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FreeSurfer Subcortical Segmentation

FreeSurfer now automatically runs automated labeling of the brain volume and this is included in all versions of the September 2005 release. In subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels, including:

However, if you processed your anatomical data using previous versions, you can just run the subcortical segmentation separately if you wish to obtain the automated labels. The September 2005 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG) to segment the white matter volume (WM). You will use the -noedit_wm_with_aseg flag to ensure that it preserves and uses the white matter volume (WM) that you edited.

recon-all -subjid <subject name> -autorecon1 -noedit_wm_with_aseg