Installation

To install the stable release version of pycortex, do the following:

# First, install some required dependencies
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+https://github.com/gallantlab/pycortex.git

Optional Dependencies

For some functionality, 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.

Demo

To test if your install went well, you can run the pycortex demo.

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 [1]: import cortex
In [2]: cortex.webshow(cortex.Volume.random("S1", "fullhead"))

If everything went well, this should pop up a web browser window with a demo subject.

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