ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies
NeuroImage, vol. 219, pp. 117031
Abstract
Arterial spin labeling (ASL) has undergone significant development since its inception, with a focus on improving standardization and reproducibility of its acquisition and quantification. In a community-wide effort towards robust and reproducible clinical ASL image processing, we developed the software package ExploreASL, allowing standardized analyses across centers and scanners. The procedures used in ExploreASL capitalize on published image processing advancements and address the challenges of multi-center datasets with scanner-specific processing and artifact reduction to limit patient exclusion. ExploreASL is self-contained, written in MATLAB and based on Statistical Parameter Mapping (SPM) and runs on multiple operating systems. To facilitate collaboration and data-exchange, the toolbox follows several standards and recommendations for data structure, provenance, and best analysis practice. ExploreASL was iteratively refined and tested in the analysis of >10,000 ASL scans using different pulse-sequences in a variety of clinical populations, resulting in four processing modules: Import, Structural, ASL, and Population that perform tasks, respectively, for data curation, structural and ASL image processing and quality control, and finally preparing the results for statistical analyses on both single-subject and group level. We illustrate ExploreASL processing results from three cohorts: perinatally HIV-infected children, healthy adults, and elderly at risk for neurodegenerative disease. We show the reproducibility for each cohort when processed at different centers with different operating systems and MATLAB versions, and its effects on the quantification of gray matter cerebral blood flow. ExploreASL facilitates the standardization of image processing and quality control, allowing the pooling of cohorts which may increase statistical power and discover between-group perfusion differences. Ultimately, this workflow may advance ASL for wider adoption in clinical studies, trials, and practice.
Authors 43
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Henk J. M. M. Mutsaerts corresponding
Rochester Institute of Technology · Utrecht University · Amsterdam UMC Location University of Amsterdam · University Medical Center Utrecht · Ghent University · Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands; Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Radiology, University Medical Center Utrecht, Utrecht, the Netherlands; Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium. Electronic address: h.j.mutsaerts@amsterdamumc.nl
Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA
Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
Radiology, University Medical Center Utrecht, Utrecht, the Netherlands
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Rochester Institute of Technology · Helmholtz-Zentrum Dresden-Rossendorf
Affiliation as printed
Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA
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Amsterdam UMC Location University of Amsterdam · Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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Affiliation as printed
Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
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Amsterdam Neuroscience · Amsterdam University Medical Centers · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
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University of Waterloo · Research Institute for Aging
Affiliation as printed
Schlegel-UW Research Institute for Aging, University of Waterloo, Waterloo, Ontario, Canada
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Lena Václavů Aachen C.J. Gorter Center for High Field MRI Department of Radiology, Leiden University Medical Center
Leiden University Medical Center
Affiliation as printed
C.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
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Affiliation as printed
Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway
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Utrecht University · University Medical Center Utrecht
Affiliation as printed
Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands
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Affiliation as printed
Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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Affiliation as printed
Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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National University of Singapore · National University Health System
Affiliation as printed
Department of Pharmacology, National University of Singapore, Singapore; Memory Aging and Cognition Center, National University Health System, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
Department of Pharmacology, National University of Singapore, Singapore
Memory Aging and Cognition Center, National University Health System, Singapore
Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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Amsterdam Neuroscience · Amsterdam University Medical Centers · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
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University Medical Center Utrecht
Affiliation as printed
Radiology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Intensive Care, University Medical Centre, Utrecht, the Netherlands
Department of Intensive Care, University Medical Centre, Utrecht, the Netherlands
Radiology, University Medical Center Utrecht, Utrecht, the Netherlands
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Amsterdam UMC Location University of Amsterdam · Amsterdam University Medical Centers
Affiliation as printed
Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands
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Affiliation as printed
School of Psychology and Centre for Brain Research, University of Auckland, Auckland, New Zealand
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Leiden University Medical Center
Affiliation as printed
Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
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Affiliation as printed
Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway
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Amsterdam UMC Location University of Amsterdam · Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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Affiliation as printed
The Anabolic Androgenic Steroid Research Group, National Advisory Unit on Substance Use Disorder Treatment, Oslo University Hospital, Oslo, Norway
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Brighton and Sussex Medical School · Ghent University
Affiliation as printed
Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
Clinical Imaging Sciences Centre, Department of Neuroscience, Brighton and Sussex Medical School, Brighton, UK
