Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)最新文献

{"title":"The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview.","authors":"Sarthak Pati, Ashish Singh, Saima Rathore, Aimilia Gastounioti, Mark Bergman, Phuc Ngo, Sung Min Ha, Dimitrios Bounias, James Minock, Grayson Murphy, Hongming Li, Amit Bhattarai, Adam Wolf, Patmaa Sridaran, Ratheesh Kalarot, Hamed Akbari, Aristeidis Sotiras, Siddhesh P Thakur, Ragini Verma, Russell T Shinohara, Paul Yushkevich, Yong Fan, Despina Kontos, Christos Davatzikos, Spyridon Bakas","doi":"10.1007/978-3-030-46643-5_38","DOIUrl":"10.1007/978-3-030-46643-5_38","url":null,"abstract":"<p><p>The purpose of this manuscript is to provide an overview of the technical specifications and architecture of the <b>Ca</b>ncer imaging <b>P</b>henomics <b>T</b>ool<b>k</b>it (CaPTk www.cbica.upenn.edu/captk), a cross-platform, open-source, easy-to-use, and extensible software platform for analyzing 2D and 3D images, currently focusing on radiographic scans of brain, breast, and lung cancer. The primary aim of this platform is to enable swift and efficient translation of cutting-edge academic research into clinically useful tools relating to clinical quantification, analysis, predictive modeling, decision-making, and reporting workflow. CaPTk builds upon established open-source software toolkits, such as the Insight Toolkit (ITK) and OpenCV, to bring together advanced computational functionality. This functionality describes specialized, as well as general-purpose, image analysis algorithms developed during active multi-disciplinary collaborative research studies to address real clinical requirements. The target audience of CaPTk consists of both computational scientists and clinical experts. For the former it provides i) an efficient image viewer offering the ability of integrating new algorithms, and ii) a library of readily-available clinically-relevant algorithms, allowing batch-processing of multiple subjects. For the latter it facilitates the use of complex algorithms for clinically-relevant studies through a user-friendly interface, eliminating the prerequisite of a substantial computational background. CaPTk's long-term goal is to provide widely-used technology to make use of advanced quantitative imaging analytics in cancer prediction, diagnosis and prognosis, leading toward a better understanding of the biological mechanisms of cancer development.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11993 ","pages":"380-394"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402244/pdf/nihms-1608130.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38232225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards Population-Based Histologic Stain Normalization of Glioblastoma.","authors":"Caleb M Grenko, Angela N Viaene, MacLean P Nasrallah, Michael D Feldman, Hamed Akbari, Spyridon Bakas","doi":"10.1007/978-3-030-46640-4_5","DOIUrl":"10.1007/978-3-030-46640-4_5","url":null,"abstract":"<p><p>Glioblastoma ( <b><i>'GBM'</i></b> ) is the most aggressive type of primary malignant adult brain tumor, with very heterogeneous radio-graphic, histologic, and molecular profiles. A growing body of advanced computational analyses are conducted towards further understanding the biology and variation in glioblastoma. To address the intrinsic heterogeneity among different computational studies, reference standards have been established to facilitate both radiographic and molecular analyses, e.g., anatomical atlas for image registration and housekeeping genes, respectively. However, there is an apparent lack of reference standards in the domain of digital pathology, where each independent study uses an arbitrarily chosen slide from their evaluation dataset for normalization purposes. In this study, we introduce a novel stain normalization approach based on a composite reference slide comprised of information from a large population of anatomically annotated hematoxylin and eosin ( <b><i>'H&E'</i></b> ) whole-slide images from the Ivy Glioblastoma Atlas Project ( <b><i>'IvyGAP'</i></b> ). Two board-certified neuropathologists manually reviewed and selected annotations in 509 slides, according to the World Health Organization definitions. We computed summary statistics from each of these approved annotations and weighted them based on their percent contribution to overall slide ( <b><i>'PCOS'</i></b> ), to form a global histogram and stain vectors. Quantitative evaluation of pre- and post-normalization stain density statistics for each annotated region with PCOS > 0.05% yielded a significant (largest <i>p</i> = 0.001, two-sided Wilcoxon rank sum test) reduction of its intensity variation for both <b><i>'H'</i></b> & <b><i>'E'</i></b> . Subject to further large-scale evaluation, our findings support the proposed approach as a potentially robust population-based reference for stain normalization.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11992 ","pages":"44-56"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394499/pdf/nihms-1608126.