Brain tumor diagnosis is a challenging task for clinicians in the modern world. Among the major reasons for cancer-related death is the brain tumor. Gliomas, a category of central nervous system (CNS) tumors, encompass diverse subregions. For accurate diagnosis of brain tumors, precise segmentation of brain images and quantitative analysis are required. A fully automatic approach to glioma segmentation is required because the manual segmentation process is laborious, prone to mistakes, as well as time-consuming. Modern techniques for segmenting gliomas are based on fully convolutional neural networks (FCNs), which can either use two-dimensional (2D) or three-dimensional (3D) convolutions. Nevertheless, 3D convolutions suffer from computational costs and memory demand, while 2D convolutions cannot fully utilize the spatial insights of volumetric clinical imaging data. To obtain an optimal solution, it is vital to balance the computational efficiency of 2D convolutions along with the spatial accuracy of 3D convolutions. This balance can potentially be realized by developing an advanced model to overcome these challenges. The 2D and 3D models implemented here are based on UNET architecture, Inception, and ResNet models. The research work has been implemented on the BraTS 2018, 2019, and 2020 datasets. The best performer of all the models' evaluations metrics for proposed methodologies offer superior potential in terms of the effective segmentation of gliomas. The ResNet model has resulted in 98.91% accuracy for 3D segmentation and 99.77 for 2D segmentations. The dice scores for 2D and 3D segmentations are 0.8312 and 0.9888, respectively. This model can be applied to various other medical applications with fine-tuning, thereby aiding clinicians in brain tumor analysis and improving the diagnosis process effectively.
Diagnostic performance of deep learning for predicting glioma isocitrate dehydrogenase and 1p/19q co-deletion in MRI: a systematic review and meta-analysis
Objectives: Glioblastomas are the most aggressive brain and central nervous system (CNS) tumors with poor prognosis in adults. The purpose of this study is to develop a machine-learning based classification method using radio-mic features of multi-parametric MRI to classify high-grade gliomas (HGG) and low-grade gliomas (LGG). Methods: Multi-parametric MRI of 80 patients, 40 HGG and 40 LGG, with gliomas from the MICCAI BRATs 2015 training database were used in this study. Each patient's T1, contrast-enhanced T1, T2, and Fluid Attenuated Inversion Recovery (FLAIR) MRIs as well as the tumor cont…
University of California San Francisco(加州大学旧金山分校);University of Pennsylvania(宾夕法尼亚大学)
Here we present the University of California San Francisco Preoperative Diffuse Glioma MRI (UCSF-PDGM) dataset. The UCSF-PDGM dataset includes 500 subjects with histopathologically-proven diffuse gliomas who were imaged with a standardized 3 Tesla preoperative brain tumor MRI protocol featuring predominantly 3D imaging, as well as advanced diffusion and perfusion imaging techniques. The dataset also includes isocitrate dehydrogenase (IDH) mutation status for all cases and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation status for World Health Organization (WHO) grade III and…
The optimal treatment strategy of newly diagnosed glioma is strongly influenced by tumour malignancy. Manual non-invasive grading based on MRI is not always accurate and biopsies to verify diagnosis negatively impact overall survival. In this paper, we propose a fully automatic 3D computer-aided diagnosis (CAD) system to non-invasively differentiate high-grade glioblastoma from lower-grade glioma. The approach consists of an automatic segmentation step to extract the tumour ROI followed by classification using a 3D convolutional neural network. Segmentation was performed using a 3D U-Net achie…
