title: BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.
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.
authors.affiliation: Department of Psychology, Stanford University, Stanford, California, United States of America.
authors.forename: Krzysztof J
authors.identifier: 0000-0003-3321-7583
authors.initials: KJ
authors.lastname: Gorgolewski
authors.affiliation: Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University, Oxford, United Kingdom.
authors.forename: Fidel
authors.identifier: 0000-0002-9133-5951
authors.initials: F
authors.lastname: Alfaro-Almagro
authors.affiliation: Department of Psychology, Royal Holloway University of London, Egham, United Kingdom.
authors.forename: Tibor
authors.initials: T
authors.lastname: Auer
authors.affiliation: Centre de Recherche de l'Institut Universitaire Gériatrique de Montréal, Montreal, Canada.|Department of computer science and operations research, Université de Montréal, Montreal, Canada.
authors.forename: Pierre
authors.identifier: 0000-0002-9111-0699
authors.initials: P
authors.lastname: Bellec
authors.affiliation: Parallel Computing Lab, Intel Corporation, Santa Clara, CA & Hillsboro, Oregon, United States of America.
authors.forename: Mihai
authors.identifier: 0000-0002-7323-2393
authors.initials: M
authors.lastname: Capotă
authors.affiliation: Douglas Mental Health University Institute, McGill University, Montreal, Canada.|Department of Psychiatry McGill University, Montreal, Canada.
authors.forename: M Mallar
authors.identifier: 0000-0002-0759-5508
authors.initials: MM
authors.lastname: Chakravarty
authors.affiliation: Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Ontario, Canada.
authors.forename: Nathan W
authors.initials: NW
authors.lastname: Churchill
authors.affiliation: Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Alexander Li
authors.identifier: 0000-0001-6557-5866
authors.initials: AL
authors.lastname: Cohen
authors.affiliation: Computational Neuroimaging Lab, Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York, United States of America.|Center for the Developing Brain, Child Mind Institute, New York, New York, United States of America.
authors.forename: R Cameron
authors.identifier: 0000-0002-4950-1303
authors.initials: RC
authors.lastname: Craddock
authors.affiliation: Douglas Mental Health University Institute, McGill University, Montreal, Canada.|Department of Psychiatry McGill University, Montreal, Canada.
authors.forename: Gabriel A
authors.identifier: 0000-0002-7766-1187
authors.initials: GA
authors.lastname: Devenyi
authors.affiliation: Department of Biomedical Engineering, Linköping University, Linköping, Sweden.|Department of Computer and Information Science, Linköping University, Linköping, Sweden.|Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden.
authors.forename: Anders
authors.identifier: 0000-0001-7061-7995
authors.initials: A
authors.lastname: Eklund
authors.affiliation: Department of Psychology, Stanford University, Stanford, California, United States of America.
authors.forename: Oscar
authors.identifier: 0000-0001-8435-6191
authors.initials: O
authors.lastname: Esteban
authors.affiliation: Wellcome Trust Centre for Neuroimaging, London, United Kingdom.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Flandin
authors.affiliation: McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Satrajit S
authors.identifier: 0000-0002-5312-6729
authors.initials: SS
authors.lastname: Ghosh
authors.affiliation: Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire, United States of America.
authors.forename: J Swaroop
authors.initials: JS
authors.lastname: Guntupalli
authors.affiliation: Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University, Oxford, United Kingdom.
authors.forename: Mark
authors.identifier: 0000-0001-6043-0166
authors.initials: M
authors.lastname: Jenkinson
authors.affiliation: UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, California, United States of America.
authors.forename: Anisha
authors.identifier: 0000-0003-3554-043X
authors.initials: A
authors.lastname: Keshavan
authors.affiliation: Center for Imaging Science, Johns Hopkins University, Baltimore, Maryland, United States of America.|Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Gregory
authors.identifier: 0000-0001-8915-496X
authors.initials: G
authors.lastname: Kiar
authors.affiliation: University Research Priority Program "Dynamics of Healthy Aging", University of Zurich, Zurich, Switzerland.
authors.forename: Franziskus
authors.identifier: 0000-0003-0646-4810
authors.initials: F
authors.lastname: Liem
authors.affiliation: Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Pradeep Reddy
authors.identifier: 0000-0003-4662-0558
authors.initials: PR
authors.lastname: Raamana
authors.affiliation: Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Raffelt
authors.affiliation: Douglas Mental Health University Institute, McGill University, Montreal, Canada.|Department of Psychiatry McGill University, Montreal, Canada.
authors.forename: Christopher J
authors.identifier: 0000-0003-1656-7928
authors.initials: CJ
authors.lastname: Steele
authors.affiliation: Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden.
authors.forename: Pierre-Olivier
authors.initials: PO
authors.lastname: Quirion
authors.affiliation: Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Smith
authors.affiliation: Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Strother
authors.affiliation: Parietal team, INRIA Saclay Ile-de-France, Palaiseau, France.
authors.forename: Gaël
authors.initials: G
authors.lastname: Varoquaux
authors.affiliation: Parallel Computing Lab, Intel Corporation, Santa Clara, CA & Hillsboro, Oregon, United States of America.
authors.forename: Yida
authors.identifier: 0000-0001-8165-840X
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Psychology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Tal
authors.identifier: 0000-0002-6558-5113
authors.initials: T
authors.lastname: Yarkoni
authors.affiliation: Department of Psychology, Stanford University, Stanford, California, United States of America.
authors.forename: Russell A
authors.identifier: 0000-0001-6755-0259
authors.initials: RA
authors.lastname: Poldrack
mesh_terms: D000465:Algorithms; D001921:Brain / Q000033:anatomy & histology*; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods; D059906:Neuroimaging / Q000379:methods*; D011873:Radiology Information Systems / Q000458:organization & administration*; D012984:Software; D014584:User-Computer Interface