Tractography with T1-weighted MRI and associated anatomical constraints on clinical quality diffusion MRI
Tian Yu, Yunhe Li, Michael E. Kim, Chenyu Gao, Qi Yang, Leon Y. Cai, Susane M. Resnick, Lori L. Beason-Held, Daniel C. Moyer, Kurt G. Schilling, Bennett A. Landman
Diffusion MRI (dMRI) streamline tractography, the gold standard for in vivo estimation of brain white matter (WM) pathways, has long been considered indicative of macroscopic relationships with WM microstructure. However, recent advances in tractography demonstrated that convolutional recurrent neural networks (CoRNN) trained with a teacher-student framework have the ability to learn and propagate streamlines directly from T1 and anatomical contexts. Training for this network has previously relied on high-resolution dMRI. In this paper, we generalize the training mechanism to traditional clinical resolution data, which allows generalizability across sensitive and susceptible study populations. We train CoRNN on a small subset of the Baltimore Longitudinal Study of Aging (BLSA), which better resembles clinical protocols. Then, we define a metric, termed the epsilon ball seeding method, to compare T1 tractography and traditional diffusion tractography at the streamline level. Under this metric, T1 tractography generated by CoRNN reproduces diffusion tractography with approximately two millimeters of error.
Harvard Medical School（哈佛医学院）；The University of Sydney（悉尼大学）；The University of New South Wales（新南威尔士大学）
The structure and variability of the brain's connections can be investigated via prediction of non-imaging phenotypes using neural networks. However, known neuroanatomical relationships between input features are generally ignored in network design. We propose TractGraphCNN, a novel, anatomically informed graph CNN framework for machine learning tasks using diffusion MRI tractography. An EdgeConv module aggregates features from anatomically similar white matter connections indicated by graph edges, and an attention module enables interpretation of predictive white matter tracts. Results in a s…
German Center for Neurodegenerative Diseases (DZNE)（德国神经退行性疾病研究中心）；A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital（马萨诸塞州总医院A. A. Martinos生物医学影像中心）；Department of Radiology, Harvard Medical School（哈佛医学院放射学系）
Deep learning approaches for diffusion MRI have so far focused primarily on voxel-based segmentation of lesions or white-matter fiber tracts. A drawback of representing tracts as volumetric labels, rather than sets of streamlines, is that it precludes point-wise analyses of microstructural or geometric features along a tract. Traditional tractography pipelines, which do allow such analyses, can benefit from detailed whole-brain segmentations to guide tract reconstruction. Here, we introduce fast, deep learning-based segmentation of 170 anatomical regions directly on diffusion-weighted MR image…
A Novel Deep Learning Tractography Fiber Clustering Framework for Functionally Consistent White Matter Parcellation Using Multimodal Diffusion MRI and Functional MRI
University of Electronic Science and Technology of China（电子科技大学）；Harvard Medical School（哈佛医学院）；Boston University（波士顿大学）
DeepMultiConnectome: Deep Multi-Task Prediction of Structural Connectomes Directly from Diffusion MRI Tractography
Eindhoven University of Technology（埃因霍温理工大学）；Brigham and Women’s Hospital（布莱尔妇女医院）；Harvard Medical School（哈佛医学院）；The University of Sydney（悉尼大学）；University of Electronic Science and Technology of China（电子科技大学）；Harvard-MIT Health Sciences and Technology（哈佛-麻省理工健康科学与技术）
Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）；University of Sydney（悉尼大学）；University of New South Wales（新南威尔士大学）；Massachusetts General Hospital（麻省总医院）
Diffusion MRI tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections. White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts. It enables quantification and visualization of whole-brain tractography. Currently, most parcellation methods focus on the deep white matter (DWM), whereas fewer methods address the superficial white matter (SWM) due to its complexity. We propose a novel two-stage deep-learning-based framework, Superficial White Matter Analysis (SupWMA), that performs an ef…