In the WHO glioma classification guidelines grade, IDH mutation and 1p19q co-deletion play a central role as they are important markers for prognosis and optimal therapy planning. Therefore, we propose a fully automatic, MRI based, 3D pipeline for glioma segmentation and classification. The designed segmentation network was a 3D U-Net achieving an average whole tumor dice score of 90%. After segmentation, the 3D tumor ROI is extracted and fed into the multi-task classification network. The network was trained and evaluated on a large heterogeneous dataset of 628 patients, collected from The Ca…
Zhengzhou University(郑州大学);Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences(中国科学院深圳先进技术研究院);Peng Cheng Laboratory(鹏城实验室);Guangdong Provincial People’s Hospital(广东省人民医院);Guangdong Academy of Medical Sciences(广东省医学科学院)
Multi-contrast magnetic resonance imaging (MRI)-based automatic auxiliary glioma diagnosis plays an important role in the clinic. Contrast-enhanced MRI sequences (e.g., contrast-enhanced T1-weighted imaging) were utilized in most of the existing relevant studies, in which remarkable diagnosis results have been reported. Nevertheless, acquiring contrast-enhanced MRI data is sometimes not feasible due to the patients physiological limitations. Furthermore, it is more time-consuming and costly to collect contrast-enhanced MRI data in the clinic. In this paper, we propose an adaptive PromptNet to …
Treatment-aware Diffusion Probabilistic Model for Longitudinal MRI Generation and Diffuse Glioma Growth Prediction
Oslo University Hospital(奥斯陆大学医院);Universitat Politècnica de València(瓦伦西亚理工大学);Instituto Universitario de Tecnologías de la Información y Comunicaciones(信息技术与通信大学学院)
Faculty of Physics and Mathematics, Benemérita Universidad Autónoma de Puebla(普埃布拉自治大学物理与数学学院)
Gliomas are brain tumors composed of different highly heterogeneous histological subregions. Image analysis techniques to identify relevant tumor substructures have high potential for improving patient diagnosis, treatment and prognosis. However, due to the high heterogeneity of gliomas, the segmentation task is currently a major challenge in the field of medical image analysis. In the present work, the database of the Brain Tumor Segmentation (BraTS) Challenge 2018, composed of multimodal MRI scans of gliomas, was studied. A segmentation methodology based on the design and application of conv…
Glioma Multimodal MRI Analysis System for Tumor Layered Diagnosis via Multi-task Semi-supervised Learning
Cancer Research Institute, Central South University(中南大学肿瘤研究所);School of Physics & Electronic Science, Changsha University of Science & Technology(长沙理工大学物理与电子科学学院);IFLYTEK Research(iFlytek研究院);School of Life Sciences, Central South University(中南大学生命科学学院);Department of Radiology, Xiangya Hospital, Central South University(中南大学湘雅医院放射科);School of Computer Science and Engineering, Central South University(中南大学计算机科学与工程学院);Department of Neurosurgery, Xiangya Hospital, Central South University(中南大学湘雅医院神经外科)
Deep learning-based group-wise registration for longitudinal MRI analysis in glioma
Erasmus MC(伊拉斯姆斯大学医学中心);Medical Delta(医疗三角洲);Delft University of Technology(代尔夫特理工大学);Amsterdam UMC / VU Medical Center(阿姆斯特丹大学医学中心/自由大学医学中心);Princess Máxima Center for Pediatric Oncology(马克西玛公主儿童肿瘤中心);The Jackson Laboratory for Genomic Medicine(杰克逊基因组医学实验室)
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, …
Hôpital Erasme(埃拉斯姆医院);Université libre de Bruxelles(布鲁塞尔自由大学);Center for Microscopy and Molecular Imaging(显微与分子成像中心)
Diffuse gliomas are highly infiltrative tumors whose early diagnosis and follow-up usually rely on magnetic resonance imaging (MRI). However, the limited sensitivity of this technique makes it impossible to directly assess the extent of the glioma cell invasion, leading to sub-optimal treatment planing. Reaction-diffusion growth models have been proposed for decades to extrapolate glioma cell infiltration beyond margins visible on MRI and predict its spatial-temporal evolution. These models nevertheless require an initial condition, that is the tumor cell density values at every location of th…
The Hong Kong University of Science and Technology(香港科技大学)
