Onboarding BIDS compliant data
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:
This command inspects the BIDS dataset, which can be provided as a
.tar.gzcompressed 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>/bidsfolders. To map the images to sessions
niifolder and generate
session.txtfile needed for further processing,
import_bidsmakes use of a supporting command
map_bids2nii. This command performs the mapping of MR images and their associated
.jsonsidecars from sessions'
session.txtfile and a
bids2nii.log, which lists exact mapping that was performed. The command is run automatically as part of the
If fieldmap images are present in the dataset
map_bids2niiwill inspect their associated
.jsonsidecar files and note which fieldmap images are associated with images listed in the
IntendedForJSON field in the
.jsonsidecar files exist for images, the parameters relevant for preprocessing will be added to the
session.txtfile. Whether and which information should be added can be specified using the
For more detailed description of the command and its parameters, please consult the online
import_bids command reference or see inline help by running