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nipoppy

Lightweight framework for neuroimaging-clinical data organization/processing

https://github.com/nipoppy/nipoppy

Science Score: 67.0%

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 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Lightweight framework for neuroimaging-clinical data organization/processing

Basic Info
Statistics
  • Stars: 33
  • Watchers: 10
  • Forks: 25
  • Open Issues: 98
  • Releases: 12
Created almost 4 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Nipoppy

DOI PyPI - Version License codecov https://github.com/psf/black Documentation Status

Nipoppy logo

Nipoppy is a lightweight framework for standardized organization and processing of neuroimaging-clinical datasets. Its goal is to help users adopt the FAIR principles and improve the reproducibility of studies.

The framework includes three components:

  1. A protocol for data organization, curation and processing, with steps that include the following:

    • Organization of raw data, including conversion of raw DICOMs (or NIfTIs) to BIDS
    • Processing of imaging data with existing or custom pipelines
    • Tracking of data availability and processing status
    • Extraction of imaging-derived phenotypes (IDPs) for downstream statistical modelling and analysis

    Nipoppy protocol

  2. A specification for dataset organization that extends the Brain Imaging Data Structure (BIDS) standard by providing additional guidelines for tabular (e.g., phenotypic) data and imaging derivatives.

    Nipoppy specification

  3. A command-line interface and Python package that provide user-friendly tools for applying the framework. The tools build upon existing technologies such as the Apptainer container platform and the Boutiques descriptor framework. Several existing containerized pipelines are supported out-of-the-box, and new pipelines can be added easily by the user.

    • We have also developed a web dashboard for interactive visualizations of imaging and phenotypic data availability.

Owner

  • Name: nipoppy
  • Login: nipoppy
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
title: nipoppy
version: 0.4.1
abstract: A lightweight framework for neuroimaging-clinical data organization/processing.
message: If you use this software, please cite it as below.
repository-code: https://github.com/nipoppy/nipoppy.git
doi: 10.5281/zenodo.8084759
contact:
  - affiliation: ORIGAMI lab, McGill University, Montréal, Canada
    family-names: Poline
    given-names: Jean-Baptiste
    orcid: https://orcid.org/0000-0002-9794-749X
authors:
  - family-names: Nipoppy contributors
  - affiliation: ORIGAMI lab, McGill University, Montréal, Canada
    email: nikhil.bhagwat@mcgill.ca
    family-names: Bhagwat
    given-names: Nikhil
    orcid: https://orcid.org/0000-0001-6073-7141
  - affiliation: ORIGAMI lab, McGill University, Montréal, Canada
    family-names: Wang
    given-names: Michelle
    orcid: https://orcid.org/0000-0002-3432-6899
  - affiliation: Big Data Infrastructures for Neuroinformatics lab, Concordia University, Montréal, Canada
    family-names: Dugré
    given-names: Mathieu
    orcid: https://orcid.org/0000-0003-2828-6031
  - affiliation: ORIGAMI lab, McGill University, Montréal, Canada
    family-names: McPherson
    given-names: Brent
    orcid: https://orcid.org/0000-0001-8378-8136
  - affiliation: ORIGAMI lab, McGill University, Montréal, Canada
    family-names: Poline
    given-names: Jean-Baptiste
    orcid: https://orcid.org/0000-0002-9794-749X
license: MIT

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 205
  • Total pull requests: 219
  • Average time to close issues: 2 months
  • Average time to close pull requests: 19 days
  • Total issue authors: 11
  • Total pull request authors: 13
  • Average comments per issue: 0.59
  • Average comments per pull request: 1.16
  • Merged pull requests: 135
  • Bot issues: 0
  • Bot pull requests: 20
Past Year
  • Issues: 159
  • Pull requests: 186
  • Average time to close issues: 29 days
  • Average time to close pull requests: 10 days
  • Issue authors: 8
  • Pull request authors: 13
  • Average comments per issue: 0.36
  • Average comments per pull request: 1.05
  • Merged pull requests: 116
  • Bot issues: 0
  • Bot pull requests: 18
View more stats
Top Authors
Issue Authors
  • michellewang (147)
  • mathdugre (21)
  • nikhil153 (13)
  • Remi-Gau (8)
  • julia-pfarr (7)
  • yarikoptic (4)
  • cindyhfls (1)
  • bcmcpher (1)
  • surchs (1)
  • emiledangremont (1)
  • dnkennedy (1)
Pull Request Authors
  • michellewang (130)
  • mathdugre (31)
  • pre-commit-ci[bot] (9)
  • Remi-Gau (9)
  • dependabot[bot] (9)
  • nikhil153 (8)
  • julia-pfarr (6)
  • asmacdo (4)
  • jacobsanz97 (4)
  • mtorabi59 (3)
  • bcmcpher (3)
  • nipoppy-bot[bot] (2)
  • alyssadai (1)
Top Labels
Issue Labels
T.1 - Enhancement (55) T.0 - Bug (45) T.3 - Documentation (18) T.2 - Maintenance (16) pipeline catalog (13) legacy (9) good first issue (9) P.2 - Minor patch (9) P.0 - Breaking change (7) C.1 - Software (6) S.2 - Todo (3) T.7 - Discussion (3) dicom-to-bids (2) E.0 - Low effort (2) C.3 - Training (2) documentation (1) priority:high (1) effort:high (1) T.5 - Deprecation (1) wontfix (1) Priority: medium (1) duplicate (1) qpn (1) help wanted (1) neurobagel (1) Priority: high (1) E.1 - Medium effort (1)
Pull Request Labels
T.1 - Enhancement (51) T.2 - Maintenance (32) T.0 - Bug (27) T.3 - Documentation (20) bot (10) P.0 - Breaking change (7) C.1 - Software (5) P.2 - Minor patch (5) pipeline catalog (4) S.3 - In progress (2) T.6 - Release (2) legacy (1) S.4 - Pending review (1)

Dependencies

.github/workflows/codespell.yml actions
  • actions/checkout v3 composite
  • codespell-project/actions-codespell v2 composite
.github/workflows/update_dataset_repos.yml actions
  • actions/checkout v3 composite
  • actions/github-script v6 composite
  • michellewang/auto-approve-action v3 composite
  • pascalgn/automerge-action v0.15.6 composite
  • peter-evans/create-pull-request v4 composite
.github/workflows/validation.yml actions
  • actions/checkout v3 composite
  • citation-file-format/cffconvert-github-action 2.0.0 composite
workflow/proc_pipe/mriqc/Dockerfile docker
  • ubuntu latest build
pyproject.toml pypi
setup.py pypi