Introduction to BIDS
The Brain Imaging Data Structure (BIDS) provides a simple and intuitive way to organize and describe your neuroimaging and behavioral data. It has been widely adopted as a standard that many processing pipelines understand.
BIDS principles can be summarized as:
- NIFTI files are the chosen imaging format
- Key data is accompanied by
json
file providing parameters and descriptions - Folder structure and files are named in a consistant manner as prescribed by the specification
Overall directories hierarchy is as follows ([] indicates optional fields):
- sub-<participant_label>[/ses-<session_label>]/<data_type>/
- [code/]
- [derivatives/]
- [stimuli/]
- [sourcedata/]
- sub-control01
- anat
- sub-control01_T1w.nii.gz sub-control01_T1w.json
- sub-control01_T2w.nii.gz sub-control01_T2w.json
- func
- sub-control01_task-nback_bold.nii.gz
- sub-control01_task-nback_bold.json
- sub-control01_task-nback_events.tsv
- sub-control01_task-nback_physio.tsv.gz
- sub-control01_task-nback_physio.json
- sub-control01_task-nback_sbref.nii.gz
- dwi
- sub-control01_dwi.nii.gz
- sub-control01_dwi.bval
- sub-control01_dwi.bvec
- fmap
- sub-control01_phasediff.nii.gz
- sub-control01_phasediff.json
- sub-control01_magnitude1.nii.gz
- sub-control01_scans.tsv
Additional files and folders containing raw data may be added as needed for special cases. They should be named using all lowercase with a name that reflects the nature of the scan (e.g., “calibration”). Naming of files within the directory should follow the same scheme as above (e.g., “sub-control01_calibration_Xcalibration.nii.gz”)
The name of the file depends on modality, acquisition parameters and other considerations. The BIDS Entity Table table compiles the entities (key-value pairs) described throughout the specification, and establishes a common order within a filename. For example, if a file has an acquisition and reconstruction label, the acquisition entity must precede the reconstruction entity.
- Filenames are case sensitive
- Recommended: Zero-padding for subjects i.e sub_01
- NOT Recommended: Zero-padding for runs and echo (and they MUST be integers)
- Units: SI
- Time: YYYY-MM-DDThh:mm:ss