Hi Ben,
The main recommendation for linear registration between modalities is to use boundary-based registration (BBR). Both the b0 and the FA should have enough WM/GM contrast for this. I’m not sure which would be better.
I would personally register the b0 to the anatomical image using the epi_reg command line tool (ignore all the optional arguments dealing with the field map, because eddy already took care of that). However, I would expect the similar result if you decide to register the FA.
Best wishes,
Michiel
> On 29 Aug 2018, at 17:03, Ben M <[log in to unmask]> wrote:
>
> Thank you Michiel!
> Would you recommend registering the FA or the b0 to the anatomical image?
> Best,
> Ben
>
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