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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