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 neural network. To solve this problem, we propose a new model called MRI Cascaded Channel-wise Attention Network (MICCAN), highlighted by three components: (i) a variant of U-net with Channel-wise Attention (UCA) module, (ii) a long skip connection and (iii) a combined loss. Our model is able to attend to salient information by filtering irrelevant features and also concentrate on high-frequency information by enforcing low-frequency information bypassed to the final output. We conduct both quantitative evaluation and qualitative analysis of our method on a cardiac dataset. The experiment shows that our method achieves very promising results in terms of three common metrics on the MRI reconstruction with low undersampled k-space data.
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)
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-…
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 …
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 …
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)
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…
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…
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…
Structural magnetic resonance imaging (MRI) has been widely utilized for analysis and diagnosis of brain diseases. Automatic segmentation of brain tumors is a challenging task for computer-aided diagnosis due to low-tissue contrast in the tumor subregions. To overcome this, we devise a novel pixel-wise segmentation framework through a convolutional 3D to 2D MR patch conversion model to predict class labels of the central pixel in the input sliding patches. Precisely, we first extract 3D patches from each modality to calibrate slices through the squeeze and excitation (SE) block. Then, the outp…
Charité – Universitätsmedizin Berlin(柏林夏里特医学院);Freie Universität Berlin(柏林自由大学);Humboldt-Universität zu Berlin(柏林洪堡大学);Berlin Institute of Health(柏林健康研究所)
Machine learning-based imaging diagnostics has recently reached or even superseded the level of clinical experts in several clinical domains. However, classification decisions of a trained machine learning system are typically non-transparent, a major hindrance for clinical integration, error tracking or knowledge discovery. In this study, we present a transparent deep learning framework relying on convolutional neural networks (CNNs) and layer-wise relevance propagation (LRP) for diagnosing multiple sclerosis (MS). MS is commonly diagnosed utilizing a combination of clinical presentation and …
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…
Enhancing Generalized Fetal Brain MRI Segmentation using A Cascade Network with Depth-wise Separable Convolution and Attention Mechanism
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University(复旦大学类脑智能科学与技术研究院);MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence(教育部计算神经科学与类脑智能重点实验室);MOE Frontiers Center for Brain Science(教育部脑科学前沿中心)
In this paper, we propose a novel learning based method for automated segmenta-tion of brain tumor in multimodal MRI images. The machine learned features from fully convolutional neural network (FCN) and hand-designed texton fea-tures are used to classify the MRI image voxels. The score map with pixel-wise predictions is used as a feature map which is learned from multimodal MRI train-ing dataset using the FCN. The learned features are then applied to random for-ests to classify each MRI image voxel into normal brain tissues and different parts of tumor. The method was evaluated on BRATS 2013 …
Massachusetts General Hospital(麻省总医院);Harvard Medical School(哈佛医学院);National Taiwan University(台湾大学);University of Southern California(南加州大学)
Assessment of cardiovascular disease (CVD) with cine magnetic resonance imaging (MRI) has been used to non-invasively evaluate detailed cardiac structure and function. Accurate segmentation of cardiac structures from cine MRI is a crucial step for early diagnosis and prognosis of CVD, and has been greatly improved with convolutional neural networks (CNN). There, however, are a number of limitations identified in CNN models, such as limited interpretability and high complexity, thus limiting their use in clinical practice. In this work, to address the limitations, we propose a lightweight and i…
Automated Detection of Multiple Sclerosis Lesions on 7-tesla MRI Using U-net and Transformer-based Segmentation
Department of Neurology, University of Maryland School of Medicine(马里兰大学医学院神经内科);Baltimore VA Medical Center, VA Maryland Healthcare System(巴尔的摩退伍军人事务医疗中心,马里兰州退伍军人医疗系统)
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…
Reliable MRI is crucial for accurate interpretation in therapeutic and diagnostic tasks. However, undersampling during MRI acquisition as well as the overparameterized and non-transparent nature of deep learning (DL) leaves substantial uncertainty about the accuracy of DL reconstruction. With this in mind, this study aims to quantify the uncertainty in image recovery with DL models. To this end, we first leverage variational autoencoders (VAEs) to develop a probabilistic reconstruction scheme that maps out (low-quality) short scans with aliasing artifacts to the diagnostic-quality ones. The VA…
