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

Identifieur interne : 001117 ( Main/Exploration ); précédent : 001116; suivant : 001118

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

Auteurs : Krzysztof J. Gorgolewski [États-Unis] ; Fidel Alfaro-Almagro [Royaume-Uni] ; Tibor Auer [Royaume-Uni] ; Pierre Bellec [Canada] ; Mihai Capot [États-Unis] ; M. Mallar Chakravarty [Canada] ; Nathan W. Churchill [Canada] ; Alexander Li Cohen [États-Unis] ; R. Cameron Craddock [États-Unis] ; Gabriel A. Devenyi [Canada] ; Anders Eklund [Suède] ; Oscar Esteban [États-Unis] ; Guillaume Flandin [Royaume-Uni] ; Satrajit S. Ghosh [États-Unis] ; J. Swaroop Guntupalli [États-Unis] ; Mark Jenkinson [Royaume-Uni] ; Anisha Keshavan [États-Unis] ; Gregory Kiar [États-Unis] ; Franziskus Liem [Suisse] ; Pradeep Reddy Raamana [Canada] ; David Raffelt [Australie] ; Christopher J. Steele [Canada] ; Pierre-Olivier Quirion [Suède] ; Robert E. Smith [Australie] ; Stephen C. Strother [Canada] ; Gaël Varoquaux [France] ; Yida Wang [États-Unis] ; Tal Yarkoni [États-Unis] ; Russell A. Poldrack [États-Unis]

Source :

RBID : PMC:5363996

Descripteurs français

English descriptors

Abstract

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. 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 comprehensiveness 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 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.


