Hi Anand,
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.
Thanks!
Rob