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resonance images using convolutional neural networks</style></title><secondary-title><style face="normal" font="default" size="100%">EURASIP Journal on Image and Video Processing</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">EURASIP Journal on Image and Video Processing</style></full-title></periodical><pages><style face="normal" font="default" size="100%">97</style></pages><volume><style face="normal" font="default" size="100%">2018</style></volume><number><style face="normal" font="default" size="100%">1</style></number><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">1687-5281</style></isbn><label><style face="normal" font="default" size="100%">RIDER Neuro MRI, Convolutional Neural Network, Deep Learning</style></label><urls></urls><electronic-resource-num><style face="normal" font="default" 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recognition</style></title><secondary-title><style face="normal" font="default" size="100%">IBM Journal of Research and Development</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">IBM Journal of Research and Development</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1: 1-1: 18</style></pages><volume><style face="normal" font="default" size="100%">59</style></volume><number><style face="normal" font="default" size="100%">2/3</style></number><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">0018-8646</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>646</rec-number><foreign-keys><key 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size="100%">Communication Papers of the Federated Conference on Computer Science and Information Systems</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Communication Papers of the Federated Conference on Computer Science and Information Systems</style></full-title></periodical><pages><style face="normal" font="default" size="100%">13-20</style></pages><volume><style face="normal" font="default" size="100%">17</style></volume><keywords><keyword><style face="normal" font="default" size="100%">SPIE-AAPM Lungx</style></keyword><keyword><style face="normal" font="default" size="100%">Haralick texture features</style></keyword><keyword><style face="normal" font="default" size="100%">support vector machine (SVM)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.15439/2018F176</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>334</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">334</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aerts, Hugo JWL</style></author><author><style face="normal" font="default" size="100%">Grossmann, Patrick</style></author><author><style face="normal" font="default" size="100%">Tan, Yongqiang</style></author><author><style face="normal" font="default" size="100%">Oxnard, Geoffrey G</style></author><author><style face="normal" font="default" size="100%">Rizvi, Naiyer</style></author><author><style face="normal" font="default" size="100%">Schwartz, Lawrence H</style></author><author><style face="normal" font="default" size="100%">Zhao, Binsheng</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Defining a Radiomic Response Phenotype: A Pilot Study using targeted therapy in NSCLC</style></title><secondary-title><style face="normal" font="default" size="100%">Scientific Reports</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><volume><style face="normal" font="default" size="100%">6</style></volume><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>84</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">84</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aerts, H. J.</style></author><author><style face="normal" font="default" size="100%">Velazquez, E. R.</style></author><author><style face="normal" font="default" size="100%">Leijenaar, R. T.</style></author><author><style face="normal" font="default" size="100%">Parmar, C.</style></author><author><style face="normal" font="default" size="100%">Grossmann, P.</style></author><author><style face="normal" font="default" size="100%">Cavalho, S.</style></author><author><style face="normal" font="default" size="100%">Bussink, J.</style></author><author><style face="normal" font="default" size="100%">Monshouwer, R.</style></author><author><style face="normal" font="default" size="100%">Haibe-Kains, B.</style></author><author><style face="normal" font="default" size="100%">Rietveld, D.</style></author><author><style face="normal" font="default" size="100%">Hoebers, F.</style></author><author><style face="normal" font="default" size="100%">Rietbergen, M. M.</style></author><author><style face="normal" font="default" size="100%">Leemans, C. R.</style></author><author><style face="normal" font="default" size="100%">Dekker, A.</style></author><author><style face="normal" font="default" size="100%">Quackenbush, J.</style></author><author><style face="normal" font="default" size="100%">Gillies, R. J.</style></author><author><style face="normal" font="default" size="100%">Lambin, P.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">1] Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands [2] Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA [3] Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA [4] Department of Biostatistics &amp; Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA [5].&#xD;1] Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands [2] Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA [3].&#xD;Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands.&#xD;1] Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands [2] Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA.&#xD;Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA.&#xD;Department of Radiation Oncology, Radboud University Medical Center Nijmegen, PB 9101, 6500HB Nijmegen, The Netherlands.&#xD;Princess Margaret Cancer Centre, University Health Network and Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada M5G 1L7.&#xD;Department of Radiation Oncology, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands.&#xD;Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands.&#xD;Department of Biostatistics &amp; Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA.&#xD;Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature communications</style></alt-title></titles><alt-periodical><full-title><style face="normal" font="default" size="100%">Nature Communications</style></full-title></alt-periodical><pages><style face="normal" font="default" size="100%">4006</style></pages><volume><style face="normal" font="default" size="100%">5</style></volume><edition><style face="normal" font="default" size="100%">2014/06/04</style></edition><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><isbn><style face="normal" font="default" size="100%">2041-1723 (Electronic)&#xD;2041-1723 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">24892406</style></accession-num><abstract><style face="normal" font="default" size="100%">Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. Radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. These data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. This may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost.</style></abstract><notes><style face="normal" font="default" size="100%">Aerts, Hugo J W L&#xD;Velazquez, Emmanuel Rios&#xD;Leijenaar, Ralph T H&#xD;Parmar, Chintan&#xD;Grossmann, Patrick&#xD;Cavalho, Sara&#xD;Bussink, Johan&#xD;Monshouwer, Rene&#xD;Haibe-Kains, Benjamin&#xD;Rietveld, Derek&#xD;Hoebers, Frank&#xD;Rietbergen, Michelle M&#xD;Leemans, C Rene&#xD;Dekker, Andre&#xD;Quackenbush, John&#xD;Gillies, Robert J&#xD;Lambin, Philippe&#xD;NIH-USA U01CA 143062-01/CA/NCI NIH HHS/United States&#xD;U01 CA143062/CA/NCI NIH HHS/United States&#xD;Research Support, N.I.H., Extramural&#xD;England&#xD;Nat Commun. 2014 Jun 3;5:4006. doi: 10.1038/ncomms5006.</style></notes><urls></urls><custom2><style face="normal" font="default" size="100%">PMC4059926</style></custom2><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/ncomms5006</style></electronic-resource-num><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider><language><style face="normal" font="default" size="100%">eng</style></language></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>85</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">85</key></foreign-keys><ref-type name="Dataset">59</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aerts, H. J.</style></author><author><style face="normal" font="default" size="100%">Velazquez, E. R.</style></author><author><style face="normal" font="default" size="100%">Leijenaar, R. T.</style></author><author><style face="normal" font="default" size="100%">Parmar, C.</style></author><author><style face="normal" font="default" size="100%">Grossmann, P.</style></author><author><style face="normal" font="default" size="100%">Cavalho, S.</style></author><author><style face="normal" font="default" size="100%">Bussink, J.</style></author><author><style face="normal" font="default" size="100%">Monshouwer, R.</style></author><author><style face="normal" font="default" size="100%">Haibe-Kains, B.</style></author><author><style face="normal" font="default" size="100%">Rietveld, D.</style></author><author><style face="normal" font="default" size="100%">Hoebers, F.</style></author><author><style face="normal" font="default" size="100%">Rietbergen, M. M.</style></author><author><style face="normal" font="default" size="100%">Leemans, C. R.</style></author><author><style face="normal" font="default" size="100%">Dekker, A.</style></author><author><style face="normal" font="default" size="100%">Quackenbush, J.</style></author><author><style face="normal" font="default" size="100%">Gillies, R. J.</style></author><author><style face="normal" font="default" size="100%">Lambin, P.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">TCIA </style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach</style></title></titles><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><pub-location><style face="normal" font="default" size="100%">Saint Louis, </style></pub-location><urls><related-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.7937/K9/TCIA.2014..ua0JGpDg</style></url></related-urls></urls><custom3><style face="normal" font="default" size="100%">DICOM Images, Clinical Data</style></custom3><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.7937/K9/TCIA.2014..ua0JGpDg</style></electronic-resource-num><remote-database-name><style face="normal" font="default" size="100%">The Cancer Imaging  Archive (TCIA)</style></remote-database-name></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>70</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">70</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aggarwal, Preeti</style></author><author><style face="normal" font="default" size="100%">Vig, Renu</style></author><author><style face="normal" font="default" size="100%">Sardana, HK</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Patient-Wise Versus Nodule-Wise Classification of Annotated Pulmonary Nodules using Pathologically Confirmed Cases</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Computers</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Journal of Computers</style></full-title></periodical><pages><style face="normal" font="default" size="100%">2245-2255</style></pages><volume><style face="normal" font="default" size="100%">8</style></volume><number><style face="normal" font="default" size="100%">9</style></number><dates><year><style face="normal" font="default" size="100%">2013</style></year></dates><isbn><style face="normal" font="default" size="100%">1796-203X</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" 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plasma volume</style></title><secondary-title><style face="normal" font="default" size="100%">NMR in Biomedicine</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">NMR in Biomedicine</style></full-title></periodical><pages><style face="normal" font="default" size="100%">e3924</style></pages><keywords><keyword><style face="normal" font="default" size="100%">DCE-MRI</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">reference region model (RRM)</style></keyword><keyword><style face="normal" font="default" size="100%">extended reference region model (ERRM)</style></keyword><keyword><style face="normal" font="default" size="100%">constrained ERRM (CERRM)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" 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face="normal" font="default" size="100%">GLISTRboost: Combining Multimodal MRI Segmentation, Registration, and Biophysical Tumor Growth Modeling with Gradient Boosting Machines for Glioma Segmentation</style></title><secondary-title><style face="normal" font="default" size="100%">Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: First International Workshop, Brainles 2015, Held in Conjunction with MICCAI 2015, Munich, Germany, October 5, 2015, Revised Selected Papers</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">144</style></pages><volume><style face="normal" font="default" size="100%">9556</style></volume><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><publisher><style face="normal" font="default" size="100%">Springer</style></publisher><isbn><style face="normal" font="default" size="100%">3319308580</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>552</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">552</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Al Mohammad, B</style></author><author><style face="normal" font="default" size="100%">Brennan, PC</style></author><author><style face="normal" font="default" size="100%">Mello-Thoms, C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A review of lung cancer screening and the role of computer-aided detection</style></title><secondary-title><style face="normal" font="default" size="100%">Clinical radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Clinical Radiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">433-442</style></pages><volume><style face="normal" font="default" size="100%">72</style></volume><number><style face="normal" font="default" size="100%">6</style></number><keywords><keyword><style face="normal" font="default" size="100%">LIDC, Lung screening</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">0009-9260</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%"> https://doi.org/10.1016/j.crad.2017.01.002</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>421</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">421</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">AL-Dabagh, Mustafa Zuhaer</style></author><author><style face="normal" font="default" size="100%">AL-Mukhtar, Firas H</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Breast Cancer Diagnostic System Based on MR images Using KPCA-Wavelet Transform and Support Vector Machine</style></title><secondary-title><style face="normal" font="default" size="100%">IJAERS</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">IJAERS</style></full-title></periodical><pages><style face="normal" font="default" size="100%">258-263</style></pages><volume><style face="normal" font="default" size="100%">4</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-BRCA, Radiomics, Breast, MRI, k-mean clustering, Morphological operators, gray scale, Texture, symmetrical, kernel, principal components analysis, Support vector machine</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">https://dx.doi.org/10.22161/ijaers.4.3.41</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>252</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">252</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Alazmani, A</style></author><author><style face="normal" font="default" size="100%">Hood, A</style></author><author><style face="normal" font="default" size="100%">Jayne, D</style></author><author><style face="normal" font="default" size="100%">Neville, A</style></author><author><style face="normal" font="default" size="100%">Culmer, P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Quantitative assessment of colorectal morphology: Implications for robotic colonoscopy</style></title><secondary-title><style face="normal" font="default" size="100%">Medical engineering &amp; physics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Medical engineering &amp; physics</style></full-title></periodical><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><isbn><style face="normal" font="default" size="100%">1350-4533</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>585</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">585</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">AlBadawy, E. A.</style></author><author><style face="normal" font="default" size="100%">Saha, A.</style></author><author><style face="normal" font="default" size="100%">Mazurowski, M. A.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Radiology, Duke University School of Medicine, Durham, NC, USA.&#xD;Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.&#xD;Duke University Medical Physics Program, Durham, NC, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Deep learning for segmentation of brain tumors: Impact of cross-institutional training and testing</style></title><secondary-title><style face="normal" font="default" size="100%">Med Phys</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Med Phys</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1150-1158</style></pages><volume><style face="normal" font="default" size="100%">45</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">Multimodal Brain Tumor Image Segmentation Benchmark (MICCAI-BraTS)</style></keyword><keyword><style face="normal" font="default" size="100%">Convolutional neural network (CNN)</style></keyword><keyword><style face="normal" font="default" size="100%">FMRIB Software Library (FSL)</style></keyword><keyword><style face="normal" font="default" size="100%">Dice similarity coefficient</style></keyword><keyword><style face="normal" font="default" size="100%">Average Hausdorff Distance</style></keyword><keyword><style face="normal" font="default" size="100%">brain tumor segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">glioblastoma</style></keyword><keyword><style face="normal" font="default" size="100%">impact of cross-institutional training</style></keyword><keyword><style face="normal" font="default" size="100%">magnetic resonance imaging</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Mar</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">2473-4209 (Electronic)&#xD;0094-2405 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29356028</style></accession-num><abstract><style face="normal" font="default" size="100%">BACKGROUND AND PURPOSE: Convolutional neural networks (CNNs) are commonly used for segmentation of brain tumors. In this work, we assess the effect of cross-institutional training on the performance of CNNs. METHODS: We selected 44 glioblastoma (GBM) patients from two institutions in The Cancer Imaging Archive dataset. The images were manually annotated by outlining each tumor component to form ground truth. To automatically segment the tumors in each patient, we trained three CNNs: (a) one using data for patients from the same institution as the test data, (b) one using data for the patients from the other institution and (c) one using data for the patients from both of the institutions. The performance of the trained models was evaluated using Dice similarity coefficients as well as Average Hausdorff Distance between the ground truth and automatic segmentations. The 10-fold cross-validation scheme was used to compare the performance of different approaches. RESULTS: Performance of the model significantly decreased (P &lt; 0.0001) when it was trained on data from a different institution (dice coefficients: 0.68 +/- 0.19 and 0.59 +/- 0.19) as compared to training with data from the same institution (dice coefficients: 0.72 +/- 0.17 and 0.76 +/- 0.12). This trend persisted for segmentation of the entire tumor as well as its individual components. CONCLUSIONS: There is a very strong effect of selecting data for training on performance of CNNs in a multi-institutional setting. Determination of the reasons behind this effect requires additional comprehensive investigation.</style></abstract><notes><style face="normal" font="default" size="100%">AlBadawy, Ehab A&#xD;Saha, Ashirbani&#xD;Mazurowski, Maciej A&#xD;eng&#xD;2018/01/23 06:00&#xD;Med Phys. 2018 Mar;45(3):1150-1158. doi: 10.1002/mp.12752. Epub 2018 Feb 8.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29356028</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1002/mp.12752</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>151</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">151</key></foreign-keys><ref-type name="Thesis">32</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Albalooshi, Fatema A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Self-organizing Approach to Learn a Level-set Function for Object Segmentation in Complex Background Environments</style></title></titles><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><publisher><style face="normal" font="default" size="100%">University of Dayton</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>402</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">402</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Albiol, Alberto</style></author><author><style face="normal" font="default" size="100%">Corbi, Alberto</style></author><author><style face="normal" font="default" size="100%">Albiol, Francisco</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Automatic intensity windowing of mammographic images based on a perceptual metric</style></title><secondary-title><style face="normal" font="default" size="100%">Medical Physics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Medical physics</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">Mammography, mutual information, algorithm development, Breast, Gabor filtering, TCGA-BRCA</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">2473-4209</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1002/mp.12144</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>623</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">623</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Alessandrino, Francesco</style></author><author><style face="normal" font="default" size="100%">Shinagare, Atul B</style></author><author><style face="normal" font="default" size="100%">Bossé, Dominick</style></author><author><style face="normal" font="default" size="100%">Choueiri, Toni K</style></author><author><style face="normal" font="default" size="100%">Krajewski, Katherine M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Radiogenomics in renal cell carcinoma</style></title><secondary-title><style face="normal" font="default" size="100%">Abdominal 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size="100%">1509044485</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>210</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">210</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">ARI, Ali</style></author><author><style face="normal" font="default" size="100%">ALPASLAN, Nuh</style></author><author><style face="normal" font="default" size="100%">HANBAY, Davut</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Beyin MR Görüntülerinden Bilgisayar Destekli Tümör Teşhisi Sistemi Computer-aided Tumor Detection System Using Brain MR Images</style></title><secondary-title><style face="normal" font="default" size="100%">Vogue</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Vogue</style></full-title></periodical><volume><style face="normal" font="default" size="100%">15</style></volume><number><style face="normal" font="default" size="100%">18</style></number><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>687</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">687</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Arimura, Hidetaka</style></author><author><style face="normal" font="default" size="100%">Soufi, Mazen</style></author><author><style face="normal" font="default" size="100%">Ninomiya, Kenta</style></author><author><style face="normal" font="default" size="100%">Kamezawa, Hidemi</style></author><author><style face="normal" font="default" size="100%">Yamada, Masahiro</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Potentials of radiomics for cancer diagnosis and treatment in comparison with computer-aided diagnosis</style></title><secondary-title><style face="normal" font="default" size="100%">Radiological Physics and Technology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiological Physics and Technology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">365-374</style></pages><volume><style face="normal" font="default" size="100%">11</style></volume><number><style face="normal" font="default" size="100%">4</style></number><keywords><keyword><style face="normal" font="default" size="100%">RIDER</style></keyword><keyword><style face="normal" font="default" size="100%">non-small cell lung cancer (NSCLC)</style></keyword><keyword><style face="normal" font="default" size="100%">computer-aided diagnosis (CAD)</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">segmentation</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">December 01</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1865-0341</style></isbn><abstract><style face="normal" font="default" size="100%">Computer-aided diagnosis (CAD) is a field that is essentially based on pattern recognition that improves the accuracy of a diagnosis made by a physician who takes into account the computer’s “opinion” derived from the quantitative analysis of radiological images. Radiomics is a field based on data science that massively and comprehensively analyzes a large number of medical images to extract a large number of phenotypic features reflecting disease traits, and explores the associations between the features and patients’ prognoses for precision medicine. According to the definitions for both, you may think that radiomics is not a paraphrase of CAD, but you may also think that these definitions are “image manipulation”. However, there are common and different features between the two fields. This review paper elaborates on these common and different features and introduces the potential of radiomics for cancer diagnosis and treatment by comparing it with CAD.</style></abstract><label><style face="normal" font="default" size="100%">Arimura2018</style></label><work-type><style face="normal" font="default" size="100%">journal article</style></work-type><urls><related-urls><url><style face="normal" font="default" size="100%">https://doi.org/10.1007/s12194-018-0486-x</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1007/s12194-018-0486-x</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>21</rec-number><foreign-keys><key app="EN" 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size="100%">Abdulkarim, Bassam</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prediction of survival with multi-scale radiomic analysis in glioblastoma patients</style></title><secondary-title><style face="normal" font="default" size="100%">Medical &amp; Biological Engineering &amp; Computing</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Medical &amp; biological engineering &amp; computing</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">radiomics, GBM</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">June 19</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1741-0444</style></isbn><abstract><style face="normal" font="default" size="100%">We propose a multiscale texture features based on Laplacian-of Gaussian (LoG) filter to predict progression free (PFS) and overall survival (OS) in patients newly diagnosed with glioblastoma (GBM). Experiments use the extracted features derived from 40 patients of GBM with T1-weighted imaging (T1-WI) and Fluid-attenuated inversion recovery (FLAIR) images that were segmented manually into areas of active tumor, necrosis, and edema. Multiscale texture features were extracted locally from each of these areas of interest using a LoG filter and the relation between features to OS and PFS was investigated using univariate (i.e., Spearman’s rank correlation coefficient, log-rank test and Kaplan-Meier estimator) and multivariate analyses (i.e., Random Forest classifier). Three and seven features were statistically correlated with PFS and OS, respectively, with absolute correlation values between 0.32 and 0.36 and p &lt; 0.05. Three features derived from active tumor regions only were associated with OS (p &lt; 0.05) with hazard ratios (HR) of 2.9, 3, and 3.24, respectively. Combined features showed an AUC value of 85.37 and 85.54% for predicting the PFS and OS of GBM patients, respectively, using the random forest (RF) classifier. We presented a multiscale texture features to characterize the GBM regions and predict he PFS and OS. The efficiency achievable suggests that this technique can be developed into a GBM MR analysis system suitable for clinical use after a thorough validation involving more patients.</style></abstract><label><style face="normal" font="default" size="100%">Chaddad2018</style></label><work-type><style face="normal" font="default" size="100%">journal article</style></work-type><urls><related-urls><url><style face="normal" font="default" size="100%">https://doi.org/10.1007/s11517-018-1858-4</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1007/s11517-018-1858-4</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>194</rec-number><foreign-keys><key app="EN" 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font="default" size="100%">Yang, Jinzhong</style></author><author><style face="normal" font="default" size="100%">Ding, Yao</style></author><author><style face="normal" font="default" size="100%">Jacobsen, Megan C</style></author><author><style face="normal" font="default" size="100%">Cardenas, Carlos E</style></author><author><style face="normal" font="default" size="100%">Fuller, Clifton D</style></author><author><style face="normal" font="default" size="100%">Howell, Rebecca M</style></author><author><style face="normal" font="default" size="100%">Li, Heng</style></author><author><style face="normal" font="default" size="100%">Stafford, R Jason</style></author><author><style face="normal" font="default" size="100%">Zhou, Shouhao</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Synthetic Head and Neck and Phantom Images for Determining Deformable Image Registration Accuracy in Magnetic Resonance 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</style></author><author><style face="normal" font="default" size="100%">Steinberg GK, </style></author><author><style face="normal" font="default" size="100%">Cheshier SH, </style></author><author><style face="normal" font="default" size="100%">Napel S, </style></author><author><style face="normal" font="default" size="100%">Zaharchuk G, </style></author><author><style face="normal" font="default" size="100%">Plevritis SK.