(model, ...
             path.get(j).getBodyName().toCharArray()');
diff --git a/src/core/motToTrc/TrcFromMot.m b/src/core/motToTrc/TrcFromMot.m
new file mode 100644
index 000000000..47e673c52
--- /dev/null
+++ b/src/core/motToTrc/TrcFromMot.m
@@ -0,0 +1,53 @@
+% This function accepts a model and .mot file and writes a .trc file that
+% contains the marker data for the given motion. Noise can be added
+% as a parameter.
+% Parameters include: 
+%   trcFileName - string - output file 
+%   dataRate - number - data rate of mot file
+%   translationNoise - number - width of gaussian noise for translational
+%       coordinates
+%   rotationNoise - number - width of gaussian noise for rotational
+%       coordinates
+
+% Copyright RNCL *change later*
+
+% (Model, string, string) -> (None)
+% Writes a .trc file from a Model and .mot file.
+function TrcFromMot(inputModel, motFileName, params)
+[model, state] = Model(inputModel);
+storage = org.opensim.modeling.Storage(motFileName);
+dataRate = dataRateOrError(params);
+table = makeTimeSeriesTableVec3(model, dataRate);
+applyValuesFromStorage(model, state, storage, table, params);
+trcFileAdapter = org.opensim.modeling.TRCFileAdapter();
+trcFileAdapter.write(table, trcFileNameOrDefault(params));
+end
+
+% (struct) -> (number)
+% Returns the dataRate if it's a number, otherwise throws an error
+function dataRate = dataRateOrError(params)
+if(isfield(params, 'dataRate'))
+    if(isnumeric(params.dataRate))
+        dataRate = params.dataRate;
+    else
+        throw(MException('dataRate must be a number'))
+    end
+else
+    throw(MException('dataRate param required'))
+end
+end
+
+% (struct) -> (string)
+% Returns the trcFileName or default value
+function fileName = trcFileNameOrDefault(params)
+if(isfield(params, 'trcFileName'))
+    if(isstring(params.trcFileName) || ischar(params.trcFileName))
+        fileName = params.trcFileName;
+    else
+        warning('params.trcFileName is not a string, using output.trc')
+        fileName = 'output.trc';
+    end
+else
+    throw(MException('trcFileName param required'))
+end
+end
\ No newline at end of file
diff --git a/src/core/motToTrc/applyValuesFromStorage.m b/src/core/motToTrc/applyValuesFromStorage.m
new file mode 100644
index 000000000..163e26476
--- /dev/null
+++ b/src/core/motToTrc/applyValuesFromStorage.m
@@ -0,0 +1,18 @@
+% This function iterates through the storage and applies the coordinate
+% values in order.
+
+% Copyright RCNL *change later*
+
+% (Model, State, Storage, TimeSeriesTableVec3, number) -> None
+function applyValuesFromStorage(model, state, storage, table, params)
+import org.opensim.modeling.*
+for i=0:storage.getSize()-1
+    for j=1:storage.getColumnLabels().size()-1
+        setValueFromStorage(model, state, storage, i, j, params);
+        model.assemble(state);
+    end
+    model.assemble(state);
+    table.appendRow(i/params.dataRate, ...
+    recordMarkersFromState(model, state));
+end
+end
\ No newline at end of file
diff --git a/src/core/motToTrc/getCoordinateFromName.m b/src/core/motToTrc/getCoordinateFromName.m
new file mode 100644
index 000000000..8e45ea156
--- /dev/null
+++ b/src/core/motToTrc/getCoordinateFromName.m
@@ -0,0 +1,18 @@
+% This function returns a mutable coordinate for changing the position of a
+% model. This coordinate can be used in coord.setValue(state, value)
+
+% Copyright RCNL *change later*
+
+% (Model, string) -> (Coordinate)
+% Returns a coordinate with the given name
+function coord = getCoordinateFromName(model, name)
+    for i=0:model.getJointSet().getSize()-1
+        joint = model.getJointSet.get(i);
+        for j=0:joint.numCoordinates()-1
+            if(joint.get_coordinates(j).getName() == name)
+                coord = joint.upd_coordinates(j);
+                return
+            end
+        end
+    end
+end
\ No newline at end of file
diff --git a/src/core/motToTrc/makeTimeSeriesTableVec3.m b/src/core/motToTrc/makeTimeSeriesTableVec3.m
new file mode 100644
index 000000000..c5a844a6d
--- /dev/null
+++ b/src/core/motToTrc/makeTimeSeriesTableVec3.m
@@ -0,0 +1,19 @@
+% This function makes a TimeSeriesTableVec3 for a given model and data rate
+% for use in a TRCFileAdapter. This function assumes units in meters.
+
+% Copyright RCNL *change later*
+
+% (Model, number) -> (TimeSeriesTableVec3)
+% Builds a TimeSeriesTableVec3 from a model and dataRate
+function table = makeTimeSeriesTableVec3(model, dataRate)
+import org.opensim.modeling.*
+table = TimeSeriesTableVec3();
+table.addTableMetaDataString("DataRate", num2str(dataRate));
+table.addTableMetaDataString("Units", "m");
+labels = StdVectorString();
+for i=0:model.getMarkerSet().getSize()-1
+    labels.add(model.getMarkerSet().get(i).getName());
+end
+table.setColumnLabels(labels);
+end
+
diff --git a/src/core/motToTrc/recordMarkersFromState.m b/src/core/motToTrc/recordMarkersFromState.m
new file mode 100644
index 000000000..63d5b96ea
--- /dev/null
+++ b/src/core/motToTrc/recordMarkersFromState.m
@@ -0,0 +1,15 @@
+% This function returns a RowVectorOfVec3 from a given state including all
+% markers in the state.
+
+% Copyright RCNL *change later*
+
+% (Model, State) -> (RowVectorOfVec3)
+% Return a RowVectorOfVec3 of marker positions for a given state
+function row = recordMarkersFromState(model, state)
+import org.opensim.modeling.*
+row = RowVectorVec3(model.getMarkerSet().getSize());
+for i=0:model.getMarkerSet().getSize()-1
+    m = model.getMarkerSet().get(i);
+    row.set(i,m.getLocationInGround(state));
+end
+end
\ No newline at end of file
diff --git a/src/core/motToTrc/setValueFromStorage.m b/src/core/motToTrc/setValueFromStorage.m
new file mode 100644
index 000000000..1471b81fd
--- /dev/null
+++ b/src/core/motToTrc/setValueFromStorage.m
@@ -0,0 +1,30 @@
+% This function sets the value of the coordinate in the given state from
+% the data within the storage object.
+
+% Copyright RCNL *change later*
+
+% (Model, State, Storage, number, number) -> None
+% Sets value of state coordinates from a Storage object row and column
+function setValueFromStorage(model, state, storage, row, column, params)
+import org.opensim.modeling.*
+dbl = ArrayDouble();
+storage.getDataColumn(column-1, dbl);
+coord = getCoordinateFromName(model, storage.getColumnLabels.get(column));
+value = dbl.get(row);
+%         applyGaussian(value, params, 'rotationNoise')*3.14/180);
+
+%     coord.setValue(state, applyGaussian(value,params, 'translationNoise'));
+coord.setValue(state, value);
+end
+
+function output = applyGaussian(value, params, fieldName)
+if(isfield(params, fieldName))
+    if(isnumeric(params.(fieldName)))
+        output = value + normrnd(0, params.(fieldName));
+    else
+        output = value;
+    end
+else
+    output = value;
+end
+end
\ No newline at end of file
diff --git a/src/core/MuscleModels/activeForceLengthCurve.m b/src/core/muscle/activeForceLengthCurve.m
similarity index 100%
rename from src/core/MuscleModels/activeForceLengthCurve.m
rename to src/core/muscle/activeForceLengthCurve.m
diff --git a/src/core/MuscleCalculations/calcMaxIsometricForce.m b/src/core/muscle/calcMaxIsometricForce.m
similarity index 100%
rename from src/core/MuscleCalculations/calcMaxIsometricForce.m
rename to src/core/muscle/calcMaxIsometricForce.m
diff --git a/src/core/MuscleCalculations/calcMetabolicCost.m b/src/core/muscle/calcMetabolicCost.m
similarity index 100%
rename from src/core/MuscleCalculations/calcMetabolicCost.m
rename to src/core/muscle/calcMetabolicCost.m
diff --git a/src/core/MuscleCalculations/calcMuscleActivations.m b/src/core/muscle/calcMuscleActivations.m
similarity index 100%
rename from src/core/MuscleCalculations/calcMuscleActivations.m
rename to src/core/muscle/calcMuscleActivations.m
diff --git a/src/core/MuscleCalculations/calcMuscleExcitations.m b/src/core/muscle/calcMuscleExcitations.m
similarity index 100%
rename from src/core/MuscleCalculations/calcMuscleExcitations.m
rename to src/core/muscle/calcMuscleExcitations.m
diff --git a/src/core/MuscleCalculations/calcMuscleJointMoments.m b/src/core/muscle/calcMuscleJointMoments.m
similarity index 100%
rename from src/core/MuscleCalculations/calcMuscleJointMoments.m
rename to src/core/muscle/calcMuscleJointMoments.m
diff --git a/src/core/MuscleCalculations/calcNeuralActivations.m b/src/core/muscle/calcNeuralActivations.m
similarity index 100%
rename from src/core/MuscleCalculations/calcNeuralActivations.m
rename to src/core/muscle/calcNeuralActivations.m
diff --git a/src/core/MuscleCalculations/calcNormalizedMuscleFiberLengthsAndVelocities.m b/src/core/muscle/calcNormalizedMuscleFiberLengthsAndVelocities.m
similarity index 100%
rename from src/core/MuscleCalculations/calcNormalizedMuscleFiberLengthsAndVelocities.m
rename to src/core/muscle/calcNormalizedMuscleFiberLengthsAndVelocities.m
diff --git a/src/core/MuscleCalculations/calcPassiveForceLengthCurve.m b/src/core/muscle/calcPassiveForceLengthCurve.m
similarity index 100%
rename from src/core/MuscleCalculations/calcPassiveForceLengthCurve.m
rename to src/core/muscle/calcPassiveForceLengthCurve.m
diff --git a/src/core/MuscleCalculations/calcPassiveMuscleMoments.m b/src/core/muscle/calcPassiveMuscleMoments.m
similarity index 99%
rename from src/core/MuscleCalculations/calcPassiveMuscleMoments.m
rename to src/core/muscle/calcPassiveMuscleMoments.m
index 137d83d57..0739ae33d 100644
--- a/src/core/MuscleCalculations/calcPassiveMuscleMoments.m
+++ b/src/core/muscle/calcPassiveMuscleMoments.m
@@ -54,10 +54,8 @@
     parallelComponentOfPennationAngle), 1);
 expandedParallelComponentOfPennationAngle(1, 1, :, 1) = ...
     parallelComponentOfPennationAngle;
-
 passiveModelMoments = experimentalData.momentArms .* ...
     expandedMaxIsometricForce .* expandedPassiveForce .* ...
     expandedParallelComponentOfPennationAngle;
-
 passiveModelMoments = permute(sum(passiveModelMoments, 3), [1 2 4 3]);
 end
diff --git a/src/core/MuscleModels/forceVelocityCurve.m b/src/core/muscle/forceVelocityCurve.m
similarity index 100%
rename from src/core/MuscleModels/forceVelocityCurve.m
rename to src/core/muscle/forceVelocityCurve.m
diff --git a/src/core/MuscleModels/passiveForceLengthCurve.m b/src/core/muscle/passiveForceLengthCurve.m
similarity index 100%
rename from src/core/MuscleModels/passiveForceLengthCurve.m
rename to src/core/muscle/passiveForceLengthCurve.m
diff --git a/src/core/optimal_control/parseGpopsSolverSettings.m b/src/core/optimal_control/parseGpopsSolverSettings.m
new file mode 100644
index 000000000..5777a4af5
--- /dev/null
+++ b/src/core/optimal_control/parseGpopsSolverSettings.m
@@ -0,0 +1,79 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function reads the optimal control settings (GPOPS-II based) from a
+% separate XML file.
+%
+% (struct) -> (Array of string)
+% Optimal control solver settings are loaded
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function solverSettings = parseGpopsSolverSettings(settingsTree)
+solverSettings.optimizationFileName = 'TreatmentOptimization';
+solverSettings.derivativeSupplier = parseTextOrAlternate( ...
+    settingsTree, 'setup_derivatives_supplier', 'sparseFD');
+solverSettings.derivativeLevel = parseTextOrAlternate( ...
+    settingsTree, 'setup_derivatives_level', 'first');
+solverSettings.derivativeDependencies = parseTextOrAlternate( ...
+    settingsTree, 'setup_derivatives_dependencies', 'sparse');
+solverSettings.scaleMethods = parseTextOrAlternate( ...
+    settingsTree, 'setup_scales_method', 'none');
+solverSettings.method = parseTextOrAlternate( ...
+    settingsTree, 'setup_method', 'RPM-Differentiation');
+solverSettings.meshMethod = parseTextOrAlternate( ...
+    settingsTree, 'setup_mesh_method', 'hp-PattersonRao');
+solverSettings.meshTolerance = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_tolerance', 10e-3);
+solverSettings.meshMaxIterations = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_max_iterations', 10);
+solverSettings.meshColpointsMin = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_colpoints_min', 3);
+solverSettings.meshColpointsMax = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_colpoints_max', 10);
+solverSettings.meshSplitMult = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_splitmult', 1.2);
+solverSettings.meshCurveRatio = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_curveratio', 2);
+solverSettings.meshR = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_R', 1.2);
+solverSettings.meshSigma = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_sigma', 0.5);
+solverSettings.numCollocationPoints = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_phase_intervals', 6);
+solverSettings.numIntervals = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_mesh_phase_colpoints_per_Interval', 10);
+solverSettings.solverType = parseTextOrAlternate( ...
+    settingsTree, 'setup_nlp_solver', 'ipopt');
+solverSettings.linearSolverType = parseTextOrAlternate( ...
+    settingsTree, 'setup_nlp_linear_solver', 'ma57');
+solverSettings.solverTolerance = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_nlp_tolerance', 1e-3);
+solverSettings.stepSize = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_nlp_step_size', 1e-8);
+solverSettings.maxIterations = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_nlp_max_iterations', 2e4);
+solverSettings.displayLevel = parseDoubleOrAlternate( ...
+    settingsTree, 'setup_display_level', 2);
+solverSettings.integralBound = parseDoubleOrAlternate( ...
+    settingsTree, "integral_bound", 1);
+end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcStepLength.m b/src/core/optimal_control/parseOptimalControlSolverSettings.m
similarity index 67%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcStepLength.m
rename to src/core/optimal_control/parseOptimalControlSolverSettings.m
index b70e0fe0b..fea19b709 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcStepLength.m
+++ b/src/core/optimal_control/parseOptimalControlSolverSettings.m
@@ -1,9 +1,5 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the step length for the specified foot for one
-% gait cycle. 
-%
-% (Array of number, Array of number) -> (Number)
 %
 
