# Coronaries Calcification

**URL:** <https://discourse.slicer.org/t/coronaries-calcification/19246>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [August 18, 2021, 9:30am UTC](https://discourse.slicer.org/t/coronaries-calcification/19246 "2021-08-18T09:30:46Z")\
**Posts on this page:** 16\
**Page:** 1

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**Author:** ![Elias\_Karabelas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/elias_karabelas/32/11286_2.png) [@Elias\_Karabelas](https://discourse.slicer.org/u/Elias_Karabelas)\
**Post date:** [August 18, 2021, 9:30am UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/1 "2021-08-18T09:30:46Z")

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Dear Team,  
I managed to segment an aorta and a coronary tree with VMTK and Slicer. However for my case I would also like to extract calcifications present in the coronaries. I managed to threshold the calcifications, but from what I got from clinicians the calcifications are not completely surrounded by lumen. So I would need a way to make the calcifications stick to parts of the wall. Is there any way of achieving this? I attached a screenshot of my current segmentation.

Best regards  
Elias

 ![Bildschirmfoto vom 2021-08-18 11-24-20](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/d/3d69062f5bb80e3226cd9fd81d622189b6bb9b7f.jpeg)

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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:** [August 20, 2021, 6:11pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/2 "2021-08-20T18:11:32Z")

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Hi,

This is an interesting project.  
Cant´you just “hollow” the vessel segmentation, then “add” the calcification segmentation via “logical operators” ?

Regards  
rudolf

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**Author:** ![Elias\_Karabelas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/elias_karabelas/32/11286_2.png) [@Elias\_Karabelas](https://discourse.slicer.org/u/Elias_Karabelas)\
**Post date:** [September 1, 2021, 9:11am UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/3 "2021-09-01T09:11:31Z")

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Hi Rudolf,  
thanks for your answer. I tried this but since the hollow algorithm removes symmetrically it will shrink the lumen also at the side where there’s no calcification present or?

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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:** [September 2, 2021, 8:54am UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/4 "2021-09-02T08:54:42Z")

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Do you have a test dataset available?

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**Author:** ![Elias\_Karabelas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/elias_karabelas/32/11286_2.png) [@Elias\_Karabelas](https://discourse.slicer.org/u/Elias_Karabelas)\
**Post date:** [September 16, 2021, 12:17pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/5 "2021-09-16T12:17:29Z")

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Hi, sorry for the late response, I was on vacation.

> **[segmentation\_new](https://box.medunigraz.at/s/A4iNN7zDrECXXKw)**
>
> Box @ Medical University of Graz - Sustainable living. learning. researching.

under this link you will find the dataset I’m currently working on.

best regards  
Elias

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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:** [September 19, 2021, 2:56pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/6 "2021-09-19T14:56:24Z")

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I was able to download the data.

Isn´t that quite good already for planning an intervention?

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/6/46c3383678f679a3ea9070c597c4a4a093c9c432.jpeg)

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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:** [September 19, 2021, 3:29pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/7 "2021-09-19T15:29:01Z")

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Made the “COMBINED” segment hollow with a thickness of 0.3 mm and enabled the “CALC” segment.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/5/35fd9ee8428f481e2f76b0f43ea83c9ef9bee414.jpeg)

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**Author:** ![Elias\_Karabelas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/elias_karabelas/32/11286_2.png) [@Elias\_Karabelas](https://discourse.slicer.org/u/Elias_Karabelas)\
**Post date:** [September 21, 2021, 12:29pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/8 "2021-09-21T12:29:00Z")

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Hi Rudolf,

yes I’m also quite happy with the segmentation, but the cardiologists I showed this dataset to told me that the calcifications are too much floating in the coronaries, they need to be stuck closest to the lumen wall, that’s why I started to redo some things and asked myself if I can get around without to much manual work.

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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:** [September 21, 2021, 5:04pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/9 "2021-09-21T17:04:15Z")

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First of all, I think you need to rework your calcification (CALC) segmentation a bit.

This slice

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/8/48ec1553ea70c15dba2efd38de09bbf61e4ae8f6.png)

produces this segmentation:

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/4/64368ab87ef6a70ecfa1282010ec820f3464e2a1.png)

which may just be a little overdone in size and smoothed too much.

