# 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?

**URL:** <https://discourse.slicer.org/t/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/10444>\
**Category:** Support\
**Tags:** segmentation, dicom\
**Created:** [February 26, 2020, 3:25pm UTC](https://discourse.slicer.org/t/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/10444 "2020-02-26T15:25:25Z")\
**Posts on this page:** 17\
**Page:** 2

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**Author:** ![Jeff\_S](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jeff_s/32/6146_2.png) [@Jeff\_S](https://discourse.slicer.org/u/Jeff_S)\
**Post date:** [June 17, 2020, 9:42am UTC](https://discourse.slicer.org/t/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/10444/22 "2020-06-17T09:42:47Z")

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

> [@lassoan](#):
>
> What kind of modeling do you plan to do?

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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 21, 2020, 5:10pm UTC](https://discourse.slicer.org/t/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/10444/23 "2020-06-21T17:10:13Z")

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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.

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**Author:** ![Farhan](https://avatars.discourse-cdn.com/v4/letter/f/b2d939/32.png) [@Farhan](https://discourse.slicer.org/u/Farhan)\
**Post date:** [September 18, 2020, 7:42pm UTC](https://discourse.slicer.org/t/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/10444/24 "2020-09-18T19:42:50Z")

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is FeBIO a open source software for student?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [September 18, 2020, 9:03pm UTC](https://discourse.slicer.org/t/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/10444/25 "2020-09-18T21:03:05Z")

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

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**Author:** ![Farhan](https://avatars.discourse-cdn.com/v4/letter/f/b2d939/32.png) [@Farhan](https://discourse.slicer.org/u/Farhan)\
**Post date:** [September 19, 2020, 12:02pm UTC](https://discourse.slicer.org/t/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/10444/26 "2020-09-19T12:02:15Z")

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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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [September 19, 2020, 7:33pm UTC](https://discourse.slicer.org/t/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/10444/27 "2020-09-19T19:33:12Z")

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

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 10, 2020, 2:58pm UTC](https://discourse.slicer.org/t/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/10444/28 "2020-10-10T14:58:25Z")

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4 posts were split to a new topic: [Exporting segmentation to Abaqus](https://discourse.slicer.org/t/exporting-segmentation-to-abaqus/13974)

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<div class="post-metadata">

**Author:** ![Jeff\_S](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jeff_s/32/6146_2.png) [@Jeff\_S](https://discourse.slicer.org/u/Jeff_S)\
**Post date:** [October 10, 2020, 3:07pm UTC](https://discourse.slicer.org/t/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/10444/29 "2020-10-10T15:07:25Z")

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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

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 10, 2020, 3:14pm UTC](https://discourse.slicer.org/t/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/10444/30 "2020-10-10T15:14:52Z")

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You need to use latest Slicer Stable Release.

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**Author:** ![Giovanni\_Cunha](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/giovanni_cunha/32/6942_2.png) [@Giovanni\_Cunha](https://discourse.slicer.org/u/Giovanni_Cunha)\
**Post date:** [March 8, 2021, 3:18pm UTC](https://discourse.slicer.org/t/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/10444/31 "2021-03-08T15:18:55Z")

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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](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/8/b803d7d96678aa05397d1f4e9ec4014bd1558d35.png)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 8, 2021, 3:37pm UTC](https://discourse.slicer.org/t/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/10444/32 "2021-03-08T15:37:57Z")

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> [@Giovanni\_Cunha](#):
>
> 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?

See explanation of all parameters [here](https://github.com/lassoan/SlicerSegmentMesher#mesh-generation-parameters).

> [@Giovanni\_Cunha](#):
>
> To perform analyses of strees distribution what are the best parameters?

Each analysis is different, you need to determine the parameters that work for you.

> [@Giovanni\_Cunha](#):
>
> 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

It does not interfere with the export. What you see is what is exported. It does not interfere with FEA analysis either - the solver will work whatever mesh you provide. Of course the results will change if you use very large elements and the computation time will be very long if you have many small elements. However, since there is almost no displacement, you can probably vary the meshing parameters in a wide range and you will still get convergence and very similar results.

> [@Giovanni\_Cunha](#):
>
> How can I change the geometric shape from triangles to tetahedral shape?

Volumetric mesh elements generated by Cleaver are already tetrahedral.

> [@Giovanni\_Cunha](#):
>
> 1. 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?

You set material properties in the pre-processor of your solver, not in Slicer. What you can do in Slicer is to create separate segments for each material (e.g., cortical bone and cancellous bone are in two separate segments), or assign CT density to each mesh point (using Probe volume with model module) and then use that information in your preprocessor. You can ask details about this on the [FEBio forum](https://febio.org/support/) (or forum of any other solver you use).