 % ----------------------------------------------------------------------- %
@@ -14,7 +10,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,22 +24,20 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function stepLength = calcStepLength(normalForce, heelPosition)
-
-normalForce = normalForce - 30; % Noise buffer
-normalForce(normalForce<0) = 0;
-slope = diff(normalForce);
-heelStrikeEvent = getHeelStrikeEvent(slope);
-if isempty(heelStrikeEvent)
-    if normalForce(1) == 0
-        heelStrikeEvent  = 1;
-        stepLength = heelPosition(heelStrikeEvent, 1) - ...
-            heelPosition(heelStrikeEvent, 2);
-    else
-        stepLength = 0;
-    end
+function inputs = parseOptimalControlSolverSettings( ...
+    tree, inputs)
+settingsFileName = getTextFromField(getFieldByNameOrError(tree, ...
+    'optimal_control_solver_settings_file'));
+solverSettingsTree = xml2struct(settingsFileName);
+verifyVersion(solverSettingsTree, "OptimalControlSolverSettings");
+tree = ...
+    solverSettingsTree.NMSMPipelineDocument.OptimalControlSolverSettings;
+if isfield(tree, 'GpopsSettings')
+    inputs.gpops = parseGpopsSolverSettings(tree);
+elseif isfield(tree, 'MocoSettings')
+    inputs.moco = parseMocoSolverSettings(tree);
 else
-    stepLength = heelPosition(heelStrikeEvent, 1) - ...
-        heelPosition(heelStrikeEvent, 2);
+    throw(MException("OptimalControlSolverSettings:UnsupportedSolver", ...
+        "Only <GpopsSettings> and <MocoSettings> are supported"))
+end
 end
-end
\ No newline at end of file
diff --git a/src/core/osimx/buildGcpContactSurface.m b/src/core/osimx/buildGcpContactSurface.m
index 4287bb85f..f0aeef189 100644
--- a/src/core/osimx/buildGcpContactSurface.m
+++ b/src/core/osimx/buildGcpContactSurface.m
@@ -65,11 +65,9 @@
 contact{i}.electrical_center_columns.Text = ...
     convertStringsToChars(strjoin(contactSurface.electricalCenterColumns));
 
-contact{i}.toes_coordinate.Comment = ...
-    'Name of the toe angle coordinate in the model file';
-contact{i}.toes_coordinate.Text = contactSurface.toesCoordinateName;
-contact{i}.toes_joint.Comment = 'Name of the toe joint in the model file';
-contact{i}.toes_joint.Text = contactSurface.toesJointName;
+contact{i}.hindfoot_body.Comment = ...
+    'Name of the hindfoot body in the model file';
+contact{i}.hindfoot_body.Text = contactSurface.hindfootBodyName;
 
 contact{i}.toe_marker.Comment = ...
     'Names of the markers used to define the foot area';
diff --git a/src/core/osimx/buildOsimxFromOsimxStruct.m b/src/core/osimx/buildOsimxFromOsimxStruct.m
index ff1f838c0..d0369fa20 100644
--- a/src/core/osimx/buildOsimxFromOsimxStruct.m
+++ b/src/core/osimx/buildOsimxFromOsimxStruct.m
@@ -1,8 +1,8 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function takes the output of parseOsimxFile(filename) and produces
-% a struct that can passed directly into writeOsimxFile() and replicate the
-% input file.
+% This function takes the output of parseOsimxFile(filename, model) and 
+% produces a struct that can passed directly into writeOsimxFile() and 
+% replicate the input file.
 %
 % This function is most commonly used to add values to an existing .osimx
 % file.
@@ -40,5 +40,8 @@
 if isfield(osimxStruct, "groundContact")
     osimx = buildGcpOsimx(osimx, osimxStruct.groundContact);
 end
+if isfield(osimxStruct, "synergyGroups")
+    osimx = buildSynergyGroupOsimx(osimx, osimxStruct.synergyGroups);
+end
 end
 
