Thanks for reporting the issue. Can you please let me know which executable were you using? Was it BDP.sh?
You can try the following workaround for now. You can simply load and save the T1 from brainsuite. It should save the header in brainsuite friendly format. Then proceed with the analysis using this saved T1.
Sorry for not replying earlier. I was using BDP.sh, for scriptability, and have never actually gotten the whole brainsuite package running. If I understand correctly though, and I think I do, I could easily manipulate the T1 to have a diagonal (non-oblique) affine matrix outside brainsuite, and carry on. I do not mind resampling the T1 for this purpose since its native resolution is much better than the dMRI’s.