afni.nimh.nih.gov

Thanks, you are right on all accounts. The spatial transformation works but the tensors need to be reoriented as well. WIth ANTs one can use ReorientTensorImage but this needs the transform that was applied to the volume and it doesn't seem to work with afni's 1D transform files. Maybe, I should move this whole routine to ANTs and stop trying to make the afni transforms work in ANTs.