Hi Matthieu,
The initial estimate for surfaces is based off the wm.mgz. Since you're wm.mgz
is incorrect (due to the large ventricles and wm abnormalities) the first pass
at a surface reconstruction is way off. The wm.mgz is created in-part from the
aseg.mgz, so it is important that you ensure your aseg.mgz is accurate.
Additionally, it will be useful to have an accurate aseg.mgz for subcortical
analyses.
I hope that answers your question.
Bram
________________________________
From: Matthieu Vanhoutte <matthieuvanhou...@gmail.com>
Sent: Friday, September 14, 2018 4:48:36 PM
To: Diamond, Bram Ryder
Cc: Freesurfer support list
Subject: Re: Troubles to determine the type of recon editing needed
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<mailto: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<https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations>.
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>>
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com<mailto:matthieuvanhou...@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>;
astev...@nmr.mgh.harvard.edu<mailto: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<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0>
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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