Installation

The best way to install pycortex currently is by getting the latest source code from github:

git clone https://github.com/gallantlab/pycortex.git
cd pycortex
checkout glrework-merged

python setup.py develop

Dependencies

The easiest way to get most of the dependencies is using Anaconda. To use pycortex with Anaconda, first install anaconda as instructed, then:

pip install numpy Cython scipy h5py nibabel matplotlib Pillow numexpr tornado lxml networkx

You will also need to install Inkscape using whatever method is appropriate for your system. On Mac OS X you will also need to enable access to Inkscape on the command line, see these instructions.

If you are running Ubuntu without Anaconda, use the following commands:

sudo apt-get install python-dev python-numpy python-scipy python-matplotlib python-h5py python-nibabel python-lxml python-shapely python-html5lib inkscape

Demo

To test if your install went well, first download the example dataset. Then run the following commands at a terminal:

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

If everything went well, this should pop up a web browser window with the same view as http://gallantlab.org/pycortex/retinotopy_demo/.

Basic Configuration

Pycortex will automatically create a database filestore when it is first installed. In Linux, this filestore is located at /usr/local/share/pycortex/. On first import, it will also create a configuration file in your user directory which allows you to specify additional options, including alternate filestore locations. In Linux, this user configuration file is located in ~/.config/pycortex/options.cfg.

You can check the location of the filestore after installing by running:

import cortex
cortex.database.default_filestore

And you can check the location of the config file by running:

import cortex
cortex.options.usercfg

If you want to move the filestore, you need to update the config file:

[basic]
filestore=/abs/path/to/filestore