A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans

Translational neuroscience requires consistent anatomical frameworks to compare brain organization across species despite differences in size and specialization. Existing atlases are species-specific, limiting cross-species analyses. Here we constructed population-averaged minimal deformation templates for rodents, nonhuman primates, and humans, and developed a hierarchical common atlas delineating homologous cortical and subcortical gray matter regions through landmark-guided boundaries and multimodal nonlinear registration. Validation against species-specific atlases confirmed strong regional correspondence and revealed systematic volumetric scaling, with humans showing expanded associative cortices and rodents emphasizing limbic and sensorimotor areas. This freely available atlas provides a unified coordinate system supporting comparative imaging, developmental analyses, and cross-species connectomics, facilitating investigations into conserved and divergent brain organization across species.