{"id":5803,"date":"2023-09-04T03:39:01","date_gmt":"2023-09-04T03:39:01","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/mrqy-quality-measures\/"},"modified":"2023-09-13T12:11:25","modified_gmt":"2023-09-13T12:11:25","slug":"mrqy-quality-measures","status":"publish","type":"tcia_analysis_result","link":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/mrqy-quality-measures\/","title":{"rendered":"MRQY-QUALITY-MEASURES"},"featured_media":8772,"template":"","cancer_types":["Glioblastoma","Cervical Squamous Cell Carcinoma","Endocervical Adenocarcinoma"],"citations":[4826,2925],"full_export":"<div class=\"columnMacro\" style=\"width:70%;min-width:70%;max-width:70%;\"><h2 style=\"margin-top: 10.0px;color: rgb(23,43,77);\" id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-Summary\">Summary<\/h2><span style=\"color: rgb(33,37,41);\">Magnetic Resonance Imaging (MRI)\u00a0<\/span>quality assessment measures were generated for\u00a0<\/p><ol><li>T1-weighted post-contrast axial MRI sequences from 133\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=1966258\">The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM)<\/a>\u00a0subjects\u00a0<\/li><li>T1-weighted post-contrast axial MRI sequences from 46\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=30671232\">The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM)<\/a>\u00a0subjects\u00a0\u00a0<\/li><li>Both T1- and T2-weighted axial MRI sequences from 54\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=19039396\">The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (TCGA-CESC)<\/a>\u00a0subjects<\/li><\/ol><p>All MRI scans for each cohort were downloaded as DICOM files from TCIA and then processed via MRQy to compute quality measures for (a) interrogating the presence of site- or equipment-specific variations within a cohort, and (b) quantifying the impact of MRI artifacts to determine what pre-analytical corrections are needed. The MRQy output can be easily interrogated via the associated HTML5 based front-end, allowing for real-time filtering and visualization. MRQy is available for download at:\u00a0<a href=\"http:\/\/github.com\/ccipd\/MRQy\" class=\"external-link\" rel=\"nofollow\">http:\/\/github.com\/ccipd\/MRQy<\/a>.\u00a0 Manifest files to download the DICOM images these results were derived from are available on the Detailed Description page.<\/p><p><br\/><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-Acknowledgements\"><span>Acknowledgements<\/span><\/h3><p><span style=\"color: rgb(32,33,36);\">Research reported in this publication was supported by:<\/span><\/p><ul><li><span style=\"color: rgb(32,33,36);\"> National Cancer Institute of the National Institutes of Health under award numbers 1U24CA199374-01, R01CA202752-01A1, R01CA208236-01A1, R01 CA216579-01A1, R01 CA220581-01A1, 1U01 CA239055-01, 1F31CA216935-01A1,\u00a0<span style=\"color: rgb(32,31,30);\">NCI 1U01CA248226-01<\/span><\/span><\/li><li><span style=\"color: rgb(32,33,36);\">National Institute for Biomedical Imaging and Bioengineering (1R43EB028736-01) <\/span><\/li><li><span style=\"color: rgb(32,33,36);\">National Center for Research Resources under award number 1 C06 RR12463-01 <\/span><\/li><li><span style=\"color: rgb(32,33,36);\">VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service<\/span><\/li><li><span style=\"color: rgb(32,33,36);\"> The DoD Breast Cancer Research Program Breakthrough Level 1 Award (W81XWH-19-1-0668)<\/span><\/li><li><span style=\"color: rgb(32,33,36);\"> The DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558)<\/span><\/li><li><span style=\"color: rgb(32,33,36);\"> The DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440)<\/span><\/li><li><span style=\"color: rgb(32,33,36);\"> The DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329, W81XWH-18-1-0404)<\/span><\/li><li><span style=\"color: rgb(32,33,36);\"> Dana Foundation David Mahoney Neuroimaging Program<\/span><\/li><li><span style=\"color: rgb(32,33,36);\">The V Foundation Translational Research Award<\/span><\/li><li><span style=\"color: rgb(32,33,36);\">The Ohio Third Frontier Technology Validation Fund<\/span><\/li><li><span style=\"color: rgb(32,33,36);\"> The Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering<\/span><\/li><li><span style=\"color: rgb(32,33,36);\">The Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University<\/span><\/li><\/ul><\/div><div class=\"columnMacro\"><p><br\/><\/p><span