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
_andreia_@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 greve@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
_andreia_@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
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