Python Cortical mapping software for fMRI data
Project description
pycortex
Pycortex is a software library that allows you to visualize fMRI or other volumetric neuroimaging data on cortical surfaces.
Quickstart
# create a virtual environment called env with Python 3
python3 -m venv env
# activate the virtual environment
source env/bin/activate
# install some prerequisite packages
pip install -U setuptools wheel numpy cython
# install the latest release of pycortex from pip
pip install -U pycortex
This command creates a new virtualenv for pycortex to resolve dependencies. Run source env/bin/activate
whenever you need pycortex.
If you want to install the latest, unreleased version of pycortex from github, instead of the last line you can run
# install unreleased version of pycortex from github
pip install -U git+git://github.com/gallantlab/pycortex.git
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:
pip install sphinx_gallery
pip install numpydoc
cd docs
make html
# open `docs/_build/html/index.html` in web browser
Demo
Pycortex is best used with IPython. Install it in your virtualenv using
source env/bin/activate
pip install ipython
To run the pycortex demo,
$ 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
Getting help
Please post on NeuroStars with the tag pycortex
to
ask questions about how to use Pycortex.
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