fix issue with ALI toolbox

Author: Remi-Gau

src/batches/lesion/setBatchLesionSegmentation.m

@@ -21,10 +21,16 @@
 
   [anatImage, anatDataDir] = getAnatFilename(BIDS, opt, subLabel);
 
-  hdr = spm_vol(fullfile(anatDataDir, anatImage));
-  voxRes = diag(hdr.mat);
-  voxRes = min(voxRes(1:3));
-  unified_segmentation.step1vox = abs(voxRes);
+  % TODO
+  % this needs to be changed
+  % - to be consistent across subject
+  % - to reslice the size of the mask that is then used for lesion detection
+  %
+  %   hdr = spm_vol(fullfile(anatDataDir, anatImage));
+  %   voxRes = diag(hdr.mat);
+  %   voxRes = min(voxRes(1:3));
+  %   unified_segmentation.step1vox = abs(voxRes);
+
   unified_segmentation.step1data{1} = fullfile(anatDataDir, anatImage);
 
   matlabbatch{end + 1}.spm.tools.ali.unified_segmentation = unified_segmentation;

src/defaults/ALI_my_defaults.m

@@ -52,8 +52,11 @@
   defaults.toolbox.ALI.outliers_detection.step3tissue.step3Lambda = -4;
 
   % specify lesion mask
-  defaults.toolbox.ALI.lesionMask = fullfile(spmDir, 'toolbox', 'ALI', ...
-                                             'Mask_image', 'mask_controls_vox2mm.nii');
+  defaults.toolbox.ALI.outliers_detection.step3mask{1} = fullfile(spmDir, ...
+                                                                  'toolbox', ...
+                                                                  'ALI', ...
+                                                                  'Mask_image', ...
+                                                                  'mask_controls_vox2mm.nii');
 
   % threshold for the mask
   defaults.toolbox.ALI.outliers_detection.step3mask_thr = 0;

src/workflows/lesion/bidsLesionAbnormalitiesDetection.m

@@ -80,6 +80,6 @@ function bidsLesionAbnormalitiesDetection(opt)
   matlabbatch = {};
   matlabbatch = setBatchLesionAbnormalitiesDetection(matlabbatch, opt, images);
 
-  saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt, subLabel);
+  saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt);
 
 end