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.
Environment Modules¶
Run module spider freesurfer to find out what environment modules are available for this application.
Environment Variables¶
- HPC_FREESURFER_DIR - installation directory
- HPC_FREESURFER_BIN - executable directory
Additional Usage Information¶
Starting with freesurfer/6.0.0 the software is available as a Singularity container. To run any executable use the 'launch_freesurfer' wrapper after loading the module.
E.g.
$ launch_freesurfer dcmunpack
Note
Freesurfer comes with Freeview software. Freeview is a completely separate software from Freesurfer and is used purely for data visualization. Freesurfer 6 includes Freeview 2.0.
Warning
Do not use the '-debug' option with the trac-all command as it can consume filesystem inodes very quickly in the Freesurfer output directory. This can exhaust inode supply and lead to a work stoppage for multiple research groups. If a user must use the '-debug' option with Freesurfer commands they must first engage UFRC staff by submitting a support request at https://support.rc.ufl.edu.
Citation¶
If you publish research that uses freesurfer you have to cite it as follows:
See this page in the Freesurfer wiki on how to correctly cite Freesurfer tools.
Categories¶
biology, neuroscience, imaging