Aligning a surface model and volume rendering of the same skull

Support
1

Hi community.

I have the DICOM files of a skull and the Surface model (in PLY format) separately.

When I load both into Slicer, and do the volume rendering of the DICOM files, I can see that they are NOT aligned.

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How can I align/superimpose both (volume rendering and surface model)?

Thanks

2

This seems like RAS vs LPS coordinate issue. What happens when you choose the coordinate system for your 3d Model explicitly during the load.

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3

Thats perfect. By changing to RAS the surface model load it was perfectly aligned. Thanks

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4

Where did you do this segmentation? If this was done in slicer, this shouldn’t have happened.

5

Yes, I did my segmentation in Slicer. My flow was:

  1. Load the skull and segment it entirely.
  2. Export model to PLY format.
  3. Load the DICOM files and do volume rendering.
  4. Load the exported PLY file.

Best

6

Can you share a one dataset of dicom and segmentaiton. This should not have happened, if you exported from Slicer.

@pieper @lassoan

1 Like
7

Hi all,

I’m facing the same problem. I export a segment as stl using:

slicer.modules.segmentations.logic().ExportSegmentsClosedSurfaceRepresentationToFiles(saveResults_path,segmentationNode,segmentIDsVTK, 'STL',False,1.0,False)

Following the documentation (link) it should save the geometry in RAS coordinates.

I need to load this geometry in slicer automatically. I tried:

modelNode = slicer.util.loadModel(path)

But it seems that it is loading the model in LPS.

When I do it manually and selecting RAS it loads the model correctly.
imagen

How can I automate this process?