How to get the boundary/edges of organs instead of the filled with color?

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1

How to get the boundary/edges of organs instead of the filled with color?

2

You can adjust segmentation visualization options in Segmentations module’s Display section. uncheck Slice fill to only see the boundary of segments without any filling.

3

@lassoan Thanks a lot! It solved my issue. By the way, how can I increase the line width? Currently, Slice Outline is showing as 1.00.

4

The 1.0 value (next to the visibility checkbox) refers to the opacity. The line thickness can be set in Display / Advanced section → Slice intersection thickness.

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5

@lassoan Solved, thanks!

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6

@lassoan Is there a way to export this as it is? I tried exporting this as a labelmap and a nrrd, but it get filled during the exporting.

Also as a side question; is there a way to separate inner and outer border (surface, as it is a 3D segment) of a particular segment?

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If you want to get a surface mesh from a segmentation then you can directly export the segmentstion to obj or stl file in Segmentations module; or export to model node and then save the model as obj, stl, ply, vtk, vtp, … file.

8

Issue in that is I am loosing my unit measure information by that (Am I wrong?). I want to measure thickness of the segment at a later point. By thickness I meant the shortest distance from outer surface to inner surface. For example, refer the below image which shows what I did using STLs.

screenshot
screenshot987×600 103 KB

To get to this results what I did was;

  1. Create segmentation
  2. Export it as a STL
  3. Separated the inner and outer surface by manually removing the faces that connects the inner and outer surface, i.e. 3 ring like faces in each branch end.
  4. Use trimesh.proximity.thickness to compute the distance between inner and outer surfaces.

I have two issues with my approach.

  1. Exporting STL make the spatial data to be lost. I don’t know the unit of measurement in the above thickness. Should I just multiply the values I received with my pixel resolution of the original dataset to get the actual thickness value? Or is this my thickness value in micro meters?
  2. I have to manually separate the inner and outer surfaces.