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?

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.

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3 posts were split to a new topic: Difference of spacing was detected during DICOM loading

vertebral model
I would like to create a volumetric model of this vertebra. I tried to mesh it with the segment mesher module in order to export it as .vtk file and the result looks like that:
meshed model
What am I doing wrong?

How to biomechanical analysis of the vertebra:

  • solidify the bone using “Wrap solidify” effect (provided by SurfaceWrapSolidify extension)
  • generate a volumetric mesh using SegmentMesher extension
  • save generated volumetric mesh with “Compress” option disabled into .vtk file
  • load .vtk file into FeBIO Studio
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Dear Mr. Lasso thank you for your reply!
Unfortunately today the extension database did not work, so I could not try the SurfaceWrapSolidify extension yet
But I am also not sure if this solidifying module can lead to the model I need, cause I think for a precise FE analysis I need to model the cancellous bone as well and with this module it seems, that the cancellous bone will be extracted? Please correct me if I am wrong

Unfortunately today the extension database did not work

Every day the Slicer Preview Release shows up around 1am EST but extension builds are completed around 10am EST, so depending on your timezone, you may not see extensions for a while. You can retry installing extensions now or install yesterday’s release (Download 3D Slicer | 3D Slicer).

The holes you see in the mesh are not there because you have such big holes in the bone. It is a segmentation error, because the average intensity of the bone decreases due to partial volume effect and it becomes so similar to soft tissue’s intensity that they become classified as soft tissue = outside segmentation.

Therefore, you need to fill in these “holes” in the segment and to reproduce material properties, you set different material properties within this mesh. You can take samples of the CT volume at every mesh point to decide where in the mesh you set material properties corresponding to cortical/cancellous bone.

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Thanks a lot for your reply!
I tried the Wrap Solidify Module, but this is the best I could get out of it. There are still holes and even peaks on the surface. What am I doing wrong with the setup?

How do I set material properties in 3DSlicer? I though it will be done for example in FEBio?

The main issue is that you have chosen to enable “Create shell” and chose thickness that is comparable to your voxel size.

If the goal is finite-element analysis then a shell is not a good model, so do not enable “Create shell” option.

You will get material IDs (corresponding to segment indices) when Segment mesher module creates a volumetric mesh using Cleaver2. You can also add CT density values to the volumetric mesh using Probe volume with model module.

Your FEM software can use these additional scalar values in your mesh to set material properties. I don’t know which FEM package can read VTK unstructured grids and which can use material IDs or density values stored in cell scalars, but you can ask their developers and report back to us what you learned.

Thank you very much for your help. I finally created a volumetric model of the vertebra with the following adjustmens:

  1. Wrap solidify module → Carve holes: 1mm
  2. Smoothing → Closing(fill holes): 1mm
  3. Gaussian Filter: 1mm
    The result looks like that:
    model

but the problem now is, if I want to mesh it, I get a very edged and reduced model. I tried different paramaters and this seems the best (but still not good enough): scale= 3; multiplier=1; grading=5
model2
Any idea, what I am doing wrong or what I should improve?

This looks really nice. Your volumetric mesh resolution looks very good, too, but of course you may want to adjust the mesh depending on what you want to model (heat transfer, mechanical stresses, etc.) and where.

Note that computational mesh does not have to be as high resolution as the visualization mesh. It would result in unnecessarily complex mesh, leading to very long computation times and robustness issues. Computational mesh surface does not have to be smooth either, except in special cases (such as when you are specifically interested in modeling surface contacts). Once the computation is complete, you can transfer displacements or other computed values over the visualization mesh.

What kind of modeling do you plan to do?

Thank you very much, without your help, I would not get so far!

I would like to model the lumbar spine (later also a osteoporotic one, if possible) with all necessary components such as intervertebral discs etc. and include pedicle screws and rods to calculate the stress distribution.

For these probably the current resolution is good. If you insert a rod then the mesh resolution will be automatically increased around the hole. I think you can also specify spatially varying mesh resolution with an image (it is called “field” in Cleaver). We don’t expose this option in Segment Mesher user interface, but you can specify additional command-line parameters.

is FeBIO a open source software for student?

Yes, it is open-source and free, even for commercial purposes.

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It worked for meshing method cleaver but not with TetGen in FeBIO Studio.
Saying:
Failed reading file:
C:/Users/CG-DTE/Documents/NewFolder/Model.vtk
ERROR: Only float data type is supported for POINT section.
How to sovle this problem. What I am doing wrong.

I would recommend to post this as an issue on the FeBIO Studio project page: https://github.com/febiosoftware/FEBioStudio/issues

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4 posts were split to a new topic: Exporting segmentation to Abaqus

Thank you very much!
Unfortunately it does not work and I get this error:
Traceback (most recent call last):
File “”, line 1, in
NameError: name ‘pip_install’ is not defined

You need to use latest Slicer Stable Release.

Hi everyone

  1. I have created a volumetric mesh from a mandible segmentation (photos). However It was necessary to change the parameters to visualize all parts of the mandible (compare the 2 photos) I have changed the values but acctually I dont know which one represents. ( the new parameters scale 0.8, multiplier 1, grading 5. Could someone explain? To perform analyses of strees distribution what are the best parameters?

  2. Regarding the mesh created: As the SCALE parameter increased the surface of the volumetric mesh has changed (more triangles). I would like to know if it could interfere when the file is exported? Manly if it can interfere in the FEA analysis

  3. How can I change the geometric shape from triangles to tetahedral shape?

  4. I have read the answer above but I was not able to understant: How can I set material properties in 3D slicer. Could someone send some prints or at least a short tutorial?

volumetric_mesh