Multi-branch Cascaded Swin Transformers with Attention to k-space Sampling Pattern for Accelerated MRI Reconstruction
Monash Biomedical Imaging, Monash University（莫纳什大学生物医学成像中心）；Department of Electrical and Computer Systems Engineering, Monash University（莫纳什大学电气与计算机系统工程系）；School of Psychological Sciences, Monash University（莫纳什大学心理科学学院）；Department of Data Science and AI, Monash University（莫纳什大学数据科学与人工智能系）
Mevan Ekanayake, Kamlesh Pawar, Mehrtash Harandi, Gary Egan, Zhaolin Chen
Global correlations are widely seen in human anatomical structures due to similarity across tissues and bones. These correlations are reflected in magnetic resonance imaging (MRI) scans as a result of close-range proton density and T1/T2 parameters. Furthermore, to achieve accelerated MRI, k-space data are undersampled which causes global aliasing artifacts. Convolutional neural network (CNN) models are widely utilized for accelerated MRI reconstruction, but those models are limited in capturing global correlations due to the intrinsic locality of the convolution operation. The self-attention-based transformer models are capable of capturing global correlations among image features, however, the current contributions of transformer models for MRI reconstruction are minute. The existing contributions mostly provide CNN-transformer hybrid solutions and rarely leverage the physics of MRI. In this paper, we propose a physics-based stand-alone (convolution free) transformer model titled, the Multi-head Cascaded Swin Transformers (McSTRA) for accelerated MRI reconstruction. McSTRA combines several interconnected MRI physics-related concepts with the transformer networks: it exploits global MR features via the shifted window self-attention mechanism; it extracts MR features belonging to different spectral components separately using a multi-head setup; it iterates between intermediate de-aliasing and k-space correction via a cascaded network with data consistency in k-space and intermediate loss computations; furthermore, we propose a novel positional embedding generation mechanism to guide self-attention utilizing the point spread function corresponding to the undersampling mask. Our model significantly outperforms state-of-the-art MRI reconstruction methods both visually and quantitatively while depicting improved resolution and removal of aliasing artifacts.
Imperial College London（帝国理工学院）；Royal Brompton Hospital（皇家布朗普顿医院）；Sun Yat-sen University（中山大学）；Beihang University（北京航空航天大学）；University of the Basque Country UPV/EHU（巴斯克大学（UPV/EHU））；TECNALIA（泰克纳利亚研究中心）；Shenzhen Second People’s Hospital（深圳市第二人民医院）；The First Affiliated Hospital of Shenzhen University Health Science Center（深圳大学医学部第一附属医院）
Magnetic resonance imaging (MRI) is an important non-invasive clinical tool that can produce high-resolution and reproducible images. However, a long scanning time is required for high-quality MR images, which leads to exhaustion and discomfort of patients, inducing more artefacts due to voluntary movements of the patients and involuntary physiological movements. To accelerate the scanning process, methods by k-space undersampling and deep learning based reconstruction have been popularised. This work introduced SwinMR, a novel Swin transformer based method for fast MRI reconstruction. The who…
National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Cardiovascular Research Centre, Royal Brompton Hospital（皇家布朗普顿医院心血管研究中心）；School of Biomedical Engineering, Sun Yat-sen University（中山大学生物医学工程学院）
Fast MRI aims to reconstruct a high fidelity image from partially observed measurements. Exuberant development in fast MRI using deep learning has been witnessed recently. Meanwhile, novel deep learning paradigms, e.g., Transformer based models, are fast-growing in natural language processing and promptly developed for computer vision and medical image analysis due to their prominent performance. Nevertheless, due to the complexity of the Transformer, the application of fast MRI may not be straightforward. The main obstacle is the computational cost of the self-attention layer, which is the co…