A Multimodal Deep Learning Approach for White Matter Shape Prediction in Diffusion MRI Tractography
Harvard Medical School（哈佛医学院）；The University of Sydney（悉尼大学）；Harvard University（哈佛大学）；Massachusetts General Hospital（麻省总医院）；Boston University（波士顿大学）；Harvard-MIT Health Sciences and Technology（哈佛-麻省理工学院健康科学与技术）
AGFS-Tractometry: A Novel Atlas-Guided Fine-Scale Tractometry Approach for Enhanced Along-Tract Group Statistical Comparison Using Diffusion MRI Tractography
University of Electronic Science and Technology of China（电子科技大学）；Brigham and Women’s Hospital, Harvard Medical School（哈佛医学院布里奇曼妇女医院）；Boston University（波士顿大学）
Université de Sherbrooke（舍布鲁克大学）；Univ. Bordeaux（波尔多大学）；CNRS（法国国家科学研究中心）；CEA（法国原子能和替代能源委员会）
Current brain white matter fiber tracking techniques show a number of problems, including: generating large proportions of streamlines that do not accurately describe the underlying anatomy; extracting streamlines that are not supported by the underlying diffusion signal; and under-representing some fiber populations, among others. In this paper, we describe a novel autoencoder-based learning method to filter streamlines from diffusion MRI tractography, and hence, to obtain more reliable tractograms. Our method, dubbed FINTA (Filtering in Tractography using Autoencoders) uses raw, unlabeled tr…
University of Sherbrooke（舍布鲁克大学）；Université de Bourgogne Franche-Comté（勃艮第-弗朗什孔泰大学）；CArdiac Simulation & Imaging Software（心脏模拟与成像软件公司）；Université de Lyon（里昂大学）
Recent publications have shown that the segmentation accuracy of modern-day convolutional neural networks (CNN) applied on cardiac MRI can reach the inter-expert variability, a great achievement in this area of research. However, despite these successes, CNNs still produce anatomically inaccurate segmentations as they provide no guarantee on the anatomical plausibility of their outcome, even when using a shape prior. In this paper, we propose a cardiac MRI segmentation method which always produces anatomically plausible results. At the core of the method is an adversarial variational autoencod…
Anatomy-guided fiber trajectory distribution estimation for cranial nerves tractography
College of Information Engineering, Zhejiang University of Technology（浙江工业大学信息工程学院）；The Hong Kong University of Science and Technology（香港科技大学）；Nuclear Industry 215 Hospital of Shaanxi Province（陕西省核工业二一五医院）；Capital Medical University Xuanwu Hospital（首都医科大学宣武医院）
High spatio-angular resolution diffusion MRI (dMRI) has been shown to provide accurate identification of complex neuronal fiber configurations, albeit, at the cost of long acquisition times. We propose a method to recover intra-voxel fiber configurations at high spatio-angular resolution relying on a 3D kq-space under-sampling scheme to enable accelerated acquisitions. Simulations and real data analysis suggest that accurate FOD mapping can be achieved from severe kq-space under-sampling regimes potentially enabling high spatio-angular resolution dMRI in the clinical setting.
Université de Sherbrooke（舍布鲁克大学）；Université Bordeaux（波尔多大学）；CNRS（法国国家科学研究中心）；CEA（法国原子能和替代能源委员会）；Imeka Solutions inc.（Imeka解决方案公司）
Current tractography methods use the local orientation information to propagate streamlines from seed locations. Many such seeds provide streamlines that stop prematurely or fail to map the true white matter pathways because some bundles are "harder-to-track" than others. This results in tractography reconstructions with poor white and gray matter spatial coverage. In this work, we propose a generative, autoencoder-based method, named GESTA (Generative Sampling in Bundle Tractography using Autoencoders), that produces streamlines achieving better spatial coverage. Compared to other deep learni…
Fiber tractography is an important tool of computational neuroscience that enables reconstructing the spatial connectivity and organization of white matter of the brain. Fiber tractography takes advantage of diffusion Magnetic Resonance Imaging (dMRI) which allows measuring the apparent diffusivity of cerebral water along different spatial directions. Unfortunately, collecting such data comes at the price of reduced spatial resolution and substantially elevated acquisition times, which limits the clinical applicability of dMRI. This problem has been thus far addressed using two principal strat…
