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Dear Omar, topup is a tool that will allow you to calculate a fieldmap based on two EPI acquisitions with different phase encodings. There is currently no way to combine that calculation with an explicitly measured (using dual echo time gradient-echo) fieldmap. When using topup we recommend using spin-echo EPI for calculating the fieldmap. The reason for that is that with spin-echo you have no/little signal dropout, which means that the whole difference between the two images can be explained by the distortions going in opposite directions. With gradient-echo EPI there is additional signal dropout. Some of this dropout (that caused by through-plane dephasing) is the same in both images, so does not present a problem. But some of it will be different in the two images. That means that the difference between the two images have two sources i) differences in distortions and ii) differences in dropout. But the model inside topup assumes that the whole difference can be explained by the distortions, so will potentially get those wrong in order to explain the difference in dropout. Exactly how much of a problem that is in practice we don’t quite know yet, and is one of the things we plan to look closer at. But for now the recommendation is to use spin-echo EPI for topup. I hope that helps. Jesper > On 22 Aug 2018, at 22:50, Omar Maximo <[log in to unmask]> wrote: > > How would someone do that? > > I got topup to work only using my resting state data, but if there is a way to implement the fieldmaps onto topup, that would be very useful. > > I have 2 fieldmaps (one for each AP and PA resting state scan). > > Thanks a lot, > Omar > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1