BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.
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 applicatio...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
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Public Library of Science
2017
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| _version_ | 1797073436651028480 |
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| author | Gorgolewski, K Alfaro-Almagro, F Auer, T Bellec, P Capotă, M Chakravarty, M Churchill, N Cohen, A Craddock, R Devenyi, G Eklund, A Esteban, O Flandin, G Ghosh, S Guntupalli, J Jenkinson, M Keshavan, A Kiar, G Liem, F Raamana, P Raffelt, D Steele, C Quirion, P Smith, R Strother, S Varoquaux, G Wang, Y Yarkoni, T Poldrack, R |
| author_facet | Gorgolewski, K Alfaro-Almagro, F Auer, T Bellec, P Capotă, M Chakravarty, M Churchill, N Cohen, A Craddock, R Devenyi, G Eklund, A Esteban, O Flandin, G Ghosh, S Guntupalli, J Jenkinson, M Keshavan, A Kiar, G Liem, F Raamana, P Raffelt, D Steele, C Quirion, P Smith, R Strother, S Varoquaux, G Wang, Y Yarkoni, T Poldrack, R |
| author_sort | Gorgolewski, K |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T23:22:07Z |
| format | Journal article |
| id | oxford-uuid:69172eb0-ccbf-4299-a66b-39a2e1da4266 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T23:22:07Z |
| publishDate | 2017 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | oxford-uuid:69172eb0-ccbf-4299-a66b-39a2e1da42662022-03-26T18:49:08ZBIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:69172eb0-ccbf-4299-a66b-39a2e1da4266EnglishSymplectic Elements at OxfordPublic Library of Science2017Gorgolewski, KAlfaro-Almagro, FAuer, TBellec, PCapotă, MChakravarty, MChurchill, NCohen, ACraddock, RDevenyi, GEklund, AEsteban, OFlandin, GGhosh, SGuntupalli, JJenkinson, MKeshavan, AKiar, GLiem, FRaamana, PRaffelt, DSteele, CQuirion, PSmith, RStrother, SVaroquaux, GWang, YYarkoni, TPoldrack, RThe 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. |
| spellingShingle | Gorgolewski, K Alfaro-Almagro, F Auer, T Bellec, P Capotă, M Chakravarty, M Churchill, N Cohen, A Craddock, R Devenyi, G Eklund, A Esteban, O Flandin, G Ghosh, S Guntupalli, J Jenkinson, M Keshavan, A Kiar, G Liem, F Raamana, P Raffelt, D Steele, C Quirion, P Smith, R Strother, S Varoquaux, G Wang, Y Yarkoni, T Poldrack, R BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. |
| title | BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. |
| title_full | BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. |
| title_fullStr | BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. |
| title_full_unstemmed | BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. |
| title_short | BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. |
| title_sort | bids apps improving ease of use accessibility and reproducibility of neuroimaging data analysis methods |
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