The Brain Imaging Data Structure and the Electrophysiology communities

By Cyril Pernet, Dora Hermes, Chris Holdgraf

We are happy to announce that the Brain Imaging Data Structure (BIDS) now supports all of the major electrophysiology modalities in human neuroscience. This means that EEG, MEG, and iEEG researchers can all store their data in a BIDS-compliant manner, making these datasets more shareable, understandable, and re-usable. This post describes the BIDS standard in general and the community around it, as well as recent changes that have brought support for electrophysiology.
 
The Brain Imaging Data Structure: BIDS
BIDS is a standard that specifies how to organize data in different folders, how to name files and how to document metadata (i.e. information about the data). It does this using community standards and dictionaries enabling efficient communication and collaboration between data users. Details about BIDS can be found at http://bids.neuroimaging.io/.

BIDS is an initiative that arose as a specific action taken in response to deliberations of the INCF, NeuroImaging Data Sharing Task Force (NIDASH), along with the NeuroImaging Data Model.  NIDM is a Semantic Web-based metadata standard that helps capture and describe experimental data, analytic workflows and statistical results that complement BIDS.
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With seeds planted in January 2015, BIDS started in September after being presented at the OHBM (June) and INCF (August) annual conferences and has rapidly been taken up by our community – starting with a specification related to sharing MRI data (basic structural, functional and diffusion) submitted in December 2015 and followed by a growing number of extensions into various modalities. The analysis of a recent survey done by the Stanford Centre for reproducible neuroscience lead to a current estimate of over 65000 subjects’ data stored and/or shared using BIDS.

Building bridges with the electrophysiology communities
In 2016, MEG BIDS was published describing how to organize and share MEG data and metadata. Right after that, Cyril Pernet used the open science space during the annual OHBM meeting in Vancouver (2016) calling for an EEG-BIDS. The first draft was done the following week with the help of Robert Oostenveld during an EEGLAB workshop. Simultaneously, the iEEG community had a need to organize and share data in a standard that matches MRI, MEG and EEG data, so Dora Hermes and Chris Holdgraf developed the iEEG-BIDS extension. For almost 2 years, the two teams developed the standards, while checking with others for consistency, with some help from the MEG-BIDS team. This work culminated with two papers published in the journal Scientific Data (Holdgraf et al., 2019, Pernet et al., 2019). Concretely, this means human brain electrophysiology data sharing is fully harmonized thanks to the effort and collaborative spirit of all involved. It also means that about 2/3 of all functional imaging data can now be organized, documented and shared efficiently (with the exception of PET, NIRS, TMS and dTCS, 34.7% of publications since January 2018 according to our PubMed search).

Repartition of functional imaging modalities according to a PubMed search ((("2018/01/01"[Date - Create] : "2020"[Date - Create])) AND keyword[Title/Abstract]) AND brain[Other Term].

BIDS is bringing neuroimagers together
While BIDS came about thanks to NIDASH, it was pushed forward by Chris Gorgolewski and the support of the Stanford Centre for reproducible neuroscience, and allows all to freely use and contribute. This approach has been extremely successful, leading to 5 published articles (Gorgolewski et al. 2016, Gorgolewski et al. 2017, Holdgraf et al., 2019, Niso et al., 2016, Pernet et al, 2019) with 86 different authors from 9 different countries. This demonstrates how much neuroimaging  community is thriving by sharing data and creating a community platform to enhance our knowledge and share our experience. Mapping those countries out, however, shows that much more work is needed to reach out to the entire OHBM community.

Geographic distribution of BIDS contributors

If you would like to start using BIDS for your own data, want to get involved in conversations around the BIDS specifications, would like to extend BIDS to cover a new use-case or modality, or would generally like to join the BIDS community, check out the BIDS starter kit, which has lots of helpful links and guides for getting more involved.
 
List of BIDS contributors:
Adeen Flinker - United States
Alexander Li Cohen - United States
Alexandre Gramfort - France
Andrea Pigorini - Italy
Ariel Rokem - United States
Arjen Stolk - United States
Arnaud Delorme - United States
Aysegul Gunduz - United States
Ben Dichter - United States
Bradley Voytek - United States
Brett Foster - United States
Brian N. Lundstrom - United States
Brian Wandell - United States
Cameron Craddock - United States
Camille Maumet - France
Christophe Phillips - Belgium
Christopher Holdgraf - United States
Christopher Honey - United States
Christopher Lee-Messer - United States
Cyril Pernet - United Kingdom
Daniel A. Handwerker - United States
David Groppe - United States
David Keator - United States
Dora Hermes - Netherlands
Elizabeth Bock - United States
Eugene P. Duff - United Kingdom
Fidel Alfaro-Almagro - United Kingdom
Francois Tadel - Canada
Gabriel A. Devenyi - Canada
Gaël Varoquaux - France
Giovanni Piantoni - Netherlands
Guillaume Flandin - United Kingdom
Guiomar Niso - Spain
Gunnar Schaefer - United States
Iris Groen - United States
Jan-Mathijs Schoffelen - Netherlands
Jean-Baptiste Poline - Canada
Jean-Philippe Lachaux - France
Jeffrey G. Ojemann - United States
Jeremy T. Moreau - France
Jessica A. Turner - United States
John Pellman - United States
Jonathan Lau - United States
Jonathan Winawer - United States
Joseph Wexler - Canada
Kai Miller - United States
Kirstie Whitaker - United Kingdom
Kristofer Bouchard - United States
Krzysztof J. Gorgolewski - United States
Liberty Hamilton - United States
Lundstrom Christopher - United States
Lyuba Zehl - Germany
M. Mallar Chakravarty - Canada
Mainak Jas - France
Michael Hanke - Germany
Mihai Capotă - United States
Nader Pouratian - United States
Natalia Petridou - Netherlands
Nathan W. Churchill - Canada
Nick ramsey Ramsey - Netherlands
Nicole C. Swann - United States
Nolan Nichols - United States
​Olivier David - France
Orrin Devinsky - United States
Pierre Bellec - Canada
Richard N. Henson - United Kingdom
Robert Knight - United States
Robert Oostenveld - Netherlands
Russell A. Poldrack - United States
Samir Das - United States
Sasha D'Ambrosio - United States
Satrajit S. Ghosh - United States
Stefan Appelhoff - Germany
Stephan Bickel - Germany
Sylvain Baillet - Canada
Teon L. Brooks - United States
Thomas E. Nichols - United Kingdom
Tibor Auer - United Kingdom
Tristan Glatard - Canada
Vanessa Sochat - United States
Vince D. Calhoun - United States
Vladimir Litvak - United Kingdom
William Triplett - United States
Xiangrui Li - United States
Yaroslav O. Halchenko - United States
Zachary Michael - United States