All Sizes Matter: Improving Volumetric Brain Segmentation on Small Lesions
Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；Deutsches Konsortium für Translationale Krebsforschung (DKTK)（德国转化癌症研究联盟（DKTK））；Helmholtz Center Munich（慕尼黑亥姆霍兹中心）
Ayhan Can Erdur, Daniel Scholz, Josef A. Buchner, Stephanie E. Combs, Daniel Rueckert, Jan C. Peeken
Brain metastases (BMs) are the most frequently occurring brain tumors. The treatment of patients having multiple BMs with stereo tactic radiosurgery necessitates accurate localization of the metastases. Neural networks can assist in this time-consuming and costly task that is typically performed by human experts. Particularly challenging is the detection of small lesions since they are often underrepresented in exist ing approaches. Yet, lesion detection is equally important for all sizes. In this work, we develop an ensemble of neural networks explicitly fo cused on detecting and segmenting small BMs. To accomplish this task, we trained several neural networks focusing on individual aspects of the BM segmentation problem: We use blob loss that specifically addresses the imbalance of lesion instances in terms of size and texture and is, therefore, not biased towards larger lesions. In addition, a model using a subtraction sequence between the T1 and T1 contrast-enhanced sequence focuses on low-contrast lesions. Furthermore, we train additional models only on small lesions. Our experiments demonstrate the utility of the ad ditional blob loss and the subtraction sequence. However, including the specialized small lesion models in the ensemble deteriorates segmentation results. We also find domain-knowledge-inspired postprocessing steps to drastically increase our performance in most experiments. Our approach enables us to submit a competitive challenge entry to the ASNR-MICCAI BraTS Brain Metastasis Challenge 2023.
A Foundation Model for Brain Lesion Segmentation with Mixture of Modality Experts
Imperial College London（帝国理工学院）；UK Dementia Research Institute（英国痴呆症研究所）；Beijing Institute of Technology（北京理工大学）；Capital Medical University（首都医科大学）；Beijing Tiantan Hospital（北京天坛医院）
University of Iceland（冰岛大学）；Landspitali - University Hospital（兰斯皮塔利大学医院）；The Icelandic Heart Association（冰岛心脏协会）；The Johns Hopkins University（约翰斯·霍普金斯大学）
Lesions that appear hyperintense in both Fluid Attenuated Inversion Recovery (FLAIR) and T2-weighted magnetic resonance images (MRIs) of the human brain are common in the brains of the elderly population and may be caused by ischemia or demyelination. Lesions are biomarkers for various neurodegenerative diseases, making accurate quantification of them important for both disease diagnosis and progression. Automatic lesion detection using supervised learning requires manually annotated images, which can often be impractical to acquire. Unsupervised lesion detection, on the other hand, does not r…
Beijing Institute of Technology（北京理工大学）；Peking University Third Hospital（北京大学第三医院）；Deepwise AI Lab（深度智耀人工智能实验室）
Brain lesion segmentation provides a valuable tool for clinical diagnosis, and convolutional neural networks (CNNs) have achieved unprecedented success in the task. Data augmentation is a widely used strategy that improves the training of CNNs, and the design of the augmentation method for brain lesion segmentation is still an open problem. In this work, we propose a simple data augmentation approach, dubbed as CarveMix, for CNN-based brain lesion segmentation. Like other "mix"-based methods, such as Mixup and CutMix, CarveMix stochastically combines two existing labeled images to generate new…
Monitoring the progression of lesions is important for clinical response. Summary statistics such as lesion volume are objective and easy to interpret, which can help clinicians assess lesion growth or decay. CNNs are commonly used in medical image segmentation for their ability to produce useful features within large contexts and their associated efficient iterative patch-based training. Many CNN architectures require hundreds of thousands parameters to yield a good segmentation. In this work, an efficient, computationally inexpensive CNN is implemented to estimate the number of lesion voxels…
Imperial College London（帝国理工学院）；UK Dementia Research Institute（英国痴呆症研究所）
