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de Vries L, van Herten RLM, Hoving JW, Išgum I, Emmer BJ, Majoie CBLM, Marquering HA, Gavves E. Spatio-temporal physics-informed learning: A novel approach to CT perfusion analysis in acute ischemic stroke. Med Image Anal 2023; 90:102971. [PMID: 37778103 DOI: 10.1016/j.media.2023.102971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/20/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023]
Abstract
CT perfusion imaging is important in the imaging workup of acute ischemic stroke for evaluating affected cerebral tissue. CT perfusion analysis software produces cerebral perfusion maps from commonly noisy spatio-temporal CT perfusion data. High levels of noise can influence the results of CT perfusion analysis, necessitating software tuning. This work proposes a novel approach for CT perfusion analysis that uses physics-informed learning, an optimization framework that is robust to noise. In particular, we propose SPPINN: Spatio-temporal Perfusion Physics-Informed Neural Network and research spatio-temporal physics-informed learning. SPPINN learns implicit neural representations of contrast attenuation in CT perfusion scans using the spatio-temporal coordinates of the data and employs these representations to estimate a continuous representation of the cerebral perfusion parameters. We validate the approach on simulated data to quantify perfusion parameter estimation performance. Furthermore, we apply the method to in-house patient data and the public Ischemic Stroke Lesion Segmentation 2018 benchmark data to assess the correspondence between the perfusion maps and reference standard infarct core segmentations. Our method achieves accurate perfusion parameter estimates even with high noise levels and differentiates healthy tissue from infarcted tissue. Moreover, SPPINN perfusion maps accurately correspond with reference standard infarct core segmentations. Hence, we show that using spatio-temporal physics-informed learning for cerebral perfusion estimation is accurate, even in noisy CT perfusion data. The code for this work is available at https://github.com/lucasdevries/SPPINN.
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Affiliation(s)
- Lucas de Vries
- Amsterdam UMC location University of Amsterdam, Biomedical Engineering and Physics, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam UMC location University of Amsterdam, Radiology and Nuclear Medicine, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands; Amsterdam Neuroscience, Amsterdam, The Netherlands.
| | - Rudolf L M van Herten
- Amsterdam UMC location University of Amsterdam, Biomedical Engineering and Physics, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Jan W Hoving
- Amsterdam UMC location University of Amsterdam, Radiology and Nuclear Medicine, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Ivana Išgum
- Amsterdam UMC location University of Amsterdam, Biomedical Engineering and Physics, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam UMC location University of Amsterdam, Radiology and Nuclear Medicine, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands; Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Bart J Emmer
- Amsterdam UMC location University of Amsterdam, Radiology and Nuclear Medicine, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charles B L M Majoie
- Amsterdam UMC location University of Amsterdam, Radiology and Nuclear Medicine, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Henk A Marquering
- Amsterdam UMC location University of Amsterdam, Biomedical Engineering and Physics, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam UMC location University of Amsterdam, Radiology and Nuclear Medicine, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands; Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands; Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Efstratios Gavves
- Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
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van Herten RLM, Chiribiri A, Breeuwer M, Veta M, Scannell CM. Physics-informed neural networks for myocardial perfusion MRI quantification. Med Image Anal 2022; 78:102399. [PMID: 35299005 PMCID: PMC9051528 DOI: 10.1016/j.media.2022.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/07/2022] [Accepted: 02/18/2022] [Indexed: 11/19/2022]
Abstract
Tracer-kinetic models allow for the quantification of kinetic parameters such as blood flow from dynamic contrast-enhanced magnetic resonance (MR) images. Fitting the observed data with multi-compartment exchange models is desirable, as they are physiologically plausible and resolve directly for blood flow and microvascular function. However, the reliability of model fitting is limited by the low signal-to-noise ratio, temporal resolution, and acquisition length. This may result in inaccurate parameter estimates. This study introduces physics-informed neural networks (PINNs) as a means to perform myocardial perfusion MR quantification, which provides a versatile scheme for the inference of kinetic parameters. These neural networks can be trained to fit the observed perfusion MR data while respecting the underlying physical conservation laws described by a multi-compartment exchange model. Here, we provide a framework for the implementation of PINNs in myocardial perfusion MR. The approach is validated both in silico and in vivo. In the in silico study, an overall decrease in mean-squared error with the ground-truth parameters was observed compared to a standard non-linear least squares fitting approach. The in vivo study demonstrates that the method produces parameter values comparable to those previously found in literature, as well as providing parameter maps which match the clinical diagnosis of patients.
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Affiliation(s)
- Rudolf L M van Herten
- Department of Biomedical Engineering, Medical Image Analysis group, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Amedeo Chiribiri
- School of Biomedical Engineering and Imaging Sciences, King's College London, United Kingdom
| | - Marcel Breeuwer
- Department of Biomedical Engineering, Medical Image Analysis group, Eindhoven University of Technology, Eindhoven, the Netherlands; Philips Healthcare, Best, the Netherlands
| | - Mitko Veta
- Department of Biomedical Engineering, Medical Image Analysis group, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Cian M Scannell
- School of Biomedical Engineering and Imaging Sciences, King's College London, United Kingdom.
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