You can install Cortex using the Python package manager pip.

$ pip install cortex

To get the most up-to-date version, you can install from the git repository:

$ pip install git+git://

However, currently the demos give the best example of how to script using cortex. So, if this is your first time using cortex, it is recommended to clone from the github repository:

$ git clone
$ cd cortex
$ python install

If you don’t have administrative rights, add the --user switch to the install commands to install the packages in your home folder. If you want to update Cortex, simply repeat the first command with the --upgrade switch added to pull the latest version from GitHub.

In either case, you need to run the setup script:

$ cortex-setup

Follow the instructions; you will be asked to specify default data and out directories. These are necessary only for the demos, and can be customized in your ~/.cortexrc file.

Basic Requirements

Neuroimaging Requirements

These are not required for basic functionality, but are necessary for neuroimaging tools. afni, in particular, needs to be installed manually.


If you want to build a local copy of the documentation, follow the instructions at the documentation development guidelines.