mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

https://github.com/nipreps/mriqc

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 8 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
10 of 47 committers (21.3%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary

Keywords

machine-learning mri neuroimaging quality-control quality-reporter

Keywords from Contributors

bids brain-imaging fmri fmri-preprocessing eeg meg closember ecog neuroscience diffusion-mri

Last synced: 6 months ago · JSON representation

Repository

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

Basic Info

Host: GitHub
Owner: nipreps
License: apache-2.0
Language: Python
Default Branch: master
Homepage: http://mriqc.readthedocs.io
Size: 269 MB

Statistics

Stars: 335
Watchers: 15
Forks: 133
Open Issues: 83
Releases: 65

Topics

machine-learning mri neuroimaging quality-control quality-reporter

Created about 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Zenodo

README.rst

mriqc: image quality metrics for quality assessment of MRI
==========================================================

|DOI| |Zenodo| |Package| |Pythons| |DevStatus| |License| |Documentation| |CircleCI| |EOSS|

MRIQC extracts no-reference IQMs (image quality metrics) from
structural (T1w and T2w), functional and diffusion MRI (magnetic resonance imaging)
data.

MRIQC is an open-source project, developed under the following
software engineering principles:

#. **Modularity and integrability**: MRIQC implements a
   `nipype `_ workflow to integrate modular
   sub-workflows that rely upon third party software toolboxes such as
   ANTs and AFNI.

#. **Minimal preprocessing**: the MRIQC workflows should be as minimal
   as possible to estimate the IQMs on the original data or their minimally
   processed derivatives.

#. **Interoperability and standards**: MRIQC follows the the `brain imaging data structure
   (BIDS) `_, and it adopts the `BIDS-App
   `_ standard.

#. **Reliability and robustness**: the software undergoes frequent vetting sprints
   by testing its robustness against data variability (acquisition parameters,
   physiological differences, etc.) using images from `OpenfMRI `_.
   Its reliability is permanently checked and maintained with
   `CircleCI `_.

Citation
--------
.. topic:: **When using MRIQC, please include the following citation:**

    Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ;
    *MRIQC: Advancing the Automatic Prediction of Image Quality in MRI from Unseen Sites*;
    PLOS ONE 12(9):e0184661; doi:`10.1371/journal.pone.0184661 `_.

Support and communication
-------------------------
The documentation of this project is found here: https://mriqc.readthedocs.io/.

Users can get help using the `mriqc-users google group `_.

All bugs, concerns and enhancement requests for this software can be submitted here:
https://github.com/nipreps/mriqc/issues.

Development
-----------
A local development build based on the latest docker build of MRIQC can be built with this command run from 
the root of this repository::

    docker build -f Dockerfile_devel -t mriqc_devel .

To test changes the local source code will need to be mounted into the development container::

    docker run --rm -v .:/src/mriqc mriqc_devel

New Python dependencies can be added in ``pyproject.toml`` under ``dependencies``.
Any time a dependency is changed or added there the docker image will need to be rebuilt
using the above ``docker build`` command.

License information
-------------------
*MRIQC* adheres to the
`general licensing guidelines `__
of the *NiPreps framework*.

*MRIQC* originally derives from, and hence is heavily influenced by, the
`PCP Quality Assessment Protocol
`__.
Please check the ``NOTICE`` file for further information.

