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pycortex

Pycortex is a python-based toolkit for surface visualization of fMRI data

https://github.com/gallantlab/pycortex

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 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    18 of 62 committers (29.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.0%) to scientific vocabulary

Keywords

fmri neuroimaging python surface-visualization

Keywords from Contributors

cloud-storage google-drive numpy-arrays brain-imaging neuroscience mvpa decoding brain-mri brain-connectivity bids
Last synced: 6 months ago · JSON representation ·

Repository

Pycortex is a python-based toolkit for surface visualization of fMRI data

Basic Info
Statistics
  • Stars: 633
  • Watchers: 46
  • Forks: 143
  • Open Issues: 103
  • Releases: 16
Topics
fmri neuroimaging python surface-visualization
Created over 12 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

pycortex

Build Status Python version License

quickflat demo

Pycortex is a software library that allows you to visualize fMRI or other volumetric neuroimaging data on cortical surfaces.

Installation

[!NOTE] Pycortex cannot be currently installed in Windows, only Linux and macOS are supported.

To install the stable release version of pycortex, do the following:

```bash

First, install some required dependencies (if not already installed)

pip install -U setuptools wheel numpy cython

Install the latest release of pycortex from pip

pip install -U pycortex ```

If you wish to install the development version of pycortex, you can install it directly from Github.

To do so, replace the second install line above with the following:

```bash

Install development version of pycortex from github

pip install -U git+https://github.com/gallantlab/pycortex.git --no-build-isolation ```

Documentation

Pycortex documentation is available at https://gallantlab.github.io/pycortex.

You can find many examples of pycortex features in the pycortex example gallery.

To build the documentation locally: ```bash

Install required dependencies for the documentation

pip install sphinx_gallery numpydoc

Move into the docs folder (assuming already in pycortex directory)

cd docs

Build a local version of the documentation site

make html ```

After you run the above, you can open docs/_build/html/index.html in a web browser to view the locally built documentation.

Demo

Pycortex is best used with IPython.

If you do not already have IPython, you can install it by running: bash pip install ipython

To run the pycortex demo, using IPython, run: ipython $ ipython In [1]: import cortex In [2]: cortex.webshow(cortex.Volume.random("S1", "fullhead"))

Citation

If you use pycortex in published work, please cite the pycortex paper:

Gao JS, Huth AG, Lescroart MD and Gallant JL (2015) Pycortex: an interactive surface visualizer for fMRI. Front. Neuroinform. 9:23. doi: 10.3389/fninf.2015.00023

Owner

  • Name: gallantlab
  • Login: gallantlab
  • Kind: organization

Citation (CITATION.cff) 

authors:
  - family-names: Gao
    given-names: James S.
  - family-names: Huth
    given-names: Alexander G.
  - family-names: Lescroart
    given-names: Mark D.
  - family-names: Gallant
    given-names: Jack L.
title: 'Pycortex: an interactive surface visualizer for fMRI'
type: software
cff-version: 1.2.0
message: 'If you use this software, please cite it using the paper from this file.'
repository: 'https://github.com/gallantlab/pycortex'
url: 'https://gallantlab.github.io/pycortex'

preferred-citation:
  authors:
    - family-names: Gao
      given-names: James S.
    - family-names: Huth
      given-names: Alexander G.
    - family-names: Lescroart
      given-names: Mark D.
    - family-names: Gallant
      given-names: Jack L.
  title: 'Pycortex: an interactive surface visualizer for fMRI'
  doi: 10.3389/fninf.2015.00023
  type: article
  journal: Frontiers in Neuroinformatics
  volume: 9
  pages: 23
  year: 2015

GitHub Events

Total
  • Create event: 8
  • Release event: 1
  • Issues event: 8
  • Watch event: 48
  • Delete event: 4
  • Issue comment event: 21
  • Push event: 15
  • Pull request review comment event: 4
  • Pull request review event: 8
  • Pull request event: 21
  • Fork event: 8
Last Year
  • Create event: 8
  • Release event: 1
  • Issues event: 8
  • Watch event: 48
  • Delete event: 4
  • Issue comment event: 21
  • Push event: 15
  • Pull request review comment event: 4
  • Pull request review event: 8
  • Pull request event: 21
  • Fork event: 8

