12.15. Using FreeSurfer

• 12.15.1. How to use FS recon-all with AFNI
  • Introduction
  • Start-to-finish FS example
  • Run recon-all faster: -parallel
  • A note of filenames/paths with FS
  • A general tcsh script for FS+SUMA
  • A note on @SUMA_Make_Spec_FS outputs
  • Minor note on FS setup
• 12.15.2. Run FS on a cluster (NIH’s Biowulf) with AFNI
  • Introduction
  • Overview
  • Module loading FS (and other things) in a script
  • Using scratch disks as temporary directories
  • A general biowulf script
  • Looping over a group of subjects
• 12.15.3. More useful outputs from @SUMA_Make_Spec_FS
  • Introduction
  • The renumbered (REN) atlas dsets
  • The fs*.nii.gz mask dsets
  • QC images
  • ROI, tissue and mask quantities (stats*.1D files)