License
~~~~~~~
Copyright (c) 2021, the *NiPreps* Developers.

As of the 21.0.x pre-release and release series, *MRIQC* is
licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
`http://www.apache.org/licenses/LICENSE-2.0
`__.

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

Acknowledgements
----------------
This work is steered and maintained by the `NiPreps Community `__.
The development of this resource was supported by
the Laura and John Arnold Foundation (RAP and KJG),
the NIBIB (R01EB020740, SSG; 1P41EB019936-01A1SSG, YOH),
the NIMH (RF1MH121867, RAP, OE; R24MH114705 and R24MH117179, RAP; 1RF1MH121885 SSG),
NINDS (U01NS103780, RAP), and NSF (CRCNS 1912266, YOH).
OE acknowledges financial support from the SNSF Ambizione project
“*Uncovering the interplay of structure, function, and dynamics of
brain connectivity using MRI*” (grant number
`PZ00P2_185872 `__).

.. topic:: **Thanks**

    * The QAP developers (C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J.
      Pellman) for the initial base of code which MRIQC was forked from.
    * W Triplett and CA Moodie for their initial contributions with bugfixes and documentation, and
    * J Varada for his contributions on the source code.


.. |DOI| image:: https://img.shields.io/badge/doi-10.1371%2Fjournal.pone.0184661-blue.svg
   :target: https://doi.org/10.1371/journal.pone.0184661
.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.2630889.svg
   :target: https://doi.org/10.5281/zenodo.2630889
.. |Package| image:: https://img.shields.io/pypi/v/mriqc.svg
   :target: https://pypi.python.org/pypi/mriqc/
.. |Pythons| image:: https://img.shields.io/pypi/pyversions/mriqc.svg
   :target: https://pypi.python.org/pypi/mriqc/
.. |DevStatus| image:: https://img.shields.io/pypi/status/mriqc.svg
   :target: https://pypi.python.org/pypi/mriqc/
.. |License| image:: https://img.shields.io/pypi/l/mriqc.svg
   :target: https://pypi.python.org/pypi/mriqc/
.. |Documentation| image:: https://readthedocs.org/projects/mriqc/badge/?version=latest
   :target: http://mriqc.readthedocs.io/en/latest/?badge=latest
.. |CircleCI| image:: https://circleci.com/gh/nipreps/mriqc/tree/master.svg?style=shield
   :target: https://circleci.com/gh/nipreps/mriqc/tree/master
.. |EOSS| image:: https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg
  :target: https://czi.co/EOSS
  :alt: CZI's Essential Open Source Software for Science

Owner

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

Website: https://nipreps.org/
Repositories: 46
Profile: https://github.com/nipreps

GitHub Events

Total

Issues event: 36
Watch event: 33
Delete event: 10
Issue comment event: 58
Push event: 66
Pull request review event: 18
Pull request review comment event: 13
Pull request event: 39
Fork event: 5
Create event: 11

Last Year

Issues event: 36
Watch event: 33
Delete event: 10
Issue comment event: 58
Push event: 66
Pull request review event: 18
Pull request review comment event: 13
Pull request event: 39
Fork event: 5
Create event: 11

Committers

Last synced: about 1 year ago

All Time

Total Commits: 2,893
Total Committers: 47
Avg Commits per committer: 61.553
Development Distribution Score (DDS): 0.232

Past Year

Commits: 284
Committers: 13
Avg Commits per committer: 21.846
Development Distribution Score (DDS): 0.37

Top Committers

Name	Email	Commits
Oscar Esteban	c**e@o**s	2,221
Krzysztof J. Gorgolewski	k**i@g**m	172
Zvi Baratz	z**z@g**m	64
Christopher J. Markiewicz	e**s@g**m	61
Eilidh MacNicol	e**l@g**m	42
NiPreps Bot	n**s@g**m	38
Teresa Gomez	4****g	35
Céline Provins	c**s@u**h	27
Dimitri Papadopoulos	3****s	25
Dylan Nielson	a**e@g**m	24
Ross Blair	r**2@s**u	21
Ariel Rokem	a**m@g**m	17
Jan Varada	j**a@n**v	14
Oscar Esteban	c**e@o**n	14
William Triplett	w**t@s**u	11