diff --git a/src/TrackingOptimization/getTrackingOptimizationValueStruct.m b/src/core/osimx/buildSynergyGroupOsimx.m
similarity index 59%
rename from src/TrackingOptimization/getTrackingOptimizationValueStruct.m
rename to src/core/osimx/buildSynergyGroupOsimx.m
index 8b6a857c4..8d5eb8ba9 100644
--- a/src/TrackingOptimization/getTrackingOptimizationValueStruct.m
+++ b/src/core/osimx/buildSynergyGroupOsimx.m
@@ -1,11 +1,14 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function parses and scales the design variables specific to
-% Tracking Optimization. If the model is synergy driven, synergy weights 
-% are properly calculated if they are fixed or being optimized.
+% This function converts the synergyGroup portion of a parsed .osimx file
+% into a new .osimx struct to be printed with writeOsimxFile(). See
+% buildOsimxFromOsimxStruct() for reference.
+%
+% The expected format of the synergyGroups comes from parseSynergyGroups() as
+% used in parseNeuralControlPersonalization()
 %
 % (struct, struct) -> (struct)
-% Design variables specific to Tracking Optimization are parsed and scaled
+% Adds synergyGroups to .osimxStruct
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -15,7 +18,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -29,17 +32,17 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function values = getTrackingOptimizationValueStruct(inputs, params)
-values = getTreatmentOptimizationValueStruct(inputs, params);
-if strcmp(params.controllerType, 'synergy_driven')
-    if params.optimizeSynergyVectors
-        synergyWeights = scaleToOriginal(inputs.parameter(1,:), ...
-            params.maxParameter, params.minParameter);
-        values.synergyWeights = getSynergyWeightsFromGroups(...
-            synergyWeights, params);
-    else
-        values.synergyWeights = getSynergyWeightsFromGroups(...
-            params.synergyWeightsGuess, params);
-    end
+function osimx = buildSynergyGroupOsimx(osimx, synergyGroups)
+osimx.NMSMPipelineDocument.OsimxModel.RCNLSynergySet.Comment = ...
+    'The set of synergies from NCP to find the values in this osimx file';
+for i = 1:length(synergyGroups)
+    synergyGroup.muscle_group_name.Comment = ['The name of the muscle ' ...
+        'group associated with this synergy'];
+    synergyGroup.muscle_group_name.Text = synergyGroups{i}.muscleGroupName;
+    synergyGroup.num_synergies.Comment = ['The number of synergies ' ...
+        'used by this synergy group'];
+    synergyGroup.num_synergies.Text = num2str(synergyGroups{i}.numSynergies);
+    osimx.NMSMPipelineDocument.OsimxModel.RCNLSynergySet.RCNLSynergy{i} = synergyGroup;
 end
 end
+
diff --git a/src/core/osimx/parseOsimxFile.m b/src/core/osimx/parseOsimxFile.m
index 442c8fd4c..c12ac255f 100644
--- a/src/core/osimx/parseOsimxFile.m
+++ b/src/core/osimx/parseOsimxFile.m
@@ -27,7 +27,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function osimx = parseOsimxFile(osimxFileName)
+function osimx = parseOsimxFile(osimxFileName, model)
 
 if strcmp(osimxFileName, "")
     osimx = struct();
@@ -87,6 +87,11 @@
         end
     end
 end
+
+rcnlSynergySetTree = getFieldByName(tree, "RCNLSynergySet");
+if isstruct(rcnlSynergySetTree)
+    osimx.synergyGroups = parseSynergyGroups(tree, model);
+end
 end
 
 function contactSurface = parseContactSurface(tree)
@@ -98,8 +103,12 @@
 contactSurface.momentColumns = parseSpaceSeparatedList(tree, "moment_columns");
 contactSurface.electricalCenterColumns = parseSpaceSeparatedList(tree, "electrical_center_columns");
 
-contactSurface.toesCoordinateName = getFieldByNameOrError(tree, "toes_coordinate").Text;
-contactSurface.toesJointName = getFieldByNameOrError(tree, "toes_joint").Text;
+hindfootBodyName = getFieldByName(tree, "hindfoot_body");
+if ~isstruct(hindfootBodyName)
+    throw(MException('', "<toes_coordinate> is replaced by <hindfoot_body> in the osimx file. Please update your osimx file."))
+else
+contactSurface.hindfootBodyName = hindfootBodyName.Text;
+end
 
 contactSurface.toeMarker = getFieldByNameOrError(tree, "toe_marker").Text;
 contactSurface.medialMarker = getFieldByNameOrError(tree, "medial_marker").Text;
diff --git a/src/core/osimx/writeMuscleTendonPersonalizationOsimxFile.m b/src/core/osimx/writeMuscleTendonPersonalizationOsimxFile.m
index 7bacaccd2..78455a417 100644
--- a/src/core/osimx/writeMuscleTendonPersonalizationOsimxFile.m
+++ b/src/core/osimx/writeMuscleTendonPersonalizationOsimxFile.m
@@ -33,7 +33,7 @@ function writeMuscleTendonPersonalizationOsimxFile(modelFileName, ...
 model = Model(modelFileName);
 
 if isfile(osimxFileName)
-    osimx = parseOsimxFile(osimxFileName);
+    osimx = parseOsimxFile(osimxFileName, model);
     [~, name, ~] = fileparts(osimxFileName);
     outfile = fullfile(results_directory, strcat(name, "_mtp.xml"));
 else
diff --git a/src/core/osimx/writeNeuralControlPersonalizationOsimxFile.m b/src/core/osimx/writeNeuralControlPersonalizationOsimxFile.m
index 80fb34f7f..f0ae596f2 100644
--- a/src/core/osimx/writeNeuralControlPersonalizationOsimxFile.m
+++ b/src/core/osimx/writeNeuralControlPersonalizationOsimxFile.m
@@ -30,13 +30,12 @@
 
 function writeNeuralControlPersonalizationOsimxFile(inputs, ...
     resultsDirectory, precalInputs)
-modelFileName = inputs.model;
-model = Model(modelFileName);
+model = Model(inputs.modelFileName);
 
 buildFromExisting = false;
 if isfield(inputs, 'osimxFileName')
     if isfile(inputs.osimxFileName)
-        osimx = parseOsimxFile(inputs.osimxFileName);
+        osimx = parseOsimxFile(inputs.osimxFileName, model);
         [~, name, ~] = fileparts(inputs.osimxFileName);
         outfile = fullfile(resultsDirectory, strcat(name, "_ncp.xml"));
         buildFromExisting = true;
@@ -52,7 +51,7 @@ function writeNeuralControlPersonalizationOsimxFile(inputs, ...
     outfile = fullfile(resultsDirectory, strcat(name, "_ncp.xml"));
 end
 osimx.modelName = name;
-osimx.model = modelFileName;
+osimx.model = inputs.modelFileName;
 if ~isfield(osimx, 'muscles')
     osimx.muscles = [];
 end
@@ -68,12 +67,13 @@ function writeNeuralControlPersonalizationOsimxFile(inputs, ...
         osimx.muscles.(inputs.muscleTendonColumnNames(i)) ...
             .tendonSlackLength = inputs.tendonSlackLength(i);
     end
-    if precalInputs.optimizeIsometricMaxForce && ...
+    if isstruct(precalInputs) && precalInputs.optimizeIsometricMaxForce && ...
             ~isfield(osimx.muscles.(inputs.muscleTendonColumnNames(i)), "maxIsometricForce")
         osimx.muscles.(inputs.muscleTendonColumnNames(i)) ...
             .maxIsometricForce = inputs.maxIsometricForce(i);
     end
 end
+osimx.synergyGroups = inputs.synergyGroups;
 
 writeOsimxFile(buildOsimxFromOsimxStruct(osimx), outfile)
 end
diff --git a/src/core/parse/findPrefixes.m b/src/core/parse/findPrefixes.m
index 14d7d0337..86f655a9a 100644
--- a/src/core/parse/findPrefixes.m
+++ b/src/core/parse/findPrefixes.m
@@ -32,7 +32,7 @@
 
