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QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures

PURPOSE: To create a realistic in silico head phantom for the second QSM reconstruction challenge and for future evaluations of processing algorithms for QSM. METHODS: We created a digital whole‐head tissue property phantom by segmenting and postprocessing high‐resolution (0.64 mm isotropic), multip...

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Autores principales: Marques, José P., Meineke, Jakob, Milovic, Carlos, Bilgic, Berkin, Chan, Kwok‐Shing, Hedouin, Renaud, van der Zwaag, Wietske, Langkammer, Christian, Schweser, Ferdinand
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048665/
https://www.ncbi.nlm.nih.gov/pubmed/33638241
http://dx.doi.org/10.1002/mrm.28716
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author Marques, José P.
Meineke, Jakob
Milovic, Carlos
Bilgic, Berkin
Chan, Kwok‐Shing
Hedouin, Renaud
van der Zwaag, Wietske
Langkammer, Christian
Schweser, Ferdinand
author_facet Marques, José P.
Meineke, Jakob
Milovic, Carlos
Bilgic, Berkin
Chan, Kwok‐Shing
Hedouin, Renaud
van der Zwaag, Wietske
Langkammer, Christian
Schweser, Ferdinand
author_sort Marques, José P.
collection PubMed
description PURPOSE: To create a realistic in silico head phantom for the second QSM reconstruction challenge and for future evaluations of processing algorithms for QSM. METHODS: We created a digital whole‐head tissue property phantom by segmenting and postprocessing high‐resolution (0.64 mm isotropic), multiparametric MRI data acquired at 7 T from a healthy volunteer. We simulated the steady‐state magnetization at 7 T using a Bloch simulator and mimicked a Cartesian sampling scheme through Fourier‐based processing. Computer code for generating the phantom and performing the MR simulation was designed to facilitate flexible modifications of the phantom in the future, such as the inclusion of pathologies as well as the simulation of a wide range of acquisition protocols. Specifically, the following parameters and effects were implemented: TR and TE, voxel size, background fields, and RF phase biases. Diffusion‐weighted imaging phantom data are provided, allowing future investigations of tissue‐microstructure effects in phase and QSM algorithms. RESULTS: The brain part of the phantom featured realistic morphology with spatial variations in relaxation and susceptibility values similar to the in vivo setting. We demonstrated some of the phantom’s properties, including the possibility of generating phase data with nonlinear evolution over TE due to partial‐volume effects or complex distributions of frequency shifts within the voxel. CONCLUSION: The presented phantom and computer programs are publicly available and may serve as a ground truth in future assessments of the faithfulness of quantitative susceptibility reconstruction algorithms.
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spelling pubmed-80486652021-04-19 QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures Marques, José P. Meineke, Jakob Milovic, Carlos Bilgic, Berkin Chan, Kwok‐Shing Hedouin, Renaud van der Zwaag, Wietske Langkammer, Christian Schweser, Ferdinand Magn Reson Med Full Papers—Computer Processing and Modeling PURPOSE: To create a realistic in silico head phantom for the second QSM reconstruction challenge and for future evaluations of processing algorithms for QSM. METHODS: We created a digital whole‐head tissue property phantom by segmenting and postprocessing high‐resolution (0.64 mm isotropic), multiparametric MRI data acquired at 7 T from a healthy volunteer. We simulated the steady‐state magnetization at 7 T using a Bloch simulator and mimicked a Cartesian sampling scheme through Fourier‐based processing. Computer code for generating the phantom and performing the MR simulation was designed to facilitate flexible modifications of the phantom in the future, such as the inclusion of pathologies as well as the simulation of a wide range of acquisition protocols. Specifically, the following parameters and effects were implemented: TR and TE, voxel size, background fields, and RF phase biases. Diffusion‐weighted imaging phantom data are provided, allowing future investigations of tissue‐microstructure effects in phase and QSM algorithms. RESULTS: The brain part of the phantom featured realistic morphology with spatial variations in relaxation and susceptibility values similar to the in vivo setting. We demonstrated some of the phantom’s properties, including the possibility of generating phase data with nonlinear evolution over TE due to partial‐volume effects or complex distributions of frequency shifts within the voxel. CONCLUSION: The presented phantom and computer programs are publicly available and may serve as a ground truth in future assessments of the faithfulness of quantitative susceptibility reconstruction algorithms. John Wiley and Sons Inc. 2021-02-26 2021-07 /pmc/articles/PMC8048665/ /pubmed/33638241 http://dx.doi.org/10.1002/mrm.28716 Text en © 2021 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Papers—Computer Processing and Modeling
Marques, José P.
Meineke, Jakob
Milovic, Carlos
Bilgic, Berkin
Chan, Kwok‐Shing
Hedouin, Renaud
van der Zwaag, Wietske
Langkammer, Christian
Schweser, Ferdinand
QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures
title QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures
title_full QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures
title_fullStr QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures
title_full_unstemmed QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures
title_short QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures
title_sort qsm reconstruction challenge 2.0: a realistic in silico head phantom for mri data simulation and evaluation of susceptibility mapping procedures
topic Full Papers—Computer Processing and Modeling
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048665/
https://www.ncbi.nlm.nih.gov/pubmed/33638241
http://dx.doi.org/10.1002/mrm.28716
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