Hi Bruce, Thank you for your quick response. Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz.
Thanks, Antonio >-----Original Message----- >From: Bruce Fischl [mailto:[EMAIL PROTECTED] >Sent: Monday, June 25, 2007 4:10 PM >To: Gallo, Antonio (NIH/NINDS) [F] >Cc: freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Segmentation > >Hi Antonio, > >I wouldn't use the wm.mgz for much of anything. It's really just an >intermediate step in the creation of the surfaces. In general we trust the >?h.white and ?h.pial surfaces first, then the aseg.mgz for things like >hippocampus, ventricles, etc... > >Bruce > > >On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: > >> Hi All, >> >> Upon reviewing subortical segmentations I see that often a mismatch >> exists between what appears on the wm.mgz and the color-coded segmented >> maps. >> >> Precisely - as an example - in the attached figure you can see that in >> the case of left insula WM, part of the tissue was classified as GM (in >> brown) in the color-coded segmented map and as WM in the wm.mgz. >> Contrariwise, the right temporal-parietal GM cortex part of the tissue >> is classified as WM (in green) the color-coded segmented map and as >> non-WM in the wm.mgz. The latter occurs in many regions of the brain >> without a clear anatomical pattern. >> >> >> >> I was wondering if this is just a display issue or it rather reflects >> some mismatch in actual tissue classification with consequential errors >> in the generated values of thickness and volumes as well? >> >> If so, is there any way I can correct for this? >> >> >> >> Thank you in advance, >> >> >> >> Antonio >> >> >> >> >> >> Antonio Gallo, MD >> >> NIB-NINDS-NIH >> >> 10 Center Drive >> >> Building 10, Room 5B16 >> >> Bethesda, MD, 20892 - USA >> >> ph #: 001-301-402.6391 >> >> fax #: 001-301-402.0373 >> >> *********************** >> >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
