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Adam NL, Kowalik G, Tyler A, Mooiweer R, Neofytou AP, McElroy S, Kunze K, Speier P, Stäb D, Neji R, Nazir MS, Razavi R, Chiribiri A, Roujol S. Fast reconstruction of SMS bSSFP myocardial perfusion images using noise map estimation network (NoiseMapNet): a head-to-head comparison with parallel imaging and iterative reconstruction. Front Cardiovasc Med 2024; 11:1350345. [PMID: 39055659 PMCID: PMC11269255 DOI: 10.3389/fcvm.2024.1350345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Background Simultaneous multi-slice (SMS) bSSFP imaging enables stress myocardial perfusion imaging with high spatial resolution and increased spatial coverage. Standard parallel imaging techniques (e.g., TGRAPPA) can be used for image reconstruction but result in high noise level. Alternatively, iterative reconstruction techniques based on temporal regularization (ITER) improve image quality but are associated with reduced temporal signal fidelity and long computation time limiting their online use. The aim is to develop an image reconstruction technique for SMS-bSSFP myocardial perfusion imaging combining parallel imaging and image-based denoising using a novel noise map estimation network (NoiseMapNet), which preserves both sharpness and temporal signal profiles and that has low computational cost. Methods The proposed reconstruction of SMS images consists of a standard temporal parallel imaging reconstruction (TGRAPPA) with motion correction (MOCO) followed by image denoising using NoiseMapNet. NoiseMapNet is a deep learning network based on a 2D Unet architecture and aims to predict a noise map from an input noisy image, which is then subtracted from the noisy image to generate the denoised image. This approach was evaluated in 17 patients who underwent stress perfusion imaging using a SMS-bSSFP sequence. Images were reconstructed with (a) TGRAPPA with MOCO (thereafter referred to as TGRAPPA), (b) iterative reconstruction with integrated motion compensation (ITER), and (c) proposed NoiseMapNet-based reconstruction. Normalized mean squared error (NMSE) with respect to TGRAPPA, myocardial sharpness, image quality, perceived SNR (pSNR), and number of diagnostic segments were evaluated. Results NMSE of NoiseMapNet was lower than using ITER for both myocardium (0.045 ± 0.021 vs. 0.172 ± 0.041, p < 0.001) and left ventricular blood pool (0.025 ± 0.014 vs. 0.069 ± 0.020, p < 0.001). There were no significant differences between all methods for myocardial sharpness (p = 0.77) and number of diagnostic segments (p = 0.36). ITER led to higher image quality than NoiseMapNet/TGRAPPA (2.7 ± 0.4 vs. 1.8 ± 0.4/1.3 ± 0.6, p < 0.001) and higher pSNR than NoiseMapNet/TGRAPPA (3.0 ± 0.0 vs. 2.0 ± 0.0/1.3 ± 0.6, p < 0.001). Importantly, NoiseMapNet yielded higher pSNR (p < 0.001) and image quality (p < 0.008) than TGRAPPA. Computation time of NoiseMapNet was only 20s for one entire dataset. Conclusion NoiseMapNet-based reconstruction enables fast SMS image reconstruction for stress myocardial perfusion imaging while preserving sharpness and temporal signal profiles.
