Hi, I am working on Ubuntu 20.04.6 LTS with the ATM’22 dataset. I have the CT volumes and the binary segmenatation mask of the pulmonary airway as nifty (.nii.gz) files. To get the centerline of the pulmonary airway, I use following steps: Load the image volume as normal volume and the segmentati…

Thanks. I have managed to get the centerline using the following code. # Reference: https://discourse.slicer.org/t/vmtk-extract-centerline-with-python-console/31596/8 # 1. load volume and segmentation print("Loading volume and segmentation:", volume) vol = slicer.util.loadVolume(vol_path) seg = sli…

[image] RomanStriker: # 2. Apply a growing operation #I am not sure how to do this This code may be an adequate example for a growing operation with the ‘Segment editor’.

I can save the nodes as follows. # Create network model storage node networkModelStorageNode = networkModelNode.CreateDefaultStorageNode() networkModelStorageNode.SetFileName(os.path.join(network_save_path, file_name + ".vtk")) networkModelStorageNode.WriteData(networkModelNode) but I still cannot…

Binary segmentation mask to centerline polydata using a python script

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RomanStriker (Roman) June 4, 2024, 10:53am 5

The code for saving the network curve with required folder structure is linked here.

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Binary segmentation mask to centerline polydata using a python script

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