Hi Rashmi,
I assume you've read the skullstrip wiki page, but I've included it below
just in case.
Have you tried different watershed thresholds? Also, you do not need to
include the -clean-bm flag every time. You can run the skullstrip step
once with the -clean-bm to start from scratch, and
Thank you Bruce,
I certainly understand your point. In my study I am trying to use whole
brain volume to normalize my volumetrics data. Due to the inclusion of the
dura into brain, I may get variation in the whole brain volume across
subjects.
In addition the current issue is affecting the grayma
Hi Rashmi
getting rid of all the dura without removing any problem is exceedingly
difficult (if not impossible). Usually we live with some remaining dura
as it doesn't affect the surface placement much.
cheers
Bruce
On Tue, 2 Oct 2012, Rashmi
Singh wrote:
Hello experts,
I am getting skul
Hello experts,
I am getting skull strip issues with FreeSurfer recon-all runs in every data.
I ran recon-all on my T1-data and noticed that the skullstrip is not so good.
Almost in every subjects there were dura included, so I tried the suggestion
of using the flags -skullstrip and -Clean–bm an
