Hi Andreia, I don't think this is a problem for the GM volume (ie, parts of the amyg or hippo getting counted twice). The thickness should be 0 in those areas, so they should not contribute to GM volume. The computation of the WM volume is done in a different way (still surface based) but automatically excludes subcortical structures. doug
_andre...@sapo.pt wrote: > Hello, > > Recalling these emails: > > "The methods are somewhat different. For the value in the aseg.stats > table, the method is to compute the total volume inside the pial surface > and subtract the total volume inside the white surface. For > mris_anatomical_stats, the method is to compute the thickness times area > of each vertex. This method will probably underestimate the total volume > because it uses the area of the white surface when it should use the > area of the surface in the middle between the white and pial surfaces. > I've added this to the list of known issues on our release page. > > doug > > Alexopoulos, Dimitrios wrote: > >> I have generated surfaces using the the centos4 build (version 5.0) >> and want to confirm that my surface-based GM and WM volumes are correct. >> For the surface-based GM calculation I originally used >> 'mris_anatomical_stats -l lh.cortex.label subjectID hemi' >> (run from within the 'label' subdirectory) and for WM i used >> 'mris_wm_volume subjectID hemi' (run from within >> the 'surf' subdirectory). >> When I add the calculated left/right cortical volumes, I get a total >> that is different from what is output in >> the 'aseg.stats' file, which in version 5.0 is noted to contain >> total surface-based GM volume >> (Cortex, CortexVol: Total cortical gray matter volume (based on >> surface-stream). >> What are the correct GM and WM surface-based volumes? >> Thanks. Jim" >> > > > I question came up to me: > > The surfaces in the hippocampus/amygdala are inaccurate and should be > ignored. However, in version 5.0 the cortical volume is surface-based, > thus it takes into account the surfaces in the hippocampus/amygdala, > is this correct? > > If so, it is expected that an error is introduced in the surface-based > calculation of cortical volume. Has anyone checked the influence of > this error? Or FS compensates for the inaccuracy of the surface > estimation of these regions somehow? > > Thanks! > > Andreia > > _______________________________________________ > 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.
