Doug, et al., We ran a few subjects through recon1, 2, and 3 in an effort to get the volume of the hippocampus bilaterally. We emailed the list to find out if we should use aseg.stats or wmparc.stats. Doug wrote back saying that the hippocampus volumes should be the same. We went back & ran more subjects and they all appear to have a discrepancy between the number of voxels in aseg.stats and wmparc.stats for the hippocampus. Some of the stats are the same-- just the NVoxels and Volume_mm3 differ between the two stat files. we've attached a set of these aseg.stats vs wmparc.stats files. Does anyone have any idea why we might be getting this bug and how we could fix it?
Thanks! Kathy & Margaret On Fri, Oct 24, 2008 at 3:32 PM, Doug Greve <[EMAIL PROTECTED]>wrote: > > They should be exactly the same. If not, it's a bug. I just looked at a few > of mine, and they are the same. > > doug > > Kathy Zhang wrote: > > Hello, I've recently started a project that involves measuring the volume > of the hippocampus and other subcortical structures, so I was also wondering > whether aseg.stats was more accurate or wmparc.stats. So far the difference > between them appears to be approximately a hundred voxels for each > right/left hippocampus. > > Thank you, > Kathy Zhang '09 > > On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi <[EMAIL PROTECTED]><[EMAIL > PROTECTED]>wrote: > >> Hi, for subcortical segmentations, is it then better to use the >> volumes in wmparc.stats than those in aseg.stats? >> >> >> >> On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <[EMAIL PROTECTED]> >> wrote: >> > >> > Actually, the construction of aparc+aseg and wmparc do use info about >> where >> > the surface is to refine the aseg cortical boundaries. This information >> is >> > stored in ribbon.mgz (and it overrides the aseg definition). At some >> point, >> > we will use the surfaces to directly refine the aseg boundaries. >> > >> > doug >> > >> > >> > >> > >> > Michael Harms wrote: >> > >> > Hi Chris, >> > Doug, please correct me if I'm wrong, but the original gm/wm >> > segmentation contained in aseg.mgz is based on the 3D volume-based >> > tissue segmentation. This original segmentation then forms the basis >> > for all subsequent additional segmentations of either GM or WM in the 3D >> > volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the >> > surface based parcellation, but only to decide the most appropriate >> > label to assign to GM/WM as defined in the already existing volume-based >> > segmentation that is contained in aseg.mgz. >> > >> > Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on >> > the 3D volume segmentation, there is no apriori reason that their >> > spatial extent will correspond precisely to the more accurate gray and >> > white mattes surfaces that come out of the surface-based processing >> > stream. (Although certainly we would hope that the discrepancies don't >> > become too large). >> > >> > cheers, >> > Mike H. >> > >> > On Thu, 2008-07-17 at 12:00 -0500, [EMAIL PROTECTED] wrote: >> > >> > >> > I have sent two images created with the following commands. >> > >> > tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white >> > -segmentation (aparc+aseg.mgz and wmparc.mgz) >> > $FREESURFER_HOME/FreesurferColorLUT.txt >> > >> > The wm segmenations go through the "main surface" and the "orig surface" >> > into the gray matter, for example in the rh-supramarginal and >> > rh-postcentral. From your last response I am unsure as to which pipeline >> > creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) >> or >> > the surface-based pipeline (i.e. ribbon.mgz) or some combination of the >> > two. It seems to me that the gm/wm parcellations are created using the >> > surface pipeline and then transferred to the closest class-matched >> voxels >> > from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg >> > segmentations. I guess the question is how are we getting from the >> surface >> > parcellations back to volume space; is there a binary? >> > In a related vein, the value from aseg.stats "surface-based-volume mm3 >> > lh-cerebral-white-matter" seems to be created with mri_segstats or is it >> > from mris_wm_volume? Thanks for all your help! >> > >> > Chris Bell >> > >> > >> > >> > >> > >> > On Jul 17 2008, Doug Greve wrote: >> > >> > >> > >> > 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, [EMAIL PROTECTED] 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 in >> > aparc.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 >> > >> > >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > >> > >> > >> > >> > _______________________________________________ Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > 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 >> > [EMAIL PROTECTED] >> > Phone Number: 617-724-2358 >> > Fax: 617-726-7422 >> > >> > In order to help us help you, please follow the steps in: >> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > ------------------------------ > > _______________________________________________ > Freesurfer mailing [EMAIL > PROTECTED]://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps > in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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