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,977
  • Total Committers: 62
  • Avg Commits per committer: 31.887
  • Development Distribution Score (DDS): 0.651
Past Year
  • Commits: 18
  • Committers: 6
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.611
Top Committers
Name Email Commits
James Gao j****s@j****m 689
Alex Huth a****h@b****u 183
alexhuth a****h@g****m 165
Storm Slivkoff s****f@g****m 95
Mark Lescroart m****t@g****m 83
Tom Dupré la Tour t****r@m****g 75
MarkLescroart m****t@b****u 70
Matteo Visconti di Oleggio Castello m****c@b****u 63
Sara Popham s****m@b****u 56
robert g****o@g****m 49
Matteo Visconti di Oleggio Castello m****c 46
James Gao j****s@l****a 46
fatma f****u@g****m 44
James Gao j****s@s****) 37
Tianjiao Zhang t****g@b****u 36
james j****s@a****) 32
Anwar Nunez-Elizalde a****z@g****m 30
mark m****k@o****u 26
James Gao j****o@g****m 17
Mark Lescroart m****t 16
christine c****e@p****b 16
Anwar Nunez-Elizalde a****z 11
Baladitya Yellapragada b****3@b****u 9
Robert Gibboni r****g@b****u 8
James Gao j****o 5
carson c****n@n****b 4
Gilles de Hollander g****r@g****m 4
Mark Lescroart m****l 4
Catherine Chen c****7@g****m 4
alebel14 a****l@a****u 3
and 32 more...
Committer Domains (Top 20 + Academic)
berkeley.edu: 12 jamesgao.com: 1 m4x.org: 1 sirius.(none): 1 arcturus.(none): 1 oxycodone.jlg.berkeley.edu: 1 pertinent-order.jlg-lab: 1 nyquil.jlg-lab: 1 austin.utexas.edu: 1 onerussian.com: 1 g.cofc.edu: 1 infocortex.com: 1 nict.go.jp: 1 hashish.jlg-lab: 1 ucsd.edu: 1 cs.cmu.edu: 1 utexas.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 66
  • Total pull requests: 153
  • Average time to close issues: 6 months
  • Average time to close pull requests: 19 days
  • Total issue authors: 51
  • Total pull request authors: 21
  • Average comments per issue: 2.47
  • Average comments per pull request: 0.66
  • Merged pull requests: 132
  • Bot issues: 0
  • Bot pull requests: 25
Past Year
  • Issues: 5
  • Pull requests: 24
  • Average time to close issues: 4 days
  • Average time to close pull requests: 4 days
  • Issue authors: 5
  • Pull request authors: 9
  • Average comments per issue: 1.2
  • Average comments per pull request: 0.54
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 11
View more stats
Top Authors
Issue Authors
  • mvdoc (7)
  • yzhlxg812 (3)
  • logogriph2 (3)
  • zengtaiping (2)
  • magehrke (2)
  • mingxue1204 (2)
  • EllieMo (2)
  • ChristianNSchmitz (2)
  • nblauch (1)
  • ryanhammonds (1)
  • geoffreyfan (1)
  • vpzgithub (1)
  • MShinkle (1)
  • dvartak (1)
  • pystar1007 (1)
Pull Request Authors
  • mvdoc (68)
  • dependabot[bot] (25)
  • TomDLT (13)
  • marklescroart (9)
  • cchen23 (6)
  • alexhuth (5)
  • kroq-gar78 (5)
  • evi-hendrikx (3)
  • MShinkle (2)
  • Matlmr (2)
  • Gilles86 (2)
  • FrancisVila (2)
  • tknapen (2)
  • smerdis (1)
  • andrewolaughlin (1)
Top Labels
Issue Labels
wontfix-windows (1)
Pull Request Labels
dependencies (25) github_actions (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 620 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 7
    (may contain duplicates)
  • Total versions: 17
  • Total maintainers: 3
pypi.org: pycortex

Python Cortical mapping software for fMRI data

  • Versions: 16
  • Dependent Packages: 1
  • Dependent Repositories: 7
  • Downloads: 620 Last month
Rankings
Stargazers count: 2.7%
Forks count: 4.2%
Dependent packages count: 4.8%
Dependent repos count: 5.5%
Average: 5.6%
Downloads: 10.7%
Maintainers (2)
jamesgao mvdoc
Last synced: 6 months ago
spack.io: py-pycortex

Python Cortical mapping software for fMRI data.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Forks count: 9.3%
Stargazers count: 10.2%
Average: 19.2%
Dependent packages count: 57.3%
Maintainers (1)
adamjstewart
Last synced: 6 months ago

Dependencies

.github/workflows/build_docs.yml actions
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  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/install_from_wheel.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/publish_to_pypi.yml actions
  • actions/checkout master composite
  • actions/setup-python v1 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/run_tests.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
requirements.txt pypi
  • cython *
  • future *
  • h5py *
  • html5lib *
  • imageio *
  • lxml *
  • matplotlib *
  • networkx >=2.1
  • nibabel >=2.1
  • numexpr *
  • numpy *
  • pillow *
  • scipy *
  • shapely *
  • six *
  • tornado >=4.3
  • wget *