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cubids

Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.

https://github.com/pennlinc/cubids

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    5 of 16 committers (31.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.5%) to scientific vocabulary

Keywords

data-curation data-organization neuroimaging neuroimaging-data-science neuroinformatics neuroscience neuroscience-methods python-package

Keywords from Contributors

bids denoising-images diffusion-mri distortion-correction motion-correction pipelines
Last synced: 6 months ago · JSON representation ·

Repository

Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.

Basic Info
Statistics
  • Stars: 28
  • Watchers: 5
  • Forks: 12
  • Open Issues: 55
  • Releases: 4
Topics
data-curation data-organization neuroimaging neuroimaging-data-science neuroinformatics neuroscience neuroscience-methods python-package
Created over 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation Authors

README.rst 

========================
CuBIDS: Curation of BIDS
========================

.. image:: https://img.shields.io/pypi/v/cubids.svg
    :target: https://pypi.python.org/pypi/cubids
    :alt: Latest Version

.. image:: https://img.shields.io/badge/Source%20Code-pennlinc%2Fcubids-purple
   :target: https://github.com/PennLINC/CuBIDS
   :alt: GitHub Repository

.. image:: https://readthedocs.org/projects/cubids/badge/?version=latest
    :target: https://cubids.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. image:: https://circleci.com/gh/PennLINC/CuBIDS.svg?style=svg
    :target: https://circleci.com/gh/PennLINC/CuBIDS
    :alt: Test Status

.. image:: https://codecov.io/gh/PennLINC/CuBIDS/branch/main/graph/badge.svg
   :target: https://app.codecov.io/gh/PennLINC/CuBIDS/tree/main
   :alt: Codecov

.. image:: https://img.shields.io/badge/NeuroImage-10.1016%2Fj.neuroimage.2022.119609-purple
   :target: https://doi.org/10.1016/j.neuroimage.2022.119609
   :alt: Publication DOI

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6514881.svg
   :target: https://doi.org/10.5281/zenodo.6514881
   :alt: Zenodo DOI

.. image:: https://img.shields.io/badge/License-MIT-green
   :target: https://opensource.org/licenses/MIT
   :alt: License


About
-----

``CuBIDS`` (Curation of BIDS) is a workflow and software package designed to facilitate
reproducible curation of neuroimaging `BIDS `_ datasets.
CuBIDS breaks down BIDS dataset curation into four main components and addresses each one using
various command line programs complete with version control capabilities.
These components are not necessarily linear but all are critical
in the process of preparing BIDS data for successful preprocessing and analysis pipeline runs.

  1.    CuBIDS facilitates the validation of BIDS data.
  2.    CuBIDS visualizes and summarizes the heterogeneity in a BIDS dataset.
  3.    CuBIDS helps users test pipelines on the entire parameter space of a BIDS dataset.
  4.    CuBIDS allows users to perform metadata-based quality control on their BIDS data.
  5.    CuBIDS helps users clean protected information in BIDS datasets,
        in order to prepare them for public sharing.

.. image:: https://github.com/PennLINC/CuBIDS/raw/main/docs/_static/cubids_workflow.png
   :width: 600

For full documentation, please visit our
`ReadTheDocs `_.


Citing CuBIDS
-------------

If you use CuBIDS in your research, please cite the following paper:

    Covitz, S., Tapera, T. M., Adebimpe, A., Alexander-Bloch, A. F., Bertolero, M. A., Feczko, E.,
    ... & Satterthwaite, T. D. (2022).
    Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets.
    NeuroImage, 263, 119609.
    doi:10.1016/j.neuroimage.2022.119609.

Please also cite the Zenodo DOI for the version you used.

