NeuroImage (Nov 2022)
Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets
- Sydney Covitz,
- Tinashe M. Tapera,
- Azeez Adebimpe,
- Aaron F. Alexander-Bloch,
- Maxwell A. Bertolero,
- Eric Feczko,
- Alexandre R. Franco,
- Raquel E. Gur,
- Ruben C. Gur,
- Timothy Hendrickson,
- Audrey Houghton,
- Kahini Mehta,
- Kristin Murtha,
- Anders J. Perrone,
- Tim Robert-Fitzgerald,
- Jenna M. Schabdach,
- Russell T Shinohara,
- Jacob W. Vogel,
- Chenying Zhao,
- Damien A. Fair,
- Michael P. Milham,
- Matthew Cieslak,
- Theodore D. Satterthwaite
Affiliations
- Sydney Covitz
- Lifespan 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. Tapera
- Lifespan 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 Adebimpe
- Lifespan 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-Bloch
- 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; Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States
- Maxwell A. Bertolero
- Lifespan 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 Feczko
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States
- Alexandre R. Franco
- Child 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. Gur
- 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
- Ruben C. Gur
- 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
- Timothy Hendrickson
- Masonic 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 Houghton
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States
- Kahini Mehta
- Lifespan 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 Murtha
- Lifespan 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. Perrone
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States
- Tim Robert-Fitzgerald
- Center 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. Schabdach
- 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; Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States
- Russell T Shinohara
- Center 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. Vogel
- Lifespan 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 Zhao
- Lifespan 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. Fair
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States
- Michael P. Milham
- Child Mind Institute, 101 E 56th St, New York, NY 10022,
- Matthew Cieslak
- Lifespan 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. Satterthwaite
- Lifespan 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; Corresponding author at: Richards Medical Labs, A504, 3700 Hamilton Walk, Philadelphia, PA 19104.
- Journal volume & issue
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Vol. 263
p. 119609
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.
