I think it should be ok. It will be a bit slower, but shouldn't reduce
accuracy I don't think. Try it and see
Bruce
On Tue, 18 Sep 2018, Matthieu
Vanhoutte wrote:
External Email - Use Caution
Hi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work well on
normal patients
without big ventricles ?
Best,
Matthieu
2018-09-18 15:56 GMT+00:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi Matthieu
yes, you will want to run all of your subjects with it
cheers
Bruce
On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Bram,
It looks like the -bigventricles flag fixed my problem with my
specific
subject. Not only, this took
into account large ventricles but also corrected grey matter
segmentation
from extra Dura tissue
that was erroneously segmented in GM.
I understand the first point of amelioration allowed by the flag
but don't
understand where the
second point come from ?
If I used the -bigventricles flag for all my atrophied and large
ventricles
patients and not for my
healthy patients, wouldn't it introduce a bias when further
statistically
comparing groups between
them ?
Best,
Matthieu
2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu>:
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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