{"id":46121,"date":"2023-11-20T05:53:23","date_gmt":"2023-11-20T11:53:23","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/mrqy-quality-measures\/"},"modified":"2024-11-07T12:23:50","modified_gmt":"2024-11-07T18:23:50","slug":"mrqy-quality-measures","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/mrqy-quality-measures\/","title":{"rendered":"MRQY-QUALITY-MEASURES"},"featured_media":9009,"template":"","class_list":["post-46121","tcia_analysis_result","type-tcia_analysis_result","status-publish","has-post-thumbnail"],"cancer_types":["Glioblastoma","Cervical Squamous Cell Carcinoma","Endocervical Adenocarcinoma"],"citations":[46109,49795,9225],"result_doi":"10.7937\/K9\/TCIA.2020.JHZ2-T694","result_download_info":"","result_downloads":[46111,46113,46115],"version_change_log_archived":"Version 1 (Current): Updated 2020\/07\/16\r\n\r\n\r\n\r\nData Type\r\nDownload all or Query\/Filter\r\nLicense\r\n\r\n\r\nTCGA-GBM MRQy results (49 kb, XLSX)\r\n\r\n\r\n\r\n Download\r\n\r\n\r\n\r\n\r\n\r\nCC BY 3.0\r\n\r\n\r\n\r\n\r\nTCGA-CESC MRQy results (49 kb, XLSX)\r\n\r\n\r\n\r\n Download\r\n\r\n\r\n\r\n\r\n\r\nCC BY 3.0\r\n\r\n\r\n\r\n\r\nCPTAC-GBM MRQy results (21 kb, XLSX)\r\n\r\n\r\n\r\n Download\r\n\r\n\r\n\r\n\r\n\r\nCC BY 3.0","versions":false,"additional_resources":"The following external resources have been made available by the data submitters.\u00a0 These are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.\r\n<ul>\r\n \t<li>Source code is available on GitHub at:\u00a0<a href=\"http:\/\/github.com\/ccipd\/MRQy\">http:\/\/github.com\/ccipd\/MRQy<\/a>.<\/li>\r\n<\/ul>","cancer_locations":["Brain","Cervix"],"publications_related":"","result_page_accessibility":"Limited","detailed_description":"The <em>spreadsheets <\/em>provided are derived analyses from subsets of images from the <a href=\"\/collection\/tcga-gbm\/\" target=\"_blank\" rel=\"noopener\">TCGA-GBM<\/a>, <a href=\"\/collection\/cptac-gbm\/\" target=\"_blank\" rel=\"noopener\">CPTAC-GBM<\/a>, and <a href=\"\/collection\/tcga-cesc\/\" target=\"_blank\" rel=\"noopener\">TCGA-CESC<\/a>\u00a0collections. To download the<em> original corresponding <\/em><em>images<\/em> for your own analysis please see the \"Collections Used In This Analysis Result\" table.","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/commons.datacite.org\/doi.org\/10.7937\/K9\/TCIA.2020.JHZ2-T694\">a list of publications<\/a>\u00a0that leveraged this dataset. If you have a manuscript you\u2019d like to add please\u00a0<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA\u2019s Helpdesk<\/a>.","result_title":"MRQy quality measures for TCIA MRI datasets","species":false,"version_number":"1","date_updated":"2020-07-16","related_collections":[43903,44721,43811],"result_short_title":"MRQy-Quality-Measures","subjects":"233","related_analysis_results":false,"result_browse_title":"MRQy quality measures for TCIA MRI datasets (MRQy-Quality-Measures)","supporting_data":["Image quality assessment measures","Software\/Source Code"],"version_change_log":"","collections":"Below is a list of the Collections used in these analyses:\r\n\r\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=\"\/wp-content\/uploads\/TCIA-Restricted-License-20220519.pdf\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a> before accessing the data.\r\n<table><colgroup> <col \/> <col \/> <col \/><\/colgroup>\r\n<tbody>\r\n<tr>\r\n<th>Source Data Type<\/th>\r\n<th>\r\n<div>\r\n\r\nDownload\r\n\r\n<\/div><\/th>\r\n<th>License<\/th>\r\n<\/tr>\r\n<tr>\r\n<td>Corresponding Original MR Images from <a href=\"https:\/\/cancerimagingarchive.net\/collection\/tcga-gbm\/\" target=\"_blank\" rel=\"noopener\">TCGA-GBM<\/a>\u00a0 (1.37GB) and <a href=\"https:\/\/cancerimagingarchive.net\/collection\/cptac-gbm\/\" target=\"_blank\" rel=\"noopener\">CPTAC-GBM<\/a>\u00a0(DICOM, 0.4 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/140313041\/CPTACandTCGA_GBM_MRQy.tcia?api=v2\"><button><i><\/i> Download<\/button><\/a>\r\n\r\n(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a> and