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freesurfer website  

Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

Required Modules


  • freesurfer

System Variables

  • HPC_{{#uppercase:freesurfer}}_DIR and FREESURFER_HOME - installation directory
  • HPC_FREESURFER_BIN - executable directory

Freesurfer configuration variables

The following variables are preset by the freesurfer module:


Matlab configuration

If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:

fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);

or load the freesurfer module and run


Additional Information

If you encounter a NVIDIA video driver compatibility issue with FreeView try the following workaround.

The freeview program uses OpenGL extensions, which appear to be driver-dependent. If you're running freeview on or you can get freeview to run within an 'xpra' session, which will handle GLX automatically. 1. Install Xpra on your client machine - see ( 2. Log into gui or gui1 node and start freeview as follows:pick a random PORT number from 1000 to 50000

For example, for user USERNAME, GUI node, and port 3223 we can do the following:

$ module load freesurfer
$ module unload python
$ xpra start :PORT --start-child=freeview

in this case

$ xpra start :3223 --start-child=freeview

Attach to the xpra session from your local machine with

$ xpra attach

A freeview window should show up on your local desktop.


If you publish research that uses freesurfer you have to cite it as follows:

See [1] in the Freesurfer wiki on how to correctly cite Freesurfer tools.