Erasmus MC(伊拉斯姆斯医学中心);Delft University of Technology(代尔夫特理工大学)
Analysis of longitudinal changes in imaging studies often involves both segmentation of structures of interest and registration of multiple timeframes. The accuracy of such analysis could benefit from a tailored framework that jointly optimizes both tasks to fully exploit the information available in the longitudinal data. Most learning-based registration algorithms, including joint optimization approaches, currently suffer from bias due to selection of a fixed reference frame and only support pairwise transformations. We here propose an analytical framework based on an unbiased learning strat…
Skolkovo Institute of Science and Technology(斯科尔科沃科学技术研究院)
Deep learning shows high potential for many medical image analysis tasks. Neural networks can work with full-size data without extensive preprocessing and feature generation and, thus, information loss. Recent work has shown that the morphological difference in specific brain regions can be found on MRI with the means of Convolution Neural Networks (CNN). However, interpretation of the existing models is based on a region of interest and can not be extended to voxel-wise image interpretation on a whole image. In the current work, we consider the classification task on a large-scale open-source…
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…
Quantitative mapping from conventional MRI using self-supervised physics-guided deep learning: applications to a large-scale, clinically heterogeneous dataset
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…
Technical University of Munich(慕尼黑工业大学);GE Global Research(通用电气全球研发中心);Harvard Medical School(哈佛医学院)
Perfusion-weighted magnetic resonance imaging (MRI) is an imaging technique that allows one to measure tissue perfusion in an organ of interest through the injection of an intravascular paramagnetic contrast agent (CA). Due to a preference for high temporal and spatial resolution in many applications, this modality could significantly benefit from accelerated data acquisitions. In this paper, we specifically address the problem of reconstructing perfusion MR image series from a subset of k-space data. Our proposed approach is motivated by the observation that temporal variations (dynamics) in …
Polytechnique Montreal(蒙特利尔理工学院);University of Montreal(蒙特利尔大学);CRIUGM(蒙特利尔大学神经科学研究所)
Despite recent improvements in medical image segmentation, the ability to generalize across imaging contrasts remains an open issue. To tackle this challenge, we implement Feature-wise Linear Modulation (FiLM) to leverage physics knowledge within the segmentation model and learn the characteristics of each contrast. Interestingly, a well-optimised U-Net reached the same performance as our FiLMed-Unet on a multi-contrast dataset (0.72 of Dice score), which suggests that there is a bottleneck in spinal MS lesion segmentation different from the generalization across varying contrasts. This bottle…
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…
University of California at Berkeley(加州大学伯克利分校);The University of Texas at Austin(德克萨斯大学奥斯汀分校);GE Global Research(通用电气全球研究院);International Computer Science Institute(国际计算机科学研究所)
Purpose: To improve reconstruction fidelity of fine structures and textures in deep learning (DL) based reconstructions. Methods: A novel patch-based Unsupervised Feature Loss (UFLoss) is proposed and incorporated into the training of DL-based reconstruction frameworks in order to preserve perceptual similarity and high-order statistics. The UFLoss provides instance-level discrimination by mapping similar instances to similar low-dimensional feature vectors and is trained without any human annotation. By adding an additional loss function on the low-dimensional feature space during training, t…
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…
Treatment-wise Glioblastoma Survival Inference with Multi-parametric Preoperative MRI
Gordon Center for Medical Imaging, Massachusetts General Hospital and Harvard Medical School(戈登医学影像中心,麻省总医院和哈佛医学院);University of Southern California(南加州大学);Yale University(耶鲁大学)
Cyclic Self-Supervised Diffusion for Ultra Low-field to High-field MRI Synthesis
Department of Bioengineering and Imperial-X, Imperial College London(生物工程系和Imperial-X,帝国理工学院伦敦分校);Department of Bioengineering, Imperial College London(生物工程系,帝国理工学院伦敦分校);School of Biomedical Engineering, Sun Yat-sen University(生物医学工程学院,中山大学);Monash Biomedical Imaging, Monash University(莫纳什大学生物医学成像)
Fetal brain magnetic resonance imaging (MRI) offers exquisite images of the developing brain but is not suitable for anomaly screening. For this ultrasound (US) is employed. While expert sonographers are adept at reading US images, MR images are much easier for non-experts to interpret. Hence in this paper we seek to produce images with MRI-like appearance directly from clinical US images. Our own clinical motivation is to seek a way to communicate US findings to patients or clinical professionals unfamiliar with US, but in medical image analysis such a capability is potentially useful, for in…
Universitat Politècnica de Catalunya. BarcelonaTech(加泰罗尼亚理工大学·巴塞罗那理工)
