Glioblastoma is one of the most aggressive and deadliest types of brain cancer, with low survival rates compared to other types of cancer. Analysis of Magnetic Resonance Imaging (MRI) scans is one of the most effective methods for the diagnosis and treatment of brain cancers such as glioblastoma. Accurate tumor segmentation in MRI images is often required for treatment planning and risk assessment of treatment methods. Here, we propose a novel pipeline, Brain Radiology Aided by Intelligent Neural NETworks (BRAINNET), which leverages MaskFormer, a vision transformer model, and generates robust tumor segmentation maks. We use an ensemble of nine predictions from three models separately trained on each of the three orthogonal 2D slice directions (axial, sagittal, and coronal) of a 3D brain MRI volume. We train and test our models on the publicly available UPenn-GBM dataset, consisting of 3D multi-parametric MRI (mpMRI) scans from 611 subjects. Using Dice coefficient (DC) and 95% Hausdorff distance (HD) for evaluation, our models achieved state-of-the-art results in segmenting all three different tumor regions -- tumor core (DC = 0.894, HD = 2.308), whole tumor (DC = 0.891, HD = 3.552), and enhancing tumor (DC = 0.812, HD = 1.608).
The Rio Hortega University Hospital Glioblastoma dataset: a comprehensive collection of preoperative, early postoperative and recurrence MRI scans (RHUH-GBM)
Future Processing Healthcare（未来医疗处理公司）；Silesian University of Technology（西里西亚工业大学）；Medical University of Silesia in Katowice（卡托维兹西里西亚医科大学）；ZSM Chorzów（霍茹夫ZSM医院）；University Clinical Centre（大学临床中心）；Roche Pharmaceutical Research & Early Development（罗氏制药研究与早期开发部）
Tumor burden assessment by magnetic resonance imaging (MRI) is central to the evaluation of treatment response for glioblastoma. This assessment is complex to perform and associated with high variability due to the high heterogeneity and complexity of the disease. In this work, we tackle this issue and propose a deep learning pipeline for the fully automated end-to-end analysis of glioblastoma patients. Our approach simultaneously identifies tumor sub-regions, including the enhancing tumor, peritumoral edema and surgical cavity in the first step, and then calculates the volumetric and bidimens…
Reutlingen University（罗伊特林根大学）；Menoufia University（梅努菲亚大学）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）
Glioblastomas are the most aggressive fast-growing primary brain cancer which originate in the glial cells of the brain. Accurate identification of the malignant brain tumor and its sub-regions is still one of the most challenging problems in medical image segmentation. The Brain Tumor Segmentation Challenge (BraTS) has been a popular benchmark for automatic brain glioblastomas segmentation algorithms since its initiation. In this year, BraTS 2021 challenge provides the largest multi-parametric (mpMRI) dataset of 2,000 pre-operative patients. In this paper, we propose a new aggregation of two …
TumorFlow: Physics-Guided Longitudinal MRI Synthesis of Glioblastoma Growth
Technical University of Munich (TUM), Germany（慕尼黑技术大学（TUM））；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心）；AI for Image-Guided Diagnosis and Therapy（图像引导诊断与治疗的AI）；Chair for AI in Healthcare and Medicine, TUM and TUM University Hospital, Munich, Germany（医疗与医学中的AI主任，慕尼黑技术大学及慕尼黑大学医院）
This thesis focuses on the research and development of the Hemodynamic Tissue Signature (HTS) method: an unsupervised machine learning approach to describe the vascular heterogeneity of glioblastomas by means of perfusion MRI analysis. The HTS builds on the concept of habitats. An habitat is defined as a sub-region of the lesion with a particular MRI profile describing a specific physiological behavior. The HTS method delineates four habitats within the glioblastoma: the High Angiogenic Tumor (HAT) habitat, as the most perfused region of the enhancing tumor; the Low Angiogenic Tumor (LAT) habi…
Segmentation of glioblastomas in early post-operative multi-modal MRI with deep neural networks
SINTEF Digital（SINTEF数字研究所）；Norwegian University of Science and Technology（挪威科技大学）；Amsterdam University Medical Centers（阿姆斯特丹大学医学中心）；Twee Steden Hospital（双城医院）；University College London（伦敦大学学院）
Quantifying intra-tumoral genetic heterogeneity of glioblastoma toward precision medicine using MRI and a data-inclusive machine learning algorithm
