Add SlicerModelsVoxelization extension

[DomenicoRiggio]

New extension

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[pieper]

This seems cool, but how is it different from what's already available in the Segmentation infrastructure? @lassoan

[DomenicoRiggio]

Hi @pieper, thank you very much for your comment,

We understand the concern. The current name/description may indeed be a bit misleading, and we would be happy to improve them to make the purpose of the extension clearer.

The extension is not meant to replicate Segment Editor functionalities. Its goal is to generate a voxel-based volumetric mesh made of regular hexahedral elements, with a user-defined pitch. The output is therefore not a labelmap and not a surface model, but a volumetric mesh with nodes and elements that can be used in FEM workflows, for example with SOFA-Slicer, or exported to other simulation tools.

The main difference from the Segment Editor / labelmap infrastructure is that the mesh resolution is controlled by the selected pitch, independently of the original image or segmentation resolution. The extension also lets users define a threshold for the minimum fraction of volume that a voxel must contain to be included in the final mesh, giving control over the boundary approximation and the trade-off between geometric fidelity, mesh size, and robustness.

Compared to Segment Mesher, that also generates volumetric meshes, the extension provides a different type of volumetric discretization: regular voxel/hexahedral elements instead of tetrahedral elements.

The extension also includes standard Boolean operations and the possibility to export the output meshes in different file formats.

We see this as a complementary workflow. Tetrahedral meshes are very useful, but tetrahedralization can require additional surface cleaning and preprocessing, especially for complex anatomical geometries. A regular voxel/hexahedral mesh can be useful when a more straightforward and robust volumetric discretization is desired, for example in preliminary, automated, or educational FEM workflows.

We presented a preliminary version of this work at the 3D Slicer Project Week in January 2026 and received encouraging feedback from participants interested in this workflow. We would be happy to discuss this further, clarify any remaining questions, and improve the extension, its name, or its documentation based on your suggestions.

[pieper]

Okay, I see, thanks for the clarification. There are some failing checks to look into.

[DomenicoRiggio]

Thank you @pieper, We have looked into the failing checks and working now on fixing the issues.

[lassoan]

It was not clear for me from the documentation what this extension can be used for. You could simply write that it provides a hexahedral mesher and give some information on the meshing strategy and intended use.

I would also recommend to consider using more of the already Slicer infrastructure and VTK, because it may dramatically reduce the amount of code that you need to maintain.

If the output is simply a uniform hexahedral mesh then vtkThreshold filter (followed by an optional append filter to merge points) could be used instead of bringing in trimesh.

Boolean operations are available for both models and segmentations (Combine Models module in Sandbox extension; and Logical operations effect in Segment Editor), and quantitative analysis is offered in Segment Statistics module. Resampling segmentations is available in Segment Editor (specify geometry) or in Crop Volume module. Saving in various formats are already available in File/Save and Export node. Additional import/export formats can be easily added by implementing file reader/writer plugins.

[kimiaghodoosi]

It was not clear for me from the documentation what this extension can be used for. You could simply write that it provides a hexahedral mesher and give some information on the meshing strategy and intended use.

I would also recommend to consider using more of the already Slicer infrastructure and VTK, because it may dramatically reduce the amount of code that you need to maintain.

If the output is simply a uniform hexahedral mesh then vtkThreshold filter (followed by an optional append filter to merge points) could be used instead of bringing in trimesh.

Boolean operations are available for both models and segmentations (Combine Models module in Sandbox extension; and Logical operations effect in Segment Editor), and quantitative analysis is offered in Segment Statistics module. Resampling segmentations is available in Segment Editor (specify geometry) or in Crop Volume module. Saving in various formats are already available in File/Save and Export node. Additional import/export formats can be easily added by implementing file reader/writer plugins.

Thanks for your comment. I am Kimia and I am one of the contributors of the project. Regarding your comments:

1. Documentation: We will add more detailed explanations to the README as soon as possible, clearly describing the extension as a hexahedral mesher intended for FEM simulation workflows.
2. Slicer infrastructure and VTK: We already use Slicer and VTK infrastructure wherever appropriate, specifically slicer.mrmlScene.AddNewNodeByClass(), CreateDefaultDisplayNodes(), vtkMassProperties, vtkSelectEnclosedPoints, and vtkTriangleFilter. The remaining custom code exists only where Slicer has no native support for our specific use case.
3. Replacing trimesh with vtkThreshold: We attempted the suggested approach: surface mesh → vtkPolyDataToImageStencil → vtkImageData → vtkThreshold → hex mesh. However, vtkPolyDataToImageStencil consistently produced empty results for arbitrary surface meshes in VTK 9.x, even when the mesh was correctly positioned within the image bounds. We tested with both world-space (RAS) coordinates and unit IJK coordinates but both failed. trimesh's mesh.voxelized(pitch).fill() is the only approach that worked reliably. We are open to suggestions on how to make vtkPolyDataToImageStencil work correctly in this context.
4. Boolean operations: Combine Models and Logical operators in Segment Editor both operate on surface meshes or segmentations at the original image resolution. Our boolean operations work on the voxelized hexahedral mesh at a user-defined pitch; operations are performed on integer voxel grid indices. The result must remain a hexahedral mesh to preserve the voxel structure for FEM export. Additionally Combine Models uses vtkbool which requires clean watertight surfaces. Voxelized hex meshes are non-manifold (adjacent cubes share faces) and cannot be processed by vtkbool.
5. Resampling in Segment Editor: Segment Editor and Crop Volume resample segmentations to a different voxel spacing while keeping the output as a segmentation or labelmap. Our extension does something fundamentally different. it converts a surface mesh or segmentation into a solid hexahedral mesh where each element is a cube of a user-defined edge size. This is a volumetric mesh suitable for FEM simulation, not a resampled segmentation. The edge size parameter controls the element size of the hex mesh, which directly affects FEM simulation accuracy and computational cost.
6. Export formats: We agree that VTK, STL, and OBJ are available through Slicer's built-in File/Save. We attempted to use slicer.util.saveNode() but it requires a storage node attached to the model node, which our programmatically created nodes do not have by default. For MSH (Gmsh 2.2), PLY, and OFF, none are available natively in Slicer. MSH is the primary format needed for our FEM workflow and is provided through a custom writer in our extension.
7. Quantitative metrics: Segment Statistics measures properties of segmentations at MRI resolution. Our metrics serve a completely different purpose, they measure voxelization error, specifically the volume difference (ΔV) between the original surface mesh and the resulting hexahedral mesh at the chosen edge size. No existing Slicer module provides this information.