Deep learning predicts total knee replacement from magnetic resonance images
University of California, Berkeley（加州大学伯克利分校）；University of California, San Francisco（加州大学旧金山分校）
Aniket A. Tolpadi, Jinhee J. Lee, Valentina Pedoia, Sharmila Majumdar
备注：
18 pages, 5 figures (4 in main article, 1 supplemental), 8 tables (5 in main article, 3 supplemental). Submitted to Scientific Reports and currently in revision
Knee Osteoarthritis (OA) is a common musculoskeletal disorder in the United States. When diagnosed at early stages, lifestyle interventions such as exercise and weight loss can slow OA progression, but at later stages, only an invasive option is available: total knee replacement (TKR). Though a generally successful procedure, only 2/3 of patients who undergo the procedure report their knees feeling ''normal'' post-operation, and complications can arise that require revision. This necessitates a model to identify a population at higher risk of TKR, particularly at less advanced stages of OA, such that appropriate treatments can be implemented that slow OA progression and delay TKR. Here, we present a deep learning pipeline that leverages MRI images and clinical and demographic information to predict TKR with AUC $0.834 \pm 0.036$ (p < 0.05). Most notably, the pipeline predicts TKR with AUC $0.943 \pm 0.057$ (p < 0.05) for patients without OA. Furthermore, we develop occlusion maps for case-control pairs in test data and compare regions used by the model in both, thereby identifying TKR imaging biomarkers. As such, this work takes strides towards a pipeline with clinical utility, and the biomarkers identified further our understanding of OA progression and eventual TKR onset.
The University of Queensland（昆士兰大学）；The Commonwealth Scientific and Industrial Research Organisation（联邦科学与工业研究组织）；University of Science and Technology of China（中国科学技术大学）；Chinese Academy of Sciences（中国科学院）；Institute of Computing Technology, CAS（中国科学院计算技术研究所）
Deep neural networks have been widely studied for predicting a medical condition, such as total knee replacement (TKR). It has shown that data of different modalities, such as imaging data, clinical variables and demographic information, provide complementary information and thus can improve the prediction accuracy together. However, the data sources of various modalities may not always be of high quality, and each modality may have only partial information of medical condition. Thus, predictions from different modalities can be opposite, and the final prediction may fail in the presence of su…
A Progressive Risk Formulation for Enhanced Deep Learning based Total Knee Replacement Prediction in Knee Osteoarthritis
Center for Data Science, New York University（纽约大学数据科学中心）；Department of Radiology, New York University Langone Health（纽约大学朗格尼健康放射科）；Bernard and Irene Schwartz Center for Biomedical Imaging, New York University Langone Health（纽约大学朗格尼健康伯纳德与艾琳·施瓦茨生物医学影像中心）
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…
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…
Duke University（杜克大学）；Duke Clinical Research Institute（杜克临床研究所）；Duke-Margolis Center for Health Policy（杜克-马戈利斯卫生政策中心）；Duke Cancer Institute（杜克癌症研究所）
The assessment of knee osteoarthritis (KOA) severity on knee X-rays is a central criteria for the use of total knee arthroplasty. However, this assessment suffers from imprecise standards and a remarkably high inter-reader variability. An algorithmic, automated assessment of KOA severity could improve overall outcomes of knee replacement procedures by increasing the appropriateness of its use. We propose a novel deep learning-based five-step algorithm to automatically grade KOA from posterior-anterior (PA) views of radiographs: (1) image preprocessing (2) localization of knees joints in the im…
RSIP Vision（RSIP Vision 公司）；Weizmann Institute of Science（魏茨曼科学研究所）
We present an end-to-end Convolutional Neural Network (CNN) approach for 3D reconstruction of knee bones directly from two bi-planar X-ray images. Clinically, capturing the 3D models of the bones is crucial for surgical planning, implant fitting, and postoperative evaluation. X-ray imaging significantly reduces the exposure of patients to ionizing radiation compared to Computer Tomography (CT) imaging, and is much more common and inexpensive compared to Magnetic Resonance Imaging (MRI) scanners. However, retrieving 3D models from such 2D scans is extremely challenging. In contrast to the commo…
