Fixing eTPM in code and readme

hMRI-group · Apr 7, 2017 · cdc4908 · cdc4908
1 parent 9c98a8d
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Showing 4 changed files with 29 additions and 24 deletions.
diff --git a/etpm/Readme.txt b/etpm/Readme.txt
@@ -6,5 +6,10 @@ The original maps provided at the time were not meeting SPM's requirements:
 	nwTPM_sl2.nii
 
 I fixed the TPM using the script: cp_update_TPM.m
-This lead to the currect TPM: 
-	unwTPM_sl2.nii
+This lead to the currect "extended TPM" : 
+	eTPM.nii
+
+
+Christophe Phillips
+University of Li�ge
+Belgium
diff --git a/etpm/cp_update_TPM.m b/etpm/cp_update_TPM.m
@@ -44,18 +44,18 @@
     fullfile(spm('dir'),'tpm','TPM.nii,4'),...
     fullfile(spm('dir'),'tpm','TPM.nii,5'),...
     fullfile(spm('dir'),'tpm','TPM.nii,6'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,1'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,2'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,3'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,4'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,5'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,6')...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,1'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,2'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,3'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,4'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,5'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,6')...
     );
 % Then display the intensities and click in a 'corner'.
 
 %% Fixing the TPms
 thr = 1e-6;
-Ptpm = fullfile(spm('dir'),'tpm','nwTPM_sl2.nii');
+Ptpm = fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii');
 Vtpm = spm_vol(Ptpm);
 tpm_orig = spm_read_vols(Vtpm);
 tpm_updt = tpm_orig;
@@ -88,7 +88,7 @@
 
 % Save updated TPMs
 Vtpm_u = spm_vol( fullfile(spm('dir'),'tpm','TPM.nii'));
-fn_TPM_upd = fullfile(spm('dir'),'tpm','unwTPM_sl2.nii');
+fn_TPM_upd = fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii');
 for ii=1:6
     Vtpm_u(ii).fname = fn_TPM_upd;
     Vtpm_u(ii) = spm_create_vol(Vtpm_u(ii));
@@ -104,17 +104,17 @@
     fullfile(spm('dir'),'tpm','TPM.nii,4'),...
     fullfile(spm('dir'),'tpm','TPM.nii,5'),...
     fullfile(spm('dir'),'tpm','TPM.nii,6'),...
-    fullfile(spm('dir'),'tpm','unwTPM_sl2.nii,1'),...
-    fullfile(spm('dir'),'tpm','unwTPM_sl2.nii,2'),...
-    fullfile(spm('dir'),'tpm','unwTPM_sl2.nii,3'),...
-    fullfile(spm('dir'),'tpm','unwTPM_sl2.nii,4'),...
-    fullfile(spm('dir'),'tpm','unwTPM_sl2.nii,5'),...
-    fullfile(spm('dir'),'tpm','unwTPM_sl2.nii,6'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,1'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,2'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,3'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,4'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,5'),...
-    fullfile(spm('dir'),'tpm','nwTPM_sl2.nii,6')...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,1'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,2'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,3'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,4'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,5'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,6'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,1'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,2'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,3'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,4'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,5'),...
+    fullfile(spm('dir'),'toolbox','hMRI','etpm','nwTPM_sl2.nii,6')...
     );
 
diff --git a/tbx_scfg_hmri_proc_US.m b/tbx_scfg_hmri_proc_US.m
@@ -127,7 +127,7 @@
 % plus use the hMRI specific TPMs.
 w_native = [[1 1];[1 1];[1 1];[0 0];[0 0];[0 0]];
 w_warped = [[1 1];[1 1];[1 1];[0 0];[0 0];[0 0]];
-fn_tpm = fullfile(spm('dir'),'toolbox','hMRI','tpm','unwTPM_sl2.nii');
+fn_tpm = fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii');
 for ii=1:size(w_native,1)
     proc_us = cfg_set_val(proc_us, 'tissues', ii, 'native', w_native(ii,:));
     proc_us = cfg_set_val(proc_us, 'tissues', ii, 'warped', w_warped(ii,:));

diff --git a/tbx_scfg_hmri_proc_smooth.m b/tbx_scfg_hmri_proc_smooth.m
@@ -74,7 +74,7 @@
 tpm.filter  = 'image';
 tpm.ufilter = '.*';
 tpm.num     = [1 1];
-tpm.val     = {{fullfile(spm('dir'),'toolbox','hMRI','tpm','unwTPM_sl2.nii,1')}};
+tpm.val     = {{fullfile(spm('dir'),'toolbox','hMRI','etpm','eTPM.nii,1')}};
 
 % ---------------------------------------------------------------------
 % Gaussian FWHM