{"id":46395,"date":"2023-11-20T06:11:53","date_gmt":"2023-11-20T12:11:53","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/a091105-tumor-annotations\/"},"modified":"2025-03-20T13:32:21","modified_gmt":"2025-03-20T18:32:21","slug":"a091105-tumor-annotations","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/a091105-tumor-annotations\/","title":{"rendered":"A091105-TUMOR-ANNOTATIONS"},"featured_media":0,"template":"","class_list":["post-46395","tcia_analysis_result","type-tcia_analysis_result","status-publish"],"cancer_types":["Non-Cancer"],"citations":[46385,9225],"result_doi":"10.7937\/T8RN-J447","result_download_info":"","result_downloads":[46387,46389],"version_change_log_archived":"Version 1 (Current): Updated 2023\/11\/13\r\nData TypeDownload all or Query\/FilterLicenseA091105 Annotations -- Segmentations, Seed Points, and Negative Findings Assessments (DICOM, 264 MB)\r\n Download\u00a0\r\n\r\n Search\u00a0\r\n(Download requires\u00a0the\u00a0NBIA Data Retriever)CC BY 4.0A091105 Annotation Metadata (CSV, 909 KB)\r\n Download\u00a0\r\nCC BY 4.0Original A0911051 Images used to create Segmentations and Seed Points (DICOM, 61.1 GB)\r\n Download\u00a0\r\n(Download requires\u00a0the\u00a0NBIA Data Retriever)\u00a0NCTN\/NCORP Data Archive License (Without Collaborative Agreement)Original A091105\u00a0 Images used to create Negative Assessment Reports (DICOM, 6.7 GB)\r\n Download\u00a0\r\n(Download requires\u00a0the\u00a0NBIA Data Retriever)NCTN\/NCORP Data Archive License (Without Collaborative Agreement)","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\/1266\">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":["Various"],"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 Sorafenib Tosylate in Treating Patients With Desmoid Tumors or Aggressive Fibromatosis","species":["Human"],"version_number":"1","date_updated":"2023-11-13","related_collections":[43621],"result_short_title":"A091105-Tumor-Annotations","subjects":"83","related_analysis_results":false,"result_browse_title":"Annotations for Sorafenib Tosylate in Treating Patients With Desmoid Tumors or Aggressive Fibromatosis (A091105-Tumor-Annotations)","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\/0WF5-SJ50\">A091105<\/a> Images used to create Segmentations and Seed Points (DICOM, 61.1 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/A091105_SourceImages-SEGSandSeedpoints-manifest_11-06-2023.tcia\" download=\"A091105_SourceImages-SEGSandSeedpoints-manifest_11-06-2023.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\/0WF5-SJ50\">A091105<\/a> Images used to create Negative Assessment reports (DICOM, 6.7 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/A091105_SourceImages-NegativeAssessments-manifest_11-06-2023.tcia\" download=\"A091105_SourceImages-NegativeAssessments-manifest_11-06-2023.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<ul>\r\n \t<li><a href=\"https:\/\/doi.org\/10.7937\/0WF5-SJ50\">Sorafenib Tosylate in Treating Patients With Desmoid Tumors or Aggressive Fibromatosis (A091105)<\/a><\/li>\r\n<\/ul>","result_summary":"This dataset contains image annotations derived from the NCI Clinical Trial \"<a href=\"https:\/\/doi.org\/10.7937\/0WF5-SJ50\">Sorafenib Tosylate in Treating Patients With Desmoid Tumors or Aggressive Fibromatosis (A091105)<\/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 otherwise 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 &lt;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 axial post contrast sequence, fat saturated if available. Occasionally, if the tumor was significantly better delineated on a STIR or T2 fat-sat sequence, it wase annotated on that sequence instead of the post contrast sequence.<\/li>\r\n \t<li>CTs were annotated using the axial post contrast series. 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 will be 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>","collection_downloads":[46391,46393],"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\/46395","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\/46395\/revisions"}],"predecessor-version":[{"id":47475,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46395\/revisions\/47475"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=46395"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}