Freesurfer

Description

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.

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.

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