Automatic segmentation of myocardial contours and relevant areas like infraction and no-reflow is an important step for the quantitative evaluation of myocardial infarction. In this work, we propose a cascaded convolutional neural network for automatic myocardial infarction segmentation from delayed-enhancement cardiac MRI. We first use a 2D U-Net to focus on the intra-slice information to perform a preliminary segmentation. After that, we use a 3D U-Net to utilize the volumetric spatial information for a subtle segmentation. Our method is evaluated on the MICCAI 2020 EMIDEC challenge dataset …
We consider an MRI reconstruction problem with input of k-space data at a very low undersampled rate. This can practically benefit patient due to reduced time of MRI scan, but it is also challenging since quality of reconstruction may be compromised. Currently, deep learning based methods dominate MRI reconstruction over traditional approaches such as Compressed Sensing, but they rarely show satisfactory performance in the case of low undersampled k-space data. One explanation is that these methods treat channel-wise features equally, which results in degraded representation ability of the neu…
Nanjing University of Science and Technology（南京理工大学）
Automatic evaluation of myocardium and pathology plays an important role in the quantitative analysis of patients suffering from myocardial infarction. In this paper, we present a cascaded convolutional neural network framework for myocardial infarction segmentation and classification in delayed-enhancement cardiac MRI. Specifically, we first use a 2D U-Net to segment the whole heart, including the left ventricle and the myocardium. Then, we crop the whole heart as a region of interest (ROI). Finally, a new 2D U-Net is used to segment the infraction and no-reflow areas in the whole heart ROI. …
Technical University of Munich（慕尼黑工业大学）；LMU Hospital Grosshadern（路德维希-马克西米利安-慕尼黑大学格罗斯哈德恩医院）
Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input …
Background and objective: Parotid gland tumors account for approximately 2% to 10% of head and neck tumors. Preoperative tumor localization, differential diagnosis, and subsequent selection of appropriate treatment for parotid gland tumors are critical. However, the relative rarity of these tumors and the highly dispersed tissue types have left an unmet need for a subtle differential diagnosis of such neoplastic lesions based on preoperative radiomics. Recently, deep learning methods have developed rapidly, especially Transformer beats the traditional convolutional neural network in computer v…
Yale University（耶鲁大学）；New York University（纽约大学）；Hyperfine Research（Hyperfine研究公司）
Multi-contrast MRI (MC-MRI) captures multiple complementary imaging modalities to aid in radiological decision-making. Given the need for lowering the time cost of multiple acquisitions, current deep accelerated MRI reconstruction networks focus on exploiting the redundancy between multiple contrasts. However, existing works are largely supervised with paired data and/or prohibitively expensive fully-sampled MRI sequences. Further, reconstruction networks typically rely on convolutional architectures which are limited in their capacity to model long-range interactions and may lead to suboptima…
SST-DUNet: Automated preclinical functional MRI skull stripping using Smart Swin Transformer and Dense UNet
School of Information Technology, Carleton University（卡尔顿大学信息技术学院）；Center for Translational NeuroImaging (CTNI), Northeastern University（东北大学转化神经影像学中心）；College of Science and Humanity Studies, Prince Sattam Bin Abdulaziz University（萨塔姆·本·阿卜杜勒阿齐兹王子大学科学与人文研究学院）；Tessellis Ltd.（泰塞利斯有限公司）
Mask-Guided Multi-Channel SwinUNETR Framework for Robust MRI Classification
Departament de Matemàtiques i Informàtica, Universitat de Barcelona, Spain（巴塞罗那大学数学与计算机系）；Computer Vision Center, Bellaterra, Spain（贝尔特拉拉计算机视觉中心）；Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain（加泰罗尼亚高级研究与教育研究所）
Unsupervised Segmentation of Fetal Brain MRI using Deep Learning Cascaded Registration
Universitat Pompeu Fabra（庞培法布拉大学）；BCNatal；Institución Catalana de Investigación y Estudios Avanzados (ICREA)（加泰罗尼亚高级研究与发展研究院）；Centre for Biomedical Research on Rare Diseases (CIBERER)（罕见疾病生物医学研究中心）；European Commission, Joint Research Centre (JRC)（欧盟委员会联合研究中心）
