Centerlines and re-slicing

[Marcela Cardenas]

Hi everyone,

Bit of background - I am currently using SimVascular to assess the semicircular canals (inner ear). The data that I need is cross-sections following the axis of the canals.

I have been using the paths and segmentation tools successfully and have created 3D models of all three canals for several of my samples. However, since I am not able to make any measurements in the system, I am interested in finding the centerline from the 3D models (have been successful in doing so), re-slicing the image following the centerline insted of my manual path, and somehow exporting the cross sections.

I have not found a way to re-slice and to export the images so far. Any help would be appreciated!

BW,
Marcela

[Gabriel Maher]

Hi Marcela,

Unfortunately you can't export the image reslices directly from within simvascular.

If you have the centerline points, you could try Paraview and using one of their slice options, e.g. "slice along plane".

Alternatively if you want to do it programmatically you could access VTK's reslice filter, see e.g. https://vtk.org/doc/nightly/html/classv ... ml#details

Here's an example of using the image reslicer in python https://github.com/gmaher/seg_regressio ... ta.py#L435

Best,

Gabriel

[Marcela Cardenas]

thank you!