Hi Peter and Paul,
Thank you once again for the clarification and help.
In my case where the B0ref is the base and the dwi scan is the input, would you think the forward transform from 3dAllineate is appropriate or backwards? When I took my T2 (aligned to B0ref) as my input and applied the inverse of the 3dAllineate matrix I was able to get it aligned to my original DWIs. This seems similar to your situation, in which case the forward may make more sense.
Thanks,
Ajay
Edited 5 time(s). Last edit at 05/26/2017 09:11AM by AjaySK.