[REF] rename variables and using bids.File instead on bids.matlab internals

demos/MoAE/moae_03_create_roi_extract_data.m

@@ -22,8 +22,8 @@
 % from the mask created by the contrast estimation in the previous step
 ffxDir = getFFXdir(subLabel, opt);
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
-p = bids.internal.parse_filename(spm_file(maskImage, 'filename'));
-conImage = spm_select('FPList', ffxDir, ['^con_' p.entities.label '.nii$']);
+bf = bids.File(spm_file(maskImage, 'filename'));
+conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
 
 %% Create ROI right auditory cortex
 saveROI = true;

demos/MoAE/moae_04_slice_display.m

@@ -27,8 +27,8 @@
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
-p = bids.internal.parse_filename(spm_file(maskImage, 'filename'));
-conImage = spm_select('FPList', ffxDir, ['^con_' p.entities.label '.nii$']);
+bf = bids.File(spm_file(maskImage, 'filename'));
+conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
 
 %% Layers to put on the figure
 layers = sd_config_layers('init', {'truecolor', 'dual', 'contour', 'contour'});
@@ -57,7 +57,7 @@
 %
 %   - t-statistics opacity-coded
 
-spmTImage = spm_select('FPList', ffxDir, ['^spmT_' p.entities.label '.nii$']);
+spmTImage = spm_select('FPList', ffxDir, ['^spmT_' bf.entities.label '.nii$']);
 layers(2).opacity.file = spmTImage;
 
 layers(2).opacity.range = [2 3];

demos/MoAE/moae_bids_app.m

@@ -12,14 +12,22 @@
 
 output_dir = fullfile(bids_dir, '..', '..', 'outputs', 'derivatives');
 
-cpp_spm(bids_dir, output_dir, 'participant', ...
+cpp_spm(bids_dir, output_dir, 'subject', ...
         'action', 'preprocess', ...
-        'task', {'auditory'});
+        'task', {'auditory'}, ...
+        'ignore', {'unwarp'}, ...
+        'space', {'IXI549Space'});
 
 %% STATS
+addpath(fullfile(pwd, '..', '..'));
+
+bids_dir = fullfile(fileparts(mfilename('fullpath')), 'inputs', 'raw');
+
+output_dir = fullfile(bids_dir, '..', '..', 'outputs', 'derivatives');
+
 preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
 
-model_file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
+model_file = fullfile(pwd, 'models', 'model-MoAE_smdl.json');
 
 opt.result.Nodes(1).Level = 'subject';
 opt.result.Nodes(1).Contrasts(1).Name = 'listening_1';
@@ -28,7 +36,7 @@
 opt.result.Nodes(1).Output.montage.slices = -4:2:16;
 opt.result.Nodes(1).Output.NIDM_results = true();
 
-cpp_spm(bids_dir, output_dir, 'participant', ...
+cpp_spm(bids_dir, output_dir, 'subject', ...
         'action', 'stats', ...
         'preproc_dir', preproc_dir, ...
         'model_file', model_file, ...

demos/face_repetition/face_rep_resolution.m

@@ -53,9 +53,9 @@
   content = spm_jsonread(opt.model.file);
   content.Name = [content.Name, ' resolution - ', num2str(iResolution)];
 
-  p = bids.internal.parse_filename(modelFile);
-  p.entities.model = [p.entities.model, ' resolution', num2str(iResolution)];
-  bf = bids.File(p);
+  bf = bids.File(modelFile);
+  bf.entities.model = [bf.entities.model, ' resolution', num2str(iResolution)];
+
   newModel = spm_file(opt.model.file, 'filename', bf.filename);
   opt.model.file = newModel;
 

src/IO/getData.m

@@ -18,15 +18,15 @@
   %
   % (C) Copyright 2020 CPP_SPM developers
 
-  p = inputParser;
+  args = inputParser;
 
