{"id":46397,"date":"2024-01-05T14:21:19","date_gmt":"2024-01-05T20:21:19","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/?post_type=tcia_analysis_result&#038;p=46397"},"modified":"2025-03-20T13:31:38","modified_gmt":"2025-03-20T18:31:38","slug":"ahep0731-tumor-annotations","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/ahep0731-tumor-annotations\/","title":{"rendered":"AHEP0731-TUMOR-ANNOTATIONS"},"featured_media":0,"template":"","class_list":["post-46397","tcia_analysis_result","type-tcia_analysis_result","status-publish"],"cancer_types":["Hepatoblastoma"],"citations":[47651,9225],"result_doi":"10.7937\/BDBN-NQ81","result_download_info":"","result_downloads":[47631,47635],"version_change_log_archived":"","versions":false,"additional_resources":"<ul>\r\n \t<li>NCTN\/NCORP Data Archive provides the\u00a0<a href=\"https:\/\/nctn-data-archive.nci.nih.gov\/node\/696\">Clinical Data files<\/a>\u00a0related to these subjects, and is also where you go to request access to the entire dataset<\/li>\r\n \t<li><a href=\"https:\/\/github.com\/kirbyju\/TCIA_Notebooks\/blob\/main\/TCIA_NCTN_Annotations.ipynb\">Jupyter notebook<\/a>\u00a0demonstrating how to use the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/NBIA+Data+Retriever+Command-Line+Interface+Guide\">NBIA Data Retriever Command-Line Interface<\/a>\u00a0application and\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/Public\/NBIA+Search+with+Authentication+REST+API+Guide\">REST API (with authentication)<\/a>\u00a0to access these data<\/li>\r\n \t<li>Instructions for\u00a0<a href=\"https:\/\/github.com\/QIICR\/TCIABrowser\/raw\/master\/User%20Guide%20for%203D%20Slicer%20TCIA%20Browser.pptx\">Visualizing these data in 3D Slicer<\/a><\/li>\r\n<\/ul>","cancer_locations":["Liver"],"publications_related":"","result_page_accessibility":"Public","detailed_description":"","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage TCIA 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":"Annotations for Risk-Based Therapy in Treating Younger Patients With Newly Diagnosed Liver Cancer","species":["Human"],"version_number":"1","date_updated":"2024-01-05","related_collections":[43509],"result_short_title":"AHEP0731-Tumor-Annotations","subjects":"80","related_analysis_results":false,"result_browse_title":"","supporting_data":false,"version_change_log":"","collections":"Below is a list of the Collections used in these analyses:\r\n<table><colgroup> <col \/> <col \/> <col \/><\/colgroup>\r\n<tbody>\r\n<tr>\r\n<th>Source Data Type<\/th>\r\n<th>Download<\/th>\r\n<th>License<\/th>\r\n<\/tr>\r\n<tr>\r\n<td>Original <a href=\"https:\/\/doi.org\/10.7937\/F2DB-8826\">AHEP0731<\/a> Images used to create Segmentations and Seed Points (DICOM, 14.8 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/www.cancerimagingarchive.net\/wp-content\/uploads\/AHEP0731_SourceImages_SEGSandSeedPoints-manifest_1-3-2024.tcia\" download=\"ARAR0331_SourceImages-SEGSandSeedpoints-manifest_11-13-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\r\n\r\n(Download requires <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:\/\/nctn-data-archive.nci.nih.gov\/sites\/default\/files\/DUA\/NCTN_NCORP_Data_Archive_DUA_CA_v2019-06-12.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">NCTN\/NCORP Data Archive License (Without Collaborative Agreement)<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Original <a href=\"https:\/\/doi.org\/10.7937\/F2DB-8826\">AHEP0731<\/a> Images used to create Negative Assessment reports (DICOM, 3.3 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/www.cancerimagingarchive.net\/wp-content\/uploads\/AHEP0731_SourceImages_NegativeAssessments-manifests_1-3-2024.tcia\" download=\"ARAR0331_SourceImages-NegativeAssessments-manifest_11-13-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\r\n\r\n(Download requires <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:\/\/nctn-data-archive.nci.nih.gov\/sites\/default\/files\/DUA\/NCTN_NCORP_Data_Archive_DUA_CA_v2019-06-12.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">NCTN\/NCORP Data Archive License (Without Collaborative Agreement)<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n&nbsp;","result_summary":"<div data-layout=\"two-equal\">\r\n<div data-type=\"normal\">\r\n\r\nThis dataset contains image annotations derived from the NCI Clinical Trial \"<a href=\"https:\/\/doi.org\/10.7937\/F2DB-8826\">Risk-Based Therapy in Treating Younger Patients With Newly Diagnosed Liver Cancer<\/a>\u201d. \u00a0This dataset was generated as part of an NCI project to augment TCIA datasets with annotations that will improve their value for cancer researchers and AI developers.