pycortex
========
Pycortex is a software library that allows you to visualize fMRI or other volumetric neuroimaging data on cortical surfaces.
Installation ------------
To install the stable release version of pycortex, do the following:
# Install the latest release of pycortex from pip
pip install -U pycortex
or, with headless rendering support:
pip install -U 'pycortex[headless]'
or, with automatic surface flattening support (see autoflatten):
pip install -U 'pycortex[autoflatten]'
or, with all optional features:
pip install -U 'pycortex[all]'If you wish to install the development version of pycortex, you can install it directly from Github.
To do so, replace the first install line above with the following:
# Install development version of pycortex from github
pip install -U git+https://github.com/gallantlab/pycortex.gitNote you will need a C compiler installed to build from scratch because there are cython code.
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 htmlAfter 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 ipythonTo 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_