class=\"confluence-embedded-file-wrapper\"><img class=\"confluence-embedded-image confluence-content-image-border\" draggable=\"false\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/MRQy%20quality%20measures%20for%20TCIA%20MRI%20datasets%20(MRQy-Quality-Measures)\/mrqy_gbm_results_v1.png?api=v2\"><\/span><p><span><span style=\"color: rgb(32,31,30);\">(a) MRQy front-end interface for interrogating TCGA-GBM cohort. (b) Outlier dataset identified on the parallel coordinate chart for the CJV quality measure found to exhibit shading artifacts\u00a0on (c) representative images, especially when compared to (d) a different dataset without this artifact. (e) t-SNE scatter plot of quality measures revealing presence of site-specific batch effects (colors correspond to different sites, note presence of site-specific clusters).<\/span><\/span><\/p><\/div><p><br\/><\/p><div class=\"tab-style-builtin\"><div class=\"localtabs-macro\"><div class=\"aui-tabs horizontal-tabs\" role=\"application\" data-aui-responsive=\"true\"><ul class=\"tabs-menu\"><li class=\"menu-item bv-localtab  active-tab \"><a href=\"#70223538b7ae160a7dec4bb0b324ad1987d1ca0d\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#70223538ab395e0175e0470ab9bbf214a983f8ec\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#702235389c007bdbe5544da3a6a59d66d0421ceb\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#70223538f95c4dab1b674224be233e35814e1024\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"70223538b7ae160a7dec4bb0b324ad1987d1ca0d\" active=\"true\" name=\"Data Access\" ><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-DataAccess\">Data Access<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup><col\/><col\/><col\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\">TCGA-GBM MRQy results (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/70223538\/TCGA_GBM_MRQy_Results.xlsx?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">TCGA-CESC MRQy results (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/70223538\/TCGA_CESC%28T1_and_T2%29_MRQy_Results.xlsx?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">CPTAC-GBM MRQy results (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/70223538\/CPTAC_GBM_MRQy_Results.xlsx\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p>Click the Versions tab for more info about data releases.<\/p><h3 style=\"text-align: left;\" id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-AdditionalResourcesforthisDataset\">Additional Resources for this Dataset<\/h3><ul><li>Source code is available on GitHub at:<span>\u00a0<\/span><a href=\"http:\/\/github.com\/ccipd\/MRQy\" class=\"external-link\" rel=\"nofollow\">http:\/\/github.com\/ccipd\/MRQy<\/a>. \u00a0<\/li><\/ul><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-CollectionsUsedinthisThirdPartyAnalysis\"><strong><span style=\"color: rgb(29,28,29);text-decoration: none;\">Collections Used in this Third Party Analysis<\/span><\/strong><\/h3><p><br style=\"text-decoration: none;text-align: left;\"\/><span style=\"color: rgb(29,28,29);text-decoration: none;\">Below is a list of the Collections used in these analyses:<br\/><\/span><span style=\"color: rgb(29,28,29);text-decoration: none;\">\nSome data in this collection contains images that could potentially be used to reconstruct a human face.  To safeguard the privacy of participants, users must sign and submit a <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\" class=\"external-link\" rel=\"nofollow\">help@cancerimagingarchive.net<\/a> before accessing the data.<\/span><\/p><div class=\"table-wrap\"><table class=\"relative-table wrapped confluenceTable\" style=\"width: 45.6664%;\"><colgroup><col style=\"width: 43.0396%;\"\/><col style=\"width: 33.7166%;\"\/><col style=\"width: 23.2292%;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\"><p>Source Data Type<\/p><\/th><th class=\"confluenceTh\"><div class=\"content-wrapper\"><p>Download<\/p><\/div><\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Corresponding Original MR Images from <a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=1966258\">TCGA-GBM<\/a>\u00a0 (1.37GB) and <a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=30671232\">CPTAC-GBM<\/a>\u00a0(DICOM, 0.4 GB)<\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/140313041\/CPTACandTCGA_GBM_MRQy.tcia?