Understanding the intensity characteristics of brain lesions is key for defining image-based biomarkers in neurological studies and for predicting disease burden and outcome. In this work, we present a novel foreground-based generative method for modelling the local lesion characteristics that can both generate synthetic lesions on healthy images and synthesize subject-specific pseudo-healthy images from pathological images. Furthermore, the proposed method can be used as a data augmentation module to generate synthetic images for training brain image segmentation networks. Experiments on mult…
Faculty of Information Technology, University of Science, VNU-HCM（越南胡志明市国家大学科学大学信息技术学院）；SBEI School №1228 ”Lefortovo”（第1228号“列福尔托沃”基础普通教育学校）
In the development of technology, there are increasing cases of brain disease, there are more treatments proposed and achieved a positive result. However, with Brain-Lesion, the early diagnoses can improve the possibility for successful treatment and can help patients recuperate better. From this reason, Brain-Lesion is one of the controversial topics in medical images analysis nowadays. With the improvement of the architecture, there is a variety of methods that are proposed and achieve competitive scores. In this paper, we proposed a technique that uses efficient-net for 3D images, especiall…
University of California, Santa Barbara（加利福尼亚大学圣巴巴拉分校）；University of California, Irvine（加利福尼亚大学欧文分校）
We propose a novel, simple and effective method to integrate lesion prior and a 3D U-Net for improving brain tumor segmentation. First, we utilize the ground-truth brain tumor lesions from a group of patients to generate the heatmaps of different types of lesions. These heatmaps are used to create the volume-of-interest (VOI) map which contains prior information about brain tumor lesions. The VOI map is then integrated with the multimodal MR images and input to a 3D U-Net for segmentation. The proposed method is evaluated on a public benchmark dataset, and the experimental results show that th…
University of Eastern Finland（东芬兰大学）；Charles River Discovery Services（查尔斯河发现服务公司）；Centro Fermi - Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi（费米中心——恩里科·费米物理历史博物馆与研究中心）；Sapienza Università di Roma（罗马第一大学）
We present a fully convolutional neural network (ConvNet), named RatLesNetv2, for segmenting lesions in rodent magnetic resonance (MR) brain images. RatLesNetv2 architecture resembles an autoencoder and it incorporates residual blocks that facilitate its optimization. RatLesNetv2 is trained end to end on three-dimensional images and it requires no preprocessing. We evaluated RatLesNetv2 on an exceptionally large dataset composed of 916 T2-weighted rat brain MRI scans of 671 rats at nine different lesion stages that were used to study focal cerebral ischemia for drug development. In addition, w…
King’s College London（伦敦国王学院）；School of Biomedical Engineering & Imaging Sciences（生物医学工程与成像科学学院）；King’s College Hospital NHS Foundation Trust（国王学院医院国民健康服务基金会信托）；NVIDIA（英伟达）；Dementia Research Centre, UCL Institute of Neurology, UCL（伦敦大学学院痴呆研究中心、伦敦大学学院神经学研究所、伦敦大学学院）；Department of Medical Physics, UCL（伦敦大学学院医学物理系）；Department of Neuroradiology（神经放射科）；St. Thomas’ Hospital（圣托马斯医院）
Brain tissue segmentation from multimodal MRI is a key building block of many neuroimaging analysis pipelines. Established tissue segmentation approaches have, however, not been developed to cope with large anatomical changes resulting from pathology, such as white matter lesions or tumours, and often fail in these cases. In the meantime, with the advent of deep neural networks (DNNs), segmentation of brain lesions has matured significantly. However, few existing approaches allow for the joint segmentation of normal tissue and brain lesions. Developing a DNN for such a joint task is currently …
Flinders University（弗林德斯大学）；Flinders Medical Centre（弗林德斯医疗中心）；Dr Jones & Partners Medical Imaging（琼斯博士及合伙人医疗影像中心）；University of Oxford（牛津大学）；University of Adelaide（阿德莱德大学）
Longitudinal imaging forms an essential component in the management and follow-up of many medical conditions. The presence of lesion changes on serial imaging can have significant impact on clinical decision making, highlighting the important role for automated change detection. Lesion changes can represent anomalies in serial imaging, which implies a limited availability of annotations and a wide variety of possible changes that need to be considered. Hence, we introduce a new unsupervised anomaly detection and localisation method trained exclusively with serial images that do not contain any…
