Multisegment merging into one model for STL export

New to using 3D slicer and have followed the cardiac segmentation video and had a question regarding export of the segments into STL. It seems that when one goes to export each segment as a model they are exported as there own segment (meaning 8 stl files for 8 segments). Is there anyway to combine the segments as one STL file? I have tried the logical operator tab Add function (not sure if I used it correctly) but am not sure if this would be the solution. I am using Slicer 4.8.

Anyway thanks for any tips and answers. This is a great program.

Latest nightly version of Slicer has a dedicated file export feature. You have the option of saving as merged STL (all segments merged into a single mesh) or OBJ (single file, segments are different objects). See details here:

Really appreciate this response and the video. Good to know the latest nightly build has this built in.

1 Like

Operating system:Windows 7
Slicer version:Slicer4.9.0
Expected behavior: stl file for the merged model
Actual behavior:error in merging the two segment model

I am working with Slicer4.9.0. I want to generate stl for a sample having two regions.

I could generate stl for both regions individually but when I try to merge model Slicer shows error and gets close.If I try to add the two segments using logical operation I get an stl but that shows error in Gmsh which I use for further mesh refinement.I have tried this process with Slicer4.8.1 also.
I don’t have dropbox to tranfer files.The mrml for segmentation and the snapshot showing errors could be sent through mail.

Use latest stable version (Slicer-4.10.1) or later.

You can use SegmentMesher extension to create high-quality multi-material meshes directly in Slicer.

You can use any other online storage provider.

Hi Andras,
I want to use gmsh within slicer. The problem I am having is I am unable to view the vtk files generated by using gmsh and meshio.

Also another problem is that I create a surface model node. how can I use this surface model node as input to gmsh. any suggestions?

Also if I use the segment mesher I found it generates a mesh from label maps but the mesh is not refined. thats Why I now jumped to gmsh. Any suggestions?

So I need to now create mesh using surface model nodes generated by slicer and using these surface model nodes to generate the mesh through gmsh. Any suggestions How can I read the surface model node in gmsh


What do you mean by “not refined”? By default mesh generation is set up to be very quick and generate a course mesh. You can adjust the parameters to preserve all relevant details of the surface mesh.

Sorry I mean fine mesh. How can I get a fine mesh using segment mesher with only one label map.

Thank you

Saima Safdar

See this tutorial: Near the end there is a step to create a finer mesh.

Hi Andras,
I checked with multiple values for scale but it always give me a mesh with some external elements which are not in the label map in segmentation.

For example see in the fig above. the label map is ok but mesh is not ok. why am i getting the mesh like this and not exactly what I needed from the label map of brain.

thank you

any suggestions please

You can add a box-shaped segment around the brain (e.g., using Scissors effect, with appropriate masking settings). You can then extract sub-meshes by thresholding based on material ID cell scalar.