Actually, you are right! Most of the non-gray matter structures in the medial wall are zeroed out, but the part that goes through the hippo and amygdala are non-zero. As Mike points out, this is going to be a very small portion of the total cortical volume, but we'll find a way to remove it. doug
_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. >> >> > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > -- 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
