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| FreeSurfer now automatically runs automated labeling of the brain volume and this is included in the BasicReconstruction workflow. | 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: |
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| However, if you have processed your anatomical data using the HistoricalReconstruction workflow, but you also wish to obtain automated labels of the neuroanatomical structures in the brain, then you must run the subcortical segmentation separately. | 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. |
[wiki:FreeSurferWorkFlows top] | [wiki:HistoricalReconstruction previous]
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.