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:

# 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
# or, with headless rendering support:
pip install -U 'pycortex[headless]'

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:

# 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:

# 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:

pip install ipython

To run the pycortex demo, using IPython, run:

$ 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