Hi Paul,
well, I axialized the subject images to an anatomical reference (mni icbn152 ACPCE) before DIFFPREP, and this seems sufficient for Tortoise, fsl dtifit and fat_proc_dwi_to_dt with Automask to mantain voxel align, but fat_proc_dwi_to_dt -mask* introduce this 3drefit step in computation:
3drefit -dxorigin .000172 -dyorigin -.000603 -dzorigin -.000828 ./dwi_DMC2dt_dwi.nii.gz
before 3dDWItoDT that seems to me just a rounding problem (0.000xxx mm?). Probably, if you could avoid this 3drefit, the analysis group of my project would not have the difficulties encountered whatever analysis they invents.
Cheers,
Giuseppe