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cff-version: 1.2.0
title: >-
  Curation of BIDS (CuBIDS)
message: If you use this software, please cite it using the metadata from this file, as well as the NeuroImage paper (doi:10.1016/j.neuroimage.2022.119609).
type: software
authors:
  - given-names: Sydney
    family-names: Covitz
    affiliation: University of Pennsylvania
    orcid: 'https://orcid.org/0000-0002-7430-4125'
  - given-names: Tinashe M.
    family-names: Tapera
  - given-names: Azeez
    family-names: Adebimpe
    affiliation: University of Pennsylvania
    orcid: 'https://orcid.org/0000-0001-9049-0135'
  - given-names: Aaron F.
    family-names: Alexander-Bloch
    affiliation: University of Pennsylvania
  - given-names: Maxwell
    family-names: Bertolero
    orcid: 'https://orcid.org/0000-0002-2691-3698'
    affiliation: University of Pennsylvania
  - given-names: Eric
    family-names: Feczko
  - given-names: Alexandre R.
    family-names: Franco
  - given-names: Raquel E.
    family-names: Gur
  - given-names: Ruben C.
    family-names: Gur
  - given-names: Timothy
    family-names: Hendrickson
  - given-names: Audrey
    family-names: Houghton
  - given-names: Kahini
    family-names: Mehta
  - given-names: Kristin
    family-names: Murtha
    affiliation: University of Pennsylvania
  - given-names: Anders J.
    family-names: Perrone
  - given-names: Tim
    family-names: Robert-Fitzgerald
  - given-names: Jenna M.
    family-names: Schabdach
  - given-names: Russell T.
    family-names: Shinohara
  - given-names: Jacob W.
    family-names: Vogel
  - given-names: Chenying
    family-names: Zhao
  - given-names: Damien A.
    family-names: Fair
  - given-names: Michael
    family-names: Milham
  - given-names: Matthew
    family-names: Cieslak
    email: matthew.cieslak@pennmedicine.upenn.edu
    affiliation: University of Pennsylvania
    orcid: 'https://orcid.org/0000-0002-1931-4734'
  - given-names: Taylor
    family-names: Salo
    email: salot@pennmedicine.upenn.edu
    affiliation: University of Pennsylvania
    orcid: 'https://orcid.org/0000-0001-9813-3167'
  - given-names: Theodore
    family-names: Satterthwaite
    affiliation: University of Pennsylvania
    orcid: 'https://orcid.org/0000-0001-7072-9399'
identifiers:
  - type: doi
    value: 10.5281/zenodo.6514881
    description: The Zenodo DOI
  - type: doi
    value: 10.1016/j.neuroimage.2022.119609
    description: The NeuroImage journal article
repository-code: 'https://github.com/PennLINC/CuBIDS'
url: 'https://cubids.readthedocs.io'
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.
keywords:
  - BIDS
  - Neuroimaging
license: MIT
version: 1.1.0
date-released: '2024-04-02'
