Try this
Bet <input> <output> -A -R -S -B -f 0.6
If not satisfied, try this:
standard_space_roi <input> <output> -b #this will register image to
MNI152_T1_2mm_brain_mask using FLIRT and will mask out the scull.
Then run bet on the results again
-P
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Yiou Li
Sent: Tuesday, September 01, 2009 11:28 AM
To: [log in to unmask]
Subject: [FSL] Problem of BET results on T1-weighted image
Hi all,
I tried using BET to extract the brain from a T1-weighted image, but
the skull can not be completely removed for some slices. As shown here
(http://cs.umbc.edu/~liyiou1/draft/Picture%201.png). I tried -R option
and the results are not improved. I think the problem might be because
the occipital part has higher intensity than the frontal part. Can you
please kindly advise?
Best,
Leo
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