afni.nimh.nih.gov

I think I solved it. I changed the 3dresample step above

3dresample -input ribbon_shft.nii -prefix ribbon_res_shft.nii -master $ct -rmode NN
to
3dresample -input ribbon_shft.nii -prefix ribbon_res_shft.nii -master ct_shft.nii -rmode NN

Anyway, it there is a more straightforward way of doing it please let me know. Also, I would like to know which -rmode option (NN, cubic) or other is the 'best', irrespective of computation time. Thank you,

Octavian