3D Model -> 2D segmentation

Provides a system for patient-specific cardiovascular modeling and simulation.
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Luke Markham
Posts: 3
Joined: Mon Oct 09, 2017 7:26 am

3D Model -> 2D segmentation

Post by Luke Markham » Mon Oct 30, 2017 1:13 am

Hi all,

I'm having a little difficulty here and was hoping someone might know how to help. SimVascular documentation does not seem to contain the information that I require.

I have an abdominal CT scan from which the aorta has been segmented. The segmentation has been specified along the axis of the aorta (by defining a path along the aorta). My question is two-fold:

1. How can I change the segmentation axis from that of the aorta to the z-axis. I've tried producing a surface from the original segmentation and then projecting that surface down onto my z-axis slices (axial slices), however I can't figure out how to do the projection.

2. How can I export a list of pixel co-ordinates (or an image binary) to denote the location of the segmented aorta in each of the axial slices.

Thanks :)
Luke
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Gabriel Maher
Posts: 32
Joined: Tue Feb 09, 2016 9:17 am

Re: 3D Model -> 2D segmentation

Post by Gabriel Maher » Mon Oct 30, 2017 11:01 am

Hi Luke,

Projecting segmentations onto arbitrary axes/extracting arbitrary cuts is currently not supported in SimVascular.

You could try exporting the polydata of the surface and using VTK along with the VTK cutter to look at cross-sections of the model in specified planes https://www.vtk.org/Wiki/VTK/Examples/Python/vtkCutter

To extract a binary image you could use the vtkPolyDataToImageStencil function https://itk.org/Wiki/VTK/Examples/Pytho ... ataStencil

Best,

Gabriel
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