use bids.File

Author: Remi-Gau

src/atlas/extractRoiByLabel.m

@@ -25,10 +25,10 @@
   p = bids.internal.parse_filename(sourceImage);
   p.entities.label = labelStruct.ROI;
   p.suffix = 'mask';
-  p.use_schema = false;
 
-  newName = bids.create_filename(p);
-  hdr.fname = spm_file(hdr.fname, 'filename', newName);
+  bidsFile = bids.File(p);
+
+  hdr.fname = spm_file(hdr.fname, 'filename', bidsFile.filename);
 
   spm_write_vol(hdr, outputVol);
   outputImage = hdr.fname;

src/atlas/extractRoiFromAtlas.m

@@ -66,13 +66,12 @@
   nameStructure = struct('entities', entities, ...
                          'suffix', 'mask', ...
                          'ext', '.nii');
-  nameStructure.use_schema = false;
-  newName = bids.create_filename(nameStructure);
+  bidsFile = bids.File(nameStructure);
 
-  movefile(roiImage, fullfile(outputDir, newName));
+  movefile(roiImage, fullfile(outputDir, bidsFile.filename));
 
   % create side car json
-  roiImage = fullfile(outputDir, newName);
+  roiImage = fullfile(outputDir, bidsFile.filename);
   json = bids.derivatives_json(roiImage);
   bids.util.jsonencode(json.filename, json.content);
 

src/atlas/labelClusters.m

@@ -19,10 +19,9 @@
   % Write new image with cluster laebelled with their voxel size
   p = bids.internal.parse_filename(sourceImage);
   p.suffix = 'dseg'; % discrete segmentation
-  p.use_schema = false;
 
-  newName = bids.create_filename(p);
-  hdr.fname = spm_file(hdr.fname, 'filename', newName);
+  bidsFile = bids.File(p);
+  hdr.fname = spm_file(hdr.fname, 'filename', bidsFile.filename);
 
   % Cluster labels as their size.
   spm_write_vol(hdr, vol);

src/roi/createRoi.m

@@ -352,8 +352,8 @@
   end
 
   p.entities.label = [label ' ' mask.label];
-  p.use_schema = false;
 
-  roiName = bids.create_filename(p);
+  bidsFile = bids.File(p);
+  roiName = bidsFile.filename;
 
 end

src/roi/keepHemisphere.m

@@ -40,10 +40,9 @@
 
   p = bids.internal.parse_filename(inputImage);
   p.entities.hemi = hemisphere;
-  p.use_schema = false;
-  newName = bids.create_filename(p);
+  bidsFile = bids.File(p);
 
-  hdr.fname = spm_file(inputImage, 'filename', newName);
+  hdr.fname = spm_file(inputImage, 'filename', bidsFile.filename);
 
   spm_write_vol(hdr, vol);
 

src/roi/renameNeuroSynth.m

@@ -31,11 +31,9 @@
   parts = strsplit(basename, '_');
   p.entities.label = ['neurosynth ' parts{1}];
 
-  p.use_schema = false;
+  bidsFile = bids.File(p);
 
-  newName = bids.create_filename(p);
-
-  outputImage = spm_file(inputImage, 'filename', newName);
+  outputImage = spm_file(inputImage, 'filename', bidsFile.filename);
 
   movefile(inputImage, outputImage);
 

src/roi/thresholdToMask.m

@@ -12,10 +12,10 @@
 
   p = bids.internal.parse_filename(inputImage);
   p.suffix = 'mask';
-  p.use_schema = false;
-  newName = bids.create_filename(p);
 
-  hdr.fname = spm_file(hdr.fname, 'filename', newName);
+  bidsFile = bids.File(p);
+
+  hdr.fname = spm_file(hdr.fname, 'filename', bidsFile.filename);
   img = img > threshold;
   spm_write_vol(hdr, img);
 

src/utils/renameFile.m

@@ -16,8 +16,8 @@
   %
   % (C) Copyright 2021 CPP ROI developers
 
-  specification.use_schema = false;
-  newName = bids.create_filename(specification, inputFile);
+  bidsFile = bids.File(inputFile, false, specification);
+  newName = bidsFile.filename;
 
   outputFile = spm_file(inputFile, 'filename', newName);