Georgia Institute of Technology（佐治亚理工学院）；Columbia University Medical Center（哥伦比亚大学医学中心）；Mayo Clinic Arizona（妙佑医疗国际亚利桑那分院）；Barrow Neurological Institute - St. Joseph’s Hospital and Medical Center（巴罗神经学研究所 - 圣约瑟夫医院和医疗中心）；University of Naples “Federico II”（那不勒斯“费德里科二世”大学）
Center for Biomedical Image Computing and Analytics（生物医学图像计算与分析中心）；University of Pennsylvania（宾夕法尼亚大学）；Comsats University Islamabad（COMSATS伊斯兰堡大学）；Wake Forest School of Medicine（维克森林医学院）；Bowman Gray Center for Medical Education（鲍曼·格雷医学教育中心）
Both radiographic (Rad) imaging, such as multi-parametric magnetic resonance imaging, and digital pathology (Path) images captured from tissue samples are currently acquired as standard clinical practice for glioblastoma tumors. Both these data streams have been separately used for diagnosis and treatment planning, despite the fact that they provide complementary information. In this research work, we aimed to assess the potential of both Rad and Path images in combination and comparison. An extensive set of engineered features was extracted from delineated tumor regions in Rad images, compris…
Multi-View MRI Approach for Classification of MGMT Methylation in Glioblastoma Patients
National Center for Artificial Intelligence (NCAI), SDAIA, Riyadh, Saudi Arabia（国家人工智能中心（NCAI）、SDAIA、沙特阿拉伯利雅得）；King Abdullah University of Science and Technology (KAUST), CEMSE Division, Thuwal, Saudi Arabia（国王阿卜杜勒阿齐兹大学科学与技术学院（KAUST）、CEMSE部门、沙特阿拉伯图瓦尔）；Aramco Research Center, R&D Center Department, Dhahran, Saudi Arabia（阿姆科研究中心、研发中心部门、沙特阿拉伯达黑兰）
Glioblastoma Overall Survival Prediction With Vision Transformers
Department of Electronic, Information and Bioengineering, Politecnico di Milano（电子、信息与生物工程系，米兰理工大学）；Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta（放射学系，IRCCS神经科学卡洛·贝斯塔研究所）
Pakistan Institute of Engineering and Applied Sciences（巴基斯坦工程与应用科学学院）
Brain tumors analysis is important in timely diagnosis and effective treatment to cure patients. Tumor analysis is challenging because of tumor morphology like size, location, texture, and heteromorphic appearance in the medical images. In this regard, a novel two-phase deep learning-based framework is proposed to detect and categorize brain tumors in magnetic resonance images (MRIs). In the first phase, a novel deep boosted features and ensemble classifiers (DBF-EC) scheme is proposed to detect tumor MRI images from healthy individuals effectively. The deep boosted feature space is achieved t…
Mohamed Bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Glioblastoma is a common brain malignancy that tends to occur in older adults and is almost always lethal. The effectiveness of chemotherapy, being the standard treatment for most cancer types, can be improved if a particular genetic sequence in the tumor known as MGMT promoter is methylated. However, to identify the state of the MGMT promoter, the conventional approach is to perform a biopsy for genetic analysis, which is time and effort consuming. A couple of recent publications proposed a connection between the MGMT promoter state and the MRI scans of the tumor and hence suggested the use o…
The concept of tumor field effect implies that cancer is a systemic disease with its impact way beyond the visible tumor confines. For instance, in Glioblastoma (GBM), an aggressive brain tumor, the increase in intracranial pressure due to tumor burden often leads to brain herniation and poor outcomes. Our work is based on the rationale that highly aggressive tumors tend to grow uncontrollably, leading to pronounced biomechanical tissue deformations in the normal parenchyma, which when combined with local morphological differences in the tumor confines on MRI scans, will comprehensively captur…
Glioblastomas are the most common malignant brain tumors in adults. Approximately 200000 people die each year from Glioblastoma in the world. Glioblastoma patients have a median survival of 12 months with optimal therapy and about 4 months without treatment. Glioblastomas appear as heterogeneous necrotic masses with irregular peripheral enhancement, surrounded by vasogenic edema. The current standard of care includes surgical resection, radiotherapy and chemotherapy, which require accurate segmentation of brain tumor subregions. For effective treatment planning, it is vital to identify the met…
College of Biomedical Engineering, Rangsit University（兰实大学生物医学工程学院）
