Hi Eric,
Hope I understand your question correctly! But, I have also had issues with registration (TBI brains 
)! So, I tried ANTS with fod images as input for template building and co-registering individual brains.
As a test, I took just the 1st volume of the fod images, and it does work!
Assuming you have the individual warps from the brains, follow this post Registration: using transformations generated from other packages
A small issue: there is a dollar sign missing in the line: do WarpImageMultiTransform 3 identity_warp${i}.nii mrtrix_warp${i}.nii
I hope this helps 
Best,
Karthik