Hi Doug, As a post-mortem to this thread, in the process of going to "tweak" the wm.mgz as you suggested, I noticed that there were actually some substantial errors in the surfaces in the calcarine, presumably due to topology correction gone astray. So, whether or not that precipitated the problem with the filling operation of mris_wm_volume, it was something that needed wm editing, and once that was done, the ensuing lhCorticalWhiteMatterVol was again normal.
cheers, -MH > On Thu, 2012-03-01 at 13:29 -0500, Douglas N Greve wrote: > It must be that the shell is not quite getting closed. Didn't Gheorghe > use a ray tracing algorithm for this? > > Bruce Fischl wrote: > > hmmmmm, I don't understand why the filling is failing then. I can't > > remember who's code this is. I think it started life as Andre's > > (shocking!), but maybe Krish or Martin has taken it over since then? > > > > On Thu, 1 Mar 2012, Douglas N Greve wrote: > > > >> > >> mris_euler_number surf/lh.white > >> euler # = v-e+f = 2g-2: 166103 - 498303 + 332202 = 2 --> 0 holes > >> F =2V-4: 332202 = 332206-4 (0) > >> 2E=3F: 996606 = 996606 (0) > >> total defect index = 0 > >> > >> mris_euler_number surf/rh.white > >> euler # = v-e+f = 2g-2: 167114 - 501336 + 334224 = 2 --> 0 holes > >> F =2V-4: 334224 = 334228-4 (0) > >> 2E=3F: 1002672 = 1002672 (0) > >> total defect index = 0 > >> > >> > >> Bruce Fischl wrote: > >>> what is the euler number for the white surface for this subject > >>> (mris_euler_number)? > >>> On Thu, 1 Mar 2012, Douglas N Greve wrote: > >>> > >>>> Hi Mike, I *think* I've found the problem with this subject. The way > >>>> that the volume inside the white surface is computed is to create a > >>>> high-res volume (.25mm iso), then create a shell based on the > >>>> intersection of the faces with the volume. The outside of the shell is > >>>> "flooded", the result is inverted to give a map of voxels inside the > >>>> white surface. This includes subcortical voxels, so the voxels > >>>> known to > >>>> be in the WM from the aseg are added. The .25mm voxels that are > >>>> labeled > >>>> as cortical gray matter are also included since these represent > >>>> partial > >>>> volume that are really WM. So far so good. I think the problem is that > >>>> the shell for this subject has a hole in it, so the flood leaks into > >>>> most the interior. When inverted, there are very few voxels left > >>>> and so > >>>> the WM volume is way too low. It might take a while to find a solution > >>>> to this, so I just wanted to give you a heads up. One possible > >>>> work-around is to make an edit that causes the surface to change. > >>>> It is > >>>> probably the case that even a small change causes the hole to fill and > >>>> everything works out. > >>>> > >>>> doug > >>>> > >>>> Michael Harms wrote: > >>>>> Hello, > >>>>> > >>>>> Anyone have a chance to look at this? Should we just forget about > >>>>> trying to get an accurate lhCorticalWhiteMatterVol value for this > >>>>> subject? > >>>>> > >>>>> thanks, > >>>>> -MH > >>>>> > >>>>> On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote: > >>>>> > >>>>>> Hi guys, > >>>>>> > >>>>>> We have a subject processed with FS v5.1 in which > >>>>>> lhCorticalWhiteMatterVol in aseg.stats is much too low -- only 33781 > >>>>>> mm^3. From what I see, the aseg.mgz looks fine. 'mris_volume > >>>>>> lh.white' > >>>>>> returns 287261 and running mri_segstats without the --excl-ctxgmwm > >>>>>> option returns a Left-Cerebral-White-Matter volume of 245169. > >>>>>> 'mris_euler_number' indicates no problems with lh.white. > >>>>>> > >>>>>> Running 'mris_wm_volume' on its own generates the same value of > >>>>>> 33781. > >>>>>> I also tried running 'mris_wm_volume' with the -v option to see > >>>>>> if any > >>>>>> interesting messages popped up, but got the message "unknown > >>>>>> option -v". > >>>>>> > >>>>>> Any idea what is going wrong here? So you can see for yourself, > >>>>>> I went > >>>>>> ahead and uploaded the subject's processed data to your FTP server > >>>>>> (110107_L206.tgz) > >>>>>> > >>>>>> thanks, > >>>>>> -MH > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
