Stroke Lesion Segmentation in Clinical Workflows: A Modular, Lightweight, and Deployment-Ready Tool
Univ Rennes（里昂大学）；Inria（法国国家信息与自动化技术研究所）；CNRS（法国国家科学研究中心）；Inserm（法国国家健康与医学研究院）；IRISA UMR 6074；Siemens Healthineers（西门子医疗）；CHU Rennes（里昂大学医院）；Centre de Kerpape（凯帕佩中心）
Deep learning frameworks such as nnU-Net achieve state-of-the-art performance in brain lesion segmentation but remain difficult to deploy clinically due to heavy dependencies and monolithic design. We introduce \textit{StrokeSeg}, a modular and lightweight framework that translates research-grade stroke lesion segmentation models into deployable applications. Preprocessing, inference, and postprocessing are decoupled: preprocessing relies on the Anima toolbox with BIDS-compliant outputs, and inference uses ONNX Runtime with \texttt{Float16} quantisation, reducing model size by about 50\%. \textit{StrokeSeg} provides both graphical and command-line interfaces and is distributed as Python scripts and as a standalone Windows executable. On a held-out set of 300 sub-acute and chronic stroke subjects, segmentation performance was equivalent to the original PyTorch pipeline (Dice difference $<10^{-3}$), demonstrating that high-performing research pipelines can be transformed into portable, clinically usable tools.
Acute stroke lesion segmentation tasks are of great clinical interest as they can help doctors make better informed treatment decisions. Magnetic resonance imaging (MRI) is time demanding but can provide images that are considered gold standard for diagnosis. Automated stroke lesion segmentation can provide with an estimate of the location and volume of the lesioned tissue, which can help in the clinical practice to better assess and evaluate the risks of each treatment. We propose a deep learning methodology for acute and sub-acute stroke lesion segmentation using multimodal MR imaging. The p…
New Jersey Institute of Technology（新泽西理工学院）；Kessler Foundation（凯斯勒基金会）；Rutgers – New Jersey Medical School（罗格斯大学新泽西医学院）；Medical College of Wisconsin（威斯康星医学院）；Rutgers University – Newark（罗格斯大学纽瓦克分校）
Automatic identification of brain lesions from magnetic resonance imaging (MRI) scans of stroke survivors would be a useful aid in patient diagnosis and treatment planning. We propose a multi-modal multi-path convolutional neural network system for automating stroke lesion segmentation. Our system has nine end-to-end UNets that take as input 2-dimensional (2D) slices and examines all three planes with three different normalizations. Outputs from these nine total paths are concatenated into a 3D volume that is then passed to a 3D convolutional neural network to output a final lesion mask. We tr…
King’s College London（伦敦国王学院）；Shanghai Jiao Tong University（上海交通大学）
Accurate stroke lesion segmentation plays a pivotal role in stroke rehabilitation research, to provide lesion shape and size information which can be used for quantification of the extent of the stroke and to assess treatment efficacy. Recently, automatic segmentation algorithms using deep learning techniques have been developed and achieved promising results. In this report, we present our stroke lesion segmentation model based on nnU-Net framework, and apply it to the Anatomical Tracings of Lesions After Stroke (ATLAS v2.0) dataset. Furthermore, we describe an effective post-processing strat…
ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset
Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar（右岸医院）；School of Medicine, Technical University of Munich（慕尼黑工业大学医学院）；icometrix（icometrix公司）；University Medical Center Hamburg-Eppendorf（汉堡埃彭多夫大学医学中心）；University of Bern（伯尔尼大学）；ARTORG Center for Biomedical Engineering Research, Univ. of Bern（伯尔尼大学生物医学工程研究ARTORG中心）；University of Southern California（南加州大学）；Chan Division of Occupational Science and Occupational Therapy, University of Southern California（南加州大学陈职业科学与职业治疗系）；TranslaTUM – Central Institute for Translational Cancer Research, Technical University of Munich（慕尼黑工业大学TranslaTUM转化癌症研究中心）
Unsupervised Detection of Post-Stroke Brain Abnormalities
Univ Rennes（里昂大学）；Inria（法国国家信息与自动化技术研究院）；CNRS（法国国家科学研究中心）；Inserm（法国国家医学研究院）；IRISA UMR 6074（里昂信息科学与自动化研究院）；CHU Rennes（里昂大学医院）；Siemens Healthineers（西门子医疗）；Centre de Kerpape（凯帕普中心）
