Hello, I am looking to utilize the vmtk module for the ‘Extract Centerline’ and ‘Cross-section Analysis’ features with a purely scripted method, similar to this issue which had a lot of great information. A brief summary of my workflow: I use other software to create an aorta segmentation, determ…

OK, I looked a little deeper into the ExtractCenterline.py code, and I think what you need is the vtkPolyData for the closed surface representation of the segment. segmentation = aorta_seg.GetSegmentation() segmentID = segmentation.GetSegmentIDBySegmentName('Segment_1') aorta_seg.CreateClosedSurfac…

Here is how to get the segment you want: segmentation = aorta_seg.GetSegmentation() segmentID = segmentation.GetSegmentIDBySegmentName('Segment_1') segment = segmentation.GetSegment(segmentID) The VMTK inputs/outputs will take a bit more research and I just have time for this quick answer at the m…

Unfortunately the segment is not the right type: TypeError: SetInputData argument 1: method requires a vtkDataObject, a vtkSegment was provided.

Thank you Mike! Your input is very appreciated, with your help I was able to generate a centerline curve from command line. I was hoping that understanding how to use one part of the vtmk module would make it easier for the next part, but I am stuck again for the cross section analysis tool. While…

[image] wesselk: While referencing the CrossSectionAnalysis code You are pointing to a former module that no longer exists as such. Please consider the latest single module ‘Cross-section analysis’ in SlicerVMTK.

This is the current code as referenced by @chir.set : https://github.com/vmtk/SlicerExtension-VMTK/blob/master/CrossSectionAnalysis/CrossSectionAnalysis.py Hopefully that will be helpful. I have not ended up using the CrossSectionAnalysis module at all in my work so I don’t have any experience or…

[image] mikebind: import ExtractCenterline Hello, I tried modifying your long code example to automatically extract centerline curves using python. However, I found that the extracted centerline curves are not labelled in the 3D view, but only in the slice views: [Screenshot 2024-01-29 at …

This section of ExtractCenterline.py shows how the centerline model is generated from the centerlinePolyData: vmtk/SlicerExtension-VMTK/blob/3787ea4a300da28ec5f0824f0715f2713b631155/ExtractCenterline/ExtractCenterline.py#L288-L302 centerlineModelNode = self._paramete…

Thanks! I tried hidding all the elements, but there is still no label of the branches in the 3D view. However, after running multiple experiments directly from the ExtractCenterline module on the 3D Slicer software, I found that whether a branch gets labelled in the 3D view seems to depend on whethe…

Hi! I also found out that if I save the centerline curves in a mrml scene file, or just .mrk.json file, when I reload the files, the labels for the curves are not showing. I am struggling to figure out how I can let it show the label in 3D Slicer, and how I can perhaps change the saved .mrk.json fil…

Hmm, that does seem like odd behavior. If you want to chase this down further, I would try examining whether the curves end up with multiple display nodes associated with them (myCurveNode.GetNumberOfDisplayNodes()), whether they are independently assigned to be visible only in certain views (che…

VMTK Extract Centerline with python console

Support

ruili (Rui Li) February 16, 2024, 2:39pm 15

Sure! I have posted this potential bug in a separate post here.

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VMTK Extract Centerline with python console

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