Hi,
BET should work fine in any orientation, but it can sometimes help to use fslreorient2std first.
We also recommend cropping the image to remove excess neck (either manually with fslroi or using the automated tool robustfov). There are also several other options to BET that you can try if this does not work.
All the best,
Mark
On 2 Mar 2013, at 15:13, "subscribe FSL Hoi Fong, Chan" <[log in to unmask]> wrote:
> Dear FSL expert,
> I am trying to do SIENAX on the T1 image acquired in Sagittal view. However, the BET result seems to be underestimated. Is it related to the orientation of the image ? ( i did the T1 BET2 first )
> I have uploaded the SIENAX file and the code is 328105.
> Thanks in advance!
> hoifong
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