NeuroImage (Oct 2020)
ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies
- Henk J.M.M. Mutsaerts,
- Jan Petr,
- Paul Groot,
- Pieter Vandemaele,
- Silvia Ingala,
- Andrew D. Robertson,
- Lena Václavů,
- Inge Groote,
- Hugo Kuijf,
- Fernando Zelaya,
- Owen O’Daly,
- Saima Hilal,
- Alle Meije Wink,
- Ilse Kant,
- Matthan W.A. Caan,
- Catherine Morgan,
- Jeroen de Bresser,
- Elisabeth Lysvik,
- Anouk Schrantee,
- Astrid Bjørnebekk,
- Patricia Clement,
- Zahra Shirzadi,
- Joost P.A. Kuijer,
- Viktor Wottschel,
- Udunna C. Anazodo,
- Dasja Pajkrt,
- Edo Richard,
- Reinoud P.H. Bokkers,
- Liesbeth Reneman,
- Mario Masellis,
- Matthias Günther,
- Bradley J. MacIntosh,
- Eric Achten,
- Michael A. Chappell,
- Matthias J.P. van Osch,
- Xavier Golay,
- David L. Thomas,
- Enrico De Vita,
- Atle Bjørnerud,
- Aart Nederveen,
- Jeroen Hendrikse,
- Iris Asllani,
- Frederik Barkhof
Affiliations
- Henk J.M.M. Mutsaerts
- 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; Corresponding author. Dep. of Radiology and Nuclear Medicine, PK -1, De Boelelaan 1117, 1081, HV, Amsterdam, the Netherlands.
- Jan Petr
- Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- Paul Groot
- Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Pieter Vandemaele
- Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
- Silvia Ingala
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
- Andrew D. Robertson
- Schlegel-UW Research Institute for Aging, University of Waterloo, Waterloo, Ontario, Canada
- Lena Václavů
- C.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
- Inge Groote
- Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway
- Hugo Kuijf
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands
- Fernando Zelaya
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Owen O’Daly
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Saima Hilal
- 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
- Alle Meije Wink
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
- Ilse Kant
- Radiology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Intensive Care, University Medical Centre, Utrecht, the Netherlands
- Matthan W.A. Caan
- Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands
- Catherine Morgan
- School of Psychology and Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Jeroen de Bresser
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
- Elisabeth Lysvik
- Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway
- Anouk Schrantee
- Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Astrid Bjørnebekk
- The Anabolic Androgenic Steroid Research Group, National Advisory Unit on Substance Use Disorder Treatment, Oslo University Hospital, Oslo, Norway
- Patricia Clement
- Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
- Zahra Shirzadi
- Sunnybrook Research Institute, University of Toronto, Toronto, Canada
- Joost P.A. Kuijer
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
- Viktor Wottschel
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
- Udunna C. Anazodo
- Department of Medical Biophysics, University of Western Ontario, London, Canada; Imaging Division, Lawson Health Research Institute, London, Canada
- Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Centre, Location Academic Medical Center, Amsterdam, the Netherlands
- Edo Richard
- 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
- Reinoud P.H. Bokkers
- Department of Radiology, Medical Imaging Center, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Liesbeth Reneman
- Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Mario Masellis
- Sunnybrook Research Institute, University of Toronto, Toronto, Canada
- Matthias Günther
- Fraunhofer MEVIS, Bremen, Germany; University of Bremen, Bremen, Germany; Mediri GmbH, Heidelberg, Germany
- Bradley J. MacIntosh
- Sunnybrook Research Institute, University of Toronto, Toronto, Canada
- Eric Achten
- Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
- Michael A. Chappell
- Institute of Biomedical Engineering, Department of Engineering Science & Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
- Matthias J.P. van Osch
- C.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
- Xavier Golay
- UCL Queen Square Institute of Neurology, University College London, London, UK
- David L. Thomas
- UCL Queen Square Institute of Neurology, University College London, London, UK
- Enrico De Vita
- 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
- Atle Bjørnerud
- Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Norway
- Aart Nederveen
- Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Jeroen Hendrikse
- Radiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Iris Asllani
- 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
- Frederik Barkhof
- 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
- Journal volume & issue
-
Vol. 219
p. 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.