Hi Russell,

Thank you for the reply. It was helpful. I think I figured out why my output parametric images are in different orientation from my input dki.nii file. It was because I allowed parametric map interpolation. When I turned that off (map_interpolation_method.flag = 0), the input and output files overlay correctly and the header information for orientation is kept the same. 

I thought the interpretation only re-sample the images. But it looks like it also interprets images to a different orientation (flipping and tilting). Is it possible to ask the program to only re-sample but no change in orientation?

Best regards,
Yi-Fen