# detailed threshold and smoothing documentation

**URL:** <https://discourse.slicer.org/t/detailed-threshold-and-smoothing-documentation/8602>\
**Category:** Support\
**Created:** [September 27, 2019, 10:21pm UTC](https://discourse.slicer.org/t/detailed-threshold-and-smoothing-documentation/8602 "2019-09-27T22:21:06Z")\
**Posts on this page:** 1\
**Showing post:** 3

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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:** [September 28, 2019, 7:40pm UTC](https://discourse.slicer.org/t/detailed-threshold-and-smoothing-documentation/8602/3 "2019-09-28T19:40:32Z")

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> [@DaveB](#):
>
> **Is there detailed documentation on the Automatic Threshold and Smoothing options? I can’t find that anywhere.** Btw, I’m mostly using Segment Editor.

We use ITK’s automatic threshold computation algorithms options. Their documentation is available [here](https://itk.org/Doxygen/html/group__ITKThresholding.html).

Smoothing pipeline consists of a number of VTK filters. See summary [here](https://discourse.slicer.org/t/segmentation-algorithm-used-in-3d-slicer/7420/3) and source code [here](https://github.com/Slicer/Slicer/blob/master/Libs/vtkSegmentationCore/vtkBinaryLabelmapToClosedSurfaceConversionRule.cxx).

> [@DaveB](#):
>
> If I use higher thresholds, then bone disappears. If I use lower thresholds to get more bone, then the facet joints get filled in regardless of the smoothing kernel size I use.

Vertebrae are very easy to separate on high-resolution CT scans, but on typical patient scans have much lower resolution.

@amine gave an excellent answer on how to approach this. In addition to his suggestions, you may also try masked grow from seeds. See [this segmentation recipe](https://lassoan.github.io/SlicerSegmentationRecipes/AortaMaskedGrowFromSeeds/) for details and this short demo video:

[![](https://img.youtube.com/vi/8Nbi1Co2rhY/maxresdefault.jpg "Femur segmentation using masked region growing in 3D Slicer") ](https://www.youtube.com/watch?v=8Nbi1Co2rhY)

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