FreeSurferAnalysis - MRC CBU Imaging Wiki
location: FreeSurferAnalysis

Analysis of MRI Data in !FreeSurfer


Further Help

  • The most important source for help is the wiki mentioned above.
  • This page outlines a basic pipeline for some types of FreeSurfer analysis (however, it is specifically designed not to work by default. You should educate yourself and make decisions based on your specific experiment). There are far too many features in FreeSurfer to cover all of them in our wiki, so do not think this page covers all of the details: DanStructurals.

Some relevant papers

Can be found toward the bottom of this page:

The code

FreeSurfer has been developed at the Martinos Center (in Boston, US). Here is its home:

At the moment, we are using "FreeSurfer 4.3.0". At the CBU, FreeSurfer is installed here:


To source the MNE tools type "freesurfer_4.3.0". Some of the tools will only be available on vncserver.glx sessions (or at a linux workstation).

A previous version "FreeSurfer 4.0.1" is available.

To source this version type "freesurfer_4.0.1".

Recent Updates

2009/04/15 Installed latest MNE



to use it [DGW]

2009/04/15 Installed latest Freesurfer



to use it[DGW]

2008/06/03 Added MNE Tutorial setup

I've added a separate mne_tutorial setup which locally sources mne in order to avoid aliasing commands with --digtrig STI101. This should only be used for the MNE Tutorial.

Instead of typin mne_setup_2.5, as you would normally, type mne_tutorial.


CbuImaging: FreeSurferAnalysis (last edited 2013-08-01 14:20:20 by RussellThompson)