{"id":46349,"date":"2023-11-20T06:08:55","date_gmt":"2023-11-20T12:08:55","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/cptac-hnscc-tumor-annotations\/"},"modified":"2025-03-20T13:34:00","modified_gmt":"2025-03-20T18:34:00","slug":"cptac-hnscc-tumor-annotations","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/cptac-hnscc-tumor-annotations\/","title":{"rendered":"CPTAC-HNSCC-TUMOR-ANNOTATIONS"},"featured_media":0,"template":"","class_list":["post-46349","tcia_analysis_result","type-tcia_analysis_result","status-publish"],"cancer_types":["Head and Neck Squamous Cell Carcinoma"],"citations":[46339,9225],"result_doi":"10.7937\/PFEC-T641","result_download_info":"","result_downloads":[46341,46343],"version_change_log_archived":"Version 1 (Current): Updated 2023\/07\/24\r\nData TypeDownload all or Query\/FilterLicenseCPTAC-HNSCC Annotations - Segmentations, Seed Points, and Negative Findings Assessments\u00a0 (DICOM, 26 MB)\r\n Download\u00a0\r\n\r\n Search\u00a0\r\n(Download requires NBIA Data Retriever)CC BY 4.0CPTAC-HNSCC Annotation Metadata (CSV, 214 kb)\r\n Search\u00a0\r\nCC BY 4.0Original CPTAC-HNSCC Images used to create Segmentations and Seed Points (DICOM, 20.3 GB)\r\n Search\u00a0\r\n(Download requires NBIA Data Retriever)TCIA RestrictedOriginal CPTAC-HNSCC Images used to create Negative Assessment reports (DICOM, 11.6 GB)\r\n Search\u00a0\r\n(Download requires NBIA Data Retriever)TCIA Restricted","versions":false,"additional_resources":"<ul>\r\n \t<li>The NCI Cancer Research Data Commons (CRDC) provides access to proteomic, genomic and clinical data related to these subjects.\r\n<ul>\r\n \t<li><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=cptac_hnscc\">Imaging Data Commons (IDC)<\/a>\u00a0(Imaging Data)<\/li>\r\n \t<li><a href=\"https:\/\/pdc.cancer.gov\/pdc\/browse\/filters\/program_name:Clinical%20Proteomic%20Tumor%20Analysis%20Consortium&amp;disease_type:Head%20and%20Neck%20Squamous%20Cell%20Carcinoma&amp;primary_site:Head%20and%20Neck\">Proteomic Data Commons (PDC)<\/a>\u00a0(Proteomic &amp; Clinical Data)<\/li>\r\n \t<li><a href=\"https:\/\/portal.gdc.cancer.gov\/exploration?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22other%20and%20ill-defined%20sites%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22CPTAC-3%22%5D%7D%7D%5D%7D&amp;searchTableTab=cases\">Genomic Data Commons (GDC)<\/a>\u00a0(Genomic &amp; Clinical Data)<\/li>\r\n<\/ul>\r\n<\/li>\r\n \t<li><a href=\"https:\/\/github.com\/kirbyju\/TCIA_Notebooks\/blob\/main\/CPTAC\/CPTAC.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":["Head-Neck"],"publications_related":"","result_page_accessibility":"Limited","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 The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection","species":["Human"],"version_number":"1","date_updated":"2023-07-24","related_collections":[44829],"result_short_title":"CPTAC-HNSCC-Tumor-Annotations","subjects":"101","related_analysis_results":false,"result_browse_title":"Annotations for The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Collection (CPTAC-HNSCC-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 scope=\"col\">Source Data Type<\/th>\r\n<th scope=\"col\">Download<\/th>\r\n<th scope=\"col\">License<\/th>\r\n<\/tr>\r\n<tr>\r\n<td>Original <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.UW45NH81\">CPTAC-HNSCC<\/a> Images used to create Segmentations and Seed Points (DICOM, 20.3 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/CPTAC-HNSCC_SourceImages_SEGSandSeedpoints-manifest-07-14-2023.tcia\" download=\"CPTAC-HNSCC_SourceImages_SEGSandSeedpoints-manifest-07-14-2023.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:\/\/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>Original <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.UW45NH81\">CPTAC-HNSCC<\/a> Images used to create Negative Assessment reports (DICOM, 11.6 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/CPTAC-HNSCC_SourceImages_NegativeAssessments-manifest-07-14-2023.tcia\" download=\"CPTAC-HNSCC_SourceImages_NegativeAssessments-manifest-07-14-2023.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:\/\/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<\/tbody>\r\n<\/table>\r\n<ul>\r\n \t<li><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.UW45NH81\">The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC)<\/a><\/li>\r\n<\/ul>","result_summary":"This dataset contains image annotations derived from \"<a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.UW45NH81\">The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC)<\/a>\u201d.\u00a0 This dataset was generated as part of a National Cancer Institute project to augment images from The Cancer Imaging Archive with tumor annotations that will improve their value for cancer researchers and artificial intelligence experts.\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>PERCIST criteria was followed for PET imaging. Specifically, the lesions estimated to have the most elevated SUVmax were annotated.<\/li>\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. Lymph nodes were annotated if &gt;1 cm in short axis. Other lesions were annotated if &gt;1 cm. The primary tumor was still annotated if &lt; 1 cm.<\/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.<\/li>\r\n \t<li>CTs were annotated using all axial post contrast series.<\/li>\r\n \t<li>PET\/CTs were annotated on the CT and attenuation corrected PET images, unless there was a diagnostic CT from the same time point, in which case the CT portion of the PET\/CT was not annotated.<\/li>\r\n \t<li>Lesions were labeled separately.<\/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\n<h4>At each time point:<\/h4>\r\n<ol>\r\n \t<li>Volume calculations were performed for each segmented structure. \u00a0These calculations are provided in the Annotation Metadata CSV.<\/li>\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>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>(719864002, SCT, \"Post-cancer treatment monitoring\")<\/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 <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":[46345,46347],"result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":"0","program":["CPTAC"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46349","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\/46349\/revisions"}],"predecessor-version":[{"id":47477,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46349\/revisions\/47477"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=46349"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}