Hi Martin,

Thanks for the quick reply! I also use a conservative DTIPrep implementation, only running slice-wise and interlace checks with pretty strict thresholds to throw out bad volumes. If you are willing to share your scripts I'd like to take a look at them. Ideally, I would like to use the QCed files as inputs to QSIPrep. To this end, since I do not want to concatenate AP-PA together for computational efficiency, I would probably need to have the AP-PA sequences have the same amount of data, so I would be interested in applying interpolation technique. In your opinion, would interpolation be better served after Eddy/Topup has been run?

Best,
Steven