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Hi again, Thanks for your prompt response. So should I apply topup to simulated data before applying eddy? If yes, how that works? I mean without having the reverse PE. you need to ask Mark about the specifics of his released data. I _think_ in the released data he hasn’t included susceptibility distortions (i.e. only eddy currents and subject movement). That means that you just run eddy without any topup information. Jesper Best, Mahmoud On Wed, Nov 30, 2016 at 11:02 AM, Jesper Andersson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Mahmoud, > > Could you please let me know how did you apply the eddy (5.0.9) to simulated diffusion data? > The explanation at Wiki page is for single shell data with AP and PA encoding but the simulated diffusion data provided by Mark Graham is multishell and just in one PE direction. that makes it even easier. Your acqp.txt will contain a single line and your index.txt will be a file of ones only. I assume Mark has provided a bvals and bvecs file? If so, just use those and that will tell eddy that this is multi-shell data. Jesper > > Thank you, > Mahmoud