Publication

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

Mutsaerts, H. J. M. M., Petr, J., Groot, P., Vandemaele, P., Ingala, S., Robertson, A. D., Vaclave, L., Groote, I., Kuijf, H., Zelaya, F., O'Daly, O., Hilal, S., Wink, A. M., Kant, I., Caan, M. W. A., Morgan, C., de Bresser, J., Lysvik, E., Schrantee, A., Bjornebekk, A., Clement, P., Shirzadi, Z., Kuijer, J. P. A., Wottschel, V., Anazodo, U. C., Pajkrt, D., Richard, E., Bokkers, R. P. H., Reneman, L., Masellis, M., Guenther, M., MacIntosh, B. J., Achten, E., Chappell, M. A., van Osch, M. J. P., Golay, X., Thomas, D. L., De Vita, E., Bjornerud, A., Nederveen, A., Hendrikse, J., Asllani, I. & Barkhof, F., 1-Oct-2020, In : Neuroimage. 219, p. 117031 17 p., 117031.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Mutsaerts, H. J. M. M., Petr, J., Groot, P., Vandemaele, P., Ingala, S., Robertson, A. D., Vaclave, L., Groote, I., Kuijf, H., Zelaya, F., O'Daly, O., Hilal, S., Wink, A. M., Kant, I., Caan, M. W. A., Morgan, C., de Bresser, J., Lysvik, E., Schrantee, A., ... Barkhof, F. (2020). ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies. Neuroimage, 219, 117031. [117031]. https://doi.org/10.1016/j.neuroimage.2020.117031

Author

Mutsaerts, Henk J. M. M. ; Petr, Jan ; Groot, Paul ; Vandemaele, Pieter ; Ingala, Silvia ; Robertson, Andrew D. ; Vaclave, Lena ; Groote, Inge ; Kuijf, Hugo ; Zelaya, Fernando ; O'Daly, Owen ; Hilal, Saima ; Wink, Alle Meije ; Kant, Ilse ; Caan, Matthan W. A. ; Morgan, Catherine ; de Bresser, Jeroen ; Lysvik, Elisabeth ; Schrantee, Anouk ; Bjornebekk, Astrid ; Clement, Patricia ; Shirzadi, Zahra ; Kuijer, Joost P. A. ; Wottschel, Viktor ; Anazodo, Udunna C. ; Pajkrt, Dasja ; Richard, Edo ; Bokkers, Reinoud P. H. ; Reneman, Liesbeth ; Masellis, Mario ; Guenther, Matthias ; MacIntosh, Bradley J. ; Achten, Eric ; Chappell, Michael A. ; van Osch, Matthias J. P. ; Golay, Xavier ; Thomas, David L. ; De Vita, Enrico ; Bjornerud, Atle ; Nederveen, Aart ; Hendrikse, Jeroen ; Asllani, Iris ; Barkhof, Frederik. / ExploreASL : An image processing pipeline for multi-center ASL perfusion MRI studies. In: Neuroimage. 2020 ; Vol. 219. pp. 117031.

Harvard

Mutsaerts, HJMM, Petr, J, Groot, P, Vandemaele, P, Ingala, S, Robertson, AD, Vaclave, L, Groote, I, Kuijf, H, Zelaya, F, O'Daly, O, Hilal, S, Wink, AM, Kant, I, Caan, MWA, Morgan, C, de Bresser, J, Lysvik, E, Schrantee, A, Bjornebekk, A, Clement, P, Shirzadi, Z, Kuijer, JPA, Wottschel, V, Anazodo, UC, Pajkrt, D, Richard, E, Bokkers, RPH, Reneman, L, Masellis, M, Guenther, M, MacIntosh, BJ, Achten, E, Chappell, MA, van Osch, MJP, Golay, X, Thomas, DL, De Vita, E, Bjornerud, A, Nederveen, A, Hendrikse, J, Asllani, I & Barkhof, F 2020, 'ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies', Neuroimage, vol. 219, 117031, pp. 117031. https://doi.org/10.1016/j.neuroimage.2020.117031

Standard

ExploreASL : An image processing pipeline for multi-center ASL perfusion MRI studies. / Mutsaerts, Henk J. M. M.; Petr, Jan; Groot, Paul; Vandemaele, Pieter; Ingala, Silvia; Robertson, Andrew D.; Vaclave, Lena; Groote, Inge; Kuijf, Hugo; Zelaya, Fernando; O'Daly, Owen; Hilal, Saima; Wink, Alle Meije; Kant, Ilse; Caan, Matthan W. A.; Morgan, Catherine; de Bresser, Jeroen; Lysvik, Elisabeth; Schrantee, Anouk; Bjornebekk, Astrid; Clement, Patricia; Shirzadi, Zahra; Kuijer, Joost P. A.; Wottschel, Viktor; Anazodo, Udunna C.; Pajkrt, Dasja; Richard, Edo; Bokkers, Reinoud P. H.; Reneman, Liesbeth; Masellis, Mario; Guenther, Matthias; MacIntosh, Bradley J.; Achten, Eric; Chappell, Michael A.; van Osch, Matthias J. P.; Golay, Xavier; Thomas, David L.; De Vita, Enrico; Bjornerud, Atle; Nederveen, Aart; Hendrikse, Jeroen; Asllani, Iris; Barkhof, Frederik.

