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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, Alexander Li Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban (+18 others)
2017 PLoS Computational Biology  
Data Structure (BIDS).  ...  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.  ...  Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capotă M, Chakravarty MM, et al. (2017) BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.  ... 
doi:10.1371/journal.pcbi.1005209 pmid:28278228 pmcid:PMC5363996 fatcat:w3lyzbawerco5k3un4ynilos4u

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

Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capota, M. Mallar Chakravarty, Nathan W. Churchill, Alexander Li Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban (+17 others)
2016 biorxiv/medrxiv   pre-print
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.  ...  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.  ...  Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capotă M, Chakravarty MM, et al. (2017) BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.  ... 
doi:10.1101/079145 fatcat:gcucphi25za2fpjslevavjaz24

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, Alexander Li Cohen, R Cameron Craddock, Gabriel A Devenyi, Anders Eklund, Oscar Esteban (+17 others)
2017
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS Computational Biology, 13(3):e1005209.  ...  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. A (2017).  ...  Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capotă M, Chakravarty MM, et al. (2017) BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.  ... 
doi:10.5167/uzh-138318 fatcat:orw533ccsncjjpwwzhs2wtsotq

(OHBM2017-Poster) BIDS Apps: Improving ease of use and reproducibility of neuroimaging data analysis methods

Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibo Auer, Pierre Bellec, Mihai Capotă, Mallar Chakravarty, Nathan W. Churchill, Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin (+15 others)
2017 Zenodo  
This is the BIDS-Apps poster that was presented at OHBM 2017.  ...  "BIDS Apps: Improving Ease of Use, Accessibility, and Reproducibility of Neuroimaging Data Analysis Methods." PLoS Computational Biology 13 (3).  ...  BIDS Apps: Improving ease of use and reproducibility of neuroimaging data analysis methods Methods BIDS Apps [1] is a framework for creating portable, easy to install neuroimaging data processing workflows  ... 
doi:10.5281/zenodo.6417362 fatcat:3o5nnyjlrzhtnftcz7vhhnd2ya

FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

Tinashe M. Tapera, Matthew Cieslak, Max Bertolero, Azeez Adebimpe, Geoffrey K. Aguirre, Ellyn R. Butler, Philip A. Cook, Diego Davila, Mark A. Elliott, Sophia Linguiti, Kristin Murtha, William Tackett (+2 others)
2021 Frontiers in Neuroinformatics  
The Brain Imaging Data Structure (BIDS) is the de facto standard for neuroimaging data, but curating neuroimaging data into BIDS can be a challenging and time-consuming task.  ...  The recent and growing focus on reproducibility in neuroimaging studies has led many major academic centers to use cloud-based imaging databases for storing, analyzing, and sharing complex imaging data  ...  Materials and Methods The FlywheelTools toolkit allows users to follow a reproducible workflow for BIDS curation and auditing of their data.  ... 
doi:10.3389/fninf.2021.678403 pmid:34239433 pmcid:PMC8258420 fatcat:bvrdtxwn2ndk5ipico3p3qwgua

Computational and informatics advances for reproducible data analysis in neuroimaging [article]

Russell A. Poldrack, Krzysztof J. Gorgolewski, Gael Varoquaux
2018 arXiv   pre-print
We outline how the open-source Python language has provided the basis for a data science platform that enables reproducible data analysis and visualization.  ...  We discuss the range of open data sharing resources that have been developed for neuroimaging data, and the role of data standards (particularly the Brain Imaging Data Structure) in enabling the automated  ...  Acknowledgments: The work described here was supported by National Institutes of Health (R24MH114705 and R24MH117179), National Science Foundation (IIS-1760950), and the Laura and John Arnold Foundation  ... 
arXiv:1809.10024v1 fatcat:pfosfxzhfrbctb5363p7plxppy

Lessons learned: A neuroimaging research center's transition to open and reproducible science

Keith A. Bush, Maegan L. Calvert, Clinton D. Kilts
2022 Frontiers in Big Data  
We group these best practices under four categories: experiment pre-registration, FAIR data principles, reproducible neuroimaging analyses, and open science.  ...  In response to these trends, neuroimaging scientists have developed principles, practices, and tools to both manage this complexity as well as to enhance the rigor and reproducibility of neuroimaging science  ...  Publisher's note All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and  ... 
doi:10.3389/fdata.2022.988084 pmid:36105538 pmcid:PMC9464934 fatcat:xhlwdjeg7rayvcc6wfcda5tszm

Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies

Alexandre Routier, Ninon Burgos, Mauricio Díaz, Michael Bacci, Simona Bottani, Omar El-Rifai, Sabrina Fontanella, Pietro Gori, Jérémy Guillon, Alexis Guyot, Ravi Hassanaly, Thomas Jacquemont (+12 others)
2021 Frontiers in Neuroinformatics  
Clinica aims for researchers to (i) spend less time on data management and processing, (ii) perform reproducible evaluations of their methods, and (iii) easily share data and results within their institution  ...  The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI, and PET data), as well as tools for statistics  ...  manuscript, and manuscript editing.  ... 
doi:10.3389/fninf.2021.689675 pmid:34483871 pmcid:PMC8415107 fatcat:dxf57rljvjhepp6y2ogbrxltru

Clinica: an open source software platform for reproducible clinical neuroscience studies [article]

