Denoising of Three-Dimensional Fast Spin Echo Magnetic Resonance Images of Knee Joints using Spatial-Variant Noise-Relevant Residual Learning of Convolution Neural Network
the Chinese University of Hong Kong（香港中文大学）
Shutian Zhao, Donal G. Cahill, Siyue Li, Fan Xiao, Thierry Blu, James F Griffith, Weitian Chen
Two-dimensional (2D) fast spin echo (FSE) techniques play a central role in the clinical magnetic resonance imaging (MRI) of knee joints. Moreover, three-dimensional (3D) FSE provides high-isotropic-resolution magnetic resonance (MR) images of knee joints, but it has a reduced signal-to-noise ratio compared to 2D FSE. Deep-learning denoising methods are a promising approach for denoising MR images, but they are often trained using synthetic noise due to challenges in obtaining true noise distributions for MR images. In this study, inherent true noise information from 2-NEX acquisition was used to develop a deep-learning model based on residual learning of convolutional neural network (CNN), and this model was used to suppress the noise in 3D FSE MR images of knee joints. The proposed CNN used two-step residual learning over parallel transporting and residual blocks and was designed to comprehensively learn real noise features from 2-NEX training data. The results of an ablation study validated the network design. The new method achieved improved denoising performance of 3D FSE knee MR images compared with current state-of-the-art methods, based on the peak signal-to-noise ratio and structural similarity index measure. The improved image quality after denoising using the new method was verified by radiological evaluation. A deep CNN using the inherent spatial-varying noise information in 2-NEX acquisitions was developed. This method showed promise for clinical MRI assessments of the knee, and has potential applications for the assessment of other anatomical structures.
University of California, San Diego（加州大学圣地亚哥分校）；Institute of Fundamental Technological Research, Polish Academy of Sciences（波兰科学院基础技术研究所）；VA San Diego Healthcare System（VA圣地亚哥医疗系统）
The purpose of this work is to develop a deep learning-based method for knee menisci segmentation in 3D ultrashort echo time (UTE) cones magnetic resonance (MR) imaging, and to automatically determine MR relaxation times, namely the T1, T1$ρ$, and T2* parameters, which can be used to assess knee osteoarthritis (OA). Whole knee joint imaging was performed using 3D UTE cones sequences to collect data from 61 human subjects. Regions of interest (ROIs) were outlined by two experienced radiologists based on subtracted T1$ρ$-weighted MR images. Transfer learning was applied to develop 2D attention U…
The aim of this study was to investigate the influence of MRI and patient data on the prediction of knee osteoarthritis (OA) incidence using different deep learning architectures. Knee OA incidence within 24 months was predicted using the intermediate-weighted turbo spin-echo (IW-TSE) sequence of 593 patients from the Osteoarthritis Initiative. To extract a region of interest containing the knee joint from the IW-TSE sequence, a U-Net model was trained and used to segment bone on a dual echo steady state (DESS) sequence. Subsequently, IW-TSE and DESS sequences were registered and the DESS segm…
MonoUNet: A Robust Tiny Neural Network for Automated Knee Cartilage Segmentation on Point-of-Care Ultrasound Devices
School of Biomedical Engineering, The University of British Columbia（生物医学工程学院，不列颠哥伦比亚大学）；Department of Kinesiology, Michigan State University（运动科学系，密歇根州立大学）；Department of Rheumatology, The University of British Columbia（风湿病学系，不列颠哥伦比亚大学）；Department of Radiology, The University of British Columbia（放射学系，不列颠哥伦比亚大学）；Department of Medicine, The University of British Columbia（医学系，不列颠哥伦比亚大学）
Utilizing 3D Fast Spin Echo Anatomical Imaging to Reduce the Number of Contrast Preparations in $T_{1ρ}$ Quantification of Knee Cartilage Using Learning-Based Methods
Robust multi-coil MRI reconstruction via self-supervised denoising
Stanford University（斯坦福大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）；Intel Corporation（英特尔公司）；MD Anderson Cancer Center（MD安德森癌症中心）；Dell Medical School Department of Diagnostic Medicine（德克萨斯大学戴维斯医学中心诊断医学系）；Oden Institute for Computational Engineering and Sciences（奥登计算工程与科学研究院）
To rapidly obtain high resolution T2, T2* and quantitative susceptibility mapping (QSM) source separation maps with whole-brain coverage and high geometric fidelity. We propose Blip Up-Down Acquisition for Spin And Gradient Echo imaging (BUDA-SAGE), an efficient echo-planar imaging (EPI) sequence for quantitative mapping. The acquisition includes multiple T2*-, T2'- and T2-weighted contrasts. We alternate the phase-encoding polarities across the interleaved shots in this multi-shot navigator-free acquisition. A field map estimated from interim reconstructions was incorporated into the joint mu…
Temporal Evolution of Knee Osteoarthritis: A Diffusion-based Morphing Model for X-ray Medical Image Synthesis
Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；University of Orleans（奥尔良大学）；IDP Institute（IDP研究所）；Jiangsu Institute of Hematology（江苏省血液研究所）；First Affiliated Hospital of Soochow University（苏州大学附属第一医院）；Cancer Hospital of Pernambuco（伯南布哥癌症医院）
Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院）；Chung-Ang University Hospital（中央大学医院）；Chung-Ang University College of Medicine（中央大学医学院）
Patient scans from MRI often suffer from noise, which hampers the diagnostic capability of such images. As a method to mitigate such artifact, denoising is largely studied both within the medical imaging community and beyond the community as a general subject. However, recent deep neural network-based approaches mostly rely on the minimum mean squared error (MMSE) estimates, which tend to produce a blurred output. Moreover, such models suffer when deployed in real-world sitautions: out-of-distribution data, and complex noise distributions that deviate from the usual parametric noise models. In…
Deep learning-based image reconstruction methods have achieved promising results across multiple MRI applications. However, most approaches require large-scale fully-sampled ground truth data for supervised training. Acquiring fully-sampled data is often either difficult or impossible, particularly for dynamic contrast enhancement (DCE), 3D cardiac cine, and 4D flow. We present a deep learning framework for MRI reconstruction without any fully-sampled data using generative adversarial networks. We test the proposed method in two scenarios: retrospectively undersampled fast spin echo knee exams…
Time-efficient combined morphologic and quantitative joint MRI based on clinical image contrasts -- An exploratory in-situ study of standardized cartilage defects
Lodz University of Technology（罗兹工业大学）；Medical University of Lodz（罗兹医科大学）；Siemens Healthcare GmbH（西门子医疗有限公司）
In this paper, we propose a method for denoising diffusion-weighted images (DWI) of the brain using a convolutional neural network trained on realistic, synthetic MR data. We compare our results to averaging of repeated scans, a widespread method used in clinics to improve signal-to-noise ratio of MR images. To obtain training data for transfer learning, we model, in a data-driven fashion, the effects of echo-planar imaging (EPI): Nyquist ghosting and ramp sampling. We introduce these effects to the digital phantom of brain anatomy (BrainWeb). Instead of simulating pseudo-random noise with a d…
Friedrich-Alexander Universität Erlangen-Nürnberg（弗里德里希-亚历山大大学埃尔兰根-纽伦堡分校）；Technical University of Applied Sciences Amberg-Weiden（安贝格-魏登应用技术大学）；Siemens Healthcare GmbH（西门子医疗有限公司）
A Magnetic Resonance Imaging (MRI) exam typically consists of the acquisition of multiple MR pulse sequences, which are required for a reliable diagnosis. Each sequence can be parameterized through multiple acquisition parameters affecting MR image contrast, signal-to-noise ratio, resolution, or scan time. With the rise of generative deep learning models, approaches for the synthesis of MR images are developed to either synthesize additional MR contrasts, generate synthetic data, or augment existing data for AI training. However, current generative approaches for the synthesis of MR images are…
Amsterdam UMC（阿姆斯特丹大学医学中心）；University of Amsterdam（阿姆斯特丹大学）；MS Center Amsterdam（阿姆斯特丹多发性硬化中心）；Amsterdam Neuroscience（阿姆斯特丹神经科学研究所）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）；Leiden University（莱顿大学）；Delft University of Technology（代尔夫特理工大学）
Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varyin…
Purpose: To present a computational procedure for accelerated, calibrationless magnetic resonance image (Cl-MRI) reconstruction that is fast, memory efficient, and scales to high-dimensional imaging. Theory and Methods: Cl-MRI methods can enable high acceleration rates and flexible sampling patterns, but their clinical application is limited by computational complexity and large memory footprint. The proposed computational procedure, HIgh-dimensional fast ConvolU-tional framework (HICU), provides fast, memory-efficient recovery of unsampled k-space points. For demonstration, HICU is applied to…
Friedrich-Alexander Universität Erlangen-Nürnberg（弗里德里希-亚历山大大学埃尔兰根-纽伦堡分校）；Technical University of Applied Sciences Amberg-Weiden（安贝格-魏登应用技术大学）；Siemens Healthineers（西门子医疗）
Purpose A Magnetic Resonance Imaging (MRI) exam typically consists of several sequences that yield different image contrasts. Each sequence is parameterized through multiple acquisition parameters that influence image contrast, signal-to-noise ratio, acquisition time, and/or resolution. Depending on the clinical indication, different contrasts are required by the radiologist to make a diagnosis. As MR sequence acquisition is time consuming and acquired images may be corrupted due to motion, a method to synthesize MR images with adjustable contrast properties is required. Methods Therefore, we …
