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 >>>> >>>> >>>> >>
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