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">TCIA</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features</style></title></titles><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><pub-location><style face="normal" font="default" size="100%">Saint Louis, </style></pub-location><urls></urls><custom3><style face="normal" font="default" size="100%">DICOM Images</style></custom3><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.7937/K9/TCIA.2014.RJEFTJBU</style></electronic-resource-num><remote-database-name><style face="normal" font="default" size="100%">The Cancer Imaging Archive (TCIA)</style></remote-database-name></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>36</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">36</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gevaert, Olivier</style></author><author><style face="normal" font="default" size="100%">Mitchell, Lex A</style></author><author><style face="normal" font="default" size="100%">Achrol, Achal S</style></author><author><style face="normal" font="default" size="100%">Xu, Jiajing</style></author><author><style face="normal" font="default" size="100%">Echegaray, Sebastian</style></author><author><style face="normal" font="default" size="100%">Steinberg, Gary K</style></author><author><style face="normal" font="default" size="100%">Cheshier, Samuel H</style></author><author><style face="normal" font="default" size="100%">Napel, Sandy</style></author><author><style face="normal" font="default" size="100%">Zaharchuk, Greg</style></author><author><style face="normal" font="default" size="100%">Plevritis, Sylvia K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features</style></title><secondary-title><style face="normal" font="default" size="100%">Radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></periodical><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><isbn><style face="normal" font="default" size="100%">0033-8419</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>139</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">139</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gevaert, O.</style></author><author><style face="normal" font="default" size="100%">Xu, J.</style></author><author><style face="normal" font="default" size="100%">Hoang, C. D.</style></author><author><style face="normal" font="default" size="100%">Leung, A. N.</style></author><author><style face="normal" font="default" size="100%">Xu, Y.</style></author><author><style face="normal" font="default" size="100%">Quon, A.</style></author><author><style face="normal" font="default" size="100%">Rubin, D. L.</style></author><author><style face="normal" font="default" size="100%">Napel, S.</style></author><author><style face="normal" font="default" size="100%">Plevritis, S. K.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results</style></title><secondary-title><style face="normal" font="default" size="100%">Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Radiology</style></alt-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></periodical><alt-periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></alt-periodical><pages><style face="normal" font="default" size="100%">387-96</style></pages><volume><style face="normal" font="default" size="100%">264</style></volume><number><style face="normal" font="default" size="100%">2</style></number><edition><style face="normal" font="default" size="100%">2012/06/23</style></edition><keywords><keyword><style face="normal" font="default" size="100%">Area Under Curve</style></keyword><keyword><style face="normal" font="default" size="100%">Carcinoma, Non-Small-Cell Lung/ genetics/radiography/radionuclide imaging</style></keyword><keyword><style face="normal" font="default" size="100%">Female</style></keyword><keyword><style face="normal" font="default" size="100%">Fluorodeoxyglucose F18/diagnostic use</style></keyword><keyword><style face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style face="normal" font="default" size="100%">Gene Expression Regulation, Neoplastic</style></keyword><keyword><style face="normal" font="default" size="100%">Humans</style></keyword><keyword><style face="normal" font="default" size="100%">Lung Neoplasms/ genetics/radiography/radionuclide imaging</style></keyword><keyword><style face="normal" font="default" size="100%">Male</style></keyword><keyword><style face="normal" font="default" size="100%">Metagenomics/ methods</style></keyword><keyword><style face="normal" font="default" size="100%">Microarray Analysis</style></keyword><keyword><style face="normal" font="default" size="100%">Positron-Emission Tomography/methods</style></keyword><keyword><style face="normal" font="default" size="100%">Predictive Value of Tests</style></keyword><keyword><style face="normal" font="default" size="100%">Prognosis</style></keyword><keyword><style face="normal" font="default" size="100%">Proportional Hazards Models</style></keyword><keyword><style face="normal" font="default" size="100%">Radiopharmaceuticals/diagnostic use</style></keyword><keyword><style face="normal" font="default" size="100%">Survival Analysis</style></keyword><keyword><style face="normal" font="default" size="100%">Tomography, X-Ray Computed/methods</style></keyword><keyword><style face="normal" font="default" size="100%">Tumor Markers, Biological/ analysis</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style face="normal" font="default" size="100%">Aug</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1527-1315 (Electronic)&#xD;0033-8419 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">22723499</style></accession-num><abstract><style face="normal" font="default" size="100%">PURPOSE: To identify prognostic imaging biomarkers in non-small cell lung cancer (NSCLC) by means of a radiogenomics strategy that integrates gene expression and medical images in patients for whom survival outcomes are not available by leveraging survival data in public gene expression data sets. MATERIALS AND METHODS: A radiogenomics strategy for associating image features with clusters of coexpressed genes (metagenes) was defined. First, a radiogenomics correlation map is created for a pairwise association between image features and metagenes. Next, predictive models of metagenes are built in terms of image features by using sparse linear regression. Similarly, predictive models of image features are built in terms of metagenes. Finally, the prognostic significance of the predicted image features are evaluated in a public gene expression data set with survival outcomes. This radiogenomics strategy was applied to a cohort of 26 patients with NSCLC for whom gene expression and 180 image features from computed tomography (CT) and positron emission tomography (PET)/CT were available. RESULTS: There were 243 statistically significant pairwise correlations between image features and metagenes of NSCLC. Metagenes were predicted in terms of image features with an accuracy of 59%-83%. One hundred fourteen of 180 CT image features and the PET standardized uptake value were predicted in terms of metagenes with an accuracy of 65%-86%. When the predicted image features were mapped to a public gene expression data set with survival outcomes, tumor size, edge shape, and sharpness ranked highest for prognostic significance. CONCLUSION: This radiogenomics strategy for identifying imaging biomarkers may enable a more rapid evaluation of novel imaging modalities, thereby accelerating their translation to personalized medicine.</style></abstract><notes><style face="normal" font="default" size="100%">Gevaert, Olivier&#xD;Xu, Jiajing&#xD;Hoang, Chuong D&#xD;Leung, Ann N&#xD;Xu, Yue&#xD;Quon, Andrew&#xD;Rubin, Daniel L&#xD;Napel, Sandy&#xD;Plevritis, Sylvia K&#xD;R01 CA160251/CA/NCI NIH HHS/United States&#xD;U01 CA142555/CA/NCI NIH HHS/United States&#xD;United States&#xD;Radiology. 2012 Aug;264(2):387-96. doi: 10.1148/radiol.12111607. Epub 2012 Jun 21.</style></notes><urls></urls><custom2><style face="normal" font="default" size="100%">PMC3401348</style></custom2><electronic-resource-num><style face="normal" font="default" size="100%">10.1148/radiol.12111607</style></electronic-resource-num><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider><language><style face="normal" font="default" size="100%">eng</style></language></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>87</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">87</key></foreign-keys><ref-type name="Dataset">59</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gevaert, O.</style></author><author><style face="normal" font="default" size="100%">Xu, J.</style></author><author><style face="normal" font="default" size="100%">Hoang, C. D.</style></author><author><style face="normal" font="default" size="100%">Leung, A. N.</style></author><author><style face="normal" font="default" size="100%">Xu, Y.</style></author><author><style face="normal" font="default" size="100%">Quon, A.</style></author><author><style face="normal" font="default" size="100%">Rubin, D. L.</style></author><author><style face="normal" font="default" size="100%">Napel, S.</style></author><author><style face="normal" font="default" size="100%">Plevritis, S. K.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">TCIA</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results.</style></title></titles><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><pub-location><style face="normal" font="default" size="100%">Saint Louis, </style></pub-location><urls></urls><custom3><style face="normal" font="default" size="100%">DICOM Images</style></custom3><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.7937/K9/TCIA.2014.X7ONY6B1</style></electronic-resource-num><remote-database-name><style face="normal" font="default" size="100%">The Cancer Imaging Archive (TCIA)</style></remote-database-name></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>484</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">484</key></foreign-keys><ref-type name="Thesis">32</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ghattas, Andrew Emile</style></author></authors><tertiary-authors><author><style face="normal" font="default" size="100%">Brian J. Smith</style></author></tertiary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Medical Imaging Segmentation Assessment via Bayesian Approaches to Fusion, Accuracy and Variability Estimation with Application to Head and Neck Cancer</style></title><secondary-title><style face="normal" font="default" size="100%">Biostatistics</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">214</style></pages><volume><style face="normal" font="default" size="100%">PhD</style></volume><number><style face="normal" font="default" size="100%">5759</style></number><keywords><keyword><style face="normal" font="default" size="100%">LIDC-IDRI</style></keyword><keyword><style face="normal" font="default" size="100%">QIN-HEADNECK</style></keyword><keyword><style face="normal" font="default" size="100%">head-neck cancer</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">The University of Iowa</style></publisher><urls><related-urls><url><style face="normal" font="default" size="100%">http://ir.uiowa.edu/etd/5759 </style></url></related-urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>518</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">518</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ghosh, Debjyoti</style></author><author><style face="normal" font="default" size="100%">Bandyopadhyay, Samir Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Brain tumor detection from MRI image: An approach</style></title><secondary-title><style face="normal" font="default" size="100%">IJAR</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">IJAR</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1152-1159</style></pages><volume><style face="normal" font="default" size="100%">3</style></volume><number><style face="normal" font="default" size="100%">6</style></number><keywords><keyword><style face="normal" font="default" size="100%">Algorithm Development, brain</style></keyword><keyword><style face="normal" font="default" size="100%">MRI</style></keyword><keyword><style face="normal" font="default" size="100%">binarization</style></keyword><keyword><style face="normal" font="default" size="100%">segmentation</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>403</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">403</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Giardino, Angela</style></author><author><style face="normal" font="default" size="100%">Gupta, Supriya</style></author><author><style face="normal" font="default" size="100%">Olson, Emmi</style></author><author><style face="normal" font="default" size="100%">Sepulveda, Karla</style></author><author><style face="normal" font="default" size="100%">Lenchik, Leon</style></author><author><style face="normal" font="default" size="100%">Ivanidze, Jana</style></author><author><style face="normal" font="default" size="100%">Rakow-Penner, Rebecca</style></author><author><style face="normal" font="default" size="100%">Patel, Midhir J</style></author><author><style face="normal" font="default" size="100%">Subramaniam, Rathan M</style></author><author><style face="normal" font="default" size="100%">Ganeshan, Dhakshinamoorthy</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Role of Imaging in the Era of Precision Medicine</style></title><secondary-title><style face="normal" font="default" size="100%">Academic Radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Academic radiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-11</style></pages><keywords><keyword><style face="normal" font="default" size="100%">TCIA-General, Radiomics</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1076-6332</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1016/j.acra.2016.11.021</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>589</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">589</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">E. Gibson</style></author><author><style face="normal" font="default" size="100%">F. Giganti</style></author><author><style face="normal" font="default" size="100%">Y. Hu</style></author><author><style face="normal" font="default" size="100%">E. Bonmati</style></author><author><style face="normal" font="default" size="100%">S. Bandula</style></author><author><style face="normal" font="default" size="100%">K. Gurusamy</style></author><author><style face="normal" font="default" size="100%">B. Davidson</style></author><author><style face="normal" font="default" size="100%">S. P. Pereira</style></author><author><style face="normal" font="default" size="100%">M. J. Clarkson</style></author><author><style face="normal" font="default" size="100%">D. C. Barratt</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Automatic Multi-organ Segmentation on Abdominal CT with Dense V-networks</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE Transactions on Medical Imaging</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">IEEE Transactions on Medical Imaging</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-1</style></pages><keywords><keyword><style face="normal" font="default" size="100%">Computed tomography</style></keyword><keyword><style face="normal" font="default" size="100%">Image segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">Kidney</style></keyword><keyword><style face="normal" font="default" size="100%">Liver</style></keyword><keyword><style face="normal" font="default" size="100%">Pancreas</style></keyword><keyword><style face="normal" font="default" size="100%">Three-dimensional displays</style></keyword><keyword><style face="normal" font="default" size="100%">Abdominal CT</style></keyword><keyword><style face="normal" font="default" size="100%">Deep learning</style></keyword><keyword><style face="normal" font="default" size="100%">Duodenum</style></keyword><keyword><style face="normal" font="default" size="100%">Esophagus</style></keyword><keyword><style face="normal" font="default" size="100%">Gallbladder</style></keyword><keyword><style face="normal" font="default" size="100%">Gastrointestinal tract</style></keyword><keyword><style face="normal" font="default" size="100%">Segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">Spleen</style></keyword><keyword><style face="normal" font="default" size="100%">Stomach</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">0278-0062</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1109/TMI.2018.2806309</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>493</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">493</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gibson, Eli</style></author><author><style face="normal" font="default" size="100%">Giganti, Francesco</style></author><author><style face="normal" font="default" size="100%">Hu, Yipeng</style></author><author><style face="normal" font="default" size="100%">Bonmati, Ester</style></author><author><style face="normal" font="default" size="100%">Bandula, Steve</style></author><author><style face="normal" font="default" size="100%">Gurusamy, Kurinchi</style></author><author><style face="normal" font="default" size="100%">Davidson, Brian R</style></author><author><style face="normal" font="default" size="100%">Pereira, Stephen P</style></author><author><style face="normal" font="default" size="100%">Clarkson, Matthew J</style></author><author><style face="normal" font="default" size="100%">Barratt, Dean C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Towards Image-Guided Pancreas and Biliary Endoscopy: Automatic Multi-organ Segmentation on Abdominal CT with Dense Dilated Networks</style></title><secondary-title><style face="normal" font="default" size="100%">International Conference on Medical Image Computing and Computer-Assisted Intervention</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">728-736</style></pages><volume><style face="normal" font="default" size="100%">10433</style></volume><keywords><keyword><style face="normal" font="default" size="100%">Algorithm Development</style></keyword><keyword><style face="normal" font="default" size="100%">abdominal CT</style></keyword><keyword><style face="normal" font="default" size="100%">segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">pancreas</style></keyword><keyword><style face="normal" font="default" size="100%">stomach</style></keyword><keyword><style face="normal" font="default" size="100%">liver</style></keyword><keyword><style face="normal" font="default" size="100%">esophagus</style></keyword><keyword><style face="normal" font="default" size="100%">deep learning</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">Springer</style></publisher><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://doi.org/10.1007/978-3-319-66182-7_83 </style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>557</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">557</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Giger, M. L.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Radiology, The University of Chicago, Chicago, Illinois. Electronic address: m-giger@uchicago.edu.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Machine Learning in Medical Imaging</style></title><secondary-title><style face="normal" font="default" size="100%">J Am Coll Radiol</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">J Am Coll Radiol</style></full-title></periodical><pages><style face="normal" font="default" size="100%">512-520</style></pages><volume><style face="normal" font="default" size="100%">15</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">Radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">Machine learning</style></keyword><keyword><style face="normal" font="default" size="100%">computer-aided diagnosis</style></keyword><keyword><style face="normal" font="default" size="100%">computer-assisted decision support</style></keyword><keyword><style face="normal" font="default" size="100%">deep learning</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 2</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1558-349X (Electronic)&#xD;1546-1440 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29398494</style></accession-num><abstract><style face="normal" font="default" size="100%">Advances in both imaging and computers have synergistically led to a rapid rise in the potential use of artificial intelligence in various radiological imaging tasks, such as risk assessment, detection, diagnosis, prognosis, and therapy response, as well as in multi-omics disease discovery. A brief overview of the field is given here, allowing the reader to recognize the terminology, the various subfields, and components of machine learning, as well as the clinical potential. Radiomics, an expansion of computer-aided diagnosis, has been defined as the conversion of images to minable data. The ultimate benefit of quantitative radiomics is to (1) yield predictive image-based phenotypes of disease for precision medicine or (2) yield quantitative image-based phenotypes for data mining with other -omics for discovery (ie, imaging genomics). For deep learning in radiology to succeed, note that well-annotated large data sets are needed since deep networks are complex, computer software and hardware are evolving constantly, and subtle differences in disease states are more difficult to perceive than differences in everyday objects. In the future, machine learning in radiology is expected to have a substantial clinical impact with imaging examinations being routinely obtained in clinical practice, providing an opportunity to improve decision support in medical image interpretation. The term of note is decision support, indicating that computers will augment human decision making, making it more effective and efficient. The clinical impact of having computers in the routine clinical practice may allow radiologists to further integrate their knowledge with their clinical colleagues in other medical specialties and allow for precision medicine.</style></abstract><notes><style face="normal" font="default" size="100%">Giger, Maryellen L&#xD;eng&#xD;2018/02/06 06:00&#xD;J Am Coll Radiol. 2018 Feb 2. pii: S1546-1440(17)31673-3. doi: 10.1016/j.jacr.2017.12.028.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29398494</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/j.jacr.2017.12.028</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>196</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">196</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gillies, Robert J</style></author><author><style face="normal" font="default" size="100%">Kinahan, Paul E</style></author><author><style face="normal" font="default" size="100%">Hricak, Hedvig</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Radiomics: Images are more than pictures, they are data</style></title><secondary-title><style face="normal" font="default" size="100%">Radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">151169</style></pages><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">0033-8419</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>521</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">521</key></foreign-keys><ref-type name="Conference Paper">47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gillmann, Christina</style></author><author><style face="normal" font="default" size="100%">Arbeláez, Pablo</style></author><author><style face="normal" font="default" size="100%">Peñaloza, José Tiberio Hernández</style></author><author><style face="normal" font="default" size="100%">Hagen, Hans</style></author><author><style face="normal" font="default" size="100%">Wischgoll, Thomas</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">B. 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JingJing</style></author><author><style face="normal" font="default" size="100%">Aurora, Tarun D</style></author><author><style face="normal" font="default" size="100%">Dunn, William D</style></author><author><style face="normal" font="default" size="100%">Scarpace, Lisa</style></author><author><style face="normal" font="default" size="100%">Mikkelsen, Tom</style></author><author><style face="normal" font="default" size="100%">Jain, Rajan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">MR Imaging Predictors of Molecular Profile and Survival: Multi-institutional Study of the TCGA Glioblastoma Data Set</style></title><secondary-title><style face="normal" font="default" size="100%">Radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></periodical><dates><year><style face="normal" font="default" 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Jayashree</style></author><author><style face="normal" font="default" size="100%">Erickson, Bradley</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer</style></title><secondary-title><style face="normal" font="default" size="100%">Frontiers in Neuroinformatics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Frontiers in Neuroinformatics</style></full-title></periodical><volume><style face="normal" font="default" size="100%">8</style></volume><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" 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font="default" size="100%">Somatic mutations associated with MRI-derived volumetric features in glioblastoma</style></title><secondary-title><style face="normal" font="default" size="100%">Neuroradiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Neuroradiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-11</style></pages><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">0028-3940</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>131</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">131</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Guvenis, A</style></author><author><style face="normal" font="default" size="100%">Koc, A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OPTIMISING DELINEATION ACCURACY OF TUMOURS IN PET FOR RADIOTHERAPY PLANNING USING BLIND DECONVOLUTION</style></title><secondary-title><style face="normal" font="default" size="100%">Radiation Protection Dosimetry</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiation Protection Dosimetry</style></full-title></periodical><pages><style face="normal" font="default" size="100%">ncv110</style></pages><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">0144-8420</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>690</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">690</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Halani, Sameer H</style></author><author><style face="normal" font="default" size="100%">Yousefi, Safoora</style></author><author><style face="normal" font="default" size="100%">Vega, Jose Velazquez</style></author><author><style face="normal" font="default" size="100%">Rossi, Michael R</style></author><author><style face="normal" font="default" size="100%">Zhao, Zheng</style></author><author><style face="normal" font="default" size="100%">Amrollahi, Fatemeh</style></author><author><style face="normal" font="default" size="100%">Holder, Chad A</style></author><author><style face="normal" font="default" size="100%">Baxter-Stoltzfus, Amelia</style></author><author><style face="normal" font="default" size="100%">Eschbacher, Jennifer</style></author><author><style face="normal" font="default" size="100%">Griffith, Brent</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways</style></title><secondary-title><style face="normal" font="default" size="100%">NPJ precision oncology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">NPJ precision oncology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">24</style></pages><volume><style face="normal" font="default" size="100%">2</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-LGG</style></keyword><keyword><style face="normal" font="default" size="100%">oligodendroglioma</style></keyword><keyword><style face="normal" font="default" size="100%">NOTCH1</style></keyword><keyword><style face="normal" font="default" size="100%">PIK3</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">2397-768X</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/s41698-018-0067-9</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>253</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">253</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Han, Hao</style></author><author><style face="normal" font="default" size="100%">Li, Lihong</style></author><author><style face="normal" font="default" size="100%">Han, Fangfang</style></author><author><style face="normal" font="default" size="100%">Zhang, Hao</style></author><author><style face="normal" font="default" size="100%">Moore, William</style></author><author><style face="normal" font="default" size="100%">Liang, Zhengrong</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Vector quantization-based automatic detection of pulmonary nodules in thoracic CT images</style></title><secondary-title><style face="normal" font="default" size="100%">Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), 2013 IEEE</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">1-4</style></pages><dates><year><style face="normal" font="default" size="100%">2013</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE</style></publisher><isbn><style face="normal" font="default" size="100%">147990533X</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>263</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">263</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Han, Hao</style></author><author><style face="normal" font="default" size="100%">Li, Lihong</style></author><author><style face="normal" font="default" size="100%">Wang, Huafeng</style></author><author><style face="normal" font="default" size="100%">Zhang, Hao</style></author><author><style face="normal" font="default" size="100%">Moore, William</style></author><author><style face="normal" font="default" size="100%">Liang, Zhengrong</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A novel computer-aided detection system for pulmonary nodule identification in CT images</style></title><secondary-title><style face="normal" font="default" size="100%">SPIE Medical Imaging</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">90352D-90352D-8</style></pages><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><publisher><style face="normal" font="default" size="100%">International Society for Optics and Photonics</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>582</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">582</key></foreign-keys><ref-type name="Conference Paper">47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Han, Lichy</style></author><author><style face="normal" font="default" size="100%">Kamdar, Maulik R.