pycortex
========
[](https://github.com/gallantlab/pycortex/actions/workflows/run_tests.yml)
[](https://www.python.org/downloads/release/python)
[](https://opensource.org/licenses/BSD-2-Clause)
[](https://gallantlab.github.io/pycortex)
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](https://gallantlab.github.io/pycortex).
You can find many examples of pycortex features in the [pycortex example gallery](https://gallantlab.github.io/pycortex/auto_examples/index.html).
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](http://dx.doi.org/10.3389/fninf.2015.00023):
_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_
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"description": "pycortex\n========\n[](https://github.com/gallantlab/pycortex/actions/workflows/run_tests.yml)\n[](https://www.python.org/downloads/release/python)\n[](https://opensource.org/licenses/BSD-2-Clause)\n\n\n[](https://gallantlab.github.io/pycortex)\n\nPycortex is a software library that allows you to visualize fMRI or other volumetric neuroimaging data on cortical surfaces.\n\nInstallation\n------------\n\n> [!NOTE]\n> Pycortex cannot be currently installed in Windows, only Linux and macOS are supported.\n\nTo install the stable release version of pycortex, do the following:\n\n```bash\n# First, install some required dependencies (if not already installed)\npip install -U setuptools wheel numpy cython\n# Install the latest release of pycortex from pip\npip install -U pycortex\n```\n\nIf you wish to install the development version of pycortex, you can install it directly from Github.\n\nTo do so, replace the second install line above with the following:\n\n```bash\n# Install development version of pycortex from github\npip install -U git+https://github.com/gallantlab/pycortex.git --no-build-isolation\n```\n\nDocumentation\n-------------\nPycortex documentation is available at [https://gallantlab.github.io/pycortex](https://gallantlab.github.io/pycortex).\n\nYou can find many examples of pycortex features in the [pycortex example gallery](https://gallantlab.github.io/pycortex/auto_examples/index.html).\n\nTo build the documentation locally:\n```bash\n# Install required dependencies for the documentation\npip install sphinx_gallery numpydoc\n# Move into the docs folder (assuming already in pycortex directory)\ncd docs\n# Build a local version of the documentation site\nmake html\n```\n\nAfter you run the above, you can open `docs/_build/html/index.html` in a web browser to view the locally built documentation.\n\nDemo\n----\nPycortex is best used with [IPython]().\n\nIf you do not already have IPython, you can install it by running:\n```bash\npip install ipython\n```\n\nTo run the pycortex demo, using IPython, run:\n```ipython\n$ ipython\nIn [1]: import cortex\nIn [2]: cortex.webshow(cortex.Volume.random(\"S1\", \"fullhead\"))\n```\n\nCitation\n--------\nIf you use pycortex in published work, please cite the [pycortex paper](http://dx.doi.org/10.3389/fninf.2015.00023):\n\n_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_\n",
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