Bugfix: Prefer TPM.nii from SPM plugin when doing CAT12 segmentation

brainstorm-tools · Oct 2, 2023 · 3a38bdb · 3a38bdb
1 parent d9f049d
commit 3a38bdb
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Showing 4 changed files with 19 additions and 8 deletions.
diff --git a/doc/license.html b/doc/license.html
@@ -5,7 +5,7 @@
 <body alink="#fff000" link="#fff000" vlink="#fff000">
     <h4><span style="font-family: Arial Black; color: #ffffff;"><strong>THERE IS NO UNDO BUTTON!<BR>SET UP A <FONT color=red>BACKUP</FONT> OF YOUR DATABASE</strong></span></h4>
 <HR>
-<!-- LICENCE_START -->Version: 3.230919 (19-Sep-2023)<br>
+<!-- LICENCE_START -->Version: 3.231002 (02-Oct-2023)<br>
 <span style="font-style: italic;">COPYRIGHT &copy; 2000-2023
 USC &amp; McGill University.<br>
 </span>

diff --git a/doc/version.txt b/doc/version.txt
@@ -1,2 +1,2 @@
 % Brainstorm
-% v. 3.230919 (19-Sep-2023)
+% v. 3.231002 (02-Oct-2023)
diff --git a/toolbox/core/bst_get.m b/toolbox/core/bst_get.m
@@ -2804,16 +2804,22 @@
         end
 
     case 'SpmTpmAtlas'
+        preferSpm = 0;
+        % CALL: bst_get('SpmTpmAtlas', 'SPM')
+        if (nargin >= 2) && strcmpi(varargin{2}, 'SPM')
+            preferSpm = 1;
+        end
+
         % Get template file
         tpmUser = bst_fullfile(bst_get('BrainstormUserDir'), 'defaults', 'spm', 'TPM.nii');
-        if file_exist(tpmUser)
+        if file_exist(tpmUser) && ~preferSpm
             argout1 = tpmUser;
             disp(['BST> SPM12 template found: ' tpmUser]);
             return;
         end
         % If it does not exist: check in brainstorm3 folder
         tpmDistrib = bst_fullfile(bst_get('BrainstormHomeDir'), 'defaults', 'spm', 'TPM.nii');
-        if file_exist(tpmDistrib)
+        if file_exist(tpmDistrib) && ~preferSpm
             argout1 = tpmDistrib;
             disp(['BST> SPM12 template found: ' tpmDistrib]);
             return;
@@ -2826,6 +2832,9 @@
                 argout1 = tpmSpm;
                 disp(['BST> SPM12 template found: ' tpmSpm]);
                 return;
+            elseif preferSpm
+               argout1 = bst_get('SpmTpmAtlas');
+               return
             end
         else
             tpmSpm = '';

diff --git a/toolbox/process/functions/process_segment_cat12.m b/toolbox/process/functions/process_segment_cat12.m
@@ -117,11 +117,11 @@
     else
         isCerebellum = 1;
     end
-    % TPM atlas
+    % % TPM atlas, preferably from SPM plugin
     if isfield(sProcess.options, 'tpmnii') && isfield(sProcess.options.tpmnii, 'Value') && ~isempty(sProcess.options.tpmnii.Value) && ~isempty(sProcess.options.tpmnii.Value{1})
         TpmNii = sProcess.options.tpmnii.Value{1};
     else
-        TpmNii = bst_get('SpmTpmAtlas');
+        TpmNii = bst_get('SpmTpmAtlas', 'SPM');
     end
     % Thickness maps
     if isfield(sProcess.options, 'extramaps') && isfield(sProcess.options.extramaps, 'Value') && ~isempty(sProcess.options.extramaps.Value)
@@ -191,7 +191,8 @@
     end
     % Check provided TPM.nii
     if isempty(TpmNii)
-        TpmNii = bst_get('SpmTpmAtlas');
+        % TPM atlas, preferably from SPM plugin
+        TpmNii = bst_get('SpmTpmAtlas', 'SPM');
     end
 
     % ===== GET SUBJECT =====
@@ -430,8 +431,9 @@ function ComputeInteractive(iSubject, iAnatomy) %#ok<DEFNU>
     end
     % Open progress bar
     bst_progress('start', 'CAT12', 'CAT12 MRI segmentation...');
+    % TPM atlas, preferably from SPM plugin
+    TpmNii = bst_get('SpmTpmAtlas', 'SPM');
     % Run CAT12
-    TpmNii = bst_get('SpmTpmAtlas');
     isInteractive = 1;
     isSphReg = 1;
     isCerebellum = 0;