FreeSurfer can be accessed from most computers on the Martinos network. This page will show you how to access the FreeSurfer program, and points you towards some tutorials to help learn how to use it.

Accessing FreeSurfer

First, consider if you need access to a stable or development version of FreeSurfer. If you are not sure you probably want to use the stable version. The development version contains new and untested features.

Copy and paste a command below into your terminal:

Stable: 

source /usr/local/freesurfer/nmr-stable60-env

Development: 

source /usr/local/freesurfer/nmr-dev-env

To ensure that worked, type  freeview  into the command prompt, press enter, and see if FreeView opened. FreeView is a tool that comes with FreeSurfer - it lets you look at the data FreeSurfer creates along with many other files common to MRI research.

Learning how to use FreeSurfer

Here is a recommended way to get up to speed on using FreeSurfer:

  1. If you are not familiar with using a Unix terminal, watch this video: https://www.youtube.com/watch?v=6eJMxh7PlOY

  2. Here is a link to online versions of a FreeSurfer course: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial

    • Each lecture has a corresponding video found here: https://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA

    • You may not be allowed the needed space to download the course data to your computer - check with someone in your lab about finding a spot to put that data.

    • To get a basic understanding of FreeSurfer it is recommended to go through all course material up to and including "Quality Checking a Recon". From there you can complete the rest to explore different specific functions of FreeSurfer, or select tutorials related to the research you plan to do.

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