Brain Imaging Data Structure: Difference between revisions

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{{Infobox technology standardstandardref

| title = Brain Imaging Data Structure

| image = [[File:BIDS Logo.png|250px]]

| status = Published

| year_started = 20142015

| version = 1.10.0<ref name="BIDS specification">{{cite web |last1=Oliver-Taylor |first1=Aaron |last2=Li |first2=Adam |last3=Thomas |first3=Adam |title=The Brain Imaging Data Structure (BIDS) Specification |url=https://zenodo.org/records/13754678 |publisher=Zenodo |access-date=19 August 2025 |doi=10.5281/zenodo.10175845 |display-authors=et al |date=12 September 2024}}</ref>

| version = 1.2.0

| version_date = March 20192024-09-12

| base_standards =

| related_standards = [[JSON]], [[Tab-separated_values|TSV]], [[Neuroimaging_Informatics_Technology_Initiative|NIfTI]]

| related_standards =

| abbreviation = BIDS

| ___domain = [[Neuroimaging]]

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}}

The '''Brain Imaging Data Structure''' ('''BIDS''') is a standard for organizing, annotating, and describing data collected during [[neuroimaging]] experiments. It is based on a formalized file/folder and directory structure and metadata files (based on [[JSON]] basedand metadata files[[Tab-separated_values|TSV]]) with [[controlled vocabulary]].<ref>{{cite journal |last1=Gorgolewski |first1=Krzysztof J. |last2=Auer |first2=Tibor |last3=Calhoun | first3=Vince D. |last4=Craddock| first4=R. Cameron |last5=Das |first5=Samir |last6=Duff |first6=Eugene P. |last7=Flandin |first7=Guillaume |last8=Ghosh |first8=Satrajit S. |last9=Glatard |first9=Tristan |last10=Halchenko |first10=Yaroslav O. | last11=Handwerker |first11=Daniel A. | last12=Hanke |first12=Michael |last13=Keator |first13=David |last14=Li |first14=Xiangrui |last15=Michael |first15=Zachary |last16=Maumet |first16=Camille |last17=Nichols |first17=B. Nolan |last18=Nichols |first18=Thomas E. |last19=Pellman |first19=John |last20=Poline |first20=Jean-Baptiste |last21=Rokem |first21=Ariel |last22=Schaefer |first22=Gunnar |last23=Sochat |first23=Vanessa |last24=Triplett |first24=William |last25=Turner |first25=Jessica A. |last26=Varoquaux |first26=Gaël |last27=Poldrack |first27=Russell A. |journal=[[Scientific Data (journal)|Scientific Data]] |volume=3|pages=160044|doi=10.1038/sdata.2016.44 |title=The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments|author=Krzysztof J|display-authors=et al |pmid=27326542 |pmc=4978148|year=2016|bibcode=2016NatSD...360044G }}</ref>

