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| = FreeSurfer Subcortical Segmentation = | = Subcortical Segmentation = |
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| In automatical subcortical segmentation, 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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| 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, Third Ventricle, Fourth Ventricle, Brain Stem, Cerebrospinal Fluid |
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| FreeSurfer now runs automated labeling of the brain volume and this is included in all versions of the January 2006 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. | FreeSurfer now runs automated labeling of the brain volume and this is included in the stable v3.0 release, [wiki:Self:ReconAllDevTable during the -autorecon2 stage]. 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. |
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| It is important to note that the January 2006 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG - in mri/aseg.mgz) to segment the white matter volume (WM - mri/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: |
To obtain automatically segmented volumes for the first time (assuming the -autorecon1 stage has completed), run: |
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| recon-all -subcortseg -segstats -subjid <subject name> | recon-all -subcortseg -subjid <subject name> |
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| The automatic subcortical segmentation can take many (11+) hours to complete. | |
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| The automatic subcortical segmentation can take many (16+) hours to complete. | It is important to note that the stable v3.0 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG - in mri/aseg.mgz) to segment the white matter volume (WM - mri/wm). In doing this the edits are different than the manual edits you may have already done in older versions of freesurfer (i.e., the ventricles are filled in completely) this creates a different folding pattern and uses different atlases. You should be sure that all of your subjects are edited in the same manner, using the same atlases (i.e., don't mix freesurfer versions). If you wish to process one subject further (i.e., to get final surfaces) and wish to maintain your edits you can use the ''' -noedit_wm_with_aseg''' flag along with the '''-old-atlas''' flag. This will preserve your manual edits and utilize the old atlases. This is not ideal, as you should process all your subjects fully with the same version of FreeSurfer. |
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| tkmedit <subject name> norm.mgz -segmentation mri/aseg.mgz $FREESURFER_HOME/tkmeditColorsCMA | tkmedit <subject name> norm.mgz -segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt |
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| If the voxels are incorrectly labeled (this is more likely to happen along the medial aspect of the brain), then you can re-label them yourself. Refer to the TkMeditGuide/TkMeditWorkingWithData/TkMeditSelectionsLabels page for detailed information on this procedure. | |
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| If the voxels are incorrectly labeled (this is more likely to happen along the medial aspect of the brain), then you can re-label them yourself. In the TkMedit Tools window, click on the Edit Label icon -- the second from the left in the top row. | = 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_2006-02-15.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. |
[wiki:FreeSurferWorkFlows top] | [wiki:HistoricalReconstruction previous]
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 now runs automated labeling of the brain volume and this is included in the stable v3.0 release, [wiki:ReconAllDevTable during the -autorecon2 stage]. 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.
To obtain automatically segmented volumes for the first time (assuming the -autorecon1 stage has completed), run:
recon-all -subcortseg -subjid <subject name>
The automatic subcortical segmentation can take many (11+) hours to complete.
It is important to note that the stable v3.0 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG - in mri/aseg.mgz) to segment the white matter volume (WM - mri/wm). In doing this the edits are different than the manual edits you may have already done in older versions of freesurfer (i.e., the ventricles are filled in completely) this creates a different folding pattern and uses different atlases. You should be sure that all of your subjects are edited in the same manner, using the same atlases (i.e., don't mix freesurfer versions). If you wish to process one subject further (i.e., to get final surfaces) and wish to maintain your edits you can use the -noedit_wm_with_aseg flag along with the -old-atlas flag. This will preserve your manual edits and utilize the old atlases. This is not ideal, as you should process all your subjects fully with the same version of FreeSurfer.
To view the segmentation, use this command:
tkmedit <subject name> norm.mgz -segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
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 (this is more likely to happen along the medial aspect of the brain), then you can re-label them yourself. Refer to the TkMeditGuide/TkMeditWorkingWithData/TkMeditSelectionsLabels page for detailed information on this procedure.
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_2006-02-15.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.