add basic support and conversion for EEG iEEG MEG BEH

Author: Remi-Gau

manualTests/dummyData/.bidsignore

@@ -0,0 +1,11 @@
+*_beh.*
+*_eeg.*
+*_ieeg.*
+*_meg.*
+
+# *_beh.tsv
+# *_eeg.edf
+# *_ieeg.edf
+# *_meg.fif
+
+# *_bold.nii.gz

manualTests/test_createBoldJson.m renamed to manualTests/test_createJson.m

@@ -1,12 +1,12 @@
-function test_suite = test_createBoldJson %#ok<*STOUT>
+function test_suite = test_createJson %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
     catch % no problem; early Matlab versions can use initTestSuite fine
     end
     initTestSuite;
 end
 
-function test_createBoldJsonExtra()
+function test_createJsonExtra()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
 
@@ -29,7 +29,7 @@ function test_createBoldJsonExtra()
 
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
 
-    createBoldJson(cfg, extraInfo);
+    createJson(cfg, extraInfo);
 
     %% check content
     fileName = strrep(cfg.fileName.events, '_events', '_bold');

manualTests/test_makeRawDataset.m

@@ -1,74 +1,75 @@
 function test_makeRawDataset()
-
+    
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
-
+    
     if isdir(outputDir)
         rmdir(outputDir, 's');
     end
-
+    
     %% set up
     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';
-
+    
     %% MRI task data
     cfg.mri.repetitionTime = 1.56;
-
+    
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-
+    
     cfg.task.name = 'testtask';
-
+    cfg.task.instructions = 'do this';
+    
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
-
+    
     cfg = createFilename(cfg);
-
+    
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
-    createBoldJson(cfg, extraInfo);
-
+    createJson(cfg, extraInfo);
+    
     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;
     logFile(end, 1).trial_type = 'MotionUp';
     logFile(end, 1).duration = 3;
     logFile(end, 1).Speed = 2;
     logFile(end, 1).is_Fixation = true;
     logFile(end, 1).LHL24 = 1:3;
-
+    
     % ROW 3: missing info (speed, LHL24)
     logFile(1, 1).onset = 3;
     logFile(end, 1).trial_type = 'static';
     logFile(end, 1).duration = 4;
     logFile(end, 1).is_Fixation = false;
-
+    
     % ROW 4: missing info (duration is missing and speed is empty)
     logFile(2, 1).onset = 4;
     logFile(end, 1).trial_type = 'BLUES';
     logFile(end, 1).Speed = [];
     logFile(end, 1).is_Fixation = true;
     logFile(end, 1).LHL24 = rand(1, 3);
-
+    
     % ROW 5: missing info (array is not the right size)
     logFile(5, 1).onset = 5;
     logFile(end, 1).trial_type = 'jazz';
     logFile(end, 1).duration = 3;
     logFile(end, 1).LHL24 = rand(1, 2);
-
+    
     saveEventsFile('save', cfg, logFile);
-
+    
     % close the file
     saveEventsFile('close', cfg, logFile);
-
+    
     % add dummy stim data
     stimLogFile = saveEventsFile('open_stim', cfg, logFile);
     for i = 1:100
@@ -82,54 +83,171 @@ function test_makeRawDataset()
     saveEventsFile('save', cfg, stimLogFile);
     saveEventsFile('close', cfg, stimLogFile);
 
-    % 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.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    
     % deal with MRI suffixes
-    cfg.mri.reconstruction = 'fast recon';
-    cfg.mri.contrastEnhancement = 'test';
-    cfg.mri.phaseEncodingDirection = 'y pos';
-    cfg.mri.echo = '1';
-    cfg.mri.acquisition = ' new tYpe';
+    cfg.suffix.reconstruction = 'fast recon';
+    cfg.suffix.contrastEnhancement = 'test';
+    cfg.suffix.phaseEncodingDirection = 'y pos';
+    cfg.suffix.echo = '1';
+    cfg.suffix.acquisition = ' new tYpe';
+    
     cfg.mri.repetitionTime = 1.56;
-
+    
     cfg.task.name = 'rest';
-
+    
     cfg = createFilename(cfg);
+    
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+    
+    
+    %% EEG data and fancy suffixes
+    clear cfg;
+    
+    cfg.dir.output = outputDir;
+    
+    cfg.testingDevice = 'eeg';
+    
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    
+    cfg.task.name = 'target practice';
+    cfg.task.instructions = 'do this';
+    
+    cfg.bids.eeg.EEGReference = 'Cz';
+    cfg.bids.eeg.SamplingFrequency = 2400;
+    cfg.bids.eeg.PowerLineFrequency = 50;
+    cfg.bids.eeg.SoftwareFilters = 'n/a';
 
