Re the image orientations, please use SPM tools at least for initial reslicing to be on the safe side (lead-DBS treats stuff as SPM does).
You can e.g. generate full-stack high-res 0.5 mm MNI files (which will be huge) by applying:
the ,0 means nn interpolations, so maps will remain binary. Can do 1 for trilinear.
will likewise reslice to the MNI space file you’re using.