I am new to freesurfer. I have been looking for an answer to this issue for days. 

I ran bbregister to align a dti scan to a t1 struc.

It worked beautifully.

I am trying to register a very abnormal looking dataset to the t1 using the registration parameters created during the first bbregister (dti to t1).

I have been unable to figure this out, but it seems like it must be a common procedure. Any advice would be greatly appreciated.