brainstat

A statistics and context decoding toolbox for neuroimaging.

https://github.com/mica-mni/brainstat

Science Score: 44.0%

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
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DOI references
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary

Keywords

matlab neuroimaging python statistics

Keywords from Contributors

brainweb

Last synced: 6 months ago · JSON representation ·

Repository

A statistics and context decoding toolbox for neuroimaging.

Basic Info

Host: GitHub
Owner: MICA-MNI
License: other
Language: Jupyter Notebook
Default Branch: master
Homepage: https://brainstat.readthedocs.io
Size: 276 MB

Statistics

Stars: 105
Watchers: 7
Forks: 24
Open Issues: 11
Releases: 26

Topics

matlab neuroimaging python statistics

Created almost 6 years ago · Last pushed over 1 year ago

Metadata Files

Readme Contributing License Code of conduct Citation Codeowners

README.rst

BrainStat : A toolbox for statistical analysis of neuroimaging data
===================================================================

.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
    :target: https://opensource.org/licenses/BSD-3-Clause
.. image:: https://github.com/MICA-MNI/BrainStat/actions/workflows/python_unittests.yml/badge.svg
    :target: https://github.com/MICA-MNI/BrainStat/actions/workflows/python_unittests.yml
.. image:: https://github.com/MICA-MNI/BrainStat/actions/workflows/MATLAB_unittests.yml/badge.svg
    :target: https://github.com/MICA-MNI/BrainStat/actions/workflows/MATLAB_unittests.yml 
.. image:: https://readthedocs.org/projects/brainstat/badge/?version=master&style=plastic
    :target: https://brainstat.readthedocs.io/en/latest/
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black
.. image:: https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg
    :target: https://www.mathworks.com/matlabcentral/fileexchange/89827-brainstat

Welcome to BrainStat's documentation!

BrainStat is a toolbox for the statistical analysis and context decoding of
neuroimaging data. It implements both univariate and multivariate linear models
and interfaces with the BigBrain Atlas, Allen Human Brain Atlas and Nimare
databases. BrainStat flexibly handles common surface, volume, and parcel level
data formats, and provides a series of interactive visualization functions. The
toolbox has been implemented in both Python and MATLAB, the two most widely
adopted programming languages in the neuroimaging and neuroinformatics
communities. It is openly available, and documented `here
`_. 

.. image:: https://github.com/MICA-LAB/BrainStat/blob/master/docs/figures/brainstat_logo_bw.png?raw=true

..
    For some reason referencing the BrainStat image locally doesn't work, so
    just linking to the image on Github instead. 

Developers
----------
.. |seyma_s|   unicode:: U+015E .. CEDILLA S

- Sara Lariviere - MICA Lab, Montreal Neurological Institute
- |seyma_s|\ eyma Bayrak - Max Planck Institute for Human Cognitive and Brain Sciences 
- Reinder Vos de Wael - MICA Lab, Montreal Neurological Institute
- Oualid Benkarim - MICA Lab, Montreal Neurological Institute
- Raul Cruces - MICA Lab, Montreal Neurological Institute
- Jessica Royer - MICA Lab, Montreal Neurological Institute
- Peer Herholz - Montreal Neurological Institute 
- Seok-Jun Hong - Sungkyunkwan University
- Sofie Valk - Max Planck Institute for Human Cognitive and Brain Sciences
- Boris Bernhardt - Montreal Neurological Institute 


License
-------

The BrainStat source code is available under the `BSD (3-Clause) license
`_.


Support
-------

If you have problems installing the software or questions about usage and
documentation, or something else related to BrainStat, you can post to the
`Issues `_ section of our repository.

Owner

Name: MICA-MNI
Login: MICA-MNI
Kind: organization
Location: Montreal

Website: mica-mni.github.io
Repositories: 8
Profile: https://github.com/MICA-MNI

Multimodal Imaging and Conenctome Analysis Lab at the Montreal Neurological Institute.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite the BrainStat manuscript."

authors:
  - family-names: "Vos de Wael"
    given-names: "Reinder"
    orcid: "https://orcid.org/0000-0003-0574-6576"
  - family-names: "Bayrak"
    given-names: "Şeyma"
  - family-names: "Benkarim"
    given-names: "Oualid"
    orcid: "https://orcid.org/0000-0003-3922-7643"
  - family-names: "Herholz"
    given-names: "Peer"
    orcid: "https://orcid.org/0000-0002-9840-6257" 
  - family-names: "Larivere"
    given-names: "Sara"
    orcid: "https://orcid.org/0000-0001-5701-1307"
  - family-names: "Rodriguez-Cruces"
    given-names: "Raul"
    orcid: "https://orcid.org/0000-0002-2917-1212"
  - family-names: "Paquola"
    given-names: "Casey"
    orcid: "https://orcid.org/0000-0002-0190-4103"
  - family-names: "Hong"
    given-names: "Seok-Jun"
    orcid: "https://orcid.org/0000-0002-1847-578X"
  - family-names: "Misic"
    given-names: "Bratislav"
    orcid: "https://orcid.org/0000-0003-0307-2862"
  - family-names: "Evans"
    given-names: "Alan"
    orcid: "https://orcid.org/0000-0003-3841-6098"
  - family-names: "Valk"
    given-names: "Sofie L."
    orcid: "https://orcid.org/0000-0003-2998-6849"
  - family-names: "Bernhardt"
    given-names: "Boris C."
    orcid: "https://orcid.org/0000-0001-9256-6041"

title: "BrainStat: a toolbox for brain-wide statistics and neuroscientific contextualization"

