There is the Allen mouse brain atlas and template. You could download that from their site. Otherwise, I’ve configured the 2011/2014 version to work with AFNI. Here is a link for you to download the datasets for that. This includes a modally smoothed version of the atlas, so the segmentation is smoother out of the coronal histology slicing plane.
http://afni.nimh.nih.gov/pub/dist/atlases/mouse/allen_mouse_waxholm.tgz
After you download these datasets, make the appropriate changes in your .afnirc file like this:
AFNI_WHEREAMI_DEC_PLACES = 2
AFNI_TEMPLATE_SPACE_LIST = allen_waxholm_mouse
AFNI_ATLAS_COLORS = Allen_Waxholm_Mouse
AFNI_SUPP_ATLAS_DIR = /directory_where_you_put_this_atlas/allen_mouse_waxholm
The 2017 version from Allen, based on more than 600 mouse brains, could also be made available. I am waiting for Allen to assign a standard coordinate system.