Automation of brain tumor segmentation in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. Moreover, most methods do not include uncertainty information, which is especially critical in medical diagnosis. This work studies 3D encoder-decoder architectures trained with patch-based techniques to reduce memory consumption and decrease the effect of unbalanced data. The different trained model…
Erasmus MC(伊拉斯谟医学中心);Delft University of Technology(代尔夫特理工大学);University of Copenhagen(哥本哈根大学)
To measure the volume of specific image structures, a typical approach is to first segment those structures using a neural network trained on voxel-wise (strong) labels and subsequently compute the volume from the segmentation. A more straightforward approach would be to predict the volume directly using a neural network based regression approach, trained on image-level (weak) labels indicating volume. In this article, we compared networks optimized with weak and strong labels, and study their ability to generalize to other datasets. We experimented with white matter hyperintensity (WMH) volum…
College of Health Science and Environmental Engineering, Shenzhen Technology University(深圳科技大学健康科学与环境工程学院);University Medical Center Göttingen(哥廷根大学医学中心);Guangdong-Hongkong-Macau CNS Regeneration Institute, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Jinan University(广东-港澳-澳门神经科学再生研究所,神经科学再生重点实验室(暨南大学)-教育部,暨南大学);Department of Radiology, The First Hospital of Tsinghua University(清华大学第一医院放射科);Center for Biomedical Imaging Research, Department of Biomedical Engineering, School of Medicine, Tsinghua University(清华大学生物医学成像研究中心,生物医学工程系,医学院);Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University(教育部生物医学工程重点实验室,生物医学工程与仪器科学学院,浙江大学);Department of Endocrinology and Metabolism, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine(浙江大学医学院邵逸夫医院内分泌科);Lab of Molecular Imaging and Medical Intelligence, Department of Radiology, Longgang Central Hospital of Shenzhen (Shenzhen Clinical Medical College, Guangzhou University of Chinese Medicine(分子成像与医学智能实验室,放射科,深圳龙岗中心医院(深圳临床医学院,广州中医药大学;龙岗临床学院,汕头大学医学院));Longgang Clinical Institute of Shantou University Medical College)
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…
Image2Flow: A hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data
Institute of Cardiovascular Science, University College London(伦敦大学学院心血管科学研究所)
A Multi-Stage Fine-Tuning and Ensembling Strategy for Pancreatic Tumor Segmentation in Diagnostic and Therapeutic MRI
German Cancer Research Center (DKFZ) Heidelberg(德国癌症研究中心(DKFZ)海德堡);Faculty of Mathematics and Computer Science(数学与计算机科学学院);Heidelberg University(海德堡大学);Helmholtz Imaging, DKFZ(海德堡影像中心,DKFZ);Pattern Analysis and Learning Group(模式分析与学习小组);Department of Radiation Oncology(放射肿瘤科);Heidelberg University Hospital(海德堡大学医院);International School of Medicine(国际医学院);Istanbul Medipol University(伊斯坦布尔梅迪波尔大学)
BrainDINO: A Brain MRI Foundation Model for Generalizable Clinical Representation Learning
Department of Radiation Oncology and Winship Cancer Institute, Emory University(放射肿瘤科和Winship癌症研究所,埃默里大学);Department of Radiation and Cellular Oncology, The University of Chicago(放射肿瘤学与细胞肿瘤学部,芝加哥大学);Department of Electrical and Computer Engineering, Georgia Institute of Technology(电气与计算机工程系,佐治亚理工学院);Department of Biomedical Engineering, Georgia Institute of Technology(生物医学工程系,佐治亚理工学院);Department of Biomedical Informatics, Emory University(生物医学信息学系,埃默里大学);Department of Medical Physics, Memorial Sloan Kettering Cancer Center(医学物理系,纪念斯隆凯特琳癌症中心)
Charité – Universitätsmedizin Berlin(柏林夏里特医学院);Freie Universität Berlin(柏林自由大学);Humboldt-Universität zu Berlin(柏林洪堡大学);Berlin Institute of Health (BIH)(柏林健康研究所)
Attribution methods are an easy to use tool for investigating and validating machine learning models. Multiple methods have been suggested in the literature and it is not yet clear which method is most suitable for a given task. In this study, we tested the robustness of four attribution methods, namely gradient*input, guided backpropagation, layer-wise relevance propagation and occlusion, for the task of Alzheimer's disease classification. We have repeatedly trained a convolutional neural network (CNN) with identical training settings in order to separate structural MRI data of patients with …
MOIS-SAM2: Exemplar-based Segment Anything Model 2 for multilesion interactive segmentation of neurofibromas in whole-body MRI
Institute for Applied Medical Informatics, Institute of Computational Neuroscience, and Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf(应用医学信息学研究所、计算神经科学研究所和生物医学人工智能中心(bAIome)、汉堡医学院中心);Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf(诊断与介入放射学及核医学系、汉堡医学院中心);Department of Neurology, University Medical Center Hamburg-Eppendorf(神经病学系、汉堡医学院中心)
MOIS-SAM2是一种基于示例的Segment Anything Model 2,用于全身体部MRI中神经纤维瘤多病灶交互分割,实现了高精度和可扩展性,支持临床应用。
Automated cardiac segmentation from magnetic resonance imaging datasets is an essential step in the timely diagnosis and management of cardiac pathologies. We propose to tackle the problem of automated left and right ventricle segmentation through the application of a deep fully convolutional neural network architecture. Our model is efficiently trained end-to-end in a single learning stage from whole-image inputs and ground truths to make inference at every pixel. To our knowledge, this is the first application of a fully convolutional neural network architecture for pixel-wise labeling in ca…