Abstract
In this paper, we introduce a novel structural holistic Atlas (holiAtlas) of human brain anatomy based on multimodal and high-resolution MRI that covers several anatomical levels from the organ level to the substructure level, using a new protocol for dense labelling generated from the fusion of multiple local protocols at different scales. This atlas was constructed by averaging images and segmentations of 75 healthy subjects from the Human Connectome Project database. Specifically, 3T MR images of T1, T2 and WMn (White Matter nulled) contrasts at 0.125 mm3 resolution were selected for this project. The images of these 75 subjects were nonlinearly registered and averaged using symmetric group-wise normalisation to construct the atlas. At the finest level, the proposed atlas has 350 different labels derived from 7 distinct delineation protocols. These labels were grouped at multiple scales, offering a coherent and consistent holistic representation of the brain across different levels of detail. This multiscale and multimodal atlas can be used to develop new ultra-high-resolution segmentation methods, potentially improving the early detection of neurological disorders. We make it publicly available to the scientific community.
Data availability
The generated holistic atlas, together with the multiscale label definitions, is publicly available through the following links: https://volbrain.net/public/data/holiatlas_v1.0.zip and https://zenodo.org/records/15690524 under a Creative Commons license.
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Acknowledgements
This work has been developed thanks to the projects PID2020-118608RB-I00 and PID2023-152127OB-I00 of the Ministerio de Ciencia e Innovacion de España. This work also benefited from the support of the projects DeepvolBrain, HoliBrain and FOLDDICO of the French National Research Agency (ANR-18-CE45-0013, ANR-23-CE45-0020-01 and ANR-20-CHIA-0027-01). Finally, this study received financial support from the French government in the framework of the University of Bordeaux’s France 2030 program / RRI “IMPACT, the PEPR StratifyAging and the IHU VBHI (ANR-23-IAHU-0001). We thank the support of ITACA (Institute of Information and Communication Technologies) at UPV (Universitat Politècnica de València).
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Author contributionJosé V. Manjón: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - Original Draft, Writing - Review & Editing, Supervision, Project administration and Funding acquisition.Sergio Morell-Ortega: Software, Validation, Investigation, Data curation, Writing - Review & Editing.Marina Ruiz-Perez: Software, Validation, Investigation, Data curation, Writing - Review & Editing, Visualization.Boris Mansencal: Methodology, Software, Validation, Formal analysis, Investigation, Writing - Review & EditingEdern Le Bot: Software, Validation, Investigation, Data curation, Writing - Review & Editing, Visualization.Marien Gadea: Conceptualization, Validation, Formal analysis, Investigation, Resources, Data curation, Review & Editing, Visualization, Supervision and Funding acquisition.Enrique Lanuza: Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationGwenaelle Catheline: Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationThomas Tourdias: Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationVincent Planche: Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationRemi Giraud: Software, Validation, Formal analysis, Investigation, Writing - Review & EditingDenis Rivière: Software, Validation, Formal analysis, Investigation, Writing - Review & Editing.Jean-Francois Mangin: Software, Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationNicole Labra-Avila: Software, Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationRoberto Vivo-Hernando: Formal analysis, Investigation, Writing - Review & Editing.Gregorio Rubio: Formal analysis, Investigation, Writing - Review & Editing.Fernando Aparici: Validation, Formal analysis, Investigation, Data curation, Writing - Review & Editing, VisualizationMaria de la Iglesia-Vaya: Formal analysis, Investigation, Resources, Data curation, Writing - Review & Editing, Visualization.Pierrick Coupé: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - Original Draft, Writing - Review & Editing, Supervision, Project administration and Funding acquisition.
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Manjón, J.V., Morell-Ortega, S., Ruiz-Perez, M. et al. Ultra-high resolution multimodal MRI densely labelled holistic structural brain atlas. Sci Rep (2026). https://doi.org/10.1038/s41598-026-40186-2
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DOI: https://doi.org/10.1038/s41598-026-40186-2