Diffusion-Weighted Magnetic Resonance Imaging (DWI) is widely used for early cerebral infarct detection caused by ischemic stroke. Manual segmentation is done by a radiologist as a common clinical process, nonetheless, challenges of cerebral infarct segmentation come from low resolution and uncertain boundaries. Many segmentation techniques have been proposed and proved by manual segmentation as gold standard. In order to reduce human error in research operation and clinical process, we adopt a semi-automatic segmentation as gold standard using Fluid-Attenuated Inversion-Recovery (FLAIR) Magne…
MIT（麻省理工学院）；Philips Research North America（飞利浦北美研究院）
We present a fully convolutional neural network for segmenting ischemic stroke lesions in CT perfusion images for the ISLES 2018 challenge. Treatment of stroke is time sensitive and current standards for lesion identification require manual segmentation, a time consuming and challenging process. Automatic segmentation methods present the possibility of accurately identifying lesions and improving treatment planning. Our model is based on the PSPNet, a network architecture that makes use of pyramid pooling to provide global and local contextual information. To learn the varying shapes of the le…
Ischemic Stroke Lesion Segmentation challenge (ISLES 2022) offers a platform for researchers to compare their solutions to 3D segmentation of ischemic stroke regions from 3D MRIs. In this work, we describe our solution to ISLES 2022 segmentation task. We re-sample all images to a common resolution, use two input MRI modalities (DWI and ADC) and train SegResNet semantic segmentation network from MONAI. The final submission is an ensemble of 15 models (from 3 runs of 5-fold cross validation). Our solution (team name NVAUTO) achieves the top place in terms of Dice metric (0.824), and overall rank…
Automatic and accurate lesion segmentation is critical for clinically estimating the lesion statuses of stroke diseases and developing appropriate diagnostic systems. Although existing methods have achieved remarkable results, further adoption of the models is hindered by: (1) inter-class indistinction, the normal brain tissue resembles the lesion in appearance. (2) intra-class inconsistency, large variability exists between different areas of the lesion. To solve these challenges in stroke segmentation, we propose a novel method, namely Attention Guided Multiscale Recovery framework (AGMR-Net…
University of Minho（米尼奥大学）；Bern University Hospital（伯尔尼大学医院）
Predicting the final ischaemic stroke lesion provides crucial information regarding the volume of salvageable hypoperfused tissue, which helps physicians in the difficult decision-making process of treatment planning and intervention. Treatment selection is influenced by clinical diagnosis, which requires delineating the stroke lesion, as well as characterising cerebral blood flow dynamics using neuroimaging acquisitions. Nonetheless, predicting the final stroke lesion is an intricate task, due to the variability in lesion size, shape, location and the underlying cerebral haemodynamic processe…
Laboratory of Imaging, Vision and Artificial Intelligence（成像、视觉与人工智能实验室）
Delineating infarcted tissue in ischemic stroke lesions is crucial to determine the extend of damage and optimal treatment for this life-threatening condition. However, this problem remains challenging due to high variability of ischemic strokes' location and shape. Recently, fully-convolutional neural networks (CNN), in particular those based on U-Net, have led to improved performances for this task. In this work, we propose a novel architecture that improves standard U-Net based methods in three important ways. First, instead of combining the available image modalities at the input, each of …
University of Chinese Academy of Sciences（中国科学院大学）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；Guizhou Provincial People’s Hospital（贵州省人民医院）；Henan Provincial People’s Hospital（河南省人民医院）；Shenzhen University（深圳大学）
Segmenting stroke lesions from T1-weighted MR images is of great value for large-scale stroke rehabilitation neuroimaging analyses. Nevertheless, there are great challenges with this task, such as large range of stroke lesion scales and the tissue intensity similarity. The famous encoder-decoder convolutional neural network, which although has made great achievements in medical image segmentation areas, may fail to address these challenges due to the insufficient uses of multi-scale features and context information. To address these challenges, this paper proposes a Cross-Level fusion and Cont…