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University of Toronto · University of Oxford · Wellcome Centre for Integrative Neuroimaging · Sunnybrook Research Institute
Affiliation as printed
Sunnybrook Research Institute, University of Toronto, Toronto, Canada
Institute of Biomedical Engineering, Department of Engineering Science & Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
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Amsterdam Neuroscience · Amsterdam University Medical Centers · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
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Amsterdam Neuroscience · Amsterdam University Medical Centers · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
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Western University · Lawson Health Research Institute
Affiliation as printed
Department of Medical Biophysics, University of Western Ontario, London, Canada; Imaging Division, Lawson Health Research Institute, London, Canada
Department of Medical Biophysics, University of Western Ontario, London, Canada
Imaging Division, Lawson Health Research Institute, London, Canada
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Amsterdam UMC Location University of Amsterdam · Emma Kinderziekenhuis · Amsterdam University Medical Centers
Affiliation as printed
Department of Pediatric Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Location Academic Medical Center, Amsterdam, the Netherlands
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Radboud University Nijmegen · Amsterdam UMC Location University of Amsterdam · Radboud University Medical Center · Amsterdam University Medical Centers · Donders Institute for Brain, Cognition and Behaviour · University of Amsterdam
Affiliation as printed
Department of Neurology, Donders Institute for Brain, Behavior and Cognition, Radboud University Medical Centre, Nijmegen, the Netherlands; Neurology, Amsterdam University Medical Center, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
Department of Neurology, Donders Institute for Brain, Behavior and Cognition, Radboud University Medical Centre, Nijmegen, the Netherlands
Neurology, Amsterdam University Medical Center, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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University Medical Center Groningen · University of Groningen
Affiliation as printed
Department of Radiology, Medical Imaging Center, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Amsterdam UMC Location University of Amsterdam · Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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University of Toronto · Sunnybrook Research Institute
Affiliation as printed
Sunnybrook Research Institute, University of Toronto, Toronto, Canada
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University of Bremen · University of Oxford · Wellcome Centre for Integrative Neuroimaging · Mediri (Germany) · Fraunhofer Institute for Digital Medicine
Affiliation as printed
Fraunhofer MEVIS, Bremen, Germany; University of Bremen, Bremen, Germany; Mediri GmbH, Heidelberg, Germany
Fraunhofer MEVIS, Bremen, Germany
Institute of Biomedical Engineering, Department of Engineering Science & Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
Mediri GmbH, Heidelberg, Germany
University of Bremen, Bremen, Germany
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University of Toronto · Mediri (Germany) · Sunnybrook Research Institute
Affiliation as printed
Sunnybrook Research Institute, University of Toronto, Toronto, Canada
Mediri GmbH, Heidelberg, Germany
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Ghent University · UCL Queen Square Institute of Neurology · University College London
Affiliation as printed
Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
UCL Queen Square Institute of Neurology, University College London, London, UK
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University of Oxford · Wellcome Centre for Integrative Neuroimaging
Affiliation as printed
Institute of Biomedical Engineering, Department of Engineering Science & Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
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Matthias J.P. van Osch Aachen C.J. Gorter Center for High Field MRI Department of Radiology, Leiden University Medical Center
Leiden University Medical Center
Affiliation as printed
C.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
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UCL Queen Square Institute of Neurology · University College London
Affiliation as printed
UCL Queen Square Institute of Neurology, University College London, London, UK
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UCL Queen Square Institute of Neurology · University College London
Affiliation as printed
UCL Queen Square Institute of Neurology, University College London, London, UK
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St Thomas' Hospital · King's College London · Kings Health Partners
Affiliation as printed
Department of Biomedical Engineering, School of Biomedical Engineering & Imaging Sciences, King's College London, King's Health Partners, St Thomas' Hospital, London, SE1 7EH, UK
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Oslo University Hospital · University of Oslo
Affiliation as printed
Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Norway
Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway
Department of Psychology, University of Oslo, Norway
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Amsterdam UMC Location University of Amsterdam · Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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Leiden University Medical Center · University Medical Center Utrecht
Affiliation as printed
Radiology, University Medical Center Utrecht, Utrecht, the Netherlands
Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
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Brighton and Sussex Medical School · Rochester Institute of Technology
Affiliation as printed
Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Clinical Imaging Sciences Centre, Department of Neuroscience, Brighton and Sussex Medical School, Brighton, UK
Clinical Imaging Sciences Centre, Department of Neuroscience, Brighton and Sussex Medical School, Brighton, UK
Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA
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Amsterdam Neuroscience · Amsterdam University Medical Centers · UCL Queen Square Institute of Neurology · University College London · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands; UCL Queen Square Institute of Neurology, University College London, London, UK; Centre for Medical Image Computing (CMIC), Faculty of Engineering Science, University College London, London, UK
Centre for Medical Image Computing (CMIC), Faculty of Engineering Science, University College London, London, UK
Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
UCL Queen Square Institute of Neurology, University College London, London, UK
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