Dear Kelly,
> I'm experiencing an error with topup when the phase encoding has been done along the z-axis (F>>H and H>>F). The error is:
>
> Exception thrown with message: Topup: msg=TopupScan::TopupScan: third element of pevec must be zero
normally it makes no sense to have PE in the z-direction (one will get data wrap-around) which is why it is disallowed. The exceptions to this rule that I have seen have been monkeys in “sphinx”-position.
>
> I have several subjects whose scans were done with this phase encoding. Can I simply fslswapdim my DTI images for topup and eddy, rewrite my acquisitionParameter.txt file accordingly, and then swap back afterwards?
Yes, that is what we did with those “sphinx” data.
Jesper
>
> Thanks,
> Kelly
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