set default json content for EEG MEG iEEG BEH

Author: Remi-Gau

README.md

@@ -105,12 +105,6 @@ The format used by the MATLAB toolbox EEGLAB (Each recording consisting of a .se
 Biosemi data format (Each recording consisting of a .bdf file) -->
 
 
-EEGReference 	REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the _channels.tsv file.
-SamplingFrequency 	REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400).
-PowerLineFrequency 	REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60).
-SoftwareFilters 	REQUIRED. A JSON object of temporal software filters applied, or "n/a" if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., {"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}.
-
-
 
 -   MEG
 

src/checkCFG.m

@@ -37,9 +37,12 @@
 
     %% BIDS
 
+    fieldsToSet = behJsonDefaults(fieldsToSet);
     fieldsToSet = datasetDescriptionDefaults(fieldsToSet);
-    fieldsToSet = mriJsonDefaults(fieldsToSet);
+    fieldsToSet = eegJsonDefaults(fieldsToSet);
+    fieldsToSet = ieegJsonDefaults(fieldsToSet);
     fieldsToSet = megJsonDefaults(fieldsToSet);
+    fieldsToSet = mriJsonDefaults(fieldsToSet);
 
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
@@ -160,6 +163,8 @@
     % removing all non alphanumeric ([a-zA-Z0-9]) characters.
     fieldsToSet.bids.meg.TaskName = [];
 
+    fieldsToSet.bids.meg.Instructions = [];
+
     % REQUIRED Sampling frequency
     fieldsToSet.bids.meg.SamplingFrequency = [];
 
@@ -190,3 +195,62 @@
     fieldsToSet.bids.meg = orderfields(fieldsToSet.bids.meg);
 
 end
+
+function fieldsToSet = eegJsonDefaults(fieldsToSet)
+    % for json for EEG data
+
+    fieldsToSet.bids.eeg.TaskName = [];
+
+    fieldsToSet.bids.eeg.Instructions = [];
+
+    fieldsToSet.bids.eeg.EEGReference = [];
+
+    fieldsToSet.bids.eeg.SamplingFrequency = [];
+
+    fieldsToSet.bids.eeg.PowerLineFrequency = [];
+
+    fieldsToSet.bids.eeg.DewarPosition = [];
+
+    fieldsToSet.bids.eeg.SoftwareFilters = [];
+
+    fieldsToSet.bids.eeg.DigitizedLandmarks = [];
+
+    fieldsToSet.bids.eeg.DigitizedHeadPoints = [];
+
+    fieldsToSet.bids.eeg = orderfields(fieldsToSet.bids.eeg);
+
+end
+
+function fieldsToSet = ieegJsonDefaults(fieldsToSet)
+    % for json for iEEG data
+
+    fieldsToSet.bids.ieeg.TaskName = [];
+
+    fieldsToSet.bids.ieeg.Instructions = [];
+
+    fieldsToSet.bids.ieeg.SamplingFrequency = [];
+
+    fieldsToSet.bids.ieeg.PowerLineFrequency = [];
+
+    fieldsToSet.bids.ieeg.DewarPosition = [];
+
+    fieldsToSet.bids.ieeg.SoftwareFilters = [];
+
+    fieldsToSet.bids.ieeg.DigitizedLandmarks = [];
+
+    fieldsToSet.bids.ieeg.DigitizedHeadPoints = [];
+
+    fieldsToSet.bids.ieeg = orderfields(fieldsToSet.bids.ieeg);
+
+end
+
+function fieldsToSet = behJsonDefaults(fieldsToSet)
+    % for json for BEH data
+
+    fieldsToSet.bids.beh.TaskName = [];
+
+    fieldsToSet.bids.beh.Instructions = [];
+
+    fieldsToSet.bids.ieeg = orderfields(fieldsToSet.bids.beh);
+
+end

src/subfun/transferInfoToBids.m

@@ -8,9 +8,20 @@
         [taskName, taskNameValid] = createValidName(cfg.task.name);
         fieldsToSet.fileName.task = taskNameValid;
         fieldsToSet.bids.meg.TaskName = taskName;
+        fieldsToSet.bids.eeg.TaskName = taskName;
+        fieldsToSet.bids.ieeg.TaskName = taskName;
+        fieldsToSet.bids.beh.TaskName = taskName;
         fieldsToSet.bids.mri.TaskName = taskName;
     end
 
+    if isfield(cfg, 'task') && isfield(cfg.task, 'instructions')
+        fieldsToSet.bids.meg.Instructions = cfg.task.instructions;
+        fieldsToSet.bids.eeg.Instructions = cfg.task.instructions;
+        fieldsToSet.bids.ieeg.Instructions = cfg.task.instructions;
+        fieldsToSet.bids.beh.Instructions = cfg.task.instructions;
+        fieldsToSet.bids.mri.Instructions = cfg.task.instructions;
+    end
+
     if isfield(cfg, 'mri') && isfield(cfg.mri, 'repetitionTime')
         fieldsToSet.bids.mri.RepetitionTime = cfg.mri.repetitionTime;
     end

tests/test_checkCFG.m

@@ -17,7 +17,10 @@ function test_checkCfgDefault()
     expectedStructure.dir.output = cfg.dir.output;
     expectedStructure.testingDevice = 'pc';
 
