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BIDS: Past, present, and future

Russell Poldrack

Stanford University

https://www.cos.io/blog/2023-is-the-year-of-open-science

Under the leadership of the White House Office of Science and Technology Policy (OSTP), all major U.S. federal agencies are participating in declaring 2023 the “Federal Year of Open Science.”

https://www.earthdata.nasa.gov/esds/open-science/oss-for-eso-workshops

Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants.

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Under the upcoming NIH Data Sharing Policy, Investigators must manage and share data as described in the approved DMS Plan, & provide updates on data management and sharing activities in annual progress reports.

In accordance with this memorandum, OSTP recommends that federal agencies:

1) Update their public access policies as soon as possible, and no later than 12/31/2025, to make publications and their supporting data resulting from federally funded research publicly accessible without an embargo on their free and public release;

2. Establish transparent procedures that ensure scientific and research integrity is maintained in public access policies

A false start for fMRI data sharing

Van Horn, 2002

This letter comes from a group of scientists who are publishing papers using fMRI to understand the links between brain and behavior. We are writing in reaction the recent announcement of the creation of the National fMRI Data Center (www.fmridc.org). In the letter announcing the creation of the center, it was also implied that leading journals in our field may require authors of all fMRI related papers accepted for publication to submit all experimental data pertaining to their paper to the Data Center. … We are particularly concerned with any journal’s decision to require all authors of all fMRI related papers accepted for publication to submit all experimental data pertaining to their paper to the Data Center.

This letter comes from a group of scientists who are publishing papers using fMRI to understand the links between brain and behavior. We are writing in reaction the recent announcement of the creation of the National fMRI Data Center (www.fmridc.org). In the letter announcing the creation of the center, it was also implied that leading journals in our field may require authors of all fMRI related papers accepted for publication to submit all experimental data pertaining to their paper to the Data Center. … We are particularly concerned with any journal’s decision to require all authors of all fMRI related papers accepted for publication to submit all experimental data pertaining to their paper to the Data Center.

2010: The year data sharing broke in neuroimaging

• “Comprehensive mapping of the functional connectome, and its subsequent exploitation to discern genetici nfluences and brain–behavior relationships, will require multicenter collaborative datasets. Here we initiate this endeavor by gathering R-fMRI data from 1,414 volunteers collected independently at 35 international centers. We demonstrate a universal architecture of positive and negative functional connections, as well as consistent loci of inter-individual variability. …”

Data sharing is becoming the norm in neuroimaging

Anonymous senior researcher circa 2019:

“OHBM has been taken over by the open science zealots!”

Milham et al., Nature Communications, 2018

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Poldrack et al., Annual Reviews in Biomedical Data Science, 2019

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Simply sharing data is not sufficient

It needs to be shared in a way that makes it useful!

https://www.youtube.com/watch?v=N2zK3sAtr-4

Data Sharing and Management Snafu in 3 Short Acts

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• I received the data, but when I opened it up it was in hexadecimal
• Yes, that is right
• I cannot read hexadecimal
• You asked for my data and I gave it to you. I have done what you asked.

…

• Is there a guide to the data anywhere?
• Yes, of course, it is the article that is published in Science.

FAIRness: Effectively open

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https://www.fosteropenscience.eu/learning/assessing-the-fairness-of-data

Toward a community standard for neuroscience data: BIDS

• A community-based open standard for neuroimaging data
• A file organization standard
• A metadata standard

Motivation for BIDS

• We shared imaging data in the OpenFMRI project (starting in 2013) using a bespoke organization scheme
• No simple way to validate whether a dataset met the scheme
• Required manual curation

Poldrack et al., 2013

The history of BIDS

• January 2015
• Initial stakeholder meeting at Stanford (funded by INCF)
• Initiated development of a draft standard

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The history of BIDS

• January 2015
• Initial stakeholder meeting at Stanford (funded by INCF)
• Initiated development of a draft standard
• September 2015
• Draft standard posted to BIDS web site with 22 example datasets
• Solicited feedback from community
• June 2016
• Published paper

September 2018

BIDS-standard Github organization started

Chris Gorgolewski

(founder,

now at Google)

BIDS Coding Sprints

Maintainers

Chris Markiewicz

Taylor Salo

Remi Gau

Steering group

Guiomar

Niso

ES

Ariel

Rokem

USA

Robert Oostenveld

NL

Yaroslav

Halchenko

USA

Ariel

Rokem

USA

Ross Blair

Anthony Galassi

Eric Earl

Christine Rogers

Principles

• Adoption is crucial
• Keep it as similar to existing practices as possible
• Don’t let technology override usability!
• Focus on engaging the community
• Don’t reinvent the wheel
• Use existing standards when possible
• 80/20 rule
• Focus on the most common use cases
• Don’t let the perfect be the enemy of the good!

BIDS extensions

• Original standard was focused raw sMRI/fMRI/dMRI
• Modality extensions:
• MEG (Niso et al., 2018)
• EEG
• iEEG/ECoG
• PET
• qMRI, ASL
• Microscopy
• fNIRS
• Ongoing work
• Eye tracking
• Motion tracking
• Data type extensions (funded by BRAIN Initiative R24s):
• Common derivatives
• Connectivity matrices (This meeting!)
• Statistical models
• Image transformations

Adoption

• Endorsed as community standard by INCF
• Used in hundreds of labs around the world
• Adopted by: ABCD Community Collection, FCP-INDI, Developing Human Connectome, SchizConnect and Donders Data repository
• Anonymized data from tens of thousands of participants formatted in BIDS are publicly available

~2.2K visitors per month

Traffic to bids.neuroimaging.io

BIDS Impact

• MRIQC Web API
• Crowdsourced database of MR QC metrics
• QC metrics from ~450K unique BOLD scans and ~360K T1w scans as of June 2023
• Publicly available:
• https://mriqc.nimh.nih.gov/

Gorgolewski et al. 2017

BIDS App: A containerized software application

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The container encapsulates all software and dependencies

- allows better reproducibility

Common command line protocol:

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bids-app /bids-directory

/output-directory

participant

[OPTIONS]

• Many application types available
• Quality control
• Anatomical processing
• Functional processing
• Diffusion processing
• Lowered friction encourages adoption
• Researchers gain easy access to tools by formatting data in BIDS
• Accepting BIDS datasets makes tools easy to try

fmriprep /data/bids/openneuro/ds000228 \

/data/processed/ds000228-fmriprep \

participant --participant-label pixar001

The future of BIDS

• Schematization of the BIDS validator
• BIDS 2.0
• Potential changes to inheritance model
• Reducing complexity
• Simplifying conversion

Thanks to the BIDS community!