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 > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