 function prefixes = findPrefixes(tree, inputDirectory)
 prefixField = getFieldByName(tree, 'trial_prefixes');
-if(isstruct(prefixField) && length(prefixField.Text) > 0)
+if isstruct(prefixField) && length(prefixField.Text) > 0
     prefixes = strsplit(prefixField.Text, ' ');
 else
     files = dir(fullfile(inputDirectory, "IDData"));
diff --git a/src/core/parse/findToolName.m b/src/core/parse/findToolName.m
new file mode 100644
index 000000000..466934cd2
--- /dev/null
+++ b/src/core/parse/findToolName.m
@@ -0,0 +1,42 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% (struct) -> (string)
+% returns the name of the tool from the settings tree
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function toolName = findToolName(tree)
+if ~isfield(tree, "NMSMPipelineDocument")
+    throw(MException("XMLParse:IncorrectDocument", ...
+        "XML files does not include <NMSMPipelineDocument"));
+end
+tree = tree.NMSMPipelineDocument;
+if isfield(tree, "TrackingOptimizationTool")
+    toolName = "TrackingOptimization";
+elseif isfield(tree, "VerificationOptimizationTool")
+    toolName = "VerificationOptimization";
+elseif isfield(tree, "DesignOptimizationTool")
+    toolName = "DesignOptimization";
+end
+end
+
diff --git a/src/core/parse/getModelOrOsimxInputs.m b/src/core/parse/getModelOrOsimxInputs.m
index 60504fefd..88192bf83 100644
--- a/src/core/parse/getModelOrOsimxInputs.m
+++ b/src/core/parse/getModelOrOsimxInputs.m
@@ -11,7 +11,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,6 +28,8 @@
 function inputs = getModelOrOsimxInputs(inputs)
 if ~isa(inputs.model, 'org.opensim.modeling.Model')
     model = Model(inputs.model);
+else
+    model = inputs.model;
 end
 inputs.optimalFiberLength = [];
 inputs.tendonSlackLength = [];
diff --git a/src/core/TreatmentOptimization/getPathConstraintTerms.m b/src/core/parse/parseController.m
similarity index 66%
rename from src/core/TreatmentOptimization/getPathConstraintTerms.m
rename to src/core/parse/parseController.m
index d56aef764..195f6f6ce 100644
--- a/src/core/TreatmentOptimization/getPathConstraintTerms.m
+++ b/src/core/parse/parseController.m
@@ -1,10 +1,11 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% Parses XML settings for a RCNLPathConstraintTerms, adding all fields 
-% included in the xml block.  
+% There are two controllers that can be used to solve optimal control
+% problems in the NMSM Pipeline. This function parses the shared inputs and
+% requests the correct subtools to be parsed.
 %
 % (struct) -> (struct)
-% Parses settings from a RCNLPathConstraintTerms.
+% parses shared controller settings from XML tree
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,18 +29,18 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function path = getPathConstraintTerms(tree)
-pathConstraintTermsTree = getFieldByName(tree, ...
-    'RCNLPathConstraintTerms');
-if(isstruct(pathConstraintTermsTree))
-    pathConstraints = getFieldByName(pathConstraintTermsTree, ...
-        'RCNLConstraintTerm');
-    if isstruct(pathConstraints) || iscell(pathConstraints)
-        path = parseRcnlConstraintTermSet(pathConstraints);
-    else
-        path = {};
-    end
-else
-    path = {};
+function inputs = parseController(tree, inputs)
+inputs = parseTreatmentOptimizationDesignVariableBounds(tree, ...
+    inputs);
+inputs.statesCoordinateNames = parseSpaceSeparatedList(tree, ...
+    "states_coordinate_list");
+
+torqueTree = getFieldByName(tree, "RCNLTorqueController");
+if isstruct(torqueTree)
+    inputs = parseTorqueController(torqueTree, inputs);
+end
+synergyTree = getFieldByName(tree, "RCNLSynergyController");
+if isstruct(synergyTree)
+    inputs = parseSynergyController(tree, inputs);
+end
 end
-end
\ No newline at end of file
diff --git a/src/core/TreatmentOptimization/makeTreatmentOptimizationInputs.m b/src/core/parse/parseControllerType.m
similarity index 66%
rename from src/core/TreatmentOptimization/makeTreatmentOptimizationInputs.m
rename to src/core/parse/parseControllerType.m
index d646dadbd..9299847ec 100644
--- a/src/core/TreatmentOptimization/makeTreatmentOptimizationInputs.m
+++ b/src/core/parse/parseControllerType.m
@@ -1,9 +1,12 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function prepares the inputs for the all treatment optimization
-% modules (tracking, verification, and design optimization. 
+% There are two controllers that can be used to solve optimal control
+% problems in the NMSM Pipeline. This function finds the correct element to
+% determine which controller is being used. This informs the XML parsing
+% logic.
 %
-% (struct, struct) -> (struct) 
+% (struct) -> (string)
+% returns "synergy" or "torque" depending on the settings file
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +16,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega, Claire V. Hammond                              %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,20 +30,17 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = makeTreatmentOptimizationInputs(inputs, params)
-if isequal(mexext, 'mexw64')
-    pointKinematicsMexWindows(inputs.mexModel);
-    inverseDynamicsMexWindows(inputs.mexModel);
+function controllerType = parseControllerType(tree)
+synergy = getFieldByName(tree, "RCNLSynergyController");
+if isstruct(synergy)
+    controllerType = "synergy";
+    return
 end
-inputs = getStateDerivatives(inputs);
-inputs = setupGroundContact(inputs);
-inputs = getSplines(inputs);
-inputs = checkStateGuess(inputs);
-inputs = checkControlGuess(inputs);
-inputs = checkParameterGuess(inputs);
-inputs = getIntegralBounds(inputs);
-inputs = getPathConstraintBounds(inputs);
-inputs = getTerminalConstraintBounds(inputs);
-inputs = getDesignVariableInputBounds(inputs);
+torque = getFieldByName(tree, "RCNLTorqueController");
+if isstruct(torque)
+    controllerType = "torque";
+    return
 end
-
+throw(MException("ParseTreatmentOptimization:NoController", ...
+    "Could not find <RCNLTorqueController> or <RCNLSynergyController>"))
+end
\ No newline at end of file
diff --git a/src/core/parse/parseDoubleOrAlternate.m b/src/core/parse/parseDoubleOrAlternate.m
new file mode 100644
index 000000000..9b8900e41
--- /dev/null
+++ b/src/core/parse/parseDoubleOrAlternate.m
@@ -0,0 +1,43 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function attempts to parse a double from a struct field. If the
+% field is not a struct or the field cannot be parsed as a double, the
+% alternate value is returned.
+%
+% (struct, string, double) => double
+% Parses a double or returns an alternate value
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                                 %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function output = parseDoubleOrAlternate(tree, field, alternate)
+    field = getFieldByName(tree, field);
+    if(isstruct(field))
+        try
+            output = str2double(field.Text);
+        catch
+            output = alternate;
+        end
+    else
+        output = alternate;
+    end
+end
diff --git a/src/core/parse/parseElementTextByNameOrAlternate.m b/src/core/parse/parseElementTextByNameOrAlternate.m
index 67367ab5d..0fcc20ea4 100644
--- a/src/core/parse/parseElementTextByNameOrAlternate.m
+++ b/src/core/parse/parseElementTextByNameOrAlternate.m
@@ -1,18 +1,45 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% (struct, string, string) -> (string)
+% Returns text or alternate
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
 function textOrAlternate = parseElementTextByNameOrAlternate(tree, ...
-        elementStringOrStringArray, alternate)
-    try
-elements = elementStringOrStringArray;
+    elementStringOrStringArray, alternate)
+try
+    elements = elementStringOrStringArray;
     if ischar(elementStringOrStringArray) || isstring(elementStringOrStringArray)
         elements = string([elementStringOrStringArray]);
     end
     for i = 1:length(elements)
-      if ~strcmp(elements(i), elements(end))
-        tree = getFieldByNameOrError(tree, elements(i));
-      else
-        textOrAlternate = getFieldByNameOrError(tree, elements(i)).Text;
-      end
-    end
-    catch
-      textOrAlternate = alternate;
+        if ~strcmp(elements(i), elements(end))
+            tree = getFieldByNameOrError(tree, elements(i));
+        else
+            textOrAlternate = getFieldByNameOrError(tree, elements(i)).Text;
+        end
     end
+catch
+    textOrAlternate = alternate;
+end
 end
diff --git a/src/core/parse/parseModel.m b/src/core/parse/parseModel.m
index db2b325fb..b4834a6c5 100644
--- a/src/core/parse/parseModel.m
+++ b/src/core/parse/parseModel.m
@@ -1,3 +1,5 @@
-function model = parseModel(tree)
-model = parseElementTextByName(tree, 'input_model_file');
+function inputs = parseModel(tree, inputs)
+fileName = parseElementTextByName(tree, 'input_model_file');
+inputs.model = Model(fileName);
+inputs.modelFileName = fileName;
 end
diff --git a/src/core/parse/parseMtpNcpSharedInputs.m b/src/core/parse/parseMtpNcpSharedInputs.m
index d39d703ac..251308797 100644
--- a/src/core/parse/parseMtpNcpSharedInputs.m
+++ b/src/core/parse/parseMtpNcpSharedInputs.m
@@ -6,7 +6,7 @@
 
 function inputs = getInputs(tree)
 
-inputs.model = parseModel(tree);
+inputs = parseModel(tree, struct());
 inputs.osimxFileName = parseElementTextByName(tree, "input_osimx_file");
 inputs.coordinateNames = parseSpaceSeparatedList(tree, "coordinate_list");
 inputs.muscleNames = getMusclesFromCoordinates(inputs.model, ...
diff --git a/src/core/parse/parseRcnlConstraintTermSet.m b/src/core/parse/parseRcnlConstraintTermSet.m
index 208a78f72..cd606fbd1 100644
--- a/src/core/parse/parseRcnlConstraintTermSet.m
+++ b/src/core/parse/parseRcnlConstraintTermSet.m
@@ -1,7 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% Parses XML settings for a RCNLCostTermSet, adding all fields included in 
-% the xml block.  
+% Parses XML settings for a RCNLCostTermSet, adding all fields included in
+% the xml block.
 %
 % (struct) -> (struct)
 % Parses settings from a RCNLCostTermSet.
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2022 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond, Spencer Williams                          %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,8 +28,10 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function costTerms = parseRcnlConstraintTermSet(tree)
-costTerms = cell(1, length(tree));
+function [path, terminal] = parseRcnlConstraintTermSet(tree, toolName, ...
+    controllerType)
+path = {};
+terminal = {};
 for term = 1:length(tree)
     if length(tree) == 1
         currentTerm = tree;
@@ -37,14 +39,20 @@
         currentTerm = tree{term};
     end
     % Find general cost term elements
-    costTerms{term}.type = getTextFromField(getFieldByNameOrError( ...
+    tempTerm.type = getTextFromField(getFieldByNameOrError( ...
         currentTerm, 'type'));
+    [isValid, isPath] = isTypeValid(tempTerm.type, toolName, controllerType);
+    if ~isValid
+        throw(MException("ConstraintTermSet:InvalidType", ...
+            strcat(tempTerm.type, " is not a valid constraint", ...
+            " term for tool ", toolName)));
+    end
     enabled = getTextFromField(getFieldByNameOrAlternate( ...
         currentTerm, 'is_enabled', 'false'));
-    costTerms{term}.isEnabled = strcmpi(enabled, 'true');
-    costTerms{term}.maxError = str2double(getTextFromField( ...
+    tempTerm.isEnabled = strcmpi(enabled, 'true');
+    tempTerm.maxError = str2double(getTextFromField( ...
         getFieldByNameOrAlternate(currentTerm, 'max_error', '1')));
-      costTerms{term}.minError = str2double(getTextFromField( ...
+    tempTerm.minError = str2double(getTextFromField( ...
         getFieldByNameOrAlternate(currentTerm, 'min_error', '-1')));
     % Find other cost term elements
     termElements = fieldnames(currentTerm);
@@ -60,9 +68,28 @@
             elseif ~isnan(str2double(contents))
                 contents = str2double(contents);
             end
-            costTerms{term}.(termElements{element}) = contents;
+            tempTerm.(termElements{element}) = contents;
         end
-    end 
+    end
+    if isPath
+        path{end + 1} = tempTerm;
+    else
+        terminal{end + 1} = tempTerm;
+    end
 end
 end
 
