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