I would like to export results of TotalSegmentator into DICOM Segmentation format. I am using latest Slicer stable 5.2.1 on Mac. I loaded input CT series from DICOM Browser. I have QuantitativeReporting extension installed. However, segmentation results are not automatically placed properly in the …

Yes, it all works! Probably the reference volume was not set in the segmentation. I’ve tried to explain this in the message in the DICOM export dialog (see red text): [image] The solution is to specify segmentation geometry using the DICOM image as source: [image] I’ve now updated TotalSegmen…

@lassoan have you ever tried this? The terminology should be good so maybe it’s just a matter of setting up the subject hierarchy to connect the segmentation results to the study. Maybe you have suggestions @cpinter ?

[image] lassoan: Probably the reference volume was not set in the segmentation. I’ve tried to explain this in the message in the DICOM export dialog (see red text): Andras, before the fix, it was not possible to get to that export dialog unless a dummy patient was created. The initial popup I…

[image] fedorov: I am working on one improvement to dcmqi that I know will help reduce this time. For the record, there was not even an attempt to optimize DICOM SEG import/export, since for smaller number of segments this is not a practical issue. I don’t know how much I can improve this, but I…

[image] lassoan: We have implemented functions in Slicer for splitting/merging overlapping/non-overlapping segments that you might find useful for this. @lassoan can you help with pointers to those relevant functions in Slicer?

I started working on adding that functionality in Add support for saving segments in a single file by fedorov · Pull Request #464 · QIICR/dcmqi · GitHub

[image] fedorov: can you help with pointers to those relevant functions in Slicer? This file is a good starting point: https://github.com/Slicer/Slicer/blob/main/Libs/vtkSegmentationCore/vtkSegmentationModifier.cxx

How to export TotalSegmentator results as DICOM SEG?

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How to export TotalSegmentator results as DICOM SEG?

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