Is it possible to do a segmentation of the lumbar spine from CT-data and use the 3D model (.igs) for further finite element analysis in ABAQUS or FEBio?

I have never worked with 3D Slicer before and I am quiet new in this field. But I would like create a 3D model out of CT-DICOM-data. It is important that the HU values of the cortical and trabecular bone will be safed in the output (as .igs) for further Finite element analysis in ABAQUS or FEBio.
Furthermore I would like to know if it is possible in 3D Slicer to do material assignment and volumetric meshing.
I would appreciate any support.
Thank you in advance

You can segment spine CT in Slicer and use Segment Mesher module (provided by SegmentMesher extension) to create a FE mesh. Segment Mesher uses Cleaver2 for mesh generation, which is developed by the same group as FEBio, so it should be compatible with it.

Thanks a lot for your fast reply Mr. Lasso, I really appreciate it. So did I understood it correctly that with the extension I can create tetrahedral (volumetric) meshes? Ho about the assignment of material properties?
I also read that I need another software like Autodesk Meshmixer to smoothen the 3D object prior FE analysis, is that correct?


The segment index is saved as cell scalar in the mesh. In your mesh preprocessor, you should be able to select part of the mesh based on this cell scalar and define material properties.

Cleaver (the mesher that Segment Mesher module uses by default) creates smooth meshes. You can adjust meshing parameters to control resolution and smoothness. You should not need any other postprocessing. Meshmixer wouldn’t work anyway, as it can only deal with surface meshes.

Dear Mr. Lasso,
finally I have created a model of an lumbar vertebra out of DICOM data. I premeshed it as you suggested via Segment Mesher Modul and eported the the model as .stl and .obj file. The problem I am facing now is that I cannot load a volume mesh into FeBio (only .stl files). Do you know how or what I should do?
Thanks a lot for your advices in advance

FeBio Studio can import CTK unstructured grid saved in legacy VTK file format in ASCII mode. You can generate such file in Slicer by choosing “Unstructured grid (.vtk)” as File Format and uncheck “Compress” option (click “Show options” checkbox if you don’t see the options). Unfortunately, FeBio Studio is still in beta and has many issues. If you find that it has trouble opening your file then report it (see feedback email address here).

Thanks a lot for your help!
I tried to safe the file as .vtk but still cannot load it into FEBio. I can only load the .stl file as binary format. Hence I wrote FEBio, if there is any other possibilitie. I will keep you updated.
Do you know if ABAQUS is better in this case?

I’ve just talked to the developer of FEBio Studio about this and he fixed unstructured grid import from ASCII VTK files today. I don’t know when he will update the FEBio download page, so ask him on the FEBio forum or at the contact email address.

Thank you so much for your efforts!
I tried to safe another 3D model in .vtk but it is showing me this error: "Cannot write data file: C:/Users/Admin/Documents/Jeffs-Data/Test/5. Trial_ Threshold_300-1800 L5/23052020_L5/LabelMapVolume.vtk.
Do you want to continue saving?
Do you know what is the problem?

Likely a permission issue. Try to save to a folder where you have right permission.

Also make sure you don’t have any special characters in any of the folder or file names.

You might find some more details in the application log.