DATA2BIDS
Note that this reference documentation is identical to the help that is displayed in MATLAB when you type “help data2bids”.
DATA2BIDS is a helper function to convert MEG, EEG, iEEG or anatomical MRI data to the Brain Imaging Data Structure. This function starts from an existing dataset on disk and creates the required sidecar files. The overall idea is that you would write a MATLAB script in which you call this function multiple times, once for each of the data files. For each data file it will write the corresponding JSON file. When operating on MEG data files, it will also write a corresponding channels.tsv and events.tsv file. Use as data2bids(cfg) or as data2bids(cfg, data) The first input argument "cfg" is the configuration structure, which contains the details for the (meta)data and which specifies the sidecar files you want to write. The optional "data" argument corresponds to preprocessed raw data according to FT_DATAYPE_RAW or an anatomical MRI according to FT_DATAYPE_VOLUME. The optional data argument allows you to write a preprocessed and realigned anatomical MRI to disk, or to write a preprocessed electrophysiological dataset to disk. The configuration structure should contains cfg.dataset = string, filename of the input data cfg.outputfile = string, optional filename for the output data, see below cfg.anat.writesidecar = string, 'yes' or 'no' (default = 'yes') cfg.anat.dicomfile = string, filename of a matching DICOM file cfg.meg.writesidecar = string, 'yes' or 'no' (default = 'yes') cfg.eeg.writesidecar = string, 'yes' or 'no' (default = 'yes') cfg.ieeg.writesidecar = string, 'yes' or 'no' (default = 'yes') cfg.channels.writesidecar = string, 'yes' or 'no' (default = 'yes') cfg.events.writesidecar = string, 'yes' or 'no' (default = 'yes') cfg.events.trl = trial definition, see below If you specify cfg.dataset without cfg.outputfile, this function will only construct and write the appropriate sidecar files matching the header details that it will get from the dataset. If you also specify cfg.outputfile, this function will furthermore read the data from the input dataset, convert it and write it to the output dataset. The output format is NIFTI for anatomical MRIs, and BrainVision for EEG and iEEG. Note that in principle you can also convert MEG data to BrainVision, but that is not recommended. You can specify cfg.anat.dicomfile in combination with a NIFTI anatomical MRI. This will cause the detailled header information with MR scanner ans sequence details to be read from the DICOM file and used to fill in the details of the JSON file. You can specify cfg.events.trl as a Nx3 matrix with the trial definition (see FT_DEFINETRIAL) or as a MATLAB table. When specified as table, the first three columns containing integer values corresponding to the begsample, endsample and offset, the additional colums can be of another type and can have any name. If you do not specify the trial definition, the events will be read from the dataset and used. General options that apply to all data types are cfg.TaskName = string cfg.InstitutionName = string cfg.InstitutionAddress = string cfg.InstitutionalDepartmentName = string cfg.Manufacturer = string cfg.ManufacturersModelName = string cfg.DeviceSerialNumber = string cfg.SoftwareVersions = string General options that apply to all functional data types are cfg.TaskDescription = string cfg.Instructions = string cfg.CogAtlasID = string cfg.CogPOID = string There are many more datatype specific options for the JSON files than can be listed here. Please open this function in the MATLAB editor to see what those are. Example with a CTF dataset on disk cfg = []; cfg.dataset = 'sub-01_ses-meg_task-language_meg.ds'; cfg.TaskName = 'language'; cfg.meg.PowerLineFrequency = 50; cfg.InstitutionName = 'Radboud University'; cfg.InstitutionalDepartmentName = 'Donders Institute for Brain, Cognition and Behaviour'; data2bids(cfg) Example with an anatomical MRI on disk cfg = []; cfg.dataset = 'sub-01_ses-mri_T1w.nii'; cfg.anat.dicomfile = '00080_1.3.12.2.1107.5.2.43.66068.2017082413175824865636649.IMA' % cfg.anat.MagneticFieldStrength = 3; % this is not needed, as it will be obtained from the DICOM file cfg.InstitutionName = 'Radboud University'; cfg.InstitutionalDepartmentName = 'Donders Institute for Brain, Cognition and Behaviour'; data2bids(cfg) Example with a NeuroScan EEG dataset on disk that needs to be converted cfg = []; cfg.dataset = 'subject01.cnt'; cfg.outputfile = 'sub-001_task-visual.vhdr'; cfg.InstitutionName = 'Radboud University'; cfg.InstitutionalDepartmentName = 'Donders Institute for Brain, Cognition and Behaviour'; data2bids(cfg) Example with preprocessed EEG data in memory cfg = []; cfg.dataset = 'subject01.cnt'; cfg.bpfilter = 'yes'; cfg.bpfreq = [0.1 40]; data = ft_preprocessing(cfg); cfg = []; cfg.outputfile = 'sub-001_task-visual.vhdr'; cfg.InstitutionName = 'Radboud University'; cfg.InstitutionalDepartmentName = 'Donders Institute for Brain, Cognition and Behaviour'; data2bids(cfg, data) Example with realigned and resliced anatomical MRI data in memory cfg = []; cfg.outputfile = 'sub-01_ses-mri_T1w.nii'; cfg.anat.MagneticFieldStrength = 3; cfg.InstitutionName = 'Radboud University'; cfg.InstitutionalDepartmentName = 'Donders Institute for Brain, Cognition and Behaviour'; data2bids(cfg, mri) This function tries to correspond to version 1.1.0 of the BIDS specification. See http://bids.neuroimaging.io/ for further details.
