Generalizable lower-limb muscle MRI segmentation and quantification on heterogeneous multisite datasets
Abstract
Abstract Neuromuscular diseases are a heterogeneous group of disorders affecting muscles and peripheral nerves, leading to progressive muscle weakness and functional impairment. Muscle MRI facilitates the assessment of muscle pathology, but current analysis relies on time-consuming manual segmentation or subjective visual scoring. Validation across diverse patient populations and imaging protocols is lacking in existing automated methods. Deep learning segmentation methods were developed to quantify intramuscular fat infiltration and muscle volume across all lower limb muscles using heterogeneous multi-site data. Three convolutional neural network architectures (U-Net, U-Net + + , and Attention U-Net + +) were evaluated on a multi-site dataset comprising 27,858 slices from 797 muscle MRI scans across 376 patients, spanning 12 neuromuscular diseases and 12 international sites. Thirty-two individual muscles across pelvis, thigh, and lower leg regions were segmented. High accuracy was achieved by all architectures (DSC = 0.97). Leave-One-Site-Out experiments revealed strong generalisability across sites (average DSC = 0.96). Automated fat quantification placed 90.9% of muscles within one point of ground truth on standard visual scales and correlated strongly with quantitative fat fraction measurements (r = 0.995, p < 0.001). High correlation with ground truth was demonstrated by cross-sectional area predictions (r = 0.94, p < 0.001). Diverse imaging protocols were handled with minimal preprocessing. Accuracy equivalent to observer variability was achieved by automated segmentation, potentially eliminating the need for manual correction in large-scale applications.
Authors 97
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José Verdú-Díaz corresponding
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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University of Antwerp · Antwerp University Hospital
Affiliation as printed
Neuromuscular Reference Center, Department of Neurology, Universitair Ziekenhuis Van Antwerpen, Universiteit Antwerpen, Antwerp, Belgium
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Agostino Gemelli University Polyclinic · Istituti di Ricovero e Cura a Carattere Scientifico
Affiliation as printed
UOC Di Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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Affiliation as printed
Centro Clinico NeMO, Pergine Valsugana, Italia
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Hospital Clínico de la Universidad de Chile · Clínica Dávila · University of Chile
Affiliation as printed
Clínica Dávila, Santiago de Chile, Chile
Hospital Clínico Universidad de Chile, Santiago de Chile, Chile
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Universitair Ziekenhuis Leuven · KU Leuven
Affiliation as printed
Department of Neurology, University Hospitals Leuven, Leuven, Belgium
Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, Leuven, Belgium
Universitair Ziekenhuis Leuven, Leuven, Belgium
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Affiliation as printed
Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
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Affiliation as printed
Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), SAPIENZA University of Rome, Rome, Italy
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Affiliation as printed
Universitätsklinikum Erlangen, Erlangen, Germany
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Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
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Hospital Universitario Puerta de Hierro Majadahonda
Affiliation as printed
Hospital Puerta de Hierro, Madrid, Spain
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Affiliation as printed
Medical University of Warsaw, Warsaw, Poland
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Affiliation as printed
University Hospital Brno, Brno, Czech Republic
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Voronezh State Medical Academy named after N.N. Burdenko
Affiliation as printed
Voronezh State Medical University, Voronezh, Russia
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University of Ljubljana · Ljubljana University Medical Centre
Affiliation as printed
Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
University Medical Centre Ljubljana, Ljubljana, Slovenia
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Fudan University · Huashan Hospital
Affiliation as printed
Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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Leeds Teaching Hospitals NHS Trust
Affiliation as printed
Leeds Teaching Hospitals NHS Trust, Leeds, UK
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Università Cattolica del Sacro Cuore · Agostino Gemelli University Polyclinic · Istituti di Ricovero e Cura a Carattere Scientifico
Affiliation as printed
Dipartimento Di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Italy
UOC Di Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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Shariati Hospital · Tehran University of Medical Sciences
Affiliation as printed
Neurology Department, Shariati Hospital, Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
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National Institute of Mental Health and Neurosciences
Affiliation as printed
National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
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Affiliation as printed
Uzhhorod National University, Uzhhorod, Ukraine
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Affiliation as printed
Advanced Imaging and AI Center, Mondino IRCCS Foundation, Pavia, Italy
Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