Magnetic Resonance Imaging (MRI) plays an important role in diagnosing the parotid tumor, where accurate segmentation of tumors is highly desired for determining appropriate treatment plans and avoiding unnecessary surgery. However, the task remains nontrivial and challenging due to ambiguous boundaries and various sizes of the tumor, as well as the presence of a large number of anatomical structures around the parotid gland that are similar to the tumor. To overcome these problems, we propose a novel anatomy-aware framework for automatic segmentation of parotid tumors from multimodal MRI. Fir…
Anatomically Faithful Artifact Suppression in SENSE Accelerated Brain MRI
East China Normal University（华东师范大学）；Affiliated Hospital of Guizhou Medical University（贵州医科大学附属医院）；West China Hospital, Sichuan University（四川大学华西医院）；Chinese Academy of Medical Sciences（中国医学科学院）；RadioDynamic Medical（镭动医疗）；Lucile Packard Children’s Hospital（露西尔·帕卡德儿童医院）
We hypothesize that probabilistic voxel-level classification of anatomy and malignancy in prostate MRI, although typically posed as near-identical segmentation tasks via U-Nets, require different loss functions for optimal performance due to inherent differences in their clinical objectives. We investigate distribution, region and boundary-based loss functions for both tasks across 200 patient exams from the publicly-available ProstateX dataset. For evaluation, we conduct a thorough comparative analysis of model predictions and calibration, measured with respect to multi-class volume segmentat…
Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）；Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins Hospital（约翰斯·霍普金斯医院）
Visualizing disease-induced scarring and fibrosis in the heart on cardiac magnetic resonance (CMR) imaging with contrast enhancement (LGE) is paramount in characterizing disease progression and quantifying pathophysiological substrates of arrhythmias. However, segmentation and scar/fibrosis identification from LGE-CMR is an intensive manual process prone to large inter-observer variability. Here, we present a novel fully-automated anatomically-informed deep learning solution for left ventricle (LV) and scar/fibrosis segmentation and clinical feature extraction from LGE-CMR. The technology invo…
Université Côte d’Azur（蔚蓝海岸大学）；Inria（法国国家信息与自动化研究所）；Centre Antoine Lacassagne（安托万·拉卡桑中心）
Planning of radiotherapy involves accurate segmentation of a large number of organs at risk, i.e. organs for which irradiation doses should be minimized to avoid important side effects of the therapy. We propose a deep learning method for segmentation of organs at risk inside the brain region, from Magnetic Resonance (MR) images. Our system performs segmentation of eight structures: eye, lens, optic nerve, optic chiasm, pituitary gland, hippocampus, brainstem and brain. We propose an efficient algorithm to train neural networks for an end-to-end segmentation of multiple and non-exclusive class…
Evaluation of 3D Counterfactual Brain MRI Generation
Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA Department of Radiology, Stanford University, Stanford, CA, USA Dept. of Psychiatry \& Behavioral Sciences, Stanford University, Stanford, CA, USA Department of Computer Science, Stanford University, Stanford, CA, USA Department of Bioengineering, Stanford University, Stanford, CA, USA Department of Electrical Engineering, Stanford University, Stanford, CA, USA
FIESTA: Autoencoders for accurate fiber segmentation in tractography
Université de Sherbrooke, Canada（舍布鲁克大学，加拿大）；Sherbrooke Connectivity Imaging Lab (SCIL)（舍布鲁克连接成像实验室（SCIL））；Videos & Images Theory and Analytics Lab (VITAL)（视频与图像理论及分析实验室（VITAL））；Department of Computer Science（计算机科学系）；Department of Radiology（放射科）；Brigham and Women’s Hospital（布莱根妇女医院）；Mass General Brigham/Harvard Medical School, USA（麻省总医院布莱根联合/哈佛医学院，美国）；Centre de Calcul Scientifique（科学计算中心）；Medical Imaging and Neuroinformatic (MINi) Lab（医学成像与神经信息学（MINi）实验室）；Groupe d’Imagerie Neurofonctionnelle (GIN)（神经功能成像小组（GIN））；CNRS, CEA, IMN, GIN, UMR 5293, F-33000 Bordeaux（法国国家科学研究中心、法国原子能委员会、神经影像研究所、神经功能成像小组、5293号联合研究单位，波尔多）；Université de Bordeaux, France（波尔多大学，法国）；Pharma Research and Early Development（制药研究与早期开发）；Neuroscience and Rare Diseases（神经科学与罕见病）；Roche Innovation Center Basel（巴塞尔罗氏创新中心）；F. Hoffmann-La Roche Ltd., Basel, Switzerland（F.霍夫曼-罗氏有限公司，巴塞尔，瑞士）