Ninon Burgos
2021 arXiv   pre-print
Clinica aims for researchers to i) spend less time on data management and processing, ii) perform reproducible evaluations of their methods, and iii) easily share data and results within their institution  ...  The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI and PET data), as well as tools for statistics  ...  Agence Nationale de la Recherche-10-IA Institut Hospitalo-Universitaire-6), ANR-11-IDEX-004 (Agence Nationale de la Recherche-11-Initiative d'Excellence-004, project LearnPETMR number SU-16-R-EMR-16) and  ... 
arXiv:2107.10256v1 fatcat:2syru7jlm5dt7o2koatmj6mqyi

Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping

Sebastien Tourbier, Joan Rue-Queralt, Katharina Glomb, Yasser Aleman-Gomez, Emeline Mullier, Alessandra Griffa, Mikkel Schöttner, Jonathan Wirsich, M. Anıl Tuncel, Jakub Jancovic, Meritxell Bach Cuadra, Patric Hagmann
2022 Journal of Open Source Software  
BIDS App, and the control of the output quality.  ...  To improve its accessibility, CMP3 comes with a graphical user interface, which supports the user in all the steps involved in the configuration of the pipelines, the configuration and execution of the  ...  All the contributors listed in the project's Zenodo and GitHub repository have contributed code and intellectual labor to further improve CMP3.  ... 
doi:10.21105/joss.04248 fatcat:tglw3fekq5ba5mkdgoq5jj6tuq

Adolescent Brain Cognitive Development (ABCD) Community MRI Collection and Utilities [article]

Eric Feczko, Greg Conan, Scott Marek, Brenden Tervo-Clemens, Michaela Cordova, Olivia Doyle, Eric Earl, Anders Perrone, Darrick Sturgeon, Rachel Klein, Gareth Harman, Dakota Kilamovich (+28 others)
2021 bioRxiv   pre-print
Section II highlights ABCC utilities that help researchers access, share, and analyze ABCD data, while section III provides two exemplar reproducibility analyses using ABCC utilities.  ...  We hope that adoption of the ABCC's data-safe, open-science framework will boost access and reproducibility, thus facilitating progress in child and adolescent mental health research.  ...  Data used in the preparation of this article were obtained from the Adolescent Brain Cognitive Development (ABCD) Study (https://abcdstudy.org), held in the NIMH Data Archive (NDA).  ... 
doi:10.1101/2021.07.09.451638 fatcat:5n5kcaa3mberbo4tybjeyz3lz4

The OpenNeuro resource for sharing of neuroscience data

Christopher J Markiewicz, Krzysztof J Gorgolewski, Franklin Feingold, Ross Blair, Yaroslav O Halchenko, Eric Miller, Nell Hardcastle, Joe Wexler, Oscar Esteban, Mathias Goncavles, Anita Jwa, Russell Poldrack
2021 eLife  
We highlight the importance of the Brain Imaging Data Structure (BIDS) standard for enabling effective curation, sharing, and reuse of data.  ...  The sharing of research data is essential to ensure reproducibility and maximize the impact of public investments in scientific research.  ...  BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methodshttps://doi.org/10.1371/journal.pcbi.1005209 PLOS Computational Biology 13 :e1005209.  ... 
doi:10.7554/elife.71774 pmid:34658334 pmcid:PMC8550750 fatcat:76jn4oic2vhavkqp67yc462ddy

Porcupine: a visual pipeline tool for neuroimaging analysis [article]

Tim van Mourik, Lukas Snoek, Tomas Knapen, David Norris
2017 biorxiv/medrxiv   pre-print
The field of neuroimaging is rapidly adopting a more reproducible approach to data acquisition and analysis.  ...  This may also be a useful tool in the education of novice neuroimaging students, considerably cutting their learning phase.  ...  Acknowledgments We would like to thank the organisation of BrainHack Global and BrainHack Amsterdam, specifically Pierre-Louis Bazin, for organising the platform that kickstarted Porcupine in its current  ... 
doi:10.1101/187344 fatcat:cdconij46beafeyqfqwvk2qu4e

Five Best Practices for fMRI research

Colleen Mills-Finnerty
2021 Journal for Reproducibility in Neuroscience  
Acknowledgements: I would like to thank Gary Glover, PhD for his input on fMRI best practices, and Halee Staggs, BS for assistance editing the commentary.  ...  BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS Computational Biology , 13 (3), e1005209.  ...  Proposals that predefine analysis plans and data and code sharing practices should be given higher appraisals for rigor, reproducibility, and data quality.  ... 
doi:10.31885/jrn.2.2021.1517 fatcat:3w4zsy4mgfcxxbcyyqurwbhcla

OpenNeuro: An open resource for sharing of neuroimaging data [article]

Christopher J Markiewicz, Krzysztof Jacek Gorgolewski, Franklin Feingold, Ross Blair, Yaroslav O Halchenko, Eric Miller, Nell Hardcastle, Joe Wexler, Oscar Esteban, Mathias Goncalves, Anita S Jwa, Russell Poldrack
2021 bioRxiv   pre-print
We highlight the importance of the Brain Imaging Data Structure (BIDS) standard for enabling effective curation, sharing, and reuse of data.  ...  The sharing of research data is essential to ensure reproducibility and maximize the impact of public investments in scientific research.  ...  Thanks to Franco Pestili for providing usage data on Brainlife.io, and Armin Thomas for helpful comments on an earlier draft.  ... 
doi:10.1101/2021.06.28.450168 fatcat:oeaxuspnubdydmj5fyfgych7dy
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