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Affiliation as printed
Programa de Doctorado en Ciencias Médicas y Especialidad, Escuela de Postgrado Facultad de Medicina, Universidad de Chile, Santiago de Chile, Chile
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Vita-Salute San Raffaele University · IRCCS Ospedale San Raffaele
Affiliation as printed
IRCCS Ospedale San Raffaele, Milan, Italy
San Raffaele Hospital, Milan, Italy
Vita-Salute San Raffaele University, Milan, Italy
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Hospital de Sant Pau · Institut de Recerca Sant Pau
Affiliation as printed
Neuromuscular Disorders Unit, Department of Neurology, Hospital de La Santa Creu I Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
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Affiliation as printed
Department of Neurology, Pusan National University School of Medicine, Busan, Republic of Korea
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Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
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Radboud University Nijmegen · Radboud University Medical Center · Donders Institute for Brain, Cognition and Behaviour
Affiliation as printed
Department of Neurology, Radboudumc Research Institute for Medical Innovation, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
Radboud University Medical Centre, Nijmegen, Netherlands
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Children's Hospital of Eastern Ontario · Ottawa Hospital
Affiliation as printed
Department of Medicine (Neurology), The Ottawa Hospital, Ottawa, Canada
Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Canada
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Affiliation as printed
Department of Neurology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
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Affiliation as printed
Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Affiliation as printed
Interdisciplinary Computing and Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
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Newcastle upon Tyne Hospitals NHS Foundation Trust · Newcastle University
Affiliation as printed
John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle Upon Tyne, UK
Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Copenhagen University Hospital · Rigshospitalet
Affiliation as printed
Copenhagen Neuromuscular Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Shariati Hospital · Tehran University of Medical Sciences
Affiliation as printed
Neurology Department, Shariati Hospital, Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Affiliation as printed
Department of Neurology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
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Affiliation as printed
Ulm University, Ulm, Germany
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Fondazione Istituto Neurologico Nazionale Casimiro Mondino
Affiliation as printed
Child and Adolescent Neuropsychiatry Department, Mondino IRCCS Foundation, Pavia, Italy
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Affiliation as printed
Medical University of Warsaw, Warsaw, Poland
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Agostino Gemelli University Polyclinic
Affiliation as printed
Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
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Great Ormond Street Hospital · University College London
Affiliation as printed
Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
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Copenhagen University Hospital · Rigshospitalet
Affiliation as printed
Copenhagen Neuromuscular Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Affiliation as printed
Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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Affiliation as printed
Medical University of Warsaw, Warsaw, Poland
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Affiliation as printed
Folkhalsan Istitute of Genetics, University of Helsinki, Helsinki, Finland
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Fudan University · Huashan Hospital
Affiliation as printed
Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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Affiliation as printed
IRCCS Ospedale San Raffaele, Milan, Italy
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Agostino Gemelli University Polyclinic
Affiliation as printed
Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
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Affiliation as printed
Musculoskeletal service, Department of Radiology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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Hospital Universitario 12 De Octubre
Affiliation as printed
Neurology Department, Neuromuscular Disorders Unit, Hospital 12 de Octubre, Madrid, Spain
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Pontificia Universidad Católica de Chile
Affiliation as printed
Department of Radiology. Pontificia, Universidad Catolica de Chile, Santiago, Chile
i-HEALTH Millennium Institute for Intelligent Healthcare Engineering, Santiago, Chile
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Leeds Teaching Hospitals NHS Trust
Affiliation as printed
Leeds Teaching Hospitals NHS Trust, Leeds, UK
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Pontificia Universidad Católica de Chile
Affiliation as printed
Hospital Sotero del Rio & Pontificia Universidad Católica de Chile, Santiago de Chile, Chile
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Vall d'Hebron Hospital Universitari
Affiliation as printed
Hospital Universitari Vall d’Hebron, Barcelona, Spain
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Centre National de la Recherche Scientifique · Aix-Marseille Université · Centre de Résonance Magnétique Biologique et Médicale
