KomaMRI.jl: An open‐source framework for general MRI simulations with GPU acceleration

To develop an open-source, high-performance, easy-to-use, extensible, cross-platform, and general MRI simulation framework (Koma). Koma was developed using the Julia programming language. Like other MRI simulators, it solves the Bloch equations with CPU and GPU parallelization. The inputs are the sc...

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Bibliographic Details
Published in:Magnetic resonance in medicine Vol. 90; no. 1; pp. 329 - 342
Main Authors: Castillo‐Passi, Carlos, Coronado, Ronal, Varela‐Mattatall, Gabriel, Alberola‐López, Carlos, Botnar, René, Irarrazaval, Pablo
Format: Journal Article
Language:English
Published: United States Wiley Subscription Services, Inc 01.07.2023
John Wiley and Sons Inc
Subjects:
Acceleration
Computer Processing and Modeling
Computer Simulation
Computers
Fingerprinting
Graphical user interface
Graphics processing units
Humans
Image reconstruction
Language
Machine learning
Magnetic resonance imaging
Magnetic Resonance Imaging - methods
Personal computers
Phantoms, Imaging
Programming languages
Scanners
Simulation
Simulators
Synthetic data
Julia
Bloch equations
open source
GUI
GPU
simulation
ISSN:0740-3194, 1522-2594, 1522-2594
Online Access:Get full text
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Description
Summary:To develop an open-source, high-performance, easy-to-use, extensible, cross-platform, and general MRI simulation framework (Koma). Koma was developed using the Julia programming language. Like other MRI simulators, it solves the Bloch equations with CPU and GPU parallelization. The inputs are the scanner parameters, the phantom, and the pulse sequence that is Pulseq-compatible. The raw data is stored in the ISMRMRD format. For the reconstruction, MRIReco.jl is used. A graphical user interface utilizing web technologies was also designed. Two types of experiments were performed: one to compare the quality of the results and the execution speed, and the second to compare its usability. Finally, the use of Koma in quantitative imaging was demonstrated by simulating Magnetic Resonance Fingerprinting (MRF) acquisitions. Koma was compared to two well-known open-source MRI simulators, JEMRIS and MRiLab. Highly accurate results (with mean absolute differences below 0.1% compared to JEMRIS) and better GPU performance than MRiLab were demonstrated. In an experiment with students, Koma was proved to be easy to use, eight times faster on personal computers than JEMRIS, and 65% of test subjects recommended it. The potential for designing acquisition and reconstruction techniques was also shown through the simulation of MRF acquisitions, with conclusions that agree with the literature. Koma's speed and flexibility have the potential to make simulations more accessible for education and research. Koma is expected to be used for designing and testing novel pulse sequences before implementing them in the scanner with Pulseq files, and for creating synthetic data to train machine learning models.
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Funding information Agencia Estatal de Investigación, Grant/Award Numbers: PID2020‐115339RB‐I00, TED2021‐130090B‐I00; ANID ‐ Millennium Science Initiative Program, Grant/Award Number: ICN2021_004; ANID Basal, Grant/Award Number: FB210024; Engineering and Physical Sciences Research Council, Grant/Award Numbers: EP/P001009, EP/P007619/1, EP/P032311/1, EP/V044087/1; Fondo Nacional de Desarrollo Científico y Tecnológico, Grant/Award Numbers: 1210637, 1210638, 121074; Millennium Nucleus, Grant/Award Number: NCN19_161; PhD program in Biological and Medical Engineering of the Pontificia Universidad Catolica de Chile; Wellcome EPSRC Centre for Medical Engineering, Grant/Award Number: NS/A000049/1; Hans Fischer Senior Fellow Award, Institute for Advanced Study at Technical University of Munich
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ISSN:0740-3194
1522-2594
1522-2594
DOI:10.1002/mrm.29635