I have run topup and applytopup to a set of positive and negative blip images to create a "hifi" image with corrected geometric distortions.

My "hifi" data is 30 directions, 2x2x2, whole brain.

Your website says the following: "topup is a tool for estimating the susceptibility induced field. In order to estimate and correct also for EC-induced distortions one will either need to run a tool like e.g. eddy_correct prior to running applytopup. Or one can feed the output from topup into the eddy tool."

Elsewhere, I have read that eddy is for data with more than 30 directions.

So, my question is, should I be running eddy_correct before topup and applytopup 

OR

eddy_correct after  topup/applytopup

OR

eddy after topup/applytopup

OR 

something else?

Thanks for all your help...I want to make sure I make optimal use of these new tools.

-Dianne

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