Automated medical image segmentation is a priority research area for computational methods. In particular, detection of cancerous tumors represents a current challenge in this area with potential for real-world impact. This paper describes a method developed in response to the 2019 Kidney Tumor Segmentation Challenge (KiTS19). Axial computed tomography (CT) scans from 210 kidney cancer patients were used to develop and evaluate this automatic segmentation method based on a logical ensemble of fully-convolutional network (FCN) architectures, followed by volumetric validation. Data was pre-proce…
University of Minho（米尼奥大学）；University Hospital Inselspital（因塞尔施皮塔尔大学医院）；University of Bern（伯尔尼大学）
Glioblastoma Multiforme is a high grade, very aggressive, brain tumor, with patients having a poor prognosis. Lower grade gliomas are less aggressive, but they can evolve into higher grade tumors over time. Patient management and treatment can vary considerably with tumor grade, ranging from tumor resection followed by a combined radio- and chemotherapy to a "wait and see" approach. Hence, tumor grading is important for adequate treatment planning and monitoring. The gold standard for tumor grading relies on histopathological diagnosis of biopsy specimens. However, this procedure is invasive, …
Case Western Reserve University（凯斯西储大学）；Cleveland Clinic（克利夫兰诊所）
A significant challenge in Glioblastoma (GBM) management is identifying pseudo-progression (PsP), a benign radiation-induced effect, from tumor recurrence, on routine imaging following conventional treatment. Previous studies have linked tumor lobar presence and laterality to GBM outcomes, suggesting that disease etiology and progression in GBM may be impacted by tumor location. Hence, in this feasibility study, we seek to investigate the following question: Can tumor location on treatment-naïve MRI provide early cues regarding likelihood of a patient developing pseudo-progression versus tumor…
University of Cambridge（剑桥大学）；Shanghai General Hospital（上海市第一人民医院）；Shanghai Jiao Tong University（上海交通大学）；Southern University of Science and Technology（南方科技大学）；University of Bath（巴斯大学）
We present an Expectation-Maximization (EM) Regularized Deep Learning (EMReDL) model for weakly supervised tumor segmentation. The proposed framework is tailored to glioblastoma, a type of malignant tumor characterized by its diffuse infiltration into the surrounding brain tissue, which poses significant challenge to treatment target and tumor burden estimation using conventional structural MRI. Although physiological MRI provides more specific information regarding tumor infiltration, the relatively low resolution hinders a precise full annotation. This has motivated us to develop a weakly su…
Differentiating tumor progression (TP) from treatment-related necrosis (TN) is critical for clinical management decisions in glioblastoma (GBM). Dynamic FDG PET (dPET), an advance from traditional static FDG PET, may prove advantageous in clinical staging. dPET includes novel methods of a model-corrected blood input function that accounts for partial volume averaging to compute parametric maps that reveal kinetic information. In a preliminary study, a convolution neural network (CNN) was trained to predict classification accuracy between TP and TN for $35$ brain tumors from $26$ subjects in th…
College of Electronic Science and Engineering, Jilin University（吉林大学电子科学与工程学院）；Wake Forest School of Medicine（维克森林医学院）
Pseudoprogression (PsP) occurs in 20-30% of patients with glioblastoma multiforme (GBM) after receiving the standard treatment. In the course of post-treatment magnetic resonance imaging (MRI), PsP exhibits similarities in shape and intensity to the true tumor progression (TTP) of GBM. So, these similarities pose challenges on the differentiation of these types of progression and hence the selection of the appropriate clinical treatment strategy. In this paper, we introduce DC-AL GAN, a novel feature learning method based on deep convolutional generative adversarial network (DCGAN) and AlexNet…
Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-re…
An Ensemble Approach for Brain Tumor Segmentation and Synthesis
Paul G. Allen School of Computer Science, University of Washington（华盛顿大学保罗G.艾伦计算机科学学院）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；Department of Bioengineering, University of Washington（华盛顿大学生物工程系）；Department of Electrical and Computer Engineering, University of Washington（华盛顿大学电气与计算机工程系）；Department of Mechanical Engineering, University of Washington（华盛顿大学机械工程系）；Watauga High School（沃托加高中）；Department of Neurological Surgery, University of Washington（华盛顿大学神经外科系）
