deal with multiple iterations renaming

Author: Remi-Gau

demos/lesion_detection/run_lesion.m

@@ -22,10 +22,10 @@
 
 bidsCopyInputFolder(opt);
 
-% Step 1: segmentation
+%% Step 1: segmentation
 bidsLesionSegmentation(opt);
 
-% % Step 2: lesion abnormalities
+%% Step 2: lesion abnormalities
 bidsLesionAbnormalitiesDetection(opt);
 
 % % Step 3: overlap map

lib/spm_2_bids

@@ -77,21 +77,24 @@
       map = map.add_mapping('prefix', [map.norm 'c4'], ...
                             'name_spec', nameSpec);
 
-      % 4th class prior next iteration
-      nameSpec = map.cfg.segment.gm_norm;
-      nameSpec.entities.label = 'PRIOR';
-      nameSpec.entities.res = 'r1pt5';
-      nameSpec.entities.desc = 'nextIte';
-      map = map.add_mapping('prefix', [map.norm 'c4prior1'], ...
-                            'name_spec', nameSpec);
-
-      % 4th class at previous iteration
-      nameSpec = map.cfg.segment.gm_norm;
-      nameSpec.entities.label = 'PRIOR';
-      nameSpec.entities.res = 'r1pt5';
-      nameSpec.entities.desc = 'prevIte';
-      map = map.add_mapping('prefix', [map.norm 'c4previous1'], ...
-                            'name_spec', nameSpec);
+      nbIteration = opt.toolbox.ALI.unified_segmentation.step1niti;
+      for i = 1:(nbIteration - 1)
+        % 4th class prior next iteration
+        nameSpec = map.cfg.segment.gm_norm;
+        nameSpec.entities.label = 'PRIOR';
+        nameSpec.entities.res = 'r1pt5';
+        nameSpec.entities.desc = sprintf('nextIte%i', i);
+        map = map.add_mapping('prefix', sprintf('%sc4prior%i', map.norm, i), ...
+                              'name_spec', nameSpec);
+
+        % 4th class at previous iteration
+        nameSpec = map.cfg.segment.gm_norm;
+        nameSpec.entities.label = 'PRIOR';
+        nameSpec.entities.res = 'r1pt5';
+        nameSpec.entities.desc = sprintf('prevIte%i', i);
+        map = map.add_mapping('prefix', sprintf('%sc4previous%i', map.norm, i), ...
+                              'name_spec', nameSpec);
+      end
 
       nameSpec = map.cfg.segment.gm_norm;
       nameSpec.entities.res = res;

src/defaults/setRenamingConfig.m

@@ -38,9 +38,7 @@ function bidsLesionSegmentation(opt)
     matlabbatch = {};
     matlabbatch = setBatchLesionSegmentation(matlabbatch, BIDS, opt, subLabel);
 
-    saveAndRunWorkflow(matlabbatch, 'LesionSegmentation', opt, subLabel);
-
-    % copyFigures(BIDS, opt, subLabel);
+    %     saveAndRunWorkflow(matlabbatch, 'LesionSegmentation', opt, subLabel);
 
   end