# Virtual septoplasty in 3D slicer

**URL:** <https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [October 25, 2021, 5:24am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329 "2021-10-25T05:24:25Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [October 25, 2021, 5:24am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/1 "2021-10-25T05:24:26Z")

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i am going to make 3D model of nasal airway with 3D slicer ,but from a data of nasal septum deviation i want to make a corrected nasal airway by virtual septoplasty , how i can do that in 3D slicer ?

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**Author:** ![caioath](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/caioath/32/9688_2.png) [@caioath](https://discourse.slicer.org/u/caioath)\
**Post date:** [October 26, 2021, 2:09am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/2 "2021-10-26T02:09:54Z")

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That might be hard because the septal deviation is only part of the asymmetry.

You may be able to erase the septum through segmenting it and masking the volume with air intensity. Then you create a new septum (again through segmentation + mask volume). But you will probably face difficulties in creating the new (straight) nasal septum because the turbinates and other structures might be in your way.

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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 26, 2021, 2:06pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/3 "2021-10-26T14:06:11Z")

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You can use landmark-based warping to simulate soft-tissue deformations using Fiducial Registration Wizard. You can specify non-deforming regions and points that are displaced and the module computes a smooth displacement field. See step-by-step instructions in this video:

[![](https://img.youtube.com/vi/GfDDQykH1iY/maxresdefault.jpg "Soft tissue deformation simulation") ](https://www.youtube.com/watch?v=GfDDQykH1iY)

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<div class="post-metadata">

**Author:** ![caioath](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/caioath/32/9688_2.png) [@caioath](https://discourse.slicer.org/u/caioath)\
**Post date:** [October 26, 2021, 6:54pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/4 "2021-10-26T18:54:00Z")

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That is amazing. Thanks!  
Will try on my dataset.

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [October 27, 2021, 12:56am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/5 "2021-10-27T00:56:51Z")

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Thank you very much, I will try this method

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [October 28, 2021, 3:07pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/6 "2021-10-28T15:07:32Z")

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is it possible to reduce septal thickness?

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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 28, 2021, 3:09pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/7 "2021-10-28T15:09:24Z")

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Yes, you can do that by placing two series of points along the septum (on both sides). If you move those points closer to each other then the septal thickness will be reduced.

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [October 29, 2021, 12:36am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/8 "2021-10-29T00:36:56Z")

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Thanks a lot for your answer .

is there any method where i can compare with the dimension of healthy septum and will reduce thickness whenever there is a deviation from healthy one? can i do it simultaneosly in 3d slicer?

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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 29, 2021, 2:42am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/9 "2021-10-29T02:42:44Z")

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You can use markups module’s line tool or specialized extensions (such as BoneThicknessMapping) or custom scripts to measure bone thickness. If you know what is the healthy thickness value then you can use that to compute how much closer you need to move the control points to each other.

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [November 1, 2021, 9:30am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/10 "2021-11-01T09:30:05Z")

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In line tool how can i ensure that whatever line i am drawing is a perfect horizontal line?

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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:** [November 11, 2021, 6:02am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/11 "2021-11-11T06:02:23Z")

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There is no such constraint during point placement, but after you have placed the line endpoints you can go to Markups module / Control points and copy-paste the coordinate values to force points to be on the same slice or line. If you need this frequently then you can automate this using a few lines of Python code.

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [November 11, 2021, 1:45pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/12 "2021-11-11T13:45:05Z")

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Hello , Is there any method where I can export STL file from 3D slicer and process it in other software and again import to 3D slicer?

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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:** [November 11, 2021, 5:17pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/13 "2021-11-11T17:17:06Z")

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Yes, you can save and load STL files in Slicer. Slicer has also a number of segment and surface editing tools. What editing operations would you like to do in the external software?

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [November 11, 2021, 5:20pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/14 "2021-11-11T17:20:14Z")

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Filling some holes , separating the regions for giving inlet ,outlet boundary conditions as As STL becomes a single file it is difficult to separate it

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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:** [November 11, 2021, 6:49pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/15 "2021-11-11T18:49:11Z")

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Filling some holes and maybe also adding inlet/outlet extensions are in Slicer’s scope. You may also generate the volumetric mesh from the segments in Slicer (using SegmentMesher extension).

Then, you use your the FEM modeler’s preprocessing software to specify boundary conditions, loads, material properties, and run the simulation.

You can then load the simulation results (meshes with computed displacements, stresses, etc.) in Slicer for visualization.

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [November 11, 2021, 6:52pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/16 "2021-11-11T18:52:14Z")

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How can I give in let outlet in slicer ?If any such tutorials are there please tell.

Thanks

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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:** [November 11, 2021, 6:55pm UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/17 "2021-11-11T18:55:27Z")

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Do you mean how to add inlet and outlet extensions? You can use “Draw Tube” effect in Segment Editor for this (provided by SegmentEditorExtraEffects extension).

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [November 12, 2021, 5:52am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/18 "2021-11-12T05:52:53Z")

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When I am using draw tube effect, my original segment is being erased , how to handle it?

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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:** [November 12, 2021, 5:57am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/19 "2021-11-12T05:57:54Z")

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You can add flow extensions as separate segments and when everything looks good then you can combine segments using “Logical operators” effect.

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**Author:** ![Sliceeeeee](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sliceeeeee/32/12358_2.png) [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Post date:** [November 12, 2021, 6:20am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329/20 "2021-11-12T06:20:08Z")

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Thank you for your reply , But again I have to make that tube hollow? For air flow simulation?

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