Hi Konstantinos,

Thanks for getting back to me so quickly. I'll try to answer your questions as  best as I can.
1) I've tried with two brain extractions, one where there is the classic "halo" around the FSL bet extraction, and another where the mask was eroded, so it was pretty much all brain matter. They both gave the same results.
2) That sounds like a good idea to put in a mask of the white matter. I will try that as well and see what the result is (although I did try two brain extractions and it didn't change much, so I don't know what the extent to which non-white matter signals affect the registration).

Would you be willing to share a subject who you normalised to the HARDI template? Do you think you could provide me with the native and registered fod image so I could compare? If you are able to discuss further, my email is eric.moulton.jr@gmail.com . I am really stumped on this, and the mrregister command doesn't let you change too many parameters, so I'm not sure what to tinker with. 

Thanks again for your quick response. If I find anything, I'll be sure to post back here.

Best,
Eric