-  addRequired(p, 'opt', @isstruct);
-  addRequired(p, 'bidsDir', @isdir);
+  addRequired(args, 'opt', @isstruct);
+  addRequired(args, 'bidsDir', @isdir);
 
-  parse(p, varargin{:});
+  parse(args, varargin{:});
 
-  opt = p.Results.opt;
-  bidsDir = p.Results.bidsDir;
+  opt = args.Results.opt;
+  bidsDir = args.Results.bidsDir;
 
   if isfield(opt, 'taskName')
     msg = sprintf('\nFOR TASK(s): %s\n', strjoin(opt.taskName, ' '));

src/IO/onsetsMatToTsv.m

@@ -16,12 +16,12 @@
   %
   % (C) Copyright 2022 CPP_SPM developers
 
-  p = inputParser;
+  args = inputParser;
   isFile = @(x) exist(x, 'file') == 2;
-  addRequired(p, 'onsetsMatFile', isFile);
-  parse(p, varargin{:});
+  addRequired(args, 'onsetsMatFile', isFile);
+  parse(args, varargin{:});
 
-  load(p.Results.onsetsMatFile, 'names', 'onsets', 'durations');
+  load(args.Results.onsetsMatFile, 'names', 'onsets', 'durations');
 
   tsvContent = struct('onset', [], 'duration', [], 'trial_type', {{}});
 
@@ -42,7 +42,7 @@
   tsvContent.trial_type = tsvContent.trial_type(idx);
   tsvContent.duration = tsvContent.duration(idx);
 
-  onsetsTsvFile = spm_file(p.Results.onsetsMatFile, 'ext', '.tsv');
+  onsetsTsvFile = spm_file(args.Results.onsetsMatFile, 'ext', '.tsv');
 
   bids.util.tsvwrite(onsetsTsvFile, tsvContent);
 

src/IO/regressorsMatToTsv.m

@@ -15,20 +15,20 @@
   %
   % (C) Copyright 2022 CPP_SPM developers
 
-  p = inputParser;
+  args = inputParser;
   isFile = @(x) exist(x, 'file') == 2;
-  addRequired(p, 'regressorsMatFile', isFile);
-  parse(p, varargin{:});
+  addRequired(args, 'regressorsMatFile', isFile);
+  parse(args, varargin{:});
 
-  load(p.Results.regressorsMatFile, 'names', 'R');
+  load(args.Results.regressorsMatFile, 'names', 'R');
 
   tsvContent = struct();
 
   for iReg = 1:numel(names) %#ok<*USENS>
     tsvContent.(names{iReg}) = R(:, iReg); %#ok<*NODEF>
   end
 
-  regressorsTsvFile = spm_file(p.Results.regressorsMatFile, 'ext', '.tsv');
+  regressorsTsvFile = spm_file(args.Results.regressorsMatFile, 'ext', '.tsv');
 
   bids.util.tsvwrite(regressorsTsvFile, tsvContent);
 

src/IO/renameSegmentParameter.m

@@ -14,15 +14,13 @@ function renameSegmentParameter(BIDS, subLabel, opt)
                                                     spm_file(anatImage, 'basename'), ...
                                                     '_seg8.mat$']);
 
-  p = bids.internal.parse_filename(anatImage);
-  p.entities.label = p.suffix;
+  bf = bids.File(anatImage);
+  bf.entities.label = bf.suffix;
 
-  p.suffix = 'segparam';
-  p.ext = '.mat';
+  bf.suffix = 'segparam';
+  bf.extension = '.mat';
 
-  bidsFile = bids.File(p);
-
-  newName = spm_file(segmentParam, 'filename',  bidsFile.filename);
+  newName = spm_file(segmentParam, 'filename',  bf.filename);
 
   if ~isempty(segmentParam)
     movefile(segmentParam, newName);

src/IO/renameUnwarpParameter.m

@@ -21,12 +21,12 @@ function renameUnwarpParameter(BIDS, subLabel, opt)
 
       inputFilename = strrep(unwarpParam(iFile, :), '_uw.', '.');
 
