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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
 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

[wiki:FreeSurferWorkFlows top] | [wiki:HistoricalReconstruction previous]

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:

  • 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 previous versions, you can just run the subcortical segmentation separately if you wish to obtain the automated labels.

SubcorticalSegmentation (last edited 2018-01-04 15:07:58 by MorganFogarty)