This standard has been adopted by a multitude of labs around the world as well as databases such as [[OpenNeuro]], SchizConnect, Developing Human Connectome Project, and FCP-INDI, and is seeing uptake in an increasing number of studies.<ref>{{cite journal|last1=Poldrack, R|first1=Russell A. |last2=Congdon | first2=Eliza |last3=Triplett |first3=William |last4=Gorgolewski |first4=Krzysztof J. |last5=Karlsgodt |first5=Katherine H. |last6=Mumford |first6=Jeanette A., et|last7=Sabb al|first7=Fred W. |last8=Freimer |first8=Nelson B. |last9=London |first9=Edythe D. |last10=Cannon |first10=Tyrone D. |last11=Bilder |first11=Robert M. |journal=[[Scientific Data (journal)|Scientific Data]] |volume=3|pages=160110|doi=10.1038/sdata.2016.110 "|title=A phenome-wide examination of neural and cognitive function."|year=2016|pmid=27922632 Scientific|pmc=5139672 data|bibcode=2016NatSD...360110P 3 (2016):|s2cid=33368149 160110.}}</ref><ref>Bigdely-Shamlo,{{cite Nima,journal|journal=[[Frontiers Scottin Makeig,Neuroinformatics]] and Kay A|volume=7|pages=10|doi=10. Robbins3389/fninf.2016.00007 "|title=Preparing laboratoryLaboratory and realReal-worldWorld EEG dataData for largeLarge-scaleScale analysisAnalysis: aA containerizedContainerized approach."Approach|last1=Bigdely-Shamlo Frontiers|first1=Nima in|last2=Makeig neuroinformatics|first2=Scott 10|last3=Robbins (2016):|first3=Kay 7A. |year=2016|pmid=27014048|pmc=4782059|doi-access=free}}</ref><ref>Nichols,{{cite Thomasjournal|journal=[[Nature E.,Neuroscience]] et al|volume=20|pages=299–303|doi=10.1038/nn.4500 "|title=Best practices in data analysis and sharing in neuroimaging using MRI."|last1=Nichols Nature|first1=Thomas neuroscienceE. 20|last2=Das |first2=Samir |last3=Eickhoff |first3=Simon B |last4=Evans |first4=Alan C.3 (2017):|last5=Glatard 299|first5=Tristan |last6=Hanke |first6=Michael |last7=Kriegeskorte |first7=Nikolaus |last8=Milham |first8=Michael P. |last9=Poldrack |first9=Russell A. |last10=Poline |first10=Jean-Baptiste |last11=Proal |first11=Erika |last12=Thirion |first12=Bertrand |last13=Van Essen |first13=David C |last14=White |first14=Tonya |last15=Yeo |first15=B. T. Thomas |year=2017|issue=3|pmid=28230846|pmc=5685169}}</ref>

While originally specified for [[Magnetic resonance imaging|MRI]] data, BIDS has been extended to several other imaging modalities such as [[Magnetoencephalography|MEG]],<ref>{{cite journal |last1=Niso |first1=Guiomar |last2=Gorgolewski |first2=Krzysztof J. |last3=Bock |first3=Elizabeth |last4=Brooks |first4=Teon L. |last5=Flandin |first5=Guillaume |last6=Gramfort |first6=Alexandre |last7=Henson |first7=Richard N. |last8=Jas |first8=Mainak |last9=Litvak |first9=Vladimir |last10=T. Moreau |first10=Jeremy |last11=Oostenveld |first11=Robert |last12=Schoffelen |first12=Jan-Mathijs |last13=Tadel |first13=Francois |last14=Wexler |first14=Joseph |last15=Baillet |first15=Sylvain |title=MEG-BIDS, the brain imaging data structure extended to magnetoencephalography |journal=[[Scientific Data (journal)|Scientific Data]] |date=19 June 2018 |volume=5 |pages=180110 |doi=10.1038/sdata.2018.110|pmid=29917016 |pmc=6007085 |bibcode=2018NatSD...580110N }}</ref> [[Electroencephalography|EEG]],<ref>{{Cite journal|lastlast1=Pernet|firstfirst1=Cyril R.|last2=Appelhoff|first2=Stefan|last3=Gorgolewski|first3=Krzysztof J.|last4=Flandin|first4=Guillaume|last5=Phillips|first5=Christophe|last6=Delorme|first6=Arnaud|last7=Oostenveld|first7=Robert|date=December 2019|title=EEG-BIDS, an extension to the brain imaging data structure for electroencephalography|url=http://www.nature.com/articles/s41597-019-0104-8|journal=[[Scientific Data (journal)|Scientific Data]] |volume=6|issue=1|doi=10.1038/s41597-019-0104-8|pmid=31239435|issn=2052-4463|pmc=6592877|page=103|bibcode=2019NatSD...6..103P}}</ref> and [[Electrocorticography|intracranial EEG]].<ref>{{Cite journal|lastlast1=Holdgraf|firstfirst1=Christopher|last2=Appelhoff|first2=Stefan|last3=Bickel|first3=Stephan|last4=Bouchard|first4=Kristofer|last5=D’Ambrosio|first5=Sasha|last6=David|first6=Olivier|last7=Devinsky|first7=Orrin|last8=Dichter|first8=Benjamin|last9=Flinker|first9=Adeen|last10=Foster|first10= Brett L.|last11= Gorgolewski|first11=Krzysztof J.|last12=Groen|first12=Iris|last13=Groppe|first13=David|last14=Gunduz|first14=Aysegul|last15=Hamilton|first15=Liberty|last16=Honey|first16=Christopher J.|last17=Jas|first17=Mainak|last18=Knight|first18=Robert|last19=Lachaux|first19=Jean-Philippe|last20=Lau|first20=Jonathan C.|last21=Lee-Messer|first21=Christopher| last22=Lundstrom|first22=Brian N.|last23=Miller|first23=Kai J.|last24=Ojemann|first24=Jeffrey G.|last25=Oostenveld|first25=Robert|last26=Petridou|first26=Natalia|last27=Piantoni|first27=Gio|last28=Pigorini|first28=Andrea|last29=Pouratian|first29=Nader|last30=Ramsey|first30=Nick F.|last31=Stolk|first31=Arjen|last32=Swann|first32=Nicole C.|last33=Tadel|first33= François|last34=Voytek|first34=Bradley|last35=Wandell|first35=Brian A.|last36=Winawer|first36=Jonathan|last37=Whitaker|first37=Kirstie|last38=Zehl|first38=Lyuba|last39=Hermes|first39=Dora|date=December 2019|title=iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology|url=http://www.nature.com/articles/s41597-019-0105-7|journal=[[Scientific Data (journal)|Scientific Data]] |volume=6|issue=1|page=102|doi=10.1038/s41597-019-0105-7|pmid=31239438|pmc=6592874|bibcode=2019NatSD...6..102H|issn=2052-4463|doi-access=free}}</ref> (see also [[#BIDS Extension Proposals|BIDS Extension Proposals]]).

