Anthony, Depending on what version of FreeSurfer you are running, you would have to run the command it would normally run to create the aseg but substitute in your atlas.
For example, in v5.1: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1
You can see the step next to -calabel: mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
Allison
On Fri, 13 Apr 2012, Anthony Dick wrote:
Hello,
I successfully created a new subcortical atlas for the cerebellum (at least I think I did--not sure how to check it without running a new segmentation). If I want to apply this to many brains, I think I want to run:
recon-all -subcortseg -subjid <subject name>
How do I tell it to call, e.g., RB_all_withskull_2012-04-13.gca instead of e.g., RB_all_withskull_2008-03-26.gca.
Basically, I want to apply the new cerebellar parcellation to existing freesurfed brains.
Anthony
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