\r\n<h3><strong>Annotation Protocol<\/strong><\/h3>\r\nFor each patient, all scans were reviewed to identify and annotate the clinically relevant time points and sequences\/series. Scans were initially annotated by an international team of radiologists holding MBBS degrees or higher, which were then reviewed by US-based board-certified radiologists to ensure accuracy. In a typical patient all available time points were annotated. The following annotation rules were followed:\r\n<ol>\r\n \t<li>RECIST 1.1 was generally followed for MR and CT imaging. A maximum of 5 lesions were annotated per patient scan (timepoint); no more than 2 per organ. The same 5 lesions were annotated at each time point. If the primary lesion was &gt;1 cm it was still annotated.<\/li>\r\n \t<li>Three-dimensional segmentations of lesions were created in the axial plane. If no axial plane was available, lesions were annotated in the coronal plane.<\/li>\r\n \t<li>MRIs were annotated using the T1-weighted post contrast sequence, fat saturated if available. Occasionally, if the tumor was significantly better delineated on a T2-weighted sequence, it was annotated on that sequence instead of the post contrast sequence.<\/li>\r\n \t<li>CTs were annotated using an axial post contrast series, preferably in the arterial phase. If not available, the non contrast series was annotated.<\/li>\r\n \t<li>Lesions were labeled separately.<\/li>\r\n \t<li>The volume of each annotated lesion was calculated and reported in cubic centimeters [cc] in the Annotation Metadata CSV.<\/li>\r\n \t<li>Seed points were automatically generated but reviewed by a radiologist.<\/li>\r\n \t<li>A \u201cnegative\u201d annotation was created for any exam without findings.<\/li>\r\n<\/ol>\r\nAt each time point:\r\n<ol>\r\n \t<li>A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSTRUCT file.<\/li>\r\n \t<li>SNOMED-CT \u201cAnatomic Region Sequence\u201d and \u201cSegmented Property Category Code Sequence\u201d and codes were inserted for all segmented structures.<\/li>\r\n \t<li>\u201cTracking ID\u201d and \u201cTracking UID\u201d tags were inserted for each segmented structure to enable longitudinal lesion tracking.<\/li>\r\n \t<li>Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.\r\n<ol>\r\n \t<li>\u201cClinical Trial Time Point ID\u201d was used to encode time point type using one of the following strings as applicable: \u201cpre-dose\u201d or \u201cpost-chemotherapy\u201d.<\/li>\r\n \t<li>Content Item in \u201cAcquisition Context Sequence\u201d was added containing \"Time Point Type\" using Concept Code Sequence (0040,A168) selected from:\r\n<ol>\r\n \t<li>(255235001, SCT, \u201cPre-dose\u201d)<\/li>\r\n \t<li>(262502001, SCT, \"Post-chemotherapy\")<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\n<h3>Important supplementary information and sample code<\/h3>\r\n<ol>\r\n \t<li>A spreadsheet containing key details about the annotations is available in the\u00a0<strong>Data Access<\/strong>\u00a0section below.<\/li>\r\n \t<li>A\u00a0Jupyter notebook demonstrating how to use the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/NBIA+Data+Retriever+Command-Line+Interface+Guide\">NBIA Data Retriever Command-Line Interface<\/a>\u00a0application and the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/Public\/NBIA+Search+with+Authentication+REST+API+Guide\">REST API<\/a>\u00a0to access these data can be found in the\u00a0<strong>Additional Resources<\/strong>\u00a0section below.<\/li>\r\n<\/ol>\r\n<\/div>\r\n<\/div>","collection_downloads":[47621,47617],"result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":"0","program":["NCI Trials"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46397","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\/46397\/revisions"}],"predecessor-version":[{"id":47473,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46397\/revisions\/47473"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=46397"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}