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View slice level annotations in OHIF using Structured Reports
- Deepa Krishnaswamy (Brigham and Women’s Hospital)
- Davide Punzo (Radical Imaging)
- Markus Herrmann (MGH)
- Chris Bridge (MGH)
- Andrey Fedorov (Brigham and Women’s Hospital)
In the last project week, we worked on an approach for enriching the DICOM metadata, specifically the body part examined.
We showed that we could classify each CT axial slice in a volume as a particular body region – head, neck, chest, abdomen, pelvis and legs. (using this approach)
In order to visualize the results of body region per slice, we used DICOM SEG objects. Though good for visualization, this is not exactly a good use of the DICOM SEG.
A better approach would be to use Structured Reports (SR), and view an annotation for each slice as you scroll. This functionality has been made available in the latest release of OHIF, and we would like to adapt our body part regression results to this format.
- Objective A. View slice level annotations using a Structured Report in the OHIF viewer.
- Objective B. Visualize the body part regression results using the above approach
Approach and Plan
- A colab notebook has been written by Andrey using highdicom library to create instances of DICOM Structured Reports that instantiate TID 1500 reporting template and include slice-level qualitative (key:value) evaluations.
- OHIF Viewer v2 was extended by Davide to enable visualization of slice-level annotations (see https://github.com/OHIF/Viewers/issues/2797)
- Deepa will adapt this notebook to create the appropriate SR for the body part regression task.
Progress and Next Steps
- We have successfully created the SR for the body part regression task and can view the CT and SR in our own instance of the OHIF viewer.
Background and References