New module: Extract Centerline (in SlicerVMTK extension)

We added a completely new module that makes vessel (or airway or any other tree structure) centerline extraction much faster, flexible, and robust. It can quickly extract a network, determine branch endpoints automatically, allows editing of endpoints, computing centerlines, branches, and quantitative metrics (radius, curvature, torsion, etc). The new “Extract Centerline” module is available in SlicerVMTK extension for latest Slicer-4.11 release (it replaces the old “Centerline Computation” module).

Video demonstrating vessel segmentation, centerline extraction, centerline curve editing, curved planar reformatting (straightening), branch extraction and quantification:

The video uses these modules:

  • SlicerVMTK extension (for “Extract Centerline” module)
  • SegmentEditorExtraEffects extension (for “Local threshold” Segment Editor effect)
  • Sandbox extension (for “Curved Planar Reformat” module)

wonderful but the “sandbox” extension does not appear to me in the Slicer version 4.11.0 2020-06-17

Sandbox extension shows up in Examples category. You only need that if you want to use the Curved Planar Reformatting module.

Fabulous, the “curved planar reformat” and “extract centerline” modules are the best, but there is some way to make the “fudicial” that are placed in the “curved planar reformat” be recognized or appear in the centerline of the segmentation ?, this in order to have more accurate measurements, as there are cases in which I need to perform the centerline from the lowest renal artery and for that I rely on the “curved planar reformat” but the fudicials do not appear in the centerline of the segmentation to be able to use the automatic centerline modules with branch recognition.

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.


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: