---------- Forwarded message ----------
From: Ryan Scotton <ryan.scotton@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 <fischl@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 <fischl@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