In: Neuroimage, Vol. 219, 117031, 01.10.2020, p. 117031.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Mutsaerts HJMM, Petr J, Groot P, Vandemaele P, Ingala S, Robertson AD et al. ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies. Neuroimage. 2020 Oct 1;219:117031. 117031. https://doi.org/10.1016/j.neuroimage.2020.117031


BibTeX

@article{f8c1d9febcb04b8dadd0df5f6ee5fd05,
title = "ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies",
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, Image processing, Multi-center, Cerebral perfusion, Quality control, CEREBRAL-BLOOD-FLOW, PARTIAL VOLUME CORRECTION, SPIN-LABELING PERFUSION, TEST-RETEST RELIABILITY, WHITE-MATTER PERFUSION, SPATIAL NORMALIZATION, ALZHEIMERS-DISEASE, SUSCEPTIBILITY DISTORTIONS, NOISE-REDUCTION, RELAXATION-TIME",
author = "Mutsaerts, {Henk J. M. M.} and Jan Petr and Paul Groot and Pieter Vandemaele and Silvia Ingala and Robertson, {Andrew D.} and Lena Vaclave and Inge Groote and Hugo Kuijf and Fernando Zelaya and Owen O'Daly and Saima Hilal and Wink, {Alle Meije} and Ilse Kant and Caan, {Matthan W. A.} and Catherine Morgan and {de Bresser}, Jeroen and Elisabeth Lysvik and Anouk Schrantee and Astrid Bjornebekk and Patricia Clement and Zahra Shirzadi and Kuijer, {Joost P. A.} and Viktor Wottschel and Anazodo, {Udunna C.} and Dasja Pajkrt and Edo Richard and Bokkers, {Reinoud P. H.} and Liesbeth Reneman and Mario Masellis and Matthias Guenther and MacIntosh, {Bradley J.} and Eric Achten and Chappell, {Michael A.} and {van Osch}, {Matthias J. P.} and Xavier Golay and Thomas, {David L.} and {De Vita}, Enrico and Atle Bjornerud and Aart Nederveen and Jeroen Hendrikse and Iris Asllani and Frederik Barkhof",
note = "Copyright {\textcopyright} 2020. Published by Elsevier Inc.",
year = "2020",
month = oct,
day = "1",
doi = "10.1016/j.neuroimage.2020.117031",
language = "English",
volume = "219",
pages = "117031",
journal = "Neuroimage",
issn = "1053-8119",
publisher = "ACADEMIC PRESS INC ELSEVIER SCIENCE",

}

RIS

TY - JOUR

T1 - ExploreASL

T2 - An image processing pipeline for multi-center ASL perfusion MRI studies

AU - Mutsaerts, Henk J. M. M.

AU - Petr, Jan

AU - Groot, Paul

AU - Vandemaele, Pieter

AU - Ingala, Silvia

AU - Robertson, Andrew D.

AU - Vaclave, Lena

AU - Groote, Inge

AU - Kuijf, Hugo

AU - Zelaya, Fernando

AU - O'Daly, Owen

AU - Hilal, Saima

AU - Wink, Alle Meije

AU - Kant, Ilse

AU - Caan, Matthan W. A.

AU - Morgan, Catherine

AU - de Bresser, Jeroen

AU - Lysvik, Elisabeth

AU - Schrantee, Anouk

AU - Bjornebekk, Astrid

AU - Clement, Patricia

AU - Shirzadi, Zahra

AU - Kuijer, Joost P. A.

AU - Wottschel, Viktor

AU - Anazodo, Udunna C.

AU - Pajkrt, Dasja

AU - Richard, Edo

AU - Bokkers, Reinoud P. H.

AU - Reneman, Liesbeth

AU - Masellis, Mario

AU - Guenther, Matthias

AU - MacIntosh, Bradley J.

AU - Achten, Eric

AU - Chappell, Michael A.

AU - van Osch, Matthias J. P.

AU - Golay, Xavier

AU - Thomas, David L.

AU - De Vita, Enrico

AU - Bjornerud, Atle

AU - Nederveen, Aart

AU - Hendrikse, Jeroen

AU - Asllani, Iris

AU - Barkhof, Frederik

N1 - Copyright © 2020. Published by Elsevier Inc.

PY - 2020/10/1

Y1 - 2020/10/1

N2 - 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.

AB - 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.

KW - Arterial spin labeling

KW - Image processing

KW - Multi-center

KW - Cerebral perfusion

KW - Quality control

KW - CEREBRAL-BLOOD-FLOW

KW - PARTIAL VOLUME CORRECTION

KW - SPIN-LABELING PERFUSION

KW - TEST-RETEST RELIABILITY

KW - WHITE-MATTER PERFUSION

KW - SPATIAL NORMALIZATION

KW - ALZHEIMERS-DISEASE

KW - SUSCEPTIBILITY DISTORTIONS

KW - NOISE-REDUCTION

KW - RELAXATION-TIME

U2 - 10.1016/j.neuroimage.2020.117031

DO - 10.1016/j.neuroimage.2020.117031

M3 - Article

C2 - 32526385

VL - 219

SP - 117031

JO - Neuroimage

JF - Neuroimage

SN - 1053-8119

M1 - 117031

ER -

ID: 132896172