[Freesurfer] Shifting hdr information in .nii?

A little off-topic maybe, but:

I am working to load external data into analysis programs using .nii format files. I have inplanes acquired at an ACPC orientation, as well as data collected and specially pre-processed through a MATLAB pathway that unfortunately strips away all orientation information. I have been trying to find a way to use the header information from the inplanes to orient the data (unfortunately, automated alignment algorithms fail due to the nature of the data).

Does anybody have any suggestions, or information on exactly which fields in the .nii header to shift?

Thanks in advance for all of the help on a thorny problem!

Joakim