Hi Marina,
BET can usually be made to work well with a bit of trial and error,
and this will likely be faster than coming up with a regime to use
the GM mask.
Do you have any other segmentations from freesurfer that you could
use, or just the GM mask?
Have you run robustfov on your structural before running BET? Have you
tried adjusting the fractional intensity threshold (-f) and the
vertical gradient (-g) settings?
If you can get BET to perform a reasonable segmentation, you can
always manually touch-up the resulting brain mask in FSLeyes/FSLView.
Cheers,
Paul
On 15/07/2019, Marina Fernandez Alvarez <[log in to unmask]> wrote:
> Dear experts,
>
> I need to get a no-skull brain. The automated no-skull brain has many errors
> and I was thinking that I could create it taking into account the gray
> matter mask (we segment manually with Freesurfer, so the mask is accurate)
> in such a way that everything outside the gray matter mask is eliminated and
> everything inside is maintained.
>
> Do you know how can I create it?
>
> Any idea will be welcome. Thank you very much.
>
> Best regards,
>
> Marina.
>
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