GlaxoSmithKline（葛兰素史克）；University College London（伦敦大学学院）；Imperial College London（帝国理工学院）
One third of stroke survivors have language difficulties. Emerging evidence suggests that their likelihood of recovery depends mainly on the damage to language centers. Thus previous research for predicting language recovery post-stroke has focused on identifying damaged regions of the brain. In this paper, we introduce a novel method where we only make use of stitched 2-dimensional cross-sections of raw MRI scans in a deep convolutional neural network setup to predict language recovery post-stroke. Our results show: a) the proposed model that only uses MRI scans has comparable performance to …
National University of Singapore（新加坡国立大学）；NIT, Tiruchirappalli（蒂鲁吉拉伯利国家技术学院）
Ischemic stroke occurs through a blockage of clogged blood vessels supplying blood to the brain. Segmentation of the stroke lesion is vital to improve diagnosis, outcome assessment and treatment planning. In this work, we propose a segmentation model with adversarial learning for ischemic lesion segmentation. We adopt U-Net with skip connection and dropout as segmentation baseline network and a fully connected network (FCN) as discriminator network. Discriminator network consists of 5 convolution layers followed by leaky-ReLU and an upsampling layer to rescale the output to the size of the inp…
CT perfusion (CTP) has been used to triage ischemic stroke patients in the early stage, because of its speed, availability, and lack of contraindications. Perfusion parameters including cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time (MTT) and time of peak (Tmax) could also be computed from CTP data. However, CTP data or the perfusion parameters, are ambiguous to locate the infarct core or tissue at risk (penumbra), which is normally confirmed by the follow-up Diffusion Weighted Imaging (DWI) or perfusion diffusion mismatch. In this paper, we propose a novel generativ…
Nanjing University of Information Science & Technology（南京信息工程大学）
Cerebrovascular accident, or commonly known as stroke, is an acute disease with extreme impact on patients and healthcare systems and is the second largest cause of death worldwide. Fast and precise stroke lesion detection and location is an extreme important process with regards to stroke diagnosis, treatment, and prognosis. Except from the manual segmentation approach, machine learning based segmentation methods are the most promising ones when considering efficiency and accuracy, and convolutional neural network based models are the first of its kind. However, most of these neural network m…
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 Bologna（博洛尼亚大学）；University of Calabria（卡拉布里亚大学）
We present a new system based on tracking the temporal evolution of stroke lesions using an image registration technique on CT exams of the patient's brain. The system is able to compare past CT exams with the most recent one related to stroke event in order to evaluate past lesions which are not related to stroke. Then, it can compare recent CT exams related to the current stroke for assessing the evolution of the lesion over time. A new similarity measure is also introduced for the comparison of the source and target images during image registration. It will result in a cheaper, faster and m…
Deep learning based disease detection and segmentation algorithms promise to improve many clinical processes. However, such algorithms require vast amounts of annotated training data, which are typically not available in the medical context due to data privacy, legal obstructions, and non-uniform data acquisition protocols. Synthetic databases with annotated pathologies could provide the required amounts of training data. We demonstrate with the example of ischemic stroke that an improvement in lesion segmentation is feasible using deep learning based augmentation. To this end, we train differ…
University of Minho（米尼奥大学）；University Hospital Inselspital and University of Bern（Inselspital大学医院与伯尔尼大学）；University of Bern（伯尔尼大学）
