{"doi":"10.1101/2025.09.08.675002","title":"A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans","abstract":"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 developed a hierarchical common atlas delineating homologous cortical and subcortical gray matter regions across mouse, rat, marmoset, rhesus macaque, and human, built upon population-averaged minimal deformation templates and uniform tissue segmentation. The atlas was validated through cross-atlas Dice similarity against established human parcellations, cross-scale containment against species-specific atlases, cross-species geometric consistency of regional positioning, and comparison of independent mouse and marmoset invasive tracer connectivity, with a per-region homology confidence index quantifying the strength of each regional assignment. Cross-species tracer comparison revealed a structured gradient of correspondence, with sensorimotor connections showing strong conservation and association connections showing progressive divergence. This freely available atlas provides a unified coordinate system for comparative neuroscience, enabling quantitative evaluation of where cross-species correspondence holds and where species-specific divergence emerges.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":559055,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8348,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1459793,"name":"Yuhe Tian","orcid":"0000-0002-2257-7666","position":1,"is_corresponding":false},{"id":1187076,"name":"W S Linn","orcid":"0009-0003-5312-6029","position":2,"is_corresponding":false},{"id":1460277,"name":"Jessica Barrios Martinez","orcid":null,"position":3,"is_corresponding":false},{"id":1460278,"name":"Harrison Mansour","orcid":null,"position":4,"is_corresponding":false},{"id":572334,"name":"James J. Cook","orcid":"0000-0001-9847-8683","position":5,"is_corresponding":false},{"id":458682,"name":"David J. Schaeffer","orcid":"0000-0003-2201-7092","position":6,"is_corresponding":false},{"id":259023,"name":"Diego Szczupak","orcid":"0000-0003-0818-9613","position":7,"is_corresponding":false},{"id":259029,"name":"Afonso C. Silva","orcid":"0000-0002-6105-7567","position":8,"is_corresponding":false},{"id":329773,"name":"G. Allan Johnson","orcid":"0000-0002-7606-5447","position":9,"is_corresponding":false},{"id":239773,"name":"Fang‐Cheng Yeh","orcid":"0000-0002-7946-2173","position":10,"is_corresponding":false},{"id":527471,"name":"Siva Venkadesh","orcid":"0000-0002-8112-0578","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T02:55:30.312295Z","pmid":"40964338","pmcid":"PMC12439950","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}