I haven’t used dtiInit in a while, so I don’t remember the exact details. What I do remember is that one of the parameters that you have to set before running dtiInit (named eddyCorrect, I believe) gives you 3 different options for correcting your data: 1 for eddy and motion correction, 0 for correcting only one of them (can’t remember which), and -1 for no correction at all. I set it to -1.
I don’t remember using a separate function for only aligning the data, but then I again maybe I didn’t need to use dtiInit and one of these functions would have sufficed. I really can’t help you there, I was pretty much following a pipeline set up by someone else, so I didn’t really explore that much. There’s a good chance the functions I used are outdated by now, I really can’t tell.
That being said, the general idea is still the same, preprocess data, align to T1, perform whole brain tractography, then run AFQ.
Sorry I couldn’t be of more help. I’m sure there’s some message board for MrVista/AFQ where you could get more help. Good luck!