keep track of segmentation batch number

Author: Remi-Gau

demos/MoAE/moae_01_bids_app.m

@@ -50,7 +50,7 @@
 cpp_spm();
 
 %% Dopwnload the dataset
-download_data = true;
+download_data = false;
 clean = true;
 download_moae_ds(download_data, clean);
 

src/batches/preproc/setBatchSegmentation.m

@@ -1,4 +1,4 @@
-function matlabbatch = setBatchSegmentation(matlabbatch, opt, imageToSegment)
+function [matlabbatch, opt] = setBatchSegmentation(matlabbatch, opt, imageToSegment)
   %
   % Creates a batch to segment the anatomical image
   %

src/workflows/preproc/bidsSegmentSkullStrip.m

@@ -57,7 +57,7 @@
       opt.segment.do = true;
     end
 
-    matlabbatch = setBatchSegmentation(matlabbatch, opt);
+    [matlabbatch, opt] = setBatchSegmentation(matlabbatch, opt);
 
     matlabbatch = setBatchSkullStripping(matlabbatch, BIDS, opt, subLabel);
 

src/workflows/preproc/bidsSpatialPrepro.m

@@ -88,6 +88,7 @@
 
     anatFile = matlabbatch{1}.cfg_basicio.cfg_named_file.files{1}{1};
 
+    % TODO refactor with bidsSegmentSkullstrip
     %% Skip segmentation / skullstripping if done previously
     if skullstripDo && ~opt.skullstrip.force && skullstrippingAlreadyDone(anatFile, BIDS)
       opt.skullstrip.do = false;
@@ -100,7 +101,7 @@
       opt.segment.do = true;
     end
 
-    matlabbatch = setBatchSegmentation(matlabbatch, opt);
+    [matlabbatch, opt] = setBatchSegmentation(matlabbatch, opt);
 
     matlabbatch = setBatchSkullStripping(matlabbatch, BIDS, opt, subLabel);
     opt.orderBatches.skullStripping = numel(matlabbatch) - 1;