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Zhao C, Jarecka D, Covitz S, Chen Y, Eickhoff SB, Fair DA, Franco AR, Halchenko YO, Hendrickson TJ, Hoffstaedter F, Houghton A, Kiar G, Macdonald A, Mehta K, Milham MP, Salo T, Hanke M, Ghosh SS, Cieslak M, Satterthwaite TD. A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps. bioRxiv 2023:2023.08.16.552472. [PMID: 37645999 PMCID: PMC10461987 DOI: 10.1101/2023.08.16.552472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Neuroimaging research faces a crisis of reproducibility. With massive sample sizes and greater data complexity, this problem becomes more acute. Software that operates on imaging data defined using the Brain Imaging Data Structure (BIDS) - BIDS Apps - have provided a substantial advance. However, even using BIDS Apps, a full audit trail of data processing is a necessary prerequisite for fully reproducible research. Obtaining a faithful record of the audit trail is challenging - especially for large datasets. Recently, the FAIRly big framework was introduced as a way to facilitate reproducible processing of large-scale data by leveraging DataLad - a version control system for data management. However, the current implementation of this framework was more of a proof of concept, and could not be immediately reused by other investigators for different use cases. Here we introduce the BIDS App Bootstrap (BABS), a user-friendly and generalizable Python package for reproducible image processing at scale. BABS facilitates the reproducible application of BIDS Apps to large-scale datasets. Leveraging DataLad and the FAIRly big framework, BABS tracks the full audit trail of data processing in a scalable way by automatically preparing all scripts necessary for data processing and version tracking on high performance computing (HPC) systems. Currently, BABS supports jobs submissions and audits on Sun Grid Engine (SGE) and Slurm HPCs with a parsimonious set of programs. To demonstrate its scalability, we applied BABS to data from the Healthy Brain Network (HBN; n=2,565). Taken together, BABS allows reproducible and scalable image processing and is broadly extensible via an open-source development model.
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Affiliation(s)
- Chenying Zhao
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dorota Jarecka
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yibei Chen
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon B. Eickhoff
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Damien A. Fair
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
- Institute of Child Development, College of Education and Human Development, University of Minnesota, Minneapolis, MN, USA
- Department of Pediatrics, University of Minnesota Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Alexandre R. Franco
- Child Mind Institute, New York, NY, USA
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Timothy J. Hendrickson
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Felix Hoffstaedter
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | | | - Austin Macdonald
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Kahini Mehta
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P. Milham
- Child Mind Institute, New York, NY, USA
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - Taylor Salo
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Hanke
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Satrajit S. Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA, USA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D. Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA, USA
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3
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Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D’Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol 2023; 21:e3002133. [PMID: 37390046 PMCID: PMC10313015 DOI: 10.1371/journal.pbio.3002133] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023] Open
Abstract
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
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Affiliation(s)
- Michael Hawrylycz
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Maryann E. Martone
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
- San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America
| | - Giorgio A. Ascoli
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, United States of America
| | - Jan G. Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hong-Wei Dong
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Satrajit S. Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David R. Haynor
- Department of Radiology, University of Washington, Seattle, Washington, United States of America
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Yufeng Liu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Partha P. Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Eran Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hanchuan Peng
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Patrick L. Ray
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Raymond Sanchez
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Aviv Regev
- Genentech, South San Francisco, California, United States of America
| | - Alex Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Shawn Zheng Kai Tan
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carol L. Thompson
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Timothy Tickle
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hagen Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, United States of America
| | - Merina Varghese
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brock Wester
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Brian Aevermann
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - David Allemang
- Kitware Inc., Albany, New York, United States of America
| | - Seth Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas L. Athey
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Cody Baker
- CatalystNeuro, Benicia, California, United States of America
| | - Katherine S. Baker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Pamela M. Baker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Anita Bandrowski
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
| | - Samik Banerjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Prajal Bishwakarma
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Ambrose Carr
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Min Chen
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Roni Choudhury
- Kitware Inc., Albany, New York, United States of America
| | - Jonah Cool
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Heather Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Florence D’Orazi
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Kylee Degatano
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | | | - Timothy P. Fliss
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - James Gee
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tom Gillespie
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
| | - Nathan Gouwens
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Guo-Qiang Zhang
- Texas Institute for Restorative Neurotechnologies, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yaroslav O. Halchenko
- Department of Psychological and Brain Sciences, Dartmouth College, Hannover, New Hampshire, United States of America
| | - Nomi L. Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Houri Hintiryan
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Gregory Hood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sam Horvath
- Kitware Inc., Albany, New York, United States of America
| | - Bingxing Huo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dorota Jarecka
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shengdian Jiang
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Farzaneh Khajouei
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Elizabeth A. Kiernan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Huseyin Kir
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Boudewijn Lelieveldt
- Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yang Li
- Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America
| | - Hanqing Liu
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America
| | - Lijuan Liu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Anup Markuhar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - James Mathews
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Kaylee L. Mathews
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Michael I. Miller
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tyler Mollenkopf
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Maja A. Puchades
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Lei Qu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Joseph P. Receveur
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America
- Ludwig Institute for Cancer Research, La Jolla, California, United States of America
| | - Nathan Sjoquist
- Microsoft Corporation, Seattle, Washington, United States of America
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Daniel Tward
- UCLA Brain Mapping Center, University of California, Los Angeles, California, United States of America
| | | | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Fangming Xie
- Department of Chemistry and Biochemistry, University of California Los Angeles, California, United States of America
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Zhixi Yun
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Yun Renee Zhang
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - W. Jim Zheng
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Brian Zingg
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
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4
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Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M. Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. Front Neuroinform 2019; 13:1. [PMID: 30792636 PMCID: PMC6374302 DOI: 10.3389/fninf.2019.00001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/17/2019] [Indexed: 11/30/2022] Open
Abstract
There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generalizes across changes in the processing approach, and sampled population, in a controlled scientific fashion. ReproNim: A Center for Reproducible Neuroimaging Computation is a recently funded initiative that seeks to facilitate the “last mile” implementations of core re-executability tools in order to reduce the accessibility barrier and increase adoption of standards and best practices at the neuroimaging research laboratory level. In this report, we summarize the overall approach and tools we have developed in this domain.
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Affiliation(s)
- David N Kennedy
- Eunice Kennedy Shriver Center, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, United States
| | - Sanu A Abraham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Julianna F Bates
- Eunice Kennedy Shriver Center, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, United States
| | | | - Satrajit Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tom Gillespie
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Mathias Goncalves
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jeffrey S Grethe
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Yaroslav O Halchenko
- Department of Psychological and Brain Sciences, Dartmouth College, Dartmouth, NH, United States
| | - Michael Hanke
- Institute of Psychology, University of Magdeburg, Magdeburg, Germany
| | - Christian Haselgrove
- Eunice Kennedy Shriver Center, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, United States
| | - Steven M Hodge
- Eunice Kennedy Shriver Center, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, United States
| | - Dorota Jarecka
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jakub Kaczmarzyk
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - David B Keator
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, United States
| | - Kyle Meyer
- Department of Psychological and Brain Sciences, Dartmouth College, Dartmouth, NH, United States
| | - Maryann E Martone
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Smruti Padhy
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jean-Baptiste Poline
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | | | - Troy Sincomb
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
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