New module: Extract Centerline (in SlicerVMTK extension)

These should be doable. Can you describe with a bit more details and sketches or screenshots about what exactly you would like to show and measure? Create a new topic.

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I followed this video step by step and got stuck at making the centerline. I was unable to select a surface input in the Extract Centerline module. I believe it has something to do with the endpoints and centerline curve shown at 1:02. Can anyone care to explain what step I’m missing? I’m using 3d Slicer 4.11.0-2020-06-27 on Windows 10 and I have MarkupsToModel, SegementEditorExtraEffects, and SlicerVMTK extentions installed.



I have been working on this module in the last couple of days. Please install the latest Slicer Preview Release (4.11.0-2020-06-30) and let me know if you run into any issues with this version.

I downloaded the 4.11.0-2020-07-04 preview release and now Extract Centerline is working as expected, thank you.

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Dear Mr. Lasso,
I would like to have tested the newest module with the newest 3D-Slicer version (4.11.0), unfortunately the program keeps crashing immediately after starting. I have reinstalled it several times and tested it on different computers (Windows 10).
I hope you can help me.

best regards

Yes, sorry, today’s build is corrupted, it’ll be fixed by tomorrow. See more information and workaround here:

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Thank you very much, I can now open the latest version of the 3D-Slicer (4.11.0), but I cannot load my CT-dataset with this version, although I do nothing else than with the stable version (4.10.2)

Use the DICOM module to import and then load the CT. If it does not work then post the details (how did you try to load the data, what error message is displayed, etc) in a new topic.

Excuse me, I have used this method to measure the vessel related morphology, and I feel it is very great. However, I have a question, does the radius measured here refer to the average radius of the vessel in this segment?

I had a quick look at the code and it seems the radius in the “Centerline properties” table is computed as the mean of the maximum inscribed sphere radii in the branch.

Thank you very much!

Hello to the community,

how are the “Curvature, Torsion, Tortuosity and StartPointPosition” defined in the “Extract Centerline” module? Which formula is the basis for the measured values?
Unfortunately, I have not found this in my research.

Greetings
Tamu

These are all computed by VMTK library. You can find detailed description of all the algorithms in Luca Antiga’s PhD thesis.

Hi, it seems that “Extract Centerline” has many more options than “Centerline Computation”. Is there a new/updated video available somewhere, presenting the functionalities, and a minimal use-case of the “Extract Centerline” module? I found only a video where “Centerline Computation” is used: Vessel segmentation and centerline extraction using 3D Slicer and VMTK - YouTube . I also asked this question in the section comments of the YouTube video as some people having similar problems may first find the video, then this post/message on the forum.

In short, my problem is that I have what seems like a legitimate segment, but I was unable to generate/extract a centerline.

Yes, there is this good video showing the workflow which works fine:

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Thank you Rudolf. I followed the video and everything worked for my segment. :+1:

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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

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

2022-11-11 (1)

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.

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’, that you should install separately from the ‘Extensions manager’.

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

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

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