I’ve installed Vascular Modelling Toolkit extension in Slicer4.11. I could find Centerline computation Level set segmentation Vesselness filtering I couldn’t find vmtknetworkextraction . I’d like to know if there a separate plugin for networkextraction.

[image] Deepa: From what I know, it is available as a python class. The page you referred to documentats usage of VMTK’s special “pypes” scripts. These scripts are not Python classes that you import and use, but scripts that you can use via command line. They are very thin wrappers over Pyth…

@lassoan Thank you very much for the clarification. I’m sorry about the confusion, I am really new to all of this. [image] lassoan: I would recommend to use the VTK classes directly instead of going through the extra layer of pypes scripts. Sure, I’d like to know how to process the branchi…

What would like to compute exactly as end result? Average vessel radius over the entire tree? Average vessel segment length over the entire tree?

@lassoan Yes, I would like to compute the average vessel segment length and average vessel segment radius of all the branches in a tree. Please check sample

I’ve added computation of branch length, average radius, curvature, torsion, and tortuosity to the centerline computation module. All you need to do to compute these metrics is to select a node for “Centerline properties”. This feature will be available in tomorrow’s Slicer Preview Release. [image…

@lassoan Excellent! I am super happy to know about this new feature. Thanks a ton. I look forward to use this. From what I understand, CellId refers to the branchid. It will be super helpful if you could also add 4 more columns branchNode0 and branchNode1, xyz_branchNode0, xyz_branchNode1. branch…

You can cross-reference the displayed curve with the computed properties in the table based on the CellId displayed in parentheses in the widget’s node name, so you can find out quite easily which numbers are for which vessel segment. Anyway, I have now added branch start and end point positions to…

@lassoan Thank you very much. This is extremely helpful. [image] lassoan: You can cross-reference the displayed curve with the computed properties in the table based on the CellId displayed in parentheses in the widget’s node name, so you can find out quite easily which numbers are for which v…

Parent/child relationships are the easiest to get from the curve hierarchy (you can get list of all immediate or all children nodes, etc.), but of course it is very easy to add any additional columns to the table, too. Could you describe what do you plan to compute and how?

[image] lassoan: but of course it is very easy to add any additional columns to the table Yes, that will be really helpful. I plan to use this as an input for CFD studies where the endpoint ids will be useful for setting up external inputs.

VMTK vessel centerline network extraction in Slicer

Support

lassoan (Andras Lasso) July 10, 2020, 5:42pm 23

Network extraction gets all branches. To search a path between two points in a network, you can use the method described here:

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VMTK vessel centerline network extraction in Slicer

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