Hi Emilie,

I ran DKE with interpolation off like you suggested and it worked!! I checked the headers of the output files and they show the same orientation as the input files, and I got no sform/qform errors as before. Thank you so much!! 

I attached the fa.nii file produced by DKE (with no interpolation), just in case you want to compare it to the files I uploaded earlier.

Thanks again!

Cheers,
Shereif