On Fri, Mar 27, 2009 at 4:49 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
yes, the thickness is independent of these. I think the only issue are the spots in the aparc+aseg, which I think we've fixed. You should be able to just rerun the very last (Fast) steps to regenerate them.
cheers,
Bruce
On Fri, 27 Mar 2009, Ryan Scotton wrote:
Hi guys,
Does this mean that the measurements are probably solid, but the
aparc+aseg.mgz volume inaccurately represents these measurements, or will I
need to recompute the last two steps (aparc2aseg and wmparc) in order to
attain accurate cortical thickness values? It doesn't like that way, since
the thickness files are generated earlier in the recon stream. I ask this
because we are trying to get the stats as fast as possible without having to
rerun all of our cases (200+) over again.
Ryan
---------- Forwarded message ----------
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Date: Fri, Mar 27, 2009 at 2:47 PM
Subject: Re: Fwd: [Freesurfer] Incorrect correspondence in the
aparc+aseg.mgz volume?
To: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Cc: Ryan Scotton <ryan.scotton@gmail.com>, Freesurfer Mailing List <
freesurfer@nmr.mgh.harvard.edu>
Hi Ryan,
I think a lot of the spottyness you are seeing is a bug in FS3 that was
fixed. Try using the new FS to just regenerate the aparc+aseg and see if it
looks better.
Bruce
On Fri, 27 Mar 2009, Nick Schmansky wrote:
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
<fischl@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.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
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