Yes, SPM uses the NIfTI spatial transforms to reorient the images. It should work regardless of whether you use SPM, dcm2nii, MRIconvert, dicm2nii or dinifti to process your files. Other tools may either ignore these transforms. As an advanced comment, the header stores two spatial transforms QForm and SForm). Some SPM processes (e.g. coregistration) will manipulate the SForm. Be aware that SPM/MRIcroGL/MRIcron gives precedence to the SForm, while other tools (e.g. those built with VTK) give precedence to the QForm. So after coregistration with SPM the orientation may appear different in different tools. I think SPM is doing the appropriate thing (retaining original coordinates and providing a affine warp to standard space), but other tools do not respect this convention.