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Pycortex is a python-based toolkit for surface visualization in fMRI data
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quickflat demo

Pycortex is a software that allows you to visualize fMRI or other volumetric mapping data on cortical surfaces.


The easiest way to get pycortex is to use the Anaconda python distribution. Download and install anaconda, then run the following commands:

$ sudo pip install nibabel
$ sudo pip install pycortex

If you are using Ubuntu, using Neurodebian is highly recommended. The following command will install all python prerequisites:

$ sudo apt-get install python-pip python-dev python-numpy python-scipy python-matplotlib python-h5py python-nibabel python-lxml python-shapely python-html5lib mayavi2 inkscape blender
$ sudo pip install pycortex


Pycortex is best used with IPython. To run this demo, please download this example dataset.

$ ipython
In [1]: import cortex
In [2]: ds = cortex.load("S1_retinotopy.hdf")
In [3]: cortex.webshow(ds)


Please find more complete documentation for pycortex at The documentation for pycortex is currently incomplete, but will be improved in the coming days.


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

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