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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 all versions of the February 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.
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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.
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So, to obtain automatically segmented volumes for the first time, run: To obtain automatically segmented volumes for the first time, 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 (16+) 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 February 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). In doing this the edits are different than the manual edits you may have already done (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. 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.

[wiki:FreeSurferWorkFlows top] | [wiki:HistoricalReconstruction previous]

FreeSurfer Subcortical Segmentation

In automatical 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 runs automated labeling of the brain volume and this is included in all versions of the February 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.

To obtain automatically segmented volumes for the first time, run:

recon-all -subcortseg -subjid <subject name>

The automatic subcortical segmentation can take many (16+) hours to complete.

It is important to note that the February 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). In doing this the edits are different than the manual edits you may have already done (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. 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/tkmeditColorsCMA

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.

SubcorticalSegmentation (last edited 2018-01-04 15:07:58 by MorganFogarty)