Difference between revisions of "Freesurfer"
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Revision as of 19:57, 31 October 2014
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
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.