Thank you very much for the response.
Attached is snapshot for the same subject (orig.mgz and wm.mgz) there are projections og white matter int he cortex. Do I need to erase these projections. Then runt he command
I apologies if my questions are simple. I am beginner and this is my first manual edit!
-------- Original Message --------
Subject: Re: [Freesurfer] recon-all
Local Time: August 25, 2017 10:09 AM
UTC Time: August 25, 2017 2:09 PM
From: fischl@nmr.mgh.harvard.edu
To: John Anderson <John.anderso@protonmail.com>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
nope, that shouldn"t matter for the cortical models (if that is what you
care about). Frequently brainstem is very far from isocenter and coil
elements, and hence low SNR causing this to happen.
cheers
Bruce
On Fri, 25 Aug 2017,
John Anderson wrote:
> Dear FS experts,
> Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of my recons
> which finished with no errors. I am reviwing the data and I see a lot of
> holes in the brain stem, Are these needs to be filled manually. Do you
> recommend to fill this type of holes or just the ones in the hemispheric
> white matter?
>
> Thanks in advance
> John
>
>
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