Difference between revisions of "Freesurfer"

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==System Variables==
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory

Revision as of 21:20, 6 December 2019


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.

Required Modules


  • freesurfer

System Variables

  • HPC_FREESURFER_DIR and FREESURFER_HOME - installation directory

Additional 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.


launch_freesurfer dcmunpack


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.


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.