I have a data-set including phase encoding (1b0+80 dir RL & 1b0+80 dir LR). Using default config file b02b0.cnf (included in attachment), an image with ghosting around brain was appeared. I also tried to change the values of the --warpres but the results got
worse.
I had a look at your data and ran topup on it. The results look perfectly fine to me, given the input data. The ghosting has not appeared as a consequence of topup. There are two bands (one in slices 31-38 and one in slices 62-90) with severe ghosting in your
input data. topup only deals with the distortions, and will not do anything about the ghosting.
I also had no problem with applytopup on your data. I think in an earlier version of applytopup the display range was not set correctly, but that would only affect the initial range that fslview (and I assume that fsleyes does the same) displays your data
with. Try changing your display range and I think you will see it has worked fine.
For future reference. If you stick all your files in a tar-ball before uploading them you will save time both for me and yourself. If you are not familiar with tar, just google “linux tar” and there will be lots of information.
Jesper