University of Oulu（奥卢大学）；KFUPM（法赫德国王石油与矿业大学）；King Fahd Specialist Hospital Dammam（达曼法赫德国王专科医院）
Introduction: Multiple Sclerosis (MS) is a chronic disease that affects millions of people across the globe. MS can critically affect different organs of the central nervous system such as the eyes, the spinal cord, and the brain. Background: To help physicians in diagnosing MS lesions, computer-aided methods are widely used. In this regard, a considerable research has been carried out in the area of automatic detection and segmentation of MS lesions in magnetic resonance images (MRIs). Methodology: In this study, we review the different approaches that have been used in computer-aided detecti…
AI Virtanen Institute for Molecular Sciences, University of Eastern Finland（东芬兰大学AI·维尔塔宁分子科学研究所）；Charles River Discovery Services（查尔斯河发现服务公司）；Centro Fermi - Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi（费米中心——恩里科·费米物理历史博物馆与研究中心）
Manual segmentation of rodent brain lesions from magnetic resonance images (MRIs) is an arduous, time-consuming and subjective task that is highly important in pre-clinical research. Several automatic methods have been developed for different human brain MRI segmentation, but little research has targeted automatic rodent lesion segmentation. The existing tools for performing automatic lesion segmentation in rodents are constrained by strict assumptions about the data. Deep learning has been successfully used for medical image segmentation. However, there has not been any deep learning approach…
Saratoga High School（萨拉托加高中）；Stanford University（斯坦福大学）
Chest X-rays of coronavirus disease 2019 (COVID-19) patients are frequently obtained to determine the extent of lung disease and are a valuable source of data for creating artificial intelligence models. Most work to date assessing disease severity on chest imaging has focused on segmenting computed tomography (CT) images; however, given that CTs are performed much less frequently than chest X-rays for COVID-19 patients, automated lung lesion segmentation on chest X-rays could be clinically valuable. There currently exists a universal shortage of chest X-rays with ground truth COVID-19 lung le…
King’s College London（伦敦国王学院）；National Hospital for Neurology and Neurosurgery（国家神经内科和神经外科医院）；Thomas Jefferson University（托马斯·杰斐逊大学）；University of Washington（华盛顿大学）
Laser interstitial thermal therapy (LITT) is a novel minimally invasive treatment that is used to ablate intracranial structures to treat mesial temporal lobe epilepsy (MTLE). Region of interest (ROI) segmentation before and after LITT would enable automated lesion quantification to objectively assess treatment efficacy. Deep learning techniques, such as convolutional neural networks (CNNs) are state-of-the-art solutions for ROI segmentation, but require large amounts of annotated data during the training. However, collecting large datasets from emerging treatments such as LITT is impractical.…
Multiple Sclerosis (MS) is a chronic neurological condition characterized by the development of lesions in the white matter of the brain. T2-fluid attenuated inversion recovery (FLAIR) brain magnetic resonance imaging (MRI) provides superior visualization and characterization of MS lesions, relative to other MRI modalities. Follow-up brain FLAIR MRI in MS provides helpful information for clinicians towards monitoring disease progression. In this study, we propose a novel modification to generative adversarial networks (GANs) to predict future lesion-specific FLAIR MRI for MS at fixed time inte…
Meta-Analysis of Transfer Learning for Segmentation of Brain Lesions
Institute for Applied Life Sciences, University of Massachusetts（马萨诸塞大学应用生命科学研究所）；Manning College of Information and Computer Sciences, University of Massachusetts（马萨诸塞大学曼宁信息与计算机科学学院）；Department of Biomedical Engineering, University of Massachusetts（马萨诸塞大学生物医学工程系）；Baystate Medical Center（贝州医疗中心）；UMass Chan Medical School - Baystate Campus（马萨诸塞大学陈医学院贝州校区）；Department of Electrical and Computer Engineering, University of Massachusetts（马萨诸塞大学电气与计算机工程系）；Department of Neurology, Baystate Medical Center（贝州医疗中心神经内科）