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Affiliation(s)
- Naledi Lenah Adam
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Grzegorz Kowalik
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Andrew Tyler
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Ronald Mooiweer
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- MR Research Collaborations, Siemens Healthcare Limited, Camberley, United Kingdom
| | - Alexander Paul Neofytou
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Sarah McElroy
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- MR Research Collaborations, Siemens Healthcare Limited, Camberley, United Kingdom
| | - Karl Kunze
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- MR Research Collaborations, Siemens Healthcare Limited, Camberley, United Kingdom
| | - Peter Speier
- Cardiovascular Predevelopment, Siemens Healthcare GmbH, Erlangen, Germany
| | - Daniel Stäb
- MR Research Collaborations, Siemens Healthcare Limited, Melbourne, VIC, Australia
| | - Radhouene Neji
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- MR Research Collaborations, Siemens Healthcare Limited, Camberley, United Kingdom
| | - Muhummad Sohaib Nazir
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- Royal Brompton Hospital, Guy’s and St Thomas NHS Foundation Trust, London, United Kingdom
| | - Reza Razavi
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Amedeo Chiribiri
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Sébastien Roujol
- School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
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Suzuki Y, Ueyama T, Sakata K, Kasahara A, Iwanaga H, Yasaka K, Abe O. High-angular resolution diffusion imaging generation using 3d u-net. Neuroradiology 2024; 66:371-387. [PMID: 38236423 DOI: 10.1007/s00234-024-03282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
PURPOSE To investigate the effects on tractography of artificial intelligence-based prediction of motion-probing gradients (MPGs) in diffusion-weighted imaging (DWI). METHODS The 251 participants in this study were patients with brain tumors or epileptic seizures who underwent MRI to depict tractography. DWI was performed with 64 MPG directions and b = 0 s/mm2 images. The dataset was divided into a training set of 191 (mean age 45.7 [± 19.1] years), a validation set of 30 (mean age 41.6 [± 19.1] years), and a test set of 30 (mean age 49.6 [± 18.3] years) patients. Supervised training of a convolutional neural network was performed using b = 0 images and the first 32 axes of MPG images as the input data and the second 32 axes as the reference data. The trained model was applied to the test data, and tractography was performed using (a) input data only; (b) input plus prediction data; and (c) b = 0 images and the 64 MPG data (as a reference). RESULTS In Q-ball imaging tractography, the average dice similarity coefficient (DSC) of the input plus prediction data was 0.715 (± 0.064), which was significantly higher than that of the input data alone (0.697 [± 0.070]) (p < 0.05). In generalized q-sampling imaging tractography, the average DSC of the input plus prediction data was 0.769 (± 0.091), which was also significantly higher than that of the input data alone (0.738 [± 0.118]) (p < 0.01). CONCLUSION Diffusion tractography is improved by adding predicted MPG images generated by an artificial intelligence model.
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Affiliation(s)
- Yuichi Suzuki
- Radiology Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Tsuyoshi Ueyama
- Radiology Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Kentarou Sakata
- Radiology Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Akihiro Kasahara
- Radiology Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Hideyuki Iwanaga
- Radiology Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Koichiro Yasaka
- Department of Radiology, The University of Tokyo Hospital, Tokyo, Japan.
| | - Osamu Abe
- Radiology Center, The University of Tokyo Hospital, Tokyo, Japan
- Department of Radiology, The University of Tokyo Hospital, Tokyo, Japan
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Wang J, Chen Z, Cai C, Cai S. Ultrafast diffusion tensor imaging based on deep learning and multi-slice information sharing. Phys Med Biol 2024; 69:035011. [PMID: 38211309 DOI: 10.1088/1361-6560/ad1d6d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/11/2024] [Indexed: 01/13/2024]
Abstract
Objective. Diffusion tensor imaging (DTI) is excellent for non-invasively quantifying tissue microstructure. Theoretically DTI can be achieved with six different diffusion weighted images and one reference image, but the tensor estimation accuracy is poor in this case. Increasing the number of diffusion directions has benefits for the tensor estimation accuracy, which results in long scan time and makes DTI sensitive to motion. It would be beneficial to decrease the scan time of DTI by using fewer diffusion-weighted images without compromising reconstruction quality.Approach. A novel DTI scan scheme was proposed to achieve fast DTI, where only three diffusion directions per slice was required under a specific direction switching manner, and a deep-learning based reconstruction method was utilized using multi-slice information sharing and correspondingT1-weighted image for high-quality DTI reconstruction. A network with two encoders developed from U-Net was implemented for better utilizing the diffusion data redundancy between neighboring slices. The method performed direct nonlinear mapping from diffusion-weighted images to diffusion tensor.Main results. The performance of the proposed method was verified on the Human Connectome Project public data and clinical patient data. High-quality mean diffusivity, fractional anisotropy, and directionally encoded colormap can be achieved with only three diffusion directions per slice.Significance. High-quality DTI-derived maps can be achieved in less than one minute of scan time. The great reduction of scan time will help push the wider application of DTI in clinical practice.