Department of Health Technology, Technical University of Denmark（丹麦技术大学健康技术系）；Department of Oncology, The Finsen Center, Rigshospitalet（哥本哈根大学医院芬森中心肿瘤学系）；Department of Clinical Physiology, Nuclear Medicine and PET, Center of Diagnostic Investigation, Rigshospitalet（哥本哈根大学医院诊断研究中心临床生理学、核医学与正电子发射断层扫描科）；Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School（哈佛医学院麻省总医院Athinoula A. Martinos生物医学成像中心）
Survival prediction models can potentially be used to guide treatment of glioblastoma patients. However, currently available MR imaging biomarkers holding prognostic information are often challenging to interpret, have difficulties generalizing across data acquisitions, or are only applicable to pre-operative MR data. In this paper we aim to address these issues by introducing novel imaging features that can be automatically computed from MR images and fed into machine learning models to predict patient survival. The features we propose have a direct biological interpretation: They measure the…
Decoding MGMT Methylation: A Step Towards Precision Medicine in Glioblastoma
National University of Computer and Emerging Sciences（国立计算机与新兴科学大学）；Oryx Universal College with Liverpool John Moores University（羚羊环球学院与利物浦约翰摩尔斯大学）；Al-Balqa Applied University（巴尔卡应用大学）
Glioblastoma, an aggressive brain cancer, is amongst the most lethal of all cancers. Expression of the O6-methylguanine-DNA-methyltransferase (MGMT) gene in glioblastoma tumor tissue is of clinical importance as it has a significant effect on the efficacy of Temozolomide, the primary chemotherapy treatment administered to glioblastoma patients. Currently, MGMT methylation is determined through an invasive brain biopsy and subsequent genetic analysis of the extracted tumor tissue. In this work, we present novel Bayesian classifiers that make probabilistic predictions of MGMT methylation status …
Accurate segmentation of different sub-regions of gliomas including peritumoral edema, necrotic core, enhancing and non-enhancing tumor core from multimodal MRI scans has important clinical relevance in diagnosis, prognosis and treatment of brain tumors. However, due to the highly heterogeneous appearance and shape, segmentation of the sub-regions is very challenging. Recent development using deep learning models has proved its effectiveness in the past several brain segmentation challenges as well as other semantic and medical image segmentation problems. Most models in brain tumor segmentati…
University of Freiburg（弗赖堡大学）；Collaborative Research Institute Intelligent Oncology (CRIION)（智能肿瘤学合作研究院（CRIION））；Facultad Latinoamericana de Ciencias Sociales (FLACSO)（拉丁美洲社会科学学院（FLACSO））；National Scientific and Technical Research Council (CONICET)（国家科学技术研究委员会（CONICET））；University Hospital of Munich (LMU)（慕尼黑大学附属医院（LMU））；Medical Center Freiburg（弗赖堡医学中心）
Cancer detection and classification from gigapixel whole slide images of stained tissue specimens has recently experienced enormous progress in computational histopathology. The limitation of available pixel-wise annotated scans shifted the focus from tumor localization to global slide-level classification on the basis of (weakly-supervised) multiple-instance learning despite the clinical importance of local cancer detection. However, the worse performance of these techniques in comparison to fully supervised methods has limited their usage until now for diagnostic interventions in domains of …
Glioblastoma Multiforme is a very aggressive type of brain tumor. Due to spatial and temporal intra-tissue inhomogeneity, location and the extent of the cancer tissue, it is difficult to detect and dissect the tumor regions. In this paper, we propose survival prognosis models using four regressors operating on handcrafted image-based and radiomics features. We hypothesize that the radiomics shape features have the highest correlation with survival prediction. The proposed approaches were assessed on the Brain Tumor Segmentation (BraTS-2020) challenge dataset. The highest accuracy of image feat…
Indian Statistical Institute（印度统计研究所）；DAV Institute of Engineering and Technology（DAV工程技术学院）
Inspired by the success of Convolutional Neural Networks (CNN), we develop a novel Computer Aided Detection (CADe) system using CNN for Glioblastoma Multiforme (GBM) detection and segmentation from multi channel MRI data. A two-stage approach first identifies the presence of GBM. This is followed by a GBM localization in each "abnormal" MR slice. As part of the CADe system, two CNN architectures viz. Classification CNN (C-CNN) and Detection CNN (D-CNN) are employed. The CADe system considers MRI data consisting of four sequences ($T_1$, $T_{1c},$ $T_2$, and $T_{2FLAIR}$) as input, and automati…
