This is probably ok. Run it all the way through and see if it affects the
surfaces. If not, you are all set
On Feb 2, 2011, at 10:30 AM, Tetiana Dadakova wrote:
> I attach a picture of what I get if I run
>
> .
>
> I feel that I need to change the -T threshold of WM intensity, does it
> make
try disabling use of gcut by adding -no-gcut to the end of recon-all.
sometimes it can cut too much (something thats fixed in the upcoming
release).
n.
On Wed, 2011-02-02 at 11:28 +0100, Tetiana Dadakova wrote:
> Dear Bruce and all,
>
> I am trying to fix the scull strip, as it affects ?h.white/
Dear Bruce and all,
I am trying to fix the scull strip, as it affects ?h.white/?h.pial
surfaces. I used -wsthresh with preflooding height of down to 1. It
didn't really help much. Therefore, I have two question:
1. Regarding mri_gcut: should I use the default intensity of 110 for
white matter mas
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't
worry about it unless it causes the ?h.white/?h.pial surfaces to be
inaccurate. In general we use the surface-based measures to estimate
gray/white morphometry and the aseg for everything else. It is a minor
s
