Segmenting Whole-Body MRI and CT for Multiorgan Anatomic Structure Delineation.

Journal: Radiology. Artificial intelligence
Published Date:

Abstract

Purpose To develop and validate MRSegmentator, a retrospective cross-modality deep learning model for multiorgan segmentation of MRI scans. Materials and Methods This retrospective study trained MRSegmentator on 1,200 manually annotated UK Biobank Dixon MRI sequences (50 participants), 221 in-house abdominal MRI sequences (177 patients), and 1228 CT scans from the TotalSegmentator-CT dataset. A human-in-the-loop annotation workflow leveraged cross-modality transfer learning from an existing CT segmentation model to segment 40 anatomic structures. The model's performance was evaluated on 900 MRI sequences from 50 participants in the German National Cohort (NAKO), 60 MRI sequences from AMOS22 dataset, and 29 MRI sequences from TotalSegmentator-MRI. Reference standard manual annotations were used for comparison. Metrics to assess segmentation quality included Dice Similarity Coefficient (DSC). Statistical analyses included organ-and sequence-specific mean ± SD reporting and two-sided tests for demographic effects. Results 139 participants were evaluated; demographic information was available for 70 (mean age 52.7 years ± 14.0 [SD], 36 female). Across all test datasets, MRSegmentator demonstrated high class wise DSC for well-defined organs (lungs: 0.81-0.96, heart: 0.81-0.94) and organs with anatomic variability (liver: 0.82-0.96, kidneys: 0.77-0.95). Smaller structures showed lower DSC (portal/splenic veins: 0.64-0.78, adrenal glands: 0.56-0.69). The average DSC on the external testing using NAKO data, ranged from 0.85 ± 0.08 for T2-HASTE to 0.91 ± 0.05 for in-phase sequences. The model generalized well to CT, achieving mean DSC of 0.84 ± 0.12 on AMOS CT data. Conclusion MRSegmentator accurately segmented 40 anatomic structures on MRI and generalized to CT; outperforming existing open-source tools. Published under a CC BY 4.0 license.

Authors

  • Hartmut Häntze
    Department of Radiology, Charite - Universitatsmedizin Berlin, Berlin, Germany.
  • Lina Xu
    Emergency Department, Beichen Hospital, Tianjin, China.
  • Christian J Mertens
    Department of Diagnostic and Interventional Radiology, School of Medicine and Health, Klinikum rechts der Isar, TUM University Hospital, Technical University of Munich, Munich, Germany.
  • Felix J Dorfner
    Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA; Department of Radiology, Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
  • Leonhard Donle
    Department of Radiology, Charite - Universitatsmedizin Berlin, Berlin, Germany.
  • Felix Busch
    Institute for Diagnostic and Interventional Radiology, TUM School of Medicine and Health, TUM University Hospital Rechts der Isar, Technical University of Munich, Munich, Germany.
  • Avan Kader
    Department of Diagnostic and Interventional Radiology, Technical University of Munich, School of Medicine and Health, Klinikum Rechts der Isar, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany.
  • Sebastian Ziegelmayer
    Department of Diagnostic and Interventional Radiology, School of Medicine, Technical University of Munich, Munich, Germany.
  • Nadine Bayerl
    Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Radiology, University Hospital Erlangen, Maximiliansplatz 3, 91054 Erlangen, Germany. Electronic address: nadine.bayerl@fau.de.
  • Nassir Navab
    Chair for Computer Aided Medical Procedures & Augmented Reality, TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
  • Daniel Rueckert
    Biomedical Image Analysis (BioMedIA) Group, Department of Computing, Imperial College London, UK. Electronic address: d.rueckert@imperial.ac.uk.
  • Julia Schnabel
  • Hugo J W L Aerts
    Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.
  • Daniel Truhn
    Department of Diagnostic and Interventional Radiology, University Hospital Düsseldorf, Düsseldorf, Germany (J.S., D.B.A., S.N.); Institute of Computer Vision and Imaging, RWTH University Aachen, Pauwelsstrasse 30, 52072 Aachen, Germany (J.S., D.M.); Department of Diagnostic and Interventional Radiology, University Hospital Aachen, Aachen, Germany (D.T., M.P., F.M., C.K., S.N.); and Faculty of Mathematics and Natural Sciences, Institute of Informatics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany (S.C.).
  • Fabian Bamberg
    Department of Diagnostic and Interventional Radiology, University Medical Center Tübingen, Tübingen, Germany.
  • Jakob Weiss
    Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA.
  • Christopher L Schlett
    From the MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, 68 Varosmajor St, 1122 Budapest, Hungary (M.K., J.K., B.M., P.M.H.); Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Mass (J.K., Y.K., A.I., M.T.L., B.F., H.J.A., U.H.); Center for Cause of Death Investigation, Faculty of Medicine, Hokkaido University, Hokkaido, Japan (Y.K.); Department for Diagnostic and Interventional Radiology, Medical Center-University of Freiburg, Freiburg, Germany (C.L.S.); and Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass (H.J.A.).
  • Steffen Ringhof
    Department of Radiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
  • Thoralf Niendorf
    Berlin Ultrahigh Field Facility, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
  • Tobias Pischon
    Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Molecular Epidemiology Research Group, Berlin, Germany.
  • Hans-Ulrich Kauczor
    Department of Diagnostic and Interventional Radiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
  • Tobias Nonnenmacher
    Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg.
  • Thomas Kröncke
    Department of Diagnostic and Interventional Radiology and Neuroradiology, Universitätsklinikum Augsburg, Augsburg, Germany.
  • Henry Völzke
    Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
  • Jeanette Schulz-Menger
    Charité-Universitätsmedizin Berlin, Experimental and Clinical Research Center, Working Group On CMR and HELIOS Klinikum Berlin Buch, Cardiology Berlin, DZHK partnersite Berlin, Berlin, Germany.
  • Klaus Maier-Hein
    Medical Image Analysis, Division Medical Image Computing, DKFZ Heidelberg, Germany.
  • Alessa Hering
    Fraunhofer Institute for Digital Medicine MEVIS, Maria-Goeppert-Str. 3, 23562, Lübeck, Germany. alessa.hering@mevis.fraunhofer.de.
  • Mathias Prokop
    Department of Radiology, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Bram van Ginneken
    Diagnostic Image Analysis Group, Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands; Fraunhofer Mevis, Bremen, Germany.
  • Marcus R Makowski
    School of Medicine and Health, Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, TUM University Hospital, Technical University of Munich, Munich, Germany.
  • Lisa C Adams
    School of Medicine and Health, Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, TUM University Hospital, Technical University of Munich, Munich, Germany.
  • Keno K Bressem
    School of Medicine and Health, Institute for Cardiovascular Radiology and Nuclear Medicine, German Heart Center Munich, TUM University Hospital, Technical University of Munich, Munich, Germany.

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