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><p class=\"auto-cursor-target\"><span style=\"color: rgb(33,37,41);\">(Download requires\u00a0the\u00a0<\/span><a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" style=\"text-decoration: none;text-align: left;\" rel=\"nofollow\">NBIA Data Retriever<\/a> and permission)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Corresponding Original MR Images from <a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=19039396\">&nbsp;TCGA-CESC<\/a> (DICOM, 2.72 GB)<\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/140313041\/TCGA_CESC_MRQy.tcia?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><p class=\"auto-cursor-target\"><span style=\"color: rgb(33,37,41);\">(Download requires\u00a0the\u00a0<\/span><a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\" style=\"text-decoration: none;text-align: left;\">NBIA Data Retriever<\/a><span style=\"color: rgb(33,37,41);\">)<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><div class=\"tabs-pane \" id=\"70223538ab395e0175e0470ab9bbf214a983f8ec\" name=\"Detailed Description\" ><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-DetailedDescription\">Detailed Description<\/h3><p><span style=\"color: rgb(32,33,36);\">The <em>spreadsheets <\/em>provided are derived analyses from subsets of images from the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=1966258\">The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM)<\/a>, <a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=30671232\">The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM)<\/a>, and\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=19039396\">The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (TCGA-CESC)<\/a> collections. To download the<em> original corresponding <\/em><\/span><em>images<\/em> <span style=\"color: rgb(32,33,36);\">for your own analysis please see the &quot;Source Data Type&quot; table.<\/span><\/p><\/div><div class=\"tabs-pane \" id=\"702235389c007bdbe5544da3a6a59d66d0421ceb\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy<\/h3><p>\n<p>\nUsers must abide by the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/x\/c4hF\" class=\"external-link\" rel=\"nofollow\">TCIA Data Usage Policy and Restrictions<\/a>. Attribution should include references to the following citations:\n<\/p><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Data Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Sadri, A. R., Janowczyk, A., Verma, R., Antunes, J., Madabhushi, A., Tiwari, P., &amp; Viswanath, S. (2020). <strong>MRQy quality measures for TCIA MRI datasets<\/strong> [Data set]. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2020.JHZ2-T694\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/K9\/TCIA.2020.JHZ2-T694<\/a><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">TCIA Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., &amp; Prior, F. (2013). <strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository.<\/strong> Journal of Digital Imaging, 26(6), 1045\u20131057. <a href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/a><\/p><\/div><\/div><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains<\/span> <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\"> a list of publications<\/a> <span> which leverage our data. <\/span> If you have a manuscript you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\">contact TCIA's Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"70223538f95c4dab1b674224be233e35814e1024\" name=\"Versions\" ><h3 id=\"MRQyqualitymeasuresforTCIAMRIdatasets(MRQyQualityMeasures)-Version1(Current):Updated2020\/07\/16\">Version 1 (Current): Updated 2020\/07\/16<\/h3><div class=\"table-wrap\"><table class=\"fixed-table wrapped confluenceTable\"><colgroup> <col style=\"width: 282.0px;\"\/> <col style=\"width: 300.0px;\"\/> <\/colgroup><tbody><tr><th colspan=\"1\" class=\"confluenceTh\">Data Type<\/th><th colspan=\"1\" class=\"confluenceTh\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">TCGA-GBM MRQy results (XLS)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/70223538\/TCGA_GBM_MRQy_Results.xlsx?version=2&amp;modificationDate=1594905520222&amp;api=v2\" data-linked-resource-id=\"70223547\" data-linked-resource-version=\"2\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"TCGA_GBM_MRQy_Results.xlsx\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet\" data-linked-resource-container-id=\"70223538\" data-linked-resource-container-version=\"29\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/MRQy%20quality%20measures%20for%20TCIA%20MRI%20datasets%20(MRQy-Quality-Measures)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">TCGA-CESC