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ACRIN 6685-Tumor-Annotations | Annotations for ACRIN-HNSCC-FDG-PET-CT Collection

DOI: 10.7937/JVGC-AQ36 | Data Citation Required | Analysis Result

Cancer Types Location Subjects Related Collections Size Supporting Data Updated
Head and Neck Squamous Cell Carcinoma Head-Neck 258 37.38MB Tumor segmentations, Seed points 2023/11/13


This dataset contains image annotations derived from the NCI Clinical Trial “ACRIN-HNSCC-FDG-PET-CT (ACRIN 6685)”.  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.

Annotation Protocol

For each patient, all scans were reviewed to identify and annotate the clinically relevant time points and sequences/series. In a typical patient all available time points were annotated. The following annotation rules were followed:

  1. PERCIST criteria was followed for PET imaging. Specifically, the lesions estimated to have the most elevated SUVmax were annotated.
  2. 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 >1 cm in short axis. Other lesions were annotated if >1 cm. If the primary lesion is < 1 cm, it was still annotated.
  3. Three-dimensional segmentations of lesions were created in the axial plane. If no axial plane was available, lesions were annotated in the coronal plane.
  4. MRIs were annotated using the T1-weighted axial post contrast sequence, fat saturated if available.
  5. CTs were annotated using the axial post contrast series. If not available, the non contrast series were annotated.
  6. PET/CTs were annotated on the CT and attenuation corrected PET images.
  7. If the post contrast CT was performed the same day as the PET/CT, the non contrast CT portion of the PET/CT was not annotated.
  8. Lesions were labeled separately.
  9. The volume of each annotated lesion was calculated and reported in cubic centimeters [cc] in the Annotation Metadata CSV.
  10. Seed points were automatically generated, but reviewed by a radiologist.
  11. A “negative” annotation was created for any exam without findings.

At each time point:

  1. A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSTRUCT file.
  2. SNOMED-CT “Anatomic Region Sequence” and “Segmented Property Category Code Sequence” and codes were inserted for all segmented structures.
  3. “Tracking ID” and “Tracking UID” tags were inserted for each segmented structure to enable longitudinal lesion tracking.
  4. Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.
    1. “Clinical Trial Time Point ID” was used to encode time point type using one of the following strings as applicable: “pre-dose” or “post-chemotherapy”.
    2. Content Item in “Acquisition Context Sequence” was added containing “Time Point Type” using Concept Code Sequence (0040,A168) selected from:
      1. (255235001, SCT, “Pre-dose”) (in this trial, both the CT/MRI and PET/CT, while being different timepoints, are pre-treatment)

Important supplementary information and sample code

  1. A spreadsheet containing key details about the annotations is available in the Data Access section below.
  2. A Jupyter notebook demonstrating how to use the NBIA Data Retriever Command-Line Interface application and the REST API to access these data can be found in the Additional Resources section below.

Data Access

Version 1: Updated 2023/11/13

Title Data Type Format Access Points Subjects Studies Series Images License
ACRIN 6685 Annotations - Segmentations, Seed Points, and Negative Findings Assessments RTSTRUCT DICOM
Download requires NBIA Data Retriever
258 481 2,085 2,085 TCIA Restricted
ACRIN 6685 Annotation Metadata CSV CC BY 4.0

Collections Used In This Analysis Result

Title Data Type Format Access Points Subjects Studies Series Images License
Original ACRIN 6685 Images used to create Segmentations and Seed Points CT, MR, PT DICOM 250 460 666 110,553 TCIA Restricted
Original ACRIN 6685 Images used to create Negative Assessment reports CT, MR, PT DICOM 16 23 31 5,525 TCIA Restricted
ACRIN 6685 Clinical Data, file set 1 ZIP and XLS CC BY 4.0
ACRIN 6685 Clinical Data, file set 2 ZIP and XLS CC BY 4.0

Additional Resources For This Dataset

Citations & Data Usage Policy

Data Citation Required: Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution must include the following citation, including the Digital Object Identifier:

Data Citation

Rozenfeld, M., & Jordan, P. (2023). Annotations for ACRIN-HNSCC-FDG-PET/CT Collection (ACRIN 6685-Tumor-Annotations) (Version 1) [Data set]. The Cancer Imaging Archive.

Publications Using This Data

TCIA maintains a list of publications which leverage TCIA data.  If you have a manuscript you’d like to add please contact TCIA’s Helpdesk.

TCIA Citation

Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC.

Collections Used In This Analysis Result

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