Registration of pre-operative and follow-up brain MRI scans is challenging due to the large variation of tissue appearance and missing correspondences in tumour recurrence regions caused by tumour mass effect. Although recent deep learning-based deformable registration methods have achieved remarkable success in various medical applications, most of them are not capable of registering images with pathologies. In this paper, we propose a 3-step registration pipeline for pre-operative and follow-up brain MRI scans that consists of 1) a multi-level affine registration, 2) a conditional deep Lapla…
OkanNet: A Lightweight Deep Learning Architecture for Classification of Brain Tumor from MRI Images
Graduate School of Natural;Applied Sciences Department of Computer Engineering Ege University Izmir, Turkey;International Computer Institute Ege University Izmir, Turkey
Washington University in St. Louis(圣路易斯华盛顿大学);Mallinckrodt Institute of Radiology(马林克罗特放射研究所);Washington University School of Medicine(华盛顿大学医学院);Institute for Informatics(信息学研究所)
Isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion status are important prognostic markers for glioma. Currently, they are determined using invasive procedures. Our goal was to develop artificial intelligence-based methods to non-invasively determine these molecular alterations from MRI. For this purpose, pre-operative MRI scans of 2648 patients with gliomas (grade II-IV) were collected from Washington University School of Medicine (WUSM; n = 835) and publicly available datasets viz. Brain Tumor Segmentation (BraTS; n = 378), LGG 1p/19q (n = 159), Ivy Glioblastoma Atlas Project (Ivy…
A Benchmark of (MRI-) Foundation Models to Predict IDH Mutational Status in Glioma
Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern(伯尔尼大学医院因塞尔斯皮塔尔放射肿瘤科);University of Bern(伯尔尼大学);Department of Digital Medicine, University of Bern(伯尔尼大学数字医学系);School of Life Sciences, FHNW University of Applied Sciences and Arts, Muttenz(FHNW应用科学与艺术大学生命科学学院);School of Business, FHNW University of Applied Sciences and Arts, Olten(FHNW应用科学与艺术学院商学院);University Children’s Hospital Basel UKBB(巴塞尔儿童医院UKBB)
Technical University of Munich(慕尼黑工业大学);LMU Hospital Grosshadern(路德维希-马克西米利安-慕尼黑大学格罗斯哈德恩医院)
Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input …
Indiana University School of Medicine(印第安纳大学医学院);Purdue University(普渡大学);Dayton Children’s Hospital(代顿儿童医院)
Background and Purpose: Biopsy is the main determinants of glioma clinical management, but require invasive sampling that fail to detect relevant features because of tumor heterogeneity. The purpose of this study was to evaluate the accuracy of a voxel-wise, multiparametric MRI radiomic method to predict features and develop a minimally invasive method to objectively assess neoplasms. Methods: Multiparametric MRI were registered to T1-weighted gadolinium contrast-enhanced data using a 12 degree-of-freedom affine model. The retrospectively collected MRI data included T1-weighted, T1-weighted ga…
Training Beyond Convergence: Grokking nnU-Net for Glioma Segmentation in Sub-Saharan MRI
Multimedia University(多媒体大学);University of British Columbia(不列颠哥伦比亚大学);McGill University(麦吉尔大学);Montreal Neurological Institute(蒙特利尔神经学研究所);Federal University of Technology Minna(明纳联邦理工大学);Medical Artificial Intelligence Laboratory(医学人工智能实验室);Friedrich-Alexander-Universität(弗里德里希-亚历山大大学)
Structural magnetic resonance imaging (MRI) has been widely utilized for analysis and diagnosis of brain diseases. Automatic segmentation of brain tumors is a challenging task for computer-aided diagnosis due to low-tissue contrast in the tumor subregions. To overcome this, we devise a novel pixel-wise segmentation framework through a convolutional 3D to 2D MR patch conversion model to predict class labels of the central pixel in the input sliding patches. Precisely, we first extract 3D patches from each modality to calibrate slices through the squeeze and excitation (SE) block. Then, the outp…
Duke University(杜克大学);Duke Kunshan University(昆山杜克大学);North Carolina State University(北卡罗来纳州立大学)
