# \#meshing

**URL:** https://discourse.slicer.org/tag/meshing/349.md

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## [Blood Vessel stl. model shows error when I used mesh in Ansys Fluent](https://discourse.slicer.org/t/blood-vessel-stl-model-shows-error-when-i-used-mesh-in-ansys-fluent/35254)

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**Author:** [@Reasat\_E\_Noor](https://discourse.slicer.org/u/Reasat_E_Noor)\
**Replies:** 0\
**Last updated:** [April 3, 2024, 12:48pm UTC](https://discourse.slicer.org/t/blood-vessel-stl-model-shows-error-when-i-used-mesh-in-ansys-fluent/35254 "2024-04-03T12:48:28Z")

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I have segmented a bifurcated small artery from Brain MRI . When I import the stl model in Ansys fluent the meshing cannot be done. I want to do a cfd simulation for my research. How to solve the issue? Please help!

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## [Merging masks of nifti format and assigning conductivities to each](https://discourse.slicer.org/t/merging-masks-of-nifti-format-and-assigning-conductivities-to-each/34401)

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**Author:** [@savvy73](https://discourse.slicer.org/u/savvy73)\
**Replies:** 3\
**Last updated:** [February 21, 2024, 3:17am UTC](https://discourse.slicer.org/t/merging-masks-of-nifti-format-and-assigning-conductivities-to-each/34401 "2024-02-21T03:17:44Z")

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Hi, I have masks of different regions of brain in niftii format. I want to combine all the masks and assign conductivities to the same after which I need to mesh the output. I wanted to know if it can be done using 3D sl…

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## [180 degree Flip in STL/PLY when imported](https://discourse.slicer.org/t/180-degree-flip-in-stl-ply-when-imported/33447)

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**Author:** [@Vignesh\_Chakravarthy](https://discourse.slicer.org/u/Vignesh_Chakravarthy)\
**Replies:** 2\
**Last updated:** [December 19, 2023, 6:33pm UTC](https://discourse.slicer.org/t/180-degree-flip-in-stl-ply-when-imported/33447 "2023-12-19T18:33:32Z")

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Hi, I am using Slicer 5.2.2. I have saved lesions and prostate from Ultrasound as landmarks in slicer. Then, imported landmarks into MATLAB for non-rigid registration. I converted them to ply/stl from pointcloud after t…

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## [FEbio reading 0 elements for Segment Mesher vtk file](https://discourse.slicer.org/t/febio-reading-0-elements-for-segment-mesher-vtk-file/28600)

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**Author:** [@fea\_99](https://discourse.slicer.org/u/fea_99)\
**Replies:** 2\
**Last updated:** [March 29, 2023, 3:09pm UTC](https://discourse.slicer.org/t/febio-reading-0-elements-for-segment-mesher-vtk-file/28600 "2023-03-29T15:09:11Z")

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Apologies, this question may be better for the FEbio community, but I am currently awaiting approval to access their support forum. Essentially I created a mesh using segment mesher (cleaver) of a vertebrae. I then expo…

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## [Building just the meshing code](https://discourse.slicer.org/t/building-just-the-meshing-code/28121)

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**Author:** [@cesss](https://discourse.slicer.org/u/cesss)\
**Replies:** 0\
**Last updated:** [March 1, 2023, 5:37pm UTC](https://discourse.slicer.org/t/building-just-the-meshing-code/28121 "2023-03-01T17:37:33Z")

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I’m interested in using the VMTK meshing code for my own CFD project. Is there any build procedure for building only the meshing code, and perhaps limiting the required dependencies to just the ones needed by the meshing…

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## [WrapSolidify is amazing for preprocessing before volumetric mesh generation](https://discourse.slicer.org/t/wrapsolidify-is-amazing-for-preprocessing-before-volumetric-mesh-generation/25961)

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**Author:** [@avarghes24](https://discourse.slicer.org/u/avarghes24)\
**Replies:** 1\
**Last updated:** [October 29, 2022, 5:58am UTC](https://discourse.slicer.org/t/wrapsolidify-is-amazing-for-preprocessing-before-volumetric-mesh-generation/25961 "2022-10-29T05:58:32Z")

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Sorry I just realized I never responded to this. I was able to segment out the entire hip joint from the sample abdomen/pelvis CT in Slicer. Previously, I was trying to run TetGen in FeBioStudio and it kept on failing be…

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## [How to generate a surface mesh from segmentation](https://discourse.slicer.org/t/how-to-generate-a-surface-mesh-from-segmentation/24751)

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**Author:** [@joanne40226](https://discourse.slicer.org/u/joanne40226)\
**Replies:** 7\
**Last updated:** [August 17, 2022, 5:19am UTC](https://discourse.slicer.org/t/how-to-generate-a-surface-mesh-from-segmentation/24751 "2022-08-17T05:19:57Z")