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**Author:** ![Giovanni\_Cunha](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/giovanni_cunha/32/6942_2.png) [@Giovanni\_Cunha](https://discourse.slicer.org/u/Giovanni_Cunha)\
**Post date:** [March 8, 2021, 4:35pm UTC](https://discourse.slicer.org/t/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/10444/34 "2021-03-08T16:35:24Z")

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Thank you Mr Iasson

**See explanation of all parameters [here]**([GitHub - lassoan/SlicerSegmentMesher: Create volumetric mesh from segmentation using Cleaver2 or TetGen](https://github.com/lassoan/SlicerSegmentMesher#mesh-generation-parameters)).

I am sorry, unfortunatelly the name of the parameters are different from Slicer, for example the **advanced options** (where the parameters are) has a different name

 ![advanced option](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/2/024a4581f673692925df044a6704495b5719287f.jpeg)

```auto
Advanced:
  -b [--background_mesh] arg input background mesh
  -I [--indicator_functions] the input files are indicator functions (boundary is defined as isosurface
                                     where image value = 0)
  -z [--sizing_field] arg sizing field path (use precomputed sizing field for adaptive mode)
  -w [--write_background_mesh] write background mesh
  --simple use simple interface approximation
  -j [--fix_tet_windup] ensure positive Jacobians with proper vertex wind-up
                                     (prevents inside-out tetrahedra in the output mesh)
                                     This flag is specified by SlicerSegmentMesher module, no need to specify it as additional option.
  -e [--strip_exterior] strip exterior tetrahedra (remove temporary elements that are added to make the volume cubic)
                                     This flag is specified by SlicerSegmentMesher module, no need to specify it as additional option.

```

I can presume that Slicer uses the Cleaver, but I was not able to identify the name of the parameters in the code above. Could you help me?

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<div class="post-metadata">

**Author:** ![Giovanni\_Cunha](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/giovanni_cunha/32/6942_2.png) [@Giovanni\_Cunha](https://discourse.slicer.org/u/Giovanni_Cunha)\
**Post date:** [March 8, 2021, 4:43pm UTC](https://discourse.slicer.org/t/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/10444/35 "2021-03-08T16:43:36Z")

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> or assign CT density to each mesh point (using Probe volume with model module) and then use that information in your preprocessor.

Where can I find this tool? I was looking for in the Models module but I did not find (photo)

 ![Models module](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/6/26b2e287ec904f76201861542e7fe5e2c9eca84b.jpeg)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 8, 2021, 4:45pm UTC](https://discourse.slicer.org/t/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/10444/36 "2021-03-08T16:45:56Z")

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> [@Giovanni\_Cunha](#):
>
> I am sorry, unfortunatelly the name of the parameters are different from Slicer, for example the **advanced options** (where the parameters are) has a different name

Adaptive mesh sizing is essentially controlled by 3 parameters, so you should be able to find which one is which.

Please use latest Slicer Stable Release. It exposes some more parameters, and the GUI contains a bit more explanations.

> [@Giovanni\_Cunha](#):
>
> > or assign CT density to each mesh point (using Probe volume with model module) and then use that information in your preprocessor.
> 
> Where can I find this tool? I was looking for in the Models module but I did not find (photo)

You can click the search icon in the module toolbar (or hit Ctrl-F) to open the module finder and type `probe`:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/b/8b652f16cf1fde7ce7a056a193a8896b21450045.png)

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<div class="post-metadata">

**Author:** ![Giovanni\_Cunha](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/giovanni_cunha/32/6942_2.png) [@Giovanni\_Cunha](https://discourse.slicer.org/u/Giovanni_Cunha)\
**Post date:** [March 8, 2021, 4:54pm UTC](https://discourse.slicer.org/t/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/10444/37 "2021-03-08T16:54:37Z")

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> [@lassoan](#):
>
> Adaptive mesh sizing is essentially controlled by 3 parameters, so you should be able to find which one is which.

OK! thanks. Just to confirm. About The – **scale** – **multiplier** and – **grading**

Scale: If the value increase the mesh improves? If the value decrease the mesh become more coarser?

Multiplier: What is its function? This tool is used to multiplier the value of the Scale?

Grading: What is its function? If the value increases the mesh become more detailed?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 8, 2021, 5:18pm UTC](https://discourse.slicer.org/t/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/10444/38 "2021-03-08T17:18:49Z")

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Multiplier (sampling rate) allows you to skip voxels. Equivalent to downsampling the input volume.

Scaling controls overall output mesh element size.

Grading controls how much the output mesh element size are allowed to change throughout the mesh.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 8, 2021, 5:28pm UTC](https://discourse.slicer.org/t/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/10444/39 "2021-03-08T17:28:12Z")

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You may find the March 15 session of the [FunkyMUG user group](https://github.com/FunkyMUG/FunkyMUG#current-schedule) useful for learning about how to create biomechanical models for FEA.

[Previous page](https://discourse.slicer.org/t/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/10444.md?page=1)