Hi Eric,

I am afraid I don't have a good answer to your question. We have not seen this shrinking for HARDI registration before. And as you mentioned we have never seen this for tensor-based registration either. But I would greatly appreciate it if you shared your solution with us in this thread when you figure it out.
A couple of questions.
1) How good is the brain extraction of your subjects? Are any signals outside the brain still left?
2) What would happen if you repeat your process after first masking the IIT HARDI template by setting a threshold of ~0.5 for both the IIT_WM_tissue_prob and IIT_GM_tissue_prob? This masking of the IIT HARDI template should eliminate signals from outside the brain. I am wondering if those signals mislead mrregister of MRtrix in your case.

Regards,
Konstantinos