I have previously used field map correction for b0 inhomogeneities when running TRACULA, however my new data set has A>P and P>A encoding. I know that topup has been shown to perform slightly better than filed map correction. I wonder if it would be possible to manually edit the 

($dob0) then # B0-inhomogeneity "correction" 

part of the code and run topup instead of epidewarp.fsl? I am trying to determine how feasible this is and was wondering if this had been tried by others? 

If not, does it make more sense to process the data with topup separately and then incorporate it into TRACULA?

Thank you for any guidance you can provide,