-    createBoldJson(cfg);
-
-    %% add dummy functional data
-    funcDir = fullfile(cfg.dir.output, 'source', 'sub-002', 'ses-003', 'func');
-    boldFilename = ['sub-002_ses-003_task-rest',  ...
+    cfg = createFilename(cfg);
+    
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+    
+    %% iEEG data and fancy suffixes
+    clear cfg;
+    
+    cfg.dir.output = outputDir;
+    
+    cfg.testingDevice = 'ieeg';
+    
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    
+    cfg.task.name = 'implanted target practice';
+    cfg.task.instructions = 'do this';
+    
+    cfg.bids.ieeg.iEEGReference = 'Cz';
+    cfg.bids.ieeg.SamplingFrequency = 2400;
+    cfg.bids.ieeg.PowerLineFrequency = 50;
+    cfg.bids.ieeg.SoftwareFilters = 'n/a';
+    
+    cfg = createFilename(cfg);
+    
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+    
+    %% MEG data and fancy suffixes
+    clear cfg;
+    
+    cfg.dir.output = outputDir;
+    
+    cfg.testingDevice = 'meg';
+    
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    
+    cfg.task.name = 'magnetic target practice';
+    cfg.task.instructions = 'do this';
+    
+    cfg.bids.meg.SamplingFrequency = 2400;
+    cfg.bids.meg.PowerLineFrequency = 60;
+    cfg.bids.meg.DewarPosition = 'upright';
+    cfg.bids.meg.SoftwareFilters = 'n/a';
+    cfg.bids.meg.DigitizedLandmarks = false;
+    cfg.bids.meg.DigitizedHeadPoints = false;
+    
+    cfg = createFilename(cfg);
+    
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+    
+    %% beh data and fancy suffixes
+    clear cfg;
+    
+    cfg.dir.output = outputDir;
+    
+    cfg.testingDevice = 'pc';
+    
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    
+    cfg.task.name = 'easy target practice';
+    cfg.task.instructions = 'do this';
+    
+    cfg = createFilename(cfg);
+    
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+    
+    %% add dummy data
+    subjectDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001');
+    funcDir = fullfile(subjectDir, 'func');
+    
+    boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
+    
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(funcDir, boldFilename));
+    
+    boldFilename = ['sub-001_ses-001_task-rest',  ...
         '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
-        '_run-004_echo-1_bold.nii.gz'];
-
+        '_run-001_echo-1_bold.nii.gz'];
+    
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
-
+    
+    eegDir = fullfile(subjectDir, 'eeg');
+    megDir = fullfile(subjectDir, 'meg');
+    ieegDir = fullfile(subjectDir, 'ieeg');
+    behDir = fullfile(subjectDir, 'beh');
+    
+    eegFilename = 'sub-001_ses-001_task-targetPractice_run-001_eeg.edf';
+    megFilename = 'sub-001_ses-001_task-magneticTargetPractice_run-001_meg.fif';
+    ieegFilename = 'sub-001_ses-001_task-implantedTargetPractice_run-001_ieeg.edf';
+    behFilename = 'sub-001_ses-001_task-easyTargetPractice_run-001_beh.tsv';
+    
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(eegDir, eegFilename));
+    
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(megDir, megFilename));
+    
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(ieegDir, ieegFilename));
+    
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(behDir, behFilename));
+    
     %% actually do the conversion of the source data thus created
     clear;
-
+    
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
     cfg.dir.output = outputDir;
     convertSourceToRaw(cfg);
-
+    
 end