The accurate reconstruction of under-sampled magnetic resonance imaging (MRI) data using modern deep learning technology, requires significant effort to design the necessary complex neural network architectures. The cascaded network architecture for MRI reconstruction has been widely used, while it suffers from the "vanishing gradient" problem when the network becomes deep. In addition, homogeneous architecture degrades the representation capacity of the network. In this work, we present an enhanced MRI reconstruction network using a residual in residual basic block. For each cell in the basic…
Tianjin University（天津大学）；Beijing Friendship Hospital, Capital Medical University（首都医科大学附属北京友谊医院）
Purpose: To introduce a dual-domain reconstruction network with V-Net and K-Net for accurate MR image reconstruction from undersampled k-space data. Methods: Most state-of-the-art reconstruction methods apply U-Net or cascaded U-Nets in image domain and/or k-space domain. Nevertheless, these methods have following problems: (1) Directly applying U-Net in k-space domain is not optimal for extracting features in k-space domain; (2) Classical image-domain oriented U-Net is heavy-weight and hence is inefficient to be cascaded many times for yielding good reconstruction accuracy; (3) Classical imag…
KTH Royal Institute of Technology（KTH皇家理工学院）；Science for Life Laboratory（生命科学实验室）
Artifacts on magnetic resonance scans are a serious challenge for both radiologists and computer-aided diagnosis systems. Most commonly, artifacts are caused by motion of the patients, but can also arise from device-specific abnormalities such as noise patterns. Irrespective of the source, artifacts can not only render a scan useless, but can potentially induce misdiagnoses if left unnoticed. For instance, an artifact may masquerade as a tumor or other abnormality. Retrospective artifact correction (RAC) is concerned with removing artifacts after the scan has already been taken. In this work, …
The need for fast acquisition and automatic analysis of MRI data is growing in the age of big data. Although compressed sensing magnetic resonance imaging (CS-MRI) has been studied to accelerate MRI by reducing k-space measurements, in current CS-MRI techniques MRI applications such as segmentation are overlooked when doing image reconstruction. In this paper, we test the utility of CS-MRI methods in automatic segmentation models and propose a unified deep neural network architecture called SegNetMRI which we apply to the combined CS-MRI reconstruction and segmentation problem. SegNetMRI is bu…
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Automated segmentation of multiple sclerosis (MS) lesions from MRI scans is important to quantify disease progression. In recent years, convolutional neural networks (CNNs) have shown top performance for this task when a large amount of labeled data is available. However, the accuracy of CNNs suffers when dealing with few and/or sparsely labeled datasets. A potential solution is to leverage the information available in large public datasets in conjunction with a target dataset which only has limited labeled data. In this paper, we propose a training framework, SSL2 (self-supervised-semi-superv…
BreastSegNet: Multi-label Segmentation of Breast MRI
Department of Biostatistics \& Bioinformatics, Duke University Department of Electrical；Computer Engineering, Duke University Department of Radiology, Duke University Medical Center Department of Computer Science, Duke University
Bilkent University（比尔肯特大学）；University of Southern California（南加利福尼亚大学）；Hacettepe University（哈杰泰佩大学）
Learning-based synthetic multi-contrast MRI commonly involves deep models trained using high-quality images of source and target contrasts, regardless of whether source and target domain samples are paired or unpaired. This results in undesirable reliance on fully-sampled acquisitions of all MRI contrasts, which might prove impractical due to limitations on scan costs and time. Here, we propose a novel semi-supervised deep generative model that instead learns to recover high-quality target images directly from accelerated acquisitions of source and target contrasts. To achieve this, the propos…
