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

doi:10.1016/j.neuroimage.2020.117031

ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies

Neuroimage. 2020 Oct 1:219:117031. doi: 10.1016/j.neuroimage.2020.117031. Epub 2020 Jun 8.

Authors

Henk J M M Mutsaerts¹, Jan Petr², Paul Groot³, Pieter Vandemaele⁴, Silvia Ingala⁵, Andrew D Robertson⁶, Lena Václavů⁷, Inge Groote⁸, Hugo Kuijf⁹, Fernando Zelaya¹⁰, Owen O'Daly¹⁰, Saima Hilal¹¹, Alle Meije Wink⁵, Ilse Kant¹², Matthan W A Caan¹³, Catherine Morgan¹⁴, Jeroen de Bresser¹⁵, Elisabeth Lysvik⁸, Anouk Schrantee³, Astrid Bjørnebekk¹⁶, Patricia Clement⁴, Zahra Shirzadi¹⁷, Joost P A Kuijer⁵, Viktor Wottschel⁵, Udunna C Anazodo¹⁸, Dasja Pajkrt¹⁹, Edo Richard²⁰, Reinoud P H Bokkers²¹, Liesbeth Reneman³, Mario Masellis¹⁷, Matthias Günther²², Bradley J MacIntosh¹⁷, Eric Achten⁴, Michael A Chappell²³, Matthias J P van Osch⁷, Xavier Golay²⁴, David L Thomas²⁴, Enrico De Vita²⁵, Atle Bjørnerud²⁶, Aart Nederveen³, Jeroen Hendrikse²⁷, Iris Asllani²⁸, Frederik Barkhof²⁹

Affiliations

¹ 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.
² Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany.
³ Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
⁴ Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium.
⁵ Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands.
⁶ Schlegel-UW Research Institute for Aging, University of Waterloo, Waterloo, Ontario, Canada.
⁷ C.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands.
⁸ Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway.
⁹ Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands.
¹⁰ Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
¹¹ 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.
¹² Radiology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Intensive Care, University Medical Centre, Utrecht, the Netherlands.
¹³ Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands.
¹⁴ School of Psychology and Centre for Brain Research, University of Auckland, Auckland, New Zealand.
¹⁵ Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands.
¹⁶ The Anabolic Androgenic Steroid Research Group, National Advisory Unit on Substance Use Disorder Treatment, Oslo University Hospital, Oslo, Norway.
¹⁷ Sunnybrook Research Institute, University of Toronto, Toronto, Canada.
¹⁸ Department of Medical Biophysics, University of Western Ontario, London, Canada; Imaging Division, Lawson Health Research Institute, London, Canada.
¹⁹ Department of Pediatric Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Location Academic Medical Center, Amsterdam, the Netherlands.
²⁰ 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.
²¹ Department of Radiology, Medical Imaging Center, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
²² Fraunhofer MEVIS, Bremen, Germany; University of Bremen, Bremen, Germany; Mediri GmbH, Heidelberg, Germany.
²³ Institute of Biomedical Engineering, Department of Engineering Science & Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK.
²⁴ UCL Queen Square Institute of Neurology, University College London, London, UK.
²⁵ 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.
²⁶ Department of Diagnostic Physics, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Norway.
²⁷ Radiology, University Medical Center Utrecht, Utrecht, the Netherlands.
²⁸ 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.
²⁹ 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.

PMID: 32526385
DOI: 10.1016/j.neuroimage.2020.117031

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.

Keywords: Arterial spin labeling; Cerebral perfusion; Image processing; Multi-center; Quality control.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Brain / diagnostic imaging*
Cerebrovascular Circulation / physiology
Humans
Image Processing, Computer-Assisted / methods*
Magnetic Resonance Angiography / methods*
Reproducibility of Results
Signal-To-Noise Ratio
Software
Spin Labels

Substances

Spin Labels

Abstract

Publication types

MeSH terms

Substances

Grants and funding