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| [wiki:Self:FreeSurferWorkFlows top] | [wiki:Self:HistoricalReconstruction previous] | [[FreeSurferWorkFlows|top]] |
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| = FreeSurfer Subcortical Segmentation Work Flow = | = Subcortical Segmentation = |
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| 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: | In automatic subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels, including: |
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| 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 |
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, Third Ventricle, Fourth Ventricle, Brain Stem, Cerebrospinal Fluid |
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| 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. | FreeSurfer runs automated labeling of the brain volume [[ReconAllDevTable|during the -autorecon2 stage]]. The automatic subcortical segmentation can take many (11+) hours to complete. |
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| 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: * [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf|Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain]], Fischl et al., (2002). Neuron, 33:341-355. 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: * Using tkmedit, label each volume in the brain. Repeat for all subjects to be included in the atlas. * Run [[mri_ca_train]] to create the atlas. See also rebuild_gca_atlas.csh script in $FREESURFER_HOME/bin. See also AtlasSubjects |
Subcortical Segmentation
In automatic 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, Third Ventricle, Fourth Ventricle, Brain Stem, Cerebrospinal Fluid
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:
Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al., (2002). Neuron, 33:341-355.
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:
- Using tkmedit, label each volume in the brain. Repeat for all subjects to be included in the atlas.
Run mri_ca_train to create the atlas.
See also rebuild_gca_atlas.csh script in $FREESURFER_HOME/bin.
See also AtlasSubjects