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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