Jon Haitz Legarreta Gorroño	j**a@g**m	9
Mathias Goncalves	g**s@g**m	9
Nikita Beliy	b**a@o**m	9
Conrad Ma	C**d@C**l	8
John A. Lee	j**h@g**m	7
Patrick Sadil	p**l@g**m	6
Yaroslav Halchenko	d**n@o**m	6
Ursula Tooley	u**y@g**m	5
Yibei Chen	y**n@g**m	5
James D. Kent	j**t@u**u	4
Bennet Fauber	b**t@u**u	3
Michael Krause	k**e@m**e	3
Pablo Velasco	p**o@n**u	3
Taylor Salo	t**6@f**u	3
Victor Férat	v**t@l**r	3
and 17 more...

Committer Domains (Top 20 + Academic)

nih.gov: 2 stanford.edu: 2 fcbg.ch: 1 uw.edu: 1 benkay.net: 1 verdurin.com: 1 live.fr: 1 fiu.edu: 1 nyu.edu: 1 mpib-berlin.mpg.de: 1 umich.edu: 1 uiowa.edu: 1 onerussian.com: 1 unil.ch: 1 oscaresteban.es: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 205
Total pull requests: 231
Average time to close issues: almost 2 years
Average time to close pull requests: 25 days
Total issue authors: 101
Total pull request authors: 22
Average comments per issue: 2.68
Average comments per pull request: 0.84
Merged pull requests: 211
Bot issues: 0
Bot pull requests: 2

Past Year

Issues: 29
Pull requests: 43
Average time to close issues: 18 days
Average time to close pull requests: 24 days
Issue authors: 19
Pull request authors: 8
Average comments per issue: 0.52
Average comments per pull request: 0.63
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

oesteban (45)
celprov (13)
chrisgorgo (8)
bpinsard (6)
araikes (5)
dkp (5)
effigies (4)
yarikoptic (3)
LuciMoore (3)
jbwexler (3)
psadil (3)
esavary (2)
WilliamFCB (2)
tclose (2)
mckenziephagen (2)

Pull Request Authors

oesteban (208)
celprov (23)
DimitriPapadopoulos (23)
jhlegarreta (19)
zvi-quantivly (12)
effigies (5)
mckenziephagen (4)
yarikoptic (4)
arokem (3)
dependabot[bot] (3)
mgxd (3)
rwblair (2)
eilidhmacnicol (2)
vferat (2)
octomike (2)

Top Labels

Issue Labels

bug (95) documentation (14) fMRI (13) feature (12) reports (11) help wanted (9) effort:low (9) impact:high (8) new iqm (7) question (4) impact:medium (4) sMRI (3) group level (3) diffusion (3) effort:medium (3) multiecho (3) containers (2) impact:low (2) effort:high (2) wontfix (2) stale (1) dMRI (1) revise (1) infant imaging (1) deprecate (1)

Pull Request Labels

dependencies (3) reports (1) github_actions (1)

Packages

Total packages: 1
Total downloads:
- pypi 628 last-month
Total docker downloads: 10

Total dependent packages: 0
Total dependent repositories: 2
Total versions: 117
Total maintainers: 4

pypi.org: mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain.

Homepage: https://github.com/nipreps/mriqc
Documentation: https://mriqc.readthedocs.io/
License: Apache Software License
Latest release: 24.0.2
published over 1 year ago

Versions: 117
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 628 Last month
Docker Downloads: 10

Rankings

Docker downloads count: 3.5%

Stargazers count: 4.2%

Forks count: 4.3%

Average: 7.8%

Dependent packages count: 10.1%

Dependent repos count: 11.5%

Downloads: 12.9%

Maintainers (4)

cjmarkie filo mgxd nipreps

Last synced: 6 months ago

Dependencies

pyproject.toml pypi

PyYAML *
importlib_resources python_version < "3.9"
markupsafe ~= 2.0.1
matplotlib *
migas *
mriqc-learn *
nibabel >= 3.0.1
nilearn >= 0.5.1
nipype ~= 1.4
nireports ~= 23.1
nitransforms ~= 23.0
niworkflows >= 1.7.7
numpy ~=1.20
pandas ~=1.0
pybids >= 0.15.6
scikit-learn *
scipy ~=1.8
statsmodels *
toml *
torch >= 1.10.2

.github/workflows/pythonpackage.yml actions

actions/cache v1 composite
actions/checkout v2 composite
actions/setup-python v1 composite

Dockerfile docker

nipreps/miniconda py39_2205.0 build

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

mriqc

Science Score: 59.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: mriqc

Rankings

Maintainers (4)

Dependencies