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

**URL:** <https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [July 1, 2020, 1:33pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320 "2020-07-01T13:33:38Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![Linford\_Briant](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/linford_briant/32/7309_2.png) [@Linford\_Briant](https://discourse.slicer.org/u/Linford_Briant)\
**Post date:** [July 1, 2020, 1:33pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320/1 "2020-07-01T13:33:39Z")

</div>

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](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/c/1ccc913123b9ce0b6469aa70df44b842010ac748.png)

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](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/2/d275499ca34976e8207273e4e49cb80cb7f530dd.png)

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](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/8/e872b8dc6950883d8fc60c082c62c3e24dc7405b.png)

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

Thanks

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [July 1, 2020, 4:21pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320/2 "2020-07-01T16:21:18Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Linford\_Briant](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/linford_briant/32/7309_2.png) [@Linford\_Briant](https://discourse.slicer.org/u/Linford_Briant)\
**Post date:** [July 1, 2020, 4:42pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320/3 "2020-07-01T16:42:42Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [July 1, 2020, 4:57pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320/4 "2020-07-01T16:57:00Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![Linford\_Briant](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/linford_briant/32/7309_2.png) [@Linford\_Briant](https://discourse.slicer.org/u/Linford_Briant)\
**Post date:** [July 2, 2020, 7:20pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320/5 "2020-07-02T19:20:37Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Linford\_Briant](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/linford_briant/32/7309_2.png) [@Linford\_Briant](https://discourse.slicer.org/u/Linford_Briant)\
**Post date:** [July 2, 2020, 7:26pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320/6 "2020-07-02T19:26:37Z")

</div>

Working now, thank you!! 🌟