SYNAPSE-Net: A Unified Framework with Lesion-Aware Hierarchical Gating for Robust Segmentation of Heterogeneous Brain Lesions
Department of Biomedical Engineering, Bangladesh University of Engineering and Technology（生物医学工程系，孟加拉国工程与技术大学）；Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology（计算机科学与工程系，孟加拉国工程与技术大学）；Department of Electrical and Electronic Engineering, Bangladesh University of Engineering and Technology（电气与电子工程系，孟加拉国工程与技术大学）
Large-kernel Attention for Efficient and Robust Brain Lesion Segmentation
Wellcome Centre for Human Neuroimaging, University College London（伦敦大学学院惠康人类神经成像中心）；NVIDIA（英伟达）；University of California, San Francisco（加州大学旧金山分校）；Helen Wills Neuroscience Institute, University of California, Berkeley（加州大学伯克利分校海伦·威尔斯神经科学研究所）；Stevens Institute for Neuroimaging and Informatics, University of Southern California（南加州大学史蒂文斯神经成像与信息学研究所）
针对 3D 脑病变分割，本文提出 U-Net 的全卷积 transformer 块变体，以大核注意力兼顾长程建模、CNN 参数效率与 transformer 归纳偏置，性能达到先进水平并开源代码。
Brain tissue segmentation from multimodal MRI is a key building block of many neuroscience analysis pipelines. It could also play an important role in many clinical imaging scenarios. Established tissue segmentation approaches have however not been developed to cope with large anatomical changes resulting from pathology. The effect of the presence of brain lesions, for example, on their performance is thus currently uncontrolled and practically unpredictable. Contrastingly, with the advent of deep neural networks (DNNs), segmentation of brain lesions has matured significantly and is achieving …
Technical University of Denmark（丹麦技术大学）；Athinoula A. Martinos Center for Biomedical Imaging（阿西努拉·A·马丁诺斯生物医学成像中心）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Technical University of Munich（慕尼黑工业大学）
In this paper we propose a novel method for the segmentation of longitudinal brain MRI scans of patients suffering from Multiple Sclerosis. The method builds upon an existing cross-sectional method for simultaneous whole-brain and lesion segmentation, introducing subject-specific latent variables to encourage temporal consistency between longitudinal scans. It is very generally applicable, as it does not make any prior assumptions on the scanner, the MRI protocol, or the number and timing of longitudinal follow-up scans. Preliminary experiments on three longitudinal datasets indicate that the …
Adaptable Segmentation Pipeline for Diverse Brain Tumors with Radiomic-Guided Subtyping and Lesion-Wise Model Ensemble
Sheikh Zayed Institute for Pediatric Surgical Innovation（Sheikh Zayed儿童外科创新研究所）；Children’s National Hospital（儿童医院）；University of Washington（华盛顿大学）；Universidad Politécnica de Madrid（马德里理工大学）；CIBER-BBN；ISCIII；School of Medicine and Health Sciences（医学与健康科学学院）
University of Chinese Academy of Sciences（中国科学院大学）；Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院保罗·C·劳特伯生物医学成像研究中心）；Guangdong General Hospital, Guangdong Academy of Medical Sciences（广东省医学科学院广东省人民医院）；Henan Provincial People’s Hospital（河南省人民医院）；Nanchang University（南昌大学）
The morbidity of brain stroke increased rapidly in the past few years. To help specialists in lesion measurements and treatment planning, automatic segmentation methods are critically required for clinical practices. Recently, approaches based on deep learning and methods for contextual information extraction have served in many image segmentation tasks. However, their performances are limited due to the insufficient training of a large number of parameters, which sometimes fail in capturing long-range dependencies. To address these issues, we propose a depthwise separable convolution based X-…
Deep Learning is the newest and the current trend of the machine learning field that paid a lot of the researchers' attention in the recent few years. As a proven powerful machine learning tool, deep learning was widely used in several applications for solving various complex problems that require extremely high accuracy and sensitivity, particularly in the medical field. In general, brain tumor is one of the most common and aggressive malignant tumor diseases which is leading to a very short expected life if it is diagnosed at higher grade. Based on that, brain tumor grading is a very critica…
Self-pruning Graph Neural Network for Predicting Inflammatory Disease Activity in Multiple Sclerosis from Brain MR Images
University of Zurich（苏黎世大学）；Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar, Technical University of Munich（慕尼黑工业大学 rechts der Isar 医院）；Imperial College London（帝国理工学院）；The First Affiliated Hospital of Xi’an Jiaotong University（西安交通大学第一附属医院）
University of Sydney（悉尼大学）；University of New South Wales（新南威尔士大学）；Sydney Neuroimaging Analysis Centre（悉尼神经影像分析中心）
Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system, characterized by the appearance of focal lesions in the white and gray matter that topographically correlate with an individual patient's neurological symptoms and signs. Magnetic resonance imaging (MRI) provides detailed in-vivo structural information, permitting the quantification and categorization of MS lesions that critically inform disease management. Traditionally, MS lesions have been manually annotated on 2D MRI slices, a process that is inefficient and prone to inter-/intra-obser…
Amirkabir University of Technology (Tehran Polytechnic)（阿米尔卡比尔理工大学（德黑兰理工学院））；South Tehran Branch Islamic Azad University (IAU)（伊斯兰阿扎德大学南德黑兰分校）；Arak University of Medical Sciences（阿拉克医科大学）
Magnetic resonance images (MRI) play an important role in supporting and substituting clinical information in the diagnosis of multiple sclerosis (MS) disease by presenting lesion in brain MR images. In this paper, an algorithm for MS lesion segmentation from Brain MR Images has been presented. We revisit the modification of properties of fuzzy -c means algorithms and the canny edge detection. By changing and reformed fuzzy c-means clustering algorithms, and applying canny contraction principle, a relationship between MS lesions and edge detection is established. For the special case of FCM, w…
P-Count: Persistence-based Counting of White Matter Hyperintensities in Brain MRI
Martinos Center for Biomedical Imaging, MGH and Harvard Medical School（马蒂诺斯生物医学成像中心，麻省总医院与哈佛医学院）；Center for Medical Image Computing, University College London（伦敦大学学院医学影像计算中心）；Amsterdam University Medical Center（阿姆斯特丹大学医学中心）；Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital（哥本哈根大学医院丹麦磁共振研究中心）；Computer Science and Artificial Intelligence Laboratory, MIT（麻省理工学院计算机科学与人工智能实验室）
Technical University of Denmark（丹麦技术大学）；Copenhagen University Hospital Hvidovre（哥本哈根大学医院维兹奥勒医院）；Medical Image Analysis Center (MIAC AG)（医学图像分析中心（MIAC AG））；Technical University of Munich（慕尼黑工业大学）；Copenhagen University Hospital Bispebjerg（哥本哈根大学医院比斯佩比约医院）；University of Copenhagen（哥本哈根大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
Here we present a method for the simultaneous segmentation of white matter lesions and normal-appearing neuroanatomical structures from multi-contrast brain MRI scans of multiple sclerosis patients. The method integrates a novel model for white matter lesions into a previously validated generative model for whole-brain segmentation. By using separate models for the shape of anatomical structures and their appearance in MRI, the algorithm can adapt to data acquired with different scanners and imaging protocols without retraining. We validate the method using four disparate datasets, showing rob…
Brain lesions, including stroke and tumours, have a high degree of variability in terms of location, size, intensity and form, making automatic segmentation difficult. We propose an improvement to existing segmentation methods by exploiting the bilateral quasi-symmetry of healthy brains, which breaks down when lesions are present. Specifically, we use nonlinear registration of a neuroimage to a reflected version of itself ("reflective registration") to determine for each voxel its homologous (corresponding) voxel in the other hemisphere. A patch around the homologous voxel is added as a set of…
National Taiwan University（台湾大学）；Santa Clara University（圣克拉拉大学）；QNAP Systems, Inc（威联通科技股份有限公司）；Taipei Hospital（台北医院）；National Taiwan University Hospital（台湾大学附属医院）
Semantic segmentation of medical images with deep learning models is rapidly developed. In this study, we benchmarked state-of-the-art deep learning segmentation algorithms on our clinical stereotactic radiosurgery dataset, demonstrating the strengths and weaknesses of these algorithms in a fairly practical scenario. In particular, we compared the model performances with respect to their sampling method, model architecture, and the choice of loss functions, identifying the suitable settings for their applications and shedding light on the possible improvements.
