Dear Stathis,
> I was wondering if any of you have run fnirt on mouse brains and
> what parameters worked best.
tiny ones.
No seriously, there are no assumptions about scale in fnirt so you
shouldn't need to do anything special. My own experience of rats is
that their brains tend to be much more similar than is the case for
humans and that you don't need to go to very high resolutions for the
non-linear warps.
What determines how you want to write the configuration file is mainly
the matrix size of your reference image. If you let me know what that
is I'll be able to give you some specific advice.
Good luck Jesper
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