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FreeSurfer

FreeSurfer is an open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images

Usage♯

The following versions of FreeSurfer are available on Picotte:

  • 5.3.0
  • 7.4.1

You can load them using modulefiles, for example:

module load freesurfer/7.4.1

In general, we recommend using the latest version of FreeSurfer. 5.3.0 is very old, and is only present to support the CBIG lab tools, which are used by some Drexel groups, and have a dependency on 5.3.0.

Once loaded, you can run FreeSurfer commands. For example, to run the recon-all command, you can do the following:

recon-all -subject <subject_id> -all

Documentation♯

The FreeSurfer documentation is available online.