you might check on the FSL list. I think I've seen some traffic 
indicating that there are some tools for doing this. I'l cc Saad as he 
might know

cheers
Bruce


On Mon, 2 Sep 2013, Douglas Greve wrote:

> Hi Shani, I don't think you can apply a FNIRT transform to a surface.
> doug
> 
> 
> On 9/2/13 8:20 AM, Shani Ben Amitay wrote:
>       Dear freesurfer people,
> Any idea whether I can apply transformation that was calculated by fsl
> fnirt on the white/pial surfaces calculated using the freesurfer
> stream?
> 
> Thanks!
> Shani
> 
> 
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>
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