Url:
DOI: 10.1371/journal.pcbi.1005209
PubMed: 28278228
PubMed Central: 5363996


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<wicri:regionArea>Center for Imaging Science, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea>
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<region type="state">Maryland</region>
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<addr-line>Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America</addr-line>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea>
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<region type="state">Maryland</region>
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<name sortKey="Liem, Franziskus" sort="Liem, Franziskus" uniqKey="Liem F" first="Franziskus" last="Liem">Franziskus Liem</name>
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<country xml:lang="fr">Suisse</country>
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<name sortKey="Raamana, Pradeep Reddy" sort="Raamana, Pradeep Reddy" uniqKey="Raamana P" first="Pradeep Reddy" last="Raamana">Pradeep Reddy Raamana</name>
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<country xml:lang="fr">Canada</country>
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<nlm:aff id="aff025">
<addr-line>Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Medical Biophysics, University of Toronto, Toronto, Ontario</wicri:regionArea>
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<name sortKey="Raffelt, David" sort="Raffelt, David" uniqKey="Raffelt D" first="David" last="Raffelt">David Raffelt</name>
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<addr-line>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia</addr-line>
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<country xml:lang="fr">Australie</country>
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<name sortKey="Steele, Christopher J" sort="Steele, Christopher J" uniqKey="Steele C" first="Christopher J." last="Steele">Christopher J. Steele</name>
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<addr-line>Douglas Mental Health University Institute, McGill University, Montreal, Canada</addr-line>
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<name sortKey="Quirion, Pierre Olivier" sort="Quirion, Pierre Olivier" uniqKey="Quirion P" first="Pierre-Olivier" last="Quirion">Pierre-Olivier Quirion</name>
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<name sortKey="Smith, Robert E" sort="Smith, Robert E" uniqKey="Smith R" first="Robert E." last="Smith">Robert E. Smith</name>
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<addr-line>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria</wicri:regionArea>
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<name sortKey="Strother, Stephen C" sort="Strother, Stephen C" uniqKey="Strother S" first="Stephen C." last="Strother">Stephen C. Strother</name>
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<addr-line>Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario</wicri:regionArea>
<wicri:noRegion>Ontario</wicri:noRegion>
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<nlm:aff id="aff025">
<addr-line>Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Medical Biophysics, University of Toronto, Toronto, Ontario</wicri:regionArea>
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<settlement type="city">Toronto</settlement>
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<name sortKey="Varoquaux, Gael" sort="Varoquaux, Gael" uniqKey="Varoquaux G" first="Gaël" last="Varoquaux">Gaël Varoquaux</name>
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<addr-line>Parietal team, INRIA Saclay Ile-de-France, Palaiseau, France</addr-line>
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<country xml:lang="fr">France</country>
<wicri:regionArea>Parietal team, INRIA Saclay Ile-de-France, Palaiseau</wicri:regionArea>
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<region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
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<name sortKey="Wang, Yida" sort="Wang, Yida" uniqKey="Wang Y" first="Yida" last="Wang">Yida Wang</name>
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<title xml:lang="en" level="a" type="main">BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods</title>
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<name sortKey="Alfaro Almagro, Fidel" sort="Alfaro Almagro, Fidel" uniqKey="Alfaro Almagro F" first="Fidel" last="Alfaro-Almagro">Fidel Alfaro-Almagro</name>
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</nlm:aff>
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</nlm:aff>
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<region type="state">Massachusetts</region>
</placeName>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<region type="state">État de New York</region>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for the Developing Brain, Child Mind Institute, New York, New York</wicri:regionArea>
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<region type="state">État de New York</region>
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<addr-line>Douglas Mental Health University Institute, McGill University, Montreal, Canada</addr-line>
</nlm:aff>
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</nlm:aff>
<country xml:lang="fr">Suède</country>
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<affiliation wicri:level="1">
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</nlm:aff>
<country xml:lang="fr">Suède</country>
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</nlm:aff>
<country xml:lang="fr">Suède</country>
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<nlm:aff id="aff001">
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Psychology, Stanford University, Stanford, California</wicri:regionArea>
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<nlm:aff id="aff016">
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</nlm:aff>
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<wicri:regionArea>Wellcome Trust Centre for Neuroimaging, London</wicri:regionArea>
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<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
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<author>
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<nlm:aff id="aff017">
<addr-line>McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America</addr-line>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts</wicri:regionArea>
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<region type="state">Massachusetts</region>
</placeName>
</affiliation>
<affiliation wicri:level="2">
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts</wicri:regionArea>
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<region type="state">Massachusetts</region>
</placeName>
</affiliation>
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<author>
<name sortKey="Guntupalli, J Swaroop" sort="Guntupalli, J Swaroop" uniqKey="Guntupalli J" first="J. Swaroop" last="Guntupalli">J. Swaroop Guntupalli</name>
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<nlm:aff id="aff019">
<addr-line>Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire</wicri:regionArea>
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<region type="state">New Hampshire</region>
</placeName>
</affiliation>
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<author>
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<nlm:aff id="aff002">
<addr-line>Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University, Oxford, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University, Oxford</wicri:regionArea>
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<nlm:aff id="aff020">
<addr-line>UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, California, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, California</wicri:regionArea>
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<region type="state">Californie</region>
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<author>
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<nlm:aff id="aff021">
