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Hi Jesper Thank you very much for the information. It is very helpful. Best Longchuan Sent from my mobile device On Jun 24, 2013, at 10:39 PM, Jesper Andersson <[log in to unmask]> wrote: > Dear Li, > >> I have just tried "eddy" and have got a very nice result. I have a question and would appreciate your help on it. From the posts, it seems the proper order for correcting susceptibility-related distortion is as follows: topup -> eddy -> applytopup. I have done the first two steps and after I ran "eddy", I got 2*129 volumes of data with movements, eddy current and susceptibility distortion corrected. So, my question is: do I still need to run "applytopup" at all, since I have all the distortion corrected already in the output of "eddy"? I compared the DTI-derived measures (FA, MD, V1, etc) based on the outputs after "eddy" with these based on "eddy" & "applytopup" and find they are almost identical. If it IS necessary to use "applytopup" after "eddy", could you tell what are the possible advantages to merge the two acquisitions with opposite phase encoding blips again using "applytopup"? > > if you run eddy you should not run/use applytopup. > > Jesper >