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Russ B Altman (Stanford), </style></author><author><style face="normal" font="default" size="100%">A Keith Dunker (Indiana University, USA), </style></author><author><style face="normal" font="default" size="100%">Lawrence Hunter (University of Colorado Health Sciences Center, USA), </style></author><author><style face="normal" font="default" size="100%">Marylyn D Ritchie (Geisinger Health System, USA), </style></author><author><style face="normal" font="default" size="100%">Tiffany A Murray (Stanford), </style></author><author><style face="normal" font="default" size="100%">Teri E Klein (Stanford)</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks</style></title><secondary-title><style face="normal" font="default" size="100%">Pacific Symposium on Biocomputing 2018</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">331-342</style></pages><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">Radiogenomics</style></keyword><keyword><style face="normal" font="default" size="100%">bi-directional convolutional neural network (CRNN)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">2018</style></date></pub-dates></dates><pub-location><style face="normal" font="default" size="100%">Kohala Coast, Hawaii, USA</style></pub-location><abstract><style face="normal" font="default" size="100%">Glioblastoma Multiforme (GBM), a malignant brain tumor, is among the most lethal of all cancers. Temozolomide is the primary chemotherapy treatment for patients diagnosed with GBM. The methylation status of the promoter or the enhancer regions of the O6− methylguanine methyltransferase (MGMT) gene may impact the efficacy and sensitivity of temozolomide, and hence may affect overall patient survival. Microscopic genetic changes may manifest as macroscopic morphological changes in the brain tumors that can be detected using magnetic resonance imaging (MRI), which can serve as noninvasive biomarkers for determining methylation of MGMT regulatory regions. In this research, we use a compendium of brain MRI scans of GBM patients collected from The Cancer Imaging Archive (TCIA) combined with methylation data from The Cancer Genome Atlas (TCGA) to predict the methylation state of the MGMT regulatory regions in these patients. Our approach relies on a bi-directional convolutional recurrent neural network architecture (CRNN) that leverages the spatial aspects of these 3-dimensional MRI scans. Our CRNN obtains an accuracy of 67% on the validation data and 62% on the test data, with precision and recall both at 67%, suggesting the existence of MRI features that may complement existing markers for GBM patient stratification and prognosis. We have additionally presented our model via a novel neural network visualization platform, which we have developed to improve interpretability of deep learning MRI-based classification models.</style></abstract><urls></urls><custom2><style face="normal" font="default" size="100%">PMC5728677</style></custom2><electronic-resource-num><style face="normal" font="default" size="100%">10.1142/9789813235533_0031</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>415</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">415</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hancock, Matthew C</style></author><author><style face="normal" font="default" size="100%">Magnan, Jerry F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Predictive capabilities of statistical learning methods for lung nodule malignancy classification using diagnostic image features: an investigation using the Lung Image Database Consortium dataset</style></title><secondary-title><style face="normal" font="default" size="100%">SPIE Medical Imaging</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">1013425-1013425-12</style></pages><keywords><keyword><style face="normal" font="default" size="100%">LIDC-IDRI</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">International Society for Optics and Photonics</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>58</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">58</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Harmon, S</style></author><author><style face="normal" font="default" size="100%">Wendelberger, B</style></author><author><style face="normal" font="default" size="100%">Jeraj, R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SU-E-J-98: Radiogenomics: Correspondence Between Imaging and Genetic Features Based On Clustering Analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Medical Physics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Medical physics</style></full-title></periodical><pages><style face="normal" font="default" size="100%">178-178</style></pages><volume><style face="normal" font="default" size="100%">41</style></volume><number><style face="normal" font="default" size="100%">6</style></number><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><urls><related-urls><url><style face="normal" font="default" size="100%">http://scitation.aip.org/content/aapm/journal/medphys/41/6/10.1118/1.4888150</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">doi:http://dx.doi.org/10.1118/1.4888150</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>674</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">674</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">He, Bo</style></author><author><style face="normal" font="default" size="100%">Zhao, Wei</style></author><author><style face="normal" font="default" size="100%">Pi, Jiang-Yuan</style></author><author><style face="normal" font="default" size="100%">Han, Dan</style></author><author><style face="normal" font="default" size="100%">Jiang, Yuan-Ming</style></author><author><style face="normal" font="default" size="100%">Zhang, Zhen-Guang</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A biomarker basing on radiomics for the prediction of overall survival in non–small cell lung cancer patients</style></title><secondary-title><style face="normal" font="default" size="100%">Respiratory research</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Respiratory research</style></full-title></periodical><pages><style face="normal" font="default" size="100%">199</style></pages><volume><style face="normal" font="default" size="100%">19</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">non-small cell lung cancer</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">1465-993X</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1186/s12931-018-0887-8</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" 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font="default" size="100%">Chen, Yiyi</style></author><author><style face="normal" font="default" size="100%">Fedorov, Andriy</style></author><author><style face="normal" font="default" size="100%">Li, Xia</style></author><author><style face="normal" font="default" size="100%">Jajamovich, Guido H</style></author><author><style face="normal" font="default" size="100%">Malyarenko, Dariya I</style></author><author><style face="normal" font="default" size="100%">Aryal, Madhava P</style></author><author><style face="normal" font="default" size="100%">LaViolette, Peter S</style></author><author><style face="normal" font="default" size="100%">Oborski, Matthew J</style></author><author><style face="normal" font="default" size="100%">O&apos;Sullivan, Finbarr</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Impact of Arterial Input Function Determination Variations on Prostate Dynamic Contrast-Enhanced Magnetic Resonance Imaging Pharmacokinetic Modeling: A Multicenter Data Analysis Challenge</style></title><secondary-title><style face="normal" font="default" size="100%">Tomography: a journal for imaging research</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Tomography: a journal for imaging research</style></full-title></periodical><pages><style face="normal" font="default" size="100%">56</style></pages><volume><style face="normal" font="default" size="100%">2</style></volume><number><style face="normal" font="default" size="100%">1</style></number><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>91</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">91</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Huang, W.</style></author><author><style face="normal" font="default" size="100%">Li, X.</style></author><author><style face="normal" font="default" size="100%">Chen, Y.</style></author><author><style face="normal" font="default" size="100%">Li, X.</style></author><author><style face="normal" font="default" size="100%">Chang, M. C.</style></author><author><style face="normal" font="default" size="100%">Oborski, M. J.</style></author><author><style face="normal" font="default" size="100%">Malyarenko, D. I.</style></author><author><style face="normal" font="default" size="100%">Muzi, M.</style></author><author><style face="normal" font="default" size="100%">Jajamovich, G. H.</style></author><author><style face="normal" font="default" size="100%">Fedorov, A.</style></author><author><style face="normal" font="default" size="100%">Tudorica, A.</style></author><author><style face="normal" font="default" size="100%">Gupta, S. N.</style></author><author><style face="normal" font="default" size="100%">Laymon, C. M.</style></author><author><style face="normal" font="default" size="100%">Marro, K. I.</style></author><author><style face="normal" font="default" size="100%">Dyvorne, H. A.</style></author><author><style face="normal" font="default" size="100%">Miller, J. V.</style></author><author><style face="normal" font="default" size="100%">Barbodiak, D. P.</style></author><author><style face="normal" font="default" size="100%">Chenevert, T. L.</style></author><author><style face="normal" font="default" size="100%">Yankeelov, T. E.</style></author><author><style face="normal" font="default" size="100%">Mountz, J. M.</style></author><author><style face="normal" font="default" size="100%">Kinahan, P. E.</style></author><author><style face="normal" font="default" size="100%">Kikinis, R.</style></author><author><style face="normal" font="default" size="100%">Taouli, B.</style></author><author><style face="normal" font="default" size="100%">Fennessy, F.</style></author><author><style face="normal" font="default" size="100%">Kalpathy-Cramer, J.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Oregon Health and Science University, Portland, OR.&#xD;Vanderbilt University, Nashville, TN.&#xD;General Electric Global Research, Niskayuna, NY.&#xD;University of Pittsburgh, Pittsburgh, PA.&#xD;University of Michigan, Ann Arbor, MI.&#xD;University of Washington, Seattle, WA.&#xD;Icahn School of Medicine at Mount Sinai, New York, NY.&#xD;Brigham and Women&apos;s Hospital and Harvard Medical School, Boston, MA.&#xD;Duke University, Durham, NC.&#xD;Massachusetts General Hospital and Harvard Medical School, Boston, MA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge</style></title><secondary-title><style face="normal" font="default" size="100%">Transl Oncol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Translational oncology</style></alt-title></titles><alt-periodical><full-title><style face="normal" font="default" size="100%">Translational oncology</style></full-title></alt-periodical><pages><style face="normal" font="default" size="100%">153-66</style></pages><volume><style face="normal" font="default" size="100%">7</style></volume><number><style face="normal" font="default" size="100%">1</style></number><edition><style face="normal" font="default" size="100%">2014/04/29</style></edition><dates><year><style face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1936-5233 (Electronic)&#xD;1936-5233 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">24772219</style></accession-num><abstract><style face="normal" font="default" size="100%">Pharmacokinetic analysis of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) time-course data allows estimation of quantitative parameters such as K (trans) (rate constant for plasma/interstitium contrast agent transfer), v e (extravascular extracellular volume fraction), and v p (plasma volume fraction). A plethora of factors in DCE-MRI data acquisition and analysis can affect accuracy and precision of these parameters and, consequently, the utility of quantitative DCE-MRI for assessing therapy response. In this multicenter data analysis challenge, DCE-MRI data acquired at one center from 10 patients with breast cancer before and after the first cycle of neoadjuvant chemotherapy were shared and processed with 12 software tools based on the Tofts model (TM), extended TM, and Shutter-Speed model. Inputs of tumor region of interest definition, pre-contrast T1, and arterial input function were controlled to focus on the variations in parameter value and response prediction capability caused by differences in models and associated algorithms. Considerable parameter variations were observed with the within-subject coefficient of variation (wCV) values for K (trans) and v p being as high as 0.59 and 0.82, respectively. Parameter agreement improved when only algorithms based on the same model were compared, e.g., the K (trans) intraclass correlation coefficient increased to as high as 0.84. Agreement in parameter percentage change was much better than that in absolute parameter value, e.g., the pairwise concordance correlation coefficient improved from 0.047 (for K (trans)) to 0.92 (for K (trans) percentage change) in comparing two TM algorithms. Nearly all algorithms provided good to excellent (univariate logistic regression c-statistic value ranging from 0.8 to 1.0) early prediction of therapy response using the metrics of mean tumor K (trans) and k ep (=K (trans)/v e, intravasation rate constant) after the first therapy cycle and the corresponding percentage changes. The results suggest that the interalgorithm parameter variations are largely systematic, which are not likely to significantly affect the utility of DCE-MRI for assessment of therapy response.</style></abstract><notes><style face="normal" font="default" size="100%">Huang, Wei&#xD;Li, Xin&#xD;Chen, Yiyi&#xD;Li, Xia&#xD;Chang, Ming-Ching&#xD;Oborski, Matthew J&#xD;Malyarenko, Dariya I&#xD;Muzi, Mark&#xD;Jajamovich, Guido H&#xD;Fedorov, Andriy&#xD;Tudorica, Alina&#xD;Gupta, Sandeep N&#xD;Laymon, Charles M&#xD;Marro, Kenneth I&#xD;Dyvorne, Hadrien A&#xD;Miller, James V&#xD;Barbodiak, Daniel P&#xD;Chenevert, Thomas L&#xD;Yankeelov, Thomas E&#xD;Mountz, James M&#xD;Kinahan, Paul E&#xD;Kikinis, Ron&#xD;Taouli, Bachir&#xD;Fennessy, Fiona&#xD;Kalpathy-Cramer, Jayashree&#xD;R00 LM009889/LM/NLM NIH HHS/United States&#xD;U01 CA151261/CA/NCI NIH HHS/United States&#xD;U01 CA154601/CA/NCI NIH HHS/United States&#xD;U01 CA154602/CA/NCI NIH HHS/United States&#xD;U01 CA166104/CA/NCI NIH HHS/United States&#xD;United States&#xD;Transl Oncol. 2014 Feb 1;7(1):153-66. eCollection 2014 Feb.</style></notes><urls></urls><custom2><style face="normal" font="default" size="100%">PMC3998693</style></custom2><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider><language><style face="normal" font="default" size="100%">eng</style></language></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>92</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">92</key></foreign-keys><ref-type name="Dataset">59</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Huang, W.</style></author><author><style face="normal" font="default" size="100%">Li, X.</style></author><author><style face="normal" font="default" size="100%">Chen, Y.</style></author><author><style face="normal" font="default" size="100%">Li, X.</style></author><author><style face="normal" font="default" size="100%">Chang, M. C.</style></author><author><style face="normal" font="default" size="100%">Oborski, M. J.</style></author><author><style face="normal" font="default" size="100%">Malyarenko, D. I.</style></author><author><style face="normal" font="default" size="100%">Muzi, M.</style></author><author><style face="normal" font="default" size="100%">Jajamovich, G. H.</style></author><author><style face="normal" font="default" size="100%">Fedorov, A.</style></author><author><style face="normal" font="default" size="100%">Tudorica, A.</style></author><author><style face="normal" font="default" size="100%">Gupta, S. N.</style></author><author><style face="normal" font="default" size="100%">Laymon, C. M.</style></author><author><style face="normal" font="default" size="100%">Marro, K. I.</style></author><author><style face="normal" font="default" size="100%">Dyvorne, H. A.</style></author><author><style face="normal" font="default" size="100%">Miller, J. V.</style></author><author><style face="normal" font="default" size="100%">Barbodiak, D. P.</style></author><author><style face="normal" font="default" size="100%">Chenevert, T. L.</style></author><author><style face="normal" font="default" size="100%">Yankeelov, T. E.</style></author><author><style face="normal" font="default" size="100%">Mountz, J. M.</style></author><author><style face="normal" font="default" size="100%">Kinahan, P. E.</style></author><author><style face="normal" font="default" size="100%">Kikinis, R.</style></author><author><style face="normal" font="default" size="100%">Taouli, B.</style></author><author><style face="normal" font="default" size="100%">Fennessy, F.</style></author><author><style face="normal" font="default" size="100%">Kalpathy-Cramer, J.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">TCIA</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge</style></title></titles><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><pub-location><style face="normal" font="default" size="100%">Saint Louis, </style></pub-location><urls></urls><custom3><style face="normal" font="default" size="100%">DICOM, Matlab, NIFTI</style></custom3><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.7937/K9/TCIA.2014.A2N1IXOX</style></electronic-resource-num><remote-database-name><style face="normal" font="default" size="100%">The Cancer Imaging Archive (TCIA)</style></remote-database-name></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>399</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">399</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hugo, Geoffrey D</style></author><author><style face="normal" font="default" size="100%">Weiss, Elisabeth</style></author><author><style face="normal" font="default" size="100%">Sleeman, William C</style></author><author><style face="normal" font="default" size="100%">Balik, Salim</style></author><author><style face="normal" font="default" size="100%">Keall, Paul J</style></author><author><style face="normal" font="default" size="100%">Lu, Jun</style></author><author><style face="normal" font="default" size="100%">Williamson, Jeffrey F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A longitudinal four‐dimensional computed tomography and cone beam computed tomography dataset for image‐guided radiation therapy research in lung cancer</style></title><secondary-title><style face="normal" font="default" size="100%">Medical Physics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Medical physics</style></full-title></periodical><pages><style face="normal" font="default" size="100%">762–771</style></pages><volume><style face="normal" 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Luke</style></author></authors><tertiary-authors><author><style face="normal" font="default" size="100%">Lawrence Court</style></author></tertiary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Radiomics of NSCLC: Quantitative CT Image Feature Characterization and Tumor Shrinkage Prediction</style></title></titles><volume><style face="normal" font="default" size="100%">MS </style></volume><dates><year><style face="normal" font="default" size="100%">2013</style></year></dates><publisher><style face="normal" font="default" size="100%">University of Texas</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>489</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">489</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hussain, Mohammad Arafat</style></author><author><style face="normal" font="default" size="100%">Amir-Khalili, Alborz</style></author><author><style face="normal" font="default" size="100%">Hamarneh, Ghassan</style></author><author><style face="normal" font="default" size="100%">Abugharbieh, Rafeef</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Collage CNN for Renal Cell Carcinoma Detection from CT</style></title><secondary-title><style face="normal" font="default" size="100%">International Workshop on Machine Learning in Medical Imaging</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">229-237</style></pages><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">Springer</style></publisher><notes><style face="normal" font="default" size="100%">TCGA-RCC; renal-cell carcinoma; image collage-based deep convolutional neural network (CNN); multiple-instance learning</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://link.springer.com/chapter/10.1007/978-3-319-67389-9_27 </style></url></related-urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>423</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">423</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hyare, Harpreet</style></author><author><style face="normal" font="default" size="100%">Thust, Steffi</style></author><author><style face="normal" font="default" size="100%">Rees, Jeremy</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Advanced MRI Techniques in the Monitoring of Treatment of Gliomas</style></title><secondary-title><style face="normal" font="default" size="100%">Current treatment options in neurology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Current treatment options in neurology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">11</style></pages><volume><style face="normal" font="default" size="100%">19</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM, glioma</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1092-8480</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>537</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">537</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Iqbal, Sajid</style></author><author><style face="normal" font="default" size="100%">Ghani, M Usman</style></author><author><style face="normal" font="default" size="100%">Saba, Tanzila</style></author><author><style face="normal" font="default" size="100%">Rehman, Amjad</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Brain tumor segmentation in multi‐spectral MRI using convolutional neural networks (CNN)</style></title><secondary-title><style face="normal" font="default" size="100%">Microscopy research and technique</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Microscopy research and technique</style></full-title></periodical><pages><style face="normal" font="default" size="100%">419-427</style></pages><volume><style face="normal" font="default" size="100%">81</style></volume><number><style face="normal" font="default" size="100%">4</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-LGG</style></keyword><keyword><style face="normal" font="default" size="100%">MICCAI-BraTS</style></keyword><keyword><style face="normal" font="default" size="100%">BRATS datasets</style></keyword><keyword><style face="normal" font="default" size="100%">convolutional neural networks</style></keyword><keyword><style face="normal" font="default" size="100%">deep 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N</style></author><author><style face="normal" font="default" size="100%">Holder, Chad</style></author><author><style face="normal" font="default" size="100%">Wintermark, Max</style></author><author><style face="normal" font="default" size="100%">Colen, Rivka R</style></author><author><style face="normal" font="default" size="100%">Kirby, Justin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic mapping and survival prediction in glioblastoma: molecular subclassification strengthened by hemodynamic imaging biomarkers</style></title><secondary-title><style face="normal" font="default" size="100%">Radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">212-220</style></pages><volume><style face="normal" font="default" size="100%">267</style></volume><number><style 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face="normal" font="default" size="100%">Rosenblum, ML</style></author><author><style face="normal" font="default" size="100%">Rempel, S</style></author><author><style face="normal" font="default" size="100%">Mikkelsen, T</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Correlation of perfusion parameters with genes related to angiogenesis regulation in glioblastoma: a feasibility study</style></title><secondary-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1343-1348</style></pages><volume><style face="normal" font="default" size="100%">33</style></volume><number><style face="normal" font="default" size="100%">7</style></number><dates><year><style face="normal" font="default" size="100%">2012</style></year></dates><isbn><style face="normal" font="default" size="100%">0195-6108</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>88</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">88</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jain, R.</style></author><author><style face="normal" font="default" size="100%">Poisson, L. M.</style></author><author><style face="normal" font="default" size="100%">Gutman, D.</style></author><author><style face="normal" font="default" size="100%">Scarpace, L.</style></author><author><style face="normal" font="default" size="100%">Hwang, S. N.</style></author><author><style face="normal" font="default" size="100%">Holder, C. A.</style></author><author><style face="normal" font="default" size="100%">Wintermark, M.</style></author><author><style face="normal" font="default" size="100%">Rao, A.</style></author><author><style face="normal" font="default" size="100%">Colen, R. R.</style></author><author><style face="normal" font="default" size="100%">Kirby, J.</style></author><author><style face="normal" font="default" size="100%">Freymann, J.</style></author><author><style face="normal" font="default" size="100%">Jaffe, C. C.</style></author><author><style face="normal" font="default" size="100%">Mikkelsen, T.</style></author><author><style face="normal" font="default" size="100%">Flanders, A.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">From the Division of Neuroradiology, Department of Radiology (R.J.), Bioinformatics Center, Department of Public Health Sciences (L.M.P.), and Department of Neurosurgery (R.J., L.S., T.M.), Henry Ford Health System, 2799 W Grand Blvd, Detroit, MI 48202; Department of Radiology, Emory University, Atlanta, Ga (D.G., C.A.H.); Department of Radiology, St Jude&apos;s Children&apos;s Research Hospital, Memphis, Tenn (S.N.H.); Department of Radiology, University of Virginia, Charlottesville, Va (M.W.); Department of Radiology, MD Anderson Cancer Center, Houston, Tex (A.R.); Department of Radiology, Brigham and Women&apos;s Hospital, Boston, Mass (R.R.C.); Clinical Research Directorate, CMRP, SAIC-Frederick, NCI-Frederick, Frederick, Md (J.K., J.F.); Department of Radiology, Boston University, Boston, Mass (C.C.J.); and Department of Radiology, Thomas Jefferson University Hospital, Philadelphia, Pa (A.F.).</style></auth-address><titles><title><style face="normal" font="default" size="100%">Outcome prediction in patients with glioblastoma by using imaging, clinical, and genomic biomarkers: focus on the nonenhancing component of the tumor</style></title><secondary-title><style face="normal" font="default" size="100%">Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Radiology</style></alt-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></periodical><alt-periodical><full-title><style face="normal" font="default" size="100%">Radiology</style></full-title></alt-periodical><pages><style face="normal" font="default" size="100%">484-93</style></pages><volume><style face="normal" font="default" size="100%">272</style></volume><number><style face="normal" font="default" size="100%">2</style></number><edition><style face="normal" font="default" size="100%">2014/03/22</style></edition><keywords><keyword><style face="normal" font="default" size="100%">Brain Neoplasms/ genetics/ pathology/surgery</style></keyword><keyword><style face="normal" font="default" size="100%">Contrast Media/diagnostic use</style></keyword><keyword><style face="normal" font="default" size="100%">Female</style></keyword><keyword><style face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style face="normal" font="default" size="100%">Glioblastoma/ genetics/ pathology/surgery</style></keyword><keyword><style face="normal" font="default" size="100%">Humans</style></keyword><keyword><style face="normal" font="default" size="100%">Image Enhancement/methods</style></keyword><keyword><style face="normal" font="default" size="100%">Image Interpretation, Computer-Assisted/methods</style></keyword><keyword><style face="normal" font="default" size="100%">Magnetic Resonance Imaging/ methods</style></keyword><keyword><style face="normal" font="default" size="100%">Male</style></keyword><keyword><style face="normal" font="default" size="100%">Predictive Value of Tests</style></keyword><keyword><style face="normal" font="default" size="100%">Prognosis</style></keyword><keyword><style face="normal" font="default" size="100%">Retrospective Studies</style></keyword><keyword><style face="normal" font="default" size="100%">Risk Factors</style></keyword><keyword><style face="normal" font="default" size="100%">Survival Rate</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style face="normal" font="default" size="100%">Aug</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1527-1315 (Electronic)&#xD;0033-8419 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">24646147</style></accession-num><abstract><style face="normal" font="default" size="100%">PURPOSE: To correlate patient survival with morphologic imaging features and hemodynamic parameters obtained from the nonenhancing region (NER) of glioblastoma (GBM), along with clinical and genomic markers. MATERIALS AND METHODS: An institutional review board waiver was obtained for this HIPAA-compliant retrospective study. Forty-five patients with GBM underwent baseline imaging with contrast material-enhanced magnetic resonance (MR) imaging and dynamic susceptibility contrast-enhanced T2*-weighted perfusion MR imaging. Molecular and clinical predictors of survival were obtained. Single and multivariable models of overall survival (OS) and progression-free survival (PFS) were explored with Kaplan-Meier estimates, Cox regression, and random survival forests. RESULTS: Worsening OS (log-rank test, P = .0103) and PFS (log-rank test, P = .0223) were associated with increasing relative cerebral blood volume of NER (rCBVNER), which was higher with deep white matter involvement (t test, P = .0482) and poor NER margin definition (t test, P = .0147). NER crossing the midline was the only morphologic feature of NER associated with poor survival (log-rank test, P = .0125). Preoperative Karnofsky performance score (KPS) and resection extent (n = 30) were clinically significant OS predictors (log-rank test, P = .0176 and P = .0038, respectively). No genomic alterations were associated with survival, except patients with high rCBVNER and wild-type epidermal growth factor receptor (EGFR) mutation had significantly poor survival (log-rank test, P = .0306; area under the receiver operating characteristic curve = 0.62). Combining resection extent with rCBVNER marginally improved prognostic ability (permutation, P = .084). Random forest models of presurgical predictors indicated rCBVNER as the top predictor; also important were KPS, age at diagnosis, and NER crossing the midline. A multivariable model containing rCBVNER, age at diagnosis, and KPS can be used to group patients with more than 1 year of difference in observed median survival (0.49-1.79 years). CONCLUSION: Patients with high rCBVNER and NER crossing the midline and those with high rCBVNER and wild-type EGFR mutation showed poor survival. In multivariable survival models, however, rCBVNER provided unique prognostic information that went above and beyond the assessment of all NER imaging features, as well as clinical and genomic features.