Python Cortical mapping software for fMRI data
Pycortex is a software library that allows you to visualize fMRI or other volumetric neuroimaging data on cortical surfaces.
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
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+git://github.com/gallantlab/pycortex.git
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.
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 : import cortex In : cortex.webshow(cortex.Volume.random("S1", "fullhead"))
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
Please post on NeuroStars with the tag
ask questions about how to use Pycortex.
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