# Removing below threshold data from segment

**URL:** <https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [August 24, 2025, 12:39am UTC](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184 "2025-08-24T00:39:49Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Learn34](https://avatars.discourse-cdn.com/v4/letter/l/c6cbf5/32.png) [@Learn34](https://discourse.slicer.org/u/Learn34)\
**Post date:** [August 24, 2025, 12:39am UTC](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184/1 "2025-08-24T00:39:49Z")

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Big picture: I want to convert the CT scan data from a SPECT of my spine into a finite element model to validate use of a novel implant in a repair thereof.  
Little picture: In attempting to follow [this workflow](https://www.youtube.com/watch?v=ToIkOpDVfpw&t=2s) for converting the CT data to an stl, I cannot figure out how to clear out the red point cloud I’m left with after thresholding the cropped segment:

 ![Capture.PNG](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/6/46d6bc9d6ef3035715cb102d101bc2ad450c1cdc.jpeg)

The documentation for the volume rendering module provides instructions for how to remove arbitrary regions, but not how to removing everything under threshold.

Help?

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 24, 2025, 7:47pm UTC](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184/2 "2025-08-24T19:47:05Z")

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After you threshold in the SegmentEditor, you can enable the Show 3D to see a surface rendering of the segmentation. You can turn off the volume rendering in the VolumeRendering module to see the surface better. If you want to see a volume rendering that takes into account the segmentation, try the [ColorizeVolume](https://discourse.slicer.org/t/new-colorize-volume-module/32254) module.

If you are planning to make a finite element model, you may want to look at the [SegmentMesher](https://github.com/lassoan/SlicerSegmentMesher) extension, although meshing tools outside of Slicer probably give better results for single-material meshes.

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**Author:** ![Learn34](https://avatars.discourse-cdn.com/v4/letter/l/c6cbf5/32.png) [@Learn34](https://discourse.slicer.org/u/Learn34)\
**Post date:** [August 24, 2025, 10:51pm UTC](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184/3 "2025-08-24T22:51:21Z")

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Yep, that did it. Now I get to figure out the best way to fill back in all the bone the thresholding took out and erase the other bits the thresholding didn’t nix.

Thanks!

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 25, 2025, 2:23pm UTC](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184/4 "2025-08-25T14:23:50Z")

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Glad you are making progress. You may also want to try the [WrapSolidify](https://github.com/sebastianandress/Slicer-SurfaceWrapSolidify) module.