Hi Michelle,
by default BET assumes that the centre of the brain is in the centre of the field of view. This is not the case if the image have lots of neck, as the centre will be too low. You can initialise the centre of gravity using the -c option in BET. Open the image in fslview and get the coordinates for what you think is approximately the centre of the brain. Then, feed these coordinates to BET, it should give you a better estimate.
Cheers,
Stam
On 7 Jul 2010, at 09:35, Michele Placci wrote:
> Dear FSL Experts, can you tell me why I get this picture after performing the function BET and pick -o option?
> I mean, why there is part of the neck and mouth in the extraction of the brain?
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> Thank you all for any help.
> Michele.
> <Copia di Anonym2.GIF>
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