Affiliation as printed
Aix-Marseille University, CRMBM, CNRS UMR 7339, Marseille, France
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Radboud University Medical Center
Affiliation as printed
Radboud University Medical Centre, Nijmegen, Netherlands
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Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Paris Est University, APHP Henri-Mondor University Hospital, Créteil, France
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Centre Hospitalier Universitaire de Montpellier
Affiliation as printed
Centre de référence des maladies du motoneurone, department of neurology, Montpellier University Hospital, Montpellier, France
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Affiliation as printed
Hospital de Clinicas, Montevideo, Uruguay
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St George’s University Hospitals NHS Foundation Trust
Affiliation as printed
George’s University and St George’s University Hospitals NHS Foundation Trust, London, United Kingdom
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Centre Hospitalier Universitaire de Montpellier
Affiliation as printed
Department of Neuroradiology, Montpellier University Hospital, I2FH platform, Montpellier, France
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Agostino Gemelli University Polyclinic
Affiliation as printed
Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
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Leiden University · Leiden University Medical Center
Affiliation as printed
Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
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Università Cattolica del Sacro Cuore
Affiliation as printed
Pediatric Neurology, Department of Woman and Child Health and Public Health, Università Cattolica del Sacro Cuore, Child Health Area, Rome, Italy
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Centre Hospitalier Universitaire de Montpellier
Affiliation as printed
Centre de référence des maladies du motoneurone, department of neurology, Montpellier University Hospital, Montpellier, France
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Hospital Clínico de la Universidad de Chile · University of Chile
Affiliation as printed
Hospital Clínico Universidad de Chile, Santiago de Chile, Chile
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National and Kapodistrian University of Athens
Affiliation as printed
National &, Kapodistrian University of Athens, Athens, Greece
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Great Ormond Street Hospital · University College London
Affiliation as printed
Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
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Copenhagen University Hospital · Rigshospitalet
Affiliation as printed
Copenhagen Neuromuscular Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Affiliation as printed
Department of Neuroscience, IRCCS Stella Maris Foundation, 56128, Pisa, Italy
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Hermien E.Kan Aachen C.J. Gorter MRI Center Department of Radiology, Leiden University Medical Center
Leiden University · Leiden University Medical Center
Affiliation as printed
C.J. Gorter MRI Centre, Department of Radiology, Leiden University Medical Centre, Leiden, The Netherlands
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Fudan University · Huashan Hospital
Affiliation as printed
Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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Affiliation as printed
Magnetic Resonance Centre, Newcastle University, Newcastle upon Tyne, United Kingdom
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Ottawa Hospital Research Institute
Affiliation as printed
Ottawa Hospital Research Institute, Ottawa, Canada
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Northern Care Alliance NHS Foundation Trust
Affiliation as printed
Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom
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UCL Queen Square Institute of Neurology · University College London
Affiliation as printed
Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
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Vall d'Hebron Hospital Universitari
Affiliation as printed
Neuromuscular Disorders Unit, Neurology Department, Hospital Universitari Vall d’Hebron, Barcelona, Spain
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Leeds Teaching Hospitals NHS Trust
Affiliation as printed
Leeds Teaching Hospitals NHS Trust, Leeds, UK
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Kyungpook National University Hospital · Kyungpook National University
Affiliation as printed
Department of Neurology, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
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Copenhagen University Hospital · Rigshospitalet
Affiliation as printed
Copenhagen Neuromuscular Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Copenhagen University Hospital · Rigshospitalet
Affiliation as printed
Copenhagen Neuromuscular Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Kyungpook National University Hospital · Kyungpook National University
Affiliation as printed
Department of Neurology, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
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Hospital Clínico de la Universidad de Chile · University of Chile
Affiliation as printed
Hospital Clínico Universidad de Chile, Santiago de Chile, Chile
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Hospital Universitario Nuestra Señora de Candelaria
Affiliation as printed
Neuromuscular Disease Unit, Neurology Department, Hospital Universitario Nuestra Señora de Candelaria, Tenerife, Spain
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