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visualqc

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

https://github.com/raamana/visualqc

Science Score: 26.0%

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
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.5%) to scientific vocabulary

Keywords

alignment anatomical-mri cortex fmri freesurfer medical-imaging mri-images neuroimaging neuroscience outlier-detection outlier-removal qc quality-control registration

Keywords from Contributors

connectivity data-structures interactive mri profiles distribution transformers integral sequences generic
Last synced: 5 months ago · JSON representation

Repository

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

Basic Info
Statistics
  • Stars: 73
  • Watchers: 5
  • Forks: 13
  • Open Issues: 38
  • Releases: 4
Topics
alignment anatomical-mri cortex fmri freesurfer medical-imaging mri-images neuroimaging neuroscience outlier-detection outlier-removal qc quality-control registration
Created over 8 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Authors

README.rst 


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

.. image:: https://app.codacy.com/project/badge/Grade/c67fbfc899d04f5aacd7a0070aeb704d
        :target: https://www.codacy.com/gh/raamana/visualqc/dashboard?utm_source=github.com&utm_medium=referral&utm_content=raamana/visualqc&utm_campaign=Badge_Grade

.. image:: https://img.shields.io/badge/say-thanks-ff69b4.svg
        :target: https://saythanks.io/to/raamana

==========================================================================================
VisualQC : software development kit for medical and neuroimaging quality control
==========================================================================================

.. image:: docs/vqc_logo_small.png



.. image:: docs/visualqc_poster_comprehensive.png


Links
-------

* Software Documentation: https://raamana.github.io/visualqc
* `User Manual `_
* Free software: Apache 2.0 license
* Pure python package (no licensing issues ala matlab, easy to install and update requiring no other external installations or maintenance)
* Generic design for API that can be adapted for other domains, imaging or medical or otherwise.


Galleries
----------

* NEW: `Defacing QC `_
* `Freesurfer `_
* `Functional MRI `_
* `Registration/Alignment quality `_
* `Structural T1w MRI `_
* `Volumetric Segmentation `_


Citation
--------------

If you used ``VisualQC`` in your analyses or projects, whether or not it was reported in the main paper, please consider citing the paper below:

- Pradeep Reddy Raamana (2023), “VisualQC: Software Development Kit for Medical and Neuroimaging Quality Control and Assurance.” Aperture Neuro 3 (March): 1–4. https://doi.org/10.52294/e130fcd2-ce83-4222-856d-c82022013a50

Bibtex:

.. code-block:: tex

    @article{Raamana_2022_VisualQCSoftware,
    	journal={Aperture Neuro},
    	doi={10.52294/e130fcd2-ce83-4222-856d-c82022013a50},
    	publisher={Organization for Human Brain Mapping},
    	title={VisualQC: software development kit for medical and neuroimaging quality control and assurance},
    	volume=3,
    	author={Reddy Raamana, Pradeep},
    	pages={1--4},
    	date={2023-03-02},
    	year=2023,
    	month=3,
    	day=2,
    }

More details at ``_

Contributions
--------------

`Contributions are welcome. `_

---

.. image:: https://img.shields.io/badge/say-thanks-ff69b4.svg
        :target: https://saythanks.io/to/raamana

Owner

  • Name: Pradeep Reddy Raamana
  • Login: raamana
  • Kind: user
  • Location: Pittsburgh, PA
  • Company: University of Pittsburgh

Neuroscientist trying to bridge the gap between clinic & computer science. Interests: Machine learning, Neuroimaging, Brain disorders, Informatics, Open science

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 3
  • Push event: 1
Last Year
  • Issues event: 2
  • Issue comment event: 3
  • Push event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 634
  • Total Committers: 3
  • Avg Commits per committer: 211.333
  • Development Distribution Score (DDS): 0.292
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pradeep Reddy Raamana r****a@g****m 449
Pradeep Reddy Raamana p****a@r****g 181
dependabot[bot] 4****] 4
Committer Domains (Top 20 + Academic)
research.baycrest.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 66
  • Total pull requests: 16
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 22
  • Total pull request authors: 2
  • Average comments per issue: 4.08
  • Average comments per pull request: 1.06
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • raamana (30)
  • atheyers (6)
  • aryamehta2006 (3)
  • MarcKhoury8 (2)
  • cfhammill (2)
  • tjiagoM (2)
  • XinQi7788 (2)
  • ericearl (2)
  • rb643 (1)
  • zswgzx (1)
  • kavandeloo97 (1)
  • araikes (1)
  • Arshitha (1)
  • tselliah (1)
  • jbramen (1)
Pull Request Authors
  • raamana (10)
  • dependabot[bot] (6)
Top Labels
Issue Labels
enhancement (3) help wanted (2)
Pull Request Labels
dependencies (6)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 109 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 31
  • Total maintainers: 1
pypi.org: visualqc

Assistive tool for the quality control of neuroimaging data

  • Versions: 31
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 109 Last month
Rankings
Dependent packages count: 4.7%
Stargazers count: 8.2%
Forks count: 9.8%
Average: 13.4%
Dependent repos count: 21.7%
Downloads: 22.7%
Maintainers (1)
raamana
Last synced: 6 months ago

Dependencies

docs/requirements_docs.txt pypi
  • matplotlib *
  • mrivis *
  • nibabel *
  • numpy *
  • numpydoc *
  • sphinx-argparse *
requirements.txt pypi
  • matplotlib >=2.1.1
  • mrivis *
  • nibabel *
  • nilearn *
  • numpy *
  • pillow *
  • pybids *
  • pyyaml >=4.2b1
  • scikit-learn *
  • scipy *
requirements_dev.txt pypi
  • Sphinx ==1.4.8 development
  • bumpversion ==0.5.3 development
  • coverage ==4.1 development
  • cryptography ==3.3.2 development
  • flake8 ==2.6.0 development
  • pip ==21.1 development
  • pytest ==2.9.2 development
  • pytest-runner ==2.11.1 development
  • pyyaml >=4.2b1 development
  • tox ==2.3.1 development
  • watchdog ==0.8.3 development
  • wheel ==0.29.0 development
.github/workflows/codeql-analysis.yml actions
  • actions/checkout v3 composite
  • github/codeql-action/analyze v2 composite
  • github/codeql-action/autobuild v2 composite
  • github/codeql-action/init v2 composite