Hi, I started using Slicer recently to create a model of pulmonary arteries and arterioles. After creating my segmentation and cleaning it up, I’m trying to use the SlicerVMTK extension to find centerlines for each vessels. I set a couple of manual endpoints and then use the auto-detect feature. Then, I check the end of each vessel and make sure it has a node. In the Outputs tab, I create a new Centerline model under the ‘Tree’ tab. After applying, Slicer loads for a bit and my segmentation becomes opaque, but no centerlines ever appear. I have also tried different combinations of network curves, network models, tree curves, and tree models, and only the network curves populate centerlines. This doesn’t work for my project since I need to export the centerlines as a .vtp file, which the curves can’t do. Other times, the centerlines miss lots of vessels and branch at random places. Any help is appreciated!
If you specify manual endpoints first then run auto-detect, then auto-detect will remove your manually specified endpoints.
Normally you either use auto-detect (and then delete or slightly move endpoints) or you specify endpoints manually.
If the endpoints are set reasonably then I don’t know why this would happen. We can have a look if you share your data or at least screenshots (make sure that no patient information is shared).
Network models and curves use the same method, so if you can get the result as curves then you can get the result as model as well. Make sure you select unique output nodes (don’t use the same node as input or centerline output or network output).
Here is are some pictures after adding endpoints and applying the centerlineModel:
(I turned the opacity up to better see the endpoints here)