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Affiliation(s)
- Jiechao Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zunquan Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, People's Republic of China
| | - Congbo Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, People's Republic of China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, People's Republic of China
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Morales MA, Manning WJ, Nezafat R. Present and Future Innovations in AI and Cardiac MRI. Radiology 2024; 310:e231269. [PMID: 38193835 PMCID: PMC10831479 DOI: 10.1148/radiol.231269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/21/2023] [Accepted: 10/26/2023] [Indexed: 01/10/2024]
Abstract
Cardiac MRI is used to diagnose and treat patients with a multitude of cardiovascular diseases. Despite the growth of clinical cardiac MRI, complicated image prescriptions and long acquisition protocols limit the specialty and restrain its impact on the practice of medicine. Artificial intelligence (AI)-the ability to mimic human intelligence in learning and performing tasks-will impact nearly all aspects of MRI. Deep learning (DL) primarily uses an artificial neural network to learn a specific task from example data sets. Self-driving scanners are increasingly available, where AI automatically controls cardiac image prescriptions. These scanners offer faster image collection with higher spatial and temporal resolution, eliminating the need for cardiac triggering or breath holding. In the future, fully automated inline image analysis will most likely provide all contour drawings and initial measurements to the reader. Advanced analysis using radiomic or DL features may provide new insights and information not typically extracted in the current analysis workflow. AI may further help integrate these features with clinical, genetic, wearable-device, and "omics" data to improve patient outcomes. This article presents an overview of AI and its application in cardiac MRI, including in image acquisition, reconstruction, and processing, and opportunities for more personalized cardiovascular care through extraction of novel imaging markers.
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Affiliation(s)
- Manuel A. Morales
- From the Department of Medicine, Cardiovascular Division (M.A.M.,
W.J.M., R.N.), and Department of Radiology (W.J.M.), Beth Israel Deaconess
Medical Center and Harvard Medical School, 330 Brookline Ave, Boston, MA
02215
| | - Warren J. Manning
- From the Department of Medicine, Cardiovascular Division (M.A.M.,
W.J.M., R.N.), and Department of Radiology (W.J.M.), Beth Israel Deaconess
Medical Center and Harvard Medical School, 330 Brookline Ave, Boston, MA
02215
| | - Reza Nezafat
- From the Department of Medicine, Cardiovascular Division (M.A.M.,
W.J.M., R.N.), and Department of Radiology (W.J.M.), Beth Israel Deaconess
Medical Center and Harvard Medical School, 330 Brookline Ave, Boston, MA
02215
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Demirel OB, Yaman B, Shenoy C, Moeller S, Weingärtner S, Akçakaya M. Signal intensity informed multi-coil encoding operator for physics-guided deep learning reconstruction of highly accelerated myocardial perfusion CMR. Magn Reson Med 2023; 89:308-321. [PMID: 36128896 PMCID: PMC9617789 DOI: 10.1002/mrm.29453] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/21/2022] [Accepted: 08/21/2022] [Indexed: 01/11/2023]
Abstract
PURPOSE To develop a physics-guided deep learning (PG-DL) reconstruction strategy based on a signal intensity informed multi-coil (SIIM) encoding operator for highly-accelerated simultaneous multislice (SMS) myocardial perfusion cardiac MRI (CMR). METHODS First-pass perfusion CMR acquires highly-accelerated images with dynamically varying signal intensity/SNR following the administration of a gadolinium-based contrast agent. Thus, using PG-DL reconstruction with a conventional multi-coil encoding operator leads to analogous signal intensity variations across different time-frames at the network output, creating difficulties in generalization for varying SNR levels. We propose to use a SIIM encoding operator to capture the signal intensity/SNR variations across time-frames in a reformulated encoding operator. This leads to a more uniform/flat contrast at the output of the PG-DL network, facilitating generalizability across time-frames. PG-DL reconstruction with the proposed SIIM encoding operator is compared to PG-DL with conventional encoding operator, split slice-GRAPPA, locally low-rank (LLR) regularized reconstruction, low-rank plus sparse (L + S) reconstruction, and regularized ROCK-SPIRiT. RESULTS Results on highly accelerated free-breathing first pass myocardial perfusion CMR at three-fold SMS and four-fold in-plane acceleration show that the proposed method improves upon the reconstruction methods use for comparison. Substantial noise reduction is achieved compared to split slice-GRAPPA, and aliasing artifacts reduction compared to LLR regularized reconstruction, L + S reconstruction and PG-DL with conventional encoding. Furthermore, a qualitative reader study indicated that proposed method outperformed all methods. CONCLUSION PG-DL reconstruction with the proposed SIIM encoding operator improves generalization across different time-frames /SNRs in highly accelerated perfusion CMR.