Purpose: To develop a neural ordinary differential equation (ODE) model for visualizing deep neural network (DNN) behavior during multi-parametric MRI (mp-MRI) based glioma segmentation as a method to enhance deep learning explainability. Methods: By hypothesizing that deep feature extraction can be modeled as a spatiotemporally continuous process, we designed a novel deep learning model, neural ODE, in which deep feature extraction was governed by an ODE without explicit expression. The dynamics of 1) MR images after interactions with DNN and 2) segmentation formation can be visualized after …
Shenzhen University(深圳大学);Islamic Azad University(伊斯兰阿扎德大学)
Magnetic resonance imaging (MRI) provides varying tissue contrast images of internal organs based on a strong magnetic field. Despite the non-invasive advantage of MRI in frequent imaging, the low contrast MR images in the target area make tissue segmentation a challenging problem. This paper demonstrates the potential benefits of image-to-image translation techniques to generate synthetic high tissue contrast (HTC) images. Notably, we adopt a new cycle generative adversarial network (CycleGAN) with an attention mechanism to increase the contrast within underlying tissues. The attention block,…
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)
Reliable and accurate registration of patient-specific brain magnetic resonance imaging (MRI) scans containing pathologies is challenging due to tissue appearance changes. This paper describes our contribution to the Registration of the longitudinal brain MRI task of the Brain Tumor Sequence Registration Challenge 2022 (BraTS-Reg 2022). We developed an enhanced unsupervised learning-based method that extends the iRegNet. In particular, incorporating an unsupervised learning-based paradigm as well as several minor modifications to the network pipeline, allows the enhanced iRegNet method to achi…
Transferring Knowledge from High-Quality to Low-Quality MRI for Adult Glioma Diagnosis
The Chinese University of Hong Kong (CUHK)(香港中文大学);CUHK Shenzhen Research Institute(香港中文大学深圳研究院);China Medical University(中国医科大学);University College London(伦敦大学学院);UCL Hawkes Institute(伦敦大学学院霍克斯研究所)
Intraoperative Glioma Segmentation with YOLO + SAM for Improved Accuracy in Tumor Resection
Carnegie Vanguard High School(卡内基先锋高中);Devon Preparatory High School(德文预备高中);Lake Travis High School(特拉维斯湖高中);Irvington High School(欧文顿高中);Algoverse AI Research(Algoverse AI研究机构)
The Hospital for Sick Children(病童医院);University of Toronto(多伦多大学);Vector Institute(矢量研究所)
Brain tumor segmentation is a critical task for tumor volumetric analyses and AI algorithms. However, it is a time-consuming process and requires neuroradiology expertise. While there has been extensive research focused on optimizing brain tumor segmentation in the adult population, studies on AI guided pediatric tumor segmentation are scarce. Furthermore, MRI signal characteristics of pediatric and adult brain tumors differ, necessitating the development of segmentation algorithms specifically designed for pediatric brain tumors. We developed a segmentation model trained on magnetic resonance…
Targeted Neural Architectures in Multi-Objective Frameworks for Complete Glioma Characterization from Multimodal MRI
School of Computer Science and Engineering, Vellore Institute of Technology(韦洛尔理工学院计算机科学与工程学院);College of Engineering, Guindy, Anna University(安娜大学金迪工程学院);Institute of Neurosurgery, Madras Medical College(马德拉斯医学院神经外科研究所)
Generative Style Transfer for MRI Image Segmentation: A Case of Glioma Segmentation in Sub-Saharan Africa
Institute of Mathematical Science, Strathmore University(斯特拉斯莫尔大学数学科学学院);Faculty of Science and Engineering, University of Hull(赫尔大学科学与工程学院);Technical University of Mombasa(蒙巴萨理工大学);Lawson Health Research Institute(劳森健康研究所);University of British Columbia(不列颠哥伦比亚大学);University of Nairobi(内罗毕大学);University of Cape Town(开普敦大学);Montreal Neurological Institute, McGill University(麦吉尔大学蒙特利尔神经学研究所);Brain Mind Institute, The Aga Khan University(阿迦汗大学脑与心智研究所);Medical Physics Unit, McGill University(麦吉尔大学医学物理部门)
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)
