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DOC: Improve segmentation DICOM export documentation
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lassoan committed May 23, 2024
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Expand Up @@ -144,10 +144,16 @@ The supported representations are listed in the Representations section. Existin
See Script repository's [Segmentations section](../../developer_guide/script_repository.md#segmentations) for examples.

### DICOM export
- The source representation is used when exporting into DICOM, therefore you need to select a source volume, create binary labelmap representation and set it as master
- DICOM Segmentation Object export if `QuantitativeReporting` extension is installed
- Legacy DICOM RT structure set export is available if `SlicerRT` extension is installed. RT structure sets are not recommended for storing segmentations, as they cannot store arbitrarily complex 3D shapes.
- Follow [these instructions](dicom.md#export-data-from-the-scene-to-dicom-database) for exporting data in DICOM format.

- Make sure the source representation is `binary labelmap` (as the source representation is used when exporting into DICOM, and currently only binary labelmap representation is supported). The source representation can be set in `Segmentations` module, `Representations` section. If the yellow star (that designates the source representation) is in the `binary labelmap` row then the representation is already good, no further action is needed. If the yellow star is in another row then click `Make source` button in the `binary labelmap` row (if that button is not shown then click `Create` button first).
- Make sure the necessary extensions are installed:
- `QuantitativeReporting` extension is required for exporting into DICOM Segmentation Object.
- `SlicerRT` extension is required for exporting into legacy DICOM RT Structure Set. RT Structure Sets are not recommended for storing segmentations, as they cannot store arbitrarily complex 3D shapes.
- If the segmented image was not loaded from the DICOM database (for example, if the image was loaded from a NRRD or NIFTI file) then a DICOM image needs to be created in the database and the segmentation must be updated to reference this image (this is necessary because a DICOM requires a segmentation to be associated with a DICOM image) by following these steps:
- [export the source volume to DICOM](dicom.md#export-data-from-the-scene-to-dicom-database) (agree to create patient and study when asked)
- load the exported volume from the DICOM database
- in `Segment Editor` module, click `Specify geometry` button, choose the loaded volume as `Source geometry`, and click OK
- Go to Data module, right-click on the segmentation, choose `Export to DICOM`, and follow [these instructions](dicom.md#export-data-from-the-scene-to-dicom-database).

## Panels and their use

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