Hi Jeff, it's going to be tricker than that to get the exact value. For
the WM volume computation, there's yet another routine that is used.
This one creates a high-resolution volume to determine which voxels are
withing the WM surface. It then loops through the voxels within the WM
surface and counts the ones that have the following labels in the aseg:
case Left_Cerebral_Cortex:
case Right_Cerebral_Cortex:
case Left_Cerebral_White_Matter:
case Right_Cerebral_White_Matter:
case Left_WM_hypointensities:
case Right_WM_hypointensities:
case CC_Posterior:
case CC_Mid_Posterior:
case CC_Central:
case CC_Mid_Anterior:
case CC_Anterior:
Note that the cortical labels are there to catch the partially volumed
voxels.
hope this helps
doug
Jeff Sadino wrote:
> Thank you Doug for your answer. After reading the wiki more, it has
> led me to another question.
>
> I am trying to duplicate the White Matter value from aseg.stats using
> FreeSurfer 5.0.0. The value from aseg.stats is 220804 (as it is also
> when running mris_wm_volume). By hand, when I run mris_volume subject
> lh.white, I get 239035. From this, I subtract:
> Left-Lateral-Ventricle
> Left-Inf-Lat-Vent
> Left-vessel
> Left-Thalamus-Proper
> Left-Caudate
> Left-Putamen
> Left-Pallidum
> Left-Accumbens-area
> Left-VentralDC
> Left-choroid-plexus
> and then I am left with 209832. Can someone please give more detail
> about how or which areas mris_wm_volume excludes?
>
> Thank you very much,
> Jeff
>
> On Wed, Nov 30, 2011 at 7:46 AM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Jeff, the total cortical gray matter is based on the volume
> between the white and pial surfaces. The other structures you
> mention below are based on the automatic volume segmentation.
> doug
>
> Jeff Sadino wrote:
>
> Hello,
>
> Thank you Bruce and Doug for your answers to my previous
> question about a bad talairach.lta file. I am now grabbing
> volumes using fs5.0.0 and would like to ask for clarification.
> On the Morphometry Stats page at
> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats, it
> says that the cortex is based on the pial surface. I am
> wondering what this includes. I loaded up the pial surface in
> tkmedit along with aseg.mgz. It looks like the following
> regions are completely outside the pial surface: cerebellum,
> 4th ventricle, Brain-Stem, optic chiasm. Is it correct that
> these regions are excluded? And then it looks like the
> hippocampus, amygdala, and inferior-lateral-ventricle are only
> halfway outside the pial surface. Is that correct? If it is,
> then is there a recommended way to exclude the hippocampus,
> amygdala, and inferior-lateral-ventricle regions in the
> cortical gray matter? Do these regions get properly accounted
> for in the subcortical gray calculation?
>
> And then for the white matter, the webpage says that it is
> based on the white surface. Looking at the white surface
> (lh.white), all of the subcortical gray matter and ventricles
> are enclosed in the surface. Can someone explain how the
> subcortical gray gets excluded?
>
> Finally, for the SubCortGray reported in aseg.stats file, does
> that exclude the following areas:
> Left-Lateral-Ventricle
> Left-Inf-Lat-Vent
> 3rd-Ventricle
> 4th-Ventricle
> CSF
> Left-vessel
> Right-Lateral-Ventricle
> Right-Inf-Lat-Vent
> Right-vessel
> 5th-Ventricle
> Left-Cerebellum-White-Matter
> Right-Cerebellum-White-Matter
> WM-hypointensities
>
> What about the brain stem? Why is the cerebellum Gray Matter
> included? I ask because the only way I can get close to the
> SubCortGray by using the aseg file is by excluding those regions.
>
> Once again, thank you for your invaluable help!
> Jeff Sadino
>
> ------------------------------------------------------------------------
>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
> <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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