Yes it is in the blue circle. I point into it and I checked the other sections. Kindly see attached.
-------- Original Message --------
Subject: Re: [Freesurfer] recon-all
Local Time: August 25, 2017 10:19 AM
UTC Time: August 25, 2017 2:19 PM
From: fischl@nmr.mgh.harvard.edu
To: John Anderson <John.anderso@protonmail.com>
Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hi John
I"m not entirely certain what you mean, but the figure you sent looked
fine. If you are thinking that the circled area is a detached piece of
wm, it is almost certainly not. Click on the center of it and look in a
different view and you will see that it is connected through-plane
cheers
Bruce
On Fri, 25 Aug 2017, John Anderson wrote:
> 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
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>