Knee Osteoarthritis Severity Prediction using an Attentive Multi-Scale Deep Convolutional Neural Network
Indian Institute of Technology Guwahati（印度古瓦哈蒂印度理工学院）；Cleveland Clinic（克利夫兰诊所）；Duke-NUS Medical School（杜克-新加坡国立大学医学院）；National University of Singapore（新加坡国立大学）
Insight Centre for Data Analytics Dublin City University（都柏林城市大学数据洞察中心）；Dublin City University（都柏林城市大学）
This work presents a comparative study of existing and new techniques to detect knee injuries by leveraging Stanford's MRNet Dataset. All approaches are based on deep learning and we explore the comparative performances of transfer learning and a deep residual network trained from scratch. We also exploit some characteristics of Magnetic Resonance Imaging (MRI) data by, for example, using a fixed number of slices or 2D images from each of the axial, coronal and sagittal planes as well as combining the three planes into one multi-plane network. Overall we achieved a performance of 93.4% AUC on …
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 University of Queensland（昆士兰大学）；Australian e-Health Research Centre（澳大利亚电子健康研究中心）；Commonwealth Scientific and Industrial Research Organisation（联邦科学与工业研究组织）
In medical image analysis, automated segmentation of multi-component anatomical structures, which often have a spectrum of potential anomalies and pathologies, is a challenging task. In this work, we develop a multi-step approach using U-Net-based neural networks to initially detect anomalies (bone marrow lesions, bone cysts) in the distal femur, proximal tibia and patella from 3D magnetic resonance (MR) images of the knee in individuals with varying grades of osteoarthritis. Subsequently, the extracted data are used for downstream tasks involving semantic segmentation of individual bone and c…
Dealing With Heterogeneous 3D MR Knee Images: A Federated Few-Shot Learning Method With Dual Knowledge Distillation
Rutgers University（罗格斯大学）；Sichuan University West China Hospital（四川大学华西医院）；Walmart Global Tech（沃尔玛全球科技）；Shanghai Jiao Tong University School of Medicine（上海交通大学医学院）；Tongren Hospital（同仁医院）；Fudan University（复旦大学）；Zhongshan Hospital（中山医院）；SenseTime Research（商汤科技研究院）
Magnetic Resonance Images (MRIs) are extremely used in the medical field to detect and better understand diseases. In order to fasten automatic processing of scans and enhance medical research, this project focuses on automatically segmenting targeted parts of MRIs and generating new MRI datasets from random noise. More specifically, a Deep Neural Network architecture called U-net is used to segment bones and cartilages of Knee MRIs, and several Generative Adversarial Networks (GANs) are compared and tuned to create new realistic and high quality brain MRIs that can be used as training set for…
Self-Auditing Residual Drifting for Pathology-Preserving Accelerated Knee MRI
Department of Radiology & Biomedical Imaging, Yale School of Medicine（放射学与生物医学成像系，耶鲁医学院）；Department of Biomedical Engineering, Rensselaer Polytechnic Institute（生物医学工程系，伦塞拉尔理工学院）
Reliability assessment and multicenter clinical application of magnetic resonance methods for knee cartilage quantification
Academy for Clinical Innovation and Translation of Shanghai Co., Ltd. (ACITS)（上海临床创新与转化研究院有限公司）；Shanghai IxCell Biotechnology Co., LTD（上海爱科百发生物科技有限公司）；Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属第九人民医院）；Nanyang Technological University（南洋理工大学）；Renji Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属仁济医院）；Shanghai Jiading District Central Hospital（上海市嘉定区中心医院）
University of Westminster（威斯敏斯特大学）；Calico Life Sciences LLC（Calico生命科学有限责任公司）
An end-to-end image analysis pipeline is presented for the abdominal MRI protocol used in the UK Biobank on the first 38,971 participants. Emphasis is on the processing steps necessary to ensure a high-level of data quality and consistency is produced in order to prepare the datasets for downstream quantitative analysis, such as segmentation and parameter estimation. Quality control procedures have been incorporated to detect and, where possible, correct issues in the raw data. Detection of fat-water swaps in the Dixon series is performed by a deep learning model and corrected automatically. B…
The University of Queensland（昆士兰大学）；The Commonwealth Scientific and Industrial Research Organisation（联邦科学与工业研究组织）；Johns Hopkins University（约翰斯·霍普金斯大学）；University of Science and Technology of China（中国科学技术大学）
