Freesurfer

Freesurfer is an open source software suite for processing and analyzing human brain MRI images: https://surfer.nmr.mgh.harvard.edu/

For a structural MRI scan, Freesurfer can:

• perform skull stripping
• segment gray matter from white matter
• label cortical and subcortical structures

This functionality is a gear on Flywheel.

Freesurfer download and installation

Follow instructions on the [Freesurfer wiki] (https://surfer.nmr.mgh.harvard.edu/fswiki)

Freesurfer integration with vistasoft

To check if Freesurfer was downloaded successfully, open Matlab and type the following in the command window:
getenv('FREESURFER_HOME')
getenv('SUBJECTS_DIR')

These Matlab calls should return paths, not empty vectors:
/Applications/freesurfer
Your/Freesurfer_subjects/directory/Freesurfer_subjects

Tip: If you use Freesurfer frequently, it might be tedious to add it to your path every time you open Matlab. Follow the instruction [HERE] (https://github.com/vistalab/vistasoft/wiki/Mac-vistasoft-software-configuration) or watch the first 2 tutorials [HERE] (http://psych.nyu.edu/winawerlab/Vistasoft%20Code%20Review/index.htm) if you want to have Freesurfer path available every time you launch Matlab.