</style></abstract><notes><style face="normal" font="default" size="100%">Jain, Rajan&#xD;Poisson, Laila M&#xD;Gutman, David&#xD;Scarpace, Lisa&#xD;Hwang, Scott N&#xD;Holder, Chad A&#xD;Wintermark, Max&#xD;Rao, Arvind&#xD;Colen, Rivka R&#xD;Kirby, Justin&#xD;Freymann, John&#xD;Jaffe, C Carl&#xD;Mikkelsen, Tom&#xD;Flanders, Adam&#xD;United States&#xD;Radiology. 2014 Aug;272(2):484-93. doi: 10.1148/radiol.14131691. Epub 2014 Mar 19.</style></notes><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1148/radiol.14131691</style></electronic-resource-num><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider><language><style face="normal" font="default" size="100%">eng</style></language></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>89</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">89</key></foreign-keys><ref-type name="Dataset">59</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jain, R.</style></author><author><style face="normal" font="default" size="100%">Poisson, L. M.</style></author><author><style face="normal" font="default" size="100%">Gutman, D.</style></author><author><style face="normal" font="default" size="100%">Scarpace, L.</style></author><author><style face="normal" font="default" size="100%">Hwang, S. N.</style></author><author><style face="normal" font="default" size="100%">Holder, C. A.</style></author><author><style face="normal" font="default" size="100%">Wintermark, M.</style></author><author><style face="normal" font="default" size="100%">Rao, A.</style></author><author><style face="normal" font="default" size="100%">Colen, R. R.</style></author><author><style face="normal" font="default" size="100%">Kirby, J.</style></author><author><style face="normal" font="default" size="100%">Freymann, J.</style></author><author><style face="normal" font="default" size="100%">Jaffe, C. 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Cancer Imaging Archive (TCIA)</style></remote-database-name></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>314</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">314</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jajamovich, Guido H</style></author><author><style face="normal" font="default" size="100%">Valiathan, Chandni R</style></author><author><style face="normal" font="default" size="100%">Cristescu, Razvan</style></author><author><style face="normal" font="default" size="100%">Somayajula, Sangeetha</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Integrative analysis of diffusion-weighted MRI and genomic 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Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lachinov, Dmitry</style></author><author><style face="normal" font="default" size="100%">Vasiliev, Evgeny</style></author><author><style face="normal" font="default" size="100%">Turlapov, Vadim</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Glioma Segmentation with Cascaded Unet</style></title><secondary-title><style face="normal" font="default" size="100%">arXiv preprint arXiv:1810.04008</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">arXiv preprint arXiv:1810.04008</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">TCGA-LGG</style></keyword><keyword><style face="normal" font="default" size="100%">BraTS</style></keyword><keyword><style face="normal" font="default" size="100%">glioma</style></keyword><keyword><style face="normal" font="default" size="100%">segmentation</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>526</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">526</key></foreign-keys><ref-type name="Thesis">32</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lambrecht, Joren</style></author></authors><tertiary-authors><author><style face="normal" font="default" size="100%">Prof. dr. Roel Van Holen</style></author></tertiary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Textural Analysis of Tumour Imaging: A Radiomics Approach</style></title><secondary-title><style face="normal" font="default" size="100%">Electronics and Information Systems</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">108</style></pages><volume><style face="normal" font="default" size="100%">MS in Biomedical Engineering</style></volume><keywords><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">NSCLC-Radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">RIDER-LUNG-CT</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA-LGG</style></keyword><keyword><style face="normal" font="default" size="100%">REMBRANDT</style></keyword><keyword><style face="normal" font="default" size="100%">VASARI</style></keyword><keyword><style face="normal" font="default" size="100%">texture analysis</style></keyword><keyword><style face="normal" font="default" size="100%">lung tumour</style></keyword><keyword><style face="normal" font="default" size="100%">CT</style></keyword><keyword><style face="normal" font="default" size="100%">brain tumour</style></keyword><keyword><style face="normal" font="default" size="100%">MRI</style></keyword><keyword><style face="normal" font="default" size="100%">clustering</style></keyword><keyword><style face="normal" font="default" size="100%">random forest</style></keyword><keyword><style face="normal" font="default" size="100%">neural network</style></keyword><keyword><style face="normal" font="default" size="100%">machine learning</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics signature</style></keyword><keyword><style face="normal" font="default" size="100%">biopsy</style></keyword><keyword><style face="normal" font="default" size="100%">tumour heterogeneity</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><pub-location><style face="normal" font="default" size="100%">Ghent, Belgium</style></pub-location><publisher><style face="normal" font="default" size="100%">Ghent University</style></publisher><urls><related-urls><url><style face="normal" font="default" size="100%">https://lib.ugent.be/nl/catalog/rug01:002367219?access=online&amp;faculty=TW-PP-GE&amp;i=1765&amp;sticky=type-access-faculty&amp;type=master  </style></url></related-urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>510</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">510</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lan, Rushi</style></author><author><style face="normal" font="default" size="100%">Zhong, Si</style></author><author><style face="normal" font="default" size="100%">Liu, Zhenbing</style></author><author><style face="normal" font="default" size="100%">Shi, Zhuo</style></author><author><style face="normal" font="default" size="100%">Luo, Xiaonan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A simple texture feature for retrieval of medical images</style></title><secondary-title><style face="normal" font="default" size="100%">Multimedia Tools and Applications</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Multimedia Tools and Applications</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-14</style></pages><keywords><keyword><style face="normal" font="default" size="100%">medical image retrieval</style></keyword><keyword><style face="normal" font="default" size="100%">texture feature</style></keyword><keyword><style face="normal" font="default" size="100%">Gabor and Schimid filtering</style></keyword><keyword><style face="normal" font="default" size="100%">BoW model</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1380-7501</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/s11042-017-5341-2</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>560</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">560</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Langer, S. G.</style></author><author><style face="normal" font="default" size="100%">Shih, G.</style></author><author><style face="normal" font="default" size="100%">Nagy, P.</style></author><author><style face="normal" font="default" size="100%">Landman, B. A.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Radiology, Mayo Clinic, Rochester, MN, USA. langer.steve@mayo.edu.&#xD;Department of Radiology, Weill Cornell Medicine, New York, NY, USA.&#xD;Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins University, Baltimore, MD, USA.&#xD;Electrical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Collaborative and Reproducible Research: Goals, Challenges, and Strategies</style></title><secondary-title><style face="normal" font="default" size="100%">J Digit Imaging</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">J Digit Imaging</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">TCIA General</style></keyword><keyword><style face="normal" font="default" size="100%">imaging biomarker</style></keyword><keyword><style face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style face="normal" font="default" size="100%">Electronic Medical Record (EMR)</style></keyword><keyword><style face="normal" font="default" size="100%">Computer analytics</style></keyword><keyword><style face="normal" font="default" size="100%">Computers in medicine</style></keyword><keyword><style face="normal" font="default" size="100%">Machine learning</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 23</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1618-727X (Electronic)&#xD;0897-1889 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29476392</style></accession-num><abstract><style face="normal" font="default" size="100%">Combining imaging biomarkers with genomic and clinical phenotype data is the foundation of precision medicine research efforts. Yet, biomedical imaging research requires unique infrastructure compared with principally text-driven clinical electronic medical record (EMR) data. The issues are related to the binary nature of the file format and transport mechanism for medical images as well as the post-processing image segmentation and registration needed to combine anatomical and physiological imaging data sources. The SiiM Machine Learning Committee was formed to analyze the gaps and challenges surrounding research into machine learning in medical imaging and to find ways to mitigate these issues. At the 2017 annual meeting, a whiteboard session was held to rank the most pressing issues and develop strategies to meet them. The results, and further reflections, are summarized in this paper.</style></abstract><notes><style face="normal" font="default" size="100%">Langer, Steve G&#xD;Shih, George&#xD;Nagy, Paul&#xD;Landman, Bennet A&#xD;eng&#xD;2018/02/25 06:00&#xD;J Digit Imaging. 2018 Feb 23. pii: 10.1007/s10278-017-0043-x. doi: 10.1007/s10278-017-0043-x.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29476392</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1007/s10278-017-0043-x</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>482</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">482</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lao, Jiangwei</style></author><author><style face="normal" font="default" size="100%">Chen, Yinsheng</style></author><author><style face="normal" font="default" size="100%">Li, Zhi-Cheng</style></author><author><style face="normal" font="default" size="100%">Li, Qihua</style></author><author><style face="normal" font="default" size="100%">Zhang, Ji</style></author><author><style face="normal" font="default" size="100%">Liu, Jing</style></author><author><style face="normal" font="default" size="100%">Zhai, Guangtao</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Deep Learning-Based Radiomics Model for Prediction of Survival in Glioblastoma Multiforme</style></title><secondary-title><style face="normal" font="default" size="100%">Scientific Reports</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><pages><style face="normal" font="default" size="100%">10353</style></pages><volume><style face="normal" font="default" size="100%">7</style></volume><dates><year><style face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style face="normal" font="default" size="100%">09/04&#xD;05/24/received&#xD;08/11/accepted</style></date></pub-dates></dates><pub-location><style face="normal" font="default" size="100%">London</style></pub-location><publisher><style face="normal" font="default" size="100%">Nature Publishing Group UK</style></publisher><isbn><style face="normal" font="default" size="100%">2045-2322</style></isbn><abstract><style face="normal" font="default" size="100%">Traditional radiomics models mainly rely on explicitly-designed handcrafted features from medical images. This paper aimed to investigate if deep features extracted via transfer learning can generate radiomics signatures for prediction of overall survival (OS) in patients with Glioblastoma Multiforme (GBM). This study comprised a discovery data set of 75 patients and an independent validation data set of 37 patients. A total of 1403 handcrafted features and 98304 deep features were extracted from preoperative multi-modality MR images. After feature selection, a six-deep-feature signature was constructed by using the least absolute shrinkage and selection operator (LASSO) Cox regression model. A radiomics nomogram was further presented by combining the signature and clinical risk factors such as age and Karnofsky Performance Score. Compared with traditional risk factors, the proposed signature achieved better performance for prediction of OS (C-index = 0.710, 95% CI: 0.588, 0.932) and significant stratification of patients into prognostically distinct groups (P &lt; 0.001, HR = 5.128, 95% CI: 2.029, 12.960). The combined model achieved improved predictive performance (C-index = 0.739). Our study demonstrates that transfer learning-based deep features are able to generate prognostic imaging signature for OS prediction and patient stratification for GBM, indicating the potential of deep imaging feature-based biomarker in preoperative care of GBM patients.</style></abstract><label><style face="normal" font="default" size="100%">TCGA-GBM; radiomics; glioblastoma multiforme (GBM); least absolute shrinkage and selection operator (LASSO) Cox regression model; deep learning; </style></label><notes><style face="normal" font="default" size="100%">10649[PII]&#xD;28871110[pmid]&#xD;Sci Rep</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583361/</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/s41598-017-10649-8</style></electronic-resource-num><remote-database-name><style face="normal" font="default" size="100%">PMC</style></remote-database-name></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>509</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">509</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Larue, Ruben THM</style></author><author><style face="normal" font="default" size="100%">Van De Voorde, Lien</style></author><author><style face="normal" font="default" size="100%">van Timmeren, Janna E</style></author><author><style face="normal" font="default" size="100%">Leijenaar, Ralph TH</style></author><author><style face="normal" font="default" size="100%">Berbée, Maaike</style></author><author><style face="normal" font="default" size="100%">Sosef, Meindert N</style></author><author><style face="normal" font="default" size="100%">Schreurs, Wendy MJ</style></author><author><style face="normal" font="default" size="100%">van Elmpt, Wouter</style></author><author><style face="normal" font="default" size="100%">Lambin, Philippe</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">4DCT imaging to assess radiomics feature stability: An investigation for thoracic cancers</style></title><secondary-title><style face="normal" font="default" size="100%">Radiotherapy and Oncology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiotherapy and Oncology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">147-153</style></pages><volume><style face="normal" font="default" size="100%">125</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">esophageal cancer</style></keyword><keyword><style face="normal" font="default" size="100%">lung cancer</style></keyword><keyword><style face="normal" font="default" size="100%">test-retest</style></keyword><keyword><style face="normal" font="default" size="100%">4D-CT</style></keyword><keyword><style face="normal" font="default" size="100%">feature stability</style></keyword><keyword><style face="normal" font="default" size="100%">RIDER_NEURO_MRI, Magnetic resonance imaging (MRI), Content based image retrieval (CBIR), Fast Wavelet Transform, kurtosis</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">0167-8140</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1016/j.radonc.2017.07.023</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>272</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">272</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lassen, BC</style></author><author><style face="normal" font="default" size="100%">Jacobs, C</style></author><author><style face="normal" font="default" size="100%">Kuhnigk, JM</style></author><author><style face="normal" font="default" size="100%">van Ginneken, B</style></author><author><style face="normal" font="default" size="100%">van Rikxoort, EM</style></author></authors></contributors><titles><title><style face="normal" 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S.</style></author><author><style face="normal" font="default" size="100%">Camara, Pablo G.</style></author><author><style face="normal" font="default" size="100%">Liu, Zhaoqi</style></author><author><style face="normal" font="default" size="100%">van Nieuwenhuizen, Patrick</style></author><author><style face="normal" font="default" size="100%">Jung, Sang Won</style></author><author><style face="normal" font="default" size="100%">Choi, Seung Won</style></author><author><style face="normal" font="default" size="100%">Kim, Junhyung</style></author><author><style face="normal" font="default" size="100%">Chen, Andrew</style></author><author><style face="normal" font="default" size="100%">Kim, Kyu-Tae</style></author><author><style face="normal" font="default" size="100%">Shin, Sang</style></author><author><style face="normal" font="default" size="100%">Seo, Yun Jee</style></author><author><style face="normal" font="default" size="100%">Oh, Jin-Mi</style></author><author><style face="normal" font="default" size="100%">Shin, Yong Jae</style></author><author><style face="normal" font="default" size="100%">Park, Chul-Kee</style></author><author><style face="normal" font="default" size="100%">Kong, Doo-Sik</style></author><author><style face="normal" font="default" size="100%">Seol, Ho Jun</style></author><author><style face="normal" font="default" size="100%">Blumberg, Andrew</style></author><author><style face="normal" font="default" size="100%">Lee, Jung-Il</style></author><author><style face="normal" font="default" size="100%">Iavarone, Antonio</style></author><author><style face="normal" font="default" size="100%">Park, Woong-Yang</style></author><author><style face="normal" font="default" size="100%">Rabadan, Raul</style></author><author><style face="normal" font="default" size="100%">Nam, Do-Hyun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Spatiotemporal genomic architecture informs precision oncology in glioblastoma</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Genet</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Nat Genet</style></full-title></periodical><pages><style face="normal" font="default" size="100%">594-599</style></pages><volume><style face="normal" font="default" size="100%">49</style></volume><number><style face="normal" font="default" size="100%">4</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM, CNS cancer, Genome informatics ,Targeted therapies</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style face="normal" font="default" size="100%">04//print</style></date></pub-dates></dates><publisher><style face="normal" font="default" size="100%">Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.</style></publisher><isbn><style face="normal" font="default" size="100%">1061-4036</style></isbn><work-type><style face="normal" font="default" size="100%">Letter</style></work-type><urls><related-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1038/ng.3806</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/ng.3806&#xD;http://www.nature.com/ng/journal/v49/n4/abs/ng.3806.html#supplementary-information</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>432</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">432</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lee, Myungeun</style></author><author><style face="normal" font="default" size="100%">Woo, Boyeong</style></author><author><style face="normal" font="default" size="100%">Kuo, Michael D</style></author><author><style face="normal" font="default" size="100%">Jamshidi, Neema</style></author><author><style face="normal" font="default" size="100%">Kim, Jong Hyo</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Quality of Radiomic Features in Glioblastoma Multiforme: Impact of Semi-Automated Tumor Segmentation Software</style></title><secondary-title><style face="normal" font="default" size="100%">Korean journal of radiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Korean journal of radiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">498-509</style></pages><volume><style face="normal" font="default" size="100%">18</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM, radiomics</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1229-6929</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>580</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">580</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lehrer, M.</style></author><author><style face="normal" font="default" size="100%">Bhadra, A.</style></author><author><style face="normal" font="default" size="100%">Aithala, S.</style></author><author><style face="normal" font="default" size="100%">Ravikumar, V.</style></author><author><style face="normal" font="default" size="100%">Zheng, Y.</style></author><author><style face="normal" font="default" size="100%">Dogan, B.</style></author><author><style face="normal" font="default" size="100%">Bonaccio, E.</style></author><author><style face="normal" font="default" size="100%">Burnside, E. S.</style></author><author><style face="normal" font="default" size="100%">Morris, E.</style></author><author><style face="normal" font="default" size="100%">Sutton, E.</style></author><author><style face="normal" font="default" size="100%">Whitman, G. J.</style></author><author><style face="normal" font="default" size="100%">Net, J.</style></author><author><style face="normal" font="default" size="100%">Brandt, K.</style></author><author><style face="normal" font="default" size="100%">Ganott, M.</style></author><author><style face="normal" font="default" size="100%">Zuley, M.</style></author><author><style face="normal" font="default" size="100%">Rao, A.</style></author><author><style face="normal" font="default" size="100%">Tcga Breast Phenotype Research Group</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.&#xD;Department of Statistics, Purdue University, West Lafayette, IN, USA.&#xD;Department of Biostatistics, Emory University, Atlanta, GA, USA.&#xD;Department of Radiology, UT Southwestern, Dallas, TX, USA.&#xD;Department of Diagnostic Radiology, Roswell Park Cancer Institute, Buffalo, NY, USA.&#xD;Department of Radiology, University of Wisconsin-Madison, Madison, WI, USA.&#xD;Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.&#xD;Department of Radiology, MD Anderson Cancer Center, Houston, TX, USA.&#xD;Department of Radiology, University of Miami Health System, Miami, FL, USA.&#xD;Department of Radiology, Mayo Clinic, Rochester, MN, USA.&#xD;Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">High-dimensional regression analysis links magnetic resonance imaging features and protein expression and signaling pathway alterations in breast invasive carcinoma</style></title><secondary-title><style face="normal" font="default" size="100%">Oncoscience</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Oncoscience</style></full-title></periodical><pages><style face="normal" font="default" size="100%">39-48</style></pages><volume><style face="normal" font="default" size="100%">5</style></volume><number><style face="normal" font="default" size="100%">1-2</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-BRCA</style></keyword><keyword><style face="normal" font="default" size="100%">MRI</style></keyword><keyword><style face="normal" font="default" size="100%">Radiogenomics</style></keyword><keyword><style face="normal" font="default" size="100%">breast invasive carcinoma</style></keyword><keyword><style face="normal" font="default" size="100%">protein expression</style></keyword><keyword><style face="normal" font="default" size="100%">signaling pathway analysis</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Jan</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">2331-4737 (Print)&#xD;2331-4737 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29556516</style></accession-num><abstract><style face="normal" font="default" size="100%">Background: Imaging features derived from MRI scans can be used for not only breast cancer detection and measuring disease extent, but can also determine gene expression and patient outcomes. The relationships between imaging features, gene/protein expression, and response to therapy hold potential to guide personalized medicine. We aim to characterize the relationship between radiologist-annotated tumor phenotypic features (based on MRI) and the underlying biological processes (based on proteomic profiling) in the tumor. Methods: Multiple-response regression of the image-derived, radiologist-scored features with reverse-phase protein array expression levels generated association coefficients for each combination of image-feature and protein in the RPPA dataset. Significantly-associated proteins for features were analyzed with Ingenuity Pathway Analysis software. Hierarchical clustering of the results of the pathway analysis determined which features were most strongly correlated with pathway activity and cellular functions. Results: Each of the twenty-nine imaging features was found to have a set of significantly correlated molecules, associated biological functions, and pathways. Conclusions: We interrogated the pathway alterations represented by the protein expression associated with each imaging feature. Our study demonstrates the relationships between biological processes (via proteomic measurements) and MRI features within breast tumors.</style></abstract><notes><style face="normal" font="default" size="100%">Lehrer, Michael&#xD;Bhadra, Anindya&#xD;Aithala, Sathvik&#xD;Ravikumar, Visweswaran&#xD;Zheng, Youyun&#xD;Dogan, Basak&#xD;Bonaccio, Emerlinda&#xD;Burnside, Elizabeth S&#xD;Morris, Elizabeth&#xD;Sutton, Elizabeth&#xD;Whitman, Gary J&#xD;Net, Jose&#xD;Brandt, Kathy&#xD;Ganott, Marie&#xD;Zuley, Margarita&#xD;Rao, Arvind&#xD;eng&#xD;P30 CA016672/CA/NCI NIH HHS/&#xD;R01 CA214955/CA/NCI NIH HHS/&#xD;P30 CA008748/CA/NCI NIH HHS/&#xD;HHSN261200800001C/RC/CCR NIH HHS/&#xD;HHSN261200800001E/CA/NCI NIH HHS/&#xD;2018/03/21 06:00&#xD;Oncoscience. 2018 Feb 26;5(1-2):39-48. doi: 10.18632/oncoscience.397. eCollection 2018 Jan.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29556516</style></url></related-urls></urls><custom2><style face="normal" font="default" size="100%">PMC5854291</style></custom2><electronic-resource-num><style face="normal" font="default" size="100%">10.18632/oncoscience.397</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>463</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">463</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lehrer, Michael</style></author><author><style face="normal" font="default" size="100%">Bhadra, Anindya</style></author><author><style face="normal" font="default" size="100%">Ravikumar, Visweswaran</style></author><author><style face="normal" font="default" size="100%">Chen, James Y</style></author><author><style face="normal" font="default" size="100%">Wintermark, Max</style></author><author><style face="normal" font="default" size="100%">Hwang, Scott N</style></author><author><style face="normal" font="default" size="100%">Holder, Chad A</style></author><author><style face="normal" font="default" size="100%">Huang, Erich P</style></author><author><style face="normal" font="default" size="100%">Fevrier-Sullivan, Brenda</style></author><author><style face="normal" font="default" size="100%">Freymann, John B</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Multiple-response regression analysis links magnetic resonance imaging features to de-regulated protein expression and pathway activity in lower grade glioma</style></title><secondary-title><style face="normal" font="default" size="100%">Oncoscience</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Oncoscience</style></full-title></periodical><pages><style face="normal" font="default" size="100%">57</style></pages><volume><style face="normal" font="default" size="100%">4</style></volume><number><style face="normal" font="default" size="100%">5-6</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-LGG, VASARI, Radiogenomics, cBioPortal, imaging-proteomics analysis, radiomics, lower grade glioma, signaling pathway activity, multiple-response regression</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" 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face="normal" font="default" size="100%">Wang, Guoliang</style></author><author><style face="normal" font="default" size="100%">Liang, Chaofeng</style></author><author><style face="normal" font="default" size="100%">Li, Zhi-Cheng</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Fully-Automatic Multiparametric Radiomics Model: Towards Reproducible and Prognostic Imaging Signature for Prediction of Overall Survival in Glioblastoma Multiforme</style></title><secondary-title><style face="normal" font="default" size="100%">Scientific reports</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><pages><style face="normal" font="default" size="100%">14331</style></pages><volume><style face="normal" font="default" 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size="100%">Li, Qian</style></author><author><style face="normal" font="default" size="100%">Balagurunathan, Yoganand</style></author><author><style face="normal" font="default" size="100%">Liu, Ying</style></author><author><style face="normal" font="default" size="100%">Qi, Jin</style></author><author><style face="normal" font="default" size="100%">Schabath, Matthew B</style></author><author><style face="normal" font="default" size="100%">Ye, Zhaoxiang</style></author><author><style face="normal" font="default" size="100%">Gillies, Robert J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparison Between Radiological Semantic Features and Lung-RADS in Predicting Malignancy of Screen-Detected Lung Nodules in the National Lung Screening Trial</style></title><secondary-title><style face="normal" font="default" size="100%">Clinical lung cancer</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Clinical lung cancer</style></full-title></periodical><volume><style face="normal" font="default" size="100%">0</style></volume><number><style face="normal" font="default" size="100%">0</style></number><keywords><keyword><style face="normal" font="default" size="100%">Lung cancer screening</style></keyword><keyword><style face="normal" font="default" size="100%">Lung-RADS</style></keyword><keyword><style face="normal" font="default" size="100%">NLST</style></keyword><keyword><style face="normal" font="default" size="100%">Predictive</style></keyword><keyword><style face="normal" font="default" size="100%">Semantic features</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1525-7304</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">https://doi.org/10.1016/j.cllc.2017.10.002</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>561</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">561</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Li, Y.</style></author><author><style face="normal" font="default" size="100%">Liu, X.</style></author><author><style face="normal" font="default" size="100%">Qian, Z.</style></author><author><style face="normal" font="default" size="100%">Sun, Z.</style></author><author><style face="normal" font="default" size="100%">Xu, K.</style></author><author><style face="normal" font="default" size="100%">Wang, K.</style></author><author><style face="normal" font="default" size="100%">Fan, X.</style></author><author><style face="normal" font="default" size="100%">Zhang, Z.</style></author><author><style face="normal" font="default" size="100%">Li, S.</style></author><author><style face="normal" font="default" size="100%">Wang, Y.</style></author><author><style face="normal" font="default" size="100%">Jiang, T.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Beijing Neurosurgical Institute, Capital Medical University, 6 Tiantanxili, Beijing, 100050, China.&#xD;Chinese Academy of Sciences, Institute of Automation, Beijing, China.&#xD;Department of Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.&#xD;Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantanxili, Beijing, 100050, China.&#xD;Neurological Imaging Center, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.&#xD;Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantanxili, Beijing, 100050, China. tiantanyinyan@126.com.&#xD;Beijing Neurosurgical Institute, Capital Medical University, 6 Tiantanxili, Beijing, 100050, China. taojiang1964@163.com.&#xD;Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantanxili, Beijing, 100050, China. taojiang1964@163.com.&#xD;Centre of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China. taojiang1964@163.com.&#xD;China National Clinical Research Center for Neurological Diseases, Beijing, China. taojiang1964@163.com.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Genotype prediction of ATRX mutation in lower-grade gliomas using an MRI radiomics signature</style></title><secondary-title><style face="normal" font="default" size="100%">Eur Radiol</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Eur Radiol</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">Radiogenomics</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA-LGG</style></keyword><keyword><style face="normal" font="default" size="100%">Biomarkers</style></keyword><keyword><style face="normal" font="default" size="100%">Genetics</style></keyword><keyword><style face="normal" font="default" size="100%">Glioma</style></keyword><keyword><style face="normal" font="default" size="100%">Machine learning</style></keyword><keyword><style face="normal" font="default" size="100%">Magnetic resonance imaging</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 5</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1432-1084 (Electronic)&#xD;0938-7994 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29404769</style></accession-num><abstract><style face="normal" font="default" size="100%">OBJECTIVES: To predict ATRX mutation status in patients with lower-grade gliomas using radiomic analysis. METHODS: Cancer Genome Atlas (TCGA) patients with lower-grade gliomas were randomly allocated into training (n = 63) and validation (n = 32) sets. An independent external-validation set (n = 91) was built based on the Chinese Genome Atlas (CGGA) database. After feature extraction, an ATRX-related signature was constructed. Subsequently, the radiomic signature was combined with a support vector machine to predict ATRX mutation status in training, validation and external-validation sets. Predictive performance was assessed by receiver operating characteristic curve analysis. Correlations between the selected features were also evaluated. RESULTS: Nine radiomic features were screened as an ATRX-associated radiomic signature of lower-grade gliomas based on the LASSO regression model. All nine radiomic features were texture-associated (e.g. sum average and variance). The predictive efficiencies measured by the area under the curve were 94.0 %, 92.5 % and 72.5 % in the training, validation and external-validation sets, respectively. The overall correlations between the nine radiomic features were low in both TCGA and CGGA databases. CONCLUSIONS: Using radiomic analysis, we achieved efficient prediction of ATRX genotype in lower-grade gliomas, and our model was effective in two independent databases. KEY POINTS: * ATRX in lower-grade gliomas could be predicted using radiomic analysis. * The LASSO regression algorithm and SVM performed well in radiomic analysis. * Nine radiomic features were screened as an ATRX-predictive radiomic signature. * The machine-learning model for ATRX-prediction was validated by an independent database.</style></abstract><notes><style face="normal" font="default" size="100%">Li, Yiming&#xD;Liu, Xing&#xD;Qian, Zenghui&#xD;Sun, Zhiyan&#xD;Xu, Kaibin&#xD;Wang, Kai&#xD;Fan, Xing&#xD;Zhang, Zhong&#xD;Li, Shaowu&#xD;Wang, Yinyan&#xD;Jiang, Tao&#xD;eng&#xD;Germany&#xD;2018/02/07 06:00&#xD;Eur Radiol. 2018 Feb 5. pii: 10.1007/s00330-017-5267-0. doi: 10.1007/s00330-017-5267-0.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29404769</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" 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size="100%">Rectosigmoid brake</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">0193-1857</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1152/ajpgi.00021.2017</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>504</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">504</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Feihong</style></author><author><style face="normal" font="default" size="100%">Feng, Jun</style></author><author><style face="normal" font="default" size="100%">Su, Wenhuo</style></author><author><style face="normal" font="default" size="100%">Lv, Zhaohui</style></author><author><style face="normal" font="default" size="100%">Xiao, Fang</style></author><author><style face="normal" font="default" size="100%">Qiu, Shi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Normalized Euclidean Super-Pixels for Medical Image Segmentation</style></title><secondary-title><style face="normal" font="default" size="100%">International Conference on Intelligent Computing</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">586-597</style></pages><keywords><keyword><style face="normal" font="default" size="100%">medical image processing</style></keyword><keyword><style face="normal" font="default" size="100%">segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">super-pixels</style></keyword><keyword><style face="normal" font="default" size="100%">local compactness</style></keyword><keyword><style face="normal" font="default" size="100%">LIDC-IDRI</style></keyword><keyword><style face="normal" font="default" size="100%">CT Lymph Nodes.</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">Springer</style></publisher><urls><related-urls><url><style face="normal" font="default" size="100%">https://link.springer.com/chapter/10.1007/978-3-319-63315-2_51 </style></url></related-urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>494</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">494</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Feng</style></author><author><style face="normal" font="default" size="100%">Hernandez-Cabronero, Miguel</style></author><author><style face="normal" font="default" size="100%">Sanchez, Victor</style></author><author><style face="normal" font="default" size="100%">Marcellin, Michael W</style></author><author><style face="normal" font="default" size="100%">Bilgin, Ali</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Current Role of Image Compression Standards in Medical Imaging</style></title><secondary-title><style face="normal" font="default" size="100%">Information</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Information</style></full-title></periodical><pages><style face="normal" font="default" size="100%">131</style></pages><volume><style face="normal" font="default" size="100%">8</style></volume><number><style face="normal" font="default" size="100%">4</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCIA General</style></keyword><keyword><style face="normal" font="default" size="100%">LIDC-IDRI</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA-BRCA</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">CT-COLONOGRAPHY</style></keyword><keyword><style face="normal" font="default" size="100%">image compression</style></keyword><keyword><style face="normal" font="default" size="100%">medical imaging</style></keyword><keyword><style face="normal" font="default" size="100%">standards</style></keyword><keyword><style face="normal" font="default" size="100%">JPEG</style></keyword><keyword><style face="normal" font="default" size="100%">JPEG-LS</style></keyword><keyword><style face="normal" font="default" size="100%">JPEG2000</style></keyword><keyword><style face="normal" font="default" size="100%">JPEG-XR</style></keyword><keyword><style face="normal" font="default" size="100%">HEVC</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.3390/info8040131 </style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>217</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">217</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, TT</style></author><author><style face="normal" font="default" size="100%">Achrol, AS</style></author><author><style face="normal" font="default" size="100%">Mitchell, LA</style></author><author><style face="normal" font="default" size="100%">Du, WA</style></author><author><style face="normal" font="default" size="100%">Loya, JJ</style></author><author><style face="normal" font="default" size="100%">Rodriguez, SA</style></author><author><style face="normal" font="default" size="100%">Feroze, A</style></author><author><style face="normal" font="default" size="100%">Westbroek, EM</style></author><author><style face="normal" font="default" size="100%">Yeom, KW</style></author><author><style face="normal" font="default" size="100%">Stuart, JM</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas</style></title><secondary-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></full-title></periodical><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><isbn><style face="normal" font="default" size="100%">0195-6108</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>376</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">376</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Tiffany T.</style></author><author><style face="normal" font="default" size="100%">Achrol, Achal S.</style></author><author><style face="normal" font="default" size="100%">Mitchell, Lex A.</style></author><author><style face="normal" font="default" size="100%">Rodriguez, Scott A.</style></author><author><style face="normal" font="default" size="100%">Feroze, Abdullah</style></author><author><style face="normal" font="default" size="100%">Michael Iv</style></author><author><style face="normal" font="default" size="100%">Kim, Christine</style></author><author><style face="normal" font="default" size="100%">Chaudhary, Navjot</style></author><author><style face="normal" font="default" size="100%">Gevaert, Olivier</style></author><author><style face="normal" font="default" size="100%">Stuart, Josh M.</style></author><author><style face="normal" font="default" size="100%">Harsh, Griffith R.</style></author><author><style face="normal" font="default" size="100%">Chang, Steven D.</style></author><author><style face="normal" font="default" size="100%">Rubin, Daniel L.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment</style></title><secondary-title><style face="normal" font="default" size="100%">Neuro-Oncology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Neuro-oncology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-11</style></pages><keywords><keyword><style face="normal" font="default" size="100%">Radiogenomics, TCGA</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style face="normal" font="default" size="100%">December 22, 2016</style></date></pub-dates></dates><abstract><style face="normal" font="default" size="100%">Background. In previous clinical trials, antiangiogenic therapies such as bevacizumab did not show efficacy in patients with newly diagnosed glioblastoma (GBM). This may be a result of the heterogeneity of GBM, which has a variety of imaging-based phenotypes and gene expression patterns. In this study, we sought to identify a phenotypic subtype of GBM patients who have distinct tumor-image features and molecular activities and who may benefit from antiangiogenic therapies.Methods. Quantitative image features characterizing subregions of tumors and the whole tumor were extracted from preoperative and pretherapy perfusion magnetic resonance (MR) images of 117 GBM patients in 2 independent cohorts. Unsupervised consensus clustering was performed to identify robust clusters of GBM in each cohort. Cox survival and gene set enrichment analyses were conducted to characterize the clinical significance and molecular pathway activities of the clusters. The differential treatment efficacy of antiangiogenic therapy between the clusters was evaluated.Results. A subgroup of patients with elevated perfusion features was identified and was significantly associated with poor patient survival after accounting for other clinical covariates (P values &lt;.01; hazard ratios &gt; 3) consistently found in both cohorts. Angiogenesis and hypoxia pathways were enriched in this subgroup of patients, suggesting the potential efficacy of antiangiogenic therapy. Patients of the angiogenic subgroups pooled from both cohorts, who had chemotherapy information available, had significantly longer survival when treated with antiangiogenic therapy (log-rank P=.022).Conclusions. Our findings suggest that an angiogenic subtype of GBM patients may benefit from antiangiogenic therapy with improved overall survival.</style></abstract><urls><related-urls><url><style face="normal" font="default" size="100%">http://neuro-oncology.oxfordjournals.org/content/early/2016/12/22/neuonc.now270.abstract</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1093/neuonc/now270</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>451</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">451</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xinglong</style></author><author><style face="normal" font="default" size="100%">Hou, Fei</style></author><author><style face="normal" font="default" size="100%">Qin, Hong</style></author><author><style face="normal" font="default" size="100%">Hao, Aimin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A CADe system for nodule detection in thoracic CT images based on artificial neural network</style></title><secondary-title><style face="normal" font="default" size="100%">Science China Information Sciences</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Science China Information Sciences</style></full-title></periodical><pages><style face="normal" font="default" size="100%">072106</style></pages><volume><style face="normal" font="default" size="100%">60</style></volume><number><style face="normal" font="default" size="100%">7</style></number><keywords><keyword><style face="normal" font="default" size="100%">LIDC-IDRI, artificial neutral network</style></keyword><keyword><style face="normal" font="default" size="100%">lung nodule</style></keyword><keyword><style face="normal" font="default" size="100%">computed tomography</style></keyword><keyword><style face="normal" font="default" size="100%">computer aided detection</style></keyword><keyword><style face="normal" font="default" size="100%">nodule detection</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1674-733X</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>678</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">678</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xing</style></author><author><style face="normal" font="default" size="100%">Li, Yiming</style></author><author><style face="normal" font="default" size="100%">Qian, Zenghui</style></author><author><style face="normal" font="default" size="100%">Sun, Zhiyan</style></author><author><style face="normal" font="default" size="100%">Xu, Kaibin</style></author><author><style face="normal" font="default" size="100%">Wang, Kai</style></author><author><style face="normal" font="default" size="100%">Liu, Shuai</style></author><author><style face="normal" font="default" size="100%">Fan, Xing</style></author><author><style face="normal" font="default" size="100%">Li, Shaowu</style></author><author><style face="normal" font="default" size="100%">Zhang, Zhong</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A radiomic signature as a non-invasive predictor of progression-free survival in patients with lower-grade gliomas</style></title><secondary-title><style face="normal" font="default" size="100%">NeuroImage: Clinical</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">NeuroImage: Clinical</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1070-1077</style></pages><volume><style face="normal" font="default" size="100%">20</style></volume><keywords><keyword><style face="normal" font="default" size="100%">Radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">Lower-grade gliomas</style></keyword><keyword><style face="normal" font="default" size="100%">Progression-free survival</style></keyword><keyword><style face="normal" font="default" size="100%">Radiogenomics</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">2213-1582</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/j.nicl.2018.10.014</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>653</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">653</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xing</style></author><author><style face="normal" font="default" size="100%">Li, Yiming</style></author><author><style face="normal" font="default" size="100%">Sun, Zhiyan</style></author><author><style face="normal" font="default" size="100%">Li, Shaowu</style></author><author><style face="normal" font="default" size="100%">Wang, Kai</style></author><author><style face="normal" font="default" size="100%">Fan, Xing</style></author><author><style face="normal" font="default" size="100%">Liu, Yuqing</style></author><author><style face="normal" font="default" size="100%">Wang, Lei</style></author><author><style face="normal" font="default" size="100%">Wang, Yinyan</style></author><author><style face="normal" font="default" size="100%">Jiang, Tao</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular profiles of tumor contrast enhancement: A radiogenomic analysis in anaplastic gliomas</style></title><secondary-title><style face="normal" font="default" size="100%">Cancer medicine</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Cancer medicine</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">glioma</style></keyword><keyword><style face="normal" font="default" size="100%">radiogenomics</style></keyword><keyword><style face="normal" font="default" size="100%">gene set enrichment analysis (GSEA)</style></keyword><keyword><style face="normal" font="default" size="100%">Molecular Signatures Database v5.1 (MSigDB)</style></keyword><keyword><style face="normal" font="default" size="100%">radiomic features</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">2045-7634</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1002/cam4.1672</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>579</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">579</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, X.</style></author><author><style face="normal" font="default" size="100%">Swen, J. J.</style></author><author><style face="normal" font="default" size="100%">Diekstra, M. H. M.</style></author><author><style face="normal" font="default" size="100%">Boven, E.</style></author><author><style face="normal" font="default" size="100%">Castellano, D.</style></author><author><style face="normal" font="default" size="100%">Gelderblom, H.</style></author><author><style face="normal" font="default" size="100%">Mathijssen, R. H. J.</style></author><author><style face="normal" font="default" size="100%">Vermeulen, S. H.</style></author><author><style face="normal" font="default" size="100%">Oosterwijk, E.</style></author><author><style face="normal" font="default" size="100%">Junker, K.</style></author><author><style face="normal" font="default" size="100%">Roessler, M.</style></author><author><style face="normal" font="default" size="100%">Alexiusdottir, K.</style></author><author><style face="normal" font="default" size="100%">Sverrisdottir, A.</style></author><author><style face="normal" font="default" size="100%">Radu, M. T.</style></author><author><style face="normal" font="default" size="100%">Ambert, V.</style></author><author><style face="normal" font="default" size="100%">Eisen, T.</style></author><author><style face="normal" font="default" size="100%">Warren, A.</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Antona, C.</style></author><author><style face="normal" font="default" size="100%">Garcia-Donas, J.</style></author><author><style face="normal" font="default" size="100%">Bohringer, S.</style></author><author><style face="normal" font="default" size="100%">Koudijs, K. K. M.</style></author><author><style face="normal" font="default" size="100%">Kiemeney, Lalm</style></author><author><style face="normal" font="default" size="100%">Rini, B. I.</style></author><author><style face="normal" font="default" size="100%">Guchelaar, H. J.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, the Netherlands.&#xD;Institute of Clinical Pharmacology, Qilu Hospital of Shandong University, Jinan, China.&#xD;Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Center, Maastricht, the Netherlands.&#xD;Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands.&#xD;Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.&#xD;Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands.&#xD;Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.&#xD;Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.&#xD;Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.&#xD;Clinic of Urology and Paediatric Urology, Saarland University, Homburg, Germany.&#xD;CESAR Central Office, CESAR Central European Society for Anticancer Drug Research-EWIV, Vienna, Austria.&#xD;Department of Medicine, Landspitali-University Hospital, Reykjavik, Iceland.&#xD;Department of Oncology, Landspitali-University Hospital, Reykjavik, Iceland.&#xD;University of Medicine and Pharmacy Carol Davila, Bucuresti, Romania.&#xD;Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke&apos;s Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom.&#xD;Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke&apos;s Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom.&#xD;Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO) and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain.&#xD;Medical Oncology, HM Hospitales, Centro Integral Oncologico HM Clara Campal, Madrid, Spain.&#xD;Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.&#xD;Department of Solid Tumor Oncology, Cleveland Clinic Taussig Cancer Institute (CCF), Cleveland, Ohio.&#xD;Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, the Netherlands. H.J.Guchelaar@lumc.nl.</style></auth-address><titles><title><style face="normal" font="default" size="100%">A Genetic Polymorphism in CTLA-4 Is Associated with Overall Survival in Sunitinib-Treated Patients with Clear Cell Metastatic Renal Cell Carcinoma</style></title><secondary-title><style face="normal" font="default" size="100%">Clin Cancer Res</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Clin Cancer Res</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">TCGA-KIRC</style></keyword><keyword><style face="normal" font="default" size="100%">Radiogenomics</style></keyword><keyword><style face="normal" font="default" size="100%">tyrosine kinase inhibitors (TKI)</style></keyword><keyword><style face="normal" font="default" size="100%">clear cell metastatic renal cell carcinoma (cc-mRCC)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 28</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1078-0432 (Print)&#xD;1078-0432 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29490989</style></accession-num><abstract><style face="normal" font="default" size="100%">Purpose: The survival of patients with clear cell metastatic renal cell carcinoma (cc-mRCC) has improved substantially since the introduction of tyrosine kinase inhibitors (TKI). With the fact that TKIs interact with immune responses, we investigated whether polymorphisms of genes involved in immune checkpoints are related to the clinical outcome of cc-mRCC patients treated with sunitinib as first TKI.Experimental Design: Twenty-seven single-nucleotide polymorphisms (SNP) in CD274 (PD-L1), PDCD1 (PD-1), and CTLA-4 were tested for a possible association with progression-free survival (PFS) and overall survival (OS) in a discovery cohort of 550 sunitinib-treated cc-mRCC patients. SNPs with a significant association (P &lt; 0.05) were tested in an independent validation cohort of 138 sunitinib-treated cc-mRCC patients. Finally, data of the discovery and validation cohort were pooled for meta-analysis.Results:CTLA-4 rs231775 and CD274 rs7866740 showed significant associations with OS in the discovery cohort after correction for age, gender, and Heng prognostic risk group [HR, 0.84; 95% confidence interval (CI), 0.72-0.98; P = 0.028, and HR, 0.73; 95% CI, 0.54-0.99; P = 0.047, respectively]. In the validation cohort, the associations of both SNPs with OS did not meet the significance threshold of P &lt; 0.05. After meta-analysis, CTLA-4 rs231775 showed a significant association with OS (HR, 0.83; 95% CI, 0.72-0.95; P = 0.008). Patients with the GG genotype had longer OS (35.1 months) compared with patients with an AG (30.3 months) or AA genotype (24.3 months). No significant associations with PFS were found.Conclusions: The G-allele of rs231775 in the CTLA-4 gene is associated with an improved OS in sunitinib-treated cc-mRCC patients and could potentially be used as a prognostic biomarker. Clin Cancer Res; 1-7. (c)2018 AACR.</style></abstract><notes><style face="normal" font="default" size="100%">Liu, Xiaoyan&#xD;Swen, Jesse J&#xD;Diekstra, Meta H M&#xD;Boven, Epie&#xD;Castellano, Daniel&#xD;Gelderblom, Hans&#xD;Mathijssen, Ron H J&#xD;Vermeulen, Sita H&#xD;Oosterwijk, Egbert&#xD;Junker, Kerstin&#xD;Roessler, Max&#xD;Alexiusdottir, Kristin&#xD;Sverrisdottir, Asgerdur&#xD;Radu, Marius T&#xD;Ambert, Valentin&#xD;Eisen, Tim&#xD;Warren, Anne&#xD;Rodriguez-Antona, Cristina&#xD;Garcia-Donas, Jesus&#xD;Bohringer, Stefan&#xD;Koudijs, Karel K M&#xD;Kiemeney, Lambertus A L M&#xD;Rini, Brian I&#xD;Guchelaar, Henk-Jan&#xD;eng&#xD;2018/03/02 06:00&#xD;Clin Cancer Res. 2018 Feb 28. pii: 1078-0432.CCR-17-2815. doi: 10.1158/1078-0432.CCR-17-2815.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29490989</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" 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size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1932-6203</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1371/journal.pone.0187209</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>3</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">3</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mongkolwat, Pattanasak</style></author><author><style face="normal" font="default" size="100%">Channin, David S</style></author><author><style face="normal" font="default" size="100%">Rubin, Vladimir Kleper Daniel 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size="100%">1475-925X</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1186/s12938-018-0529-x</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>140</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">140</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stephen M. 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Prior</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">De-identification of Medical Images with Retention of Scientific Research Value</style></title><secondary-title><style face="normal" font="default" size="100%">RadioGraphics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiographics</style></full-title></periodical><pages><style face="normal" font="default" size="100%">727-735</style></pages><volume><style face="normal" font="default" size="100%">35</style></volume><number><style face="normal" font="default" size="100%">3</style></number><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><abstract><style face="normal" font="default" size="100%">Online public repositories for sharing research data allow investigators to validate existing research or perform secondary research without the expense of collecting new data. Patient data made publicly available through such repositories may constitute a breach of personally identifiable information if not properly de-identified. Imaging data are especially at risk because some intricacies of the Digital Imaging and Communications in Medicine (DICOM) format are not widely understood by researchers. If imaging data still containing protected health information (PHI) were released through a public repository, a number of different parties could be held liable, including the original researcher who collected and submitted the data, the original researcher’s institution, and the organization managing the repository. To minimize these risks through proper de-identification of image data, one must understand what PHI exists and where that PHI resides, and one must have the tools to remove PHI without compromising the scientific integrity of the data. DICOM public elements are defined by the DICOM Standard. Modality vendors use private elements to encode acquisition parameters that are not yet defined by the DICOM Standard, or the vendor may not have updated an existing software product after DICOM defined new public elements. Because private elements are not standardized, a common de-identification practice is to delete all private elements, removing scientifically useful data as well as PHI. 