Dear Dr Bruce, Thank you very much for the response.
Kindly I have one additional question and I highly appreciate your answer! 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 recon-all -s <subject> -autorecon2-wm -autorecon3
Is this correct? 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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