Subcortical Segmentation

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

FreeSurfer runs automated labeling of the brain volume during the -autorecon2 stage.

The automatic subcortical segmentation can take many (11+) hours to complete.

To view just the segmentation, use this command:

tkmedit <subject name> norm.mgz -aseg 

Float your cursor over any voxel and the label assigned to it will be displayed in the TkMeditTools window.

If the voxels are incorrectly labeled, then you can re-label them yourself although we suggest contacting the freesurfer mailing list first to see if there is an automatic procedure that can be used to re-label them.. Refer to the TkMeditGuide/TkMeditWorkingWithData/TkMeditSelectionsLabels page for detailed information on manually editing the aseg.

Aseg Atlas

Automatic subcortical segmentation of a brain volume is based upon the existence of an atlas containing probablistic information on the location of structures. This is decribed here:

The atlas included with the Freesurfer distribution is found in the 'average' directory, and is called 'RB_all_2008-03-26.gca'. It is possible to construct your own atlas. This is described next.

Constructing an Aseg Atlas

Basic steps:

See also rebuild_gca_atlas.csh script in $FREESURFER_HOME/bin.

See also AtlasSubjects

For accuracy evaluations see also SubcorticalSegmentationAccuracy


The original CMA segmentation scheme used for subcortical segmentation training is defined by (Filipek, et al, Cerebral Cortex, 1994) (paper). However, with better imaging resolution, anatomists Verne Caviness and Nikos Mkris developed the separation of the "thalamus proper" from a "ventral diencephalon" region that subtends many of the smaller nuclei and structures in the area inferior to the thalamus, such as hypothalamus, red nuclei, later and medial geniculate, ect. The first definition of the ventral diencephalon method is provided in Am J Med Genet. 1997 Sep 19;74(5):507-14. (paper).