# Vessel branch extraction

**URL:** <https://discourse.slicer.org/t/vessel-branch-extraction/13815>\
**Category:** Support\
**Created:** [October 2, 2020, 11:08am UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815 "2020-10-02T11:08:52Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![Andreas](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Post date:** [October 2, 2020, 11:08am UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/1 "2020-10-02T11:08:52Z")

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Hi all,

is it possible with the stable release version (4.10.2) to segment individual vascular branches of a vascular tree using Centerline Computation?

I have already tried the AddOn “SlicerExtension-VMTK” and the Youtube video “New vessel branch module extraction for 3D Slicer” but unfortunately without success.

> **[vmtk/SlicerExtension-VMTK](https://github.com/vmtk/SlicerExtension-VMTK)**
>
> Contribute to vmtk/SlicerExtension-VMTK development by creating an account on GitHub.

Can you please give me instructions on how to proceed step by step?

Best regards

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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:** [October 2, 2020, 11:54pm UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/2 "2020-10-02T23:54:08Z")

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Please use the new stable release (version 4.11.20200930) and let us know if it works as you expect.

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**Author:** ![Andreas](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Post date:** [October 3, 2020, 9:16pm UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/3 "2020-10-03T21:16:51Z")

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Many thanks for your help. With the latest version it worked now. However, I don’t know how to remove the individual branches from the trunk. Maybe it is only possible to hide individual branches.  
I would also like to know whether the geometry of the vessels can be changed in terms of length or diameter.  
I would be very grateful for your help.

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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:** [October 4, 2020, 1:04am UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/4 "2020-10-04T01:04:47Z")

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If you want to delete branches from centerline/network then just remove the vessel endpoints that you don’t need (before you start centerline/network extraction).

If you get the result as curves then you can show/hide/remove/edit each branch using GUI provided by Markups module. If you are comfortable processing the network/centerline tree in Python then you can use either the markups curve or model (vtkPolyData) representation. The best choice also depends on the next processing/analysis step. What is your end goal?

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**Author:** ![Andreas](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Post date:** [October 4, 2020, 8:16pm UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/5 "2020-10-04T20:16:32Z")

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Thank you for your quick reply.

In the attachment you can see how I try to delete vessel branches using the markups module. Unfortunately, nothing is removed from my vessel model  
Unfortunately I am not familiar with Python.

 ![Vessel branch extraction](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/5/551df88fb3f2bb88f97a55ebb925e15aa6c1f0ff.jpeg)

In the end, I am trying to create reproducibility for the removal of vascular branches. I don’t want to do this with scissors as this result is not reproducible.

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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:** [October 4, 2020, 11:33pm UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/6 "2020-10-04T23:33:46Z")

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Removing endpoints only removes branches from the centerline tree. The input model is not modified.

There are many options for removing branches. The best choice depends on why you need to remove branches. What is your end goal? CFD analysis?

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**Author:** ![Andreas](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Post date:** [October 5, 2020, 10:18pm UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/7 "2020-10-05T22:18:41Z")

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Thank you for your help.

Isn’t it possible to remove the branches at the endpoints of the actual input model?

Can you please tell me which processing tools are recommended in addition to scissors?

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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:** [October 5, 2020, 11:07pm UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/8 "2020-10-05T23:07:07Z")

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> [@Andreas](#):
>
> Can you please tell me which processing tools are recommended in addition to scissors?

There are many options for removing branches. The best choice depends on why you need to remove branches. What is your end goal? 3D printing, CFD analysis, simulation, visualization, …?

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**Author:** ![Andreas](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Post date:** [October 7, 2020, 10:50am UTC](https://discourse.slicer.org/t/vessel-branch-extraction/13815/9 "2020-10-07T10:50:20Z")

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I want to 3D print vessel models and remove small diameter branches.