# Segmentation by thresholding doesnt correspond to HU units

**URL:** <https://discourse.slicer.org/t/segmentation-by-thresholding-doesnt-correspond-to-hu-units/14900>\
**Category:** Support\
**Created:** [December 5, 2020, 4:00pm UTC](https://discourse.slicer.org/t/segmentation-by-thresholding-doesnt-correspond-to-hu-units/14900 "2020-12-05T16:00:12Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Cesar\_Puga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cesar_puga/32/6926_2.png) [@Cesar\_Puga](https://discourse.slicer.org/u/Cesar_Puga)\
**Post date:** [December 5, 2020, 4:00pm UTC](https://discourse.slicer.org/t/segmentation-by-thresholding-doesnt-correspond-to-hu-units/14900/1 "2020-12-05T16:00:13Z")

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Hello Everyone,

Im trying to segment the bones from a set of CT scans, actually i’ve done this actions both in Slicer and in Python, i have read the segmentation recipes for extracting skeletons but when i apply a threshold for the common bone HU (\>225 or \>300) values i seem to be extracting incomplete ribcages/bones along with extra artifacts (blood vessels, kidneys)

could this be an error of how the CT scan was taken, i researched and the parameters used for the HU unit calculation are the rescale Slope and rescale intercept

 ![segbones](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/d/5d4c02b04e96a314b4a8f0ca7b89202dc5bd5ba1.jpeg) , my scans have all values of 1 and -1024 respectively, is there a workaround for mapping the HU units of my CT scans to properly encompass bone between a certain range and blood,

i attach images of the segmentation when applying a thrreshold of 225 HU

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [December 5, 2020, 4:14pm UTC](https://discourse.slicer.org/t/segmentation-by-thresholding-doesnt-correspond-to-hu-units/14900/2 "2020-12-05T16:14:04Z")

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Hounsfield Unit ranges cannot be used for accurate segmentation of different materials for many reasons - noise, partial volume effect, patient-specific bone density differences, etc.

Check out segmentation tutorials here to learn more about segmentation tools: [https://slicer.readthedocs.io/en/latest/user\_guide/modules/segmenteditor.html#tutorials](https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#tutorials)