ArticleNeuroImage2022
Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets.
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Article in NeuroImage, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26citing papers in PubMed
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Who cites it
26 citing papers in PubMed, 28 citations in OpenAlex.
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- Two axes of white matter development.Nature communications · 2026Article
- Anatomical White Matter Tracts Span the Cortical Hierarchy to Support Cognitive Diversity.bioRxiv : the preprint server for biology · 2025Article
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- An Open, Fully-processed, Longitudinal Data Resource to Study Brain Development and Transdiagnostic Executive Function.bioRxiv : the preprint server for biology · 2025Article
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- Systematic protocol to identify 'clinical controls' for paediatric neuroimaging research from clinically acquired brain MRIs.BMJ open · 2025Article
- A systematic protocol to identify "clinical controls" for pediatric neuroimaging research from clinically acquired brain MRIs.bioRxiv : the preprint server for biology · 2025Article
- Human thalamocortical structural connectivity develops in line with a hierarchical axis of cortical plasticity.Nature neuroscience · 2025Article
- Sharing Neuroimaging Data with Squirrel - A Relational Data Format to Store Raw to Analyzed Data and Everything in Between.Neuroinformatics · 2025Article
- Investigating mood and cognition in people with multiple sclerosis: a prospective cross-sectional study protocol.BMJ open · 2025Article
- Heterochronous laminar maturation in the human prefrontal cortex.bioRxiv : the preprint server for biology · 2025Article
- Automated algorithm for medical data structuring, and segmentation using artificial intelligence within secured environment for dataset creation.European journal of radiology open · 2024Article
- Integration across biophysical scales identifies molecular and cellular correlates of person-to-person variability in human brain connectivity.Nature neuroscience · 2024Article
- Investigating Mood and Cognition in People with Multiple Sclerosis: A Prospective Study Protocol.medRxiv : the preprint server for health sciences · 2024Article
- Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA.Neuroinformatics · 2024Article
- MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology.Neuroinformatics · 2024Article
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Authors and funding
23 authors at 7 institutions in 1 country.
Sydney CovitzLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Tinashe M TaperaLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Azeez AdebimpeLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Aaron F Alexander-BlochPenn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States.
Maxwell A BertoleroLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Eric FeczkoMasonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States.
Alexandre R FrancoChild Mind Institute, 101 E 56th St, New York, NY 10022,; Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA; Department of Psychiatry, NYU Grossman School of Medicine, New York, NY 10016, USA.
Raquel E GurPenn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Ruben C GurPenn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Timothy HendricksonMasonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States; University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, United States.
Audrey HoughtonMasonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States.
Kahini MehtaLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Kristin MurthaLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Anders J PerroneMasonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States.
Tim Robert-FitzgeraldCenter for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA.
Jenna M SchabdachPenn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States.
Russell T ShinoharaCenter for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA.
Jacob W VogelLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Chenying ZhaoLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
Damien A FairMasonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States.
Michael P MilhamChild Mind Institute, 101 E 56th St, New York, NY 10022.
Matthew CieslakLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Theodore D SatterthwaiteLifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: sattertt@pennmedicine.upenn.edu.
