I only have data from the human connectome project, I usually don't collect data myself. Right now I'm only interested in the motion correction, not the eddy current correction, as I just recently started with DTI (worked with fMRI for a long time).

I have a pretty good registration algorithm, and I want to test how it performs compared to other algorithms for DTI. For DTI data, there are large differences in the image intensity and the noise level for different b-values. This makes it hard(er) to correct for motion between different b-values, like 1000, 2000 and 3000. My registration algorithm is designed for handling large intensity differences, and a quick test shows that it is more robust than flirt in FSL for my DTI data (but I don't know how common it is to use flirt for DTI).