Installing FreeSurfer

FreeSurfer is software for analysis and visualization of MRI data. In the MNE ecosystem, freesurfer is used to convert structural MRI scans into models of the scalp, inner/outer skull, and cortical surfaces, which are used to

1. model how changes in the electrical and magnetic field caused by neural activity propagate to the sensor locations (part of computing the “forward solution”), and

2. constrain the estimates of where brain activity may have occurred (in the “inverse imaging” step of source localization).

System requirements, setup instructions, and test scripts are provided on the FreeSurfer download page. Note that if you don’t already have it, you will need to install tcsh for FreeSurfer to work; tcsh is usually pre-installed with macOS, and is available in the package repositories for Linux-based systems (e.g., sudo apt install tcsh on Ubuntu-like systems).