== History ==

The project is a community-driven effort. BIDS, originally OBIDS (Open Brain Imaging Data Structure), was initiated during an [[INCF]] sponsored data sharing working group meeting (January 2015) at [[Stanford University]]. It was subsequently spearheaded and maintained by [[Chris Gorgolewski]]. Since October 2019, the project is headed by a [https://bids.neuroimaging.io/governance.html#bids-steering-group Steering Group]<ref>{{Cite web|url=https://bids.neuroimaging.io/2019/12/31/meet-the-bids-steering-group.html|title = Meet the BIDS Steering Group|date = 31 December 2019}}</ref> and maintained by a separate team of maintainers, the [https://bids.neuroimaging.io/governance.html#bids-maintainers-group Maintainers Group], according to a [https://bids.neuroimaging.io/governance.html governance document] that was approved of by the BIDS community in a vote. BIDS has advanced under the direction and effort of contributors, the community of researchers that appreciate the value of standardizing neuroimaging data to facilitate sharing and analysis.

== BIDS Extension Proposals ==

BIDS can be extended in a backwards compatible way and is evolving over time. This is accomplished through BIDS Extension Proposals (BEPs), which are community-driven processes following [https://bids.neuroimaging.io/bep_guide.html agreed-upon guidelines]. A full list of finalized BEPs and BEPs in progress can be found on the [https://bids.neuroimaging.io/get_involved.html#extending-the-bids-specification BIDS website]

== References ==

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== External links ==

* [httphttps://bids.neuroimaging.io bids.neuroimaging.ioOfficial BIDS website]

* [https://github.com/bids-standard/bids-specification.readthedocs.io HTML version of the BIDS github.com/bids-standard/bids-specification]

* [https://github.com/bids-standard/bids-specification Source of the BIDS specification on GitHub]

[[Category:Data management]]