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:
copyfile(‘vat_right.nii’,’backup_vat_right.nii’);
ea_conformspaceto([ea_space,’t1.nii’],’vat_right.nii’,0);
the ,0 means nn interpolations, so maps will remain binary. Can do 1 for trilinear.
ea_conformspaceto(‘/path/to/your_mni_space.nii’,’vat_right.nii’,0);
will likewise reslice to the MNI space file you’re using.
Best, Andy
