adapt to bids-matlab dev

Author: Remi-Gau

src/atlas/extractRoiByLabel.m

@@ -10,7 +10,7 @@
 
   p = bids.internal.parse_filename(sourceImage);
   p.label = labelStruct.ROI;
-  p.type = 'mask';
+  p.suffix = 'mask';
   newName = createFilename(p);
   hdr.fname = spm_file(hdr.fname, 'filename', newName);
 

src/atlas/extractRoiFromAtlas.m

@@ -22,12 +22,12 @@
 
   roiImage = extractRoiByLabel(sourceImage, labelStruct);
 
-  nameStructure = struct( ...
-                         'space', 'MNI', ...
-                         'hemi', hemisphere, ...
-                         'desc', atlas, ...
-                         'label', roiName, ...
-                         'type', 'mask', ...
+  entities = struct('space', 'MNI', ...
+      'hemi', hemisphere, ...
+      'desc', atlas, ...
+      'label', roiName);
+  nameStructure = struct('entities', entities, ...                         
+                         'suffix', 'mask', ...
                          'ext', '.nii');
   newName = createFilename(nameStructure);
 

src/atlas/labelClusters.m

@@ -18,7 +18,7 @@
 
   % Write new image with cluster laebelled with their voxel size
   p = bids.internal.parse_filename(sourceImage);
-  p.type = 'dseg'; % discrete segmentation
+  p.suffix = 'dseg'; % discrete segmentation
   newName = createFilename(p);
   hdr.fname = spm_file(hdr.fname, 'filename', newName);
 

src/roi/createRoi.m

@@ -327,14 +327,14 @@
 
     p.filename = '';
     p.ext = '.nii';
-    p.type = 'mask';
+    p.suffix = 'mask';
 
     if ~isempty(volumeDefiningImage)
       tmp = bids.internal.parse_filename(volumeDefiningImage);
 
       % if the volume defining image has a space entity we reuse it
       if isfield(p, 'space')
-        p.space = tmp.space;
+        p.entities.space = tmp.space;
       end
 
     end
@@ -347,10 +347,10 @@
 
   label = '';
   if isfield(p, 'label')
-    label = p.label;
+    label = p.entities.label;
   end
 
-  p.label = [label ' ' mask.label];
+  p.entities.label = [label ' ' mask.label];
 
   roiName = createFilename(p);
 

src/roi/keepHemisphere.m

@@ -33,7 +33,7 @@
   vol(discard, :, :) = NaN;
 
   p = bids.internal.parse_filename(inputImage);
-  p.hs = lower(hemisphere);
+  p.entities.hs = lower(hemisphere);
   newName = createFilename(p);
 
   hdr.fname = spm_file(inputImage, 'filename', newName);

src/roi/renameNeuroSynth.m

@@ -7,13 +7,13 @@
   %
 
   p.filename = spm_file(inputImage, 'filename');
-  p.type = 'probseg';
+  p.suffix = 'probseg';
   p.ext = '.nii';
-  p.space = 'MNI';
+  p.entities.space = 'MNI';
 
   basename = spm_file(inputImage, 'basename');
   parts = strsplit(basename, '_');
-  p.label = ['neurosynth ' parts{1}];
+  p.entities.label = ['neurosynth ' parts{1}];
 
   newName = createFilename(p);
 

src/roi/thresholdToMask.m

@@ -9,7 +9,7 @@
   img = spm_read_vols(hdr);
 
   p = bids.internal.parse_filename(inputImage);
-  p.type = 'mask';
+  p.suffix = 'mask';
   newName = createFilename(p);
   hdr.fname = spm_file(hdr.fname, 'filename', newName);
 

src/utils/createFilename.m

@@ -2,16 +2,15 @@
 
 function newName = createFilename(p)
 
-  entities = fieldnames(p);
+  entities = fieldnames(p.entities);
 
   newName = '';
   for iEntity = 1:numel(entities)
 
     thisEntity = entities{iEntity};
 
-    if ~any(strcmp(thisEntity, {'filename', 'type', 'ext'})) && ...
-            ~isempty(p.(thisEntity))
-      thisLabel = convertToValidCamelCase(p.(thisEntity));
+    if ~isempty(p.entities.(thisEntity))
+      thisLabel = convertToValidCamelCase(p.entities.(thisEntity));
       newName = [newName '_' thisEntity '-' thisLabel]; %#ok<AGROW>
     end
 
@@ -21,7 +20,7 @@
   newName(1) = [];
 
   ext = p.ext;
-  suffix = p.type;
+  suffix = p.suffix;
   newName = [newName '_', suffix ext];
 
 end

src/utils/renameFile.m

@@ -8,7 +8,7 @@
   entitiesToChange = fieldnames(specification);
 
   for iEntity = 1:numel(entitiesToChange)
-    p.(entitiesToChange{iEntity}) = specification.(entitiesToChange{iEntity});
+    p.entities.(entitiesToChange{iEntity}) = specification.(entitiesToChange{iEntity});
   end
 
   newName = createFilename(p);