d.
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on
behalf of Matthieu Vanhoutte
Sent: Tuesday, September 18, 2018 12:45:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubles to determine the type of recon editing
needed
on behalf of Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com>
> *Sent:* Tuesday, September 18, 2018 12:45:23 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Troubles to determine the type of recon
> editing needed
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Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed
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Ok I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands following
manual editing of brainmask, white matter,...etc or
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Ok I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands
following manual editing of brainmask, white matter,...etc or just once at
the first recon-all -all command ?
Best,
Matthieu
Le mar. 18 sept. 20
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:
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Hi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work we
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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 :
> Hi Matthieu
>
> yes, you will want to run all of your subject
Hi Matthieu
yes, you will want to run all of your subjects with it
cheers
Bruce
On Tue, 18 Sep 2018,
Matthieu Vanhoutte wrote:
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Dear Bram,
It looks like the -bigventricles flag fixed my problem with my specific
subject. Not only, this took
into
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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 un
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 he
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
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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
st
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 th
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