Evaluating the Predictive Value of Preoperative MRI for Erectile Dysfunction Following Radical Prostatectomy
University of Amsterdam（阿姆斯特丹大学）；Antoni van Leeuwenhoek-Netherlands Cancer Institute（安托尼·范·列文霍克-荷兰癌症研究所）；Department of Urology（泌尿科部）；AI Technology for Life（人工智能技术生命）；Utrecht University（乌特勒支大学）；GROW School for Oncology and Developmental Biology（GROW肿瘤学与发育生物学学院）
Rutgers University（罗格斯大学）；United Imaging Intelligence（联影智能）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Accurate estimation of shape thickness from medical images is crucial in clinical applications. For example, the thickness of myocardium is one of the key to cardiac disease diagnosis. While mathematical models are available to obtain accurate dense thickness estimation, they suffer from heavy computational overhead due to iterative solvers. To this end, we propose novel methods for dense thickness estimation, including a fast solver that estimates thickness from binary annular shapes and an end-to-end network that estimates thickness directly from raw cardiac images.We test the proposed model…
University of Dundee（邓迪大学）；University of Cambridge（剑桥大学）；University of Bath（巴斯大学）；East China Normal University（华东师范大学）
MRI synthesis promises to mitigate the challenge of missing MRI modality in clinical practice. Diffusion model has emerged as an effective technique for image synthesis by modelling complex and variable data distributions. However, most diffusion-based MRI synthesis models are using a single modality. As they operate in the original image domain, they are memory-intensive and less feasible for multi-modal synthesis. Moreover, they often fail to preserve the anatomical structure in MRI. Further, balancing the multiple conditions from multi-modal MRI inputs is crucial for multi-modal synthesis. …
Carotid artery vessel wall thickness measurement is an essential step in the monitoring of patients with atherosclerosis. This requires accurate segmentation of the vessel wall, i.e., the region between an artery's lumen and outer wall, in black-blood magnetic resonance (MR) images. Commonly used convolutional neural networks (CNNs) for semantic segmentation are suboptimal for this task as their use does not guarantee a contiguous ring-shaped segmentation. Instead, in this work, we cast vessel wall segmentation as a multi-task regression problem in a polar coordinate system. For each carotid a…
Global Context Is All You Need for Parallel Efficient Tractography Parcellation
University of Bonn（波恩大学）；Center for X-ray and Nano Science CXNS, DESY（欧洲同步辐射中心X射线与纳米科学中心）；University Hospital Bonn（波恩大学医院）；German Center for Neurodegenerative Diseases (DZNE)（德国神经退行性疾病中心）；Lamarr Institute for Machine Learning and Artificial Intelligence（拉马尔机器学习与人工智能研究院）
Fine-Tuning TransMorph with Gradient Correlation for Anatomical Alignment
University Hospital Augsburg（奥格斯堡大学医院）；Technical University of Munich（慕尼黑工业大学）；Institute of Digital Medicine, University Hospital Augsburg（奥格斯堡大学医院数字医学研究所）
Pseudo-MRI-Guided PET Image Reconstruction Method Based on a Diffusion Probabilistic Model
Washington University in St. Louis（圣路易斯华盛顿大学）；Yale University（耶鲁大学）；Western University（西安大略大学）；Lawson Health Research Institute（劳森健康研究所）；McGill University（麦吉尔大学）；Siemens Healthineers AG（西门子医疗保健公司）；Mallinckrodt Institute of Radiology（马林克罗特放射学研究所）
FS-RWKV: Leveraging Frequency Spatial-Aware RWKV for 3T-to-7T MRI Translation
Faculty of Science and Technology, University of Macau（澳门大学科学与技术学院）；School of Electronic and Communication Engineering, Shenzhen Polytechnic University（深圳职业技术学院电子与通信工程学院）；Department of Cardiology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China（广东省人民医院心内科（广东省医学科学院））；Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China（广东省心血管病研究院，广东省人民医院，广东省医学科学院，广州，中国）
