Pooled two-cohort MRI body composition phenotyping with open-source deep learning
Communications Medicine, vol. 6
Abstract
BACKGROUND: Body mass index fails to capture variation in fat and muscle distribution that determines metabolic health and disease risk. MRI enables radiation-free quantification of regional body composition, yet scalable open-source tools applied in pooled cohorts with differing acquisition protocols have been lacking. METHODS: MRSegmentator, an open-source nnU-Net-based pipeline, was applied to quantify visceral adipose tissue (VAT), abdominal subcutaneous adipose tissue (ASAT), gluteofemoral adipose tissue (GFAT), trunk musculature, and the liver mask used for liver fat-fraction estimation in 45,851 adults from the German National Cohort (n = 26,877, 3 T multi-centre Siemens) and UK Biobank (n = 18,974, 1.5 T Siemens). Population-scale compartment volumes were segmented from stitched in-phase gradient-echo (GRE) images in both cohorts; liver fat fraction was calculated from fat-only and water-only images. The annotated development data comprised NAKO T2-HASTE and UKB Dixon reconstructions. A single pooled model was applied without site-specific adaptation. A separate two-reader agreement study used 50 scans from these annotated development-sequence domains. Associations between BMI-adjusted body composition and cardiometabolic conditions were estimated using generalized linear mixed-effects models. Incremental discrimination beyond age, BMI, and waist-to-hip ratio was assessed. RESULTS: Five-fold participant-stratified internal cross-validation against curated human-in-the-loop development references comprising UKB Dixon and NAKO T2-HASTE yielded a mean Dice of 0.91. In a separate 50-scan reader study on these annotated development-sequence images, overall reader-reader Dice was 0.937 and overall algorithm-reader Dice was 0.908. The trained pipeline was then used to segment compartment volumes from stitched in-phase GRE inputs in both cohorts, while liver fat fraction was calculated from fat-only and water-only images; direct sequence-matched validation on NAKO GRE was not performed. VAT showed the strongest positive associations with cardiometabolic conditions, while GFAT showed inverse associations, most prominently for type 2 diabetes (OR 0.69, 95% CI 0.66 to 0.72). Disease-specific body-composition phenotypes were identified, with type 2 diabetes characterized by elevated VAT, reduced GFAT, and increased liver fat. MRI-derived compartments modestly improved discrimination for type 2 diabetes and hyperlipidemia beyond anthropometric measures. CONCLUSIONS: A single open-source deep-learning pipeline enabled pooled body-composition phenotyping in two cohorts and captured distributional variation in fat and muscle beyond BMI. High agreement in internal cross-validation (mean Dice 0.91) and the separate two-reader study support the annotated development-sequence analysis, while the population-scale application identified distinct disease-associated phenotypes and modest incremental discrimination beyond conventional anthropometry.
