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 naming conventions used in this chapter are explained on page about preparation of QuNex study folder hierarchy.

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 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.

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.