Dear Mark,
> 1) The Further Information wiki page endorses the least squares method. Does that mean that, at least as far as topup is concerned, the optimal DTI acquisition scheme would be to repeat the full DWI sequence with reversed PE direction?
It would have some advantages, provided you are still sampling the diffusion sphere with enough directions. If for example you have time/money to collect 120 volumes than I believe that getting two sets of 60 volumes with different blip directions would be sufficient. If you can only collect 60 volumes then I think you are better off using only a single blip-direction.
> 2) Is there any reason why FUGUE could not (or should not) be used to perform the distortion correction using the topup determined field map?
Yes. Fugue doesn't know how to read the output from topup.
Good luck Jesper
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