# How to extract 3D vessels segmentation quickly and accurately?

**URL:** <https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [July 16, 2020, 9:51am UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571 "2020-07-16T09:51:53Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![wwx992881](https://avatars.discourse-cdn.com/v4/letter/w/ebca7d/32.png) [@wwx992881](https://discourse.slicer.org/u/wwx992881)\
**Post date:** [July 16, 2020, 9:51am UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/1 "2020-07-16T09:51:53Z")

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Hi,All!  
I need to extract 3D vessels segmentation from 3d TOF MRA,I want to do that more quickly and accurately .Now I use threshold and islands in segment editor to that and my segmentation as follow.But is there a better way to do?

 ![QQ图片20200716175054](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/1/81c729ddb784a40d1e2340eeb0e8fd1649cc73b8.png)

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [July 16, 2020, 1:02pm UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/2 "2020-07-16T13:02:01Z")

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As a start I’d suggest oversampling the segmentation. Then you might try [VMTK](https://github.com/vmtk/SlicerExtension-VMTK) vesselness filtering and other tools.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/6/d67cf10d9aefdc34312aa18162eb850d94719143.jpeg)

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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:** [July 16, 2020, 1:22pm UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/3 "2020-07-16T13:22:07Z")

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Yes, oversampling is a good idea (if you need to segment thinner vessels and they are breaking up), and vesselness filtering can be useful too (to improve contrast of tubular structures in images). VMTK’s vessel segmentation methods only worked for me for very simple geometries (up to a few branches).

It seems that you get decent results with simple global thresholding and islands, which means that you would probably get even better results and faster by using “Local Threshold” effect (provided by SegmentEditorExtraEffects extension):

[![](https://img.youtube.com/vi/yi07mjr3JeU/maxresdefault.jpg "New vessel branch extraction module for 3D Slicer") ](https://www.youtube.com/watch?v=yi07mjr3JeU)

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**Author:** ![wwx992881](https://avatars.discourse-cdn.com/v4/letter/w/ebca7d/32.png) [@wwx992881](https://discourse.slicer.org/u/wwx992881)\
**Post date:** [July 17, 2020, 8:37am UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/4 "2020-07-17T08:37:12Z")

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Thank for you help! 😀

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**Author:** ![wwx992881](https://avatars.discourse-cdn.com/v4/letter/w/ebca7d/32.png) [@wwx992881](https://discourse.slicer.org/u/wwx992881)\
**Post date:** [July 17, 2020, 9:03am UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/5 "2020-07-17T09:03:49Z")

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hi~I click OK and I didn’t see any change?Is something wrong with me?

 ![微信图片_20200717165950](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/2/5223dbd1decb06c45d348a9c8051c29b398c7456.png)

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<div class="post-metadata">

**Author:** ![wwx992881](https://avatars.discourse-cdn.com/v4/letter/w/ebca7d/32.png) [@wwx992881](https://discourse.slicer.org/u/wwx992881)\
**Post date:** [July 17, 2020, 9:18am UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/6 "2020-07-17T09:18:16Z")

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> [@lassoan](#):
>
> Yes, oversampling is a good idea (if you need to segment thinner vessels and they are breaking up), and vesselness filtering can be useful too (to improve contrast of tubular structures in images). VMTK’s vessel segmentation methods only worked for me for very simple geometries (up to a few branches).
> 
> It seems that you get decent results with simple global thresholding and islands, which means that you would probably get even better results and faster by using “Local Threshold” effect (provided by SegmentEditorExtraEffects extension):

Hi,andras,Yes,I tried it follow the tutorial step by step,but I don’t see 3d segmentation,why?(I have clicked ‘show 3d’ button)

 ![微信图片_20200717171003](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/3/4320920b919220dbc805e1c4cb0908966a00af4f.png)

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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:** [July 17, 2020, 4:34pm UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/7 "2020-07-17T16:34:33Z")

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> [@wwx992881](#):
>
> hi~I click OK and I didn’t see any change?Is something wrong with me?

This is normal. Changing resolution does not change what you have already segmented, but if you apply smoothing or make further edits then you will see the effect of increased resolution.

> [@wwx992881](#):
>
> Hi,andras,Yes,I tried it follow the tutorial step by step,but I don’t see 3d segmentation,why?(I have clicked ‘show 3d’ button)

You will not see any structures that are smaller than the minimum diameter. Decrease that value to 1-2mm or less.

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<div class="post-metadata">

**Author:** ![wwx992881](https://avatars.discourse-cdn.com/v4/letter/w/ebca7d/32.png) [@wwx992881](https://discourse.slicer.org/u/wwx992881)\
**Post date:** [July 20, 2020, 1:45pm UTC](https://discourse.slicer.org/t/how-to-extract-3d-vessels-segmentation-quickly-and-accurately/12571/8 "2020-07-20T13:45:15Z")

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okok~thanks! 😊