Hi Matthieu
the aseg is used to automatically edit the wm.mgz, which helps the creation
of cortical surfaces. For example, the ventricles are filled using the
aseg. I think in your case with greatly expanded ventricles, some of the
ventricular voxels were incorrectly labeled in the aseg and hence resulted
in incorrect surfaces.
cheers
Bruce
On Fri, 14 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Bram,
Thank you for your answer. As soon as possible I will run recon-all with the
-bigventricles flag.
Concerning the manual editing I don't understand well the aim of editing
aseg.mgz since it seems to
most concern subcortical structures and statistics and not have an impact on
surfaces computed ?
Best,
Matthieu
Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
a écrit :
If you haven't already, you may want to run the subject through recon-all
with the
-bigventricles flag since it looks like the lateral ventricle was
significantly
mislabeled in the aseg. If using the -bigventricles flag doesn't fix your
problem, you
can edit the aseg.mgz manually by following the directions in this
tutorial. Then run
the following command (again, substituting <subj_id> for your subject's
id):
recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best,
Bram
____________________________________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on
behalf of Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor
surfaces in the
posterior right hemisphere you were referring to in your message. It looks like
your subject
has a combination of abnormally large ventricles and significant wm
abnormalities, so I'm
surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more
accurately represent
the wm from slice 84 to 39. You can take a look at the white matter edits
tutorial for details
on how to do that. Then run the following command (substituting <subj_id> for
your
subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral
ventricle in the
wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us
the surfaces
for the left hemisphere. Before you do that, edit the wm.mgz as explained in
the tutorial and
tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598
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