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size="100%">Kim, Donnie</style></author><author><style face="normal" font="default" size="100%">Aithala, Sathvik</style></author><author><style face="normal" font="default" size="100%">Heimberger, Amy B</style></author><author><style face="normal" font="default" size="100%">Ahmed, Salmaan</style></author><author><style face="normal" font="default" size="100%">Rao, Dinesh</style></author><author><style face="normal" font="default" size="100%">Rao, Ganesh</style></author><author><style face="normal" font="default" size="100%">Rao, Arvind</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Tumor image-derived texture features are associated with CD3 T-cell infiltration status in glioblastoma</style></title><secondary-title><style face="normal" font="default" size="100%">Oncotarget</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Oncotarget</style></full-title></periodical><pages><style face="normal" font="default" size="100%">101244</style></pages><volume><style face="normal" font="default" size="100%">8</style></volume><number><style face="normal" font="default" size="100%">60</style></number><keywords><keyword><style face="normal" font="default" size="100%">glioma</style></keyword><keyword><style face="normal" font="default" size="100%">imaging-genomics analysis</style></keyword><keyword><style face="normal" font="default" size="100%">texture analysis</style></keyword><keyword><style face="normal" font="default" size="100%">immune activity</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.18632/oncotarget.20643</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>562</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">562</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Narayanan, B. N.</style></author><author><style face="normal" font="default" size="100%">Hardie, R. C.</style></author><author><style face="normal" font="default" size="100%">Kebede, T. M.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">University of Dayton, Department of Electrical and Computer Engineering, Dayton, Ohio, United States.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Performance analysis of a computer-aided detection system for lung nodules in CT at different slice thicknesses</style></title><secondary-title><style face="normal" font="default" size="100%">J Med Imaging (Bellingham)</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">J Med Imaging (Bellingham)</style></full-title></periodical><pages><style face="normal" font="default" size="100%">014504</style></pages><volume><style face="normal" font="default" size="100%">5</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">LIDC-IDRI</style></keyword><keyword><style face="normal" font="default" size="100%">Algorithm Development</style></keyword><keyword><style face="normal" font="default" size="100%">computed tomography</style></keyword><keyword><style face="normal" font="default" size="100%">computer-aided detection</style></keyword><keyword><style face="normal" font="default" size="100%">downsampling</style></keyword><keyword><style face="normal" font="default" size="100%">lung nodules</style></keyword><keyword><style face="normal" font="default" size="100%">slice thickness</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Jan</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">2329-4302 (Print)&#xD;2329-4302 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29487880</style></accession-num><abstract><style face="normal" font="default" size="100%">We study the performance of a computer-aided detection (CAD) system for lung nodules in computed tomography (CT) as a function of slice thickness. In addition, we propose and compare three different training methodologies for utilizing nonhomogeneous thickness training data (i.e., composed of cases with different slice thicknesses). These methods are (1) aggregate training using the entire suite of data at their native thickness, (2) homogeneous subset training that uses only the subset of training data that matches each testing case, and (3) resampling all training and testing cases to a common thickness. We believe this study has important implications for how CT is acquired, processed, and stored. We make use of 192 CT cases acquired at a thickness of 1.25 mm and 283 cases at 2.5 mm. These data are from the publicly available Lung Nodule Analysis 2016 dataset. In our study, CAD performance at 2.5 mm is comparable with that at 1.25 mm and is much better than at higher thicknesses. Also, resampling all training and testing cases to 2.5 mm provides the best performance among the three training methods compared in terms of accuracy, memory consumption, and computational time.</style></abstract><notes><style face="normal" font="default" size="100%">Narayanan, Barath Narayanan&#xD;Hardie, Russell Craig&#xD;Kebede, Temesguen Messay&#xD;eng&#xD;2018/03/01 06:00&#xD;J Med Imaging (Bellingham). 2018 Jan;5(1):014504. doi: 10.1117/1.JMI.5.1.014504. 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size="100%">101331G-101331G-8</style></pages><keywords><keyword><style face="normal" font="default" size="100%">Phantom FDA, Algorithms</style></keyword><keyword><style face="normal" font="default" size="100%">Image segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">Lung</style></keyword><keyword><style face="normal" font="default" size="100%">Volume segmentation</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">International Society for Optics and Photonics</style></publisher><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1117/12.2254583 </style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>364</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">364</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Parks, Connie L</style></author><author><style face="normal" font="default" size="100%">Monson, Keith L</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Automated Facial Recognition of Computed Tomography-Derived Facial Images: Patient Privacy Implications</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Digital Imaging</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Journal of Digital Imaging</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-11</style></pages><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><isbn><style face="normal" font="default" size="100%">0897-1889</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>452</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">452</key></foreign-keys><ref-type name="Thesis">32</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Parmar, Chintan</style></author></authors><tertiary-authors><author><style face="normal" font="default" size="100%">Lambin, Philippe; Aerts, H.J.W.</style></author></tertiary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Machine learning applications for Radiomics: towards robust non-invasive predictors in clinical oncology</style></title></titles><pages><style face="normal" font="default" size="100%">187</style></pages><volume><style face="normal" font="default" size="100%">PhD</style></volume><dates><year><style face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style face="normal" font="default" size="100%">5/18/2017</style></date></pub-dates></dates><pub-location><style face="normal" font="default" size="100%">Maastricht, NL</style></pub-location><publisher><style face="normal" font="default" size="100%">Maastricht University</style></publisher><notes><style face="normal" font="default" size="100%">oncology, precision medicine, medical imaging, radiomic analyses, artificial intelligence, machine learning methods, LIDC</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://cris.maastrichtuniversity.nl/portal/en/publications/chromosome-instability(121d5068-f9a9-4cf7-893a-1541bf792eb9).html</style></url></related-urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>180</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">180</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Parmar, C.</style></author><author><style face="normal" font="default" size="100%">Grossmann, P.</style></author><author><style face="normal" font="default" size="100%">Bussink, J.</style></author><author><style face="normal" font="default" size="100%">Lambin, P.</style></author><author><style face="normal" font="default" size="100%">Aerts, H. J.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">1] Departments of Radiation Oncology [2] Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, Maastricht, the Netherlands [3] Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.&#xD;1] Departments of Radiation Oncology [2] Department of Biostatistics &amp;Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.&#xD;Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands.&#xD;Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, Maastricht, the Netherlands.&#xD;1] Departments of Radiation Oncology [2] Radiology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, MA, USA [3] Department of Biostatistics &amp;Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Machine Learning methods for Quantitative Radiomic Biomarkers</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Scientific reports</style></alt-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><alt-periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></alt-periodical><pages><style face="normal" font="default" size="100%">13087</style></pages><volume><style face="normal" font="default" size="100%">5</style></volume><edition><style face="normal" font="default" size="100%">2015/08/19</style></edition><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">2045-2322 (Electronic)&#xD;2045-2322 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">26278466</style></accession-num><abstract><style face="normal" font="default" size="100%">Radiomics extracts and mines large number of medical imaging features quantifying tumor phenotypic characteristics. Highly accurate and reliable machine-learning approaches can drive the success of radiomic applications in clinical care. In this radiomic study, fourteen feature selection methods and twelve classification methods were examined in terms of their performance and stability for predicting overall survival. A total of 440 radiomic features were extracted from pre-treatment computed tomography (CT) images of 464 lung cancer patients. To ensure the unbiased evaluation of different machine-learning methods, publicly available implementations along with reported parameter configurations were used. Furthermore, we used two independent radiomic cohorts for training (n = 310 patients) and validation (n = 154 patients). We identified that Wilcoxon test based feature selection method WLCX (stability = 0.84 +/- 0.05, AUC = 0.65 +/- 0.02) and a classification method random forest RF (RSD = 3.52%, AUC = 0.66 +/- 0.03) had highest prognostic performance with high stability against data perturbation. Our variability analysis indicated that the choice of classification method is the most dominant source of performance variation (34.21% of total variance). Identification of optimal machine-learning methods for radiomic applications is a crucial step towards stable and clinically relevant radiomic biomarkers, providing a non-invasive way of quantifying and monitoring tumor-phenotypic characteristics in clinical practice.</style></abstract><notes><style face="normal" font="default" size="100%">Parmar, Chintan&#xD;Grossmann, Patrick&#xD;Bussink, Johan&#xD;Lambin, Philippe&#xD;Aerts, Hugo J W L&#xD;England&#xD;Sci Rep. 2015 Aug 17;5:13087. doi: 10.1038/srep13087.</style></notes><urls></urls><custom2><style face="normal" font="default" size="100%">PMC4538374</style></custom2><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/srep13087</style></electronic-resource-num><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider><language><style face="normal" font="default" size="100%">eng</style></language></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>181</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">181</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Parmar, C.</style></author><author><style face="normal" font="default" size="100%">Leijenaar, R. T.</style></author><author><style face="normal" font="default" size="100%">Grossmann, P.</style></author><author><style face="normal" font="default" size="100%">Rios Velazquez, E.</style></author><author><style face="normal" font="default" size="100%">Bussink, J.</style></author><author><style face="normal" font="default" size="100%">Rietveld, D.</style></author><author><style face="normal" font="default" size="100%">Rietbergen, M. M.</style></author><author><style face="normal" font="default" size="100%">Haibe-Kains, B.</style></author><author><style face="normal" font="default" size="100%">Lambin, P.</style></author><author><style face="normal" font="default" size="100%">Aerts, H. J.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">1] Departments of Radiation Oncology [2] Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, Maastricht, the Netherlands [3] Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.&#xD;Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, Maastricht, the Netherlands.&#xD;1] Departments of Radiation Oncology [2] Department of Biostatistics &amp;Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.&#xD;Departments of Radiation Oncology.&#xD;Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands.&#xD;Department of Radiation Oncology, VU University Medical Center, Amsterdam, The Netherlands.&#xD;Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.&#xD;1] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada [2] Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada.&#xD;1] Departments of Radiation Oncology [2] Radiology, Dana-Farber Cancer Institute, Brigham and Women&apos;s Hospital, Harvard Medical School, Boston, MA, USA [3] Department of Biostatistics &amp;Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Radiomic feature clusters and Prognostic Signatures specific for Lung and Head &amp;Neck cancer</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Scientific reports</style></alt-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><alt-periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></alt-periodical><pages><style face="normal" font="default" size="100%">11044</style></pages><volume><style face="normal" font="default" size="100%">5</style></volume><edition><style face="normal" font="default" size="100%">2015/08/08</style></edition><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">2045-2322 (Electronic)&#xD;2045-2322 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">26251068</style></accession-num><abstract><style face="normal" font="default" size="100%">Radiomics provides a comprehensive quantification of tumor phenotypes by extracting and mining large number of quantitative image features. To reduce the redundancy and compare the prognostic characteristics of radiomic features across cancer types, we investigated cancer-specific radiomic feature clusters in four independent Lung and Head &amp;Neck (H) cancer cohorts (in total 878 patients). Radiomic features were extracted from the pre-treatment computed tomography (CT) images. Consensus clustering resulted in eleven and thirteen stable radiomic feature clusters for Lung and H cancer, respectively. These clusters were validated in independent external validation cohorts using rand statistic (Lung RS = 0.92, p &lt; 0.001, H RS = 0.92, p &lt; 0.001). Our analysis indicated both common as well as cancer-specific clustering and clinical associations of radiomic features. Strongest associations with clinical parameters: Prognosis Lung CI = 0.60 +/- 0.01, Prognosis H CI = 0.68 +/- 0.01; Lung histology AUC = 0.56 +/- 0.03, Lung stage AUC = 0.61 +/- 0.01, H HPV AUC = 0.58 +/- 0.03, H stage AUC = 0.77 +/- 0.02. Full utilization of these cancer-specific characteristics of image features may further improve radiomic biomarkers, providing a non-invasive way of quantifying and monitoring tumor phenotypic characteristics in clinical practice.</style></abstract><notes><style face="normal" font="default" size="100%">Parmar, Chintan&#xD;Leijenaar, Ralph T H&#xD;Grossmann, Patrick&#xD;Rios Velazquez, Emmanuel&#xD;Bussink, Johan&#xD;Rietveld, Derek&#xD;Rietbergen, Michelle M&#xD;Haibe-Kains, Benjamin&#xD;Lambin, Philippe&#xD;Aerts, Hugo J W L&#xD;England&#xD;Sci Rep. 2015 Jun 5;5:11044. doi: 10.1038/srep11044.</style></notes><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/srep11044</style></electronic-resource-num><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider><language><style face="normal" font="default" size="100%">eng</style></language></record><record><database name="Pubs_basedon_TCIA.enl" 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face="normal" font="default" size="100%">1-12</style></pages><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">seed-based segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">key slice</style></keyword><keyword><style face="normal" font="default" size="100%">tumor plot</style></keyword><keyword><style face="normal" font="default" size="100%">brain volumes</style></keyword><keyword><style face="normal" font="default" size="100%">BRaTS: Multimodal Brain Tumor Segmentation Challenge MICCAI 2012</style></keyword><keyword><style face="normal" font="default" size="100%">support vector machine (SVM) classification</style></keyword><keyword><style face="normal" font="default" size="100%">boundary-based methods</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">1609-0985</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>65</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">65</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Patel, Nikhilkumar P</style></author><author><style face="normal" font="default" size="100%">Parmar, Shankar K</style></author><author><style face="normal" font="default" size="100%">Jain, Kavindra R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Swift Pre Rendering Volumetric Visualization of Magnetic Resonance Cardiac Images based on Isosurface Technique</style></title><secondary-title><style face="normal" font="default" size="100%">Procedia Technology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Procedia Technology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">422-429</style></pages><volume><style face="normal" font="default" size="100%">14</style></volume><dates><year><style face="normal" font="default" size="100%">2014</style></year></dates><isbn><style face="normal" font="default" size="100%">2212-0173</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>693</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">693</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pathak, Yadunath</style></author><author><style face="normal" font="default" size="100%">Arya, KV</style></author><author><style face="normal" font="default" size="100%">Tiwari, Shailendra</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An efficient low-dose CT reconstruction technique using partial derivatives based guided image filter</style></title><secondary-title><style face="normal" font="default" size="100%">Multimedia Tools and Applications</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Multimedia Tools and Applications</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-20</style></pages><keywords><keyword><style face="normal" font="default" size="100%">TCGA-LUAD</style></keyword><keyword><style face="normal" font="default" size="100%">low-dose CT</style></keyword><keyword><style face="normal" font="default" size="100%">Filtered back projection (FBP)</style></keyword><keyword><style face="normal" font="default" size="100%">adaptive statistical iterative reconstruction (ASIR)</style></keyword><keyword><style face="normal" font="default" size="100%">model-based iterative reconstruction (MBIR)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">1380-7501</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1007/s11042-018-6840-5</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>379</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">379</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Patil, Ravindra</style></author><author><style face="normal" font="default" size="100%">Mahadevaiah, Geetha</style></author><author><style face="normal" font="default" size="100%">Dekker, Andre</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An Approach Toward Automatic Classification of Tumor Histopathology of Non–Small Cell Lung Cancer Based on Radiomic Features</style></title><secondary-title><style face="normal" font="default" size="100%">Tomography: a journal for imaging research</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Tomography: a journal for imaging research</style></full-title></periodical><pages><style face="normal" font="default" size="100%">374-377</style></pages><volume><style face="normal" font="default" size="100%">2</style></volume><number><style face="normal" font="default" size="100%">4</style></number><keywords><keyword><style face="normal" font="default" size="100%">NSCLC-radiomics, lung cancer, tumor histopathology</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>563</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">563</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Peeken, J. C.</style></author><author><style face="normal" font="default" size="100%">Hesse, J.</style></author><author><style face="normal" font="default" size="100%">Haller, B.</style></author><author><style face="normal" font="default" size="100%">Kessel, K. A.</style></author><author><style face="normal" font="default" size="100%">Nusslin, F.</style></author><author><style face="normal" font="default" size="100%">Combs, S. E.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Semantic imaging features predict disease progression and survival in glioblastoma multiforme patients</style></title><secondary-title><style face="normal" font="default" size="100%">Strahlenther Onkol</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Strahlenther Onkol</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">Radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">Semantic features</style></keyword><keyword><style face="normal" font="default" size="100%">VASARI</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">REMBRANDT</style></keyword><keyword><style face="normal" font="default" size="100%">Biomarker</style></keyword><keyword><style face="normal" font="default" size="100%">Prognostic model</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 13</style></date></pub-dates></dates><orig-pub><style face="normal" font="default" size="100%">Semantische Bildeigenschaften prognostizieren Tumorprogression und Uberleben von Patienten mit Glioblastoma multiforme.</style></orig-pub><isbn><style face="normal" font="default" size="100%">1439-099X (Electronic)&#xD;0179-7158 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29442128</style></accession-num><abstract><style face="normal" font="default" size="100%">BACKGROUND: For glioblastoma (GBM), multiple prognostic factors have been identified. Semantic imaging features were shown to be predictive for survival prediction. No similar data have been generated for the prediction of progression. The aim of this study was to assess the predictive value of the semantic visually accessable REMBRANDT [repository for molecular brain neoplasia data] images (VASARI) imaging feature set for progression and survival, and the creation of joint prognostic models in combination with clinical and pathological information. METHODS: 189 patients were retrospectively analyzed. Age, Karnofsky performance status, gender, and MGMT promoter methylation and IDH mutation status were assessed. VASARI features were determined on pre- and postoperative MRIs. Predictive potential was assessed with univariate analyses and Kaplan-Meier survival curves. Following variable selection and resampling, multivariate Cox regression models were created. Predictive performance was tested on patient test sets and compared between groups. The frequency of selection for single variables and variable pairs was determined. RESULTS: For progression free survival (PFS) and overall survival (OS), univariate significant associations were shown for 9 and 10 VASARI features, respectively. Multivariate models yielded concordance indices significantly different from random for the clinical, imaging, combined, and combined+ MGMT models of 0.657, 0.636, 0.694, and 0.716 for OS, and 0.602, 0.604, 0.633, and 0.643 for PFS. &quot;Multilocality,&quot; &quot;deep white-matter invasion,&quot; &quot;satellites,&quot; and &quot;ependymal invasion&quot; were over proportionally selected for multivariate model generation, underlining their importance. CONCLUSIONS: We demonstrated a predictive value of several qualitative imaging features for progression and survival. 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face="normal" font="default" size="100%">Journal of neurosurgery</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Journal of neurosurgery</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1008-1017</style></pages><volume><style face="normal" font="default" size="100%">124</style></volume><number><style face="normal" font="default" size="100%">4</style></number><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><isbn><style face="normal" font="default" size="100%">0022-3085</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>578</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">578</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reeves, A. P.</style></author><author><style face="normal" font="default" size="100%">Xie, Y.</style></author><author><style face="normal" font="default" size="100%">Liu, S.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">School of Electrical and Computer Engineering, Cornell University, Ithaca, NY, 14850, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Automated image quality assessment for chest CT scans</style></title><secondary-title><style face="normal" font="default" size="100%">Med Phys</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Med Phys</style></full-title></periodical><pages><style face="normal" font="default" size="100%">561-578</style></pages><volume><style face="normal" font="default" size="100%">45</style></volume><number><style face="normal" font="default" size="100%">2</style></number><keywords><keyword><style face="normal" font="default" size="100%">Phantom FDA</style></keyword><keyword><style face="normal" font="default" size="100%">Lung Image Database Consortium (LIDC)</style></keyword><keyword><style face="normal" font="default" size="100%">lung cancer</style></keyword><keyword><style face="normal" font="default" size="100%">chest anthropomorphic phantom</style></keyword><keyword><style face="normal" font="default" size="100%">segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">CT image calibration assessment</style></keyword><keyword><style face="normal" font="default" size="100%">CT image noise assessment</style></keyword><keyword><style face="normal" font="default" size="100%">automatic image quality measurement</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">2473-4209 (Electronic)&#xD;0094-2405 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29239005</style></accession-num><abstract><style face="normal" font="default" size="100%">PURPOSE: Medical image quality needs to be maintained at standards sufficient for effective clinical reading. Automated computer analytic methods may be applied to medical images for quality assessment. METHODS: For chest CT scans in a lung cancer screening context, an automated quality assessment method is presented that characterizes image noise and image intensity calibration. This is achieved by image measurements in three automatically segmented homogeneous regions of the scan: external air, trachea lumen air, and descending aorta blood. Profiles of CT scanner behavior are also computed. RESULTS: The method has been evaluated on both phantom and real low-dose chest CT scans and results show that repeatable noise and calibration measures may be realized by automated computer algorithms. Noise and calibration profiles show relevant differences between different scanners and protocols. CONCLUSIONS: Automated image quality assessment may be useful for quality control for lung cancer screening and may enable performance improvements to automated computer analysis methods.</style></abstract><notes><style face="normal" font="default" size="100%">Reeves, Anthony P&#xD;Xie, Yiting&#xD;Liu, Shuang&#xD;eng&#xD;2017/12/15 06:00&#xD;Med Phys. 2018 Feb;45(2):561-578. doi: 10.1002/mp.12729. Epub 2018 Jan 8.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29239005</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1002/mp.12729</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>577</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">577</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ren, Yacheng</style></author><author><style face="normal" font="default" size="100%">Ma, Jingchen</style></author><author><style face="normal" font="default" size="100%">Xiong, Junfeng</style></author><author><style 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size="100%">MRI</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">0972-7272</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>473</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">473</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Saltz, Joel</style></author><author><style face="normal" font="default" size="100%">Almeida, Jonas</style></author><author><style face="normal" font="default" size="100%">Gao, Yi</style></author><author><style face="normal" font="default" size="100%">Sharma, Ashish</style></author><author><style face="normal" font="default" size="100%">Bremer, Erich</style></author><author><style face="normal" font="default" size="100%">DiPrima, Tammy</style></author><author><style face="normal" font="default" size="100%">Saltz, Mary</style></author><author><style face="normal" font="default" size="100%">Kalpathy-Cramer, Jayashree</style></author><author><style face="normal" font="default" size="100%">Kurc, Tahsin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Towards Generation, Management, and Exploration of Combined Radiomics and Pathomics Datasets for Cancer Research</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA Summits on Translational Science Proceedings</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">AMIA Summits on Translational Science Proceedings</style></full-title></periodical><pages><style face="normal" font="default" size="100%">85-94</style></pages><volume><style face="normal" font="default" size="100%">2017</style></volume><keywords><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">pathomics</style></keyword><keyword><style face="normal" font="default" size="100%">non small cell lung cancer (NSCLC)</style></keyword><keyword><style face="normal" font="default" size="100%">glioblastoma multiforme (GBM)</style></keyword><keyword><style face="normal" font="default" size="100%">JSON</style></keyword><keyword><style face="normal" font="default" size="100%">GeoJSON</style></keyword><keyword><style face="normal" font="default" size="100%">NoSQL</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>576</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">576</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Saltz, J.</style></author><author><style face="normal" font="default" size="100%">Gupta, R.</style></author><author><style face="normal" font="default" size="100%">Hou, L.</style></author><author><style face="normal" font="default" size="100%">Kurc, T.