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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:
Left/Right Cerebral White Matter Left/Right Cerebral Cortex Left/Right Lateral Ventricle Left/Right Inferior Lateral Ventricle Left/Right Cerebellum White Matter Left/Right Cerebellum Cortex Left/Right Thalamus Left/Right Caudate Left/Right Putamen Left/Right Pallidum Left/Right Hippocampus Left/Right Amygdala Left/Right Lesion Left/Right Accumbens area Left/Right 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.