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Dear Ben, there is a random selection of voxels within the brain mask that is used to calculate the hyperparameters of the Gaussian process in eddy. That is what gives the nondeterministic behaviour. For the next release there will be a switch that allows you to specify a seed for the random number generator which will then ensure a identical results for repeated runs. Jesper On 9 Mar 2015, at 15:03, Ben Jeurissen <[log in to unmask]> wrote: > Dear eddy experts, > > I routinely use topup and eddy to correct DWI images for motion and EPI and EC distortions. > > Recently, I noticed that the output of eddy is nondeterministic. While topup, produces the same output every time I run it with the same input, repeated runs of eddy do not produce the same output (although they are close). > > Is this expected behavior? Are there any nondeterministic steps in the eddy process? Or should I worry that my hardware is failing? > > Kind regards, > Ben