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| = FreeSurfer Subcortical Segmentation Work Flow = | = FreeSurfer 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 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, Central Diencephalon, 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 now automatically runs automated labeling of the brain volume and this is included in all versions of the September 2005 release. However, if you processed your anatomical data using previous versions and you wish to obtain the automated labels, you can just run the subcortical segmentation separately. It is important to note that the September 2005 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG) to segment the white matter volume (WM). You must therefore use the -noedit_wm_with_aseg flag to ensure that it preserves and uses the white matter volume (WM) edits that you made, ''if'' you rerun any later steps on your previously edited data -- e.g. if for some reason you wish to regenerate final surfaces. So, to obtain automatically segmented volumes for the first time, run: {{{ recon-all -subcortseg -segstats -subjid <subject name> }}} |
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| The automatic subcortical segmentation can take many hours to complete. To view the segmentation, use this command: {{{ tkmedit <subject name> norm.mgz -segmentation mri/aseg $FREESURFER_HOME/tkmeditColorsCMA }}} |
[wiki:FreeSurferWorkFlows top] | [wiki:HistoricalReconstruction previous]
FreeSurfer Subcortical Segmentation
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
FreeSurfer now automatically runs automated labeling of the brain volume and this is included in all versions of the September 2005 release. However, if you processed your anatomical data using previous versions and you wish to obtain the automated labels, you can just run the subcortical segmentation separately. It is important to note that the September 2005 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG) to segment the white matter volume (WM). You must therefore use the -noedit_wm_with_aseg flag to ensure that it preserves and uses the white matter volume (WM) edits that you made, if you rerun any later steps on your previously edited data -- e.g. if for some reason you wish to regenerate final surfaces.
So, to obtain automatically segmented volumes for the first time, run:
recon-all -subcortseg -segstats -subjid <subject name>
The automatic subcortical segmentation can take many hours to complete.
To view the segmentation, use this command:
tkmedit <subject name> norm.mgz -segmentation mri/aseg $FREESURFER_HOME/tkmeditColorsCMA