Magnetic resonance (MR) images exhibit various contrasts and appearances based on factors such as different acquisition protocols, views, manufacturers, scanning parameters, etc. This generally accessible appearance-related side information affects deep learning-based undersampled magnetic resonance imaging (MRI) reconstruction frameworks, but has been overlooked in the majority of current works. In this paper, we investigate the use of such side information as normalisation parameters in a convolutional neural network (CNN) to improve undersampled MRI reconstruction. Specifically, a Side Info…
Facebook AI Research (FAIR)（Facebook人工智能研究院（FAIR））；NYU School of Medicine（纽约大学医学院）
The slow acquisition speed of magnetic resonance imaging (MRI) has led to the development of two complementary methods: acquiring multiple views of the anatomy simultaneously (parallel imaging) and acquiring fewer samples than necessary for traditional signal processing methods (compressed sensing). While the combination of these methods has the potential to allow much faster scan times, reconstruction from such undersampled multi-coil data has remained an open problem. In this paper, we present a new approach to this problem that extends previously proposed variational methods by learning ful…
Gordon Center for Medical Imaging, Massachusetts General Hospital and Harvard Medical School（马萨诸塞总医院与哈佛医学院戈登医学影像中心）；Texas A&M University（德克萨斯A&M大学）；Texas A&M Institute of Data Science, Texas A&M University（德克萨斯A&M大学数据科学研究所）；Texas A&M University at Qatar（德克萨斯A&M大学卡塔尔分校）
Magnetic resonance imaging (MRI) is one of the noninvasive imaging modalities that can produce high-quality images. However, the scan procedure is relatively slow, which causes patient discomfort and motion artifacts in images. Accelerating MRI hardware is constrained by physical and physiological limitations. A popular alternative approach to accelerated MRI is to undersample the k-space data. While undersampling speeds up the scan procedure, it generates artifacts in the images, and advanced reconstruction algorithms are needed to produce artifact-free images. Recently deep learning has emer…
Facebook AI Research（脸书人工智能研究院）；McGill University（麦吉尔大学）
Deep learning approaches have recently shown great promise in accelerating magnetic resonance image (MRI) acquisition. The majority of existing work have focused on designing better reconstruction models given a pre-determined acquisition trajectory, ignoring the question of trajectory optimization. In this paper, we focus on learning acquisition trajectories given a fixed image reconstruction model. We formulate the problem as a sequential decision process and propose the use of reinforcement learning to solve it. Experiments on a large scale public MRI dataset of knees show that our proposed…
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…
Second Affiliated Hospital of Xiamen Medical College（厦门医学院附属第二医院）；Neusoft Medical System（东软医疗系统）
Magnetic resonance imaging has been widely applied in clinical diagnosis, however, is limited by its long data acquisition time. Although imaging can be accelerated by sparse sampling and parallel imaging, achieving promising reconstruction images with a fast reconstruction speed remains a challenge. Recently, deep learning approaches have attracted a lot of attention for its encouraging reconstruction results but without a proper interpretability. In this letter, to enable high-quality image reconstruction for the parallel magnetic resonance imaging, we design the network structure from the p…
Ege University（埃杰大学）；University of Central Florida（中佛罗里达大学）；University of Pennsylvania（宾夕法尼亚大学）
The diagnosis, prognosis, and treatment of patients with musculoskeletal (MSK) disorders require radiology imaging (using computed tomography, magnetic resonance imaging(MRI), and ultrasound) and their precise analysis by expert radiologists. Radiology scans can also help assessment of metabolic health, aging, and diabetes. This study presents how machinelearning, specifically deep learning methods, can be used for rapidand accurate image analysis of MRI scans, an unmet clinicalneed in MSK radiology. As a challenging example, we focus on automatic analysis of knee images from MRI scans and stu…