Automatic segmentation is essential for the brain tumor diagnosis, disease prognosis, and follow-up therapy of patients with gliomas. Still, accurate detection of gliomas and their sub-regions in multimodal MRI is very challenging due to the variety of scanners and imaging protocols. Over the last years, the BraTS Challenge has provided a large number of multi-institutional MRI scans as a benchmark for glioma segmentation algorithms. This paper describes our contribution to the BraTS 2022 Continuous Evaluation challenge. We propose a new ensemble of multiple deep learning frameworks namely, De…
University of Cambridge(剑桥大学);Nanyang Technological University(南洋理工大学);University of Bath(巴斯大学)
Glioma is a common malignant brain tumor with distinct survival among patients. The isocitrate dehydrogenase (IDH) gene mutation provides critical diagnostic and prognostic value for glioma. It is of crucial significance to non-invasively predict IDH mutation based on pre-treatment MRI. Machine learning/deep learning models show reasonable performance in predicting IDH mutation using MRI. However, most models neglect the systematic brain alterations caused by tumor invasion, where widespread infiltration along white matter tracts is a hallmark of glioma. Structural brain network provides an ef…
University of Electronic Science and Technology of China(电子科技大学)
Past few years have witnessed the artificial intelligence inspired evolution in various medical fields. The diagnosis and treatment of gliomas -- one of the most commonly seen brain tumors with low survival rate -- rely heavily on the computer assisted segmentation process undertaken on the magnetic resonance imaging (MRI) scans. Although the encoder-decoder shaped deep learning networks have been the de facto standard style for semantic segmentation tasks in medical imaging analysis, enormous effort is still required to be spent on designing the detailed architecture of the down-sampling and …
Massachusetts General Hospital(麻省总医院);Harvard University(哈佛大学);General Electric Healthcare(通用电气医疗集团);Indian Institute of Science(印度科学学院)
Gliomas are one of the most frequent brain tumors and are classified into high grade and low grade gliomas. The segmentation of various regions such as tumor core, enhancing tumor etc. plays an important role in determining severity and prognosis. Here, we have developed a multi-threshold model based on attention U-Net for identification of various regions of the tumor in magnetic resonance imaging (MRI). We propose a multi-path segmentation and built three separate models for the different regions of interest. The proposed model achieved mean Dice Coefficient of 0.59, 0.72, and 0.61 for enhan…
Department of Computer Science, University of Rochester(罗切斯特大学计算机科学系);Department of Electrical Engineering, University of Rochester(罗切斯特大学电气工程系);Department of Biomedical Engineering, University of Rochester(罗切斯特大学生物医学工程系);Department of Imaging Sciences, University of Rochester(罗切斯特大学影像科学系);Faculty of Medicine and Institute of Clinical Radiology, Ludwig Maximilian University(路德维希-马克西米利安大学医学院及临床放射学研究所)
Glioma is one of the most common and aggressive types of primary brain tumors. The accurate segmentation of subcortical brain structures is crucial to the study of gliomas in that it helps the monitoring of the progression of gliomas and aids the evaluation of treatment outcomes. However, the large amount of required human labor makes it difficult to obtain the manually segmented Magnetic Resonance Imaging (MRI) data, limiting the use of precise quantitative measurements in the clinical practice. In this work, we try to address this problem by developing a 3D Convolutional Neural Network~(3D C…
Rectified flow-based prediction of post-treatment brain MRI from pre-radiotherapy priors for patients with glioma
Amsterdam UMC, Department of Radiation Oncology(阿姆斯特丹大学医学中心放射肿瘤科);Cancer Center Amsterdam, Imaging and Biomarkers(阿姆斯特丹癌症中心影像与生物标志物);Department of Radiology and Nuclear Medicine(放射科与核医学科);Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Brain Imaging(阿姆斯特丹大学医学中心、阿姆斯特丹自由大学、阿姆斯特丹神经科学、脑成像)