Owner

  • Name: Lifespan Informatics and Neuroimaging Center
  • Login: PennLINC
  • Kind: organization

The Lifespan Informatics and Neuroimaging Center at the University of Pennylvannia

Citation (CITATION.cff) 

# 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: 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'

GitHub Events

Total
  • Create event: 55
  • Release event: 1
  • Issues event: 89
  • Watch event: 5
  • Delete event: 48
  • Member event: 3
  • Issue comment event: 127
  • Push event: 286
  • Pull request review comment event: 87
  • Pull request review event: 127
  • Pull request event: 128
  • Fork event: 5
Last Year
  • Create event: 55
  • Release event: 1
  • Issues event: 89
  • Watch event: 5
  • Delete event: 48
  • Member event: 3
  • Issue comment event: 127
  • Push event: 286
  • Pull request review comment event: 87
  • Pull request review event: 127
  • Pull request event: 128
  • Fork event: 5

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 677
  • Total Committers: 16
  • Avg Commits per committer: 42.313
  • Development Distribution Score (DDS): 0.251
Past Year
  • Commits: 42
  • Committers: 7
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.238
Top Committers
Name Email Commits
Sydney Covitz s****z@g****m 507
Matt Cieslak m****k@g****m 55
TinasheMTapera t****a@g****m 52
Sydney Covitz 7****z 34
Sydney Covitz s****1@s****u 10
Tinashe Michael Tapera t****s@y****m 4
Taylor Salo s****t@p****u 3
jaberbasma 6****a 3
Margaret Gardner 9****n 2
Matthew Cieslak Matthew.Cieslak@pennmedicine.upenn.edu c****m@c****u 1
Philip Cook c****a@p****u 1
Taylor Salo t****0@g****m 1
Yaroslav Halchenko d****n@o****m 1
jaberbasma j****a@g****m 1
krmurtha k****a@p****u 1
krmurtha 4****a 1
Committer Domains (Top 20 + Academic)
pennmedicine.upenn.edu: 3 onerussian.com: 1 cubic-login3.uphs.upenn.edu: 1 swarthmore.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 183
  • Total pull requests: 224
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 23
  • Total pull request authors: 15
  • Average comments per issue: 0.75
  • Average comments per pull request: 0.7
  • Merged pull requests: 176
  • Bot issues: 0
  • Bot pull requests: 41
Past Year
  • Issues: 60
  • Pull requests: 121
  • Average time to close issues: 20 days
  • Average time to close pull requests: 11 days
  • Issue authors: 9
  • Pull request authors: 10
  • Average comments per issue: 0.65
  • Average comments per pull request: 0.91
  • Merged pull requests: 91
  • Bot issues: 0
  • Bot pull requests: 25
View more stats
Top Authors
Issue Authors
  • scovitz (81)
  • tsalo (59)
  • mattcieslak (9)
  • gabridele (6)
  • tientong98 (4)
  • singlesp (3)
  • B-Sevchik (3)
  • ericearl (2)
  • yarikoptic (2)
  • jhauneuro (1)
  • jmschabdach (1)
  • fpichardo-umn (1)
  • TinasheMTapera (1)
  • dependabot[bot] (1)
  • araikes (1)
Pull Request Authors
  • tsalo (75)
  • dependabot[bot] (65)
  • scovitz (50)
  • singlesp (16)
  • tientong98 (15)
  • gabridele (14)
  • mattcieslak (9)
  • TinasheMTapera (6)
  • megardn (3)
  • smeisler (3)
  • B-Sevchik (2)
  • ashleychari (2)
  • shivaram-k (2)
  • yarikoptic (2)
  • cookpa (1)
Top Labels
Issue Labels
enhancement (38) bug (33) documentation (12) priority: high (11) breaking-change (7) priority: medium (5) refactor (5) testing (4) priority: low (4) question (3) maintenance (3) ignore-for-release (1)
Pull Request Labels
maintenance (83) ignore-for-release (73) bug (26) documentation (22) enhancement (20) testing (12) breaking-change (8) refactor (6)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 45 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 11
  • Total maintainers: 2
pypi.org: cubids

Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.

  • Homepage: https://github.com/PennLINC/cubids
  • Documentation: https://www.cubids.readthedocs.io
  • License: MIT License Copyright (c) 2020 Lifespan Informatics and Neuroimaging Center Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 1.2.0
    published 12 months ago
  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 45 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 11.9%
Stargazers count: 14.6%
Average: 26.3%
Downloads: 27.8%
Dependent repos count: 67.1%
Maintainers (2)
tsalo scovitz
Last synced: 6 months ago

Dependencies

.readthedocs/environment.yaml conda
  • pip >=20.1
  • python 3.7.*
package-lock.json npm
  • 244 dependencies
package.json npm
  • pip ^0.0.1