# 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`](../../api/gmri/import_bids.rst)

    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`](../../api/gmri/import_bids.rst) command reference or see inline help by running `qunex import_bids --help`.