Prepare labelmap for parenchyma analysis

Support
1

I want to use the Parenchyma Analysis module, but want to use a segmentation that was done by different software.

What I tried:

  • Convert the surface mesh to a label map using the Model to Label Map module.
  • Use this label map as Label Map Volume in Parenchyma Analysis.

This did not work, my next idea was to try and devide the lung mesh into upper, middle and lower parts for the left and right lungs by:

  1. Let the Parenchyma Analysis module generate a partial lung label map.
  2. Convert the partial lung label map to a model with the Model Maker module.
  3. Importing the surface mesh as a model in the Segmentations module, as well as the model created in step 2.
  4. My idea was to cut the model from the surface mesh, to devide it into the upper, middle and lower parts as the model created in step 2 has. However, when trying to use any of the Effects in the Segmentation module, a window opens and asks to change the master representation from closed surface to binary labelmap. After clicking on Yes, 3D Slicer does not respond and I need to restart the software.

What would be a solution to be able to use my surface mesh?
Thanks.

2

Use the latest nightly version of Slicer, it has lots of improvements and fixes.

No need. Import it directly into the Segmentation node (in Segmentations module, Import/export … section).

This should work correctly with the latest nightly version, but if not then let us know.

3

Thanks for the tip to import the labelmap directly, I had overlooked this option.
After reducing the size of the imported mesh it worked, although converting to binary labelmap still took some time (about an hour). I think it was a memory problem.

4

Thanks for the update, I’m glad that it worked.

You can usually reduce size of high-resolution meshes by 80-95% without any visible difference by using Surface toolbox module decimate function with a factor of 0.8 to 0.95.

5

Hi, did you finally geti it? I’m trying to do the same - use the parenchyma analysis with a segmentation made by another software, but I can’t even start. In what format has the segmentation to be saved for a correct import in 3d slicer?
Thanks

6

What software did you use to create the initial segmentation? What file formats it can save into?

7

Hello, sorry for this late answer, I had to drop my project but now I have some time to spend on it!I hope to find you well.
I use pulmonary toolkit to create the initial segmentation, a plugin on Mat-Lab. It can save the segmentaion in: dicom (.dcm), Matlab matrix (.mat), nifti (.nii) and metaheader and raw data (mhd).

8

Pulmonary toolkit can also generate “lobe mesh”, but when I import it, the position is incorrect (coordinates are different between ct-scan and imported mesh).

9

Most likely it is a RAS/LPS coordinate system mismatch. In recent Slicer Preview Releases, you can choose preferred coordinate system when opening a model in Add data dialog.

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