permission)\r\n\r\n<\/div><\/td>\r\n<td>\r\n<div>\r\n\r\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>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Corresponding Original MR Images from <a href=\"https:\/\/cancerimagingarchive.net\/collection\/tcga-cesc\/\" target=\"_blank\" rel=\"noopener\">\u00a0TCGA-CESC<\/a> (DICOM, 2.72 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/140313041\/TCGA_CESC_MRQy.tcia?api=v2\"><button><i><\/i> Download<\/button><\/a>\r\n\r\n(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)\r\n\r\n<\/div><\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\">CC BY 3.0<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n&nbsp;","result_summary":"Magnetic Resonance Imaging (MRI)\u00a0quality assessment measures were generated for\r\n<ol>\r\n \t<li>T1-weighted post-contrast axial MRI sequences from 133 <a href=\"\/collection\/tcga-gbm\/\" target=\"_blank\" rel=\"noopener\">TCGA-GBM<\/a>\u00a0subjects<\/li>\r\n \t<li>T1-weighted post-contrast axial MRI sequences from 46 <a href=\"\/collection\/cptac-gbm\/\" target=\"_blank\" rel=\"noopener\">CPTAC-GBM<\/a>\u00a0subjects<\/li>\r\n \t<li>Both T1- and T2-weighted axial MRI sequences from 54 <a href=\"\/collection\/tcga-cesc\/\" target=\"_blank\" rel=\"noopener\">TCGA-CESC<\/a>\u00a0subjects<\/li>\r\n<\/ol>\r\nAll 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 in the \"Collections Used In This Analysis Result\" table.\r\n\r\nIn the figure, see (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 on (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).","collection_downloads":[46117,46119],"result_featured_image":{"ID":"9009","post_author":"29","post_date":"2023-09-14 01:04:45","post_date_gmt":"2023-09-14 06:04:45","post_content":"(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 on (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).","post_title":"mrqy_gbm_results_v1","post_excerpt":"(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 on (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).","post_status":"inherit","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"mrqy_gbm_results_v1","to_ping":"","pinged":"","post_modified":"2024-02-28 19:27:56","post_modified_gmt":"2024-02-29 01:27:56","post_content_filtered":"","post_parent":"46121","guid":"https:\/\/stage.cancerimagingarchive.net\/mrqy_gbm_results_v1\/","menu_order":"0","post_type":"attachment","post_mime_type":"image\/png","comment_count":"0","pod_item_id":"9009"},"result_acknowledgements":"Research reported in this publication was supported by:\r\n<ul>\r\n \t<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>\r\n \t<li>National Institute for Biomedical Imaging and Bioengineering (1R43EB028736-01)<\/li>\r\n \t<li>National Center for Research Resources under award number 1 C06 RR12463-01<\/li>\r\n \t<li>VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service<\/li>\r\n \t<li>The DoD Breast Cancer Research Program Breakthrough Level 1 Award (W81XWH-19-1-0668)<\/li>\r\n \t<li>The DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558)<\/li>\r\n \t<li>The DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440)<\/li>\r\n \t<li>The DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329, W81XWH-18-1-0404)<\/li>\r\n \t<li>Dana Foundation David Mahoney Neuroimaging Program<\/li>\r\n \t<li>The V Foundation Translational Research Award<\/li>\r\n \t<li>The Ohio Third Frontier Technology Validation Fund<\/li>\r\n \t<li>The Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering<\/li>\r\n \t<li>The Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University<\/li>\r\n<\/ul>","hide_from_browse_table":"0","program":["Community"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46121","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/types\/tcia_analysis_result"}],"version-history":[{"count":1,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46121\/revisions"}],"predecessor-version":[{"id":47227,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46121\/revisions\/47227"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media\/9009"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=46121"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}