University of Pennsylvania · USLifespan · USUniversity of Minnesota · USChildren's Hospital of Philadelphia · USChild Mind Institute · USPenn Center for AIDS Research · USUniversity of Minnesota System · US
Funding
ABCD-USA Consortium: Research ProjectU01DA041148 · NIDA · OREGON HEALTH & SCIENCE UNIVERSITY · PI Damien A Fair, Rebekah S Huber · 2015 to 2026
$22.3MLongitudinal Mapping of Network Development Underlying Executive Dysfunction in AdolescenceR01MH113550 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI Danielle Smith Bassett, Theodore Satterthwaite · 2018 to 2026
$6.9MPersonalized Functional Network Modeling to Characterize and Predict Psychopathology in YouthR01EB022573 · NIBIB · UNIVERSITY OF PENNSYLVANIA · PI Yong Fan, Theodore Satterthwaite · 2016 to 2026
$6.0MInter-modal Coupling Image AnalyticsR01MH112847 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI Theodore Satterthwaite, Russell Takeshi Shinohara · 2017 to 2026
$5.9MPrecision mapping of individualized executive networks in youthR37MH125829 · NIMH · UNIVERSITY OF MINNESOTA · PI Damien A Fair, Theodore Satterthwaite · 2021 to 2026
$4.7MHarmonization of Multi-Site Neuroimaging Data from Complex Study DesignsR01MH123550 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI SHINOHARA, RUSSELL TAKESHI · 2020 to 2025
$4.0MReproducible imaging-based brain growth charts for psychiatryR01MH120482 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI MILHAM, MICHAEL PETER, SATTERTHWAITE, THEODORE · 2019 to 2023
$3.5MAdvanced Statistical Analytics of MRI in MSR01NS112274 · NINDS · UNIVERSITY OF PENNSYLVANIA · PI SHINOHARA, RUSSELL TAKESHI · 2020 to 2024
$2.8MNetwork Control and Functional Context: Mechanisms for TMS ResponseRF1MH116920 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI BASSETT, DANIELLE SMITH, OATHES, DESMOND · 2018 to 2018
$2.8MSemiparametric Inference for Psychiatric NeuroimagingR01MH123563 · NIMH · VANDERBILT UNIVERSITY MEDICAL CENTER · PI VANDEKAR, SIMON NEIL · 2020 to 2024
$2.1MBiomedical Image Computing and Informatics ClusterS10OD023495 · OD · UNIVERSITY OF PENNSYLVANIA · PI DAVATZIKOS, CHRISTOS · 2017 to 2017
$1.9MNIPreps: integrating neuroimaging preprocessing workflows across modalities, populations, and speciesRF1MH121867 · NIMH · STANFORD UNIVERSITY · PI POLDRACK, RUSSELL A, ROKEM, ARIEL SHALOM · 2021 to 2022
$1.6MNIBIB NIH HHS R01 EB022573NIDA NIH HHS U01 DA041148NIH HHS S10 OD023495NIMH NIH HHS R01 MH112847NIMH NIH HHS R01 MH113550NIMH NIH HHS R01 MH120482NIMH NIH HHS R01 MH123550NIMH NIH HHS R01 MH123563NIMH NIH HHS R37 MH125829NIMH NIH HHS RF1 MH116920NIMH NIH HHS RF1 MH121867NINDS NIH HHS R01 NS112274
Abstract
The Brain Imaging Data Structure (BIDS) is a specification accompanied by a software ecosystem that was designed to create reproducible and automated workflows for processing neuroimaging data. BIDS Apps flexibly build workflows based on the metadata detected in a dataset. However, even BIDS valid metadata can include incorrect values or omissions that result in inconsistent processing across sessions. Additionally, in large-scale, heterogeneous neuroimaging datasets, hidden variability in metadata is difficult to detect and classify. To address these challenges, we created a Python-based software package titled "Curation of BIDS" (CuBIDS), which provides an intuitive workflow that helps users validate and manage the curation of their neuroimaging datasets. CuBIDS includes a robust implementation of BIDS validation that scales to large samples and incorporates DataLad--a version control software package for data--as an optional dependency to ensure reproducibility and provenance tracking throughout the entire curation process. CuBIDS provides tools to help users perform quality control on their images' metadata and identify unique combinations of imaging parameters. Users can then execute BIDS Apps on a subset of participants that represent the full range of acquisition parameters that are present, accelerating pipeline testing on large datasets.
Indexed as
EcosystemSoftwareHumansNeuroimagingReproducibility of ResultsWorkflowBIDSBrainCurationHeterogeneityMetadataMRINeuroimagingSoftwareValidationVersion control
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