+    expectedStructure = orderfields(expectedStructure);
+
     %% test
+    assertEqual(expectedStructure.bids.ieeg, cfg.bids.ieeg);
     assertEqual(expectedStructure, cfg);
 
 end
@@ -62,8 +65,11 @@ function test_checkCfgBasic()
     expectedStructure.fileName.task = 'testTask';
 
     expectedStructure.bids.mri.RepetitionTime = 1.56;
-    expectedStructure.bids.mri.TaskName = 'test Task';
 
+    expectedStructure.bids.mri.TaskName = 'test Task';
+    expectedStructure.bids.beh.TaskName = 'test Task';
+    expectedStructure.bids.ieeg.TaskName = 'test Task';
+    expectedStructure.bids.eeg.TaskName = 'test Task';
     expectedStructure.bids.meg.TaskName = 'test Task';
 
     expectedStructure.bids.datasetDescription.Name = 'dummy';
@@ -99,13 +105,36 @@ function test_checkCfgBasic()
     expectedCfgStructure.suffix.repetitionTime = [];
     expectedCfgStructure.suffix.recording = [];
 
+    expectedCfgStructure.bids.beh.TaskName = '';
+    expectedCfgStructure.bids.beh.Instructions = '';
+
     expectedCfgStructure.bids.mri.RepetitionTime = [];
     expectedCfgStructure.bids.mri.SliceTiming = '';
     expectedCfgStructure.bids.mri.TaskName = '';
     expectedCfgStructure.bids.mri.Instructions = '';
     expectedCfgStructure.bids.mri.TaskDescription = '';
 
+    expectedCfgStructure.bids.eeg.TaskName = '';
+    expectedCfgStructure.bids.eeg.Instructions = '';
+    expectedCfgStructure.bids.eeg.EEGReference = [];
+    expectedCfgStructure.bids.eeg.SamplingFrequency = [];
+    expectedCfgStructure.bids.eeg.PowerLineFrequency = [];
+    expectedCfgStructure.bids.eeg.DewarPosition = [];
+    expectedCfgStructure.bids.eeg.SoftwareFilters = [];
+    expectedCfgStructure.bids.eeg.DigitizedLandmarks = [];
+    expectedCfgStructure.bids.eeg.DigitizedHeadPoints = [];
+
+    expectedCfgStructure.bids.ieeg.TaskName = '';
+    expectedCfgStructure.bids.ieeg.Instructions = '';
+    expectedCfgStructure.bids.ieeg.SamplingFrequency = [];
+    expectedCfgStructure.bids.ieeg.PowerLineFrequency = [];
+    expectedCfgStructure.bids.ieeg.DewarPosition = [];
+    expectedCfgStructure.bids.ieeg.SoftwareFilters = [];
+    expectedCfgStructure.bids.ieeg.DigitizedLandmarks = [];
+    expectedCfgStructure.bids.ieeg.DigitizedHeadPoints = [];
+
     expectedCfgStructure.bids.meg.TaskName = '';
+    expectedCfgStructure.bids.meg.Instructions = '';
     expectedCfgStructure.bids.meg.SamplingFrequency = [];
     expectedCfgStructure.bids.meg.PowerLineFrequency = [];
     expectedCfgStructure.bids.meg.DewarPosition = [];
@@ -123,6 +152,8 @@ function test_checkCfgBasic()
     expectedCfgStructure.bids.datasetDescription.ReferencesAndLinks = {''};
     expectedCfgStructure.bids.datasetDescription.DatasetDOI = '';
 
+    expectedCfgStructure.bids = orderfields(expectedCfgStructure.bids);
+
     expectedCfgStructure = orderfields(expectedCfgStructure);
 
 end

tests/test_transferInfoToBids.m

@@ -23,13 +23,22 @@ function test_transferInfoToBidsTaskname()
     % make sure the file name gets trasnferred where it should
 
     cfg.task.name = 'foo bar';
+    cfg.task.instructions = 'do this';
 
     fieldsToSet = struct();
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
     expectedStruct.fileName.task = 'fooBar';
     expectedStruct.bids.meg.TaskName = 'foo Bar';
+    expectedStruct.bids.eeg.TaskName = 'foo Bar';
+    expectedStruct.bids.ieeg.TaskName = 'foo Bar';
+    expectedStruct.bids.beh.TaskName = 'foo Bar';
     expectedStruct.bids.mri.TaskName = 'foo Bar';
+    expectedStruct.bids.meg.Instructions = 'do this';
+    expectedStruct.bids.eeg.Instructions = 'do this';
+    expectedStruct.bids.ieeg.Instructions = 'do this';
+    expectedStruct.bids.beh.Instructions = 'do this';
+    expectedStruct.bids.mri.Instructions = 'do this';
 
     assert(isequal(expectedStruct, fieldsToSet));