Get involved in making BIDS better

The easiest way to contribute to BIDS is to ask questions you have about the specification on Neurostars. If your question has a bids tag it will be much easier for others to find the answer.

You can also get involved by answering questions on Neurostars!

You can contribute to the BIDS specification by opening Issues and proposing changes via Pull Requests on GitHub.

To make improvements to the website that you are reading right now, you can also open an Issue and propose changes via Pull Requests at the BIDS website GitHub repository.

There are so many ways to help us build this community. You could help someone else learn the benefits of BIDS, give a talk in your local organisation, or build a BIDS App!

The only requirement is that everyone who contributes adheres to our BIDS Code of Conduct.

Thank you for your contributions!

Extending the BIDS specification

The BIDS specification can be extended in a backwards compatible way and will evolve over time. These are accomplished with BIDS Extension Proposals (BEPs), which are community-driven processes.

Do you want to extend BIDS to a new modality or set of data types? Please draft a BIDS Extension Proposal (BEP) following the BIDS Extension Proposals Guide.

You can also contribute to ongoing BIDS Extension Proposals. Below is a table of currently-active BEPs. The “Extension label” column provides a direct link to the documentation.

Please find our latest BEP update presented in the Open Science Room at OHBM.

Note that all of the extension ideas that are not backwards compatible and thus will have to wait for BIDS 2.0 are listed on the Issues page of the bids-2-devel GitHub repository.


Extension Title Lead(s) Last update Blocking point(s)
BEP002

The BIDS Models Specification

  • Tal Yarkoni

  • Chris Markiewcz

Reworked structure:

  • list of steps is now a directed graph,
  • Model zoo,
  • Abstracted transformations, to ease interoperability of implementations.

Stat Models released v1.0.0-rc1 in June 2021 - Please review!

BEP004

Susceptibility Weighted Imaging (SWI)

Looking for a new leader.

Looking for a new leader.

BEP011

The structural preprocessing derivatives

  • Viviana Siless

Opened pull request.

Features:

  • surfaces,
  • scalar maps on surfaces
  • morphometrics.

Need to conform with final Common Derivatives and gather community feedback.

Blocked by BIDS-validator extending and PyBIDS implementation for common derivatives

BEP012

The functional preprocessing derivatives

  • Chris Markiewicz

Opened the pull request.

Features:

  • Derivative images (mean, ALFF, ReHo, etc.),
  • Time series (confounds, decompositions, etc.)

Blocked by BIDS-validator extending and PyBIDS implementation

BEP013

The resting state fMRI derivatives

  • Steven Giavasis

Merged into BEP012.

None

BEP014

The affine transformations and nonlinear field warps

  • Oscar Esteban

In progress.

BEP016

The diffusion weighted imaging derivatives

  • Franco Pestilli

  • Oscar Esteban

  • Being discussed here.
  • Coordinating with BEP017.
  • Diffusion-weighted model description merged, but must comply to this.
  • Upcoming integration across DWI, Tractography, Tractometry, and Connectivity (from fMRI and DWI)

None

BEP017

Generic BIDS connectivity data schema

  • Eugene Duff

  • Current state.
  • Intended as a meeting point for minimal harmonisation of connectivity-based formats across modalities.
  • Seeking use cases spanning modalities and input defining connectivity based formats

None

BEP019

DICOM Metadata

  • Satrajit Ghosh

Not active. Could be a NIDM extension rather than in BIDS.

None

BEP020

Eye Tracking including Gaze Position and Pupil Size

  • Dejan Draschkow

  • BEP close to PR submission, examples and validator under development.
  • Seeking additional BEP lead to help incoporate into standard contact dejan to get involved.

None

BEP021

Common Electrophysiological Derivatives

  • Stefan Appelhoff

  • Arnaud Delorme

  • Dora Hermes

  • Mainak Jas

  • Guiomar Niso

  • Robert Oostenveld

  • Cyril Pernet

  • Discussion here UCSD to include head models with BIDS EEG data.
  • Developments of BIDS M/EEG pipelines will trigger discussion on storing derived data.

Mostly on hold.

BEP022

Magnetic Resonance Spectroscopy (MRS)

  • Mark Mikkelsen

  • William Clarke

  • Martin Wilson

  • Group discussions here and here.
  • Developed NifTI standard for MRS data - presented abstract at ISMRM; manuscript in preparation.

None

BEP023

PET Preprocessing derivatives

  • Martin Noergaard

  • Graham Searle

  • Melanie Ganz

  • Work in progress following BEP009 incorporation into spec.
  • Coord. kickoff scheduled Sept. 2021 to capture various experimental designs and needs for preprocessing and pharmacokinetic modeling.
  • Focused on staying aligned with derivatives for MRI (structural, functional, ASL, diffusion)

Progressing and soliciting input from senior PET experts.

