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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