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Hi, recently i’m building mesh from segmetation. However i only need the informations of the voxel/vertex on the surface. So, i’m wondering if there is a way to only generate surface mesh from a segmented 3D model? Than…

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## [Need help making a 3D mesh given co-ordinates of the vertices and vertex indices of each face for 3D Slicer - trimesh/vtkwrite/etc](https://discourse.slicer.org/t/need-help-making-a-3d-mesh-given-co-ordinates-of-the-vertices-and-vertex-indices-of-each-face-for-3d-slicer-trimesh-vtkwrite-etc/24536)

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**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 2\
**Last updated:** [July 28, 2022, 3:19pm UTC](https://discourse.slicer.org/t/need-help-making-a-3d-mesh-given-co-ordinates-of-the-vertices-and-vertex-indices-of-each-face-for-3d-slicer-trimesh-vtkwrite-etc/24536 "2022-07-28T15:19:45Z")

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Hi all, Given the following data: The Cartesian co-ordinates of the vertices in the surface mesh: n vertices x 3 The vertex indices of each face in the surface mesh: n faces x 3 I’m trying to make some 3D file that I…

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## [Segmentation to CFD Mesh](https://discourse.slicer.org/t/segmentation-to-cfd-mesh/23693)

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**Author:** [@Elias\_Karabelas](https://discourse.slicer.org/u/Elias_Karabelas)\
**Replies:** 5\
**Last updated:** [June 20, 2022, 2:44pm UTC](https://discourse.slicer.org/t/segmentation-to-cfd-mesh/23693 "2022-06-20T14:44:59Z")

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Hey there, I have a question concerning the transition from segmentation to meshing. I managed to segment some coronary arteries with the aorta and also have the centerline in there (see my slicer screenshot) In a n…

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## [myvmtkmeshDlabeling](https://discourse.slicer.org/t/myvmtkmeshdlabeling/22959)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 2\
**Last updated:** [April 14, 2022, 5:51pm UTC](https://discourse.slicer.org/t/myvmtkmeshdlabeling/22959 "2022-04-14T17:51:20Z")

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I’m working with macOS operating system on mac with M1 processor. I’m having problems in order to obtain a meshDxx.vtu (starting from 2 files meshR.vtu and Dxx.mhd) which associates the values of the tensor built in Dxx…

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## [Problem with myvmtkmeshDlabeling](https://discourse.slicer.org/t/problem-with-myvmtkmeshdlabeling/22953)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 0\
**Last updated:** [April 13, 2022, 10:09pm UTC](https://discourse.slicer.org/t/problem-with-myvmtkmeshdlabeling/22953 "2022-04-13T22:09:08Z")

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I’m working with macOS operating system on mac with M1 processor. I’m having problems in order to obtain a meshDxx.vtu (starting from 2 files meshR.vtu and Dxx.mhd) which associates the values of the tensor built in Dxx…

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## [creating an unstructured grid (ascii) with surface elements, volume and points](https://discourse.slicer.org/t/creating-an-unstructured-grid-ascii-with-surface-elements-volume-and-points/22459)

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**Author:** [@oliver\_gruhn](https://discourse.slicer.org/u/oliver_gruhn)\
**Replies:** 1\
**Last updated:** [March 13, 2022, 5:40am UTC](https://discourse.slicer.org/t/creating-an-unstructured-grid-ascii-with-surface-elements-volume-and-points/22459 "2022-03-13T05:40:11Z")

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Dear Slicer Team, dear Slicer community i am working on a monte carlo simulation on soft tissue analysis including Slicer. For the last weeks I tried to find a solution for the upcoming issue that I hope you can help m…

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## [Generating surface triangulation (mesh) based on sequence of segmentation](https://discourse.slicer.org/t/generating-surface-triangulation-mesh-based-on-sequence-of-segmentation/22324)

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**Author:** [@BraveDistribution](https://discourse.slicer.org/u/BraveDistribution)\
**Replies:** 3\
**Last updated:** [March 10, 2022, 12:03am UTC](https://discourse.slicer.org/t/generating-surface-triangulation-mesh-based-on-sequence-of-segmentation/22324 "2022-03-10T00:03:30Z")

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Hi all, I have a motion dataset tracking liver with segmentation available throughout the whole sequence. I’d like to generate a mesh from the first segmentation and then continuously deform it throughout the time. Of c…

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## [Visualize the difference between two meshes](https://discourse.slicer.org/t/visualize-the-difference-between-two-meshes/20729)