+function [isValid, isPath] = isTypeValid(type, toolName, controllerType)
+[~, allowedTypes] = ...
+    generateConstraintTermStruct("path", controllerType, ...
+    toolName);
+isPath = true;
+isValid = any(strcmp(type, allowedTypes));
+if ~isValid
+    [~, allowedTypes] = ...
+        generateConstraintTermStruct("terminal", controllerType, ...
+        toolName);
+    isPath = false;
+    isValid = any(strcmp(type, allowedTypes));
+end
+end
diff --git a/src/core/parse/parseSelectMomentArms.m b/src/core/parse/parseSelectMomentArms.m
index 256516ef7..b7b1493d7 100644
--- a/src/core/parse/parseSelectMomentArms.m
+++ b/src/core/parse/parseSelectMomentArms.m
@@ -11,7 +11,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -25,22 +25,19 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cells = parseSelectMomentArms(directories, coordinateNames, muscleNames)
+function cells = parseSelectMomentArms(directory, coordinateNames, muscleNames)
 import org.opensim.modeling.Storage
-firstTrial = parseSpecificMuscleAnalysisCoordinates(directories(1), ...
+firstTrial = parseSpecificMuscleAnalysisCoordinates(directory, ...
     coordinateNames, muscleNames);
-cells = zeros([length(directories) size(firstTrial)]);
+cells = zeros([1 size(firstTrial)]);
 cells(1, :, :, :) = firstTrial;
-for i=2:length(directories)
-    cells(i, :, :, :) = parseSpecificMuscleAnalysisCoordinates(directories(i), ...
-        coordinateNames, muscleNames);
-end
 end
 
 function cells = parseSpecificMuscleAnalysisCoordinates(inputDirectory, ...
     coordinateNames, muscleNames)
 import org.opensim.modeling.Storage
-coordFileNames = findSpecificMuscleAnalysisCoordinateFiles(inputDirectory, coordinateNames);
+coordFileNames = findSpecificMuscleAnalysisCoordinateFiles( ...
+    inputDirectory, coordinateNames);
 firstFile = storageToDoubleMatrix(Storage(coordFileNames(1)));
 columnNames = getStorageColumnNames(Storage(coordFileNames(1)));
 cells = zeros([length(coordFileNames) size(firstFile)]);
diff --git a/src/core/parse/parseSpaceSeparatedList.m b/src/core/parse/parseSpaceSeparatedList.m
index 3178a147e..2317a931d 100644
--- a/src/core/parse/parseSpaceSeparatedList.m
+++ b/src/core/parse/parseSpaceSeparatedList.m
@@ -32,9 +32,10 @@
 function prefixes = parseSpaceSeparatedList(tree, elementName)
 prefixField = getFieldByName(tree, elementName);
 if ~isfield(prefixField, "Text")
-    throw(MException('', strcat(prefixField, " is not in the xml file.")))
+    throw(MException('', strcat(elementName, " is not in the xml file.")))
 end
-if ~isempty(prefixField.Text)
+prefixField.Text = strip(prefixField.Text);
+if ~isempty(convertStringsToChars(prefixField.Text))
     if(strcmp(prefixField.Text(1), ' '))
         prefixField.Text = prefixField.Text(2:end);
     end
diff --git a/src/core/parse/parseSynergyController.m b/src/core/parse/parseSynergyController.m
new file mode 100644
index 000000000..463064c45
--- /dev/null
+++ b/src/core/parse/parseSynergyController.m
@@ -0,0 +1,73 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% There are two controllers that can be used to solve optimal control
+% problems in the NMSM Pipeline. This function parses the synergy
+% controller settings inside <RCNLSynergyController>
+%
+% (struct) -> (struct)
+% parses synergy controller settings from XML tree
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Claire V. Hammond                                            %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function inputs = parseSynergyController(tree, inputs)
+inputs.synergyGroups = inputs.osimx.synergyGroups;
+inputs.numSynergies = getNumSynergies(inputs.synergyGroups);
+inputs.surrogateModelCoordinateNames = parseSpaceSeparatedList(tree, ...
+    "surrogate_model_coordinate_list");
+[~, ~, statesOrder] = intersect(inputs.statesCoordinateNames, ...
+    inputs.surrogateModelCoordinateNames, 'stable');
+inputs.surrogateModelCoordinateNames = ...
+    inputs.surrogateModelCoordinateNames(statesOrder);
+inputs.muscleNames = getMusclesFromCoordinates(inputs.model, ...
+    inputs.surrogateModelCoordinateNames);
+inputs.numMuscles = length(inputs.muscleNames);
+inputs.epsilon = str2double(parseElementTextByNameOrAlternate(tree, ...
+    "epsilon", "1e-4"));
+inputs.polynomialDegree = str2double(parseElementTextByNameOrAlternate( ...
+    tree, "surrogate_model_polynomial_degree", "5"));
+inputs.performLatinHyperCubeSampling = strcmpi( ...
+    parseElementTextByNameOrAlternate(tree, ...
+    "perform_latin_hypercube_sampling", "false"), "true");
+if inputs.performLatinHyperCubeSampling
+    inputs.lhsRangeMultiplier = str2double( ...
+        parseElementTextByName(tree, "latin_hypercube_range_multiplier"));
+    inputs.lhsNumPoints = str2double( ...
+        parseElementTextByName(tree, "latin_hypercube_number_of_points"));
+end
+inputs.dataDirectory = parseElementTextByName(tree, "data_directory");
+inputs.vMaxFactor = str2double(parseElementTextByNameOrAlternate(tree, ...
+    "maximum_shortening_velocity_multiplier", "10"));
+inputs.optimizeSynergyVectors = getBooleanLogic(...
+    parseElementTextByNameOrAlternate(tree, "optimize_synergy_vectors", 0));
+inputs.maxControlSynergyActivations = parseDoubleOrAlternate(tree, ...
+    'maximum_allowable_synergy_activation', 10);
+if ~isfield(inputs, "torqueControllerCoordinateNames")
+    inputs.torqueControllerCoordinateNames = [];
+end
+inputs = getModelOrOsimxInputs(inputs);
+inputs.saveSurrogate = getBooleanLogicFromField( ...
+    getFieldByNameOrAlternate(tree, 'save_surrogate_model', false));
+inputs.loadSurrogate = getBooleanLogicFromField( ...
+    getFieldByNameOrAlternate(tree, 'load_surrogate_model', false));
+end
+
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMetabolicCost.m b/src/core/parse/parseTextOrAlternate.m
similarity index 79%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMetabolicCost.m
rename to src/core/parse/parseTextOrAlternate.m
index 0e9c64d9b..4d76cdeac 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMetabolicCost.m
+++ b/src/core/parse/parseTextOrAlternate.m
@@ -1,9 +1,7 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function minimizes the metabolic cost.
 %
-% (struct, struct, struct) -> (Array of number)
-% 
+
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
 % optimization of neuromusculoskeletal models through OpenSim. See        %
@@ -12,7 +10,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -26,10 +24,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingMetabolicCost(values, modeledValues, ...
-    params)
-
-metabolicCost = calcMetabolicCost(values.time, ...
-    values.statePositions, modeledValues.muscleActivations, params);
-cost = calcMinimizingCostArrayTerm(metabolicCost);
-end
\ No newline at end of file
+function text = parseTextOrAlternate(tree, field, alternate)
+text = getTextFromField( ...
+    getFieldByNameOrAlternate(tree, field, alternate));
+end
diff --git a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkControlGuess.m b/src/core/parse/parseTorqueController.m
similarity index 72%
rename from src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkControlGuess.m
rename to src/core/parse/parseTorqueController.m
index d91d6e5b2..cc41fe910 100644
--- a/src/core/TreatmentOptimization/OptimalControlSetupFunctions/checkControlGuess.m
+++ b/src/core/parse/parseTorqueController.m
@@ -1,10 +1,11 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function checks that the initial guess control file is in the 
-% correct order
+% There are two controllers that can be used to solve optimal control
+% problems in the NMSM Pipeline. This function parses the torque
+% controller settings inside <RCNLTorqueController>
 %
 % (struct) -> (struct)
-% 
+% parses torque controller settings from XML tree
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +15,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,16 +29,11 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function inputs = checkControlGuess(inputs)
-if isfield(inputs.initialGuess, 'control')
-    for i = 1 : inputs.numCoordinates
-        for k = 1 : length(inputs.initialGuess.controlLabels)
-            if strcmpi(inputs.coordinateNames(i), inputs.initialGuess.controlLabels(k))
-                controlIndex(i) = k;
-            end
-        end 
-    end
-    inputs.initialGuess.control(:, 1:inputs.numCoordinates) = ...
-        inputs.initialGuess.control(:, controlIndex);
+function inputs = parseTorqueController(tree, inputs)
+inputs.torqueControllerCoordinateNames = parseSpaceSeparatedList(tree, ...
+    "coordinate_list");
+inputs.maxTorqueControlsMultiple = parseDoubleOrAlternate(tree, ...
+    'torque_controls_range_scale_factor', 1);
+inputs.numSynergies = 0;
+inputs.surrogateModelCoordinateNames = [];
 end
-end
\ No newline at end of file
diff --git a/src/core/parse/parseTreatmentOptimizationDataDirectory.m b/src/core/parse/parseTreatmentOptimizationDataDirectory.m
index 1862754b4..29ed26762 100644
--- a/src/core/parse/parseTreatmentOptimizationDataDirectory.m
+++ b/src/core/parse/parseTreatmentOptimizationDataDirectory.m
@@ -16,7 +16,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -31,74 +31,142 @@
 % ----------------------------------------------------------------------- %
 
 function inputs = parseTreatmentOptimizationDataDirectory(tree, inputs)
+[dataDirectory, inputs.previousResultsDirectory] = findDataDirectory(tree, inputs);
+inputs.trialName = parseTrialName(tree);
+inputs = parseExperimentalData(tree, inputs, dataDirectory);
+inputs = parseSynergyExperimentalData(tree, inputs, dataDirectory);
+inputs = parseInitialValues(tree, inputs);
+inputs.numCoordinates = size(inputs.experimentalJointAngles, 2);
+end
+
+function [dataDirectory, previousResultsDirectory] = ...
+    findDataDirectory(tree, inputs)
 dataDirectory = parseDataDirectory(tree);
-previousResultsDirectoryElement = getFieldByName(tree, 'previous_results_directory');
-if isstruct(previousResultsDirectoryElement)
-    previousResultsDirectory = previousResultsDirectoryElement.Text;
-else
-    previousResultsDirectory = [];
+previousResultsDirectory = ...
+    parseTextOrAlternate(tree, "previous_results_directory", "");
+if strcmp(previousResultsDirectory, "") && ...
+        strcmp(inputs.controllerType, 'synergy')
+    throw(MException("ParseError:RequiredElement", ...
+        strcat("Element <previous_results_directory> required", ...
+        " for <RCNLSynergyController>, this can be an NCP", ...
+        " or Treatment Optimization results directory")))
 end
-if strcmp(previousResultsDirectory, "")
-        previousResultsDirectory = [];
 end
-prefix = findPrefixes(tree, dataDirectory);
 