BEP024

Computed Tomography scan (CT)

  • Hugo Boniface

Lead seeking more contributors and experts.

None

BEP025

Medical Imaging Data structure (MIDS)

  • Jose Manuel

  • Saborit Torres

  • Maria de la Iglesia Vayá

None

BEP026

Microelectrode Recordings

BEP is open to new leadership, see also BEP032 (animal electrophys)

Searching for a new leader.

BEP027

BIDS Applications 2.0

  • Chris Markiewicz

  • Greg Kiar

  • Focusing on: command-line conventions, I/O interface descriptors, and common behavior (for example, exit codes for failure modes); relies upon the Boutiques standard.
  • Re-conception of BIDS Apps

None

BEP028

Provenance

  • Satra Ghosh

  • Camille Maumet

  • BEP aims to provide a description of data manipulation and transformations steps related to a BIDS data element via BIDS structured sidecar JSON-LD files.
  • Can be used to describe provenance at different levels of granularity.
  • Discussions held in this repository.
  • A set of examples and user stories are being refined.

None

BEP029

Virtual and physical motion data

  • Sein Jeung

  • Julius Welzel

BEP is developing and starting to finalize as discussions concerning example datasets are completed.

None

BEP032

Animal electrophysiology

  • Sylvain Takerkart

  • Julia Sprenger

  • New BEP, collecting comments and community feedback which may be submitted here, directly to Sylvain & Julia, or here during the ~monthly meeting.
  • Example datasets here.
  • Supporting early stage interaction with: ProbeInterface & SpikeInterface, AnDO, interoperability with NWB and NIX data/metadata formats.

None

BEP033

Advanced Diffusion Weighted Imaging (aDWI)

  • James Gholam

  • Leandro Beltrachini

  • Filip Szczepankiewicz

  • New BEP, seeking contributors and collecting community feedback relating to: priority sequences to support, best supported binary structured formats (e.g. CBOR? HDF5? MsgPack?).
  • Comments may be submitted directly on the document.
  • Generating example datasets here and determining best practice w/ vendors to record data in-sequence

None

BEP034

Computational modeling

  • Michael Schirner

  • Petra Ritter

BEP Computational Models: PR open for review and discussion here

None

BEP035

Modular extensions for individual participant data mega-analyses with non-compliant derivatives

  • Giuseppe Gallitto

  • Balint Kincses

  • Tamas Spisak

  • BEP revised: now collecting further comments and community feedback.
  • Collaborators with mega-analysis experience or with actual example use-cases (planned/ongoing/finished mega analyses) welcome!

None

BEP036

Phenotypic Data Guidelines

  • BEP drafted.
  • Poster presentation at OHBM 2022.
  • Now collecting community comments and feedback.
  • All collaborators are welcome.

More reviews and discussions are necessary.

BEP037

Non-Invasive Brain Stimulation (NIBS)

New BEP, collecting community comments and feedback. All collaborators are welcome.

None


Completed BEPs

When an extension reaches maturity it is merged into the main body of the specification. Below is a table of BEPs that have been merged.

The references of the final publication for those BEPS can be found in the BIDS specification.

Extension label Title Moderators/leads
BEP001 Quantitative MRI (qMRI) Gilles de Hollander and Kirstie Whitaker
BEP003 Common Derivatives Chris Markiewicz
BEP005 Arterial Spin Labeling (ASL) Henk-Jan Mutsaerts, Patricia Clement, Jan Petr, and Marco Castellaro
BEP006 Electroencephalography (EEG) Cyril Pernet, Stefan Appelhoff, and Robert Oostenveld
BEP007 Hierarchical Event Descriptor (HED) Tags Chris Gorgolewski
BEP008 Magnetoencephalography (MEG) Guiomar Niso
BEP009 Positron Emission Tomography (PET) Melanie Ganz
BEP010 intracranial Electroencephalography (iEEG) Chris Holdgraf and Dora Hermes
BEP018 Genetic information Cyril R Pernet, Clara Moreau, and Thomas Nichols
BEP030 Near Infrared Spectroscopy (NIRS) Robert Luke and Luca Pollonini
BEP031 Microscopy Marie-Hélène Bourget and Julien Cohen-Adad


Some proposals that set out to extend the BIDS specification have instead become tools for handling BIDS. See the table below.

Extension label Title Moderators/leads Tool name
BEP015 Mapping file Eric Earl, Camille Maumet, and Vasudev Raguram File mapper