Bugfix: Running CAT12 for the default anatomy folder

brainstorm-tools · Jan 18, 2022 · bbc699d · bbc699d
1 parent 10bfe72
commit bbc699d
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Showing 4 changed files with 17 additions and 13 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 - SET UP A BACKUP OF YOUR DATABASE</strong></span></h4>
 <HR>
-<!-- LICENCE_START -->Version: 3.220115 (15-Jan-2022)<br>
+<!-- LICENCE_START -->Version: 3.220118 (18-Jan-2022)<br>
 <span style="font-style: italic;">COPYRIGHT &copy; 2000-2022
 USC &amp; McGill University.<br>
 </span>

diff --git a/doc/version.txt b/doc/version.txt
@@ -1,2 +1,2 @@
 % Brainstorm
-% v. 3.220115 (15-Jan-2022)
+% v. 3.220118 (18-Jan-2022)
diff --git a/toolbox/io/import_anatomy_cat_2020.m b/toolbox/io/import_anatomy_cat_2020.m
@@ -593,11 +593,11 @@
 end
 
 %% ===== IMPORT THICKNESS MAPS =====
-if isExtraMaps && ~isempty(CentralHiFile)
+if isExtraMaps && ~isempty(CentralHiFile) && (iSubject > 0)
     % Create a condition "CAT12"
     iStudy = db_add_condition(iSubject, 'CAT12');
     % Import cortical thickness
-    if ~isempty(ThickLhFile) && ~isempty(ThickLhFile)
+    if ~isempty(ThickLhFile) && ~isempty(ThickRhFile)
         import_sources(iStudy, CentralHiFile, ThickLhFile, ThickRhFile, 'FS', 'thickness');
     end
     % Import gyrification

diff --git a/toolbox/process/functions/process_segment_cat12.m b/toolbox/process/functions/process_segment_cat12.m
@@ -352,8 +352,8 @@
     elseif ~isSphReg && isCerebellum
         matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 6;   % 6: lh+rh+cerebellum  (fast, no registration, quick review only)
     end
-    % Extract additional surface parameters: Cortical thickness, Gyrification index, Sulcal depth
-    if isExtraMaps
+    % Extract additional surface parameters: Cortical thickness, Gyrification index, Sulcal depth (can't be imported for default anatomy)
+    if isExtraMaps && (iSubject > 0)
         matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 1;  % Thickness maps
         % Separate SPM process (second element in the batch)
         matlabbatch{2}.spm.tools.cat.stools.surfextract.data_surf(1) = cfg_dep('CAT12: Segmentation (current release): Left Central Surface', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','lhcentral', '()',{':'}));
@@ -427,13 +427,17 @@ function ComputeInteractive(iSubject, iAnatomy) %#ok<DEFNU>
     if isCancel
         return
     end
-    % Ask for cortical maps
-    [isExtraMaps, isCancel] = java_dialog('confirm', ['Compute cortical maps?' 10 10 ...
-        ' - Cortical thickness', 10 ...
-        ' - Gyrification index', 10 ...
-        ' - Sulcal depth', 10 10], 'CAT12 MRI segmentation');
-    if isCancel
-        return
+    % Ask for cortical maps (not for default anatomy)
+    if (iSubject > 0)
+        [isExtraMaps, isCancel] = java_dialog('confirm', ['Compute cortical maps?' 10 10 ...
+            ' - Cortical thickness', 10 ...
+            ' - Gyrification index', 10 ...
+            ' - Sulcal depth', 10 10], 'CAT12 MRI segmentation');
+        if isCancel
+            return
+        end
+    else
+        isExtraMaps = 0;
     end
     % Open progress bar
     bst_progress('start', 'CAT12', 'CAT12 MRI segmentation...');