RC-aware nnU-Netv2 for Pre-treatment and Post-treatment Glioma Segmentation Using Multimodal MRI
School of Statistics, East China Normal University(华东师范大学统计学院);Department of Biostatistics, School of Global Public Health, New York University(纽约大学全球公共卫生学院生物统计学系)
Quantifying U-Net Uncertainty in Multi-Parametric MRI-based Glioma Segmentation by Spherical Image Projection
Duke University(杜克大学);Duke Kunshan University(昆山杜克大学);The University of Texas MD Anderson Cancer Center(德克萨斯大学MD安德森癌症中心);The University of Texas MD Anderson Graduate School of Biomedical Science(德克萨斯大学MD安德森生物医学研究生院)
Shanghai United Imaging Intelligence Co. Ltd(上海联影智能医疗科技有限公司);Southern Medical University(南方医科大学)
In brain tumor diagnosis and surgical planning, segmentation of tumor regions and accurate analysis of surrounding normal tissues are necessary for physicians. Pathological variability often renders difficulty to register a well-labeled normal atlas to such images and to automatic segment/label surrounding normal brain tissues. In this paper, we propose a new registration approach that first segments brain tumor using a U-Net and then simulates missed normal tissues within the tumor region using a partial convolutional network. Then, a standard normal brain atlas image is registered onto such …
Recent analysis identified distinct genomic subtypes of lower-grade glioma tumors which are associated with shape features. In this study, we propose a fully automatic way to quantify tumor imaging characteristics using deep learning-based segmentation and test whether these characteristics are predictive of tumor genomic subtypes. We used preoperative imaging and genomic data of 110 patients from 5 institutions with lower-grade gliomas from The Cancer Genome Atlas. Based on automatic deep learning segmentations, we extracted three features which quantify two-dimensional and three-dimensional …
City University of Hong Kong(香港城市大学);Kwong Wah Hospital(广华医院)
Automatically segmenting sub-regions of gliomas (necrosis, edema and enhancing tumor) and accurately predicting overall survival (OS) time from multimodal MRI sequences have important clinical significance in diagnosis, prognosis and treatment of gliomas. However, due to the high degree variations of heterogeneous appearance and individual physical state, the segmentation of sub-regions and OS prediction are very challenging. To deal with these challenges, we utilize a 3D dilated multi-fiber network (DMFNet) with weighted dice loss for brain tumor segmentation, which incorporates prior volume …
Courant Institute of Mathematical Sciences(库朗数学科学研究所);New York University(纽约大学);Vilcek Institute of Graduate Biomedical Sciences(维尔切克生物医学研究生科学研究所)
Multi-modal magnetic resonance imaging (MRI) is a crucial method for analyzing the human brain. It is usually used for diagnosing diseases and for making valuable decisions regarding the treatments - for instance, checking for gliomas in the human brain. With varying degrees of severity and detection, properly diagnosing gliomas is one of the most daunting and significant analysis tasks in modern-day medicine. Our primary focus is on working with different approaches to perform the segmentation of brain tumors in multimodal MRI scans. Now, the quantity, variability of the data used for trainin…
Tencent(腾讯);Beijing Neurosurgical Institute(北京神经外科研究所);Capital Medical University(首都医科大学);Beijing Tiantan Hospital(北京天坛医院);Sinovation Ventures AI Institute(创新工场人工智能研究院)
Knowledge of molecular subtypes of gliomas can provide valuable information for tailored therapies. This study aimed to investigate the use of deep convolutional neural networks (DCNNs) for noninvasive glioma subtyping with radiological imaging data according to the new taxonomy announced by the World Health Organization in 2016. Methods: A DCNN model was developed for the prediction of the five glioma subtypes based on a hierarchical classification paradigm. This model used three parallel, weight-sharing, deep residual learning networks to process 2.5-dimensional input of trimodal MRI data, i…