Convert unstructured grid model to volume

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1

Hi,
I tried loading the volumetric mesh (vtkUnstructuredGrid) by using both the interface Load Data as Volume and using “slicer.util.loadVolume(’/path/to/file’)” on the Python interactor to no avail. Slicer simply doesn’t load it up. However, loading it as Model would always work. How do I load it as Volume?

Here’s a sample unstructuredgrid below:

vtk DataFile Version 3.0

2D scalar data
ASCII

DATASET UNSTRUCTURED_GRID
POINTS 18 float
0 0 2
1 0 2
1 1 2
0 1 2
2 0 2
3 0 2
3 1 2
2 1 2
4 5 6
2 2 4
4 4 4
6 5 2
7 2 4
3 4 2
2 4 6
1 3 5
2 9 8
8 7 5

CELLS 4 44
10 0 1 2 8 9 4 5 13 12 11
10 0 2 3 15 16 4 6 1 17 10
10 1 4 2 9 10 11 12 13 14 16
10 9 8 7 6 5 4 3 2 1 0

CELL_TYPES 4
24
24
24
24

2

Surface and volumetric meshes are represented in Slicer as model nodes. You can convert a volumetric mesh to volume by sampling the mesh at each voxel using vtkProbeFilter. Here is a complete example of how to do that: https://github.com/lassoan/SlicerNotebooks/blob/master/UnstructuredGridToVolume.ipynb

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3

I was able to make it work thanks to your help. One thing I noticed was that the vtkUnstructuredGrid mesh must have CELL_DATA and POINT_DATA for Slicer to work correctly. I’m a beginner at vtk in general, so I guess my question would be which part of your code requires those two pieces of data? Or does volumetric mesh in general needs to have those in Slicer? I was able to generate volumes without those in vtkpython on conda and Paraview. Thanks a lot Andras!

1 Like
4

Maybe vtkProbeFilter specifically needs cell or point data (I don’t think you need both). You can convert between point and cell data as needed using vtkPointDataToCellData and vtkCellDataToPointData.

5

hi this page has been taken down. would you mind reuploading it, im having a similar issue

6

A post was split to a new topic: Convert mesh to volume