Deep cerebellar nuclei are a key structure of the cerebellum that are involved in processing motor and sensory information. It is thus a crucial step to accurately segment deep cerebellar nuclei for the understanding of the cerebellum system and its utility in deep brain stimulation treatment. However, it is challenging to clearly visualize such small nuclei under standard clinical magnetic resonance imaging (MRI) protocols and therefore precise segmentation is not feasible. Recent advances in 7 Tesla (T) MRI technology and great potential of deep neural networks facilitate automatic patient-specific segmentation. In this paper, we propose a novel deep learning framework (referred to as DCN-Net) for fast, accurate, and robust patient-specific segmentation of deep cerebellar dentate and interposed nuclei on 7T diffusion MRI. DCN-Net effectively encodes contextual information on the patch images without consecutive pooling operations and adding complexity via proposed dilated dense blocks. During the end-to-end training, label probabilities of dentate and interposed nuclei are independently learned with a hybrid loss, handling highly imbalanced data. Finally, we utilize self-training strategies to cope with the problem of limited labeled data. To this end, auxiliary dentate and interposed nuclei labels are created on unlabeled data by using DCN-Net trained on manual labels. We validate the proposed framework using 7T B0 MRIs from 60 subjects. Experimental results demonstrate that DCN-Net provides better segmentation than atlas-based deep cerebellar nuclei segmentation tools and other state-of-the-art deep neural networks in terms of accuracy and consistency. We further prove the effectiveness of the proposed components within DCN-Net in dentate and interposed nuclei segmentation.
DeepCERES: A Deep learning method for cerebellar lobule segmentation using ultra-high resolution multimodal MRI
Instituto de Aplicaciones de las Tecnologías de la Información y de las Comunicaciones Avanzadas (ITACA), Universitat Politècnica de València（瓦伦西亚理工大学先进信息与通信技术应用研究所（ITACA））；Department of Psychobiology, Faculty of Psychology, Universitat de Valencia（瓦伦西亚大学心理学院心理生物学系）；Instituto de Automática e Informática Industrial, Universitat Politècnica de València（瓦伦西亚理工大学自动化和工业信息学研究所）；Departamento de matemática aplicada, Universitat Politècnica de València（瓦伦西亚理工大学应用数学系）；Área de Imagen Médica. Hospital Universitario y Politécnico La Fe（拉费大学理工医院医学影像科）；Unidad Mixta de Imagen Biomédica FISABIO-CIPF. Fundación para el Fomento de la Investigación Sanitario y Biomédica de la Comunidad Valenciana（FISABIO-CIPF生物医学成像联合单位，瓦伦西亚自治区卫生与生物医学研究促进基金会）；Univ. Bordeaux, CNRS, UMR 5287, Institut de Neurosciences Cognitives et Intégratives d’Aquitaine（波尔多大学，国家科学研究中心，UMR 5287，阿基坦认知与整合神经科学研究所）；CNRS, Univ. Bordeaux, Bordeaux INP, LABRI, UMR5800, in2brain（国家科学研究中心，波尔多大学，波尔多国立理工学院，LABRI，UMR5800，in2brain）
As the largest human cerebellar nucleus, the dentate nucleus (DN) functions significantly in the communication between the cerebellum and the rest of the brain. Structural connectivity-based parcellation has the potential to reveal the topography of the DN and enable the study of its subregions. In this paper, we investigate a deep nonnegative matrix factorization clustering method (DNMFC) for parcellation of the human DN based on its structural connectivity using diffusion MRI tractography. We propose to describe the connectivity of the DN using a set of curated tractography fiber clusters wi…
University College London（伦敦大学学院）；Basque Center on Cognition, Brain and Language（巴斯克认知、大脑与语言中心）；University of Castilla-La Mancha（卡斯蒂利亚-拉曼恰大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Technical University of Denmark（丹麦技术大学）
The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are known to have different functions and to be connected to different areas of the cerebral cortex, it is of great interest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manual delineation of 26 thalamic nuclei on the…
Samsung Medical Center（三星医疗中心）；Sungkyunkwan University School of Medicine（成均馆大学医学院）；Sungkyunkwan University（成均馆大学）；Columbia University（哥伦比亚大学）；University of Maryland（马里兰大学）
Automated segmentation and volumetry of brain magnetic resonance imaging (MRI) scans are essential for the diagnosis of Parkinson's disease (PD) and Parkinson's plus syndromes (P-plus). To enhance the diagnostic performance, we adopt deep learning (DL) models in brain segmentation and compared their performance with the gold-standard non-DL method. We collected brain MRI scans of healthy controls (n=105) and patients with PD (n=105), multiple systemic atrophy (n=132), and progressive supranuclear palsy (n=69) at Samsung Medical Center from January 2017 to December 2020. Using the gold-standard…
