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FreeSurfer Subcortical Segmentation

In subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels, including:

FreeSurfer now automatically runs automated labeling of the brain volume and this is included in all versions of the September 2005 release. However, if you processed your anatomical data using previous versions and you wish to obtain the automated labels, you can just run the subcortical segmentation separately. It is important to note that the September 2005 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG) to segment the white matter volume (WM). You must therefore use the -noedit_wm_with_aseg flag to ensure that it preserves and uses the white matter volume (WM) edits that you made, if you rerun any later steps on your previously edited data -- e.g. if for some reason you wish to regenerate final surfaces.

So, to obtain automatically segmented volumes for the first time, run:

recon-all -subcortseg -segstats -subjid <subject name>

The automatic subcortical segmentation can take many hours to complete.

To view the segmentation, use this command:

tkmedit <subject name> norm.mgz -segmentation mri/aseg $FREESURFER_HOME/tkmeditColorsCMA