MRQy results (XLS)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/70223538\/TCGA_CESC%28T1_and_T2%29_MRQy_Results.xlsx?version=1&amp;modificationDate=1594905696762&amp;api=v2\" data-linked-resource-id=\"70227230\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"TCGA_CESC(T1_and_T2)_MRQy_Results.xlsx\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet\" data-linked-resource-container-id=\"70223538\" data-linked-resource-container-version=\"29\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/MRQy%20quality%20measures%20for%20TCIA%20MRI%20datasets%20(MRQy-Quality-Measures)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">CPTAC-GBM MRQy results (XLS)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/70223538\/CPTAC_GBM_MRQy_Results.xlsx?version=1&amp;modificationDate=1594905520390&amp;api=v2\" data-linked-resource-id=\"70227229\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"CPTAC_GBM_MRQy_Results.xlsx\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet\" data-linked-resource-container-id=\"70223538\" data-linked-resource-container-version=\"29\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/MRQy%20quality%20measures%20for%20TCIA%20MRI%20datasets%20(MRQy-Quality-Measures)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div>","make_new_version_button":"","related_collections":["TCGA-GBM","CPTAC-GBM","TCGA-CESC"],"result_doi":"10.7937\/K9\/TCIA.2020.JHZ2-T694","versions":false,"cancer_locations":["Brain","Cervix"],"publications_related":"","result_download_info":"Click the Versions tab for more info about data releases.","result_downloads":[5451,5452,5453],"result_page_accessibility":"Public","version_change_log_archived":"","additional_resources":"<ul><li>Source code is available on GitHub at:\u00a0<a href=\"http:\/\/github.com\/ccipd\/MRQy\">http:\/\/github.com\/ccipd\/MRQy<\/a>. \u00a0<\/li><\/ul>","date_updated":"2020-07-22","publications_using":"TCIA maintains <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\"> a list of publications<\/a>  which leverage our data.  If you have a manuscript you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a>.","result_title":"MRQy quality measures for TCIA MRI datasets","subjects":"233","detailed_description":"The <em>spreadsheets <\/em>provided are derived analyses from subsets of images from the <a href=\"\/pages\/viewpage.action?pageId=1966258\">The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM)<\/a>, <a href=\"\/pages\/viewpage.action?pageId=30671232\">The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM)<\/a>, and\u00a0<a href=\"\/pages\/viewpage.action?pageId=19039396\">The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (TCGA-CESC)<\/a> collections. To download the<em> original corresponding <\/em><em>images<\/em> for your own analysis please see the \"Source Data Type\" table.","result_short_title":"MRQy-Quality-Measures","supporting_data":["Image quality assessment measures"],"version_change_log":"","collections":"<br\/>Below is a list of the Collections used in these analyses:<br\/>\nSome data in this collection contains images that could potentially be used to reconstruct a human face.  To safeguard the privacy of participants, users must sign and submit a <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a> before accessing the data.\n<table><colgroup><col\/><col\/><col\/><\/colgroup><tbody><tr><th><p>Source Data Type<\/p><\/th><th><div><p>Download<\/p><\/div><\/th><th>License<\/th><\/tr><tr><td><p>Corresponding Original MR Images from <a href=\"\/pages\/viewpage.action?pageId=1966258\">TCGA-GBM<\/a>\u00a0 (1.37GB) and <a href=\"\/pages\/viewpage.action?pageId=30671232\">CPTAC-GBM<\/a>\u00a0(DICOM, 0.4 GB)<\/p><\/td><td><div><p><br\/>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/140313041\/CPTACandTCGA_GBM_MRQy.tcia?api=v2\"><button><i> <\/i> Download<\/button><\/a>\u00a0\n<\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a> and permission)<\/p><\/div><\/td><td><div><p>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">TCIA Restricted<\/a><\/p><\/div><\/td><\/tr><tr><td><p>Corresponding Original MR Images from <a href=\"\/pages\/viewpage.action?pageId=19039396\">\u00a0TCGA-CESC<\/a> (DICOM, 2.72 