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Affiliation(s)
- Omer Burak Demirel
- Department of Electrical and Computer EngineeringUniversity of MinnesotaMinneapolisMinnesotaUSA,Center for Magnetic Resonance ResearchUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Burhaneddin Yaman
- Department of Electrical and Computer EngineeringUniversity of MinnesotaMinneapolisMinnesotaUSA,Center for Magnetic Resonance ResearchUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Chetan Shenoy
- Department of Medicine (Cardiology)University of MinnesotaMinneapolisMinnesotaUSA
| | - Steen Moeller
- Center for Magnetic Resonance ResearchUniversity of MinnesotaMinneapolisMinnesotaUSA
| | | | - Mehmet Akçakaya
- Department of Electrical and Computer EngineeringUniversity of MinnesotaMinneapolisMinnesotaUSA,Center for Magnetic Resonance ResearchUniversity of MinnesotaMinneapolisMinnesotaUSA
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Reinhard S, Helmerich DA, Boras D, Sauer M, Kollmannsberger P. ReCSAI: recursive compressed sensing artificial intelligence for confocal lifetime localization microscopy. BMC Bioinformatics 2022; 23:530. [PMID: 36482307 PMCID: PMC9732995 DOI: 10.1186/s12859-022-05071-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Localization-based super-resolution microscopy resolves macromolecular structures down to a few nanometers by computationally reconstructing fluorescent emitter coordinates from diffraction-limited spots. The most commonly used algorithms are based on fitting parametric models of the point spread function (PSF) to a measured photon distribution. These algorithms make assumptions about the symmetry of the PSF and thus, do not work well with irregular, non-linear PSFs that occur for example in confocal lifetime imaging, where a laser is scanned across the sample. An alternative method for reconstructing sparse emitter sets from noisy, diffraction-limited images is compressed sensing, but due to its high computational cost it has not yet been widely adopted. Deep neural network fitters have recently emerged as a new competitive method for localization microscopy. They can learn to fit arbitrary PSFs, but require extensive simulated training data and do not generalize well. A method to efficiently fit the irregular PSFs from confocal lifetime localization microscopy combining the advantages of deep learning and compressed sensing would greatly improve the acquisition speed and throughput of this method. RESULTS Here we introduce ReCSAI, a compressed sensing neural network to reconstruct localizations for confocal dSTORM, together with a simulation tool to generate training data. We implemented and compared different artificial network architectures, aiming to combine the advantages of compressed sensing and deep learning. We found that a U-Net with a recursive structure inspired by iterative compressed sensing showed the best results on realistic simulated datasets with noise, as well as on real experimentally measured confocal lifetime scanning data. Adding a trainable wavelet denoising layer as prior step further improved the reconstruction quality. CONCLUSIONS Our deep learning approach can reach a similar reconstruction accuracy for confocal dSTORM as frame binning with traditional fitting without requiring the acquisition of multiple frames. In addition, our work offers generic insights on the reconstruction of sparse measurements from noisy experimental data by combining compressed sensing and deep learning. We provide the trained networks, the code for network training and inference as well as the simulation tool as python code and Jupyter notebooks for easy reproducibility.
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Affiliation(s)
- Sebastian Reinhard
- Department of Biotechnology and Biophysics, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Dominic A Helmerich
- Department of Biotechnology and Biophysics, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Dominik Boras
- Department of Biotechnology and Biophysics, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, University of Wuerzburg, Klara-Oppenheimer-Weg 32, 97074, Wuerzburg, Germany.
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Methodology for Interactive Labeling of Patched Asphalt Pavement Images Based on U-Net Convolutional Neural Network. SUSTAINABILITY 2022. [DOI: 10.3390/su14020861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Image recognition based on deep learning generally demands a huge sample size for training, for which the image labeling becomes inevitably laborious and time-consuming. In the case of evaluating the pavement quality condition, many pavement distress patching images would need manual screening and labeling, meanwhile the subjectivity of the labeling personnel would greatly affect the accuracy of image labeling. In this study, in order for an accurate and efficient recognition of the pavement patching images, an interactive labeling method is proposed based on the U-Net convolutional neural network, using active learning combined with reverse and correction labeling. According to the calculation results in this paper, the sample size required by the interactive labeling is about half of the traditional labeling method for the same recognition precision. Meanwhile, the accuracy of interactive labeling method based on the mean intersection over union (mean_IOU) index is 6% higher than that of the traditional method using the same sample size and training epochs. In addition, the accuracy analysis of the noise and boundary of the prediction results shows that this method eliminates 92% of the noise in the predictions (the proportion of noise is reduced from 13.85% to 1.06%), and the image definition is improved by 14.1% in terms of the boundary gray area ratio. The interactive labeling is considered as a significantly valuable approach, as it reduces the sample size in each epoch of active learning, greatly alleviates the demand for manpower, and improves learning efficiency and accuracy.
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