That is basically correct. mri_segstats uses the same functions internally that mris_volume and mris_wm_volume use. doug
Alexopoulos, Dimitrios wrote: > Just for clarification, the surface-based cortical GM volumes in the > 'aseg.stats' file are calculated using: > mris_volume hem.pial AND mris_volume hem.white > For each hemisphere, determine the total volume inside the pial surface and > subtract > the total volume inside the white surface. > > Cortical WM volumes in the 'aseg.stats' are determined using" > mris_wm_volume subject hem > > Is this correct? > > Jim > > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, November 30, 2011 11:46 AM > To: Jeff Sadino > Cc: andrei.sherstyuk; skoga...@gmail.com; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Brain Volume measures > > 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. > > > The materials in this email are private and may contain Protected Health > Information. If you are not the intended recipient, be advised that any > unauthorized use, disclosure, copying, distribution or the taking of any > action in reliance on the contents of this information is strictly > prohibited. If you have received this email in error, please immediately > notify the sender via telephone or return email. > > > -- 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