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38228884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting Clinical Outcome of Stroke Patients with Tractographic Feature.","authors":"Po-Yu Kao,&nbsp;Jeffereson W Chen,&nbsp;B S Manjunath","doi":"10.1007/978-3-030-46640-4_4","DOIUrl":"https://doi.org/10.1007/978-3-030-46640-4_4","url":null,"abstract":"<p><p>The volume of stroke lesion is the gold standard for predicting the clinical outcome of stroke patients. However, the presence of stroke lesion may cause neural disruptions to other brain regions, and these potentially damaged regions may affect the clinical outcome of stroke patients. In this paper, we introduce the tractographic feature to capture these potentially damaged regions and predict the modified Rankin Scale (mRS), which is a widely used outcome measure in stroke clinical trials. The tractographic feature is built from the stroke lesion and average connectome information from a group of normal subjects. The tractographic feature takes into account different functional regions that may be affected by the stroke, thus complementing the commonly used stroke volume features. The proposed tractographic feature is tested on a public stroke benchmark Ischemic Stroke Lesion Segmentation 2017 and achieves higher accuracy than the stroke volume and the state-of-the-art feature on predicting the mRS grades of stroke patients. Also, the tractographic feature yields a lower average absolute error than the commonly used stroke volume feature.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11992 ","pages":"32-43"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8557637/pdf/nihms-1750890.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39687053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: 5th International Workshop, BrainLes 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 17, 2019, Revised Selected Papers, Part I","authors":"A. Crimi, S. Bakas, E. Bertino","doi":"10.1007/978-3-030-46640-4","DOIUrl":"https://doi.org/10.1007/978-3-030-46640-4","url":null,"abstract":"","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90878283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Skull-Stripping of Glioblastoma MRI Scans Using 3D Deep Learning.","authors":"Siddhesh P Thakur, Jimit Doshi, Sarthak Pati, Sung Min Ha, Chiharu Sako, Sanjay Talbar, Uday Kulkarni, Christos Davatzikos, Guray Erus, Spyridon Bakas","doi":"10.1007/978-3-030-46640-4_6","DOIUrl":"10.1007/978-3-030-46640-4_6","url":null,"abstract":"<p><p>Skull-stripping is an essential pre-processing step in computational neuro-imaging directly impacting subsequent analyses. Existing skull-stripping methods have primarily targeted non-pathologicallyaffected brains. Accordingly, they may perform suboptimally when applied on brain Magnetic Resonance Imaging (MRI) scans that have clearly discernible pathologies, such as brain tumors. Furthermore, existing methods focus on using only T1-weighted MRI scans, even though multi-parametric MRI (mpMRI) scans are routinely acquired for patients with suspected brain tumors. Here we present a performance evaluation of publicly available implementations of established 3D Deep Learning architectures for semantic segmentation (namely DeepMedic, 3D U-Net, FCN), with a particular focus on identifying a skull-stripping approach that performs well on brain tumor scans, and also has a low computational footprint. We have identified a retrospective dataset of 1,796 mpMRI brain tumor scans, with corresponding manually-inspected and verified gold-standard brain tissue segmentations, acquired during standard clinical practice under varying acquisition protocols at the Hospital of the University of Pennsylvania. Our quantitative evaluation identified DeepMedic as the best performing method (<i>Dice</i> = 97.9, <i>Hausdorf f</i> ₉₅ = 2.68). We release this pre-trained model through the Cancer Imaging Phenomics Toolkit (CaPTk) platform.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11992 ","pages":"57-68"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311100/pdf/nihms-1597912.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38082780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-stage Association Analysis of Glioblastoma Gene Expressions with Texture and Spatial Patterns.","authors":"Samar S M Elsheikh, Spyridon Bakas, Nicola J Mulder, Emile R Chimusa, Christos Davatzikos, Alessandro Crimi","doi":"10.1007/978-3-030-11723-8_24","DOIUrl":"10.1007/978-3-030-11723-8_24","url":null,"abstract":"<p><p>Glioblastoma is the most aggressive malignant primary brain tumor with a poor prognosis. Glioblastoma heterogeneous neuroimaging, pathologic, and molecular features provide opportunities for subclassification, prognostication, and the development of targeted therapies. Magnetic resonance imaging has the capability of quantifying specific phenotypic imaging features of these tumors. Additional insight into disease mechanism can be gained by exploring genetics foundations. Here, we use the gene expressions to evaluate the associations with various quantitative imaging phenomic features extracted from magnetic resonance imaging. We highlight a novel correlation by carrying out multi-stage genomewide association tests at the gene-level through a non-parametric correlation framework that allows testing multiple hypotheses about the integrated relationship of imaging phenotype-genotype more efficiently and less expensive computationally. Our result showed several novel genes previously associated with glioblastoma and other types of cancers, as the LRRC46 (chromosome 17), EPGN (chromosome 4) and TUBA1C (chromosome 12), all associated with our radiographic tumor features.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11383 ","pages":"239-250"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719702/pdf/nihms-1035734.