TY - JOUR
T1 - KomaMRI.jl
T2 - An open-source framework for general MRI simulations with GPU acceleration
AU - Castillo-Passi, Carlos
AU - Coronado, Ronal
AU - Varela-Mattatall, Gabriel
AU - Alberola-López, Carlos
AU - Botnar, René
AU - Irarrazaval, Pablo
N1 - 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 Funding information
Funding Information:
Authors wish to acknowledge funding by the PhD program in Biological and Medical Engineering of the Pontificia Universidad Católica de Chile; by ANID ‐ Millennium Science Initiative Program ICN2021_004; by Fondecyt 121074, 1210637, and 1210638; by the Agencia Estatal de Investigación PID2020‐115339RB‐I00, and TED2021‐130090B‐I00; by EPSRC EP/P001009, EP/P032311/1, EP/P007619/1, and EP/V044087/1; by Wellcome EPSRC Centre for Medical Engineering NS/A000049/1; ANID Basal FB210024; by Millennium Nucleus NCN19_161; and Hans Fischer Senior Fellow Award, Institute for Advanced Study at Technical University of Munich. Finally, the authors also wish to thank Boris Oróstica for his help with Koma's documentation.
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 - 2023/7
Y1 - 2023/7
N2 - Purpose: To develop an open-source, high-performance, easy-to-use, extensible, cross-platform, and general MRI simulation framework (Koma). Methods: 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. Results: 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. Conclusions: 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.
AB - Purpose: To develop an open-source, high-performance, easy-to-use, extensible, cross-platform, and general MRI simulation framework (Koma). Methods: 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. Results: 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. Conclusions: 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.
KW - Bloch equations
KW - GPU
KW - GUI
KW - Julia
KW - open source
KW - simulation
UR - http://www.scopus.com/inward/record.url?scp=85149703612&partnerID=8YFLogxK
U2 - 10.1002/mrm.29635
DO - 10.1002/mrm.29635
M3 - Article
C2 - 36877139
AN - SCOPUS:85149703612
SN - 0740-3194
VL - 90
SP - 329
EP - 342
JO - Magnetic resonance in medicine
JF - Magnetic resonance in medicine
IS - 1
ER -