Automated Dentate Nucleus Segmentation from QSM Images Using Deep Learning
Abstract
Abstract Purpose To develop a dentate nucleus (DN) segmentation tool using deep learning (DL) applied to brain quantitative susceptibility mapping (QSM) images. Materials and Methods Brain QSM images from 132 healthy controls and 170 individuals with cerebellar ataxia or multiple sclerosis were collected from nine different datasets worldwide for this retrospective study. Manual delineation of the DN (gray matter and white matter hilus) was first undertaken by experienced raters with a robust quality control process. Performance of automated segmentation was compared following training using several DL architectures. A two-step approach was implemented, composed of a localization model followed by DN segmentation. Results The manual tracing protocol produced ground-truth data with high intra-rater (average ICC 0.906) and inter-rater reliability (average ICC 0.776). Initial DL architecture exploration indicated that the nnU-Net framework performed best. The two-step localization plus segmentation pipeline achieved a Dice score of 0.898±0.031 and 0.894±0.036 for left and right DN, respectively. In external validation, our algorithm outperformed the leading existing automated tool (left/right DN Dice 0.863±0.038/0.843±0.066 vs. 0.568±0.222/0.582±0.239). The model demonstrated generalizability across unseen datasets during the training step. The measures showed a superior correlation index with manual annotations and performed well in both isotropic and anisotropic QSM datasets. Conclusion We provide a model that accurately and efficiently segments the DN from brain QSM images. The model can be readily deployed for use in observational, natural history, and treatment trials for biomarker discovery.
Authors 35
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil;
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil
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Affiliation as printed
School of Psychological Sciences, The Turner Institute for Brain and Mental Health, Monash University, Clayton, Victoria, Australia;
School of Psychological Sciences, The Turner Institute for Brain and Mental Health, Monash University, Clayton, Victoria, Australia
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Affiliation as printed
Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, United States of America;
Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, United States of America
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University of Naples Federico II
Affiliation as printed
Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy;
Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
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Murdoch Children's Research Institute
Affiliation as printed
Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia;
Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
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Affiliation as printed
University Clinic and Outpatient Clinic for Radiology, Department for Radiation Medicine, University Hospital Halle (Saale), University Medicine Halle, Halle (Saale), Germany;
University Clinic and Outpatient Clinic for Radiology, Department for Radiation Medicine, University Hospital Halle (Saale), University Medicine Halle, Halle (Saale), Germany
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Murdoch Children's Research Institute
Affiliation as printed
Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia;
Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
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Affiliation as printed
Department of Neurology, RWTH Aachen University, Aachen, Germany;
Department of Neurology, RWTH Aachen University, Aachen, Germany
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Children's Hospital of Philadelphia
Affiliation as printed
Department of Radiology and Program in Advanced Imaging Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America;
Department of Radiology and Program in Advanced Imaging Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
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Affiliation as printed
School of Psychological Sciences, The Turner Institute for Brain and Mental Health, Monash University, Clayton, Victoria, Australia;
School of Psychological Sciences, The Turner Institute for Brain and Mental Health, Monash University, Clayton, Victoria, Australia
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Affiliation as printed
University Clinic and Outpatient Clinic for Radiology, Department for Radiation Medicine, University Hospital Halle (Saale), University Medicine Halle, Halle (Saale), Germany;
University Clinic and Outpatient Clinic for Radiology, Department for Radiation Medicine, University Hospital Halle (Saale), University Medicine Halle, Halle (Saale), Germany
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Fondazione IRCCS Istituto Neurologico Carlo Besta
Affiliation as printed
Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy;
Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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Affiliation as printed
Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, United States of America;
Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, United States of America
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil;
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil
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Affiliation as printed
Department of Neurology, Medical University of Graz, Graz, Austria;
Department of Neurology, Medical University of Graz, Graz, Austria
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Affiliation as printed
Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, United States of America;
Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, United States of America
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Affiliation as printed
Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America;
Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil;
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil
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Affiliation as printed
Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America;
Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
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Children's Hospital of Philadelphia
Affiliation as printed
Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America;
Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
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Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America;
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
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Institute of Biostructure and Bioimaging · National Research Council
Affiliation as printed
Institute of Biostructures and Bioimaging, Italian National Research Council, Naples, Italy;
Institute of Biostructures and Bioimaging, Italian National Research Council, Naples, Italy
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Fondazione IRCCS Istituto Neurologico Carlo Besta
Affiliation as printed
Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy;
Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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Affiliation as printed
Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada;
Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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Affiliation as printed
Department of Neurology, RWTH Aachen University, Aachen, Germany;
Department of Neurology, RWTH Aachen University, Aachen, Germany
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Children's Hospital of Philadelphia
Affiliation as printed
Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America;
Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
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Affiliation as printed
Department of Neurology, RWTH Aachen University, Aachen, Germany;
Department of Neurology, RWTH Aachen University, Aachen, Germany
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Affiliation as printed
Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada;
Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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University of Naples Federico II
Affiliation as printed
Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy;
Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
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Affiliation as printed
Department of Neurology, RWTH Aachen University, Aachen, Germany;
Department of Neurology, RWTH Aachen University, Aachen, Germany
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University of Florida Health · University of Florida
Affiliation as printed
Department of Neurology and the Fixel Institute for Neurological Diseases, University of Florida, Gainesville, Florida, United States of America;
Department of Neurology and the Fixel Institute for Neurological Diseases, University of Florida, Gainesville, Florida, United States of America
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Essen University Hospital · University of Duisburg-Essen
Affiliation as printed
Department of Neurology and Center for Translational and Behavioral Neuroscience (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany;
Department of Neurology and Center for Translational and Behavioral Neuroscience (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil;
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil
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QIMR Berghofer Medical Research Institute
Affiliation as printed
QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia;
QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Thiago Junqueira Ribeiro de Rezende corresponding
Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil;
Department of Neurology, School of Medical Sciences, University of Campinas (Unicamp), Campinas, Brazil
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