Graph Theory and GNNs to Unravel the Topographical Organization of Brain Lesions in Variants of Alzheimer's Disease Progression
Sorbonne Université（索邦大学）；Paris Brain Institute - ICM（巴黎脑研究所 - ICM）；CNRS（法国国家科学研究中心）；Inria（法国国家信息与自动化研究所）；Inserm（法国国家健康与医学研究院）；AP-HP（巴黎公共医疗集团）；Hôpital de la Pitié Salpêtrière（皮蒂-萨尔皮特里耶医院）
Deep neural networks have become the gold-standard approach for the automated segmentation of 3D medical images. Their full acceptance by clinicians remains however hampered by the lack of intelligible uncertainty assessment of the provided results. Most approaches to quantify their uncertainty, such as the popular Monte Carlo dropout, restrict to some measure of uncertainty in prediction at the voxel level. In addition not to be clearly related to genuine medical uncertainty, this is not clinically satisfying as most objects of interest (e.g. brain lesions) are made of groups of voxels whose …
TU Munich（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；ETH Zurich（苏黎世联邦理工学院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Brain pathologies can vary greatly in size and shape, ranging from few pixels (i.e. MS lesions) to large, space-occupying tumors. Recently proposed Autoencoder-based methods for unsupervised anomaly segmentation in brain MRI have shown promising performance, but face difficulties in modeling distributions with high fidelity, which is crucial for accurate delineation of particularly small lesions. Here, similar to these previous works, we model the distribution of healthy brain MRI to localize pathologies from erroneous reconstructions. However, to achieve improved reconstruction fidelity at hi…
Geisel School of Medicine at Dartmouth（达特茅斯盖泽尔医学院）；Dartmouth College（达特茅斯学院）；Dartmouth-Hitchcock Medical Center（达特茅斯-希区柯克医学中心）
In this paper, we demonstrate the feasibility and performance of deep residual neural networks for volumetric segmentation of irreversibly damaged brain tissue lesions on T1-weighted MRI scans for chronic stroke patients. A total of 239 T1-weighted MRI scans of chronic ischemic stroke patients from a public dataset were retrospectively analyzed by 3D deep convolutional segmentation models with residual learning, using a novel zoom-in&out strategy. Dice similarity coefficient (DSC), Average symmetric surface distance (ASSD), and Hausdorff distance (HD) of the identified lesions were measured by…
University of Alberta（阿尔伯塔大学）；Alberta Machine Intelligence Institute（阿尔伯塔机器智能研究所）
As one of the leading causes of mortality and disability worldwide, Acute Ischemic Stroke (AIS) occurs when the blood supply to the brain is suddenly interrupted because of a blocked artery. Within seconds of AIS onset, the brain cells surrounding the blocked artery die, which leads to the progression of the lesion. The automated and precise prediction of the existing lesion plays a vital role in the AIS treatment planning and prevention of further injuries. The current standard AIS assessment method, which thresholds the 3D measurement maps extracted from Computed Tomography Perfusion (CTP) i…
Warren Alpert Medical School of Brown University（布朗大学沃伦·阿尔珀特医学院）；Emory University School of Medicine（埃默里大学医学院）；University of Florida School of Medicine（佛罗里达大学医学院）；Brown University（布朗大学）
Automated segmentation of medical imaging is of broad interest to clinicians and machine learning researchers alike. The goal of segmentation is to increase efficiency and simplicity of visualization and quantification of regions of interest within a medical image. Image segmentation is a difficult task because of multiparametric heterogeneity within the images, an obstacle that has proven especially challenging in efforts to automate the segmentation of brain lesions from non-contrast head computed tomography (CT). In this research, we have experimented with multiple available deep learning a…
