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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). If, after generating an ASEG volume for your previously processed data, you wish for whatever reason to recreate the final surfaces for data previously processed using the HistoricalReconstruction workflow, then you must specify that it preserves and uses the white matter volume (WM) that you edited. Simply use this flag: