Hi Gabor,
It would probably not be a problem, but it is easier to input the non-betted images into FSLVBM or SIENA. You can then specify the additional bet options that you want to use (i.e. -B) on the command line like this:
fslvbm_1_bet -b -B
siena input1.nii.gz input2.nii.gz -B "-B”
Best,
Eelke
> On 21 Apr 2016, at 09:39, Gabor Perlaki <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> The brain extraction works well on our images using the Bias field & neck cleanup (can be useful in SIEANA) BET option. Since the *_brain output images of BET are already bias field corrected my question is whether using this option in FSL_VBM or in SIENA is OK or not? As far as I know both FSL_VBM and SIEANA will use FAST in the processing pipeline which will run bias field correction again, so the images will be bias-field corrected twice. Is it a problem?
>
> Best regards,
> Gabor
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