</style></author><author><style face="normal" font="default" size="100%">Singh, P.</style></author><author><style face="normal" font="default" size="100%">Nguyen, V.</style></author><author><style face="normal" font="default" size="100%">Samaras, D.</style></author><author><style face="normal" font="default" size="100%">Shroyer, K. R.</style></author><author><style face="normal" font="default" size="100%">Zhao, T.</style></author><author><style face="normal" font="default" size="100%">Batiste, R.</style></author><author><style face="normal" font="default" size="100%">Van Arnam, J.</style></author><author><style face="normal" font="default" size="100%">Cancer Genome Atlas Research, Network</style></author><author><style face="normal" font="default" size="100%">Shmulevich, I.</style></author><author><style face="normal" font="default" size="100%">Rao, A. U. K.</style></author><author><style face="normal" font="default" size="100%">Lazar, A. J.</style></author><author><style face="normal" font="default" size="100%">Sharma, A.</style></author><author><style face="normal" font="default" size="100%">Thorsson, V.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Biomedical Informatics, Stony Brook Medicine, Stony Brook, NY 11794, USA. Electronic address: joel.saltz@stonybrookmedicine.edu.&#xD;Department of Biomedical Informatics, Stony Brook Medicine, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA.&#xD;Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA.&#xD;Department of Biomedical Informatics, Stony Brook Medicine, Stony Brook, NY 11794, USA.&#xD;Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.&#xD;Department of Pathology, Stony Brook Medicine, Stony Brook, NY 11794, USA.&#xD;Department of Pathology and Laboratory Medicine, Perelman School at the University of Pennsylvania, Philadelphia, PA 19104, USA.&#xD;Institute for Systems Biology, Seattle, WA 98109, USA.&#xD;Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.&#xD;Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.&#xD;Department of Biomedical Informatics, Emory University, Atlanta, GA 30322, USA.&#xD;Institute for Systems Biology, Seattle, WA 98109, USA. Electronic address: vesteinn.thorsson@systemsbiology.org.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images</style></title><secondary-title><style face="normal" font="default" size="100%">Cell Rep</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Cell Rep</style></full-title></periodical><pages><style face="normal" font="default" size="100%">181-193 e7</style></pages><volume><style face="normal" font="default" size="100%">23</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCIA General</style></keyword><keyword><style face="normal" font="default" size="100%">artificial intelligence</style></keyword><keyword><style face="normal" font="default" size="100%">bioinformatics</style></keyword><keyword><style face="normal" font="default" size="100%">computer vision</style></keyword><keyword><style face="normal" font="default" size="100%">deep learning</style></keyword><keyword><style face="normal" font="default" size="100%">digital pathology</style></keyword><keyword><style face="normal" font="default" size="100%">immuno-oncology</style></keyword><keyword><style face="normal" font="default" size="100%">lymphocytes</style></keyword><keyword><style face="normal" font="default" size="100%">machine learning</style></keyword><keyword><style face="normal" font="default" size="100%">tumor microenvironment</style></keyword><keyword><style face="normal" font="default" size="100%">tumor-infiltrating lymphocytes</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Apr 3</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">2211-1247 (Electronic)</style></isbn><accession-num><style face="normal" font="default" size="100%">29617659</style></accession-num><abstract><style face="normal" font="default" size="100%">Beyond sample curation and basic pathologic characterization, the digitized H&amp;E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&amp;E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment.</style></abstract><notes><style face="normal" font="default" size="100%">Saltz, Joel&#xD;Gupta, Rajarsi&#xD;Hou, Le&#xD;Kurc, Tahsin&#xD;Singh, Pankaj&#xD;Nguyen, Vu&#xD;Samaras, Dimitris&#xD;Shroyer, Kenneth R&#xD;Zhao, Tianhao&#xD;Batiste, Rebecca&#xD;Van Arnam, John&#xD;Shmulevich, Ilya&#xD;Rao, Arvind U K&#xD;Lazar, Alexander J&#xD;Sharma, Ashish&#xD;Thorsson, Vesteinn&#xD;eng&#xD;2018/04/05 06:00&#xD;Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29617659</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/j.celrep.2018.03.086</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>405</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">405</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Samala, Ravi K</style></author><author><style face="normal" font="default" size="100%">Chan, Heang-Ping</style></author><author><style face="normal" font="default" size="100%">Hadjiiski, Lubomir</style></author><author><style face="normal" font="default" size="100%">Helvie, Mark A</style></author><author><style face="normal" font="default" size="100%">Kim, Renaid</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Samuel G. Armato III, </style></author><author><style face="normal" font="default" size="100%">Nicholas A. Petrick</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Identifying key radiogenomic associations between DCE-MRI and micro-RNA expressions for breast cancer</style></title><secondary-title><style face="normal" font="default" size="100%">Medical Imaging 2017: Computer-Aided Diagnosis</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">1-7</style></pages><volume><style face="normal" font="default" size="100%">10134</style></volume><keywords><keyword><style face="normal" font="default" size="100%">breast cancer, radiomics, miRNA, DCE-MRI, LASSO</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">SPIE</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>268</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">268</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sarathi, Mangipudi Partha</style></author><author><style face="normal" font="default" size="100%">Ansari, MA</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A scheme for patient study retrieval from 3D brain MR volumes</style></title><secondary-title><style face="normal" font="default" size="100%">Green Computing and Internet of Things (ICGCIoT), 2015 International Conference on</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">214-218</style></pages><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>400</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">400</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sargent, Dustin</style></author><author><style face="normal" font="default" size="100%">Park, Sun Young</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Semi-automatic 3D lung nodule segmentation in CT using dynamic programming</style></title><secondary-title><style face="normal" font="default" size="100%">SPIE Medical Imaging</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">101332R-101332R-9</style></pages><keywords><keyword><style face="normal" font="default" size="100%">Phantom FDA, SPIE 2016 lung nodule classification challenge, Computer programming</style></keyword><keyword><style face="normal" font="default" size="100%">Image segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">Lung</style></keyword><keyword><style face="normal" font="default" size="100%">Tissues</style></keyword><keyword><style face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style face="normal" font="default" size="100%">Chest</style></keyword><keyword><style face="normal" font="default" size="100%">Diseases and disorders</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">International Society for Optics and Photonics</style></publisher><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1117/12.2254575 </style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>273</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">273</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sathyan, Pratheesh</style></author><author><style face="normal" font="default" size="100%">Zinn, Pascal O</style></author><author><style face="normal" font="default" size="100%">Marisetty, Anantha L</style></author><author><style face="normal" font="default" size="100%">Liu, Bin</style></author><author><style face="normal" font="default" size="100%">Kamal, Mohamed Mostafa</style></author><author><style face="normal" font="default" size="100%">Singh, Sanjay K</style></author><author><style face="normal" font="default" size="100%">Bady, Pierre</style></author><author><style face="normal" font="default" size="100%">Lu, Li</style></author><author><style face="normal" font="default" size="100%">Wani, Khalida M</style></author><author><style face="normal" font="default" size="100%">Veo, Bethany L</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mir-21–Sox2 Axis Delineates Glioblastoma Subtypes with Prognostic Impact</style></title><secondary-title><style face="normal" font="default" size="100%">The Journal of Neuroscience</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">The Journal of Neuroscience</style></full-title></periodical><pages><style face="normal" font="default" size="100%">15097-15112</style></pages><volume><style face="normal" font="default" size="100%">35</style></volume><number><style face="normal" font="default" size="100%">45</style></number><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">0270-6474</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>604</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">604</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sawant, Aaswad</style></author><author><style face="normal" font="default" size="100%">Bhandari, Mayur</style></author><author><style face="normal" font="default" size="100%">Yadav, Ravikumar</style></author><author><style face="normal" font="default" size="100%">Yele, Rohan</style></author><author><style face="normal" font="default" size="100%">Bendale, Mrs Sneha</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">BRAIN CANCER DETECTION FROM MRI: A MACHINE LEARNING APPROACH (TENSORFLOW)</style></title><secondary-title><style face="normal" font="default" size="100%">BRAIN</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">BRAIN</style></full-title></periodical><volume><style face="normal" font="default" size="100%">5</style></volume><number><style face="normal" font="default" size="100%">04</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>575</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">575</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Scarpelli, M.</style></author><author><style face="normal" font="default" size="100%">Eickhoff, J.</style></author><author><style face="normal" font="default" size="100%">Cuna, E.</style></author><author><style face="normal" font="default" size="100%">Perlman, S.</style></author><author><style face="normal" font="default" size="100%">Jeraj, R.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Medical Physics, University of Wisconsin, 1111 Highland Ave, Room 1005, Madison, WI 53792, United States of America.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Optimal transformations leading to normal distributions of positron emission tomography standardized uptake values</style></title><secondary-title><style face="normal" font="default" size="100%">Phys Med Biol</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Phys Med Biol</style></full-title></periodical><pages><style face="normal" font="default" size="100%">035021</style></pages><volume><style face="normal" font="default" size="100%">63</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">Head-Neck Cetuximab</style></keyword><keyword><style face="normal" font="default" size="100%">RTOG-0522</style></keyword><keyword><style face="normal" font="default" size="100%">Radiation Therapy Oncology Group (RTOG)</style></keyword><keyword><style face="normal" font="default" size="100%">head and neck squamous cell carcinoma</style></keyword><keyword><style face="normal" font="default" size="100%">positron emission tomography (PET)</style></keyword><keyword><style face="normal" font="default" size="100%">standardized uptake value (SUV)</style></keyword><keyword><style face="normal" font="default" size="100%">18F-FDG</style></keyword><keyword><style face="normal" font="default" size="100%">18F-FLT</style></keyword><keyword><style face="normal" font="default" size="100%">Box-Cox transform</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Jan 30</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1361-6560 (Electronic)&#xD;0031-9155 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29235988</style></accession-num><abstract><style face="normal" font="default" size="100%">The statistical analysis of positron emission tomography (PET) standardized uptake value (SUV) measurements is challenging due to the skewed nature of SUV distributions. This limits utilization of powerful parametric statistical models for analyzing SUV measurements. An ad-hoc approach, which is frequently used in practice, is to blindly use a log transformation, which may or may not result in normal SUV distributions. This study sought to identify optimal transformations leading to normally distributed PET SUVs extracted from tumors and assess the effects of therapy on the optimal transformations. METHODS: The optimal transformation for producing normal distributions of tumor SUVs was identified by iterating the Box-Cox transformation parameter (lambda) and selecting the parameter that maximized the Shapiro-Wilk P-value. Optimal transformations were identified for tumor SUVmax distributions at both pre and post treatment. This study included 57 patients that underwent (18)F-fluorodeoxyglucose ((18)F-FDG) PET scans (publically available dataset). In addition, to test the generality of our transformation methodology, we included analysis of 27 patients that underwent (18)F-Fluorothymidine ((18)F-FLT) PET scans at our institution. RESULTS: After applying the optimal Box-Cox transformations, neither the pre nor the post treatment (18)F-FDG SUV distributions deviated significantly from normality (P &gt; 0.10). Similar results were found for (18)F-FLT PET SUV distributions (P &gt; 0.10). For both (18)F-FDG and (18)F-FLT SUV distributions, the skewness and kurtosis increased from pre to post treatment, leading to a decrease in the optimal Box-Cox transformation parameter from pre to post treatment. There were types of distributions encountered for both (18)F-FDG and (18)F-FLT where a log transformation was not optimal for providing normal SUV distributions. CONCLUSION: Optimization of the Box-Cox transformation, offers a solution for identifying normal SUV transformations for when the log transformation is insufficient. The log transformation is not always the appropriate transformation for producing normally distributed PET SUVs.</style></abstract><notes><style face="normal" font="default" size="100%">Scarpelli, Matthew&#xD;Eickhoff, Jens&#xD;Cuna, Enrique&#xD;Perlman, Scott&#xD;Jeraj, Robert&#xD;eng&#xD;England&#xD;2017/12/14 06:00&#xD;Phys Med Biol. 2018 Jan 30;63(3):035021. doi: 10.1088/1361-6560/aaa175.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29235988</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1088/1361-6560/aaa175</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>616</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">616</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Schmainda, KM</style></author><author><style face="normal" font="default" size="100%">Prah, MA</style></author><author><style face="normal" font="default" size="100%">Rand, SD</style></author><author><style face="normal" font="default" size="100%">Liu, Y</style></author><author><style face="normal" font="default" size="100%">Logan, B</style></author><author><style face="normal" font="default" size="100%">Muzi, M</style></author><author><style face="normal" font="default" size="100%">Rane, SD</style></author><author><style face="normal" font="default" size="100%">Da, X</style></author><author><style face="normal" font="default" size="100%">Yen, Y-F</style></author><author><style face="normal" font="default" size="100%">Kalpathy-Cramer, J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Multisite Concordance of DSC-MRI Analysis for Brain Tumors: Results of a National Cancer Institute Quantitative Imaging Network Collaborative Project</style></title><secondary-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-9</style></pages><keywords><keyword><style face="normal" font="default" size="100%">DSC-MRI, QIN</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">0195-6108</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" 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</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>650</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">650</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Soike, Michael H</style></author><author><style face="normal" font="default" size="100%">McTyre, Emory R</style></author><author><style face="normal" font="default" size="100%">Shah, Nameeta</style></author><author><style face="normal" font="default" size="100%">Puchalski, Ralph B</style></author><author><style face="normal" font="default" size="100%">Holmes, Jordan A</style></author><author><style face="normal" font="default" size="100%">Paulsson, Anna K</style></author><author><style face="normal" font="default" size="100%">Miller, Lance D</style></author><author><style face="normal" font="default" size="100%">Cramer, Christina K</style></author><author><style face="normal" font="default" size="100%">Lesser, Glenn J</style></author><author><style face="normal" font="default" size="100%">Strowd, Roy E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Glioblastoma radiomics: can genomic and molecular characteristics correlate with imaging response patterns?</style></title><secondary-title><style face="normal" font="default" size="100%">Neuroradiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Neuroradiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-9</style></pages><keywords><keyword><style face="normal" font="default" size="100%">IVY Gap</style></keyword><keyword><style face="normal" font="default" size="100%">glioblastoma</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">pseudoprogression (PSP)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">0028-3940</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1007/s00234-018-2060-y</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>372</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">372</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Song, Jiangdian</style></author><author><style face="normal" font="default" size="100%">Liu, Zaiyi</style></author><author><style face="normal" font="default" size="100%">Zhong, Wenzhao</style></author><author><style face="normal" font="default" size="100%">Huang, Yanqi</style></author><author><style face="normal" font="default" size="100%">Ma, Zelan</style></author><author><style face="normal" font="default" size="100%">Dong, Di</style></author><author><style face="normal" font="default" size="100%">Liang, Changhong</style></author><author><style face="normal" font="default" size="100%">Tian, Jie</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Non-small cell lung cancer: quantitative phenotypic analysis of CT images as a potential marker of prognosis</style></title><secondary-title><style face="normal" font="default" size="100%">Scientific Reports</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><pages><style face="normal" font="default" size="100%">1-9</style></pages><volume><style face="normal" font="default" size="100%">6:38282</style></volume><keywords><keyword><style face="normal" font="default" size="100%">Radiomics, NSCLC, Lung</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/srep38282</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>443</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">443</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Song, QingZeng</style></author><author><style face="normal" font="default" size="100%">Zhao, Lei</style></author><author><style face="normal" font="default" size="100%">Luo, XingKe</style></author><author><style face="normal" font="default" size="100%">Dou, XueChen</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Using Deep Learning for Classification of lung nodules on Computed Tomography Images</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Healthcare Engineering </style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Journal of Healthcare Engineering</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-10</style></pages><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><notes><style face="normal" font="default" size="100%">LIDC-IDRI, Classifier, convolutional neural network, deep neural network</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">http://downloads.hindawi.com/journals/jhe/aip/8314740.pdf</style></url></related-urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>346</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">346</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Song, Sung Eun</style></author><author><style face="normal" font="default" size="100%">Bae, Min Sun</style></author><author><style face="normal" font="default" size="100%">Chang, Jung Min</style></author><author><style face="normal" font="default" size="100%">Cho, Nariya</style></author><author><style face="normal" font="default" size="100%">Ryu, Han Suk</style></author><author><style face="normal" font="default" size="100%">Moon, Woo Kyung</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">MR and mammographic imaging features of HER2-positive breast cancers according to hormone receptor status: a retrospective comparative study</style></title><secondary-title><style face="normal" font="default" size="100%">Acta Radiologica</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Acta Radiologica</style></full-title></periodical><pages><style face="normal" font="default" size="100%">0284185116673119</style></pages><keywords><keyword><style face="normal" font="default" size="100%">TCGA-Breast</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><isbn><style face="normal" font="default" size="100%">0284-1851</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>667</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">667</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Soufi, Mazen</style></author><author><style face="normal" font="default" size="100%">Arimura, Hidetaka</style></author><author><style face="normal" font="default" size="100%">Nagami, Noriyuki</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identification of optimal mother wavelets in survival prediction of lung cancer patients using wavelet decomposition‐based radiomic features</style></title><secondary-title><style face="normal" font="default" size="100%">Medical physics</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Medical physics</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">radiomics-nsclc</style></keyword><keyword><style face="normal" font="default" size="100%">rider</style></keyword><keyword><style face="normal" font="default" size="100%">lung</style></keyword><keyword><style face="normal" font="default" size="100%">pet-ct</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><isbn><style face="normal" font="default" size="100%">0094-2405</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1002/mp.13202</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>574</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">574</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Soufi, M.</style></author><author><style face="normal" font="default" size="100%">Arimura, H.</style></author><author><style face="normal" font="default" size="100%">Nakamoto, T.</style></author><author><style face="normal" font="default" size="100%">Hirose, T. A.</style></author><author><style face="normal" font="default" size="100%">Ohga, S.</style></author><author><style face="normal" font="default" size="100%">Umezu, Y.</style></author><author><style face="normal" font="default" size="100%">Honda, H.</style></author><author><style face="normal" font="default" size="100%">Sasaki, T.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Graduate School of Medical Sciences, Kyushu University 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Research Fellow at Japan Society for the Promotion of Science 5-3-1, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan.&#xD;Faculty of Medical Sciences, Kyushu University 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. Electronic address: arimurah@med.kyushu-u.ac.jp.&#xD;Graduate School of Medical Sciences, Kyushu University 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.&#xD;Faculty of Medical Sciences, Kyushu University 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.&#xD;Kyushu University Hospital 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Exploration of temporal stability and prognostic power of radiomic features based on electronic portal imaging device images</style></title><secondary-title><style face="normal" font="default" size="100%">Phys Med</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Phys Med</style></full-title></periodical><pages><style face="normal" font="default" size="100%">32-44</style></pages><volume><style face="normal" font="default" size="100%">46</style></volume><keywords><keyword><style face="normal" font="default" size="100%">NSCLC-Radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">Radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">multiplication of intraclass correlation coefficient (mICC)</style></keyword><keyword><style face="normal" font="default" size="100%">Matlab</style></keyword><keyword><style face="normal" font="default" size="100%">Kaplan-Meier survival analysis</style></keyword><keyword><style face="normal" font="default" size="100%">EPID image</style></keyword><keyword><style face="normal" font="default" size="100%">Prognostic prediction</style></keyword><keyword><style face="normal" font="default" size="100%">Radiomic feature</style></keyword><keyword><style face="normal" font="default" size="100%">Temporal stability</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1724-191X (Electronic)&#xD;1120-1797 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29519407</style></accession-num><abstract><style face="normal" font="default" size="100%">PURPOSE: We aimed to explore the temporal stability of radiomic features in the presence of tumor motion and the prognostic powers of temporally stable features. METHODS: We selected single fraction dynamic electronic portal imaging device (EPID) (n=275 frames) and static digitally reconstructed radiographs (DRRs) of 11 lung cancer patients, who received stereotactic body radiation therapy (SBRT) under free breathing. Forty-seven statistical radiomic features, which consisted of 14 histogram-based features and 33 texture features derived from the graylevel co-occurrence and graylevel run-length matrices, were computed. The temporal stability was assessed by using a multiplication of the intra-class correlation coefficients (ICCs) between features derived from the EPID and DRR images at three quantization levels. The prognostic powers of the features were investigated using a different database of lung cancer patients (n=221) based on a Kaplan-Meier survival analysis. RESULTS: Fifteen radiomic features were found to be temporally stable for various quantization levels. Among these features, seven features have shown potentials for prognostic prediction in lung cancer patients. CONCLUSIONS: This study suggests a novel approach to select temporally stable radiomic features, which could hold prognostic powers in lung cancer patients.</style></abstract><notes><style face="normal" font="default" size="100%">Soufi, Mazen&#xD;Arimura, Hidetaka&#xD;Nakamoto, Takahiro&#xD;Hirose, Taka-Aki&#xD;Ohga, Saiji&#xD;Umezu, Yoshiyuki&#xD;Honda, Hiroshi&#xD;Sasaki, Tomonari&#xD;eng&#xD;Italy&#xD;2018/03/10 06:00&#xD;Phys Med. 2018 Feb;46:32-44. doi: 10.1016/j.ejmp.2017.11.037. Epub 2018 Jan 19.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29519407</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/j.ejmp.2017.11.037</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>71</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">71</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Soysal, Omer M</style></author><author><style face="normal" font="default" size="100%">Chen, P</style></author><author><style face="normal" font="default" size="100%">Schneider, Helmut</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An Image Processing Tool for Efficient Feature Extraction in Computer-Aided Detection Systems</style></title><secondary-title><style face="normal" font="default" size="100%">Granular Computing (GrC), 2010 IEEE International Conference on</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">438-442</style></pages><dates><year><style face="normal" font="default" size="100%">2010</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE</style></publisher><isbn><style face="normal" font="default" size="100%">1424479649</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>172</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">172</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Steed, TC</style></author><author><style face="normal" font="default" size="100%">Treiber, JM</style></author><author><style face="normal" font="default" size="100%">Patel, KS</style></author><author><style face="normal" font="default" size="100%">Taich, Z</style></author><author><style face="normal" font="default" size="100%">White, NS</style></author><author><style face="normal" font="default" size="100%">Treiber, ML</style></author><author><style face="normal" font="default" size="100%">Farid, N</style></author><author><style face="normal" font="default" size="100%">Carter, BS</style></author><author><style face="normal" font="default" size="100%">Dale, AM</style></author><author><style face="normal" font="default" size="100%">Chen, CC</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Iterative Probabilistic Voxel Labeling: Automated Segmentation for Analysis of The Cancer Imaging Archive Glioblastoma Images</style></title><secondary-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">American Journal of Neuroradiology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">678-685</style></pages><volume><style face="normal" font="default" size="100%">36</style></volume><number><style face="normal" font="default" size="100%">4</style></number><dates><year><style face="normal" font="default" size="100%">2015</style></year></dates><isbn><style face="normal" font="default" size="100%">0195-6108</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>564</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">564</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Steed, T. C.</style></author><author><style face="normal" font="default" size="100%">Treiber, J. M.</style></author><author><style face="normal" font="default" size="100%">Brandel, M. G.</style></author><author><style face="normal" font="default" size="100%">Patel, K. S.