Dear Derek,
> I noticed that TOPUP-EDDY runs with single phase encodings in FSL 5.0.11.
I am not really sure what you mean by topup-eddy here. I assume you simply mean running topup followed by eddy.
If so, I guess the question is “What happens if I run topup with no phase-reversed data followed by an eddy where I feed those topup results in?”
I must admit to thinking that it wouldn’t be possible to run topup with only identically acquired images and identical rows in the acqpar.txt, but it seems I don’t explicitly check for that so it is in principle possible. Though it is of course not possible to estimate the field in that way. I will put it on my todo-list to implement such a check.
> In these cases (i.e. where none of the B0's are reverse-phase encoded), is the susceptibility correction simply skipped? If so, what is TOPUP actually estimating (particularly since it still seems to run for 30 min or so)? If the output is simply a 'null' warp, is it still safe to apply it to images at the Eddy stage?
I would be very cautious about doing that. My gut feeling is that it would estimate a field that is very close to zero, and that it would therefore not be much different to running eddy without --topup. But I would not want to bank on that without a fair amount of testing to ensure the field really stays “zero”, and even if it is “very close to zero” it will not be exactly zero and that deviation from zero will essentially be “noise" that gets propagated into the final results.
Jesper
>
> Cheers,
> Derek
>
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