Towards a deep learning approach for classifying treatment response in glioblastomas
Institute for Systems and Robotics - Lisbon and Department of Bioengineering of Instituto Superior Técnico（系统与机器人研究所 - 里斯本及 Instituto Superior Técnico 生物工程系）；Hospital da Luz Learning Health（Luz医院学习健康中心）；Imaging Department, Hospital da Luz（Luz医院影像部门）
Postoperative glioblastoma segmentation: Development of a fully automated pipeline using deep convolutional neural networks and comparison with currently available models
Río Hortega University Hospital（里奥·奥尔特加大学医院）；Universidad de Valladolid（巴利亚多利德大学）；Center for Biomedical Research in Network of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN)（生物工程、生物材料和纳米医学网络生物医学研究中心）；Albacete University Hospital（阿尔瓦塞特大学医院）；La Princesa University Hospital（拉普林塞萨大学医院）；UiT The Arctic University of Norway（挪威北极大学）；University Hospital of North Norway（北挪威大学医院）；St. Olavs University Hospital（圣奥拉夫大学医院）；Norwegian University of Science and Technology（挪威科技大学）；St. Olavs Hospital, Trondheim University Hospital（圣奥拉夫医院，特隆赫姆大学医院）；de Octubre University Hospital (i + 12)（10月12日大学医院）；Complutense University（马德里康普顿斯大学）；Instituto de Investigación Sanitaria, 12 de Octubre University Hospital (i + 12)（10月12日大学医院卫生研究所）；Institute for Research in Mathematics (IMUVA), University of Valladolid（巴利亚多利德大学数学研究所）
Patient-specific prediction of glioblastoma growth via reduced order modeling and neural networks
Mathematics Area, mathLab, SISSA（SISSA数学区mathLab）；Dipartimento di Matematica e Fisica “N. Tartaglia”, Università Cattolica del Sacro Cuore（圣心大学N. Tartaglia数学与物理系）；Department of Neurosurgery – Fondazione I.R.C.C.S. Istituto Neurologico Carlo Besta（卡尔·贝斯塔神经科学研究所神经外科部）
Raidionics: an open software for pre- and postoperative central nervous system tumor segmentation and standardized reporting
SINTEF Digital（挪威科技工业研究院数字分院）；Norwegian University of Science and Technology (NTNU)（挪威科技大学（NTNU））；St. Olavs hospital, Trondheim University Hospital（特隆赫姆大学医院圣奥拉夫斯医院）
We proposed a fully automatic workflow for glioblastoma (GBM) survival prediction using deep learning (DL) methods. 285 glioma (210 GBM, 75 low-grade glioma) patients were included. 163 of the GBM patients had overall survival (OS) data. Every patient had four pre-operative MR scans and manually drawn tumor contours. For automatic tumor segmentation, a 3D convolutional neural network (CNN) was trained and validated using 122 glioma patients. The trained model was applied to the remaining 163 GBM patients to generate tumor contours. The handcrafted and DL-based radiomic features were extracted …
Convolutional neural networks have achieved excellent results in automatic medical image segmentation. In this study, we proposed a novel 3D multi-path DenseNet for generating the accurate glioblastoma (GBM) tumor contour from four multi-modal pre-operative MR images. We hypothesized that the multi-path architecture could achieve more accurate segmentation than a single-path architecture. 258 GBM patients were included in this study. Each patient had four MR images (T1-weighted, contrast-enhanced T1-weighted, T2-weighted, and FLAIR) and the manually segmented tumor contour. We built a 3D multi…
National University of Singapore（新加坡国立大学）；University of Moratuwa（莫拉图瓦大学）
The accurate prognosis of Glioblastoma Multiforme (GBM) plays an essential role in planning correlated surgeries and treatments. The conventional models of survival prediction rely on radiomic features using magnetic resonance imaging (MRI). In this paper, we propose a radiogenomic overall survival (OS) prediction approach by incorporating gene expression data with radiomic features such as shape, geometry, and clinical information. We exploit TCGA (The Cancer Genomic Atlas) dataset and synthesize the missing MRI modalities using a fully convolutional network (FCN) in a conditional Generative …
Automated ensemble method for pediatric brain tumor segmentation
Manning College of Information and Computer Sciences, University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校曼宁信息与计算机科学学院）；Institute for Applied Life Sciences, University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校应用生命科学研究所）；UMass Chan Medical School - Baystate Campus（马萨诸塞大学陈医学院贝塞特校区）；Baystate Medical Center（贝塞特医疗中心）
