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 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 and ?gcut in my
recon-all command line for one subject. Forexmaple:
I ran reconall using the following command lin:
recon-all ?skullstrip first -clean?bm ?gcut ?sAA***.T* -all -use?mritotal
The run was complete and I looked at the brainmask.mgz file of the output.
But I didn't see any correction.
I am attaching the jpg image of the sagittal view of brainmask.nii ( I
converted the mgz file to nii to view tham in afni)
SubjFS: is the image from recon-all run
SubjFS: is the image from recon-all that was run with
Skullstrip/clean-bm/gcut options included.
Did I do anything wrong?
Your guidance and suggestion needed.
Thanks,
Rashmi.
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