Hi Matteo,
You might find answers to your question here Denoising and unringing before eddy and here https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1901&L=FSL&P=R48437&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
Basically, there are differing opinions on whether one should apply denoising (and Gibbs ringing correction, which I also recommend -> mrdegibbs) prior to running eddy. I have yet to see eddy fail on denoised and/or de-Gibbs-ed DWI data (the problem described in my post to the FSL forum was a field map issue).
Best,
Matthias