As @eilidhmacnicol points out, mouse template alignment has some difficulties like the differences in scale that can happen between mouse subjects and the template. A couple solutions can work though - first allow for the alignment to search over a large range of scale. Another approach is to prescale the data before or as part of the alignment procedure using an approximate scale factor. In AFNI, we include those methods in @animal_warper (options -super_size, -init_scale) along with -feature_size that allows for different size animals to be aligned. The output can then be used with afni_proc.py.
Here is the latest Allen Brain mouse CCF3 template converted to a convenient NIFTI format with voxel dimensions and a useful orientation. I put the 0,0,0 coordinate over anterior commissure. The left and right are almost completely symmetric, and there is no online definition from Allen on how to tell the difference.
https://afni.nimh.nih.gov/pub/dist/atlases/mouse/AllenCCF3_2020/AFNI_AllenMouseCCF3.tgz