</style></author><author><style face="normal" font="default" size="100%">Dale, A. M.</style></author><author><style face="normal" font="default" size="100%">Carter, B. S.</style></author><author><style face="normal" font="default" size="100%">Chen, C. C.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Department of Neurosurgery, Emory University, Atlanta, GA, USA.&#xD;Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA.&#xD;Department of Neurosurgery, University of California San Diego, La Jolla, CA, USA.&#xD;Department of Neurosurgery, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.&#xD;Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA, USA.&#xD;Department of Radiology, University of California San Diego, La Jolla, CA, USA.&#xD;Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA.&#xD;Department of Neurosurgery, University of Minnesota, Minneapolis, MN, USA. ccchen@umn.edu.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Quantification of glioblastoma mass effect by lateral ventricle displacement</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Sci Rep</style></full-title><abbr-1><style face="normal" font="default" size="100%">Scientific reports</style></abbr-1></periodical><pages><style face="normal" font="default" size="100%">2827</style></pages><volume><style face="normal" font="default" size="100%">8</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">TCGA-GBM</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword><keyword><style face="normal" font="default" size="100%">glioblastoma</style></keyword><keyword><style face="normal" font="default" size="100%">lateral ventricle displacement (LVd)</style></keyword><keyword><style face="normal" font="default" size="100%">iterative probabilistic voxel labeling (IPVL)</style></keyword><keyword><style face="normal" font="default" size="100%">contrast enhancing volumes (CEV)</style></keyword><keyword><style face="normal" font="default" size="100%">FLAIR hyper-intensity volumes (FHV)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 12</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">2045-2322 (Electronic)&#xD;2045-2322 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29434275</style></accession-num><abstract><style face="normal" font="default" size="100%">Mass effect has demonstrated prognostic significance for glioblastoma, but is poorly quantified. Here we define and characterize a novel neuroimaging parameter, lateral ventricle displacement (LVd), which quantifies mass effect in glioblastoma patients. LVd is defined as the magnitude of displacement from the center of mass of the lateral ventricle volume in glioblastoma patients relative to that a normal reference brain. Pre-operative MR images from 214 glioblastoma patients from The Cancer Imaging Archive (TCIA) were segmented using iterative probabilistic voxel labeling (IPVL). LVd, contrast enhancing volumes (CEV) and FLAIR hyper-intensity volumes (FHV) were determined. Associations with patient survival and tumor genomics were investigated using data from The Cancer Genome Atlas (TCGA). Glioblastoma patients had significantly higher LVd relative to patients without brain tumors. The variance of LVd was not explained by tumor volume, as defined by CEV or FLAIR. LVd was robustly associated with glioblastoma survival in Cox models which accounted for both age and Karnofsky&apos;s Performance Scale (KPS) (p = 0.006). Glioblastomas with higher LVd demonstrated increased expression of genes associated with tumor proliferation and decreased expression of genes associated with tumor invasion. Our results suggest LVd is a quantitative measure of glioblastoma mass effect and a prognostic imaging biomarker.</style></abstract><notes><style face="normal" font="default" size="100%">Steed, Tyler C&#xD;Treiber, Jeffrey M&#xD;Brandel, Michael G&#xD;Patel, Kunal S&#xD;Dale, Anders M&#xD;Carter, Bob S&#xD;Chen, Clark C&#xD;eng&#xD;R01 NS097649/NS/NINDS NIH HHS/&#xD;England&#xD;2018/02/13 06:00&#xD;Sci Rep. 2018 Feb 12;8(1):2827. doi: 10.1038/s41598-018-21147-w.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29434275</style></url></related-urls></urls><custom2><style face="normal" font="default" size="100%">PMC5809591</style></custom2><electronic-resource-num><style face="normal" font="default" size="100%">10.1038/s41598-018-21147-w</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded 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size="100%">Dale, Anders M</style></author><author><style face="normal" font="default" size="100%">Chow, LM</style></author><author><style face="normal" font="default" size="100%">Chen, Clark C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Differential localization of glioblastoma subtype: implications on glioblastoma pathogenesis</style></title><secondary-title><style face="normal" font="default" size="100%">Oncotarget</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Oncotarget</style></full-title></periodical><pages><style face="normal" font="default" size="100%">24899-24907</style></pages><volume><style face="normal" font="default" size="100%">7</style></volume><number><style face="normal" font="default" size="100%">18</style></number><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><isbn><style face="normal" font="default" size="100%">1949-2553</style></isbn><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>377</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">377</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stoll, Markus</style></author><author><style face="normal" font="default" size="100%">Stoiber, Eva Maria</style></author><author><style face="normal" font="default" size="100%">Grimm, Sarah</style></author><author><style face="normal" font="default" size="100%">Debus, Jürgen</style></author><author><style face="normal" font="default" size="100%">Bendl, Rolf</style></author><author><style face="normal" font="default" size="100%">Giske, 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size="100%">Dang, Jun</style></author><author><style face="normal" font="default" size="100%">Chang, Panchun</style></author><author><style face="normal" font="default" size="100%">Yin, Fang-Fang</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Effect of machine learning methods on predicting NSCLC overall survival time based on Radiomics analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Radiation Oncology</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Radiation Oncology</style></full-title></periodical><pages><style face="normal" font="default" size="100%">197</style></pages><volume><style face="normal" font="default" size="100%">13</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">NSCLC</style></keyword><keyword><style 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size="100%">Sutton, Elizabeth J</style></author><author><style face="normal" font="default" size="100%">Huang, Erich P</style></author><author><style face="normal" font="default" size="100%">Drukker, Karen</style></author><author><style face="normal" font="default" size="100%">Burnside, Elizabeth S</style></author><author><style face="normal" font="default" size="100%">Li, Hui</style></author><author><style face="normal" font="default" size="100%">Net, Jose M</style></author><author><style face="normal" font="default" size="100%">Rao, Arvind</style></author><author><style face="normal" font="default" size="100%">Whitman, Gary J</style></author><author><style face="normal" font="default" size="100%">Zuley, Margarita</style></author><author><style face="normal" font="default" size="100%">Ganott, Marie</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Breast MRI radiomics: comparison of computer-and human-extracted imaging phenotypes</style></title><secondary-title><style face="normal" font="default" size="100%">European Radiology Experimental</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">European Radiology Experimental</style></full-title></periodical><pages><style face="normal" font="default" size="100%">22</style></pages><volume><style face="normal" font="default" size="100%">1</style></volume><number><style face="normal" font="default" size="100%">1</style></number><keywords><keyword><style face="normal" font="default" size="100%">breast cancer</style></keyword><keyword><style face="normal" font="default" size="100%">magnetic resonance imaging</style></keyword><keyword><style face="normal" font="default" size="100%">inter-observer variability</style></keyword><keyword><style face="normal" font="default" size="100%">machine learning</style></keyword><keyword><style face="normal" font="default" size="100%">radiomics</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><isbn><style face="normal" font="default" size="100%">2509-9280</style></isbn><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">http://dx.doi.org/10.1186/s41747-017-0025-2 </style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>406</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">406</key></foreign-keys><ref-type name="Book Section">5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sutton, Elizabeth J</style></author><author><style face="normal" font="default" size="100%">Purvis, Nina</style></author><author><style face="normal" font="default" size="100%">Pinker-Domenig, Katja</style></author><author><style face="normal" font="default" size="100%">Morris, Elizabeth A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Personalized Medicine, Biomarkers of Risk and Breast MRI</style></title><secondary-title><style face="normal" font="default" size="100%">Breast Oncology: Techniques, Indications, and Interpretation</style></secondary-title></titles><pages><style face="normal" font="default" size="100%">337-349</style></pages><keywords><keyword><style face="normal" font="default" size="100%">Breast cancer, radiomics,</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><publisher><style face="normal" font="default" size="100%">Springer</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>448</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">448</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Suzan, A Melody</style></author><author><style face="normal" font="default" size="100%">Prathibha, G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Classification of Benign and Malignant Tumors of Lung Using Bag of Features</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Scientific &amp; Engineering Research</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Journal of Scientific &amp; Engineering Research</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-4</style></pages><volume><style face="normal" font="default" size="100%">8</style></volume><number><style face="normal" font="default" size="100%">3</style></number><keywords><keyword><style face="normal" font="default" size="100%">SPIE-AAPM-NCI Lung Nodule Classification Challenge Dataset, Bag-of-features, KNN, Lung Cancer, ROI, SIFT</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2017</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>573</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">573</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Taghanaki, S. A.</style></author><author><style face="normal" font="default" size="100%">Duggan, N.</style></author><author><style face="normal" font="default" size="100%">Ma, H.</style></author><author><style face="normal" font="default" size="100%">Hou, X.</style></author><author><style face="normal" font="default" size="100%">Celler, A.</style></author><author><style face="normal" font="default" size="100%">Benard, F.</style></author><author><style face="normal" font="default" size="100%">Hamarneh, G.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Medical Image Analysis Lab, Simon Fraser University, Canada. Electronic address: sasagarit@sfu.ca.&#xD;Medical Image Analysis Lab, Simon Fraser University, Canada. Electronic address: nduggan@sfu.ca.&#xD;Medical Imaging Research Group, Department of Radiology, University of British Columbia, Vancouver, Canada. Electronic address: mah@phas.ubc.ca.&#xD;Medical Imaging Research Group, Department of Radiology, University of British Columbia, Vancouver, Canada. Electronic address: xinchi.hou@ubc.ca.&#xD;Medical Imaging Research Group, Department of Radiology, University of British Columbia, Vancouver, Canada. Electronic address: aceller@physics.ubc.ca.&#xD;British Columbia Cancer Agency Research Centre, Vancouver, Canada. Electronic address: fbenard@bccrc.ca.&#xD;Medical Image Analysis Lab, Simon Fraser University, Canada. Electronic address: hamarneh@sfu.ca.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Segmentation-free direct tumor volume and metabolic activity estimation from PET scans</style></title><secondary-title><style face="normal" font="default" size="100%">Comput Med Imaging Graph</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Comput Med Imaging Graph</style></full-title></periodical><pages><style face="normal" font="default" size="100%">52-66</style></pages><volume><style face="normal" font="default" size="100%">63</style></volume><keywords><keyword><style face="normal" font="default" size="100%">QIN-HEADNECK</style></keyword><keyword><style face="normal" font="default" size="100%">Algorithm development</style></keyword><keyword><style face="normal" font="default" size="100%">Direct estimation</style></keyword><keyword><style face="normal" font="default" size="100%">Ensemble learning</style></keyword><keyword><style face="normal" font="default" size="100%">Positron emission tomography</style></keyword><keyword><style face="normal" font="default" size="100%">Segmentation</style></keyword><keyword><style face="normal" font="default" size="100%">Segmentation-free</style></keyword><keyword><style face="normal" font="default" size="100%">Total lesion glucose</style></keyword><keyword><style face="normal" font="default" size="100%">Tumor activity quantification</style></keyword><keyword><style face="normal" font="default" size="100%">Tumor volume quantification</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Jan</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1879-0771 (Electronic)&#xD;0895-6111 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29336922</style></accession-num><abstract><style face="normal" font="default" size="100%">Tumor volume and metabolic activity are two robust imaging biomarkers for predicting early therapy response in F-fluorodeoxyglucose (FDG) positron emission tomography (PET), which is a modality to image the distribution of radiotracers and thereby observe functional processes in the body. To date, estimation of these two biomarkers requires a lesion segmentation step. While the segmentation methods requiring extensive user interaction have obvious limitations in terms of time and reproducibility, automatically estimating activity from segmentation, which involves integrating intensity values over the volume is also suboptimal, since PET is an inherently noisy modality. Although many semi-automatic segmentation based methods have been developed, in this paper, we introduce a method which completely eliminates the segmentation step and directly estimates the volume and activity of the lesions. We trained two parallel ensemble models using locally extracted 3D patches from phantom images to estimate the activity and volume, which are derivatives of other important quantification metrics such as standardized uptake value (SUV) and total lesion glycolysis (TLG). For validation, we used 54 clinical images from the QIN Head and Neck collection on The Cancer Imaging Archive, as well as a set of 55 PET scans of the Elliptical Lung-Spine Body Phantomwith different levels of noise, four different reconstruction methods, and three different background activities, namely; air, water, and hot background. In the validation on phantom images, we achieved relative absolute error (RAE) of 5.11%+/-3.5% and 5.7%+/-5.25% for volume and activity estimation, respectively, which represents improvements of over 20% and 6% respectively, compared with the best competing methods. From the validation performed using clinical images, we found that the proposed method is capable of obtaining almost the same level of agreement with a group of trained experts, as a single trained expert is, indicating that the method has the potential to be a useful tool in clinical practice.</style></abstract><notes><style face="normal" font="default" size="100%">Taghanaki, Saeid Asgari&#xD;Duggan, Noirin&#xD;Ma, Hillgan&#xD;Hou, Xinchi&#xD;Celler, Anna&#xD;Benard, Francois&#xD;Hamarneh, Ghassan&#xD;eng&#xD;2018/01/18 06:00&#xD;Comput Med Imaging Graph. 2018 Jan;63:52-66. doi: 10.1016/j.compmedimag.2017.12.004. Epub 2017 Dec 27.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29336922</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/j.compmedimag.2017.12.004</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>259</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">259</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tan, Maxine</style></author><author><style face="normal" font="default" size="100%">Deklerck, Rudi</style></author><author><style face="normal" font="default" size="100%">Jansen, 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font="default" size="100%">Milhem, Mohammed</style></author><author><style face="normal" font="default" size="100%">Sigmund, Rita</style></author><author><style face="normal" font="default" size="100%">Godwin, Andrew K.</style></author><author><style face="normal" font="default" size="100%">Madan, Rashna</style></author><author><style face="normal" font="default" size="100%">Rosenthal, Howard G.</style></author><author><style face="normal" font="default" size="100%">Adebamowo, Clement</style></author><author><style face="normal" font="default" size="100%">Adebamowo, Sally N.</style></author><author><style face="normal" font="default" size="100%">Boussioutas, Alex</style></author><author><style face="normal" font="default" size="100%">Beer, David</style></author><author><style face="normal" font="default" size="100%">Giordano, Thomas</style></author><author><style face="normal" font="default" size="100%">Mes-Masson, Anne-Marie</style></author><author><style face="normal" font="default" size="100%">Saad, Fred</style></author><author><style face="normal" font="default" size="100%">Bocklage, Therese</style></author><author><style face="normal" font="default" size="100%">Landrum, Lisa</style></author><author><style face="normal" font="default" size="100%">Mannel, Robert</style></author><author><style face="normal" font="default" size="100%">Moore, Kathleen</style></author><author><style face="normal" font="default" size="100%">Moxley, Katherine</style></author><author><style face="normal" font="default" size="100%">Postier, Russel</style></author><author><style face="normal" font="default" size="100%">Walker, Joan</style></author><author><style face="normal" font="default" size="100%">Zuna, Rosemary</style></author><author><style face="normal" font="default" size="100%">Feldman, Michael</style></author><author><style face="normal" font="default" size="100%">Valdivieso, Federico</style></author><author><style face="normal" font="default" size="100%">Dhir, Rajiv</style></author><author><style face="normal" font="default" size="100%">Luketich, James</style></author><author><style face="normal" font="default" size="100%">Pinero, Edna M. Mora</style></author><author><style face="normal" font="default" size="100%">Quintero-Aguilo, Mario</style></author><author><style face="normal" font="default" size="100%">Carlotti, Carlos Gilberto, Jr.</style></author><author><style face="normal" font="default" size="100%">Dos Santos, Jose SebastiÃ£o</style></author><author><style face="normal" font="default" size="100%">Kemp, Rafael</style></author><author><style face="normal" font="default" size="100%">Sankarankuty, Ajith</style></author><author><style face="normal" font="default" size="100%">Tirapelli, Daniela</style></author><author><style face="normal" font="default" size="100%">Catto, James</style></author><author><style face="normal" font="default" size="100%">Agnew, Kathy</style></author><author><style face="normal" font="default" size="100%">Swisher, Elizabeth</style></author><author><style face="normal" font="default" size="100%">Creaney, Jenette</style></author><author><style face="normal" font="default" size="100%">Robinson, Bruce</style></author><author><style face="normal" font="default" size="100%">Shelley, Carl Simon</style></author><author><style face="normal" font="default" size="100%">Godwin, Eryn M.</style></author><author><style face="normal" font="default" size="100%">Kendall, Sara</style></author><author><style face="normal" font="default" size="100%">Shipman, Cassaundra</style></author><author><style face="normal" font="default" size="100%">Bradford, Carol</style></author><author><style face="normal" font="default" size="100%">Carey, Thomas</style></author><author><style face="normal" font="default" size="100%">Haddad, Andrea</style></author><author><style face="normal" font="default" size="100%">Moyer, Jeffey</style></author><author><style face="normal" font="default" size="100%">Peterson, Lisa</style></author><author><style face="normal" font="default" size="100%">Prince, Mark</style></author><author><style face="normal" font="default" size="100%">Rozek, Laura</style></author><author><style face="normal" font="default" size="100%">Wolf, Gregory</style></author><author><style face="normal" font="default" size="100%">Bowman, Rayleen</style></author><author><style face="normal" font="default" size="100%">Fong, Kwun M.</style></author><author><style face="normal" font="default" size="100%">Yang, Ian</style></author><author><style face="normal" font="default" size="100%">Korst, Robert</style></author><author><style face="normal" font="default" size="100%">Rathmell, W. Kimryn</style></author><author><style face="normal" font="default" size="100%">Fantacone-Campbell, J. Leigh</style></author><author><style face="normal" font="default" size="100%">Hooke, Jeffrey A.</style></author><author><style face="normal" font="default" size="100%">Kovatich, Albert J.</style></author><author><style face="normal" font="default" size="100%">Shriver, Craig D.</style></author><author><style face="normal" font="default" size="100%">DiPersio, John</style></author><author><style face="normal" font="default" size="100%">Drake, Bettina</style></author><author><style face="normal" font="default" size="100%">Govindan, Ramaswamy</style></author><author><style face="normal" font="default" size="100%">Heath, Sharon</style></author><author><style face="normal" font="default" size="100%">Ley, Timothy</style></author><author><style face="normal" font="default" size="100%">Van Tine, Brian</style></author><author><style face="normal" font="default" size="100%">Westervelt, Peter</style></author><author><style face="normal" font="default" size="100%">Rubin, Mark A.</style></author><author><style face="normal" font="default" size="100%">Lee, Jung Il</style></author><author><style face="normal" font="default" size="100%">Aredes, NatÃ¡lia D.</style></author><author><style face="normal" font="default" size="100%">Mariamidze, Armaz</style></author><author><style face="normal" font="default" size="100%">Lazar, Alexander J.</style></author><author><style face="normal" font="default" size="100%">Serody, Jonathan S.</style></author><author><style face="normal" font="default" size="100%">Demicco, Elizabeth G.</style></author><author><style face="normal" font="default" size="100%">Disis, Mary L.</style></author><author><style face="normal" font="default" size="100%">Vincent, Benjamin G.</style></author><author><style face="normal" font="default" size="100%">Shmulevich, llya</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Immune Landscape of Cancer</style></title><secondary-title><style face="normal" font="default" size="100%">Immunity</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Immunity</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">TCIA General</style></keyword><keyword><style face="normal" font="default" size="100%">TCGA</style></keyword><keyword><style face="normal" font="default" size="100%">tumor microenvironment (TME)</style></keyword><keyword><style face="normal" font="default" size="100%">spatial fraction of tumor regions with tumor-infiltrating lymphocytes (TILs)</style></keyword><keyword><style face="normal" font="default" size="100%">H&amp;E-stained slides</style></keyword><keyword><style face="normal" font="default" size="100%">NCI Genomic Data Commons (GDC)</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year></dates><abstract><style face="normal" font="default" size="100%">We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes—wound healing, IFN-</style><style face="normal" font="default" charset="161" size="100%">γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant</style><style face="normal" font="default" size="100%">—characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.</style></abstract><urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/j.immuni.2018.03.023</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>275</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">275</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tiwari, Arvind Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PREDICTION OF LUNG CANCER USING IMAGE PROCESSING TECHNIQUES: A REVIEW</style></title><secondary-title><style face="normal" font="default" size="100%">Advanced Computational Intelligence: An International Journal</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Advanced Computational Intelligence: An International Journal</style></full-title></periodical><pages><style face="normal" font="default" size="100%">1-9</style></pages><volume><style face="normal" font="default" size="100%">3</style></volume><number><style face="normal" font="default" size="100%">1</style></number><dates><year><style face="normal" font="default" size="100%">2016</style></year></dates><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>152</rec-number><foreign-keys><key app="EN" 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size="100%">2015</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE</style></publisher><urls></urls></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded Research/TCIA/Pubs_basedon_TCIA.enl">Pubs_basedon_TCIA.enl</database><source-app name="EndNote" version="18.2">EndNote</source-app><rec-number>568</rec-number><foreign-keys><key app="EN" db-id="rpw92fz5pwafdtez0wq5sww2x0af0sxt05vd">568</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhao, X.</style></author><author><style face="normal" font="default" size="100%">Liu, L.</style></author><author><style face="normal" font="default" size="100%">Qi, S.</style></author><author><style face="normal" font="default" size="100%">Teng, Y.</style></author><author><style face="normal" font="default" size="100%">Li, J.</style></author><author><style face="normal" font="default" size="100%">Qian, W.</style></author></authors></contributors><auth-address><style face="normal" font="default" size="100%">Sino-Dutch Biomedical and Information Engineering School, Northeastern University, Life Science Building, 500 Zhihui Street, Hun&apos;nan District, Shenyang, 110169, China.&#xD;Sino-Dutch Biomedical and Information Engineering School, Northeastern University, Life Science Building, 500 Zhihui Street, Hun&apos;nan District, Shenyang, 110169, China. qisl@bmie.neu.edu.cn.&#xD;College of Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas, 79968, USA.</style></auth-address><titles><title><style face="normal" font="default" size="100%">Agile convolutional neural network for pulmonary nodule classification using CT images</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Comput Assist Radiol Surg</style></secondary-title></titles><periodical><full-title><style face="normal" font="default" size="100%">Int J Comput Assist Radiol Surg</style></full-title></periodical><keywords><keyword><style face="normal" font="default" size="100%">LIDC-IDRI</style></keyword><keyword><style face="normal" font="default" size="100%">Convolutional neural network</style></keyword><keyword><style face="normal" font="default" size="100%">Deep learning</style></keyword><keyword><style face="normal" font="default" size="100%">Lung cancer</style></keyword><keyword><style face="normal" font="default" size="100%">Nodule classification</style></keyword></keywords><dates><year><style face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style face="normal" font="default" size="100%">Feb 23</style></date></pub-dates></dates><isbn><style face="normal" font="default" size="100%">1861-6429 (Electronic)&#xD;1861-6410 (Linking)</style></isbn><accession-num><style face="normal" font="default" size="100%">29473129</style></accession-num><abstract><style face="normal" font="default" size="100%">OBJECTIVE: To distinguish benign from malignant pulmonary nodules using CT images is critical for their precise diagnosis and treatment. A new Agile convolutional neural network (CNN) framework is proposed to conquer the challenges of a small-scale medical image database and the small size of the nodules, and it improves the performance of pulmonary nodule classification using CT images. METHODS: A hybrid CNN of LeNet and AlexNet is constructed through combining the layer settings of LeNet and the parameter settings of AlexNet. A dataset with 743 CT image nodule samples is built up based on the 1018 CT scans of LIDC to train and evaluate the Agile CNN model. Through adjusting the parameters of the kernel size, learning rate, and other factors, the effect of these parameters on the performance of the CNN model is investigated, and an optimized setting of the CNN is obtained finally. RESULTS: After finely optimizing the settings of the CNN, the estimation accuracy and the area under the curve can reach 0.822 and 0.877, respectively. The accuracy of the CNN is significantly dependent on the kernel size, learning rate, training batch size, dropout, and weight initializations. The best performance is achieved when the kernel size is set to [Formula: see text], the learning rate is 0.005, the batch size is 32, and dropout and Gaussian initialization are used. CONCLUSIONS: This competitive performance demonstrates that our proposed CNN framework and the optimization strategy of the CNN parameters are suitable for pulmonary nodule classification characterized by small medical datasets and small targets. The classification model might help diagnose and treat pulmonary nodules effectively.</style></abstract><notes><style face="normal" font="default" size="100%">Zhao, Xinzhuo&#xD;Liu, Liyao&#xD;Qi, Shouliang&#xD;Teng, Yueyang&#xD;Li, Jianhua&#xD;Qian, Wei&#xD;eng&#xD;61672146/National Natural Science Foundation of China&#xD;81671773/National Natural Science Foundation of China&#xD;Germany&#xD;2018/02/24 06:00&#xD;Int J Comput Assist Radiol Surg. 2018 Feb 23. pii: 10.1007/s11548-017-1696-0. doi: 10.1007/s11548-017-1696-0.</style></notes><urls><related-urls><url><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29473129</style></url></related-urls></urls><electronic-resource-num><style face="normal" font="default" size="100%">10.1007/s11548-017-1696-0</style></electronic-resource-num></record><record><database name="Pubs_basedon_TCIA.enl" path="/Users/fprior01/PC_H/mir_h/Funded 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