{"id":5812,"date":"2023-09-04T03:39:45","date_gmt":"2023-09-04T03:39:45","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/aren0534-tumor-annotations\/"},"modified":"2023-09-13T21:48:29","modified_gmt":"2023-09-13T21:48:29","slug":"aren0534-tumor-annotations","status":"publish","type":"tcia_analysis_result","link":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/aren0534-tumor-annotations\/","title":{"rendered":"AREN0534-TUMOR-ANNOTATIONS"},"featured_media":0,"template":"","cancer_types":["Wilms Tumor"],"citations":[4841,2925],"full_export":"

Summary<\/h1>

This dataset contains image annotations derived from the NCI Clinical Trial "Combination Chemotherapy and Surgery in Treating Young Patients With Wilms Tumor (AREN0534)<\/a>\u201d.\u00a0 This 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.<\/p>

Annotation Protocol<\/strong><\/h3>

For each patient, every DICOM Study and DICOM Series was reviewed to identify and annotate the clinically relevant time points and sequences. In a typical patient the following time points were annotated:<\/span><\/p>

  1. Pre-surgical CT chest and CT\/MRI abdomen<\/span><\/li>
  2. CT chest and\/or CT\/MRI abdomen at 6 weeks<\/span><\/li>
  3. Possible CT\/MRI abdomen at 12 weeks.\u00a0<\/span><\/li>
  4. Any negative imaging included past 12 weeks was annotated as negative. If any included imaging past 12 weeks is positive for tumor, the last positive exam was annotated.\u00a0<\/span><\/li><\/ol>

    In a typical patient the following annotation rules were followed:<\/span><\/p>

    1. The primary renal tumor(s) were annotated on post-contrast axial series. <\/span>Normal renal parenchyma were excluded.\u00a0<\/span><\/li>
    2. 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.\u00a0 RECIST 1.1 principles were followed for lesion annotation, however, if <5 lesions measuring >1 cm were present, then smaller lesions were annotated, again up to 2 lesions per organ or 5 lesions per patient scan. Bone lesions were included if other lesions were not present.\u00a0<\/span><\/li>
    3. Lesions were labeled separately.<\/span><\/li>
    4. Seed points were automatically generated but reviewed by a radiologist.<\/span><\/li>
    5. To ensure a high standard of accuracy and data quality, each annotation was reviewed by a secondary reader.<\/span><\/li><\/ol>

      At each time point:<\/span><\/p>

      1. A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSS file.\u00a0<\/span><\/li>
      2. SNOM<\/span>ED-CT \u201cAnatomic Region Sequence\u201d and \u201cSegmented Property Category Code Sequence\u201d and codes were inserted for all segmented structures.<\/span><\/li>
      3. Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.\u00a0<\/span>
        1. \u201cClinical Trial Time Point ID\u201d was used to encode time point type using one of the following strings as applicable: \u201cpre-dose\u201d, \u201cpost-chemotherapy\u201d, or \u201cpost-operative\u201d.<\/span><\/li>
        2. Content Item in \u201cAcquisition Context Sequence\u201d will be added containing "Time Point Type" using Concept Code Sequence (0040,A168) selected from:<\/span><\/li>
          1. (255235001, SCT, \u201cPre-dose\u201d)<\/span><\/li>
          2. (262502001, SCT, "Post-chemotherapy")\u00a0<\/span><\/li>
          3. (262061000, SCT, "Post-operative")<\/span><\/li><\/ol><\/ol><\/li><\/ol>

            Important supplementary information and sample code<\/h3>
            1. A spreadsheet containing key details about the annotations is available in the Data Access<\/strong>\u00a0section below.<\/li>
            2. A\u00a0Jupyter notebook demonstrating how to use the\u00a0NBIA Data Retriever Command-Line Interface<\/a> application and the REST API (with authentication)<\/a>\u00a0to access these data can be found in the\u00a0Additional Resources<\/strong>\u00a0section below.<\/li><\/ol>