Ryan, Be sure to have a look at ribbon.mgz, as that is a volume file created using the white and pial surfaces (from mris_volmask), and would be the most accurate of the volume files in regards to gm segmentation.
Nick On Fri, 2009-03-27 at 10:53 -0400, Ryan Scotton wrote: > Hi Bruce, > > I've uploaded an example of a case with fairly accurate white and pial > boundries when viewed on top of the wm.mgz volume, and GM areas that > are not segmented and others > which have a very fuzzy/noisy boundary within the aparc+aseg.mgz > volume. > > Also, I'm not sure what email client you're using, but since my first > email failed to come through, I ended up forwarding it and sending it > to you again yesterday, which is the one you received. I noticed that > in gmail, it will hide the quoted text, which contained my best > description of the problems we're seeing and my FS version (3.0.4). > You may have already read it, I'm not sure, but just in case, it's > inline with this email. > > The file I uploaded is named 5008-003-02_scotton.tar.gz > > Thanks so much for your help, > > Ryan > > On Thu, Mar 26, 2009 at 5:36 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: > Hi Ryan, > > I still don't quite understand what I'm looking at. Maybe you > can put a problem subject somewhere we can get to it? > > cheers, > Bruce > > > > On Thu, 26 Mar 2009, Ryan Scotton wrote: > > For whatever reason, my email from this morning > doesn't seem to have gone > through. Hopefully it will work this time... > > Ryan > > ---------- Forwarded message ---------- > From: Ryan Scotton <ryan.scot...@gmail.com> > Date: Thu, Mar 26, 2009 at 10:25 AM > Subject: Re: [Freesurfer] Incorrect correspondence in > the aparc+aseg.mgz > volume? > To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > > > Hello again Bruce, > > We used FreeSurfer version 3.0.4, so an older > version. I've attached 9 > screen shots...the first 6 are from the same subject, > and the last three > (the jpgs with _2 at the end of them) were included > just to give a better > idea of the problems we're seeing in the aparc > +aseg.mgz volume, despite good > surfaces in the wm.mgz volume (screenshots of the > wm.mgz were not included > for the 2nd volume...they are equally accurate as the > first case I sent). > You'll notice that there are many GM areas that are > not segmented and others > which have a very fuzzy/noisy boundary. Do you think > that there is some > kind of error occuring in the spherical registration > step? If so, how can > one QC this step? Or is it some other issue entirely? > > Thanks for your help, > > Ryan > > > > On Tue, Mar 24, 2009 at 5:01 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu>wrote: > > Hi Ryan, > > what version are you using? And when you say > "bad" what exactly do you > mean? Can you send some snapshots? If you're > doing a thickness study the > aparc+aseg is irrelevant - just the white and > pial surfaces matter (and the > spherical registration of course) > > > cheers > Bruce > > On Tue, 24 Mar 2009, Ryan Scotton wrote: > > Hi FreeSurfers, > > After a months of QC'ing FreeSurfer > results, my team and I are now working > toward end stage analysis of our > cortical thickness data. All along, > we > have been aiming to make improvements > in the wm.mgz volume so that we can > assure that the white matter and gray > matter surfaces are as accurate as > possible. This was under the > assumption that if the white matter > and gray > matter surfaces are accurate, then the > voxel-wise representation of the > white and gray matter in the aparc > +aseg.mgz file would be accurate. > However, in almost all of our cases, > the aparc+aseg.mgz segmentation looks > very bad. The bad aparc+aseg.mgz > representation of what seem to be > accurate > white and gray matter segmentations in > the wm.mgz file is leading us to > believe that the cortical > correspondences created after template > mapping > are > wrong. > > Does anyone else have an explanation > for such a discrepancy? Is this a > common problem and if so, is there any > way to remedy this situation? > > Thanks, > > Ryan > > > > > _______________________________________________ > 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
