Setting up your experiment

Configuration

src.checkCFG(cfg)

Check the fields of the configuration structure cfg. If a required field is missing the default value will be assigned to that field. If this field already exists then the existing value will not be replaced.

USAGE:

cfg = checkCFG([cfg])
Parameters:

cfg (structure) – The configuration variable to check.

Returns:

cfg:

(structure)

This function reuses a lot of code and comment from the BIDS starter kit:

https://github.com/bids-standard/bids-starter-kit/tree/master/matlabCode

Fields descriptions:

The following section describes the main fields set by checkCFG() with their associated default value.

  • cfg.testingDevice = 'pc' sets the way the experiment is run and the different options match the imaging modality:

    • pc or beh is for behavioral test

    • mri is for fMRI

    • eeg is for EEG…

  • cfg.verbose = 0 sets how talkative the code will be. Possible values range from 0 to 2.

    • 0: “I don’t want to hear anything from CPP_BIDS.”

    • 1: “I want to get my warnings.”

    • 2: “Tell me everything!”

    For implementation see utils/talkToMe and utils/throwWarning.

  • cfg.useGUI = false sets whether a graphic interface should be used for the userInputs() to query about group name, as well as for session, subject and run number.

  • cfg.dir.output sets where the data will be saved.

Filename options:

sets options that will help in creating the filenames.

  • cfg.fileName.task = '' sets the name to be given to the task

  • cfg.fileName.zeroPadding = 3 sets the amount of 0 padding the subject, session and run number.

  • cfg.fileName.dateFormat = 'yyyymmddHHMM' sets the format of the date and time stamp that will be appended to all files.

The following fields can be used to specify certain of the labels that are used to specify certain of the acquisition conditions of certain experimental runs in a BIDS data set. These are mostly for MRI and, if set, will be ignored for most other modalities. See tests/test_createFilename() for details on how to use these.

  • cfg.suffix.ce = []

  • cfg.suffix.dir = []

  • cfg.suffix.rec = []

  • cfg.suffix.echo = []

  • cfg.suffix.acq = []

  • cfg.suffix.recording = []

Group and session options:

All the fields of cfg.subject can be set using the userInputs() function but can also be set “manually” directly into the cfg structure.

  • cfg.subject.subjectGrp = '' is set to empty in case no group was provided.

  • cfg.subject.sessionNb = 1 always sets to 1 in case no session was provided.

  • cfg.subject.askGrpSess = [true true] means that userInputs() will always ask for group and session by default.

Eyetracker options:

Those options are mostly work in progress at the moment but should allow to track the some of the metadata regarding eyetracking data acquisition.

  • cfg.eyeTracker.do = false

  • cfg.eyeTracker.SamplingFrequency = []

  • cfg.eyeTracker.PupilPositionType = ''

  • cfg.eyeTracker.RawSamples =  []

  • cfg.eyeTracker.Manufacturer = ''

  • cfg.eyeTracker.ManufacturersModelName = ''

  • cfg.eyeTracker.SoftwareVersions = ''

  • cfg.eyeTracker.CalibrationType = 'HV5'

  • cfg.eyeTracker.CalibrationPosition = ''

  • cfg.eyeTracker.CalibrationDistance = ''

  • cfg.eyeTracker.MaximalCalibrationError = []

  • cfg.eyeTracker.AverageCalibrationError = []

  • cfg.eyeTracker.RawDataFilters = {}

cfg.bids:

checkCFG() will also initialize cfg.bids that contains any information related to a BIDS data set and that will end up in in one of the JSON “sidecar” files containing the metadata of your experiment.

If the content of some fields of cfg has been set before running checkCFG(), that content might be copied into the relevant field in cfg.bids. For example, if you have set the field cfg.mri.repetitionTime, then when you run checkCFG(), its content will also be copied into cfg.bids.mri.RepetitionTime.

cfg.bids is further sub-divided into several fields for the different “imaging modalities”.

  • cfg.bids.datasetDescription will be there for all type of experiments

  • cfg.bids.beh is for purely behavioral experiment with no associated imaging

  • cfg.bids.mri is for fMRI experiments

  • cfg.bids.eeg is for EEG experiments

  • cfg.bids.meg is for MEG experiments

  • cfg.bids.ieeg is for iEEG experiments

The content of each of those subfields matches the different “keys” one can find in the JSON file for each modality. The content of those different keys is detailed in the code of checkCFG(), but a more extensive and updated descriptions will be found in the BIDS specifications themselves.

https://bids-specification.readthedocs.io/en/stable/

For the content of the datasetDescription.json files:

cfg.bids.datasetDescription.Name = '';
cfg.bids.datasetDescription.BIDSVersion =  '';
cfg.bids.datasetDescription.License = '';
cfg.bids.datasetDescription.Authors = {''};
cfg.bids.datasetDescription.Acknowledgements = '';
cfg.bids.datasetDescription.HowToAcknowledge = '';
cfg.bids.datasetDescription.Funding = {''};
cfg.bids.datasetDescription.ReferencesAndLinks = {''};
cfg.bids.datasetDescription.DatasetDOI = '';

For the content of the JSON files for behavioral data:

cfg.bids.beh.TaskName = [];
cfg.bids.beh.Instructions = [];

For the content of the JSON files for fMRI data:

cfg.bids.mri.TaskName = '';
cfg.bids.mri.Instructions = '';
cfg.bids.mri.RepetitionTime = [];
cfg.bids.mri.SliceTiming = '';
cfg.bids.mri.TaskDescription = '';

For the content of the JSON files for EEG:

cfg.bids.eeg.TaskName = '';
cfg.bids.eeg.Instructions = '';
cfg.bids.eeg.EEGReference = '';
cfg.bids.eeg.SamplingFrequency = [];
cfg.bids.eeg.PowerLineFrequency = 50;
cfg.bids.eeg.SoftwareFilters = 'n/a';

For the content of the JSON files for iEEG:

cfg.bids.ieeg.TaskName = '';
cfg.bids.ieeg.Instructions = '';
cfg.bids.ieeg.iEEGReference = '';
cfg.bids.ieeg.SamplingFrequency = [];
cfg.bids.ieeg.PowerLineFrequency = 50;
cfg.bids.ieeg.SoftwareFilters = 'n/a';

For the content of the JSON files for MEG:

cfg.bids.meg.TaskName = '';
cfg.bids.meg.Instructions = '';
cfg.bids.meg.SamplingFrequency = [];
cfg.bids.meg.PowerLineFrequency = [];
cfg.bids.meg.DewarPosition = [];
cfg.bids.meg.SoftwareFilters = [];
cfg.bids.meg.DigitizedLandmarks = [];
cfg.bids.meg.DigitizedHeadPoints = [];
src.utils.transferInfoToBids(fieldsToSet, cfg)

Transfers any info that might have been provided by the user in cfg to the relevant field of fieldsToSet for its reuse later for BIDS filenames or JSON.

USAGE:

fieldsToSet = transferInfoToBids(fieldsToSet, cfg)
Parameters:

  • fieldsToSet (structure) – List of the fields to set. See checkCFG().

  • cfg (structure) – The configuration variable where the user has predefined some fields. See checkCFG().

Returns:

fieldsToSet:

Updated list of the fields to set.

This can be used for example to make sure that the repetition time set manually in cfg.mri.repetitionTime or in cfg.task.name will be passed to the correct field in right fields of cfg.bids.

Group, subject, session and run

You can use the userInputs() function to easily set the group name as well as the subject, session and run number. You can ask the function to not bother you with group and session