you need to register them.

cheers
Bruce
On Wed, 10 Oct 2012, dgw wrote:

> Hi,
>
>> From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms), I
> can see that mri_ms_fitparms can accept and afi map. Can someone tell
> me what assumptions the -afi subcommand makes about the position of
> the afi map relative to the flash volumes? does it calculate
> everything in scanner coordinates, or do I need to register them to
> one another?
>
> Thanks,
> D
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>
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