Hi,
Have you tried using different BET options (via the —betfparam).
Also, the method used by fsl_anat involves registration to the standard space, using the MNI152 template, and this might not be appropriate for your infants. So you might want to try just running BET rather than fsl_anat, or turning off the registration within fsl_anat.
All the best,
Mark
> On 19 Nov 2014, at 15:12, Keren Lesinger <[log in to unmask]> wrote:
>
> Hi ,
> I am using fsl_anat on anatomical fmri scams of adults and infants.
> it seems that the T1_biascorr_brain.nii.gz of adults extract the brain ok.
> However , the infants brain are over cutt by fsl_anat.
> (I'm using fsl_anat for the purpose of brain extraction and the registration functional images using fsl piplines with bbr (which use fsl_anat outputs).
> is there something I can do to improve the infants brain extraction?
>
> Thanks,
> Keren
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