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hMRI-group · Mar 26, 2024 · ca895d2 · ca895d2
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commit ca895d2
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Showing 5 changed files with 11 additions and 16 deletions.
diff --git a/hmri_make_dMT.m → hmri_calc_dMT.m b/hmri_make_dMT.m → hmri_calc_dMT.m
@@ -1,4 +1,4 @@
-function dMT = hmri_make_dMT(SPD,ST1,SMT,dSPD,dST1,dSMT,alpha_PD,alpha_T1,alpha_MT,TRPD,TRT1,TRMT,small_angle_approximation)
+function dMT = hmri_calc_dMT(SPD,ST1,SMT,dSPD,dST1,dSMT,alpha_PD,alpha_T1,alpha_MT,TRPD,TRT1,TRMT,small_angle_approximation)
 % Calculate propagation of uncertainty for MT map
 % (https://en.wikipedia.org/wiki/Propagation_of_uncertainty).
 % Taking the total differential from Eq. A9 in Tabelow et al., NI, 2019

diff --git a/hmri_make_dPD.m → hmri_calc_dPD.m b/hmri_make_dPD.m → hmri_calc_dPD.m
@@ -1,4 +1,4 @@
-function dPD = hmri_make_dPD(SPD,ST1,dSPD,dST1,alpha_PD,alpha_T1,TRPD,TRT1,f_T,small_angle_approximation)
+function dPD = hmri_calc_dPD(SPD,ST1,dSPD,dST1,alpha_PD,alpha_T1,TRPD,TRT1,f_T,small_angle_approximation)
 % Calculate propagation of uncertainty for PD map
 % (https://en.wikipedia.org/wiki/Propagation_of_uncertainty).
 % % S.Mohammadi 06.09.2019

diff --git a/hmri_make_dR1.m → hmri_calc_dR1.m b/hmri_make_dR1.m → hmri_calc_dR1.m
@@ -1,4 +1,4 @@
-function dR1 = hmri_make_dR1(SPD,ST1,dSPD,dST1,alpha_PD,alpha_T1,TRPD,TRT1,f_T,small_angle_approximation)
+function dR1 = hmri_calc_dR1(SPD,ST1,dSPD,dST1,alpha_PD,alpha_T1,TRPD,TRT1,f_T,small_angle_approximation)
 % Calculate propagation of uncertainty for R1 map
 % (https://en.wikipedia.org/wiki/Propagation_of_uncertainty).
 % S.Mohammadi 06.09.2019

diff --git a/hmri_code_tests/hmri_make_errormaps_test.m → hmri_code_tests/hmri_calc_errormaps_test.m b/hmri_code_tests/hmri_make_errormaps_test.m → hmri_code_tests/hmri_calc_errormaps_test.m
@@ -1,9 +1,9 @@
 %% Main function to generate tests
-function tests = hmri_make_errormaps_test
+function tests = hmri_calc_errormaps_test
 tests = functiontests(localfunctions);
 end
 
-function hmri_make_dR1_test(testCase)
+function hmri_calc_dR1_test(testCase)
 htu = hmri_test_utils;
 
 % Define reasonable parameter set
@@ -51,7 +51,7 @@ function hmri_make_dR1_test(testCase)
 
 R1est=hmri_calc_R1(PDwErr,T1wErr,B1map);
 
-errorinR1=hmri_make_dR1(PDwErr.data,T1wErr.data,errorinPD,errorinT1,PDwErr.fa,T1wErr.fa,PDwErr.TR,T1wErr.TR,B1map,R1est);
+errorinR1=hmri_calc_dR1(PDwErr.data,T1wErr.data,errorinPD,errorinT1,PDwErr.fa,T1wErr.fa,PDwErr.TR,T1wErr.TR,B1map,R1est);
 
 merrorinR1 = mean(errorinR1,4);
 
@@ -67,7 +67,7 @@ function hmri_make_dR1_test(testCase)
 end
 
 
-function hmri_make_dPD_test(testCase)
+function hmri_calc_dPD_test(testCase)
 htu = hmri_test_utils;
 
 % Define reasonable parameter set
@@ -115,7 +115,7 @@ function hmri_make_dPD_test(testCase)
 
