When the volume is created, a decision has to be made at each voxel as to what to classify it as. This is used when the aseg.mgz and ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from these files. When using mri_segstats with --pv, it will take the volume of a 1mm3 voxel and divide it up so that it can contribute to more than one region. But there's not a way to put the partial volume information into the segmentation itself. Not sure why that do not appear alingned, but we've been recently looking into this for other reasons. Can you send a pic.?
doug
On Wed, 16 Jul 2008, bell0368@umn.edu wrote:
I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help.
Chris Bell
the interior voxels are only included in the volume if they are one of the following in the aseg.mgz:
case Left_Cerebral_Cortex: case Right_Cerebral_Cortex: case Left_Cerebral_White_Matter: case Right_Cerebral_White_Matter: case Left_WM_hypointensities: case Right_WM_hypointensities:
cheers, Bruce
On Tue, 15 Jul 2008, Marin Richardson wrote:
OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats?
Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included?
Marin
Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>>It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels.
doug
Marin Richardson wrote:
Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region inaparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use?
Thanks, Marin
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