Discriminative convolutional neural networks (CNNs), for which a voxel-wise conditional Multinoulli distribution is assumed, have performed well in many brain lesion segmentation tasks. For a trained discriminative CNN to be used in clinical practice, the patient's radiological features are inputted into the model, in which case a conditional distribution of segmentations is produced. Capturing the uncertainty of the predictions can be useful in deciding whether to abandon a model, or choose amongst competing models. In practice, however, we never know the ground truth segmentation, and theref…
New Jersey Institute of Technology（新泽西理工学院）；Kessler Foundation（凯斯勒基金会）；Emory University（埃默里大学）；Atlanta VA Medical Center（亚特兰大退伍军人事务医疗中心）；Medical College of Wisconsin（威斯康星医学院）；Rutgers University - Newark（罗格斯大学纽瓦克分校）
We propose a fully 3D multi-path convolutional network to predict stroke lesions from 3D brain MRI images. Our multi-path model has independent encoders for different modalities containing residual convolutional blocks, weighted multi-path feature fusion from different modalities, and weighted fusion modules to combine encoder and decoder features. Compared to existing 3D CNNs like DeepMedic, 3D U-Net, and AnatomyNet, our networks achieves the highest statistically significant cross-validation accuracy of 60.5% on the large ATLAS benchmark of 220 patients. We also test our model on multi-modal…
Stanford University（斯坦福大学）；Oslo University Hospital（奥斯陆大学医院）
Deep learning has proven to be an essential tool for medical image analysis. However, the need for accurately labeled input data, often requiring time- and labor-intensive annotation by experts, is a major limitation to the use of deep learning. One solution to this challenge is to allow for use of coarse or noisy labels, which could permit more efficient and scalable labeling of images. In this work, we develop a lopsided loss function based on entropy regularization that assumes the existence of a nontrivial false negative rate in the target annotations. Starting with a carefully annotated b…
Exploiting learning algorithms under scarce data regimes is a limitation and a reality of the medical imaging field. In an attempt to mitigate the problem, we propose a data augmentation protocol based on generative adversarial networks. We condition the networks at a pixel-level (segmentation mask) and at a global-level information (acquisition environment or lesion type). Such conditioning provides immediate access to the image-label pairs while controlling global class specific appearance of the synthesized images. To stimulate synthesis of the features relevant for the segmentation task, a…
Make-A-Volume: Leveraging Latent Diffusion Models for Cross-Modality 3D Brain MRI Synthesis
The University of Hong Kong（香港大学）；The Chinese University of Hong Kong（香港中文大学）；Qilu Hospital of Shandong University（山东大学齐鲁医院）；Nanyang Technological University（南洋理工大学）
Deep learning and classical computer vision techniques in medical image analysis: Case studies on brain MRI tissue segmentation, lung CT COPD registration, and skin lesion classification
University of Exeter（埃克塞特大学）；Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）；Sorbonne Université（索邦大学）
University of Brescia（布雷西亚大学）；University of Glasgow（格拉斯哥大学）
Many functional and structural neuroimaging studies call for accurate morphometric segmentation of different brain structures starting from image intensity values of MRI scans. Current automatic (multi-) atlas-based segmentation strategies often lack accuracy on difficult-to-segment brain structures and, since these methods rely on atlas-to-scan alignment, they may take long processing times. Recently, methods deploying solutions based on Convolutional Neural Networks (CNNs) are making the direct analysis of out-of-the-scanner data feasible. However, current CNN-based solutions partition the t…
