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CITATION.cff
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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
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: Tien
family-names: Tong
affiliation: University of Pennsylvania
orcid: 'https://orcid.org/0000-0002-1940-3198'
- 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: Brooke L.
family-names: Sevchik
affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- given-names: Shivaram
family-names: Karandikar
affiliation: Lifespan Brain Institute (LiBI) of the Children's Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, PA
orcid: 'https://orcid.org/0009-0003-0649-9260'
- given-names: Gabriele
family-names: De Leonardis
affiliation: Department of Clinical Sciences Malmö, Faculty of Medicine, SciLifeLab, Lund University, Lund, Sweden
orcid: 'https://orcid.org/0009-0006-9947-4768'
- given-names: Steven
family-names: Meisler
affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
orcid: 'https://orcid.org/0000-0002-8888-1572'
- given-names: S. Parker
family-names: Singleton
affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
orcid: 'https://orcid.org/0000-0002-7102-7820'
- given-names: Damien A.
family-names: Fair
- given-names: Michael
family-names: Milham
- given-names: Matthew
family-names: Cieslak
email: [email protected]
affiliation: University of Pennsylvania
orcid: 'https://orcid.org/0000-0002-1931-4734'
- given-names: Taylor
family-names: Salo
email: [email protected]
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'