Hi Anastasia,
indeed, it's enlarging quite artificially the cortex in the T1 image even beyond the fa cortex/background boundaries. Jesper might be able to explain why (and why it's not doing so on my set of images!)...
But as far as I can see, it's doing a very good job on the white matter (try to threshold your t1_to_fa image at 1400 and overlap it with the fa image). So hopefully your ROIs are defined in the white matter or the deep grey matter, in which case the result is fine.
Cheers,
Gwenaelle
--- En date de : Jeu 11.9.08, Anastasia A Ford <[log in to unmask]> a écrit :
> De: Anastasia A Ford <[log in to unmask]>
> Objet: Re: [FSL] FNIRT bzero to T1
> À: [log in to unmask]
> Date: Jeudi 11 Septembre 2008, 17h21
> Thank you for taking a look. I included the T1 fnirted to FA
> as well as the
> warpcoef file.
>
> The upload number is 732999.
>
> Sincerely,
>
> Anastasia
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