# How to get the boundary/edges of organs instead of the filled with color?

**URL:** <https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [December 20, 2022, 12:16am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836 "2022-12-20T00:16:09Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Js165](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/js165/32/14631_2.png) [@Js165](https://discourse.slicer.org/u/Js165)\
**Post date:** [December 20, 2022, 12:16am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/1 "2022-12-20T00:16:09Z")

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How to get the boundary/edges of organs instead of the filled with color?

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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 20, 2022, 5:39am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/2 "2022-12-20T05:39:50Z")

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You can adjust segmentation visualization options in `Segmentations` module’s `Display` section. uncheck `Slice fill` to only see the boundary of segments without any filling.

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**Author:** ![Js165](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/js165/32/14631_2.png) [@Js165](https://discourse.slicer.org/u/Js165)\
**Post date:** [December 20, 2022, 1:50pm UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/3 "2022-12-20T13:50:08Z")

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@lassoan Thanks a lot! It solved my issue. By the way, how can I increase the line width? Currently, `Slice Outline` is showing as 1.00.

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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 20, 2022, 7:14pm UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/4 "2022-12-20T19:14:22Z")

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The 1.0 value (next to the visibility checkbox) refers to the opacity. The line thickness can be set in `Display` / `Advanced` section → `Slice intersection thickness`.

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<div class="post-metadata">

**Author:** ![Js165](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/js165/32/14631_2.png) [@Js165](https://discourse.slicer.org/u/Js165)\
**Post date:** [December 20, 2022, 7:22pm UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/5 "2022-12-20T19:22:53Z")

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@lassoan Solved, thanks!

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**Author:** ![Windy](https://avatars.discourse-cdn.com/v4/letter/w/91b2a8/32.png) [@Windy](https://discourse.slicer.org/u/Windy)\
**Post date:** [May 1, 2024, 2:09am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/6 "2024-05-01T02:09:08Z")

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@lassoan Is there a way to export this as it is? I tried exporting this as a labelmap and a nrrd, but it get filled during the exporting.

Also as a side question; is there a way to separate inner and outer border (surface, as it is a 3D segment) of a particular segment?

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<div class="post-metadata">

**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:** [May 1, 2024, 3:15am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/7 "2024-05-01T03:15:29Z")

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If you want to get a surface mesh from a segmentation then you can directly export the segmentstion to obj or stl file in Segmentations module; or export to model node and then save the model as obj, stl, ply, vtk, vtp, … file.

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**Author:** ![Windy](https://avatars.discourse-cdn.com/v4/letter/w/91b2a8/32.png) [@Windy](https://discourse.slicer.org/u/Windy)\
**Post date:** [May 1, 2024, 4:06am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836/8 "2024-05-01T04:06:25Z")

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Issue in that is I am loosing my unit measure information by that (Am I wrong?). I want to measure thickness of the segment at a later point. By thickness I meant the shortest distance from outer surface to inner surface. For example, refer the below image which shows what I did using STLs.

 ![screenshot](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/6/c6810dfd90035da2aefd0f90f256c96a34d076fa.png)

To get to this results what I did was;

1. Create segmentation
2. Export it as a STL
3. Separated the inner and outer surface by manually removing the faces that connects the inner and outer surface, i.e. 3 ring like faces in each branch end.
4. Use trimesh.proximity.thickness to compute the distance between inner and outer surfaces.

I have two issues with my approach.

1. Exporting STL make the spatial data to be lost. I don’t know the unit of measurement in the above thickness. Should I just multiply the values I received with my pixel resolution of the original dataset to get the actual thickness value? Or is this my thickness value in micro meters?
2. I have to manually separate the inner and outer surfaces.