Onboarding BIDS compliant data#

When sharing dataset or importing data from a publicly shared repository, the data is often stored and organized according to Brain Imaging Data Structure (BIDS) specification. For more information on BIDS visit http://bids.neuroimaging.io. QuNex provides commands that map BIDS data to QuNex data structure so that the data can be easily processed and used.

The main command for importing BIDS formatted dataset is:

  • import_bids

    This command inspects the BIDS dataset, which can be provided as a .zip, .tar.gz compressed package, a folder with expanded data, or a folder with individual compressed packages, and maps the data into the correct folders. Specifically, study general data is mapped to <study folder>/info/bids/<bids dataset name> folder, session specific data are mapped to <sessions folder>/<session>_<session>/bids folders. To map the images to sessions nii folder and generate session.txt file needed for further processing, import_bids makes use of a supporting command map_bids2nii. This command performs the mapping of MR images and their associated .json sidecars from sessions' bids folder to nii folder, creates session.txt file and a bids2nii.log, which lists exact mapping that was performed. The command is run automatically as part of the import_bids command. If fieldmap images are present in the dataset map_bids2nii will inspect their associated .json sidecar files and note which fieldmap images are associated with images listed in the IntendedFor JSON field in the session.txt. If .json sidecar files exist for images, the parameters relevant for preprocessing will be added to the session.txt file. Whether and which information should be added can be specified using the sequenceinfo parameter.

For more detailed description of the command and its parameters, please consult the online import_bids command reference or see inline help by running qunex import_bids --help.