Behavior and Neuroimaging Core User Manual
  • About
  • Infrastructure Overview
  • XNAT
    • Getting Started
    • Accessing XNAT
    • BIDS Ready Protocols
    • New XNAT projects
    • Uploading Data
    • Downloading Data
  • Demo Dataset
    • Introduction
    • How to access it
    • Protocol Information
    • Basic analysis example: checks task
  • XNAT to BIDS
    • Getting Started
    • XNAT2BIDS Software
    • Exporting to BIDS using Oscar
      • Oscar Utility Script
        • Running xnat2bids using default configuration
        • Running xnat2bids with a custom configuration
        • Syncing your XNAT project & Oscar data directory
        • Extra tools & features
      • Step-wise via Interact Session
    • BIDS Validation
      • Oscar
      • Docker
    • Converting non-MR data
      • Physiological data
      • EEG data
  • XNAT TO BIDS (Legacy)
    • Oscar SBATCH Scripts
  • BIDS and BIDS Containers
    • Introduction to BIDS
    • mriqc
    • fmriprep
    • BIDS to NIMH Data Archive (NDA)
  • Analysis Pipelines
    • Freesurfer
    • 🚧CONN Toolbox
    • FSL topup and eddy
    • Tractography: DSI Studio
    • Brown University MRS Data Collection and Preprocessing Protocol
    • LC Model
      • Installation
      • Example Run
      • Running LCModel on your own data
    • Quantitative Susceptibility Mapping (QSM)
  • Standalone Tools
    • Multi-session spectroscopy with voxalign
    • dicomsort: a tool to organize DICOM files
    • ironmap
    • convert enhanced multi-frame DICOMs to legacy single-frame
    • DICOM anonymization
  • MRF GUIDES
    • MRI simulator room
      • Motion Trainer: Balloon Task
      • Simulating scanner triggers
    • Stimulus display & response collection
    • Eyetracking at the scanner
    • Exporting data via scannershare
    • EEG in the scanner
    • Exporting spectroscopy RDA files
  • Community
    • MRF/BNC user community meetings
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  • BIDS Specification
  • Organization Principles
  • Directory Structure

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  1. BIDS and BIDS Containers

Introduction to BIDS

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Last updated 1 year ago

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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

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

The name of the file depends on modality, acquisition parameters and other considerations. The 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.

https://bids-specification.readthedocs.io/en/stable/
BIDS Entity Table