In multi-contrast magnetic resonance imaging (MRI), compressed sensing theory can accelerate imaging by sampling fewer measurements within each contrast. The conventional optimization-based models suffer several limitations: strict assumption of shared sparse support, time-consuming optimization and "shallow" models with difficulties in encoding the rich patterns hiding in massive MRI data. In this paper, we propose the first deep learning model for multi-contrast MRI reconstruction. We achieve information sharing through feature sharing units, which significantly reduces the number of paramet…
Northeastern University（东北大学）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）
Kidney function evaluation using dynamic contrast-enhanced MRI (DCE-MRI) images could help in diagnosis and treatment of kidney diseases of children. Automatic segmentation of renal parenchyma is an important step in this process. In this paper, we propose a time and memory efficient fully automated segmentation method which achieves high segmentation accuracy with running time in the order of seconds in both normal kidneys and kidneys with hydronephrosis. The proposed method is based on a cascaded application of two 3D convolutional neural networks that employs spatial and temporal informatio…
Imperial College London（帝国理工学院）；Royal Brompton Hospital（皇家布朗普顿医院）
Magnetic resonance imaging (MRI) is a widely used non-radiative and non-invasive method for clinical interrogation of organ structures and metabolism, with an inherently long scanning time. Methods by k-space undersampling and deep learning based reconstruction have been popularised to accelerate the scanning process. This work focuses on investigating how powerful transformers are for fast MRI by exploiting and comparing different novel network architectures. In particular, a generative adversarial network (GAN) based Swin transformer (ST-GAN) was introduced for the fast MRI reconstruction. T…
Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited…
Dual-Encoder Transformer-Based Multimodal Learning for Ischemic Stroke Lesion Segmentation Using Diffusion MRI
Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University（麻醉学、围术期与疼痛医学系，斯坦福大学）；Department of Biomedical Sciences, Seoul National University（生物医学科学系，首尔国立大学）；Department of Computer Engineering, National University of Sciences and Technology (NUST)（计算机工程系，国立科学与技术大学（NUST））；Department of Computer Science, The University of Alabama（计算机科学系，阿拉巴马大学）；Department of Computer Science, Hanyang University（计算机科学系，翰阳大学）
ImViA Laboratory, University of Burgundy（勃艮第大学ImViA实验室）；CHU Dijon（第戎大学医院）；CGFL；Institut Curie（居里研究所）
In this paper, we propose a new deep learning framework for an automatic myocardial infarction evaluation from clinical information and delayed enhancement-MRI (DE-MRI). The proposed framework addresses two tasks. The first task is automatic detection of myocardial contours, the infarcted area, the no-reflow area, and the left ventricular cavity from a short-axis DE-MRI series. It employs two segmentation neural networks. The first network is used to segment the anatomical structures such as the myocardium and left ventricular cavity. The second network is used to segment the pathological area…
Lightweight Hypercomplex MRI Reconstruction: A Generalized Kronecker-Parameterized Approach
Bioengineering Department（生物工程系）；Imperial-X, Imperial College London（帝国理工学院Imperial-X）；Imperial College London（帝国理工学院）；National Heart and Lung Institute, Imperial College London（国家心脏和肺 institute, 帝国理工学院）；Cardiovascular Research Centre, Royal Brompton Hospital（心血管研究中心, 罗伊·布罗姆普顿医院）；School of Biomedical Engineering and Imaging Sciences, King’s College London（生物医学工程与成像科学学院, 伦敦国王学院）
Anatomy-Guided Multitask Learning for MRI-Based Classification of Placenta Accreta Spectrum and its Subtypes
Sun Yat-sen University（中山大学）；The Third Affiliated Hospital of Guangzhou Medical University（广州医科大学附属第三医院）；Hainan General Hospital, Hainan Medical University（海南医科大学附属海南医院）
Department of Computing, Imperial College London（帝国理工学院计算机系）；National Heart & Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Cardiovascular Research Centre, Royal Brompton Hospital（皇家布朗普顿医院心血管研究中心）
