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.

Note that starting with Freesurfer-6.0.0 the software is installed in a container. To launch any programs use the launch_freesurfer command. E.g.

launch_freesurfer mri_diff

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