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41221746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-Institutional Deep Learning Modeling Without Sharing Patient Data: A Feasibility Study on Brain Tumor Segmentation.","authors":"Micah J Sheller,&nbsp;G Anthony Reina,&nbsp;Brandon Edwards,&nbsp;Jason Martin,&nbsp;Spyridon Bakas","doi":"10.1007/978-3-030-11723-8_9","DOIUrl":"https://doi.org/10.1007/978-3-030-11723-8_9","url":null,"abstract":"<p><p>Deep learning models for semantic segmentation of images require large amounts of data. In the medical imaging domain, acquiring sufficient data is a significant challenge. Labeling medical image data requires expert knowledge. Collaboration between institutions could address this challenge, but sharing medical data to a centralized location faces various legal, privacy, technical, and data-ownership challenges, especially among international institutions. In this study, we introduce the first use of federated learning for multi-institutional collaboration, enabling deep learning modeling without sharing patient data. Our quantitative results demonstrate that the performance of federated semantic segmentation models (Dice=0.852) on multimodal brain scans is similar to that of models trained by sharing data (Dice=0.862). We compare federated learning with two alternative collaborative learning methods and find that they fail to match the performance of federated learning.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11383 ","pages":"92-104"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-030-11723-8_9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37354792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patient-Specific Registration of Pre-operative and Post-recurrence Brain Tumor MRI Scans.","authors":"Xu Han, Spyridon Bakas, Roland Kwitt, Stephen Aylward, Hamed Akbari, Michel Bilello, Christos Davatzikos, Marc Niethammer","doi":"10.1007/978-3-030-11723-8_10","DOIUrl":"10.1007/978-3-030-11723-8_10","url":null,"abstract":"<p><p>Registering brain magnetic resonance imaging (MRI) scans containing pathologies is challenging primarily due to large deformations caused by the pathologies, leading to missing correspondences between scans. However, the registration task is important and directly related to personalized medicine, as registering between <i>baseline pre-operative</i> and <i>post-recurrence</i> scans may allow the evaluation of tumor infiltration and recurrence. While many registration methods exist, most of them do not specifically account for pathologies. Here, we propose a framework for the registration of longitudinal image-pairs of individual patients diagnosed with glioblastoma. Specifically, we present a combined image registration/reconstruction approach, which makes use of a patient-specific principal component analysis (PCA) model of image appearance to register baseline pre-operative and post-recurrence brain tumor scans. Our approach uses the post-recurrence scan to construct a patient-specific model, which then guides the registration of the pre-operative scan. Quantitative and qualitative evaluations of our framework on 10 patient image-pairs indicate that it provides excellent registration performance without requiring (1) any human intervention or (2) prior knowledge of tumor location, growth or appearance.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"11383 ","pages":"105-114"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599177/pdf/nihms-1032951.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37105936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glioblastoma and Survival Prediction.","authors":"Zeina Shboul, Lasitha Vidyaratne, Mahbubul Alam, Syed M S Reza, Khan M Iftekharuddin","doi":"10.1007/978-3-319-75238-9_31","DOIUrl":"10.1007/978-3-319-75238-9_31","url":null,"abstract":"<p><p>Glioblastoma is a stage IV highly invasive astrocytoma tumor. Its heterogeneous appearance in MRI poses critical challenge in diagnosis, prognosis and survival prediction. This work extracts a total of 1207 different types of texture and other features, tests their significance and prognostic values, and then utilizes the most significant features with Random Forest regression model to perform survival prediction. We use 163 cases from BraTS17 training dataset for evaluation of the proposed model. A 10-fold cross validation offers normalized root mean square error of 30% for the training dataset and the cross validated accuracy of 63%, respectively.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"10670 ","pages":"358-368"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-319-75238-9_31","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36318573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dice Overlap Measures for Objects of Unknown Number: Application to Lesion Segmentation.","authors":"Ipek Oguz,&nbsp;Aaron Carass,&nbsp;Dzung L Pham,&nbsp;Snehashis Roy,&nbsp;Nagesh Subbana,&nbsp;Peter A Calabresi,&nbsp;Paul A Yushkevich,&nbsp;Russell T Shinohara,&nbsp;Jerry L Prince","doi":"10.1007/978-3-319-75238-9_1","DOIUrl":"https://doi.org/10.1007/978-3-319-75238-9_1","url":null,"abstract":"<p><p>The Dice overlap ratio is commonly used to evaluate the performance of image segmentation algorithms. While Dice overlap is very useful as a standardized quantitative measure of segmentation accuracy in many applications, it offers a very limited picture of segmentation quality in complex segmentation tasks where the number of target objects is not known <i>a priori</i>, such as the segmentation of white matter lesions or lung nodules. While Dice overlap can still be used in these applications, segmentation algorithms may perform quite differently in ways not reflected by differences in their Dice score. Here we propose a new set of evaluation techniques that offer new insights into the behavior of segmentation algorithms. We illustrate these techniques with a case study comparing two popular multiple sclerosis (MS) lesion segmentation algorithms: OASIS and LesionTOADS.</p>","PeriodicalId":72455,"journal":{"name":"Brainlesion : glioma, multiple sclerosis, stroke and traumatic brain injuries. BrainLes (Workshop)","volume":"10670 ","pages":"3-14"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-319-75238-9_1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36058092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}