TY - JOUR
T1 - Contrast-agent-based perfusion MRI code repository and testing framework
T2 - ISMRM Open Science Initiative for Perfusion Imaging (OSIPI)
AU - van Houdt, Petra J.
AU - Ragunathan, Sudarshan
AU - Berks, Michael
AU - Ahmed, Zaki
AU - Kershaw, Lucy E.
AU - Gurney-Champion, Oliver J.
AU - Tadimalla, Sirisha
AU - Arvidsson, Jonathan
AU - Sun, Yu
AU - Kallehauge, Jesper
AU - Dickie, Ben
AU - Lévy, Simon
AU - Bell, Laura
AU - Sourbron, Steven
AU - Thrippleton, Michael J.
N1 - Publisher Copyright: © 2023 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.
PY - 2023
Y1 - 2023
N2 - Purpose: Software has a substantial impact on quantitative perfusion MRI values. The lack of generally accepted implementations, code sharing and transparent testing reduces reproducibility, hindering the use of perfusion MRI in clinical trials. To address these issues, the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) aimed to establish a community-led, centralized repository for sharing open-source code for processing contrast-based perfusion imaging, incorporating an open-source testing framework. Methods: A repository was established on the OSIPI GitHub website. Python was chosen as the target software language. Calls for code contributions were made to OSIPI members, the ISMRM Perfusion Study Group, and publicly via OSIPI websites. An automated unit-testing framework was implemented to evaluate the output of code contributions, including visual representation of the results. Results: The repository hosts 86 implementations of perfusion processing steps contributed by 12 individuals or teams. These cover all core aspects of DCE- and DSC-MRI processing, including multiple implementations of the same functionality. Tests were developed for 52 implementations, covering five analysis steps. For T1 mapping, signal-to-concentration conversion and population AIF functions, different implementations resulted in near-identical output values. For the five pharmacokinetic models tested (Tofts, extended Tofts-Kety, Patlak, two-compartment exchange, and two-compartment uptake), differences in output parameters were observed between contributions. Conclusions: The OSIPI DCE-DSC code repository represents a novel community-led model for code sharing and testing. The repository facilitates the re-use of existing code and the benchmarking of new code, promoting enhanced reproducibility in quantitative perfusion imaging.
AB - Purpose: Software has a substantial impact on quantitative perfusion MRI values. The lack of generally accepted implementations, code sharing and transparent testing reduces reproducibility, hindering the use of perfusion MRI in clinical trials. To address these issues, the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) aimed to establish a community-led, centralized repository for sharing open-source code for processing contrast-based perfusion imaging, incorporating an open-source testing framework. Methods: A repository was established on the OSIPI GitHub website. Python was chosen as the target software language. Calls for code contributions were made to OSIPI members, the ISMRM Perfusion Study Group, and publicly via OSIPI websites. An automated unit-testing framework was implemented to evaluate the output of code contributions, including visual representation of the results. Results: The repository hosts 86 implementations of perfusion processing steps contributed by 12 individuals or teams. These cover all core aspects of DCE- and DSC-MRI processing, including multiple implementations of the same functionality. Tests were developed for 52 implementations, covering five analysis steps. For T1 mapping, signal-to-concentration conversion and population AIF functions, different implementations resulted in near-identical output values. For the five pharmacokinetic models tested (Tofts, extended Tofts-Kety, Patlak, two-compartment exchange, and two-compartment uptake), differences in output parameters were observed between contributions. Conclusions: The OSIPI DCE-DSC code repository represents a novel community-led model for code sharing and testing. The repository facilitates the re-use of existing code and the benchmarking of new code, promoting enhanced reproducibility in quantitative perfusion imaging.
KW - OSIPI
KW - dynamic contrast-enhanced MRI
KW - dynamic susceptibility-contrast MRI
KW - open source
KW - perfusion
KW - software
UR - http://www.scopus.com/inward/record.url?scp=85169819612&partnerID=8YFLogxK
U2 - https://doi.org/10.1002/mrm.29826
DO - https://doi.org/10.1002/mrm.29826
M3 - Article
C2 - 37667526
SN - 0740-3194
JO - Magnetic resonance in medicine
JF - Magnetic resonance in medicine
ER -