Hi,
We recommend using a T1-weighted intermediate image.
You register the FLAIR to the T1-weighted image with FLIRT
and 6 DOF and then you register the T1-weighted image to
the MNI152 with FLIRT and FNIRT. After this you combine
the transforms (or apply them together with a single call to
applywarp) in order to go from the FLAIR to the MNI space.
All the best,
Mark
On 12 Jan 2012, at 04:07, John Smith wrote:
> Hi,
>
> Can anyone give me some tips on normalising FLAIR images to the MNI-152 template using FSL?
>
> I have tried fnirt after flirt but the result is poor.
>
> Thank you
>
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