Longitudinal reproducibility is an essential concern in automated medical image segmentation, yet has proven to be an elusive objective as manual brain structure tracings have shown more than 10% variability. To improve reproducibility, lon-gitudinal segmentation (4D) approaches have been investigated to reconcile tem-poral variations with traditional 3D approaches. In the past decade, multi-atlas la-bel fusion has become a state-of-the-art segmentation technique for 3D image and many efforts have been made to adapt it to a 4D longitudinal fashion. However, the previous methods were either limited by using application specified energy function (e.g., surface fusion and multi model fusion) or only considered tem-poral smoothness on two consecutive time points (t and t+1) under sparsity as-sumption. Therefore, a 4D multi-atlas label fusion theory for general label fusion purpose and simultaneously considering temporal consistency on all time points is appealing. Herein, we propose a novel longitudinal label fusion algorithm, called 4D joint label fusion (4DJLF), to incorporate the temporal consistency modeling via non-local patch-intensity covariance models. The advantages of 4DJLF include: (1) 4DJLF is under the general label fusion framework by simul-taneously incorporating the spatial and temporal covariance on all longitudinal time points. (2) The proposed algorithm is a longitudinal generalization of a lead-ing joint label fusion method (JLF) that has proven adaptable to a wide variety of applications. (3) The spatial temporal consistency of atlases is modeled in a prob-abilistic model inspired from both voting based and statistical fusion. The pro-posed approach improves the consistency of the longitudinal segmentation while retaining sensitivity compared with original JLF approach using the same set of atlases. The method is available online in open-source.
The Hong Kong University of Science and Technology（香港科技大学）
In this paper, a novel label fusion method is proposed for brain magnetic resonance image segmentation. This label fusion method is formulated on a graph, which embraces both label priors from atlases and anatomical priors from target image. To represent a pixel in a comprehensive way, three kinds of feature vectors are generated, including intensity, gradient and structural signature. To select candidate atlas nodes for fusion, rather than exact searching, randomized k-d tree with spatial constraint is introduced as an efficient approximation for high-dimensional feature matching. Feature Sen…
Xi’an Jiaotong University（西安交通大学）；National Engineering Laboratory for Big Data Algorithm and Analysis Technology（大数据算法与分析技术国家工程实验室）；Shanghai Jiaotong University（上海交通大学）
Multi-atlas segmentation approach is one of the most widely-used image segmentation techniques in biomedical applications. There are two major challenges in this category of methods, i.e., atlas selection and label fusion. In this paper, we propose a novel multi-atlas segmentation method that formulates multi-atlas segmentation in a deep learning framework for better solving these challenges. The proposed method, dubbed deep fusion net (DFN), is a deep architecture that integrates a feature extraction subnet and a non-local patch-based label fusion (NL-PLF) subnet in a single network. The netw…
Wuhan University（武汉大学）；Rensselaer Polytechnic Institute (RPI)（伦斯勒理工学院（RPI））
Medical image segmentation is a fundamental task in medical image analysis. Despite that deep convolutional neural networks have gained stellar performance in this challenging task, they typically rely on large labeled datasets, which have limited their extension to customized applications. By revisiting the superiority of atlas based segmentation methods, we present a new framework of One-pass aligned Atlas Set for Images Segmentation (OASIS). To address the problem of time-consuming iterative image registration used for atlas warping, the proposed method takes advantage of the power of deep …
Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）；School of Computer and Control Engineering, Yantai University（烟台大学计算机与控制工程学院）；Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）
A novel multi-atlas based image segmentation method is proposed by integrating a semi-supervised label propagation method and a supervised random forests method in a pattern recognition based label fusion framework. The semi-supervised label propagation method takes into consideration local and global image appearance of images to be segmented and segments the images by propagating reliable segmentation results obtained by the supervised random forests method. Particularly, the random forests method is used to train a regression model based on image patches of atlas images for each voxel of th…
Multi-atlas segmentation (MAS) is a popular image segmentation technique for medical images. In this work, we improve the performance of MAS by correcting registration errors before label fusion. Specifically, we use a volumetric displacement field to refine registrations based on image anatomical appearance and predicted labels. We show the influence of the initial spatial alignment as well as the beneficial effect of using label information for MAS performance. Experiments demonstrate that the proposed refinement approach improves MAS performance on a 3D magnetic resonance dataset of the kne…
