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+git://github.com/gallantlab/pycortex.git
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.
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 : import cortex In : cortex.webshow(cortex.Volume.random("S1", "fullhead"))
If everything went well, this should pop up a web browser window with a demo subject.
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
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: