# 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](../UsageDocs/PreparingStudy).

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`.

````{seealso}
[BIDS support within QuNex](../Overview/QuNexBIDS)
````