-if ~isempty(previousResultsDirectory) && ...
-        exist(fullfile(previousResultsDirectory, "optimal"), 'dir')
-    directory = findFirstLevelSubDirectoriesFromPrefixes( ...
-        previousResultsDirectory, "optimal");
-    if ~isempty(directory)
-        model = Model(inputs.model);
-        [inputs.experimentalJointMoments, inputs.inverseDynamicMomentLabels] = ...
-            parseTreatmentOptimizationData(directory, 'inverseDynamics', model);
-        [inputs.experimentalJointAngles, inputs.coordinateNames] = ...
-            parseTreatmentOptimizationData(directory, 'inverseKinematics', model);
-        experimentalTime = parseTimeColumn(findFileListFromPrefixList(...
-            directory, "inverseKinematics"))';
-        inputs.kinematicsFile = findFileListFromPrefixList(...
-            directory, "inverseKinematics");
-        inputs.experimentalTime = experimentalTime - experimentalTime(1);
-        if exist(fullfile(dataDirectory, "groundReactions"), 'dir')
-            inputs.grfFileName = findFileListFromPrefixList(...
-                directory, "groundReactions");
-        end
-        if strcmp(inputs.controllerType, 'synergy_driven')
-            [inputs.experimentalMuscleActivations, inputs.muscleLabels] = ...
-                parseTreatmentOptimizationData(directory, 'muscleActivations', model);
-        end
+function inputs = parseExperimentalData(tree, inputs, dataDirectory)
+[inputs.experimentalJointMoments, ...
+    inputs.inverseDynamicsMomentLabels] = ...
+    parseTrialDataTryDirectories( ...
+    fullfile(inputs.previousResultsDirectory, "IDData"), ...
+    fullfile(dataDirectory, "IDData"), inputs.trialName, inputs.model);
+[inputs.experimentalJointAngles, inputs.coordinateNames, ...
+    experimentalTime] = parseTrialDataTryDirectories( ...
+    fullfile(inputs.previousResultsDirectory, "IKData"), ...
+    fullfile(dataDirectory, "IKData"), inputs.trialName, inputs.model);
+inputs.coordinateNames = cellstr(inputs.coordinateNames);
+inputs.experimentalTime = experimentalTime - experimentalTime(1);
+inputs.initialTime = inputs.experimentalTime;
+if isfield(inputs.osimx, 'groundContact') && ...
+        isfield(inputs.osimx.groundContact, 'contactSurface')
+    inputs.contactSurfaces = inputs.osimx.groundContact.contactSurface;
+    for surfaceIndex = 1:length(inputs.contactSurfaces)
+        [inputs.contactSurfaces{surfaceIndex} ...
+            .experimentalGroundReactionForces, ...
+            inputs.contactSurfaces{surfaceIndex} ...
+            .experimentalGroundReactionMoments, ...
+            inputs.contactSurfaces{surfaceIndex} ...
+            .electricalCenter] = parseGroundReactionDataWithoutTime( ...
+            inputs, dataDirectory, surfaceIndex);
     end
 else
-    directory = findFirstLevelSubDirectoriesFromPrefixes(dataDirectory, "IDData");
-    model = Model(inputs.model);
-    [inputs.experimentalJointMoments, inputs.inverseDynamicMomentLabels] = ...
-        parseTreatmentOptimizationData(directory, prefix, model);
-    directory = findFirstLevelSubDirectoriesFromPrefixes(dataDirectory, "IKData");
-    [inputs.experimentalJointAngles, inputs.coordinateNames] = ...
-        parseTreatmentOptimizationData(directory, prefix, model);
-    experimentalTime = parseTimeColumn(findFileListFromPrefixList(...
-        fullfile(dataDirectory, "IKData"), prefix))';
-    inputs.kinematicsFile = findFileListFromPrefixList( ...
-        fullfile(dataDirectory, "IKData"), prefix);
-    inputs.experimentalTime = experimentalTime - experimentalTime(1);
-    if exist(fullfile(dataDirectory, "GRFData"), 'dir')
-        inputs.grfFileName = findFileListFromPrefixList(...
-            fullfile(dataDirectory, "GRFData"), prefix);
-    end
-    if strcmp(inputs.controllerType, 'synergy_driven')
-        directory = findFirstLevelSubDirectoriesFromPrefixes(dataDirectory, "ActData");
-        [inputs.experimentalMuscleActivations, inputs.muscleLabels] = ...
-            parseTreatmentOptimizationData(directory, prefix, model);
-    end
+inputs.contactSurfaces = {};
+end
 end
 
-if strcmp(inputs.controllerType, 'synergy_driven')
-    directories = findFirstLevelSubDirectoriesFromPrefixes(fullfile( ...
-        dataDirectory, "MAData"), prefix);
-    inputs.momentArms = parseSelectMomentArms(directories, ...
+function inputs = parseSynergyExperimentalData(tree, inputs, dataDirectory)
+if strcmp(inputs.controllerType, "synergy")
+    [inputs.experimentalMuscleActivations, inputs.muscleLabels] = ...
+        parseTrialData(inputs.previousResultsDirectory, ...
+        strcat(inputs.trialName, "_combinedActivations"), inputs.model);
+    [inputs.synergyWeights, inputs.synergyWeightsLabels] = ...
+    parseTrialData(inputs.previousResultsDirectory, ...
+        "synergyWeights", inputs.model);
+    directory = fullfile(dataDirectory, "MAData", inputs.trialName);
+    inputs.momentArms = parseSelectMomentArms(directory, ...
         inputs.surrogateModelCoordinateNames, inputs.muscleNames);
     inputs.momentArms = reshape(permute(inputs.momentArms, [1 4 2 3]), [], ...
         length(inputs.surrogateModelCoordinateNames), length(inputs.muscleNames));
     inputs = getMuscleSpecificSurrogateModelData(inputs);
 end
-inputs.numCoordinates = size(inputs.experimentalJointAngles, 2);
-end
\ No newline at end of file
+end
+
+function inputs = parseInitialValues(tree, inputs)
+initialGuess = [];
+try
+    [inputs.initialStates, inputs.initialStatesLabels, inputs.initialTime] = ...
+        parseTrialData(inputs.previousResultsDirectory, ...
+        strcat(inputs.trialName, "_states"), inputs.model);
+catch; end
+try
+    [inputs.initialAccelerations, inputs.initialAccelerationsLabels] = ...
+        parseTrialData(inputs.previousResultsDirectory, ...
+        strcat(inputs.trialName, "_accelerations"), inputs.model);
+catch; end
+try
+    [inputs.initialTorqueControls, inputs.initialTorqueControlsLabels] = ...
+        parseTrialData(inputs.previousResultsDirectory, ...
+        strcat(inputs.trialName, "_torqueControls"), inputs.model);
+catch;end
+if strcmp(inputs.controllerType, "synergy")
+    [inputs.initialSynergyControls, inputs.initialSynergyControlsLabels] = ...
+        parseTrialData(inputs.previousResultsDirectory, ...
+        strcat(inputs.trialName, "_synergyCommands"), inputs.model);
+end
+end
+
+function [data, labels, time] = parseTrialDataTryDirectories( ...
+    previousResultsDirectory, dataDirectory, trialName, model)
+if ~strcmp(previousResultsDirectory, "")
+    try
+        [data, labels, time] = parseTrialData(...
+            previousResultsDirectory, trialName, model);
+    catch
+        [data, labels, time] = parseTrialData( ...
+            dataDirectory, trialName, model);
+    end
+else
+    [data, labels, time] = parseTrialData(dataDirectory, trialName, model);
+end
+end
+
+function [forces, moments, ec] = parseGroundReactionDataWithoutTime( ...
+    inputs, dataDirectory, surfaceIndex)
+import org.opensim.modeling.Storage
+[grfData, grfColumnNames, grfTime] = parseTrialDataTryDirectories( ...
+    fullfile(inputs.previousResultsDirectory, "GRFData"), ...
+    fullfile(dataDirectory, "GRFData"), inputs.trialName, inputs.model);
+forces = NaN(length(grfTime), 3);
+moments = NaN(length(grfTime), 3);
+ec = NaN(length(grfTime), 3);
+for i=1:size(grfColumnNames')
+    label = grfColumnNames(i);
+    for j = 1:3
+        if strcmpi(label, inputs.osimx.groundContact ...
+                .contactSurface{surfaceIndex}.forceColumns(j))
+            forces(:, j) = grfData(:, i);
+        end
+        if strcmpi(label, inputs.osimx.groundContact ...
+                .contactSurface{surfaceIndex}.momentColumns(j))
+            moments(:, j) = grfData(:, i);
+        end
+        if strcmpi(label, inputs.osimx.groundContact ...
+                .contactSurface{surfaceIndex}.electricalCenterColumns(j))
+            ec(:, j) = grfData(:, i);
+        end
+    end
+end
+if any([isnan(forces) isnan(moments) isnan(ec)])
+    throw(MException('', ['Unable to parse GRF file, check that ' ...
+        'all necessary column labels are present']))
+end
+end
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingMuscleActivationIntegrand.m b/src/core/parse/parseTreatmentOptimizationDesignVariableBounds.m
similarity index 75%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingMuscleActivationIntegrand.m
rename to src/core/parse/parseTreatmentOptimizationDesignVariableBounds.m
index 8ec37297d..3ba4b29e8 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMaximizingMuscleActivationIntegrand.m
+++ b/src/core/parse/parseTreatmentOptimizationDesignVariableBounds.m
@@ -1,9 +1,6 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function maximizes the muscle activation for the specified muscle.
 %
-% (2D matrix, struct, Array of string) -> (Array of number)
-% 
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +10,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Marleny Vega, Claire V. Hammond                                                 %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,10 +24,12 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMaximizingMuscleActivationIntegrand(...
-    muscleActivations, params, muscleName)
-
-indx = find(strcmp(convertCharsToStrings(params.muscleNames), ...
-    muscleName));
-cost = calcMaximizingCostArrayTerm(muscleActivations(:, indx));
-end
\ No newline at end of file
+function inputs = parseTreatmentOptimizationDesignVariableBounds( ...
+    tree, inputs)
+inputs.jointPositionsMultiple = parseDoubleOrAlternate(tree, ...
+    'joint_position_range_scale_factor', 2);
+inputs.jointVelocitiesMultiple = parseDoubleOrAlternate(tree, ...
+    'joint_velocity_range_scale_factor', 1.5);
+inputs.jointAccelerationsMultiple = parseDoubleOrAlternate(tree, ...
+    'joint_acceleration_range_scale_factor', 1);
+end
diff --git a/src/core/parse/parseTreatmentOptimizationInputs.m b/src/core/parse/parseTreatmentOptimizationInputs.m
new file mode 100644
index 000000000..a92a1c0b2
--- /dev/null
+++ b/src/core/parse/parseTreatmentOptimizationInputs.m
@@ -0,0 +1,109 @@
+% This function is part of the NMSM Pipeline, see file for full license.
+%
+% This function parses the settings tree resulting from xml2struct from the
+% settings XML file common to all treatment optimizatin modules (trackning,
+% verification, and design optimization).
+%
+% (struct) -> (struct, struct)
+% returns the input values for all treatment optimization modules
+
+% ----------------------------------------------------------------------- %
+% The NMSM Pipeline is a toolkit for model personalization and treatment  %
+% optimization of neuromusculoskeletal models through OpenSim. See        %
+% nmsm.rice.edu and the NOTICE file for more information. The             %
+% NMSM Pipeline is developed at Rice University and supported by the US   %
+% National Institutes of Health (R01 EB030520).                           %
+%                                                                         %
+% Copyright (c) 2021 Rice University and the Authors                      %
+% Author(s): Marleny Vega, Claire V. Hammond                              %
+%                                                                         %
+% Licensed under the Apache License, Version 2.0 (the "License");         %
+% you may not use this file except in compliance with the License.        %
+% You may obtain a copy of the License at                                 %
+% http://www.apache.org/licenses/LICENSE-2.0.                             %
+%                                                                         %
+% Unless required by applicable law or agreed to in writing, software     %
+% distributed under the License is distributed on an "AS IS" BASIS,       %
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
+% implied. See the License for the specific language governing            %
+% permissions and limitations under the License.                          %
+% ----------------------------------------------------------------------- %
+
+function inputs = parseTreatmentOptimizationInputs(tree)
+inputs = parseBasicInputs(tree);
+inputs.osimx = parseOsimxFileWithCondition(tree, inputs);
+inputs = parseController(tree, inputs);
+inputs = parseTreatmentOptimizationDataDirectory(tree, inputs);
+inputs = parseOptimalControlSolverSettings(tree, inputs);
+inputs.costTerms = parseRcnlCostTermSetHelper( ...
+    getFieldByNameOrError(tree, 'RCNLCostTermSet'));
+if isequal(mexext, 'mexw64') 
+    inputs.calculateAngularMomentum = any(all([ ...
+        strcmp(cellfun(@(term) term.type, inputs.costTerms, ...
+        'UniformOutput', false), {'angular_momentum_minimization'}) ...
+        ; ...
+        cell2mat(cellfun(@(term) term.isEnabled, inputs.costTerms, ...
+        'UniformOutput', false)) ...
+        ], 1));
+    inputs.calculateMetabolicCost = any(all([ ...
+        strcmp(cellfun(@(term) term.type, inputs.costTerms, ...
+        'UniformOutput', false), {'relative_metabolic_cost_per_time'}), ...
+        strcmp(cellfun(@(term) term.type, inputs.costTerms, ...
+        'UniformOutput', false), {'relative_metabolic_cost_per_distance'}) ...
+        ; ...
+        cell2mat(cellfun(@(term) term.isEnabled, inputs.costTerms, ...
+        'UniformOutput', false)), ...
+        cell2mat(cellfun(@(term) term.isEnabled, inputs.costTerms, ...
+        'UniformOutput', false)) ...
+        ], 1));
+end
+[inputs.path, inputs.terminal] = parseRcnlConstraintTermSetHelper( ...
+    getFieldByNameOrError(tree, 'RCNLConstraintTermSet'), ...
+    inputs.controllerType, inputs.toolName);
+end
+
+function inputs = parseBasicInputs(tree)
+inputs.toolName = findToolName(tree);
+inputs.resultsDirectory = getTextFromField(getFieldByName(tree, ...
+    'results_directory'));
+if(isempty(inputs.resultsDirectory)); inputs.resultsDirectory = pwd; end
+inputs.controllerType = parseControllerType(tree);
+inputs = parseModel(tree, inputs);
+end
+
+function osimx = parseOsimxFileWithCondition(tree, inputs)
+osimxFileName = parseTextOrAlternate(tree, "input_osimx_file", "");
+osimx = parseOsimxFile(osimxFileName, inputs.model);
+if strcmp(inputs.controllerType, "synergy")
+    if strcmp(osimxFileName, "")
+        throw(MException("", ...
+            strcat("<input_osimx_file> must be specified", ...
+            " for <RCNLSynergyController>")))
+    end
+    if ~isfield(osimx, "synergyGroups")
+        throw(MException("", ...
+            strcat("<RCNLSynergySet> must be specified in the", ...
+            " osimx file for <RCNLSynergyController>. Have you run NCP yet?")))
+    end
+end
+end
+
+function costTerms = parseRcnlCostTermSetHelper(tree)
+if isfield(tree, "RCNLCostTerm")
+    costTerms = parseRcnlCostTermSet(tree.RCNLCostTerm);
+else
+    costTerms = parseRcnlCostTermSet({});
+end
+end
+
+function [path, terminal] = parseRcnlConstraintTermSetHelper(tree, ...
+    controllerType, toolName)
+if isfield(tree, "RCNLConstraintTerm")
+    [path, terminal] = parseRcnlConstraintTermSet( ...
+        tree.RCNLConstraintTerm, toolName, controllerType);
+else
+    [path, terminal] = parseRcnlConstraintTermSet({}, controllerType, ...
+        toolName);
+end
+end
+
diff --git a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityXIntegrand.m b/src/core/parse/parseTreatmentOptimizationParams.m
similarity index 79%
rename from src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityXIntegrand.m
rename to src/core/parse/parseTreatmentOptimizationParams.m
index 831fa0b34..e45215032 100644
--- a/src/core/TreatmentOptimization/IntegrandTerms/calcMinimizingMassCenterVelocityXIntegrand.m
+++ b/src/core/parse/parseTreatmentOptimizationParams.m
@@ -1,9 +1,6 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function minimizes the center of mass velocity in the x direction.
 %
-% (struct, struct) -> (Array of number)
-% 
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -13,7 +10,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -27,9 +24,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function cost = calcMinimizingMassCenterVelocityXIntegrand(values, params)
-
-massCenterVelocity = calcMassCenterVelocity(values, params.model, ...
-    params.coordinateNames);
-cost = calcMinimizingCostArrayTerm(massCenterVelocity(:, 1));
-end
\ No newline at end of file
+function params = parseTreatmentOptimizationParams(tree)
+params.experimentalBSplineCutoffFrequency = ...
+    parseDoubleOrAlternate(tree, "experimental_bspline_cutoff_frequency", 6);
+end
diff --git a/src/GroundContactPersonalization/Modeling/prepareModel.m b/src/core/parse/parseTrialData.m
similarity index 59%
rename from src/GroundContactPersonalization/Modeling/prepareModel.m
rename to src/core/parse/parseTrialData.m
index d145d254a..66485b30d 100644
--- a/src/GroundContactPersonalization/Modeling/prepareModel.m
+++ b/src/core/parse/parseTrialData.m
@@ -1,12 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function returns an isolated foot model with spring markers and its 
-% associated kinematics expressed in its seven coordinates (toe angle, 
-% three hindfoot rotations, three hindfoot translations).
+% This function looks in the given directory for all files that match the
+% trialName, if there is only one, parse the file into data and data labels
 %
-% (string, string, string, string, string, string, struct, double, double, 
-% logical) -> (Model, Array of double, Array of double)
-% Create foot model and kinematics in seven coordinates.
+% (string, string, Model) -> (2D matrix of number, 1D array of string)
+% returns a 3D matrix of the loaded muscle tendon length data
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -30,23 +28,29 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function [footModel, footPosition, footVelocity] = prepareModel( ...
-    modelName, motionFileName, hindfootBodyName, toesBodyName, ...
-    toesJointName, toesCoordinateName, markerNames, gridWidth, ...
-    gridHeight, isLeftFoot)
-
-import org.opensim.modeling.Storage
-
-model = Model(modelName);
-time = findTimeColumn(Storage(motionFileName));
-coordinatesOfInterest = findGCPFreeCoordinates(model, toesBodyName);
-
-footPosition = makeFootKinematics(model, motionFileName, ...
-    coordinatesOfInterest, hindfootBodyName, toesCoordinateName);
-footVelocity = calcDerivative(time, footPosition);
-
-footModel = makeFootModel(model, toesJointName);
-footModel = addSpringsToModel(footModel, markerNames, gridWidth, ...
-    gridHeight, hindfootBodyName, toesBodyName, isLeftFoot);
+function [data, dataLabels, time] = parseTrialData(directory, ...
+    trialName, model)
+files = findDirectoryFileNames(directory);
+matchedFiles = [];
+for i = 1:length(files)
+    [~, name, ~] = fileparts(files(i));
+    if contains(name, trialName)
+        matchedFiles(end + 1) = i;
+    end
+end
+if isempty(matchedFiles)
+    throw(MException("ParseError:TrialNameFile", ...
+        strcat("Cannot find file: ", trialName, " in directory ", ...
+        strrep(directory, '\', '\\'))))
+end
+if length(matchedFiles) ~= 1
+    throw(MException("ParseError:TrialNameFile", ...
+        strcat("Multiple files contain: ", trialName, " in directory ", ...
+        strrep(directory, '\', '\\'))))
+end
+[dataLabels, time, data] = parseMotToComponents(model, ...
+     org.opensim.modeling.Storage(files(matchedFiles(1))));
+data = data';
+time = time';
 end
 
diff --git a/src/TrackingOptimization/calcTrackingOptimizationObjective.m b/src/core/parse/parseTrialName.m
similarity index 80%
rename from src/TrackingOptimization/calcTrackingOptimizationObjective.m
rename to src/core/parse/parseTrialName.m
index 6b8eef71d..485baa353 100644
--- a/src/TrackingOptimization/calcTrackingOptimizationObjective.m
+++ b/src/core/parse/parseTrialName.m
@@ -1,10 +1,10 @@
 % This function is part of the NMSM Pipeline, see file for full license.
 %
-% This function calculates the cost function objective for tracking 
-% optimization.
+% trialName indicates which trial is used for Treatment Optimization and
+% this indicates which file should be parsed from the various data sources.
 %
-% (Number, Array of number, Number, struct) -> (Number)
-% Returns objective
+% (struct) -> (string)
+% parses the <trial_name> element
 
