Dear Ignacio,
There was no attachment (they are not allowed on the list for large files) so I cannot see the kind of tumour you are dealing with. If it is a very large tumour like a stroke tumour then it is often very difficult to get BET to work automatically on just the T1 image. You will probably have to edit the brain extraction manually (in FSLView) or use a different modality, possibly with registration (you could try fsl_anat or the registration tools) although these will probably require a tumour mask to work well, which you would also need to create manually.
All the best,
Mark
On 29 Apr 2013, at 18:09, Ignacio Letelier <[log in to unmask]> wrote:
> Dear Experts.
>
> Could you please give me a hand with this issue. I'm trying to remove non brain regions using the Bias field & neck cleanup option in BET , but it also removes some part off the tumor (see attached image). I' ve tried different thresholds without succes.
>
> I would really appreciate your help.
>
> Thanks in advance.
>
>
>
> --
> Ignacio.
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