Understanding the structure of the heart at the microscopic scale of cardiomyocytes and their aggregates provides new insights into the mechanisms of heart disease and enables the investigation of effective therapeutics. Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) is a unique non-invasive technique that can resolve the microscopic structure, organisation, and integrity of the myocardium without the need for exogenous contrast agents. However, this technique suffers from relatively low signal-to-noise ratio (SNR) and frequent signal loss due to respiratory and cardiac motion. Current D…
Polytechnique Montreal（蒙特利尔理工学院）；Mila, Quebec AI Institute（米拉魁北克人工智能研究所）；Beijing Tiantan Hospital, Capital Medical University（首都医科大学附属北京天坛医院）；Université de Montréal（蒙特利尔大学）
Spinal cord tumors lead to neurological morbidity and mortality. Being able to obtain morphometric quantification (size, location, growth rate) of the tumor, edema, and cavity can result in improved monitoring and treatment planning. Such quantification requires the segmentation of these structures into three separate classes. However, manual segmentation of 3-dimensional structures is time-consuming and tedious, motivating the development of automated methods. Here, we tailor a model adapted to the spinal cord tumor segmentation task. Data were obtained from 343 patients using gadolinium-enha…
TinyViT-Batten: Few-Shot Vision Transformer with Explainable Attention for Early Batten-Disease Detection on Pediatric MRI
Department of Applied Medical Sciences（应用医学科学系）；RareGen Youth Network 501(c)(3)（RareGen青年网络501(c)(3)）；Harvard University（哈佛大学）；Carnegie Mellon University（卡内基梅隆大学）；Mellon College of Science（梅隆科学学院）
Deformable image registration is a key task in medical image analysis. The Brain Tumor Sequence Registration challenge (BraTS-Reg) aims at establishing correspondences between pre-operative and follow-up scans of the same patient diagnosed with an adult brain diffuse high-grade glioma and intends to address the challenging task of registering longitudinal data with major tissue appearance changes. In this work, we proposed a two-stage cascaded network based on the Inception and TransMorph models. The dataset for each patient was comprised of a native pre-contrast (T1), a contrast-enhanced T1-w…
Three-dimensional end-to-end deep learning for brain MRI analysis
Technical University Dresden（德累斯顿工业大学）；University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden（德累斯顿工业大学卡尔·古斯塔夫·卡鲁斯大学医院及医学院）；National Center for Tumor Diseases Dresden（德累斯顿国家肿瘤疾病中心）；University Hospital Heidelberg（海德堡大学医院）；National Center for Tumor Diseases（国家肿瘤疾病中心）；University Hospital Aachen（亚琛大学医院）；Carl Gustav Carus University Hospital, Technische Universität Dresden（德累斯顿工业大学卡尔·古斯塔夫·卡鲁斯大学医院）
MSR:Hybrid Field Modeling for CT-MRI Rigid-Deformable Registration of the Cervical Spine with an Annotated Dataset
School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China.（南方医科大学生物医学工程学院）；Guangdong Provincial Key Laboratory of Medical Image Processing, Guangzhou, 510515, China.（广东省医学图像处理重点实验室）；Guangdong Province Engineering Laboratory for Medical Imaging（广东省医学影像与诊断技术工程实验室）；Information Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.（南方医科大学南华医院信息中心）；Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China.（南方医科大学南华医院骨科脊柱外科）
Spatio-Temporal Mixture-of-Modality-Experts Diffusion for Quantitative DCE-MRI Synthesis from Incomplete MR Sequences
Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine（首尔大学医学院癌症生物学跨学科项目）；Department of Radiology, Seoul National University Hospital（首尔大学医院放射科）；Department of Radiology, Seoul National University College of Medicine（首尔大学医学院放射科）；Healthcare AI Research Institute, Seoul National University Hospital（首尔大学医院医疗人工智能研究所）
Interpretable Prostate Cancer Detection using a Small Cohort of MRI Images
Department of Computer Science, Boston University Metropolitan College（波士顿大学计算机科学系）；Department of Radiology, McMaster University（麦斯特大学放射科）；Department of Radiology, School of Medicine, 5th Azar Hospital, Golestan University of Medical Sciences（戈兰大学医学学院放射科，第五阿扎尔医院）；Department of Medical Imaging, Niagara Health System（尼亚加拉健康系统医学影像科）；Center of Excellence in Precision Medicine and Digital Health, Department of Physiology, Chulalongkorn University（朱拉隆梭大学精准医学与数字健康中心，生理学系）
