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
