What tool are you using to view your data - is it possible that your image viewer is not aware of the spatial transformation matrices stored in the NIfTI header? I would suggest you use a tool like MRIcroGL or SPM to view your data (as these leverage the NIfTI header). One thought is that these are 3D images, which dcm2niix is losslessly rotating to the nearest orthogonal rotation to match an identity matrix. When the software does reorient the images in this manner, it updates the spatial transformation information stored in the header.

I am not familiar with nibabel, but I think it is aware of the coordinate systm, but initially shows you the raw data without applying the transform
http://nipy.org/nibabel/coordinate_syste...