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The Brain Imaging Data Structure: a standard for organizing and describing outputs of neuroimaging experiments

View ORCID ProfileKrzysztof J. Gorgolewski, Tibor Auer, Vince D. Calhoun, R. Cameron Craddock, Samir Das, Eugene P. Duff, Guillaume Flandin, Satrajit S. Ghosh, Tristan Glatard, Yaroslav O. Halchenko, Daniel A. Handwerker, Michael Hanke, David Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B. Nolan Nichols, Thomas E. Nichols, Jean-Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, Jessica A. Turner, Gaël Varoquaux, Russell A. Poldrack
doi: https://doi.org/10.1101/034561
Krzysztof J. Gorgolewski
1Department of Psychology, Stanford University, Stanford, CA, USA
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  • ORCID record for Krzysztof J. Gorgolewski
Tibor Auer
17MRC Cognition and Brain Sciences Unit, Cambridge, UK
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Vince D. Calhoun
14The Mind Research Network, Albuquerque, NM, USA
15Department of Electrical and Computer Engineering, The University of New Mexico, Albuquerque, NM, USA
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R. Cameron Craddock
23Computational Neuroimaging Lab, Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
24Center for the Developing Brain, Child Mind Institute, New York, NY, USA
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Samir Das
28McGill Centre for Integrative Neuroscience, Ludmer Centre, Montreal Neurological Institute, Montreal, Quebec, Canada
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Eugene P. Duff
25FMRIB Centre, University of Oxford, Oxford, UK
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Guillaume Flandin
22Wellcome Trust Centre for Neuroimaging, University College London, UK
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Satrajit S. Ghosh
4McGovern Institute for Brain Research, MIT, Cambridge, USA
5Department of Otology and Laryngology, Harvard Medical School, Boston, USA
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Tristan Glatard
28McGill Centre for Integrative Neuroscience, Ludmer Centre, Montreal Neurological Institute, Montreal, Quebec, Canada
29Université de Lyon, CREATIS; CNRS UMR5220; Inserm U1044; INSA-Lyon ; Université Claude Bernard Lyon 1, France.
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Yaroslav O. Halchenko
8Department of Psychological and Brain Sciences, Dartmouth College, Hanover NH, USA
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Daniel A. Handwerker
13Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
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Michael Hanke
9Department of Psychology II, Otto-von-Guericke-University, Magdeburg, Germany
10Center for Behavioral Brain Sciences, Magdeburg, Germany
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David Keator
11Department of Psychiatry and Human Behavior, University of California, Irvine, USA
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Xiangrui Li
20Center for Cognitive and Behavioral Brain Imaging, The Ohio State University, Columbus OH 43210, USA
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Zachary Michael
16Squishymedia, Portland, OR, USA
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Camille Maumet
19WMG, University of Warwick, Coventry, UK
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B. Nolan Nichols
6Center for Health Sciences, SRI International, Menlo Park, CA, USA
7Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
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Thomas E. Nichols
12Department of Statistics, University of Warwick, Coventry, UK
19WMG, University of Warwick, Coventry, UK
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Jean-Baptiste Poline
27Henry Wheeler Jr. Brain Imaging Center, Helen Wills Neuroscience Institute, University of California Berkeley, CA, USA
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Ariel Rokem
2The University of Washington eScience Institute, Seattle, WA, USA
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Gunnar Schaefer
1Department of Psychology, Stanford University, Stanford, CA, USA
21Flywheel Exchange, LLC, Minneapolis, MN, USA
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Vanessa Sochat
3Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
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Jessica A. Turner
14The Mind Research Network, Albuquerque, NM, USA
18Department of Psychology & the Neuroscience Institute, Georgia State University, Atlanta, GA USA
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Gaël Varoquaux
26Parietal team, INRIA Saclay, Palaiseau, FR
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Russell A. Poldrack
1Department of Psychology, Stanford University, Stanford, CA, USA
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Abstract

The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible, and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard format and comprehensive protocol for organizing and describing MRI datasets. The BIDS protocol uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 05, 2016.
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The Brain Imaging Data Structure: a standard for organizing and describing outputs of neuroimaging experiments
Krzysztof J. Gorgolewski, Tibor Auer, Vince D. Calhoun, R. Cameron Craddock, Samir Das, Eugene P. Duff, Guillaume Flandin, Satrajit S. Ghosh, Tristan Glatard, Yaroslav O. Halchenko, Daniel A. Handwerker, Michael Hanke, David Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B. Nolan Nichols, Thomas E. Nichols, Jean-Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, Jessica A. Turner, Gaël Varoquaux, Russell A. Poldrack
bioRxiv 034561; doi: https://doi.org/10.1101/034561
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The Brain Imaging Data Structure: a standard for organizing and describing outputs of neuroimaging experiments
Krzysztof J. Gorgolewski, Tibor Auer, Vince D. Calhoun, R. Cameron Craddock, Samir Das, Eugene P. Duff, Guillaume Flandin, Satrajit S. Ghosh, Tristan Glatard, Yaroslav O. Halchenko, Daniel A. Handwerker, Michael Hanke, David Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B. Nolan Nichols, Thomas E. Nichols, Jean-Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, Jessica A. Turner, Gaël Varoquaux, Russell A. Poldrack
bioRxiv 034561; doi: https://doi.org/10.1101/034561

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