Just as a followup regarding MRTrix3 for the FSL format (http://mrtrix.readthedocs.io/en/latest/concepts/dw_scheme.html)

"It is important to note that in this format, the gradient vectors are provided with respect to the image axes, not in real or scanner coordinates (actually, it’s a little bit more complicated than that, refer to the FSL wiki for details). This is a rich source of confusion, since seemingly innocuous changes to the image can introduce inconsistencies in the b-vectors. For example, simply reformatting the image from sagittal to axial will effectively rotate the b-vectors, since this operation changes the image axes. It is also important to remember that a particular bvals/bvecs pair is only valid for the particular image that it corresponds to."

I can output the files in " real formats".
"It is important to note that in this format, the direction vectors are assumed to be provided with respect to real or scanner coordinates. This is the same convention as is used in the DICOM format."

Does the "FSL" or real format match better to 3dAllineate to apply rotation of bvecs?

Thanks,
Ajay