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A primer to BIDS
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Ghislain Vaillant | A primer to BIDS | Inria Digital Health Meetup 2022

A primer to BIDS

A 10-minute (or so) introduction to the Brain Imaging Data Structure for busy engineers.

Learning objectives

  • Understand what BIDS is
  • Introduce the core concepts
  • Overview of available tools

The Brain Imaging Data Structure

Definition

A simple and intuitive way to organize and describe your neuroimaging and behavioral data.

The Brain Imaging Data Structure (BIDS) is a standard specifying the description of neuroimaging data in a filesystem hierarchy and of the metadata associated with the imaging data.

Governance

BIDS is a community-driven effort.

The specification is opensource and contributions are accepted through submission of issues and requests to the GitHub repository.

Governance is driven by a formal leadership structure, which ensures strict application of contribution policies and the code of conduct.

Extensions

Requests for improvement are handled through BIDS Extension Proposals (BEP).

BEPs are incubated within special interest groups, prior to proposal for inclusion to the specification.

Once accepted, the BEP is officially included in the next release of the specification.

Notable BEPs: EEG, MEG, PET, Microscopy WIP: DWI derivatives, PET derivatives, Provenance

Concepts

  • Datasets
  • File collections
  • Metadata

Datasets

  • Source, raw and derivative datasets
  • Minimal requirements
  • Storage convention

Types of dataset

Raw dataset

  • A BIDS-compliant dataset containing the raw data of the study.

Source dataset

  • A non BIDS-compliant dataset containing the source data of the study before normalisation to BIDS.

Derivative dataset

  • A BIDS-like dataset containing artifacts processed from a raw dataset and other derivatives possibly.

Minimal requirements

dataset_description.json

{
    "Name": "This dataset",
    "BIDSVersion": "1.8.0",
    "DatasetType": "raw" | "derivative",
}

Storage convention (1)

Embedded (in-tree)

rawdata/
    dataset_description.json
    derivatives/
        pipeline-foo/
            dataset_description.json
       pipeline-bar/
            dataset_description.json 
    sourcedata/

Storage convention (2)

Standalone (out-of-tree)

sourcedata/
rawdata/
    dataset_description.json
derivatives/
    pipeline-foo/
        dataset_description.json
    pipeline-bar/
        dataset_description.json

File collections

  • File naming convention
  • Components and entities
  • Derivatives

Anatomy of a BIDS file

sub-P01/
    ses-M00/
        anat/
            sub-P01_ses-M00_T1w.nii.gz

Components and entities

sub-P01/
    ses-M00/
        anat/
            sub-P01_ses-M00_run-01_T1w.nii.gz
            sub-P01_ses-M00_run-02_T1w.nii.gz

Entities: sub, ses, run Datatype: anat Suffix: T1w Extension: .nii.gz

Supported entities by modality.

Derivatives

sub-P01/
    ses-M00/
        anat/
            sub-P01_ses-M00_desc-preproc_T1w.nii.gz

Source entities: sub, ses Derivative entities: desc

BIDS derivatives are still a work-in-progress. Consider checking for in-progress BEP first, before reaching for your own implementation.

Metadata

  • Modality-agnostic metadata
  • Modality-specific metadata
  • Inheritence principle

Modality-agnostic metadata

Modality-agnostic metadata are defined in tabular format and serialised to TSV.

participants.tsv                        # participant-level metadata
sub-P01/
    sub-P01_sessions.tsv                # session-level metadata
    ses-M00/
        sub-P01_ses-M00_scans.tsv       # scan-level metadata

Example: participants.tsv

participant_id age sex handedness group
sub-P01 36 M n/a control

Modality-specific metadata

Modality-specific metadata are defined in dictionary format and serialised to JSON.

sub-P01/
    ses-M00/
        anat/
            sub-P01_ses-M00_T1w.nii.gz
            sub-P01_ses-M00_T1w.json    # Modality-specific metadata

Example sidecar JSON metadata:

{
    "MagneticFieldStrength": 3,         /* DICOM tag 0018, 0087 */
    "MRAcquisitionType": "3D",          /* DICOM tag 0018, 0023 */
    "EchoTime": 0.00298                 /* DICOM tag 0018, 0081 */
}

Inheritence principle

⚠️ OPTIONAL

T1w.json                                # Dataset-wide definition
sub-P01/
    sub-P01_T1w.json                    # Participant-specific overrides
    ses-M00/
        anat/
            sub-P01_T1w.nii.gz
            sub-P01_T1w.json            # Modality-specific overrides

Modality-specific metadata computed by dictionary merging from root to leaf.

Ecosystem around BIDS

  • Publicly available datasets
  • Official tools and libraries
  • Starter kit

https://github.com/bids-standard/bids-examples

https://openneuro.org/

Official libraries

Converters

Validator

https://github.com/bids-standard/bids-validator

Starter kit

https://bids-standard.github.io/bids-starter-kit/

Questions

Thank you for your attention.