Hi Maria,
If the brain extraction has very minor imperfections, I have found that robust BET improves results (-R option).
If the brain extraction has more significant imperfections, I use bias field and neck cleanup (-B option) with an -f value of 0.2 or 0.15. This method takes longer (between 15 and 30 minutes), but works well for me.
Thanks,
Rohan
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