# How to exclude area through thresholding?

**URL:** <https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703>\
**Category:** Support\
**Created:** [June 11, 2024, 4:19pm UTC](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703 "2024-06-11T16:19:33Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![kev1n](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/kev1n/32/70430_2.png) [@kev1n](https://discourse.slicer.org/u/kev1n)\
**Post date:** [June 11, 2024, 4:19pm UTC](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703/1 "2024-06-11T16:19:33Z")

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Hi there,

I’m trying to segment out a CT w/ contrast of the L hip. I’m trying to use a threshold to segment just the bone but the contrast has the same intensity as the bone and I’m unable to effectively separate out the two. I was able to set the threshold to just include the contrast and I was wondering if there was a way to exclude this and paint over the bone or a way to inverse it? I’m still new to slicer and could use any tips or tricks! Thank you!

![Screenshot 2024-06-11 103519](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/b/db9cfb01fae56886c7ef999f6a8419d87aa59635.png)

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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:** [June 11, 2024, 4:23pm UTC](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703/2 "2024-06-11T16:23:40Z")

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You can use tools in the Segment Editor to separate bones from contrasted vessels. Easiest is to use `Islands` effect, choose `Keep selected island` mode, and click on the component you want to keep. You can also remove islands using the same effect, or use `Scissors` effect, etc.

However, normally you don’t need to do any of these manually anymore. AI segmentation tools, such as `MONAI Auto3DSeg` and `TotalSegmentator` extensions in Slicer can segment all major bones and vessels fully automatically in a few minutes.

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**Author:** ![kev1n](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/kev1n/32/70430_2.png) [@kev1n](https://discourse.slicer.org/u/kev1n)\
**Post date:** [June 11, 2024, 5:36pm UTC](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703/3 "2024-06-11T17:36:53Z")

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Thank you for that. I have been trying out MONAI Auto3D and for some reason after I run it and hit apply- it doesn’t seem to be working. Does that software only work for the sample data it comes with?

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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:** [June 11, 2024, 6:38pm UTC](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703/4 "2024-06-11T18:38:46Z")

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MONAI Auto3DSeg and TotalSegmentator are very robust and work well with any CT images.