University College London（伦敦大学学院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；MIT（麻省理工学院）；Technical University of Denmark（丹麦技术大学）
Segmentation of structural and diffusion MRI (sMRI/dMRI) is usually performed independently in neuroimaging pipelines. However, some brain structures (e.g., globus pallidus, thalamus and its nuclei) can be extracted more accurately by fusing the two modalities. Following the framework of Bayesian segmentation with probabilistic atlases and unsupervised appearance modeling, we present here a novel algorithm to jointly segment multi-modal sMRI/dMRI data. We propose a hierarchical likelihood term for the dMRI defined on the unit ball, which combines the Beta and Dimroth-Scheidegger-Watson distrib…
Automated Fetal Brain MRI Biometry in Healthy and Pathological Cases
Faculty of Medicine, University of Ljubljana（卢布尔雅那大学医学院）；University Medical Centre Ljubljana（卢布尔雅那大学医学中心）；Faculty of Electrical Engineering, University of Ljubljana（卢布尔雅那大学电气工程学院）
Interpretable machine learning predicts Parkinson's disease severity using motion-corrected QSM MRI and multiband multiecho fMRI features
Lyda Hill Department of Bioinformatics（Lyda Hill 生物信息学系）；Department of Biomedical Engineering（生物医学工程系）；University of Texas Southwestern Medical Center, Dallas, Texas, USA（德克萨斯西南医学中心，德克萨斯州达拉斯）
DeepThalamus: A novel deep learning method for automatic segmentation of brain thalamic nuclei from multimodal ultra-high resolution MRI
Institute of Applications of Information and Advanced Communication Technologies (ITACA), Polytechnic University of Valencia（瓦伦西亚理工大学信息应用与高级通信技术研究所）；University de Valencia（瓦伦西亚大学）；Institute of Automation and Industrial Informatics, Polytechnic University of Valencia（瓦伦西亚理工大学自动化与工业信息学研究所）；La Fe University and Polytechnic Hospital（拉费大学及综合医院）；Foundation for the Promotion of Health and Biomedical Research of the Valencian Community（瓦伦西亚社区健康与生物医学研究促进基金会）；University Bordeaux（波尔多大学）；CNRS（法国国家科学研究中心）；Bordeaux INP（波尔多国立综合理工学院）；LABRI（法国国家科学研究中心、波尔多大学、波尔多国立综合理工学院联合实验室（LABRI））
Escola Politécnica, Universidade de São Paulo（圣保罗大学理工学院）；Brain Institute, IIEP Albert Einstein（阿尔伯特·爱因斯坦教育与研究学院脑研究所）；Faculdade de Medicina, Universidade de São Paulo（圣保罗大学医学院）；University of California San Francisco（加州大学旧金山分校）；University of Würzburg（维尔茨堡大学）；Athinoula A. Martinos Center for Biomedical Imaging, MGH/HST（麻省总医院/哈佛-麻省理工健康科学与技术部阿西诺拉·A·马丁诺斯生物医学成像中心）
Although the latest advances in MRI technology have allowed the acquisition of higher resolution images, reliable delineation of cytoarchitectural or subcortical nuclei boundaries is not possible. As a result, histological images are still required to identify the exact limits of neuroanatomical structures. However, histological processing is associated with tissue distortion and fixation artifacts, which prevent a direct comparison between the two modalities. Our group has previously proposed a histological procedure based on celloidin embedding that reduces the amount of artifacts and yields…
Britton Chance Center for Biomedical Photonics（布里顿·钱斯生物医学光子学研究中心）；Wuhan National Laboratory for Optoelectronics（武汉光电国家研究中心）；MoE Key Laboratory for Biomedical Photonics（教育部生物医学光子学重点实验室）；Collaborative Innovation Center for Biomedical Engineering（生物医学工程协同创新中心）；School of Engineering Sciences, Huazhong University of Science and Technology（华中科技大学工程科学学院）
Registration of brain MRI images requires to solve a deformation field, which is extremely difficult in aligning intricate brain tissues, e.g., subcortical nuclei, etc. Existing efforts resort to decomposing the target deformation field into intermediate sub-fields with either tiny motions, i.e., progressive registration stage by stage, or lower resolutions, i.e., coarse-to-fine estimation of the full-size deformation field. In this paper, we argue that those efforts are not mutually exclusive, and propose a unified framework for robust brain MRI registration in both progressive and coarse-to-…
Detailed delineation of the fetal brain in diffusion MRI via multi-task learning
Harvard Medical School（哈佛医学院）；Elmhurst Hospital Center（埃尔姆赫斯特医院中心）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；Massachusetts General Hospital（麻省总医院）；University of California Irvine（加州大学欧文分校）
