this usually happens when niftis are not in standard nifti orientation and maybe were not imported from DICOM properly. Please make sure to do the DICOM import with a new version of Lead-DBS.
Also maybe try to make some experiences with other datasets that work first.
Finally, if it all persists, trick is to manually prealign volumes to MNI space (e.g. using 3D slicer) first and then run Lead-DBS based normalization – but this is pretty involved and cannot be explained easily here.