There is also cortical_extraction.sh, which can be run from bash on Mac or Linux. It sets all of the parameters to be the same as the GUI. If necessary, you can copy it and edit it if you need to make any changes. If you do edit it, then you will want to make sure that BrainSuiteDir is set to the installation path. If it is not set, then the script will try to find the files based on location of the script.