 % ----------------------------------------------------------------------- %
 % The NMSM Pipeline is a toolkit for model personalization and treatment  %
@@ -14,7 +14,7 @@
 % National Institutes of Health (R01 EB030520).                           %
 %                                                                         %
 % Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
+% Author(s): Claire V. Hammond                                            %
 %                                                                         %
 % Licensed under the Apache License, Version 2.0 (the "License");         %
 % you may not use this file except in compliance with the License.        %
@@ -28,7 +28,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function objective = calcTrackingOptimizationObjective(integral)
-continuousObjective = sum(integral) / length(integral);
-objective = continuousObjective;
-end
\ No newline at end of file
+function trialName = parseTrialName(tree)
+trialName = getFieldByNameOrError(tree, "trial_name").Text;
+end
+
diff --git a/src/core/parse/reorderPreprocessedDataByMuscleNames.m b/src/core/parse/reorderPreprocessedDataByMuscleNames.m
index 9a75d8b0d..12e41b93a 100644
--- a/src/core/parse/reorderPreprocessedDataByMuscleNames.m
+++ b/src/core/parse/reorderPreprocessedDataByMuscleNames.m
@@ -1,7 +1,7 @@
 function inputs = reorderPreprocessedDataByMuscleNames(inputs, muscleNames)
 
-indexesInParsedMuscleData = ...
-    ismember(inputs.muscleTendonColumnNames, muscleNames);
+[~, ~, indexesInParsedMuscleData] = intersect( ...
+    muscleNames, inputs.muscleTendonColumnNames, 'stable');
 
 inputs.muscleTendonColumnNames = ...
     inputs.muscleTendonColumnNames(indexesInParsedMuscleData);
@@ -10,16 +10,10 @@
 inputs.muscleTendonVelocity = inputs.muscleTendonVelocity(:, ...
     indexesInParsedMuscleData, :);
 
-indexesInParsedCoordinateData = ...
-    ismember( ...
-        inputs.inverseDynamicsMomentsColumnNames, ...
-        inputs.coordinateNames ...
-    );
-indexesInParsedMuscleAnalysisData = ...
-    ismember( ...
-        inputs.momentArmsCoordinateNames, ...
-        inputs.coordinateNames ...
-    );
+[~, ~, indexesInParsedCoordinateData] = intersect( ...
+    inputs.coordinateNames, inputs.inverseDynamicsMomentsColumnNames, 'stable');
+[~, ~, indexesInParsedMuscleAnalysisData] = intersect( ...
+    inputs.coordinateNames, inputs.momentArmsCoordinateNames, 'stable');
 
 inputs.inverseDynamicsMoments = ...
     inputs.inverseDynamicsMoments(:, indexesInParsedCoordinateData, :);
@@ -27,13 +21,13 @@
     indexesInParsedMuscleData, :);
 
 if (isfield(inputs, "mtpActivationsColumnNames"))
-indexesInParsedActivationData = ...
-    ismember(inputs.mtpActivationsColumnNames, muscleNames);
+    [~, ~, indexesInParsedActivationData] = ...
+        intersect(muscleNames, inputs.mtpActivationsColumnNames, 'stable');
 
-inputs.mtpActivationsColumnNames = ...
-    inputs.mtpActivationsColumnNames(indexesInParsedActivationData);
-inputs.mtpActivations = ...
-    inputs.mtpActivations(:, indexesInParsedActivationData, :);
+    inputs.mtpActivationsColumnNames = ...
+        inputs.mtpActivationsColumnNames(indexesInParsedActivationData);
+    inputs.mtpActivations = ...
+        inputs.mtpActivations(:, indexesInParsedActivationData, :);
 end
 
 end
diff --git a/src/core/synergies/getNumSynergyWeights.m b/src/core/synergies/getNumSynergyWeights.m
deleted file mode 100644
index 66ef3d04f..000000000
--- a/src/core/synergies/getNumSynergyWeights.m
+++ /dev/null
@@ -1,34 +0,0 @@
-% This function is part of the NMSM Pipeline, see file for full license.
-%
-% () -> ()
-% 
-
-% ----------------------------------------------------------------------- %
-% The NMSM Pipeline is a toolkit for model personalization and treatment  %
-% optimization of neuromusculoskeletal models through OpenSim. See        %
-% nmsm.rice.edu and the NOTICE file for more information. The             %
-% NMSM Pipeline is developed at Rice University and supported by the US   %
-% National Institutes of Health (R01 EB030520).                           %
-%                                                                         %
-% Copyright (c) 2021 Rice University and the Authors                      %
-% Author(s): Marleny Vega                                                 %
-%                                                                         %
-% Licensed under the Apache License, Version 2.0 (the "License");         %
-% you may not use this file except in compliance with the License.        %
-% You may obtain a copy of the License at                                 %
-% http://www.apache.org/licenses/LICENSE2.0.                             %
-%                                                                         %
-% Unless required by applicable law or agreed to in writing, software     %
-% distributed under the License is distributed on an "AS IS" BASIS,       %
-% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %
-% implied. See the License for the specific language governing            %
-% permissions and limitations under the License.                          %
-% ----------------------------------------------------------------------- %
-
-function numSynergyWeights = getNumSynergyWeights(synergyGroups)
-numSynergyWeights = 0;
-for i = 1 : length(synergyGroups)
-    numSynergyWeights = numSynergyWeights + ...
-        length(synergyGroups{i}.muscleNames) * synergyGroups{i}.numSynergies;
-end
-end
\ No newline at end of file
diff --git a/src/core/synergies/getSynergyWeightsFromGroups.m b/src/core/synergies/getSynergyWeightsFromGroups.m
index 6c670c457..3aa39f9dc 100644
--- a/src/core/synergies/getSynergyWeightsFromGroups.m
+++ b/src/core/synergies/getSynergyWeightsFromGroups.m
@@ -29,20 +29,20 @@
 % ----------------------------------------------------------------------- %
 
 function synergyWeightsReformatted = getSynergyWeightsFromGroups(...
-    synergyWeights, params)
-synergyWeightsReformatted = zeros(params.numSynergies, params.numMuscles);
+    synergyWeights, inputs)
+synergyWeightsReformatted = zeros(inputs.numSynergies, inputs.numMuscles);
 valuesIndex = 1;
 row = 1;
 column = 1; % the sum of the muscles in the previous synergy groups
-for i = 1:length(params.synergyGroups)
-    for j = 1: params.synergyGroups{i}.numSynergies
+for i = 1:length(inputs.synergyGroups)
+    for j = 1: inputs.synergyGroups{i}.numSynergies
         synergyWeightsReformatted(row, column : ...
-            column + length(params.synergyGroups{i}.muscleNames) - 1) = ...
+            column + length(inputs.synergyGroups{i}.muscleNames) - 1) = ...
             synergyWeights(valuesIndex : ...
-            valuesIndex + length(params.synergyGroups{i}.muscleNames) - 1);
-        valuesIndex = valuesIndex + length(params.synergyGroups{i}.muscleNames);
+            valuesIndex + length(inputs.synergyGroups{i}.muscleNames) - 1);
+        valuesIndex = valuesIndex + length(inputs.synergyGroups{i}.muscleNames);
         row = row + 1;
     end
-    column = column + length(params.synergyGroups{i}.muscleNames);
+    column = column + length(inputs.synergyGroups{i}.muscleNames);
 end
 end
\ No newline at end of file
diff --git a/src/core/synergies/getSynergyGroups.m b/src/core/synergies/parseSynergyGroups.m
similarity index 98%
rename from src/core/synergies/getSynergyGroups.m
rename to src/core/synergies/parseSynergyGroups.m
index c48917c9d..ac8abdc00 100644
--- a/src/core/synergies/getSynergyGroups.m
+++ b/src/core/synergies/parseSynergyGroups.m
@@ -27,7 +27,7 @@
 % permissions and limitations under the License.                          %
 % ----------------------------------------------------------------------- %
 
-function groups = getSynergyGroups(tree, model)
+function groups = parseSynergyGroups(tree, model)
 synergySetTree = getFieldByNameOrError(tree, "RCNLSynergySet");
 groupsTree = getFieldByNameOrError(synergySetTree, "RCNLSynergy");
 groups = {};
diff --git a/src/core/verify/getPipelineVersion.m b/src/core/verify/getPipelineVersion.m
index 678e184cd..6c4b59065 100644
--- a/src/core/verify/getPipelineVersion.m
+++ b/src/core/verify/getPipelineVersion.m
@@ -38,5 +38,5 @@
 % ----------------------------------------------------------------------- %
 
 function version = getPipelineVersion()
-version = "1.0.1";
+version = "1.1.0";
 end