ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies
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 soft...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-10-01
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| Series: | NeuroImage |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1053811920305176 |
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Article |
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DOAJ |
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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 |
| spellingShingle |
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 ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies NeuroImage Arterial spin labeling Image processing Multi-center Cerebral perfusion Quality control |
| author_facet |
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 |
| author_sort |
Henk J.M.M. Mutsaerts |
| title |
ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies |
| title_short |
ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies |
| title_full |
ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies |
| title_fullStr |
ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies |
| title_full_unstemmed |
ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies |
| title_sort |
exploreasl: an image processing pipeline for multi-center asl perfusion mri studies |
| publisher |
Elsevier |
| series |
NeuroImage |
| issn |
1095-9572 |
| publishDate |
2020-10-01 |
| description |
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. |
| topic |
Arterial spin labeling Image processing Multi-center Cerebral perfusion Quality control |
| url |
http://www.sciencedirect.com/science/article/pii/S1053811920305176 |
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doaj-9ca02ec737244e5dbd9512f7639b54582020-11-25T03:03:33ZengElsevierNeuroImage1095-95722020-10-01219117031ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studiesHenk J.M.M. Mutsaerts0Jan Petr1Paul Groot2Pieter Vandemaele3Silvia Ingala4Andrew D. Robertson5Lena Václavů6Inge Groote7Hugo Kuijf8Fernando Zelaya9Owen O’Daly10Saima Hilal11Alle Meije Wink12Ilse Kant13Matthan W.A. Caan14Catherine Morgan15Jeroen de Bresser16Elisabeth Lysvik17Anouk Schrantee18Astrid Bjørnebekk19Patricia Clement20Zahra Shirzadi21Joost P.A. Kuijer22Viktor Wottschel23Udunna C. Anazodo24Dasja Pajkrt25Edo Richard26Reinoud P.H. Bokkers27Liesbeth Reneman28Mario Masellis29Matthias Günther30Bradley J. MacIntosh31Eric Achten32Michael A. Chappell33Matthias J.P. van Osch34Xavier Golay35David L. Thomas36Enrico De Vita37Atle Bjørnerud38Aart Nederveen39Jeroen Hendrikse40Iris Asllani41Frederik Barkhof42Department 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.Kate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, GermanyRadiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the NetherlandsGhent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, BelgiumDepartment of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the NetherlandsSchlegel-UW Research Institute for Aging, University of Waterloo, Waterloo, Ontario, CanadaC.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the NetherlandsDepartment of Diagnostic Physics, Oslo University Hospital, Oslo, NorwayImage Sciences Institute, University Medical Center Utrecht, Utrecht, the NetherlandsDepartment of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UKDepartment of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UKDepartment 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, SingaporeDepartment of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the NetherlandsRadiology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Intensive Care, University Medical Centre, Utrecht, the NetherlandsDepartment of Biomedical Engineering and Physics, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the NetherlandsSchool of Psychology and Centre for Brain Research, University of Auckland, Auckland, New ZealandDepartment of Radiology, Leiden University Medical Center, Leiden, the NetherlandsDepartment of Diagnostic Physics, Oslo University Hospital, Oslo, NorwayRadiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the NetherlandsThe Anabolic Androgenic Steroid Research Group, National Advisory Unit on Substance Use Disorder Treatment, Oslo University Hospital, Oslo, NorwayGhent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, BelgiumSunnybrook Research Institute, University of Toronto, Toronto, CanadaDepartment of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the NetherlandsDepartment of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, the NetherlandsDepartment of Medical Biophysics, University of Western Ontario, London, Canada; Imaging Division, Lawson Health Research Institute, London, CanadaDepartment of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Centre, Location Academic Medical Center, Amsterdam, the NetherlandsDepartment 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 NetherlandsDepartment of Radiology, Medical Imaging Center, University Medical Center Groningen, University of Groningen, Groningen, the NetherlandsRadiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the NetherlandsSunnybrook Research Institute, University of Toronto, Toronto, CanadaFraunhofer MEVIS, Bremen, Germany; University of Bremen, Bremen, Germany; Mediri GmbH, Heidelberg, GermanySunnybrook Research Institute, University of Toronto, Toronto, CanadaGhent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, BelgiumInstitute of Biomedical Engineering, Department of Engineering Science & Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UKC.J. Gorter Center for High Field MRI, Department of Radiology, Leiden University Medical Center, Leiden, the NetherlandsUCL Queen Square Institute of Neurology, University College London, London, UKUCL Queen Square Institute of Neurology, University College London, London, UKDepartment of Biomedical Engineering, School of Biomedical Engineering & Imaging Sciences, King’s College London, King’s Health Partners, St Thomas’ Hospital, London, SE1 7EH, UKDepartment of Diagnostic Physics, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, NorwayRadiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, the NetherlandsRadiology, University Medical Center Utrecht, Utrecht, the NetherlandsKate Gleason College of Engineering, Rochester Institute of Technology, NY, USA; Clinical Imaging Sciences Centre, Department of Neuroscience, Brighton and Sussex Medical School, Brighton, UKDepartment 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, UKArterial 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.http://www.sciencedirect.com/science/article/pii/S1053811920305176Arterial spin labelingImage processingMulti-centerCerebral perfusionQuality control |