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**Author:** [@suranga](https://discourse.slicer.org/u/suranga)\
**Replies:** 1\
**Last updated:** [November 23, 2021, 7:07am UTC](https://discourse.slicer.org/t/visualize-the-difference-between-two-meshes/20729 "2021-11-23T07:07:31Z")

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I have two volumetric liver meshes in .vtk format (i.e. ground-truth and predicted versions) and I want to plot the error i.e., for example, the difference between the ground-truth and the predicted liver meshes on the p…

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## [How to save labelmap information in a volumetric mesh?](https://discourse.slicer.org/t/how-to-save-labelmap-information-in-a-volumetric-mesh/19163)

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**Author:** [@Matheus](https://discourse.slicer.org/u/Matheus)\
**Replies:** 5\
**Last updated:** [August 17, 2021, 6:01pm UTC](https://discourse.slicer.org/t/how-to-save-labelmap-information-in-a-volumetric-mesh/19163 "2021-08-17T18:01:13Z")

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Hello everyone! I segmented some DICOM files and turned the segmentation into a volumetric mesh. I have different segments for different biological tissues and I want to store the segment ID information after transformi…

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## [How to read a volumetric mesh in python?](https://discourse.slicer.org/t/how-to-read-a-volumetric-mesh-in-python/18974)

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**Author:** [@Matheus](https://discourse.slicer.org/u/Matheus)\
**Replies:** 2\
**Last updated:** [August 2, 2021, 6:17pm UTC](https://discourse.slicer.org/t/how-to-read-a-volumetric-mesh-in-python/18974 "2021-08-02T18:17:17Z")

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Hello everyone! I segmented some DICOM files and turned the segmentation into a volumetric mesh. I want to read and plot this file correctly in python. Can you tell me how to do this the best way without losing informat…

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## [Issue with Mesh to Label Map](https://discourse.slicer.org/t/issue-with-mesh-to-label-map/17875)

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**Author:** [@quan](https://discourse.slicer.org/u/quan)\
**Replies:** 2\
**Last updated:** [June 1, 2021, 5:18am UTC](https://discourse.slicer.org/t/issue-with-mesh-to-label-map/17875 "2021-06-01T05:18:30Z")

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I’m trying to generate a SPHARM-PDM mesh from a .stl file. I imported the .stl and used “Mesh to Label Map” to obtain the .nrrd. However, the .nrrd is inverted (the white space are supposed to be black and vice versa). T…

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## [Volumetric mesh of vertebrae - difficulty with meshing the interior](https://discourse.slicer.org/t/volumetric-mesh-of-vertebrae-difficulty-with-meshing-the-interior/17376)

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**Author:** [@michxu98](https://discourse.slicer.org/u/michxu98)\
**Replies:** 12\
**Last updated:** [April 30, 2021, 7:19pm UTC](https://discourse.slicer.org/t/volumetric-mesh-of-vertebrae-difficulty-with-meshing-the-interior/17376 "2021-04-30T19:19:06Z")

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Hello, I am trying to obtain a volumetric mesh of a single vertebrae from a segmentation as seen here: I have separated one vertebrae into its own segmentation by copying the segment from the main segmentation. So …

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## [Volume mesh with uniform element size](https://discourse.slicer.org/t/volume-mesh-with-uniform-element-size/17319)

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**Author:** [@michxu98](https://discourse.slicer.org/u/michxu98)\
**Replies:** 1\
**Last updated:** [April 26, 2021, 1:45am UTC](https://discourse.slicer.org/t/volume-mesh-with-uniform-element-size/17319 "2021-04-26T01:45:05Z")

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Hello, I am trying to generate a volume mesh with uniform element size from a segmentation using Cleaver in the Segment Mesher module, however the output mesh does not seem to have uniform element sizes: Slicer vers…

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## [What finite element systems do you use with Slicer?](https://discourse.slicer.org/t/what-finite-element-systems-do-you-use-with-slicer/17278)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 4\
**Last updated:** [April 23, 2021, 10:07pm UTC](https://discourse.slicer.org/t/what-finite-element-systems-do-you-use-with-slicer/17278 "2021-04-23T22:07:21Z")

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Hi - We are doing large deformation mechanical simulation project that currently uses matlab and comsol and would like to switch to something more Slicer-like (free, python-based, extendable, etc). What packages have p…

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## [Voxelization of mesh](https://discourse.slicer.org/t/voxelization-of-mesh/4942)

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**Author:** [@zjx1805](https://discourse.slicer.org/u/zjx1805)\
**Replies:** 13\
**Last updated:** [February 9, 2021, 11:40am UTC](https://discourse.slicer.org/t/voxelization-of-mesh/4942 "2021-02-09T11:40:30Z")

