Hi Min
unfortunately there's not much we can do as these artifacts make the gray
matter look just like white matter. Do you see this in many subjects?
sorry
Bruce
On Thu, 17 Mar 2016, Min Liu wrote:
Dear Bruce,
Many thanks for looking into this. I tried to post orig.mgz to the mailing
list yesterday but the email didn't get through because the file size
exceeds 1000KB. So I screen-captured two images to showcase the overall
quality of T1 and where the problem is. Although the bright rim doesn't
occur everywhere, it is mostly seen in the left hemisphere. I hope there is
a way to counteract such acquisition defects.
Thanks,
Min
On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Min
that looks like it might be a normalization problem. Can you
post the orig.mgz and see what it looks like? Is there a bright
rim in it also?
cheers
Bruce
On Wed, 16 Mar 2016, Min Liu wrote:
Dear Freesufer users,
We have some T1 images having a rim of bright signal
in the GM at some spots
like the one showing in the attached Figure 1. The
WM surface goes out to
include this bright signal and the cortex ends up
artificially thin. We
followed the standard WM edit procedure, which is to
erase the bright signal
in wm.mgz. As shown in Figure 2, the bright rim is
replaced with intensity 1
(red). However, that doesn't improve the situation.
Does anyone know a way
to prevent the surface from going out?
Thanks,
--
Min
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