From the literature, the thickness of the coronary artery wall is around 0.75 mm.

Use this as the thickness in the “Hollow” tool With the hollow tool settings of

_thickness: 0.75 and_  
_Use current segment as: medial surface_

I get this result

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/5/8507dd5b322030260678cad21f3385ae2ab3c3de.jpeg)

with your segmentation which leaves the calcifications sticking or very close to the artery walls.  
If you rework the CALC segmentation maybe you can switch to

_Use current segment as: inside surface_

which should actually be the case here.

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<div class="post-metadata">

**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:** [September 21, 2021, 6:17pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/10 "2021-09-21T18:17:39Z")

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… you may also try a combination of volume rendering as shown here:

[![](https://img.youtube.com/vi/aeOFl19fh_c/maxresdefault.jpg "Coronary vessel segmentation on cardiac CT images") ](https://www.youtube.com/watch?v=aeOFl19fh_c)

and adding the calcifications as separate segmentations

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**Author:** ![ames](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ames/32/8989_2.png) [@ames](https://discourse.slicer.org/u/ames)\
**Post date:** [September 23, 2021, 6:13am UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/11 "2021-09-23T06:13:57Z")

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Hi Elias,

May I ask how you segmented the coronary arteries and what threshold you are using to identify the calcifications? Thanks in advance!

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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:** [October 9, 2021, 5:13pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/12 "2021-10-09T17:13:33Z")

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> [@Elias\_Karabelas](#):
>
> the calcifications are too much floating in the coronaries, they need to be stuck closest to the lumen wall

I could segment the LAD with [this](https://github.com/chir-set/MetaCenterlineExtraction/tree/main/CurveCenterlineExtraction/) tool (with calcifications outside the lumen). The key part is placing control points as close as possible to its center for such small arteries. That’s tedious still.

 ![Screenshot](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/0/b05ae23316db4b53f5c8c7f6414067084c14ccd7.jpeg)

Used parameters :

27 control points  
Intensity tolerance : 60  
Neighbourhood size : 2.0  
Tube diameter : 4 mm

The calcifications were segmented with usual tools of the ‘Segment editor’:  
Threshold  
Masking  
Paint : with sphere brush in 3D.

Centerline extraction failed, I suppose because of a very tight stenosis.

N.B : This tool is still experimental and not conventional inside. And it’s one tube at a time.

Regards.

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**Author:** ![suculent](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/suculent/32/80131_2.png) [@suculent](https://discourse.slicer.org/u/suculent)\
**Post date:** [May 19, 2025, 2:23pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/14 "2025-05-19T14:23:16Z")

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@chir.set Can you share which tool you used (link doesn’t work), is this tool available as a module in 3D Slicer?

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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:** [May 19, 2025, 2:40pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/15 "2025-05-19T14:40:07Z")

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> [@suculent](#):
>
> (link doesn’t work)

Yep, I even forgot I ever had this repository.

It’s `Guided artery segmentation` module in the [SlicerVMTK](https://github.com/vmtk/SlicerExtension-VMTK) extension. Many things have changed since this post. If you have segmented a coronary, you can segment the calcifications very quickly with `Arterial calcification pre-processor` module in the same extension. Other kinds of tinkering can be helpful to segment coronaries when they are not too diseased, it’s still tedious however. Since I don’t work with these arteries, I did not spend too much time with this.

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**Author:** ![liam26](https://avatars.discourse-cdn.com/v4/letter/l/858c86/32.png) [@liam26](https://discourse.slicer.org/u/liam26)\
**Post date:** [December 22, 2025, 10:33pm UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/16 "2025-12-22T22:33:56Z")

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I’m trying to evaluatate calcification, but I’m a bit confussed on your process. I used the arterial calcification pre-processor. Is that a subsitute for using threshold?

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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:** [December 23, 2025, 7:53am UTC](https://discourse.slicer.org/t/coronaries-calcification/19246/17 "2025-12-23T07:53:03Z")

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> [@liam26](#):
>
> a subsitute

No, it’s just one more tool. You can use any tool with which you are comfortable. With `Arterial calcification pre-processor`, you need a lumen segment first, that’s the hardest part, for tiny blood vessels like coronaries.