We present an end-to-end 3D reconstruction method for a scene by directly regressing a truncated signed distance function (TSDF) from a set of posed RGB images. Traditional approaches to 3D reconstruction rely on an intermediate representation of depth maps prior to estimating a full 3D model of a scene. We hypothesize that a direct regression to 3D is more effective. A 2D CNN extracts features from each image independently which are then back-projected and accumulated into a voxel volume using the camera intrinsics and extrinsics. After accumulation, a 3D CNN refines the accumulated features …
In this work, we improve the performance of multi-atlas segmentation (MAS) by integrating the recently proposed VoteNet model with the joint label fusion (JLF) approach. Specifically, we first illustrate that using a deep convolutional neural network to predict atlas probabilities can better distinguish correct atlas labels from incorrect ones than relying on image intensity difference as is typical in JLF. Motivated by this finding, we propose VoteNet+, an improved deep network to locally predict the probability of an atlas label to differs from the label of the target image. Furthermore, we …
Longitudinal fetal brain atlas is a powerful tool for understanding and characterizing the complex process of fetus brain development. Existing fetus brain atlases are typically constructed by averaged brain images on discrete time points independently over time. Due to the differences in onto-genetic trends among samples at different time points, the resulting atlases suffer from temporal inconsistency, which may lead to estimating error of the brain developmental characteristic parameters along the timeline. To this end, we proposed a multi-stage deep-learning framework to tackle the time in…
Deep learning (DL) approaches are state-of-the-art for many medical image segmentation tasks. They offer a number of advantages: they can be trained for specific tasks, computations are fast at test time, and segmentation quality is typically high. In contrast, previously popular multi-atlas segmentation (MAS) methods are relatively slow (as they rely on costly registrations) and even though sophisticated label fusion strategies have been proposed, DL approaches generally outperform MAS. In this work, we propose a DL-based label fusion strategy (VoteNet) which locally selects a set of reliable…
National Institutes of Health（美国国立卫生研究院）；University of California, Irvine School of Medicine（加州大学欧文分校医学院）
The precise and accurate segmentation of the vertebral column is essential in the diagnosis and treatment of various orthopedic, neurological, and oncological traumas and pathologies. Segmentation is especially challenging in the presence of pathology such as vertebral compression fractures. In this paper, we propose a method to produce segmentations for osteoporotic compression fractured vertebrae by applying a multi-atlas joint label fusion technique for clinical CT images. A total of 170 thoracic and lumbar vertebrae were evaluated using atlases from five patients with varying degrees of sp…
Fuzhou University（福州大学）；Fudan University（复旦大学）；Shanghai Jiao Tong University（上海交通大学）；King’s College London（伦敦国王学院）
Both image registration and label fusion in the multi-atlas segmentation (MAS) rely on the intensity similarity between target and atlas images. However, such similarity can be problematic when target and atlas images are acquired using different imaging protocols. High-level structure information can provide reliable similarity measurement for cross-modality images when cooperating with deep neural networks (DNNs). This work presents a new MAS framework for cross-modality images, where both image registration and label fusion are achieved by DNNs. For image registration, we propose a consiste…
In this work, we attempt the segmentation of cardiac structures in late gadolinium-enhanced (LGE) magnetic resonance images (MRI) using only minimal supervision in a two-step approach. In the first step, we register a small set of five LGE cardiac magnetic resonance (CMR) images with ground truth labels to a set of 40 target LGE CMR images without annotation. Each manually annotated ground truth provides labels of the myocardium and the left ventricle (LV) and right ventricle (RV) cavities, which are used as atlases. After multi-atlas label fusion by majority voting, we possess noisy labels fo…
Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation. Generally, MAS methods register multiple atlases, i.e., medical images with corresponding labels, to a target image; and the transformed atlas labels can be combined to generate target segmentation via label fusion schemes. Many conventional MAS methods employed the atlases from the same modality as the target image. However, the number of atlases with the same modality may be limited or even missing in many clinical applications. Besides, conventional MAS methods suffer from the computational burden of reg…
Murdoch University（莫道克大学）；Harry Butler Institute, Murdoch University（莫道克大学哈里·巴特勒研究所）；University of South Australia（南澳大学）；TU Berlin（柏林工业大学）；Durham University（杜伦大学）；Ohio State University（俄亥俄州立大学）；University of Western Australia（西澳大学）；Florida State University（佛罗里达州立大学）
