Using vmtk scripts within Slicer with vmtk-extension

Community VMTK
1

Hi, I have a vessel modelling workflow written in python which makes use of vmtk to convert a surface file (.vtk) to a mesh file (.vtu). I would like to migrate the workflow to use the Slicer environment as well as replace some of the scripts (e.g. vmtkcenterlines, vmtkcenterlinesnetwork) with those used in the slicer vmtk-extension.

The workflow makes use of the following vmtk scripts: vmtksurfacereader, vmtksurfacekiteremoval, vmtksurfacesmoothing, vmtkvmtkcenterlines, vmtkcenterlinesnetwork, vmtksurfaceclipper, vmtkbranchclipper, vmtksurfaceconnectivity, vmtkflowextensions, vmtkdistancetocenterlines, vmtksurfaceremeshing, vmtkmeshgenerator, vmtksurfacewriter, vmtkmeshwriter. Apart from the above vmtk rendering scripts like vmtksurfaceviewer, etc… were used as well. Visualization can be handled by Slicer so I did not include those to the list.

May I confirm that all the vmtk scripts are contained within slicer when I install the extension, or is access limited to those used for the functions present within the extension? (e.g. Can I use vmtkmeshgenerator from within the slicer python interactor?)

Additionally, how to access vmtk from slicer? I can’t import vmtk within the slicer python interactor. I get the following error when I input import vmtk

Traceback (most recent call last):
  File "<console>", line 1, in <module>
ModuleNotFoundError: No module named 'vmtk'
1 Like
2

I believe the packaging is different in the extension. Have a look in the scripted modules to see how they access the vmtk filters and you should be able to do the same.

3

Doodads, did you have any success. I’m struggling with the same problem.