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 greve@nmr.mgh.harvard.eduwrote:
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/MorphometryStatshttp://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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