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