preferred-citation: 
  authors:
  - family-names: "Vos de Wael"
    given-names: "Reinder"
    orcid: "https://orcid.org/0000-0003-0574-6576"
  - family-names: "Bayrak"
    given-names: "Şeyma"
  - family-names: "Benkarim"
    given-names: "Oualid"
    orcid: "https://orcid.org/0000-0003-3922-7643"
  - family-names: "Herholz"
    given-names: "Peer"
    orcid: "https://orcid.org/0000-0002-9840-6257" 
  - family-names: "Larivere"
    given-names: "Sara"
    orcid: "https://orcid.org/0000-0001-5701-1307"
  - family-names: "Rodriguez-Cruces"
    given-names: "Raul"
    orcid: "https://orcid.org/0000-0002-2917-1212"
  - family-names: "Paquola"
    given-names: "Casey"
    orcid: "https://orcid.org/0000-0002-0190-4103"
  - family-names: "Hong"
    given-names: "Seok-Jun"
    orcid: "https://orcid.org/0000-0002-1847-578X"
  - family-names: "Misic"
    given-names: "Bratislav"
    orcid: "https://orcid.org/0000-0003-0307-2862"
  - family-names: "Evans"
    given-names: "Alan"
    orcid: "https://orcid.org/0000-0003-3841-6098"
  - family-names: "Valk"
    given-names: "Sofie L."
    orcid: "https://orcid.org/0000-0003-2998-6849"
  - family-names: "Bernhardt"
    given-names: "Boris C."
    orcid: "https://orcid.org/0000-0001-9256-6041"

  title: "BrainStat: a toolbox for brain-wide statistics and neuroscientific contextualization"
  doi: 10.1101/2022.01.18.476795
  date-released: 2022-01-21
  url: "https://www.biorxiv.org/content/10.1101/2022.01.18.476795v1"
  journal: bioRxiv
  type: article

GitHub Events

Total

Issues event: 6
Watch event: 8
Issue comment event: 4
Fork event: 1

Last Year

Issues event: 6
Watch event: 8
Issue comment event: 4
Fork event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 726
Total Committers: 13
Avg Commits per committer: 55.846
Development Distribution Score (DDS): 0.49

Past Year

Commits: 14
Committers: 1
Avg Commits per committer: 14.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Reinder Vos de Wael	r**l@g**m	370
Şeyma Bayrak	s**a@g**m	228
saratheriver	s**r@g**m	54
Boris Bernhardt	b**t@g**m	29
Enning Yang	e**0@g**m	14
Ruediger Meier	r**r@g**l	12
rcruces	r**s@i**x	6
PeerHerholz	h**r@g**m	4
oualidbenkarim	L**p@r**5	4
Sofie	s**k@g**m	2
Ross Markello	r**o@g**m	1
NicolasGensollen	n**n@g**m	1
Ghislain Vaillant	g****l	1

Committer Domains (Top 20 + Academic)

inb.unam.mx: 1 ga-group.nl: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 41
Total pull requests: 89
Average time to close issues: 11 months
Average time to close pull requests: about 1 month
Total issue authors: 27
Total pull request authors: 7
Average comments per issue: 1.07
Average comments per pull request: 0.07
Merged pull requests: 81
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 9
Pull requests: 7
Average time to close issues: 23 days
Average time to close pull requests: about 3 hours
Issue authors: 8
Pull request authors: 1
Average comments per issue: 0.67
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ReinderVosDeWael (11)
knutj (2)
JohannesWiesner (2)
NicolasGensollen (2)
YH2010 (2)
tomug (1)
mtsotras (1)
qiruizhangqirui (1)
GerardYu (1)
RuiWang0805 (1)
dancebean (1)
iamnielsjanssen (1)
araikes (1)
fhaos123 (1)
jihoonkim2100 (1)

Pull Request Authors

saratheriver (42)
ReinderVosDeWael (33)
zihuaihuai (13)
neuroimagingdatascience (6)
NicolasGensollen (2)
ghisvail (2)
lassemadsen (1)

Top Labels

Issue Labels

Python (7) bug (5) on hold (4) Documentation (3) enhancement (3) low priority (3) Github (2) MATLAB (1) high priority (1)

Pull Request Labels

Python (59) Documentation (52) MATLAB (35) Github (17)

Dependencies

docs/requirements.txt pypi

Sphinx ==3.5.4
plotly *
sphinx-gallery *
sphinx_rtd_theme *
sphinxcontrib-matlabdomain *
wordcloud *

requirements.txt pypi

abagen >=0.1
brainspace >=0.1.1
h5py *
matplotlib >=2.0.0
netneurotools >=0.2.3
neurosynth *
nibabel *
nilearn >=0.7.0
nimare *
numpy >=1.16.5
pandas *
scikit_learn *
scipy >=1.3.3
templateflow *
trimesh *

setup.py pypi

abagen >=0.1
brainspace >=0.1.2
h5py *
netneurotools *
neurosynth *
nibabel *
nilearn >=0.7.0
nimare *
numpy >=1.16.5
pandas *
scikit_learn *
scipy >=1.3.3
templateflow *
trimesh *

.github/workflows/MATLAB_unittests.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
matlab-actions/run-tests v0 composite
matlab-actions/setup-matlab v0 composite

.github/workflows/development_release.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/label.yml actions

actions/labeler v2 composite

.github/workflows/python_unittests.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
psf/black stable composite

.github/workflows/tagged_release.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
marvinpinto/action-automatic-releases latest composite
matlab-actions/setup-matlab v0 composite
pypa/gh-action-pypi-publish master composite

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Open Source Science

brainstat

Science Score: 44.0%

Keywords

Keywords from Contributors

Repository

Basic Info

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Topics

Metadata Files

README.rst

Owner

Citation (CITATION.cff)

GitHub Events

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Committers

All Time

Past Year

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Committer Domains (Top 20 + Academic)

Issues and Pull Requests

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Dependencies