FreeSurfer

Introduction

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.

General use

The FS wiki has many tutorials for the different commands in FreeSurfer. Andy's Brain Book! also has a good intro tutorial for FreeSurfer

Before you use FreeSurfer, you'll need to download a free license available here

Recon-all

The most important command is recon-all which manages the full cortical surface reconstruction pipeline

• This can be broken down into autorecon1, autorecon2, and autorecon3 depending on which stage of the pipeline you want to run (or re-run), but recon-all -all will run everything too

FreeView

• Visualisation software for FreeSurfer surfaces and outputs
• On MASSIVE specifically, visualisation software will require the addition of ‘vglrun’ before any commands when using the command line interface *Manual edits to cortical surfaces can be conducted within FreeSurfer through the edit mode in FreeView