Hi Natalia,
no, it's actually not a problem to "play" a bit with the different BET options to obtain a better brain extraction... If this is worth including this subject in the study, then you should try some other options but I'm unfortunately not the best person to recommend them - apart from the obvious -f one. Steve, MJ?
Otherwise, have you tried the -N option in fslvbm_1_bet or some iterative bettings?
Cheers,
Gwenaelle
--- En date de : Jeu 17.4.08, Natalia <[log in to unmask]> a écrit :
> De: Natalia <[log in to unmask]>
> Objet: [FSL] BET problem in fsl-vbm
> À: [log in to unmask]
> Date: Jeudi 17 Avril 2008, 15h21
> Hi,
>
> I have one subject out of 45 whose brain hasn't
> segmented very well
> because some of the skull / dura etc. has been included in
> the grey and
> white matter maps - see attached segmentation image. Should
> I exclude this
> subject from my fsl-vbm analysis? I understand it's not
> advisable to apply
> different BET thresholds to different subjects. I tried to
> increase the -f
> but there is still some skull 'attached' to the
> brain.
>
> Many thanks,
>
> Natalia
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