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Is there a way in 3D Slicer to voxelize a 3D mesh (preferably through python interpreter)? I would also like to be able to specify the voxel size and shape, if possible. BTW, my complete mesh consists of 100+ separate .v…

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## [Wrong face normals after Mesh conversion (OpenFOAM)](https://discourse.slicer.org/t/wrong-face-normals-after-mesh-conversion-openfoam/15738)

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**Author:** [@haontaler](https://discourse.slicer.org/u/haontaler)\
**Replies:** 3\
**Last updated:** [January 30, 2021, 5:58pm UTC](https://discourse.slicer.org/t/wrong-face-normals-after-mesh-conversion-openfoam/15738 "2021-01-30T17:58:30Z")

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Hello everyone, I am not sure if this is the correct forum to post questions about VMTK mesh generation and conversion as it is not available in Slicer directly afaik. But I hope that you can still give me a hint to sol…

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## [Meshing: Self-intersecting faces](https://discourse.slicer.org/t/meshing-self-intersecting-faces/13588)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 13\
**Last updated:** [October 2, 2020, 1:25am UTC](https://discourse.slicer.org/t/meshing-self-intersecting-faces/13588 "2020-10-02T01:25:13Z")

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Hello, These question may be a little outside the realm of Slicer, but it never hurts to ask! Our team has been using Cleaver to create some amazing multi-material, conforming meshes. However, we have found mesh qualit…

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## [Voxel-based finite element modeling](https://discourse.slicer.org/t/voxel-based-finite-element-modeling/11223)

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**Author:** [@Vasyl](https://discourse.slicer.org/u/Vasyl)\
**Replies:** 6\
**Last updated:** [April 24, 2020, 12:32am UTC](https://discourse.slicer.org/t/voxel-based-finite-element-modeling/11223 "2020-04-24T00:32:19Z")

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Hy everybody! I’m only a beginner in segmentation and meshing models and I have one precise question: how can I create voxel-based FE model. I’ve already read some articles dedicated to this topic (GitHub - lassoan/Sli…

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## [Mesh multiple objects](https://discourse.slicer.org/t/mesh-multiple-objects/10384)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 11\
**Last updated:** [March 2, 2020, 9:03pm UTC](https://discourse.slicer.org/t/mesh-multiple-objects/10384 "2020-03-02T21:03:40Z")

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Hello all, I have multiple parts of an organ (which are in contact with each other) and I want to mesh them in a way that they be conformal (having same nodes on their contact region). I can generate separate meshes for…

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## [Runtime of SegmentMesher](https://discourse.slicer.org/t/runtime-of-segmentmesher/10193)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 2\
**Last updated:** [February 11, 2020, 1:50am UTC](https://discourse.slicer.org/t/runtime-of-segmentmesher/10193 "2020-02-11T01:50:09Z")

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Hello all, Is there any way to speed up generating mesh using SegmentMesher? Is it possible to use GPU for these calculations or is it possible to run in parallel? or are there any other suggestions? Thanks for your h…

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## [Meshing separate parts in SegmentMesher](https://discourse.slicer.org/t/meshing-separate-parts-in-segmentmesher/10188)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 5\
**Last updated:** [February 10, 2020, 6:42pm UTC](https://discourse.slicer.org/t/meshing-separate-parts-in-segmentmesher/10188 "2020-02-10T18:42:57Z")

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Hello all, I use SegmentMesher to mesh two segments that are in contact with each other. The slicer gives me just one vtk file (for both segments). I know that I have to use codes such as meshio to convert these files i…

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## [Save Mesh VTK without Cleaver Background Mesh](https://discourse.slicer.org/t/save-mesh-vtk-without-cleaver-background-mesh/9767)

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**Author:** [@lausiv](https://discourse.slicer.org/u/lausiv)\
**Replies:** 3\
**Last updated:** [January 14, 2020, 5:41am UTC](https://discourse.slicer.org/t/save-mesh-vtk-without-cleaver-background-mesh/9767 "2020-01-14T05:41:15Z")

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Would you Know How to eliminate Box(Background) Mesh on the Cleaver when saving VTK file? or mesh generating parameter

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## [FEM Mesh Analysis & Visualization in Model Module](https://discourse.slicer.org/t/fem-mesh-analysis-visualization-in-model-module/9376)

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**Author:** [@lausiv](https://discourse.slicer.org/u/lausiv)\
**Replies:** 37\
**Last updated:** [December 18, 2019, 1:50am UTC](https://discourse.slicer.org/t/fem-mesh-analysis-visualization-in-model-module/9376 "2019-12-18T01:50:35Z")

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FEM Mesh Analysis & Visualization in Model Module (refers below picture :-)) in other words, for example. each mesh, i want to calculate mesh volume and display different color corresponding to the volume.