Stroke is the second most common cause of death in developed countries, where rapid clinical intervention can have a major impact on a patient's life. To perform the revascularization procedure, the decision making of physicians considers its risks and benefits based on multi-modal MRI and clinical experience. Therefore, automatic prediction of the ischemic stroke lesion outcome has the potential to assist the physician towards a better stroke assessment and information about tissue outcome. Typically, automatic methods consider the information of the standard kinetic models of diffusion and p…
Local Gamma Augmentation for Ischemic Stroke Lesion Segmentation on MRI
University of Copenhagen（哥本哈根大学）；Cerebriu A/S（Cerebriu公司）；Rigshospitalet, Copenhagen, Denmark（哥本哈根大学医院）；Pioneer Centre for Artificial Intelligence, University of Copenhagen（哥本哈根大学人工智能先锋中心）
Nankai University（南开大学）；Guilin University of Electronic Technology（桂林电子科技大学）；Tianjin Huanhu Hospital（天津市环湖医院）
Ischemic stroke is a common disease in the elderly population, which can cause long-term disability and even death. However, the time window for treatment of ischemic stroke in its acute stage is very short. To fast localize and quantitively evaluate the acute ischemic stroke (AIS) lesions, many deep-learning-based lesion segmentation methods have been proposed in the literature, where a deep convolutional neural network (CNN) was trained on hundreds of fully labeled subjects with accurate annotations of AIS lesions. Despite that high segmentation accuracy can be achieved, the accurate labels …
Fudan University（复旦大学）；Shanghai Center for Brain Science and Brain-inspired Technology（上海脑科学与类脑研究中心）
There are considerable interests in automatic stroke lesion segmentation on magnetic resonance (MR) images in the medical imaging field, as stroke is an important cerebrovascular disease. Although deep learning-based models have been proposed for this task, generalizing these models to unseen sites is difficult due to not only the large inter-site discrepancy among different scanners, imaging protocols, and populations, but also the variations in stroke lesion shape, size, and location. To tackle this issue, we introduce a self-adaptive normalization network, termed SAN-Net, to achieve adaptiv…
Domain-Agnostic Stroke Lesion Segmentation Using Physics-Constrained Synthetic Data
Department of Imaging Neuroscience, University College London（影像神经科学系，伦敦大学学院）；Institute of Cognitive Neuroscience, University College London（认知神经科学研究所，伦敦大学学院）
University of Electronic Science and Technology of China（电子科技大学）；SenseTime Research（商汤科技研究院）；Huashan Hospital, Fudan University（复旦大学附属华山医院）；Fudan University（复旦大学）；Jing’an District Centre Hospital of Shanghai（上海市静安区中心医院）
Ischemic stroke lesion segmentation from Computed Tomography Perfusion (CTP) images is important for accurate diagnosis of stroke in acute care units. However, it is challenged by low image contrast and resolution of the perfusion parameter maps, in addition to the complex appearance of the lesion. To deal with this problem, we propose a novel framework based on synthesized pseudo Diffusion-Weighted Imaging (DWI) from perfusion parameter maps to obtain better image quality for more accurate segmentation. Our framework consists of three components based on Convolutional Neural Networks (CNNs) a…
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-…
Automated Segmentation of Ischemic Stroke Lesions in Non-Contrast Computed Tomography Images for Enhanced Treatment and Prognosis
Kwame Nkrumah University of Science and Technology（库马西科技大学）；Department of Computer Engineering（计算机工程系）；Kumasi Centre for Collaborative Research in Tropical Medicine（库马西热带医学协作研究中心）；Komfo Anokye Teaching Hospital（科莫福·阿诺耶教学医院）
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…
Philips Research North America（飞利浦北美研究院）；MIT（麻省理工学院）
Infarcted brain tissue resulting from acute stroke readily shows up as hyperintense regions within diffusion-weighted magnetic resonance imaging (DWI). It has also been proposed that computed tomography perfusion (CTP) could alternatively be used to triage stroke patients, given improvements in speed and availability, as well as reduced cost. However, CTP has a lower signal to noise ratio compared to MR. In this work, we investigate whether a conditional mapping can be learned by a generative adversarial network to map CTP inputs to generated MR DWI that more clearly delineates hyperintense re…
