Hi Doug, I was comparing the aseg.mgz and aparc+aseg.mgz segmentations (FS v4.0.2), and recalled a previous thread on this issue in which you corrected me on an aspect of how the aparc+aseg.mgz is affected by the surfaces.
>From what I can tell looking at this again, voxels labeled as "None" in the aseg.mgz are also still ALWAYS labelled as "None" in the aparc +aseg.mgz, even if those voxels are clearly interior to the final pial surface. However, voxels interior to the white surface that are labeled as "Cortex" in the aseg.mgz get converted to "None" in aparc+aseg.mgz. That is, it appears that a voxel must be in ribbon.mgz to be eligible for one of the "ctx" parcellation labels in aparc+aseg.mgz, but not necessarily all voxels in the ribbon will be labelled as "ctx" (some will remain labeled as "None", apparently propagated from aseg.mgz). Do I have this summary correct? thanks, Mike H. On Tue, 2008-07-22 at 14:54 -0400, Doug Greve 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
