Multi-class glioma segmentation on real-world data with missing MRI sequences: comparison of three deep learning algorithms.

Journal: Scientific reports
Published Date: Nov 2, 2023

Abstract

This study tests the generalisability of three Brain Tumor Segmentation (BraTS) challenge models using a multi-center dataset of varying image quality and incomplete MRI datasets. In this retrospective study, DeepMedic, no-new-Unet (nn-Unet), and NVIDIA-net (nv-Net) were trained and tested using manual segmentations from preoperative MRI of glioblastoma (GBM) and low-grade gliomas (LGG) from the BraTS 2021 dataset (1251 in total), in addition to 275 GBM and 205 LGG acquired clinically across 12 hospitals worldwide. Data was split into 80% training, 5% validation, and 15% internal test data. An additional external test-set of 158 GBM and 69 LGG was used to assess generalisability to other hospitals' data. All models' median Dice similarity coefficient (DSC) for both test sets were within, or higher than, previously reported human inter-rater agreement (range of 0.74-0.85). For both test sets, nn-Unet achieved the highest DSC (internal = 0.86, external = 0.93) and the lowest Hausdorff distances (10.07, 13.87 mm, respectively) for all tumor classes (p < 0.001). By applying Sparsified training, missing MRI sequences did not statistically affect the performance. nn-Unet achieves accurate segmentations in clinical settings even in the presence of incomplete MRI datasets. This facilitates future clinical adoption of automated glioma segmentation, which could help inform treatment planning and glioma monitoring.

Authors

  • Hugh G Pemberton
    Centre for Medical Image Computing (CMIC), University College London, London, UK.
  • Jiaming Wu
    Centre for Medical Image Computing (CMIC), University College London, London, UK.
  • Ivar Kommers
    Neurosurgical Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
  • Domenique M J Müller
    Neurosurgical Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
  • Yipeng Hu
    Centre for Medical Image Computing (CMIC), Departments of Medical Physics & Biomedical Engineering and Computer Science, University College London, UK.
  • Olivia Goodkin
    Centre for Medical Image Computing (CMIC), University College London, London, UK.
  • Sjoerd B Vos
    From the Translational and Clinical Research Institute (N.S.), Faculty of Medical Sciences, and Computational Neuroscience, Neurology, and Psychiatry Lab (N.S., Y.W., N.M.d.S., P.N.T.), Interdisciplinary Computing and Complex BioSystems Group, School of Computing, Newcastle University, Newcastle Upon Tyne; NIHR University College London Hospitals Biomedical Research Centre (Y.W., A.M., A.W.M., J.d.T., S.B.V., G.P.W., J.S.D., P.N.T.), UCL Institute of Neurology, Queen Square; Centre for Medical Image Computing (S.B.V.), University College London; Epilepsy Society MRI Unit (S.B.V., G.P.W., J.S.D), Chalfont St Peter, UK; and Department of Medicine (G.P.W.,), Division of Neurology, Queen's University, Kingston, Ontario, Canada.
  • Sotirios Bisdas
    Queen Square Institute of Neurology, University College London, Queen Square 7, London WC1N 3BG, UK.
  • Pierre A Robe
    Department of Neurology & Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands.
  • Hilko Ardon
    Department of Neurosurgery, St. Elisabeth Hospital, Tilburg, The Netherlands.
  • Lorenzo Bello
    Department of Oncology and Hematology-Oncology, Universitá degli Studi di Milano, Milan, Italy.
  • Marco Rossi
    Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy.
  • Tommaso Sciortino
    Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy.
  • Marco Conti Nibali
    Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy.
  • Mitchel S Berger
    Department of Neurological Surgery, University of California San Fransisco, San Francisco, CA 94143-0112, USA.
  • Shawn L Hervey-Jumper
    Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA.
  • Wim Bouwknegt
    Department of Neurosurgery, Medical Center Slotervaart, Amsterdam, The Netherlands.
  • Wimar A Van den Brink
    Department of Neurosurgery, Isala Hospital, Zwolle, The Netherlands.
  • Julia Furtner
    Department of Biomedical Imaging and Image-Guided Therapy, Medical University Vienna, Vienna, Austria.
  • Seunggu J Han
    Department of Neurological Surgery, Stanford University, Stanford, USA.
  • Albert J S Idema
    Department of Neurosurgery, Northwest Clinics, Alkmaar, The Netherlands.
  • Barbara Kiesel
    Department of Neurosurgery, Medical University of Vienna, Vienna, Austria; and.
  • Georg Widhalm
    Department of Neurosurgery, Medical University Vienna, Vienna, Austria.
  • Alfred Kloet
    Department of Neurosurgery, Medical Center Haaglanden, The Hague, The Netherlands.
  • Michiel Wagemakers
    Department of Neurosurgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
  • Aeilko H Zwinderman
    Amsterdam UMC, University of Amsterdam, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam, The Netherlands.
  • Sandro M Krieg
    Klinik und Poliklinik für Neurochirurgie, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675, München, Deutschland. sandro.krieg@tum.de.
  • Emmanuel Mandonnet
    Department of Neurosurgery, Lariboisière Hospital , Paris , France.
  • Ferran Prados
    Queen Square MS Centre, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK; Center for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
  • Philip de Witt Hamer
    Neurosurgical Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
  • Frederik Barkhof
    MS Center Amsterdam, Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam UMC location VUmc, the Netherlands.
  • Roelant S Eijgelaar
    Department of Neurosurgery, Cancer Center Amsterdam, Brain Tumor Center, Amsterdam UMC, Amsterdam, Netherlands.

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