Dear Daniel,
you should leave those b0 volumes in there, _and_ make sure that the first volume in your 4D input to topup is also the first volume in the concatenated PA-AP data set. That is how you ensure that the fieldmap from topup is perfectly registered to the data you apply it to.
Jesper
> On 27 Feb 2018, at 21:53, Daniel Levitas <[log in to unmask]> wrote:
>
> Okay, great. And I would combine the full PA and AP files (i.e. including the b0 reference volumes), or does the combined PA AP file need to have those removed?
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