include MRI suffixes to the bids-validator test

Author: Remi-Gau

manualTests/test_makeRawDataset.m

@@ -7,37 +7,34 @@ function test_makeRawDataset()
     end
 
     %% set up
-
-    %%% set up
-
-    cfg.subject.subjectNb = 1;
-    cfg.subject.runNb = 1;
-
-    cfg.task.name = 'testtask';
-
     cfg.dir.output = outputDir;
 
     cfg.bids.datasetDescription.Name = 'dummy';
     cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
     cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
+    
+    cfg.testingDevice = 'mri';
 
-    cfg.bids.mri.RepetitionTime = 1.56;
+    %% MRI task data
+    cfg.mri.repetitionTime = 1.56;
 
-    cfg.testingDevice = 'mri';
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
 
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
 
-    %%% do stuff
-
     cfg = createFilename(cfg);
 
-    % create the events file and header
-    logFile = saveEventsFile('open', cfg, logFile);
-
     createBoldJson(cfg);
+    
     createDatasetDescription(cfg);
+    
+    % create the events file and header
+    logFile = saveEventsFile('open', cfg, logFile);
 
     % ROW 2: normal events : all info is there
     logFile(1, 1).onset = 2;
@@ -74,11 +71,48 @@ function test_makeRawDataset()
     % add dummy functional data
     funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
+    
     copyfile( ...
         fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
+    
+    %% MRI bold rest data and fancy suffixes
+    clear cfg
+    
+    cfg.dir.output = outputDir;
+    
+    cfg.testingDevice = 'mri';
+
+    cfg.subject.subjectNb = 2;
+    cfg.subject.sessionNb = 3;
+    cfg.subject.runNb = 4;
+    
+    cfg.mri.reconstruction = 'fast recon';
+    cfg.mri.contrastEnhancement = 'test';
+    cfg.mri.phaseEncodingDirection = 'y pos';
+    cfg.mri.echo = '1';
+    cfg.mri.acquisition = ' new tYpe';
+    cfg.mri.repetitionTime = 1.56;
+    
+    cfg.task.name = 'rest';
 
-    %%
+    cfg = createFilename(cfg);
 
+    createBoldJson(cfg);
+
+    % add dummy functional data
+    funcDir = fullfile(cfg.dir.output, 'source', 'sub-002', 'ses-003', 'func');
+    boldFilename = ['sub-002_ses-003_task-rest',  ...
+        '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
+        '_run-004_echo-1_bold.nii.gz'];
+    
+    copyfile( ...
+        fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
+        fullfile(funcDir, boldFilename));
+    
+    %% 
+    clear
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+    cfg.dir.output = outputDir;
     convertSourceToRaw(cfg);
 end

src/convertSourceToRaw.m

@@ -11,7 +11,7 @@ function convertSourceToRaw(cfg)
     sourceDir = fullfile(cfg.dir.output, 'source');
     rawDir = fullfile(cfg.dir.output, 'rawdata');
 
-    % add dummy readme and change file
+    % add dummy README and CHANGE file
     copyfile(fullfile( ...
         fileparts(mfilename('fullpath')), '..', 'dummyData', 'README'), ...
         sourceDir);
@@ -28,6 +28,7 @@ function convertSourceToRaw(cfg)
         error('No subjects found in BIDS directory.');
     end
 
+    % go through the subject files and parses them to remove the date suffix
     for su = 1:numel(subjects)
 
         sess = cellstr(file_utils('List', fullfile(rawDir, subjects{su}), 'dir', '^ses-.*$'));

src/createFilename.m

@@ -1,4 +1,6 @@
 function cfg = createFilename(cfg)
+    % cfg = createFilename(cfg)
+    %
     % create the BIDS compliant directories and fileNames for the behavioral output
     % for this subject / session / run using the information from cfg and expParameters.
     % Will also create the right fileName for the eyetracking data file.