 Aest=hmri_calc_A(PDwErr,T1wErr,B1map);
 
-modelerrorinPD=hmri_make_dPD(PDwErr.data,T1wErr.data,errorinPD,errorinT1,PDwErr.fa,T1wErr.fa,PDwErr.TR,T1wErr.TR,B1map,Aest);
+modelerrorinPD=hmri_calc_dPD(PDwErr.data,T1wErr.data,errorinPD,errorinT1,PDwErr.fa,T1wErr.fa,PDwErr.TR,T1wErr.TR,B1map,Aest);
 
 mmodelerrorinPD = mean(modelerrorinPD,4);
 

diff --git a/hmri_create_MTProt.m b/hmri_create_MTProt.m
@@ -444,11 +444,6 @@
             PR2s_OLS_error{ccon}    = fullfile(calcpath,[outbasename '_' 'R2s_errorESTATICS' '.nii']);
             Ni = hmri_create_nifti(PR2s_OLS_error{ccon},V_pdw(1),dt,'Error map for R2s contrast');
             NEmap(ccon) = Ni;
-
-            % this is unused
-            PR2s_OLS_mSNR    = fullfile(calcpath,[outbasename '_' 'R2s_mSNR' '.nii']);
-            Ni      = hmri_create_nifti(PR2s_OLS_mSNR,V_pdw(1),dt,'Standarized map for R2s contrast');
-            NSMmap = Ni;
         end
     end % init nifti objects for fullOLS case
 
@@ -678,7 +673,7 @@
             Edata.PDw = hmri_read_vols(Verror(PDwidx),V_ref,p,mpm_params.interp);
             Edata.T1w = hmri_read_vols(Verror(T1widx),V_ref,p,mpm_params.interp);
 
-            dR1 = hmri_make_dR1(PDw,T1w,Edata.PDw,Edata.T1w,fa_pdw_rad,fa_t1w_rad,TR_pdw,TR_t1w,f_T,mpm_params.small_angle_approx);
+            dR1 = hmri_calc_dR1(PDw,T1w,Edata.PDw,Edata.T1w,fa_pdw_rad,fa_t1w_rad,TR_pdw,TR_t1w,f_T,mpm_params.small_angle_approx);
 
             if ISC.enabled&&~isempty(f_T)
                 % Use chain rule to include the imperfect spoiling 
@@ -783,7 +778,7 @@
             Edata.PDw = hmri_read_vols(Verror(PDwidx),V_ref,p,mpm_params.interp);
             Edata.T1w = hmri_read_vols(Verror(T1widx),V_ref,p,mpm_params.interp);
 
-            dPD = hmri_make_dPD(PDw,T1w,Edata.PDw,Edata.T1w,fa_pdw_rad,fa_t1w_rad,TR_pdw,TR_t1w,f_T,mpm_params.small_angle_approx);
+            dPD = hmri_calc_dPD(PDw,T1w,Edata.PDw,Edata.T1w,fa_pdw_rad,fa_t1w_rad,TR_pdw,TR_t1w,f_T,mpm_params.small_angle_approx);
 
             % truncate PD error maps
             dPD(isinf(dPD)) = 0;
@@ -843,7 +838,7 @@
             if mpm_params.errormaps
                 Edata.MTw = hmri_read_vols(Verror(MTwidx),V_ref,p,mpm_params.interp);
 
-                dMT = hmri_make_dMT(PDw,T1w,MTw,Edata.PDw,Edata.T1w,Edata.MTw,fa_pdw_rad,fa_t1w_rad,fa_mtw_rad,TR_pdw,TR_t1w,TR_mtw,mpm_params.small_angle_approx) * 100;
+                dMT = hmri_calc_dMT(PDw,T1w,MTw,Edata.PDw,Edata.T1w,Edata.MTw,fa_pdw_rad,fa_t1w_rad,fa_mtw_rad,TR_pdw,TR_t1w,TR_mtw,mpm_params.small_angle_approx) * 100;
 
                 if (~isempty(f_T))&&(~mpm_params.UNICORT.R1 || mpm_params.UNICORT.MT)
                     % use chain rule to include MTsat B1 correction in error maps