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dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

https://github.com/nipreps/dmriprep

Science Score: 59.0%

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

  • ○
    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
  • ✓
    Committers with academic emails
    5 of 17 committers (29.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary

Keywords

bids bids-apps diffusion-mri magnetic-resonance-imaging preprocessing

Keywords from Contributors

brain-imaging fmri fmri-preprocessing neuroimaging
Last synced: 6 months ago · JSON representation

Repository

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

Basic Info
Statistics
  • Stars: 67
  • Watchers: 12
  • Forks: 24
  • Open Issues: 39
  • Releases: 8
Topics
bids bids-apps diffusion-mri magnetic-resonance-imaging preprocessing
Created almost 7 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog Contributing License Roadmap Zenodo

README.rst 

========
dMRIPrep
========

.. image:: https://img.shields.io/badge/chat-mattermost-blue
    :target: https://mattermost.brainhack.org/brainhack/channels/dmriprep

.. image:: https://img.shields.io/badge/docker-nipreps/dmriprep-brightgreen.svg?logo=docker&style=flat
  :target: https://hub.docker.com/r/nipreps/dmriprep/tags/

.. image:: https://img.shields.io/pypi/v/dmriprep.svg
    :target: https://pypi.python.org/pypi/dmriprep

.. image:: https://circleci.com/gh/nipreps/dmriprep.svg?style=svg
    :target: https://circleci.com/gh/nipreps/dmriprep

.. image:: https://github.com/nipreps/dmriprep/workflows/Python%20package/badge.svg
    :target: https://github.com/nipreps/dmriprep/actions

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3392201.svg
    :target: https://doi.org/10.5281/zenodo.3392201

[`Documentation `__]
[`Support at neurostars.org `__]

About
-----
The preprocessing of diffusion MRI (dMRI) involves numerous steps to clean and standardize
the data before fitting a particular model.
Generally, researchers create ad-hoc preprocessing workflows for each dataset,
building upon a large inventory of available tools.
The complexity of these workflows has snowballed with rapid advances in
acquisition and processing.
dMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and
reproducible preprocessing for whole-brain dMRI data.
dMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of
virtually any dataset, ensuring high-quality preprocessing without manual intervention.
dMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing
workflow, which can help ensure the validity of inference and the interpretability
of results.

The workflow is based on `Nipype `__ and
encompasses a large set of tools from other neuroimaging packages.
This pipeline was designed to provide the best software implementation for each state of
preprocessing, and will be updated as newer and better neuroimaging software
becomes available.

dMRIPrep performs basic preprocessing steps such as head-motion correction,
susceptibility-derived distortion correction, eddy current correction, etc.
providing outputs that can be easily submitted to a variety of diffusion models.

Getting involved
----------------
We welcome all contributions!
We'd like to ask you to familiarize yourself with our `contributing guidelines `__.
For ideas for contributing to *dMRIPrep*, please see the current list of `issues `__.
For making your contribution, we use the GitHub flow, which is
nicely explained in the chapter `Contributing to a Project `__ in Pro Git
by Scott Chacon and also in the `Making a change section `__ of our guidelines.
If you're still not sure where to begin, feel free to pop into `Mattermost `__ and introduce yourself!
Our project maintainers will do their best to answer any question or concerns and will be happy to help you find somewhere to get started.

Want to learn more about our future plans for developing `dMRIPrep`?
Please take a look at our `milestones board `__ and `project roadmap `__.

We ask that all contributors to `dMRIPrep` across all project-related spaces (including but not limited to: GitHub, Mattermost, and project emails), adhere to our `code of conduct `__.

Owner

  • Name: NeuroImaging PREProcessing toolS
  • Login: nipreps
  • Kind: organization
  • Email: nipreps@gmail.com

GitHub Events

Total
  • Issues event: 1
  • Watch event: 6
  • Issue comment event: 11
  • Pull request event: 2
  • Fork event: 2
Last Year
  • Issues event: 1
  • Watch event: 6
  • Issue comment event: 11
  • Pull request event: 2
  • Fork event: 2

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 545
  • Total Committers: 17
  • Avg Commits per committer: 32.059
  • Development Distribution Score (DDS): 0.552
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Oscar Esteban c****e@o****s 244
Michael Joseph j****2@g****m 73
Anisha Keshavan a****n@g****m 58
Ariel Rokem a****m@b****u 48
Adam Richie-Halford r****d@u****u 47
Salim Mansour s****r@g****m 28
pyup-bot g****t@p****o 21
Anisha Keshavan a****a@c****g 6
Derek Pisner d****r@u****u 6
Garikoitz Lerma-Usabiaga g****z@g****m 3
James D. Kent j****t@u****u 3
Celine Provins c****s@u****h 2
Anisha Keshavan a****n 2
nrajamani3 n****3@g****u 1
Erin W Dickie e****e 1
Derek Pisner 1****s 1
snyk-test s****t@s****o 1
Committer Domains (Top 20 + Academic)
snyk.io: 1 gatech.edu: 1 unil.ch: 1 uiowa.edu: 1 utexas.edu: 1 childmind.org: 1 pyup.io: 1 uw.edu: 1 berkeley.edu: 1 oscaresteban.es: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 47
  • Total pull requests: 59
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 17
  • Total pull request authors: 9
  • Average comments per issue: 1.83
  • Average comments per pull request: 2.29
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 8.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • oesteban (23)
  • josephmje (4)
  • arokem (2)
  • h-w-k (2)
  • GalKepler (2)
  • esavary (2)
  • levchenkoegor (2)
  • Meryam1985 (1)
  • nabaruns (1)
  • LangFiL (1)
  • man-shu (1)
  • richford (1)
  • maryjis (1)
  • celprov (1)
  • alienx-zero (1)
Pull Request Authors
  • oesteban (31)
  • josephmje (9)
  • GalKepler (5)
  • arokem (4)
  • dPys (3)
  • celprov (2)
  • slimnsour (2)
  • edickie (2)
  • jhlegarreta (1)
  • mattcieslak (1)
Top Labels
Issue Labels
bug (8) impact: high (6) NiPreps Grant (5) effort: high (4) effort: medium (3) enhancement (2) depends: SDCFlows (2) impact: medium (2) validation / evaluation (1) effort: low (1) good first issue (1)
Pull Request Labels
documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 70 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 8
  • Total maintainers: 1
pypi.org: dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data.

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 70 Last month
Rankings
Forks count: 8.1%
Stargazers count: 8.6%
Dependent packages count: 10.0%
Average: 14.6%
Dependent repos count: 21.7%
Downloads: 24.5%
Maintainers (1)
nipreps
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • nbsphinx *
  • nipype *
  • niworkflows >=1.4.0rc5,<1.5
  • packaging *
  • pydot >=1.2.3
  • pydotplus *
  • sdcflows *
  • smriprep >=0.8.0rc2
  • sphinx >=2.1.2,<3.0
  • sphinx-argparse *
  • sphinx_rtd_theme *
  • sphinxcontrib-apidoc *
  • sphinxcontrib-napoleon 0dc3f28a309ad602be5f44a9049785a1026451b3
  • sphinxcontrib-versioning 39b40b0b84bf872fc398feff05344051bbce0f63
  • templateflow *
  • toml *
.github/workflows/pythonpackage.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
Dockerfile docker
  • ubuntu xenial-20201030 build