Dear Ken,
> I want to coregister the output of eddy to an anatomical image using, for example, flirt.
> Which volume of the output of eddy should I use? The first b=0 volume? The mean of the b=0 volumes?
>
> I don't think this should make much of a difference, but my dMRI dataset has 60 b=1000sec/mm^2 volumes with 5 b=0 volumes interspersed evenly among the diffusion-weighted volumes.
I think you can do either, and it wouldn’t make much/any difference. An average of the b=0 would have better SNR, but even a single b0 usually have oodles of SNR.
Jesper
>
> Thanks!
> Ken
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