Nankai University（南开大学）；Tianjin Huanhu Hospital（天津市环湖医院）；the University of Aizu（会津大学）；Tianjin Medical University（天津医科大学）；College of Electronic Information and Optical Engineering, Nankai University（南开大学电子信息与光学工程学院）；School of Computer Science and Engineering, the University of Aizu（会津大学计算机科学与工程学院）；School of Basic Medical Sciences, Tianjin Medical University（天津医科大学基础医学院）；Department of Medical Imaging, Tianjin Huanhu Hospital（天津市环湖医院医学影像科）；Key Laboratory for Cerebral Artery and Neural Degeneration of Tianjin（天津市脑血管及神经变性重点实验室）；Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology（天津市光电传感器与传感网络技术重点实验室）
The patient with ischemic stroke can benefit most from the earliest possible definitive diagnosis. While the high quality medical resources are quite scarce across the globe, an automated diagnostic tool is expected in analyzing the magnetic resonance (MR) images to provide reference in clinical diagnosis. In this paper, we propose a deep learning method to automatically segment ischemic stroke lesions from multi-modal MR images. By using atrous convolution and global convolution network, our proposed residual-structured fully convolutional network (Res-FCN) is able to capture features from la…
Dual-Encoder Transformer-Based Multimodal Learning for Ischemic Stroke Lesion Segmentation Using Diffusion MRI
Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University（麻醉学、围术期与疼痛医学系，斯坦福大学）；Department of Biomedical Sciences, Seoul National University（生物医学科学系，首尔国立大学）；Department of Computer Engineering, National University of Sciences and Technology (NUST)（计算机工程系，国立科学与技术大学（NUST））；Department of Computer Science, The University of Alabama（计算机科学系，阿拉巴马大学）；Department of Computer Science, Hanyang University（计算机科学系，翰阳大学）
Stroke Locus Net: Occluded Vessel Localization from MRI Modalities
Department of Electrical Engineering, College of Engineering, Qatar University, Doha, Qatar（电气工程系，工程学院，卡塔尔大学，多哈，卡塔尔）；Department of Mathematics and Statistics, College of Arts and Sciences, Qatar University, Doha, Qatar（数学与统计学系，艺术与科学学院，卡塔尔大学，多哈，卡塔尔）
本研究提出端到端深度学习流水线 Stroke Locus Net，结合 nnUNet 分割、动脉图谱与 pGAN 生成，仅用 MRI 扫描实现闭塞血管定位，为更快速的中风诊断提供潜力。
Generalizable automated ischaemic stroke lesion segmentation with vision transformers
University College London（伦敦大学学院）；UCL Queen Square Institute of Neurology（伦敦大学学院女王广场神经病学研究所）；National Hospital for Neurology and Neurosurgery（国家神经病学与神经外科医院）；King’s College London（伦敦国王学院）；Institut des Maladies Neurodégénératives（神经退行性疾病研究所）；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）；University of Bordeaux（波尔多大学）
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）
Shenzhen University（深圳大学）；University of Sydney（悉尼大学）；Northwestern Polytechnical University（西北工业大学）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）
Assessing the location and extent of lesions caused by chronic stroke is critical for medical diagnosis, surgical planning, and prognosis. In recent years, with the rapid development of 2D and 3D convolutional neural networks (CNN), the encoder-decoder structure has shown great potential in the field of medical image segmentation. However, the 2D CNN ignores the 3D information of medical images, while the 3D CNN suffers from high computational resource demands. This paper proposes a new architecture called dimension-fusion-UNet (D-UNet), which combines 2D and 3D convolution innovatively in the…
Ischemic Stroke Segmentation and Net Water Uptake Quantification on Multicenter Non-Contrast CT Using Supervised Target-Domain Adaptation
University Medical Center Hamburg-Eppendorf（汉堡-埃彭多夫大学医学中心）；University Hospital Marburg（马尔堡大学医院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；HELIOS Medical Center Schwerin（HELIOS什未林医疗中心）；MSH Medical School Hamburg（汉堡MSH医学院）；MSH Research, Development and Innovation GmbH（MSH研究开发与创新有限公司）；MSH Medical University of Applied Sciences and Medical University（MSH应用科学医科大学与医科大学）
Acute ischemic stroke lesion segmentation in non-contrast CT images using 3D convolutional neural networks
Novosibirsk State University（新西伯利亚国立大学）；International Tomography Center SB RAS（西伯利亚分院国际断层扫描中心）；Sobolev Institute of Mathematics SB RAS（西伯利亚分院索博列夫数学研究所）
State-of-the-Art Stroke Lesion Segmentation at 1/1000th of Parameters
Center for Data Science, Nell Hodgson Woodruff School of Nursing（内尔·霍奇森·伍德拉夫护理学院数据科学中心）；Emory University（埃默里大学）；University of South Carolina（南卡罗来纳大学）；Georgia State University（佐治亚州立大学）
Comparative evaluation of training strategies using partially labelled datasets for segmentation of white matter hyperintensities and stroke lesions in FLAIR MRI