Authors 36
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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Radboud University Nijmegen · TUM Klinikum · Radboud University Medical Center · Technical University of Munich
Affiliation as printed
Diagnostic Image Analysis Group, Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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Heidelberg University · University Hospital Heidelberg · National Center for Tumor Diseases · University Hospital Carl Gustav Carus · Else Kröner Fresenius Center for Digital Health
Affiliation as printed
Department of Medicine I, University Hospital Dresden, Dresden, Germany
Else Kroener Fresenius Center for Digital Health, Dresden University of Technology, Dresden, Germany
Medical Oncology, National Center for Tumour Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
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Affiliation as printed
Department for Diagnostic and Interventional Radiology, University Hospital Aachen, Aachen, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Department of Diagnostic and Interventional Neuroradiology, School of Medicine and Health, TUM Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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University of Freiburg · University Medical Center Freiburg
Affiliation as printed
Department of Diagnostic and Interventional Radiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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University of Freiburg · University Medical Center Freiburg
Affiliation as printed
Department of Diagnostic and Interventional Radiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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University of Freiburg · University Medical Center Freiburg
Affiliation as printed
Department of Diagnostic and Interventional Radiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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University of Freiburg · University Medical Center Freiburg
Affiliation as printed
Department of Diagnostic and Interventional Radiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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University of Freiburg · University Medical Center Freiburg
Affiliation as printed
Department of Diagnostic and Interventional Radiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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Max Delbrück Center · Humboldt-Universität zu Berlin · German Centre for Cardiovascular Research · Helios Hospital Berlin-Buch · Charité - Universitätsmedizin Berlin
Affiliation as printed
Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, ECRC Experimental and Clinical Research Center, Berlin, Germany
DZHK (German Centre for Cardiovascular Research), Berlin, Germany
Department of Cardiology and Nephrology, Helios Hospital Berlin-Buch, Berlin, Germany
Working Group on CMR, Experimental and Clinical Research Center, a Joint Cooperation Between the Max-Delbrück-Center for Molecular Medicine and the Charité, Universitätsmedizin Berlin, Berlin, Germany
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Max Delbrück Center · Charité - Universitätsmedizin Berlin
Affiliation as printed
Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility (B.U.F.F.), Berlin, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Department of Gynecology and Center for Hereditary Breast and Ovarian Cancer, Technical University of Munich (TUM), School of Medicine and Health, Klinikum rechts der Isar, TUM University Hospital, Munich, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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Radboud University Nijmegen · Radboud University Medical Center
Affiliation as printed
Diagnostic Image Analysis Group, Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
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Stiftung Charité · Charité - Universitätsmedizin Berlin
Affiliation as printed
Department of Neuroradiology, Charité Universitätsmedizin Berlin, Berlin, Germany
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Stiftung Charité · Charité - Universitätsmedizin Berlin
Affiliation as printed
Department of Neuroradiology, Charité Universitätsmedizin Berlin, Berlin, Germany
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University of Potsdam · German Institute of Human Nutrition
Affiliation as printed
Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
Institute of Nutrition Science, University of Potsdam, Nuthetal, Germany
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Humboldt-Universität zu Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
Institute of Social Medicine, Epidemiology and Health Economics, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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Humboldt-Universität zu Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
Institute of Social Medicine, Epidemiology and Health Economics, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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Humboldt-Universität zu Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
Institute of Social Medicine, Epidemiology and Health Economics, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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Deutsches Herzzentrum München · Technical University of Munich
Affiliation as printed
Department of Cardiovascular Radiology and Nuclear Medicine, German Heart Center Munich, TUM University Hospital, Munich, Germany
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Universitätsmedizin Greifswald · Universität Greifswald
Affiliation as printed
Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
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Technical University of Munich
Affiliation as printed
Center for Translational Cancer Research (TranslaTUM), Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
Department of Medicine III, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
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TUM Klinikum · Munich Center for Machine Learning · Imperial College London · Technical University of Munich
Affiliation as printed
Chair of AI in Healthcare and Medicine, Technical University of Munich (TUM) and TUM University Hospital, Munich, Germany
Department of Computing, Imperial College London, London, UK
Munich Center for Machine Learning (MCML), Munich, Germany
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Max Delbrück Center · Humboldt-Universität zu Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biobank Technology Platform, Berlin, Germany
Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Technische Universität of Munich, School of Medicine and Health, TUM University Hospital Rechts der Isar, Institute of AI and Informatics in Medicine and Institute of General Practice and Health Services Research, Munich, Germany
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TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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TUM Klinikum · Deutsches Herzzentrum München · Technical University of Munich
Affiliation as printed
Department of Cardiovascular Radiology and Nuclear Medicine, German Heart Center Munich, TUM University Hospital, Munich, Germany
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany
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Lisa C. Adams corresponding
TUM Klinikum · Technical University of Munich
Affiliation as printed
Institute for Diagnostic and Interventional Radiology, School of Medicine and Health, TUM Klinikum, Technical University of Munich (TUM), Munich, Germany. lisa.adams@tum.de
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