# Segmentation of Alveolar cleft

**URL:** <https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104>\
**Category:** Support\
**Created:** [December 17, 2020, 12:57am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104 "2020-12-17T00:57:33Z")\
**Posts on this page:** 10\
**Page:** 1

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**Author:** ![manjula](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/manjula/32/80981_2.png) [@manjula](https://discourse.slicer.org/u/manjula)\
**Post date:** [December 17, 2020, 12:57am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/1 "2020-12-17T00:57:33Z")

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I am trying to find a predictable way to measure the volume of an alveolar bone cleft in cleft lip and palate children with CBCT.

 ![image_00001](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/2/d2c873b11059cad415aaab49e2c3ccdde258290a.jpeg) ![image_00002](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/8/f857d8ae1def112c76de0e746a1810badedcfea8.jpeg)

Several papers describe that they have done it but it is very vague. The main problem is to define the anterior and posterior limits of the alveolar bone.

So far the best result I got was with the fill between slice option. Looking for a better and predictable way of segmenting this area to measure the volume which is not very nice in the anterior margin. (Superior and Inferior is not a problem as it can be defined with landmarks.

 ![image_00031](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/8/187bbc37556551d93dd21d324dc15a42f1d5c937.jpeg)

What would be the best way to do this?

Thank you

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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 17, 2020, 1:15am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/2 "2020-12-17T01:15:35Z")

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The images are very helpful but it is still not very clear what the main challenge is. Could you join the segmentation breakout session tomorrow at 2pm EST and bring this as a case to look at?

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**Author:** ![Tina\_Kapur](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tina_kapur/32/3140_2.png) [@Tina\_Kapur](https://discourse.slicer.org/u/Tina_Kapur)\
**Post date:** [December 17, 2020, 2:50am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/3 "2020-12-17T02:50:47Z")

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Btw, the Project Week Segmentation breakout session is at 11am EST tomorrow (not 2pm)

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>
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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 17, 2020, 2:56am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/4 "2020-12-17T02:56:17Z")

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We agreed on Monday to move the segmentation session to the afternoon because we wanted to have a segmentation storage format discussion and we could not find any other timeslot that worked for everyone. I updated the time in the breakout list, but not in the calendar. This afternoon I fixed this, they are now in sync.

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**Author:** ![manjula](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/manjula/32/80981_2.png) [@manjula](https://discourse.slicer.org/u/manjula)\
**Post date:** [December 17, 2020, 6:19am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/5 "2020-12-17T06:19:12Z")

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I will try to add better photos.  
I can come.today and bring this data for the breakout session. Thanks you

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**Author:** ![manjula](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/manjula/32/80981_2.png) [@manjula](https://discourse.slicer.org/u/manjula)\
**Post date:** [December 17, 2020, 10:09am UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/6 "2020-12-17T10:09:42Z")

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Dear Prof @lassoan

Idea is to calculate the volume of the bony cleft in cleft lip and palte children.

The area we want to segment is like a pyramid.

Defining the superior and inferior margins and the lateral and medial margins are no problem.

![1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/0/408a796b521452d1b3687976792635d511c389a3.png)

The problem is with the anterior and posterior walls. ![2](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/0/007919c3966940ff15aadeeabb1f2daeb9f14631.png)

People have tried different methods.

1, Marked the area in each slice and has multiplied that by spacing  
 ![Screenshot from 2020-12-17 10-25-45](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/c/0ceb46a90e59f01b86af934c0f9e775d8ff224e6.png)

But my idea is to replicate the method described here with the 3D Slicer in a much simpler way

[https://www.oooojournal.net/article/S2212-4403(17)30181-5/fulltext](https://www.oooojournal.net/article/S2212-4403(17)30181-5/fulltext)

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**Author:** ![TomAlexanderSchr](https://avatars.discourse-cdn.com/v4/letter/t/aeb1de/32.png) [@TomAlexanderSchr](https://discourse.slicer.org/u/TomAlexanderSchr)\
**Post date:** [April 6, 2023, 3:26pm UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/7 "2023-04-06T15:26:19Z")

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> [@manjula](#):
>
> find a predictable way to measure the volume of an alveolar bone cleft in cleft lip and palate children with CBCT.

Hello  
Have you found a predictable way to measure the volume of an alveolar bone cleft in cleft lip and palate children with CBCT ?

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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:** [April 6, 2023, 10:05pm UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/8 "2023-04-06T22:05:43Z")

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You can use the “Markups to model” module (provided by MarkupsToModel extension) to define the pyramid model by dropping a couple of markup points. You can get the volume of the model in Models module / Information section.

[![](https://img.youtube.com/vi/lqABW0_ohi4/maxresdefault.jpg "Quick volume measurement using boundary points") ](https://www.youtube.com/watch?v=lqABW0_ohi4)

You can improve the accuracy by importing the model into a segmentation and refine the shape in the Segment Editor module.

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<div class="post-metadata">

**Author:** ![TomAlexanderSchr](https://avatars.discourse-cdn.com/v4/letter/t/aeb1de/32.png) [@TomAlexanderSchr](https://discourse.slicer.org/u/TomAlexanderSchr)\
**Post date:** [April 22, 2023, 1:46pm UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/9 "2023-04-22T13:46:49Z")

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Dear Prof @lassoan

This workflow is tremendously helpful.  
Thank you a lot!

All the best

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<div class="post-metadata">

**Author:** ![TomAlexanderSchr](https://avatars.discourse-cdn.com/v4/letter/t/aeb1de/32.png) [@TomAlexanderSchr](https://discourse.slicer.org/u/TomAlexanderSchr)\
**Post date:** [March 28, 2025, 8:21pm UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104/10 "2025-03-28T20:21:34Z")

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Dear Prof @lassoan

I have found a problem that I unfortunately cannot solve myself.  
If I markup points in different planes, the inner points (middle plane) are not taken into account in the volume calculation.

See the markup points in the coronar plane below:

 ![{1FD4B7B3-8E66-4814-A4F8-78247DE37703}](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/e/1e2b821b13b76a2aa5a527bfbec1958023ea0309.png)  
 ![{5D36D2F7-F447-49E1-9361-79CCEAF286B0}](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/8/a8837adb4b3af11e78f0e25a5796fd92f3e8960c.png)  
 ![{59DCA9B3-4566-4F8F-90C4-7142107F4BBF}](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/8/b884fbb8860c850f1fb971abb2b99ca673900e4e.png)

The main problem in the volume calculation is the sandglass-shaped configuration of the alveolar cleft.

Thx in advance