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Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation

Landheer, Karl ; Swanberg, Kelley M LU orcid and Juchem, Christoph (2021) In NMR in Biomedicine 34(5).
Abstract

The aim of this study was to develop a novel software platform for the simulation of magnetic resonance spin systems, capable of simulating a large number of spatial points (1283 ) for large in vivo spin systems (up to seven coupled spins) in a time frame of the order of a few minutes. The quantum mechanical density-matrix formalism is applied, a coherence pathway filter is utilized for handling unwanted coherence pathways, and the 1D projection method, which provides a substantial reduction in computation time for a large number of spatial points, is extended to include sequences of an arbitrary number of RF pulses. The novel software package, written in MATLAB, computes a basis set of 23 different metabolites (including the two... (More)

The aim of this study was to develop a novel software platform for the simulation of magnetic resonance spin systems, capable of simulating a large number of spatial points (1283 ) for large in vivo spin systems (up to seven coupled spins) in a time frame of the order of a few minutes. The quantum mechanical density-matrix formalism is applied, a coherence pathway filter is utilized for handling unwanted coherence pathways, and the 1D projection method, which provides a substantial reduction in computation time for a large number of spatial points, is extended to include sequences of an arbitrary number of RF pulses. The novel software package, written in MATLAB, computes a basis set of 23 different metabolites (including the two anomers of glucose, seven coupled spins) with 1283 spatial points in 26 min for a three-pulse experiment on a personal desktop computer. The simulated spectra are experimentally verified with data from both phantom and in vivo MEGA-sLASER experiments. Recommendations are provided regarding the various assumptions made when computing a basis set for in vivo MRS with respect to the number of spatial points simulated and the consideration of relaxation.

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Please use this url to cite or link to this publication:
author
; and
publishing date
type
Contribution to journal
publication status
published
keywords
Adult, Algorithms, Computer Simulation, Creatinine/analysis, Humans, Lactic Acid/analysis, Magnetic Resonance Spectroscopy, Reproducibility of Results, Software, Time Factors, gamma-Aminobutyric Acid/analysis
in
NMR in Biomedicine
volume
34
issue
5
article number
e4129
publisher
John Wiley & Sons Inc.
external identifiers
  • scopus:85068524197
  • pmid:31313877
ISSN
0952-3480
DOI
10.1002/nbm.4129
language
English
LU publication?
no
additional info
© 2019 John Wiley & Sons, Ltd.
id
916a1a24-a69a-4aa2-ba4a-9e357240896f
date added to LUP
2023-09-18 15:01:28
date last changed
2024-04-19 00:55:26
@article{916a1a24-a69a-4aa2-ba4a-9e357240896f,
  abstract     = {{<p>The aim of this study was to develop a novel software platform for the simulation of magnetic resonance spin systems, capable of simulating a large number of spatial points (1283 ) for large in vivo spin systems (up to seven coupled spins) in a time frame of the order of a few minutes. The quantum mechanical density-matrix formalism is applied, a coherence pathway filter is utilized for handling unwanted coherence pathways, and the 1D projection method, which provides a substantial reduction in computation time for a large number of spatial points, is extended to include sequences of an arbitrary number of RF pulses. The novel software package, written in MATLAB, computes a basis set of 23 different metabolites (including the two anomers of glucose, seven coupled spins) with 1283 spatial points in 26 min for a three-pulse experiment on a personal desktop computer. The simulated spectra are experimentally verified with data from both phantom and in vivo MEGA-sLASER experiments. Recommendations are provided regarding the various assumptions made when computing a basis set for in vivo MRS with respect to the number of spatial points simulated and the consideration of relaxation.</p>}},
  author       = {{Landheer, Karl and Swanberg, Kelley M and Juchem, Christoph}},
  issn         = {{0952-3480}},
  keywords     = {{Adult; Algorithms; Computer Simulation; Creatinine/analysis; Humans; Lactic Acid/analysis; Magnetic Resonance Spectroscopy; Reproducibility of Results; Software; Time Factors; gamma-Aminobutyric Acid/analysis}},
  language     = {{eng}},
  number       = {{5}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{NMR in Biomedicine}},
  title        = {{Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation}},
  url          = {{http://dx.doi.org/10.1002/nbm.4129}},
  doi          = {{10.1002/nbm.4129}},
  volume       = {{34}},
  year         = {{2021}},
}