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BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods

View ORCID ProfileKrzysztof J. Gorgolewski, View ORCID ProfileFidel Alfaro-Almagro, Tibor Auer, View ORCID ProfilePierre Bellec, View ORCID ProfileMihai Capotă, View ORCID ProfileM. Mallar Chakravarty, Nathan W. Churchill, View ORCID ProfileR. Cameron Craddock, View ORCID ProfileGabriel A. Devenyi, View ORCID ProfileAnders Eklund, View ORCID ProfileOscar Esteban, View ORCID ProfileGuillaume Flandin, View ORCID ProfileSatrajit S. Ghosh, View ORCID ProfileJ. Swaroop Guntupalli, View ORCID ProfileMark Jenkinson, View ORCID ProfileAnisha Keshavan, View ORCID ProfileGregory Kiar, View ORCID ProfilePradeep Reddy Raamana, View ORCID ProfileDavid Raffelt, View ORCID ProfileChristopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, View ORCID ProfileStephen C. Strother, View ORCID ProfileGaël Varoquaux, View ORCID ProfileTal Yarkoni, Yida Wang, View ORCID ProfileRussell A. Poldrack
doi: https://doi.org/10.1101/079145
Krzysztof J. Gorgolewski
Department of Psychology, Stanford University, Stanford, CA, 94305
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  • ORCID record for Krzysztof J. Gorgolewski
Fidel Alfaro-Almagro
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University, UK.
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Tibor Auer
Department of Psychology, Royal Holloway University of London. Egham, UK
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Pierre Bellec
Centre de Recherche de l’Institut Universitaire Gériatrique de MontréalDepartment of computer science and operations research, Université de Montréal, CA
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Mihai Capotă
Parallel Computing Lab, Intel Corporation, Santa Clara, CA & Hillsboro, OR
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M. Mallar Chakravarty
Douglas Mental Health University Institute, McGill University, Montreal, CADepartment of Psychiatry McGill University, Montreal, CA
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  • ORCID record for M. Mallar Chakravarty
Nathan W. Churchill
Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael’s Hospital
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R. Cameron Craddock
Computational Neuroimaging Lab, Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NYCenter for the Developing Brain, Child Mind Institute, New York, NY
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Gabriel A. Devenyi
Douglas Mental Health University Institute, McGill University, Montreal, CADepartment of Psychiatry McGill University, Montreal, CA
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Anders Eklund
Department of Biomedical Engineering, Linköping University, Linköping, SwedenDepartment of Computer and Information Science, Linköping University, Linköping, SwedenCenter for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
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Oscar Esteban
Department of Psychology, Stanford University, Stanford, CA, 94305
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Guillaume Flandin
Wellcome Trust Centre for Neuroimaging, London, UK
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Satrajit S. Ghosh
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MADepartment of Otolaryngology, Harvard Medical School, Boston, MA
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J. Swaroop Guntupalli
Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, US
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  • ORCID record for J. Swaroop Guntupalli
Mark Jenkinson
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University, UK.
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  • ORCID record for Mark Jenkinson
Anisha Keshavan
UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA, US
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Gregory Kiar
Center for Imaging Science, Johns Hopkins University, Baltimore, MDDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
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Pradeep Reddy Raamana
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada.Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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David Raffelt
Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
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  • ORCID record for David Raffelt
Christopher J. Steele
Douglas Mental Health University Institute, McGill University, Montreal, CADepartment of Psychiatry McGill University, Montreal, CA
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Pierre-Olivier Quirion
Centre de Recherche de l’Institut Universitaire Gériatrique de Montréal
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Robert E. Smith
Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
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Stephen C. Strother
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada.Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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Gaël Varoquaux
Parietal team, INRIA Saclay Ile-de-France, Palaiseau, France
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Tal Yarkoni
Department of Psychology, University of Texas at Austin, Austin, TX
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Yida Wang
Parallel Computing Lab, Intel Corporation, Santa Clara, CA & Hillsboro, OR
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Russell A. Poldrack
Department of Psychology, Stanford University, Stanford, CA, 94305
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  • ORCID record for Russell A. Poldrack
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Abstract

In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the richness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 19 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.

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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 October 05, 2016.
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BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods
Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Tal Yarkoni, Yida Wang, Russell A. Poldrack
bioRxiv 079145; doi: https://doi.org/10.1101/079145
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BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods
Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Tal Yarkoni, Yida Wang, Russell A. Poldrack
bioRxiv 079145; doi: https://doi.org/10.1101/079145

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