How do I get the ID number from subject hierarchy information for a segmentation?

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1

I want to get the ID number present in the subject hierarchy information. I want to do that to access the children segments through the ID number. Heres a picture of what I want to get using python. How can I do this?

id
id696×429 16.6 KB

2

Hi. You can do it like this:

shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
segmentationItemID = shNode.GetItemByName("Segmentation")
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3

Thanks, that’s great. How can I do this for the children?

4

There is a segmentation data node, there isn’t a segment data node for each segment
You can access segments from a segmentation like this:

segmentationDataNode = shNode.GetItemDataNode(segmentationItemID)

segmentIDinPosition0 = segmentationDataNode.GetSegmentation().GetNthSegmentID(0)
segmentInPosition0 = segmentationDataNode.GetSegmentation().GetSegment(segmentIDinPosition0)

upperAirwaySegmentID = segmentationDataNode.GetSegmentation().GetSegmentIdBySegmentName('upper_airway')
upperAirwaySegment = segmentationDataNode.GetSegmentation().GetSegment(upperAirwaySegmentID)
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5

Is there a way of doing this by vtk ID, so that the name of the segmentation doesn’t have to be used, as it can be ambiguous?

6

Yes, sure, the segment ID is stored in the segmentID attribute of the subject hierarchy item:

image
image987×1233 62 KB

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7

You may use GetItemAttribute method to get the segmentID from the vtk ID:

shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
segmentID = shNode.GetItemAttribute(vtkID, "segmentID")