-      p = bids.internal.parse_filename(inputFilename);
-      p.entities.label = p.suffix;
-      p.suffix = 'unwarpparam';
-      p.ext = '.mat';
+      bf = bids.File(inputFilename);
+      bf.entities.label = bf.suffix;
+      bf.suffix = 'unwarpparam';
+      bf.extension = '.mat';
 
-      bidsFile = bids.File(p);
+      bidsFile = bids.File(bf);
 
       newName = spm_file(unwarpParam(iFile, :), 'filename',  bidsFile.filename);
 

src/IO/saveSpmScript.m

@@ -17,30 +17,30 @@
 
   % TODO add header to output .m file
 
-  p = inputParser;
+  args = inputParser;
 
   defaultOutputFilename = '';
 
   isCellOrMatFile = @(x) iscell(x) || ...
                          (exist(x, 'file') == 2 && ...
                           strcmp(spm_file(x, 'ext'), 'mat'));
 
-  addRequired(p, 'input', isCellOrMatFile);
-  addOptional(p, 'outputFilename', defaultOutputFilename, @ischar);
+  addRequired(args, 'input', isCellOrMatFile);
+  addOptional(args, 'outputFilename', defaultOutputFilename, @ischar);
 
-  parse(p, varargin{:});
+  parse(args, varargin{:});
 
-  outputFilename = p.Results.outputFilename;
+  outputFilename = args.Results.outputFilename;
 
-  if iscell(p.Results.input)
-    matlabbatch = p.Results.input;
+  if iscell(args.Results.input)
+    matlabbatch = args.Results.input;
 
   else
     % assumes the job was saved in a matlabbatch variable
-    load(p.Results.input, 'matlabbatch');
+    load(args.Results.input, 'matlabbatch');
 
     if strcmp(outputFilename, '')
-      outputFilename = spm_file(p.Results.input, 'ext', '.m');
+      outputFilename = spm_file(args.Results.input, 'ext', '.m');
     end
 
   end

src/QA/anatomicalQA.m

@@ -54,19 +54,19 @@ function anatomicalQA(opt)
     outputDir = fullfile(anatDataDir, '..', 'reports');
     spm_mkdir(outputDir);
 
-    p = bids.internal.parse_filename(anatImage);
-    p.entities.label = p.suffix;
+    bf = bids.File(anatImage);
+    bf.entities.label = bf.suffix;
 
-    p.suffix = 'qametrics';
-    p.ext = '.json';
-    bidsFile = bids.File(p);
-    bids.util.jsonwrite(fullfile(outputDir, bidsFile.filename), anatQA);
+    bf.suffix = 'qametrics';
+    bf.extension = '.json';
+
+    bids.util.jsonwrite(fullfile(outputDir, bf.filename), anatQA);
+
+    bf.suffix = 'qa';
+    bf.extension = '.png';
 
-    p.suffix = 'qa';
-    p.ext = '.png';
-    bidsFile = bids.File(p);
     movefile(fullfile(pwd, 'spmup_QC-Brain Mask_001.png'), ...
-             fullfile(outputDir,  bidsFile.filename));
+             fullfile(outputDir,  bf.filename));
 
     delete(fullfile(anatDataDir, [spm_file(anatImage, 'basename') '_anatQA.txt']));
 

src/QA/functionalQA.m

@@ -167,33 +167,33 @@ function functionalQA(opt)
           outputDir = fullfile(subFuncDataDir, '..', 'reports');
           spm_mkdir(outputDir);
 
-          p = bids.internal.parse_filename(funcImage);
-          p.entities.label = p.suffix;
-          p.prefix = '';
+          bf = bids.File(funcImage);
+          bf.entities.label = bf.suffix;
+          bf.prefix = '';
 