Swiss Federal Institute of Technology (ETH) Zürich（苏黎世联邦理工学院）；Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins School of Medicine（约翰斯·霍普金斯大学医学院）；University of Maryland School of Medicine（马里兰大学医学院）
The thalamus is a subcortical gray matter structure that plays a key role in relaying sensory and motor signals within the brain. Its nuclei can atrophy or otherwise be affected by neurological disease and injuries including mild traumatic brain injury. Segmenting both the thalamus and its nuclei is challenging because of the relatively low contrast within and around the thalamus in conventional magnetic resonance (MR) images. This paper explores imaging features to determine key tissue signatures that naturally cluster, from which we can parcellate thalamic nuclei. Tissue contrasts include T1…
GE Research（通用电气研究院）；GE Healthcare（通用电气医疗）；Mayo Clinic（妙佑医疗国际）；Walter Reed National Military Medical Center（沃尔特里德国家军事医疗中心）；Uniformed Services University（美国三军卫生科学大学）
Purpose: To accelerate brain 3D MRI scans by using a deep learning method for reconstructing images from highly-undersampled multi-coil k-space data Methods: DL-Speed, an unrolled optimization architecture with dense skip-layer connections, was trained on 3D T1-weighted brain scan data to reconstruct complex-valued images from highly-undersampled k-space data. The trained model was evaluated on 3D MPRAGE brain scan data retrospectively-undersampled with a 10-fold acceleration, compared to a conventional parallel imaging method with a 2-fold acceleration. Scores of SNR, artifacts, gray/white ma…
University of Cambridge（剑桥大学）；University of Granada（格拉纳达大学）
Deep learning models for MRI classification face two recurring problems: they are typically limited by low sample size, and are abstracted by their own complexity (the "black box problem"). In this paper, we train a convolutional neural network (CNN) with the largest multi-source, functional MRI (fMRI) connectomic dataset ever compiled, consisting of 43,858 datapoints. We apply this model to a cross-sectional comparison of autism (ASD) vs typically developing (TD) controls that has proved difficult to characterise with inferential statistics. To contextualise these findings, we additionally pe…
The thalamus consists of several histologically and functionally distinct nuclei increasingly implicated in brain pathology and important for treatment, motivating the need for development of fast and accurate thalamic segmentation. The contrast between thalamic nuclei as well as between the thalamus and surrounding tissues is poor in T1 and T2 weighted magnetic resonance imaging (MRI), inhibiting efforts to date to segment the thalamus using standard clinical MRI. Automatic segmentation techniques have been developed to leverage thalamic features better captured by advanced MRI methods, inclu…
Segmenting Thalamic Nuclei: T1 Maps Provide a Reliable and Efficient Solution
Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health（行为神经科学实验室，国家老龄化研究所，国家卫生研究院）；Department of Computer Science, Johns Hopkins University（计算机科学系，约翰霍普金斯大学）；Department of Neurology, Johns Hopkins School of Medicine（神经病学系，约翰霍普金斯医学院）
Purpose: Thalamic nuclei are largely invisible in conventional MRI due to poor contrast. Thalamus Optimized Multi-Atlas Segmentation (THOMAS) provides automatic segmentation of 12 thalamic nuclei using white-matter-nulled (WMn) MPRAGE sequence at 7T. Application of THOMAS to Magnetization Prepared 2 Rapid Gradient Echo (MP2RAGE) sequence acquired at 7T has been investigated in this study. Methods: 8 healthy volunteers and 5 pediatric-onset multiple sclerosis patients were recruited at the Children's Hospital of Philadelphia and scanned at Siemens 7T with WMn-MPRAGE and multi-echo MP2RAGE (ME-M…
Concordia University（康考迪亚大学）；Concordia Institute for Information Systems Engineering（康考迪亚信息系统工程研究所）；London Health Sciences Centre（伦敦健康科学中心）；Western University（韦仕敦大学）；SpinTech MRI（SpinTech磁共振成像公司）；York University（约克大学）；Wayne State University（韦恩州立大学）
Brain iron deposition, in particular deep gray matter nuclei, increases with advancing age. Hereditary Hemochromatosis (HH) is the most common inherited disorder of systemic iron excess in Europeans and recent studies claimed high brain iron accumulation in patient with Hemochromatosis. In this study, we focus on Artificial Intelligence (AI)-based differential diagnosis of brain iron deposition in HH via Quantitative Susceptibility Mapping (QSM), which is an established Magnetic Resonance Imaging (MRI) technique to study the distribution of iron in the brain. Our main objective is investigatin…
