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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 Specification

The main specification lives here

Organization Principles

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

Directory Structure

Overall directories hierarchy is as follows ([] indicates optional fields):
  • sub-<participant_label>[/ses-<session_label>]/<data_type>/
  • [code/]
  • [derivatives/]
  • [stimuli/]
  • [sourcedata/]

Single Session Example

  • 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”)

BIDS Entity Table

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.

Format considerations

  • 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