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Flexible numerical simulation framework for dynamic PET-MR data

Mayer, J; Brown, R; Thielemans, K; Ovtchinnikov, E; Pasca, E; Atkinson, D; Gillman, A; ... Kolbitsch, C; + view all (2020) Flexible numerical simulation framework for dynamic PET-MR data. Physics in Medicine & Biology , 65 (14) , Article 145003. 10.1088/1361-6560/ab7eee. Green open access

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Abstract

This paper presents a simulation framework for dynamic PET-MR. The main focus of this framework is to provide motion-resolved MR and PET data and ground truth motion information. This can be used in the optimisation and quantitative evaluation of image registration and in assessing the error propagation due to inaccuracies in motion estimation in complex motion-compensated reconstruction algorithms. Contrast and tracer kinetics can also be simulated and are available as ground truth information. To closely emulate medical examination, input and output of the simulation are files in standardised open-source raw data formats. This enables the use of existing raw data as a template input and ensures seamless integration of the output into existing reconstruction pipelines. The proposed framework was validated in PET-MR and image registration applications. It was used to simulate a FDG-PET-MR scan with cardiac and respiratory motion. Ground truth motion information could be utilised to optimise parameters for PET and synergistic PET-MR image registration. In addition, a free-breathing dynamic contrast enhancement (DCE) abdominal scan of a patient with hepatic lesions was simulated. In order to correct for breathing motion, a motion-corrected image reconstruction scheme was used and a Toft’s model was fit to the DCE data to obtain quantitative DCE-MRI parameters. Utilising the ground truth motion information, the dependency of quantitative DCE-MR images on the accuracy of the motion estimation was evaluated. We demonstrated that respiratory motion had to be available with an average accuracy of at least the spatial resolution of the DCE-MR images in order to ensure an improvement in lesions visualisation and quantification compared to no motion correction. The proposed framework provides a valuable tool with a wide range of scientific PET and MR applications and will be available as part of the open-source project Synergistic Image Reconstruction Framework (SIRF).

Type: Article
Title: Flexible numerical simulation framework for dynamic PET-MR data
Open access status: An open access version is available from UCL Discovery
DOI: 10.1088/1361-6560/ab7eee
Publisher version: https://doi.org/10.1088/1361-6560/ab7eee
Language: English
Additional information: Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 license. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. http://creativecommons.org/licenses/by/3.0/
Keywords: PET-MR, motion correction, simulation, image registration, open source
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine > Department of Imaging
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine > Experimental and Translational Medicine
URI: https://discovery.ucl.ac.uk/id/eprint/10106457
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