Hi Anastasia,
by using only 6 DOF, you impose a simple translation and rotation to this skull-stripped T1, which can not match the template.
6 DOF are generally used for intra-subject registration or to just rotate the brain so that AC and PC would be in the same axial plane for instance... If you use 12 DOF instead, that should do the trick.
Cheers,
Gwenaelle
--- En date de : Mer 22.4.09, Anastasia A Ford <[log in to unmask]> a écrit :
> De: Anastasia A Ford <[log in to unmask]>
> Objet: [FSL] Using FLIRT to register anatomic to MNI
> À: [log in to unmask]
> Date: Mercredi 22 Avril 2009, 18h40
> hi,
>
> I am trying to register a skull-stripped anatomical image
> to MNI template.
> First I used t he MNI_1mm_brain template as the reference
> image, as my
> anatomicals are 1x1x1 mm. I also used 6 DOF. As a result,
> the registered
> anatomical is much smaller than the template (i.e. the
> cerebellum of the
> original image is overlapping with the occipital lobe of
> the template).
> Could you suggest changes to the command line options so
> that the size of
> the images will match up?
>
> Sincerely,
>
>
> anastasia
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