High-quality magnetic resonance (MR) image, i.e., with near isotropic voxel spacing, is desirable in various scenarios of medical image analysis. However, many MR acquisitions use large inter-slice spacing in clinical practice. In this work, we propose a novel deep-learning-based super-resolution algorithm to generate high-resolution (HR) MR images with small slice spacing from low-resolution (LR) inputs of large slice spacing. Notice that most existing deep-learning-based methods need paired LR and HR images to supervise the training, but in clinical scenarios, usually no HR images will be ac…
University of California, San Francisco（加州大学旧金山分校）；University of California, Berkeley（加州大学伯克利分校）
Deep Learning (DL) has shown potential in accelerating Magnetic Resonance Image acquisition and reconstruction. Nevertheless, there is a dearth of tailored methods to guarantee that the reconstruction of small features is achieved with high fidelity. In this work, we employ adversarial attacks to generate small synthetic perturbations, which are difficult to reconstruct for a trained DL reconstruction network. Then, we use robust training to increase the network's sensitivity to these small features and encourage their reconstruction. Next, we investigate the generalization of said approach to…
Xiamen University（厦门大学）；Xiamen University of Technology（厦门理工学院）；United Imaging Research Institute of Intelligent Imaging（联影智能影像研究院）；Nanjing Medical University（南京医科大学）；University of Texas at Austin（德克萨斯大学奥斯汀分校）
Deep learning has shown astonishing performance in accelerated magnetic resonance imaging (MRI). Most state-of-the-art deep learning reconstructions adopt the powerful convolutional neural network and perform 2D convolution since many magnetic resonance images or their corresponding k-space are in 2D. In this work, we present a new approach that explores the 1D convolution, making the deep network much easier to be trained and generalized. We further integrate the 1D convolution into the proposed deep network, named as One-dimensional Deep Low-rank and Sparse network (ODLS), which unrolls the …
Deep learning based image reconstruction methods outperform traditional methods. However, neural networks suffer from a performance drop when applied to images from a different distribution than the training images. For example, a model trained for reconstructing knees in accelerated magnetic resonance imaging (MRI) does not reconstruct brains well, even though the same network trained on brains reconstructs brains perfectly well. Thus there is a distribution shift performance gap for a given neural network, defined as the difference in performance when training on a distribution $P$ and train…
The MRI Scanner as a Diagnostic: Image-less Active Sampling
School of Engineering, The University of Edinburgh（爱丁堡大学工程学院）；Krannert Cardiovascular Research Center, Indiana University School of Medicine（印第安纳大学医学院克兰纳特心血管研究中心）；The Alan Turing Institute（阿兰·图灵研究所）
Mannheim University of Applied Science（曼海姆应用科技大学）；UT Southwestern Medical Center（德克萨斯大学西南医学中心）；DZHK (German Centre for Cardiovascular Research)（德国心血管研究中心）；German Heart Centre Munich（慕尼黑德国心脏中心）；Hannover Medical School（汉诺威医学院）；Heidelberg University Hospital（海德堡大学医院）
Planning the optimal time of intervention for pulmonary valve replacement surgery in patients with the congenital heart disease Tetralogy of Fallot (TOF) is mainly based on ventricular volume and function according to current guidelines. Both of these two biomarkers are most reliably assessed by segmentation of 3D cardiac magnetic resonance (CMR) images. In several grand challenges in the last years, U-Net architectures have shown impressive results on the provided data. However, in clinical practice, data sets are more diverse considering individual pathologies and image properties derived fr…
Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）
Magnetic Resonance Imaging (MRI) scans are time consuming and precarious, since the patients remain still in a confined space for extended periods of time. To reduce scanning time, some experts have experimented with undersampled k spaces, trying to use deep learning to predict the fully sampled result. These studies report that as many as 20 to 30 minutes could be saved off a scan that takes an hour or more. However, none of these studies have explored the possibility of using masked image modeling (MIM) to predict the missing parts of MRI k spaces. This study makes use of 11161 reconstructed…
