Segment Editor; Thresholding intensity range not working with discrete Hounsfield Units of [0,1,2]

Support
1

Dear Slicer Community,

I have been using the Segment Editor to segment an image that takes on 3 discrete Hounsfield Units (0,1,2). The images contain 2 cells, cell1 is in HU=1, cell2 is in HU=2. The background is HU=0.

screenshot_hu
screenshot_hu1564×1076 90 KB

I must not be using the Thresholding tool properly, because even if I set the intensity range correctly to get cell2 but not cell1 (thresholding with HU>1.88) it will still segment both cells:

screenshot_hu1
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Alternatively, if I set the intensity range for threshold to be between 0.9 and 1.1 to segment out cell1 (and not cell2), it includes all the background!

screenshot_hu2
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What am I doing wrong? Any help would be really appreciated!!

Thanks

2

This looks like a labelmap. Why don’t you import the volume as a labelmap and then convert to segmentation?

3

Thanks muratmaga for your help. How do I do this?

4

Go to volumes module, and then expand the Volume information, and click the convert to label map.
Then go to segmentations module and under then import/export section, import the newly created labelmap as a segmentation.

5

OK, thanks muratmaga. Now I have done this, what do I do? How do I show them in 3D?

6

Working now, thank you!! :star2: