Extract Centerline computational troubleshooting

Support
1

I was trying to use Extract Centerline to generate a centerline tree of what I think is a relatively simple shape (compared to what I want to input later). I’ve got 128gb RAM, 8GB NVIDIA card, 2TB SSD, and Intel i7-14700HX processor, which I would think would be enough to process at least this.

The model was imported as a .ply from an Avizo export because the lab I’m in segments in Avizo (and not going to change). It was about 42k points, I used decimate set at 0.9 and it output a 23k-point mesh.

If I did not run pre-processing, the network outputs rendered very quickly, though missing a couple branching points I had marked with endpoints, and the centerline outputs haven’t finished after 30min. If I did run pre-processing, Slicer stays pre-processing for over 30min. I’ve tried changing curve sampling distance to 0.001mm because the scan resolution is 0.006mm; I saw that was an issue in a previous post. I’ve also tried increasing target point count. It pre-processes fast when set to 23k (basically no more decimating), then spends tens of min on the centerline curve and table generation. When I set target point count for 15k, then it takes a very long time to pre-process again, I haven’t seen it finish either step yet.

If this was the most complicated tree structure I wanted a centerline tree of, then I’d be more patient. But I have much more complex structures that I will need trees from too, so I was wondering if there was anything else I could do to optimize computation time or if I was missing something obvious. Avizo has a similar module, but it finishes the computation in a minute or two, though the line isn’t always in the center and it’s harder to edit/refine (talking with them about that too), so I was hoping to use Slicer’s.

Thank you for any ideas!

2

Your data has a tree_smooth and a decimate tree models.

With multiple combinations of Preprocess input surface, Target point count and Subdivide, a centerline model only (Tree) is generated in a few seconds with either input model.

Trouble starts while generating centerline curves, it runs and runs and there’s no console output hinting at anything.

If the bifurcated centerline (11K+ points) is processed with vtkCleanPolyData and a new model is created from its output (4K+ points), and the clean centerline model is processed in Centerline disassembly, its components as models are created in a few mins. But it keeps running when curve components are requested. Centerline disassembly relies on Extract centerline to generate curves.

If the bifurcated centerline itself is processed in Centerline disassembly (without cleaning), the same observations can be made.

So the lengthy computation happens with centerline curve generation in Extract centerline for unknown reasons. I’m afraid you’ll have to work with centerline models for now.

Someone else may have a better idea.