<addr-line>Center for Imaging Science, Johns Hopkins University, Baltimore, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Imaging Science, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea>
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<region type="state">Maryland</region>
</placeName>
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<nlm:aff id="aff022">
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea>
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<region type="state">Maryland</region>
</placeName>
</affiliation>
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<author>
<name sortKey="Liem, Franziskus" sort="Liem, Franziskus" uniqKey="Liem F" first="Franziskus" last="Liem">Franziskus Liem</name>
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<nlm:aff id="aff023">
<addr-line>University Research Priority Program "Dynamics of Healthy Aging", University of Zurich, Zurich, Switzerland</addr-line>
</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>University Research Priority Program "Dynamics of Healthy Aging", University of Zurich, Zurich</wicri:regionArea>
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<name sortKey="Raamana, Pradeep Reddy" sort="Raamana, Pradeep Reddy" uniqKey="Raamana P" first="Pradeep Reddy" last="Raamana">Pradeep Reddy Raamana</name>
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<nlm:aff id="aff024">
<addr-line>Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario</wicri:regionArea>
<wicri:noRegion>Ontario</wicri:noRegion>
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<affiliation wicri:level="4">
<nlm:aff id="aff025">
<addr-line>Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Medical Biophysics, University of Toronto, Toronto, Ontario</wicri:regionArea>
<orgName type="university">Université de Toronto</orgName>
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<settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
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<nlm:aff id="aff026">
<addr-line>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria</wicri:regionArea>
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<addr-line>Douglas Mental Health University Institute, McGill University, Montreal, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Douglas Mental Health University Institute, McGill University, Montreal</wicri:regionArea>
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<affiliation wicri:level="3">
<nlm:aff id="aff008">
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</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Psychiatry McGill University, Montreal</wicri:regionArea>
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<addr-line>Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden</addr-line>
</nlm:aff>
<country xml:lang="fr">Suède</country>
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<nlm:aff id="aff026">
<addr-line>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria</wicri:regionArea>
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<nlm:aff id="aff025">
<addr-line>Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Medical Biophysics, University of Toronto, Toronto, Ontario</wicri:regionArea>
<orgName type="university">Université de Toronto</orgName>
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<settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Varoquaux, Gael" sort="Varoquaux, Gael" uniqKey="Varoquaux G" first="Gaël" last="Varoquaux">Gaël Varoquaux</name>
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<addr-line>Parietal team, INRIA Saclay Ile-de-France, Palaiseau, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Parietal team, INRIA Saclay Ile-de-France, Palaiseau</wicri:regionArea>
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<region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Palaiseau</settlement>
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</author>
<author>
<name sortKey="Wang, Yida" sort="Wang, Yida" uniqKey="Wang Y" first="Yida" last="Wang">Yida Wang</name>
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<addr-line>Parallel Computing Lab, Intel Corporation, Santa Clara, CA & Hillsboro, Oregon, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Parallel Computing Lab, Intel Corporation, Santa Clara, CA & Hillsboro, Oregon</wicri:regionArea>
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<region type="state">Oregon</region>
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<author>
<name sortKey="Yarkoni, Tal" sort="Yarkoni, Tal" uniqKey="Yarkoni T" first="Tal" last="Yarkoni">Tal Yarkoni</name>
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<addr-line>Department of Psychology, University of Texas at Austin, Austin, Texas, United States of America</addr-line>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Psychology, University of Texas at Austin, Austin, Texas</wicri:regionArea>
<placeName>
<region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
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<orgName type="university">Université du Texas à Austin</orgName>
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<author>
<name sortKey="Poldrack, Russell A" sort="Poldrack, Russell A" uniqKey="Poldrack R" first="Russell A." last="Poldrack">Russell A. Poldrack</name>
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<addr-line>Department of Psychology, Stanford University, Stanford, California, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Psychology, Stanford University, Stanford, California</wicri:regionArea>
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<series>
<title level="j">PLoS Computational Biology</title>
<idno type="ISSN">1553-734X</idno>
<idno type="eISSN">1553-7358</idno>
<imprint>
<date when="2017">2017</date>
</imprint>
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<profileDesc>
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<keywords scheme="KwdEn" xml:lang="en">
<term>Algorithms</term>
<term>Brain (anatomy & histology)</term>
<term>Humans</term>
<term>Image Interpretation, Computer-Assisted (methods)</term>
<term>Magnetic Resonance Imaging (methods)</term>
<term>Neuroimaging (methods)</term>
<term>Radiology Information Systems (organization & administration)</term>
<term>Software</term>
<term>User-Computer Interface</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Algorithmes</term>
<term>Encéphale (anatomie et histologie)</term>
<term>Humains</term>
<term>Imagerie par résonance magnétique ()</term>
<term>Interface utilisateur</term>
<term>Interprétation d'image assistée par ordinateur ()</term>
<term>Logiciel</term>
<term>Neuroimagerie ()</term>
<term>Systèmes d'information de radiologie (organisation et administration)</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr">
<term>Encéphale</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en">
<term>Brain</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en">
<term>Image Interpretation, Computer-Assisted</term>
<term>Magnetic Resonance Imaging</term>
<term>Neuroimaging</term>
</keywords>
<keywords scheme="MESH" qualifier="organisation et administration" xml:lang="fr">
<term>Systèmes d'information de radiologie</term>
</keywords>
<keywords scheme="MESH" qualifier="organization & administration" xml:lang="en">
<term>Radiology Information Systems</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Algorithms</term>
<term>Humans</term>
<term>Software</term>
<term>User-Computer Interface</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Algorithmes</term>
<term>Humains</term>
<term>Imagerie par résonance magnétique</term>
<term>Interface utilisateur</term>
<term>Interprétation d'image assistée par ordinateur</term>
<term>Logiciel</term>
<term>Neuroimagerie</term>
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</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. 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 comprehensiveness 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 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.</p>
</div>
</front>
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