# New module: Extract Centerline (in SlicerVMTK extension)

**URL:** <https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117>\
**Category:** Support\
**Tags:** feature\
**Created:** [June 19, 2020, 4:45pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117 "2020-06-19T16:45:30Z")\
**Posts on this page:** 15\
**Page:** 2

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**Author:** ![Peter\_Horvath](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/peter_horvath/32/17295_2.png) [@Peter\_Horvath](https://discourse.slicer.org/u/Peter_Horvath)\
**Post date:** [November 11, 2022, 5:27pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/23 "2022-11-11T17:27:41Z")

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Hi! I would like to use the vmtk library to extract centerline of airways. When I install the extension through the wizard, everything seems fine:

 ![2022-11-11](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/7/1719dc48c6d9109f7357fb968f372bf9d8433808.png)

However, when I try to actualy use the module, the following happens:

 ![2022-11-11 (1)](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/6/26432f89492551a932fdf21f8ebad9057c84b989.png)

If I double-click the name of the extension, nothing happens. Same for the curve centerline extraction module. How can I load these modules? I have tried installing-deleting the modules and slicer itself, but it does not help.

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [November 11, 2022, 5:50pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/24 "2022-11-11T17:50:55Z")

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> [@Peter\_Horvath](#):
>
> Same for the curve centerline extraction module.

As for “Curve centerline extraction” module, it is a helper module, that combines and automates a segmentation process relative to an arbitrary curve, followed optionally by centerline extraction. It has a dependency on ‘[Slicer segmentation extra effects](https://github.com/lassoan/SlicerSegmentEditorExtraEffects)’, that you should install separately from the ‘Extensions manager’.

Select ‘Centerline extraction’ module instead. If this one does not work, there’s another problem.

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**Author:** ![Peter\_Horvath](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/peter_horvath/32/17295_2.png) [@Peter\_Horvath](https://discourse.slicer.org/u/Peter_Horvath)\
**Post date:** [November 11, 2022, 7:27pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/25 "2022-11-11T19:27:16Z")

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Thank you, my bad. Centerline extraction works fine, and that is what I need.

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [November 11, 2022, 8:48pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/26 "2022-11-11T20:48:52Z")

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Set one point at the top of the trachea and autgenerate the others.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/8/987ad405dc37887303296f44fe1ba2ea22a33479.png)  
Relatively easy

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**Author:** ![Peter\_Horvath](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/peter_horvath/32/17295_2.png) [@Peter\_Horvath](https://discourse.slicer.org/u/Peter_Horvath)\
**Post date:** [November 11, 2022, 8:51pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/27 "2022-11-11T20:51:24Z")

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Thanks, works as expected.

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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:** [March 22, 2023, 4:24pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/28 "2023-03-22T16:24:44Z")

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4 posts were split to a new topic: [Construct a model of coronaries from CCTA scans](https://discourse.slicer.org/t/construct-a-model-of-coronaries-from-ccta-scans/28527)

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**Author:** ![Yuri\_Cocati](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/yuri_cocati/32/65637_2.png) [@Yuri\_Cocati](https://discourse.slicer.org/u/Yuri_Cocati)\
**Post date:** [April 16, 2023, 8:40pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/29 "2023-04-16T20:40:41Z")

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Hello everyone,

If anyone knows and can help me, I would like how the parameters (like torsion, curvature, radius, …) are obtained. For example, in this image, I applied Extract Centerline in the trachea, but the table with the parameters returned me just one value for each one. I did not understand if it is an average for the entire trachea or just the calculation of a specific region…

Thank you very much in advance

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/f/bfadb8498ed285b224b2902270b87897f93264ba.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:** [April 17, 2023, 1:05am UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/30 "2023-04-17T01:05:43Z")

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The values in the metrics table are summary statistics (one value is computed for each branch).

Radius, curvature, and torsion values are available as curve measurement data for each curve point. How would you like to use these values?

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**Author:** ![Mudrika](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@Mudrika](https://discourse.slicer.org/u/Mudrika)\
**Post date:** [May 2, 2023, 3:43pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/31 "2023-05-02T15:43:30Z")

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I have a similar query. I have a model of the aortic root dividing into the coronary arteries. I am able to calculate the parameters for the different centreline curves but is there any way to obtain these parameters for the whole geometry in the form of a contour where I can see the variation as a whole?

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:** [May 2, 2023, 7:05pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/32 "2023-05-02T19:05:45Z")

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What do you mean by the whole geometry? To the entire segmented tree?

What variation you would like to see? The radius, curvature, and torsion varies from point to point in a curve and you access these values in curve measurements. Radius is retrieved during centerline extraction; while torsion and curvature are computed from the curve on-the-fly.

Length and tortuosity only makes sense for a curve segment (a branch).

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**Author:** ![Mudrika](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@Mudrika](https://discourse.slicer.org/u/Mudrika)\
**Post date:** [May 3, 2023, 8:16am UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/33 "2023-05-03T08:16:03Z")

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Yes, by the whole geometry I meant to say the whole segmented tree.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/1/619da8252e6a7072d19448de3f9f1d0400a518a9.jpeg)  
This is taken from the article by Piccinelli _et al. 2009._

I want to obtain the variation in a similar way.

What I have done till now is: Imported my .vtp geometry and then the centerline extraction which creates a centerline model. For different centerline curves, I am able to see to the quantification in the tabular format but I want to study the variation in this format.

I hope, I am able to explain my problem!

Thank you!

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**Author:** ![gdisalle](https://avatars.discourse-cdn.com/v4/letter/g/f17d59/32.png) [@gdisalle](https://discourse.slicer.org/u/gdisalle)\
**Post date:** [June 30, 2023, 3:12pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/34 "2023-06-30T15:12:35Z")

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Dear Mr. Lasso,  
How do I access the value of the curvature at a given point of the centerline? In the “curve measurements” section I can only see the mean and max curvature, which refer to the entire vessel. Thank you in advance.

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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:** [June 30, 2023, 4:34pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/35 "2023-06-30T16:34:02Z")

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See this topic: [Exporting Curvature Data](https://discourse.slicer.org/t/exporting-curvature-data/23181)

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**Author:** ![Hamed\_Yousefiroshan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hamed_yousefiroshan/32/69324_2.png) [@Hamed\_Yousefiroshan](https://discourse.slicer.org/u/Hamed_Yousefiroshan)\
**Post date:** [February 12, 2024, 11:41pm UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/36 "2024-02-12T23:41:23Z")

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Hi, the new interface with the vertical segment editor looks nice, however, I am used to older versions where we could easily find MakeModeleffect and other effects. It would be appreciative if you put a new vid for this Centerline Exct module with the new editor. Thanks.

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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:** [February 13, 2024, 5:29am UTC](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117/37 "2024-02-13T05:29:55Z")

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Segmentations store labelmap and surface meshes and their content is synchronized in real-time, so times are long gone when you had to do manual export to models using Make model effect or Model maker module.

Once you segmented the vessels, you can go directly to Extract Centerline module and choose the segmentation as input.

There are several videos of this on [[https://m.youtube.com/user/PerkLabResearch](https://m.youtube.com/user/PerkLabResearch)](our lab’s YouTube channel) and many more created by others. Can you send a couple of links to videos that you found to be so old that was hard to follow?

[Previous page](https://discourse.slicer.org/t/new-module-extract-centerline-in-slicervmtk-extension/12117.md?page=1)