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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
