Brain Imaging Data Structure: Difference between revisions

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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 structure and [[JSON]] based metadata files with [[controlled vocabulary]].<ref>{{cite journal |last1=KrzysztofGorgolewski |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|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|display-authors=et al |pmid=27326542 |pmc=4978148|year=2016}}</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 |first1=Russell A. |last2=Congdon | first2=Eliza |last3=Triplett |first3=first24=William |last4=Gorgolewski |first4=Krzysztof J. |last5=Karlsgodt |first5=Katherine H. |last6=Mumford |first6=Jeanette A. |last7=Sabb |first7=Fred W. |last8=Freimer |fist8=Nelson B. |last9=London |first9=Edythe D. |last10=Cannon |first10=Tyrone D. |last11=Bilder |first11=Robert M. |journal=Scientific Data|volume=3|pages=160110|doi=10.1038/sdata.2016.110 |title=A phenome-wide examination of neural and cognitive function|author=Poldrack, R. A.|display-authors=et al|year=2016}}</ref><ref>{{cite journal|journal=Frontiers in neuroinformatics|volume=7|pages=10|doi=10.3389/fninf.2016.00007 |title=Preparing Laboratory and Real-World EEG Data for Large-Scale Analysis: A Containerized Approach|authorlast1=Bigdely-Shamlo, |first1=Nima |display-authorslast2=etMakeig |first2=Scott |last3=Robbins |first3=Kay A. al|year=2016}}</ref><ref>{{cite journal|journal=Nature Neuroscience|volume=20|pages=299|doi=10.1038/nn.4500 |title=Best practices in data analysis and sharing in neuroimaging using MRI.|authorlast1=Nichols, |first1=Thomas E. |displaylast2=Das |first2=Samir |last3=Eickhoff |first3=Simon B |last4=Evans |first4=Alan C. |last5=Glatard |first5=Tristan |last6=Hanke |first6=Michael |last7=Kriegeskorte |first7=Nikolaus |last8=Milham |first8=Michael P. |last9=Poldrack |first9=Russell A. |last10=Poline |first10=Jean-authorsBaptiste |last11=etProal |first11=Erika |last12=Thirion |first12=Bertrand |last13=Van Essen |first13=David C |last14=White |first14=Tonya |last15=Yeo |first15=B. T. Thomas al|year=2017}}</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 |date=19 June 2018 |volume=5 |pages=180110 |doi=10.1038/sdata.2018.110|pmid=29917016 |pmc=6007085 }}</ref> [[Electroencephalography|EEG]],<ref>{{Cite journal|last=Pernet|first=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|journal=Scientific Data|volume=6|issue=1|doi=10.1038/s41597-019-0104-8|pmid=31239435|issn=2052-4463|pmc=6592877|page=103}}</ref> and [[Electrocorticography|intracranial EEG]].<ref>{{Cite journal|last=Holdgraf|first=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|date=December 2019|title=iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology|journal=Scientific Data|volume=6|issue=1|doi=10.1038/s41597-019-0105-7|issn=2052-4463|doi-access=free}}</ref>