GB)<\/p><\/td><td><div><p><br\/>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/140313041\/TCGA_CESC_MRQy.tcia?api=v2\"><button><i> <\/i> Download<\/button><\/a>\u00a0\n<\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td><div><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table>","result_browse_title":"","version_number":[],"collection_downloads":[5860,5861],"result_summary":"Magnetic Resonance Imaging (MRI)\u00a0quality assessment measures were generated for\u00a0<ol><li>T1-weighted post-contrast axial MRI sequences from 133\u00a0<a href=\"\/pages\/viewpage.action?pageId=1966258\">The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM)<\/a>\u00a0subjects\u00a0<\/li><li>T1-weighted post-contrast axial MRI sequences from 46\u00a0<a href=\"\/pages\/viewpage.action?pageId=30671232\">The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM)<\/a>\u00a0subjects\u00a0\u00a0<\/li><li>Both T1- and T2-weighted axial MRI sequences from 54\u00a0<a href=\"\/pages\/viewpage.action?pageId=19039396\">The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (TCGA-CESC)<\/a>\u00a0subjects<\/li><\/ol><p>All MRI scans for each cohort were downloaded as DICOM files from TCIA and then processed via MRQy to compute quality measures for (a) interrogating the presence of site- or equipment-specific variations within a cohort, and (b) quantifying the impact of MRI artifacts to determine what pre-analytical corrections are needed. The MRQy output can be easily interrogated via the associated HTML5 based front-end, allowing for real-time filtering and visualization. MRQy is available for download at:\u00a0<a href=\"http:\/\/github.com\/ccipd\/MRQy\">http:\/\/github.com\/ccipd\/MRQy<\/a>.\u00a0 Manifest files to download the DICOM images these results were derived from are available on the Detailed Description page.<\/p>","result_featured_image":{"ID":"8772","post_author":"6","post_date":"2023-09-13 04:24:17","post_date_gmt":"2023-09-13 04:24:17","post_content":"","post_title":"mrqy_gbm_results_v1","post_excerpt":"","post_status":"inherit","comment_status":"open","ping_status":"closed","post_password":"","post_name":"mrqy_gbm_results_v1","to_ping":"","pinged":"","post_modified":"2023-09-13 12:11:25","post_modified_gmt":"2023-09-13 12:11:25","post_content_filtered":"","post_parent":"5803","guid":"https:\/\/cm.vastapps.dev\/wp-content\/uploads\/mrqy_gbm_results_v1.png","menu_order":"0","post_type":"attachment","post_mime_type":"image\/png","comment_count":"0","pod_item_id":"8772"},"result_acknowledgements":"Research reported in this publication was supported by:\n<ul><li> National Cancer Institute of the National Institutes of Health under award numbers 1U24CA199374-01, R01CA202752-01A1, R01CA208236-01A1, R01 CA216579-01A1, R01 CA220581-01A1, 1U01 CA239055-01, 1F31CA216935-01A1,\u00a0NCI 1U01CA248226-01<\/li><li>National Institute for Biomedical Imaging and Bioengineering (1R43EB028736-01) <\/li><li>National Center for Research Resources under award number 1 C06 RR12463-01 <\/li><li>VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service<\/li><li> The DoD Breast Cancer Research Program Breakthrough Level 1 Award (W81XWH-19-1-0668)<\/li><li> The DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558)<\/li><li> The DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440)<\/li><li> The DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329, W81XWH-18-1-0404)<\/li><li> Dana Foundation David Mahoney Neuroimaging Program<\/li><li>The V Foundation Translational Research Award<\/li><li>The Ohio Third Frontier Technology Validation Fund<\/li><li> The Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering<\/li><li>The Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University<\/li><\/ul>\n<br\/>\n\n(a) MRQy front-end interface for interrogating TCGA-GBM cohort. (b) Outlier dataset identified on the parallel coordinate chart for the CJV quality measure found to exhibit shading artifacts\u00a0on (c) representative images, especially when compared to (d) a different dataset without this artifact. (e) t-SNE scatter plot of quality measures revealing presence of site-specific batch effects (colors correspond to different sites, note presence of site-specific clusters).\n<br\/>","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results\/5803"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_analysis_result"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media\/8772"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5803"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}