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FreeSurfer Subcortical Segmentation Work Flow

FreeSurfer now automatically runs automated labeling of the brain volume and this is included in the BasicReconstruction workflow. Each voxel in the normalized brain volume is assigned one of about 40 labels, including:

Cerebral White Matter, Cerebral Cortex, Lateral Ventricle, Inferior Lateral Ventricle, Cerebellum White Matter, Cerebellum Cortex, Thalamus, Caudate, Putamen, Pallidum, Hippocampus, Amygdala, Lesion, Accumbens area, Vessel, Central Diencephalon Third Ventricle, Fourth Ventricle, Brain Stem, Cerebrospinal Fluid

However, if you processed your anatomical data using the HistoricalReconstruction workflow, you must run the subcortical segmentation separately if you wish to obtain the automated labels.