Fetal brain magnetic resonance imaging (MRI) offers exquisite images of the developing brain but is not suitable for second-trimester anomaly screening, for which ultrasound (US) is employed. Although expert sonographers are adept at reading US images, MR images which closely resemble anatomical images are much easier for non-experts to interpret. Thus in this paper we propose to generate MR-like images directly from clinical US images. In medical image analysis such a capability is potentially useful as well, for instance for automatic US-MRI registration and fusion. The proposed model is end…
Yantai University（烟台大学）；University of Rochester（罗切斯特大学）；The Chinese University of Hong Kong（香港中文大学）；Fudan University（复旦大学）；The Hong Kong Polytechnic University（香港理工大学）
Magnetic resonance imaging (MRI) can present multi-contrast images of the same anatomical structures, enabling multi-contrast super-resolution (SR) techniques. Compared with SR reconstruction using a single-contrast, multi-contrast SR reconstruction is promising to yield SR images with higher quality by leveraging diverse yet complementary information embedded in different imaging modalities. However, existing methods still have two shortcomings: (1) they neglect that the multi-contrast features at different scales contain different anatomical details and hence lack effective mechanisms to mat…
Self-Supervised Diffusion MRI Denoising via Iterative and Stable Refinement
School of Biomedical Engineering, Division of Life Sciences and Medicine, USTC（中国科学技术大学生命科学与医学部生物医学工程学院）；MIRACLE Center, Suzhou Institute for Advance Research, USTC（中国科学技术大学苏州研究院MIRACLE中心）；State Key Laboratory of Precision and Intelligent Chemistry, USTC（中国科学技术大学精准与智能化学国家重点实验室）；Key Laboratory of Intelligent Information Processing of CAS, Institute of Computing Technology, CAS（中国科学院计算技术研究所中国科学院智能信息处理重点实验室）
The surface Boundary Element Method (BEM) is one of the most commonly employed formulations to solve the forward problem in electroencephalography, but the applicability of its classical incarnations is lamentably limited to piece-wise homogeneous media. Several head tissues, however, are strongly anisotropic due to their complex underlying micro-structure. This implies that standard boundary integral formulations oversimplify the electrical properties of the head and produce unrealistic solutions, something that drastically limits the suitability and impact of BEM technologies to brain imagin…
Current deep learning approaches for diffusion MRI modeling circumvent the need for densely-sampled diffusion-weighted images (DWIs) by directly predicting microstructural indices from sparsely-sampled DWIs. However, they implicitly make unrealistic assumptions of static $q$-space sampling during training and reconstruction. Further, such approaches can restrict downstream usage of variably sampled DWIs for usages including the estimation of microstructural indices or tractography. We propose a generative adversarial translation framework for high-quality DWI synthesis with arbitrary $q$-space…
Multiscale Structure-Guided Latent Diffusion for Multimodal MRI Translation
Computer Science and Engineering, Northeastern University, Shenyang, China（东北大学计算机科学与工程系，沈阳，中国）；Key Laboratory of Intelligent Computing in Medical Image of Ministry of Education, Northeastern University, Shenyang, China（教育部医学图像智能计算重点实验室，东北大学，沈阳，中国）；National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Shenyang, China（工业智能与系统优化国家级前沿科学中心，沈阳，中国）；Amii, University of Alberta, Edmonton, Alberta, Canada（阿尔伯塔大学阿米人工智能研究所，埃德蒙顿，阿尔伯塔，加拿大）；AiShiWeiLai AI Research, Beijing, China（人工智能研究（北京）有限公司，北京，中国）
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…
The various speech sounds of a language are obtained by varying the shape and position of the articulators surrounding the vocal tract. Analyzing their variations is crucial for understanding speech production, diagnosing speech disorders and planning therapy. Identifying key anatomical landmarks of these structures on medical images is a pre-requisite for any quantitative analysis and the rising amount of data generated in the field calls for an automatic solution. The challenge lies in the high inter- and intra-speaker variability, the mutual interaction between the articulators and the mode…
