# Conversion to binary labelmap freezes Slicer

**URL:** https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733
**Category:** Support
**Created:** [April 25, 2024, 2:43pm UTC](https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733 "2024-04-25T14:43:41Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![koenterheegde](https://avatars.discourse-cdn.com/v4/letter/k/67e7ee/32.png) [@koenterheegde](https://discourse.slicer.org/u/koenterheegde)
#### Post date: [April 25, 2024, 2:43pm UTC](https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733/1 "2024-04-25T14:43:41Z")

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Hey everyone,

I have been using Slicer a lot to generate a .STL from a segmentation. The nice thing in here was that I could apply smoothing very easily. I’m doing the segmentation myself now, and generate a .STL from it (own program). However, I can’t manage to smooth it and wanted to see if Slicer could do it for me. I import the .STL and set the geometry to that of the .STL. I then want to smooth it, but Slicer asks me to change the source representation to a binary labelmap. When I click ‘Yes’, Slicer completely freezes. I looked at this issue: [Retrieving statistics from RTSTRUCT and scalar volume - binary labelmap representation computation is very slow](https://discourse.slicer.org/t/retrieving-statistics-from-rtstruct-and-scalar-volume-binary-labelmap-representation-computation-is-very-slow/28100), but for me there is no option to select the “Planar contour → Ribbon model → Binary labelmap” path to create the binary labelmap. What is the issue here?

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/d/8d3a34427a655296a7c7d3622261f47238279079.png)

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### Author: ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)
#### Post date: [April 25, 2024, 2:46pm UTC](https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733/2 "2024-04-25T14:46:25Z")

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Did you try the smoothing in Surface toolbox? That does not require changing the representation to segmentation.

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### Author: ![koenterheegde](https://avatars.discourse-cdn.com/v4/letter/k/67e7ee/32.png) [@koenterheegde](https://discourse.slicer.org/u/koenterheegde)
#### Post date: [April 25, 2024, 2:56pm UTC](https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733/3 "2024-04-25T14:56:56Z")

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I just did, but it doesn’t lead to the result I want. In the Surface Toolbox, the only options are Taubin and Laplacian Smoothing. The smoothing used in the segment editor is Median Smoothing if I understood correctly. This is the result after applying Laplacian smoothing with 500 iterations and relaxation factor of 0.5:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/7/771d64022f8b755f33f71884a74e5d904dfa719c.png)

And I want to get something like this:

 ![Schermafbeelding 2024-03-13 123413 (1)](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/4/e42d2b087a34e141cebd2927bd828119c023c9aa.jpeg)

Important difference is to know that the in the first picture I did the segmentation in my own program and in the second picture it was done in Slicer.

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### Author: ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)
#### Post date: [April 25, 2024, 7:18pm UTC](https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733/4 "2024-04-25T19:18:47Z")

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What happens when you drag and drop the STL into slicer scene, and as opposed to loading it as Model, choose Segmentation in the options?

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### Author: ![koenterheegde](https://avatars.discourse-cdn.com/v4/letter/k/67e7ee/32.png) [@koenterheegde](https://discourse.slicer.org/u/koenterheegde)
#### Post date: [April 26, 2024, 7:18am UTC](https://discourse.slicer.org/t/conversion-to-binary-labelmap-freezes-slicer/35733/5 "2024-04-26T07:18:36Z")

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I’ve now loaded it in using ‘Add data’ and then select the .STL. Haven’t converted it into a model and then I can make it a binary labelmap in the ‘Segmentations’ module using just the standard ‘Create’ option, so not even using the advanced option. However, I still need a model in order to smooth it in the segment editor and I don’t have a model now.