We propose a novel framework to learn the spatiotemporal variability in longitudinal 3D shape data sets, which contain observations of objects that evolve and deform over time. This problem is challenging since surfaces come with arbitrary parameterizations and thus, they need to be spatially registered. Also, different deforming objects, also called 4D surfaces, evolve at different speeds and thus they need to be temporally aligned. We solve this spatiotemporal registration problem using a Riemannian approach. We treat a 3D surface as a point in a shape space equipped with an elastic Riemanni…
Multi-Atlas Brain Network Classification through Consistency Distillation and Complementary Information Fusion
College of Computing and Data Science, Nanyang Technological University（计算与数据科学学院，南洋理工大学）；Saw Swee Hock School of Public Health at National University of Singapore（新加坡国立大学 Saw Swee Hock 公共卫生学院）；Cognitive Neuroimaging Centre and Lee Kong Chian School of Medicine, Nanyang Technological University（认知神经影像中心和 Lee Kong Chian 医学院，南洋理工大学）
Convolutional networks (ConvNets) have achieved promising accuracy for various anatomical segmentation tasks. Despite the success, these methods can be sensitive to data appearance variations. Considering the large variability of scans caused by artifacts, pathologies, and scanning setups, robust ConvNets are vital for clinical applications, while have not been fully explored. In this paper, we propose to mitigate the challenge by enabling ConvNets' awareness of the underlying anatomical invariances among imaging scans. Specifically, we introduce a fully convolutional Constraint Adoption Modul…
University of Pennsylvania（宾夕法尼亚大学）；Lund University（隆德大学）
Deep learning (DL) is the state-of-the-art methodology in various medical image segmentation tasks. However, it requires relatively large amounts of manually labeled training data, which may be infeasible to generate in some applications. In addition, DL methods have relatively poor generalizability to out-of-sample data. Multi-atlas segmentation (MAS), on the other hand, has promising performance using limited amounts of training data and good generalizability. A hybrid method that integrates the high accuracy of DL and good generalizability of MAS is highly desired and could play an importan…
University College London（伦敦大学学院）；Centre for Medical Image Computing（医学图像计算中心）
Accurate segmentation of the right ventricle (RV) is a crucial step in the assessment of the ventricular structure and function. Yet, due to its complex anatomy and motion segmentation of the RV has not been as largely studied as the left ventricle. This paper presents a fully automatic method for the segmentation of the RV in cardiac magnetic resonance images (MRI). The method uses a coarse-to-fine segmentation strategy in combination with a multi-atlas propagation segmentation framework. Based on a cross correlation metric, our method selects the best atlases for propagation allowing the ref…
White Matter Hyperintensities (WMH) are the most common manifestation of cerebral small vessel disease (cSVD) on the brain MRI. Accurate WMH segmentation algorithms are important to determine cSVD burden and its clinical consequences. Most of existing WMH segmentation algorithms require both fluid attenuated inversion recovery (FLAIR) images and T1-weighted images as inputs. However, T1-weighted images are typically not part of standard clinicalscans which are acquired for patients with acute stroke. In this paper, we propose a novel brain atlas guided attention U-Net (BAGAU-Net) that leverage…
GLOMIA-Pro: A Generalizable Longitudinal Medical Image Analysis Framework for Disease Progression Prediction
School of Medical Technology, Beijing Institute of Technology（北京理工大学医学技术学院）；Department of Thoracic Surgery, Sun Yat-sen University Cancer Center（中山大学肿瘤医院胸外科部门）；Department of Radiology, The Fifth Affiliated Hospital of Sun Yat-sen University（中山大学第五附属医院放射科部门）；Beijing Duanliu Medical Technology Co., Ltd.（北京杜流医疗科技有限公司）
AtlasSeg: Atlas Prior Guided Dual-U-Net for Cortical Segmentation in Fetal Brain MRI
College of Biomedical Engineering & Instrument Science, Zhejiang University（浙江大学生物医学工程与仪器科学学院）；Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences（中国医学科学院北京医院国家老年医学中心老年医学研究所）；Shandong Provincial Hospital Affiliated to Shandong First Medical University（山东第一医科大学附属山东省立医院）；State Key Lab of CAD&CG, Zhejiang University（浙江大学CAD&CG国家重点实验室）
UNC Chapel Hill（北卡罗来纳大学教堂山分校）；University of Pennsylvania（宾夕法尼亚大学）
Registration of images with pathologies is challenging due to tissue appearance changes and missing correspondences caused by the pathologies. Moreover, mass effects as observed for brain tumors may displace tissue, creating larger deformations over time than what is observed in a healthy brain. Deep learning models have successfully been applied to image registration to offer dramatic speed up and to use surrogate information (e.g., segmentations) during training. However, existing approaches focus on learning registration models using images from healthy patients. They are therefore not desi…
Multi-Atlas Segmentation and Spatial Alignment of the Human Embryo in First Trimester 3D Ultrasound
Erasmus MC, University Medical Center Rotterdam（伊拉斯姆斯医学中心鹿特丹大学医学中心）；Delft University of Technology（代尔夫特理工大学）；Erasmus MC, University Medical Center（伊拉斯姆斯医学中心大学医学中心）
