Dear Gabor,
>
> We're planning to measure DTI with two different PE polarity/directions. How to combine eddy_correct and TOPUP in this case? Which one is the first? Is it worth to combine them?
I suggest you consider using the new eddy tool (not the same as eddy_correct) since that is designed to be used together with topup.
The principle for combining them is to run topup to calculate a fieldmap, but not resample the images, and then pass that to eddy together with the original images to estimate and correct for eddy currents and movements.
The wiki pages gives a decent description of how to use the tolls, and also how you need to acquire your images in order to use them.
Good luck Jesper
>
> Thanks,
> Gabor
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