Hi Andreia, The XhCortexVol measures in the aseg.stats of FS v5.1 are identical to: `mris_volume Xh.pial` - `mris_volume Xh.white`
To my knowledge, that measure is therefore simply the difference of the volume encapsulated by the two surfaces. My point was that the surface "inaccuracies" in the hippocampus and amygdala are tiny compared to the overall variation in CortexVol across individuals, so if you want a measure of CortexVol I wouldn't worry about the fact that parts of those structures are included (and parts are excluded) from XhCortexVol. cheers, -MH On Tue, 2011-12-20 at 15:59 +0000, _andre...@sapo.pt wrote: > Hi Michael and Doug, > > Michael: > "As you noted, the surfaces bisect the hippocampus and amygdala, so the > small amount of tissue outside the pial surface is not included in the > surface based measures of total GM volume. Compared to the overall > variation in brain size, this should be inconsequential. > > cheers, > -MH" > > I got a little confused with your answer. The calculation is > everything inside the pial surface - everything inside the wm surface. > What is outside is half hippocampus/amygdala and is not included, ok. > But the other halves are inside the surfaces, being then included, > right? > > Doug: > > If the thickness was 0 in those areas that would make sense. But do > the surfaces "have" the information that in those regions the > structures are hippocampus and amygdala? > > I checked if the thickness was 0 and from what I'm understanding it is > 5mm. What I did was to open tkmedit with aparc+aseg and open tksurfer > (for both hemispheres). Then, I used the buttons "Save point" and "Go > to saved point" to go from tkmedit to tksurfer. What happened was that > when the point was located in the hippocampus or amygdala in tkmedit > it had a correspondence in tksurfer in regions which have a thickness > value. > > Please see figures in attachement (green arrows are amygdala poinst > and blue arrows are hippocampus points) > > Am I missing something? > > Thank you, > Andreia > > > > > Citando Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > > 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. > > > > > > _______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