           % TODO find an ouput format that is leaner than a 3 Gb json file!!!
-          p.suffix = 'qametrics';
-          p.ext = '.json';
-          bidsFile = bids.File(p);
-          bids.util.jsonwrite(fullfile(outputDir, bidsFile.filename), jsonContent);
-
-          p.suffix = 'qa';
-          p.ext = '.pdf';
-          bidsFile = bids.File(p);
+          bf.suffix = 'qametrics';
+          bf.extension = '.json';
+
+          bids.util.jsonwrite(fullfile(outputDir, bf.filename), jsonContent);
+
+          bf.suffix = 'qa';
+          bf.extension = '.pdf';
+
           movefile(fullfile(subFuncDataDir, 'spmup_QC.ps'), ...
-                   fullfile(outputDir, bidsFile.filename));
+                   fullfile(outputDir, bf.filename));
 
-          p.entities.desc = 'confounds';
-          p.entities.label = '';
-          p.suffix = 'regressors';
-          p.ext = '.tsv';
-          bidsFile = bids.File(p);
-          bids.util.tsvwrite(spm_file(funcImage, 'filename', bidsFile.filename), tsvContent);
+          bf.entities.desc = 'confounds';
+          bf.entities.label = '';
+          bf.suffix = 'regressors';
+          bf.extension = '.tsv';
+
+          bids.util.tsvwrite(spm_file(funcImage, 'filename', bf.filename), tsvContent);
 
           jsonContent = createDataDictionary(tsvContent);
-          p.ext = '.json';
-          bidsFile = bids.File(p);
-          bids.util.jsonwrite(spm_file(funcImage, 'filename', bidsFile.filename), jsonContent);
+          bf.extension = '.json';
+
+          bids.util.jsonwrite(spm_file(funcImage, 'filename', bf.filename), jsonContent);
 
           delete(outputFiles.design);
           delete(realignParamFile);

src/QA/plotRoiTimeCourse.m

@@ -28,34 +28,34 @@
   %
   % (C) Copyright 2022 CPP_SPM developers
 
-  p = inputParser;
+  args = inputParser;
 
   isFile = @(x) exist(x, 'file') == 2;
 
-  addRequired(p, 'tsvFile', isFile);
-  addOptional(p, 'verbose', true, @islogical);
-  addParameter(p, 'colors', twelveClassesColorMap(), @isnumeric);
-  addParameter(p, 'roiName', '', @ischar);
+  addRequired(args, 'tsvFile', isFile);
+  addOptional(args, 'verbose', true, @islogical);
+  addParameter(args, 'colors', twelveClassesColorMap(), @isnumeric);
+  addParameter(args, 'roiName', '', @ischar);
 
-  parse(p, varargin{:});
+  parse(args, varargin{:});
 
-  tsvFile = p.Results.tsvFile;
+  tsvFile = args.Results.tsvFile;
   timeCourse = bids.util.tsvread(tsvFile);
   conditionNames = fieldnames(timeCourse);
 
   visible = 'off';
-  if p.Results.verbose
+  if args.Results.verbose
     visible = 'on';
   end
 
-  if strcmp(p.Results.roiName, '')
+  if strcmp(args.Results.roiName, '')
     bf = bids.File(tsvFile);
     figName = ['ROI: ' bf.entities.label];
     if isfield(bf.entities, 'hemi')
       figName = [figName ' - ' bf.entities.hemi];
     end
   else
-    figName = ['ROI: ' p.Results.roiName];
+    figName = ['ROI: ' args.Results.roiName];
   end
 
   for i = 1:numel(conditionNames)
@@ -68,7 +68,7 @@
 
   secs = [0:size(timeCourse, 1) - 1] * jsonContent.SamplingFrequency;
 
-  colors = p.Results.colors;
+  colors = args.Results.colors;
   if size(timeCourse, 2) > size(colors, 1)
     colors = repmat(colors, 2, 1);
   end