Freesurfer
Description
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
Serial
- 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:
- SUBJECTS_DIR
- FUNCTIONALS_DIR
- FSFAST_HOME
- MNI_DIR
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);
path(path,fsfasttoolbox);
or load the freesurfer module and run
source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh
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 gui.rc.ufl.edu or gui1.rc.ufl.edu you can get freeview to run within an 'xpra' session, which will handle GLX automatically. 1. Install Xpra on your client machine - see (https://www.xpra.org) 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 gui1.rc.ufl.edu, 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 ssh:USERNAME@gui1.rc.ufl.edu:3223
A freeview window should show up on your local desktop.
Citation
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.