Hi Rick,
I have been modifying different parts of the header, but still have not had any luck aligning the functionals and anatomicals. I was wondering whether any of the fields determine the geometrical origin of the image, and then just setting those to 0. I'm guessing it isn't that simple, but it would be a good starting point. If you have any recommendations, or can point me towards a reference section outlining the function of the different nifti fields, please let me know.
Thank you,
-Andrew