# \#segmentmesher

**URL:** https://discourse.slicer.org/tag/segmentmesher/269.md

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## [How to understand SegmentMesher with Image spacing and Image Dimensions](https://discourse.slicer.org/t/how-to-understand-segmentmesher-with-image-spacing-and-image-dimensions/44632)

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**Author:** [@Shajia\_Ali](https://discourse.slicer.org/u/Shajia_Ali)\
**Replies:** 1\
**Last updated:** [October 2, 2025, 9:10pm UTC](https://discourse.slicer.org/t/how-to-understand-segmentmesher-with-image-spacing-and-image-dimensions/44632 "2025-10-02T21:10:04Z")

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Hello everyone, I am using SegmentMesher for meshing, and so far things are going well. However, I am still trying to understand how image dimensions and voxel spacing influence the element size and the total number of …

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## [SegmentMesher in Slicer 5.2 and 5.3 fail: Error: 'vtkmodules.vtkFiltersCore.vtkThreshold' object has no attribute 'ThresholdByUpper'](https://discourse.slicer.org/t/segmentmesher-in-slicer-5-2-and-5-3-fail-error-vtkmodules-vtkfilterscore-vtkthreshold-object-has-no-attribute-thresholdbyupper/27894)

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**Author:** [@Mat](https://discourse.slicer.org/u/Mat)\
**Replies:** 4\
**Last updated:** [September 26, 2025, 2:15pm UTC](https://discourse.slicer.org/t/segmentmesher-in-slicer-5-2-and-5-3-fail-error-vtkmodules-vtkfilterscore-vtkthreshold-object-has-no-attribute-thresholdbyupper/27894 "2025-09-26T14:15:23Z")

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Operating system: Windows 11 Slicer version: 5.3 Expected behavior: complete successfully Actual behavior: fails I’m trying to create a volume mesh using segmentMesher and it keeps failing: Generating volumetric mes…

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## [Convert file of .vtk of Segment Mesher](https://discourse.slicer.org/t/convert-file-of-vtk-of-segment-mesher/37351)

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**Author:** [@khajta](https://discourse.slicer.org/u/khajta)\
**Replies:** 4\
**Last updated:** [July 14, 2024, 3:57am UTC](https://discourse.slicer.org/t/convert-file-of-vtk-of-segment-mesher/37351 "2024-07-14T03:57:53Z")

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I am a new of using Segment Mesher and mesh phantom. I can export the segmented organ using Cleaver method and save as .vtk. However, the input for phits program need .node and .ele. How to convert this file?

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## [Best Practices for Segment Mesher, Cleaver](https://discourse.slicer.org/t/best-practices-for-segment-mesher-cleaver/10796)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 3\
**Last updated:** [April 20, 2024, 3:47pm UTC](https://discourse.slicer.org/t/best-practices-for-segment-mesher-cleaver/10796 "2024-04-20T15:47:12Z")

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Hello, Our team is trying to use the segment mesher extension on a multi-material model of breast tissue, segmented from an MRI dataset. We are having great success, but still have some questions related to best practic…

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## [IA-FEMesh extension for Abaqus](https://discourse.slicer.org/t/ia-femesh-extension-for-abaqus/13317)

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**Author:** [@nithin](https://discourse.slicer.org/u/nithin)\
**Replies:** 14\
**Last updated:** [September 1, 2023, 9:13pm UTC](https://discourse.slicer.org/t/ia-femesh-extension-for-abaqus/13317 "2023-09-01T21:13:59Z")

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Dear all, I am trying to apply material mapping to the vertebral model and analyze in Abaqus. I exported image data and surface model (.stl) from the 3D slicer, but when the same are imported IA-FEMesh, there is no over…

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## [SegmentMesher, Error: Command 'cleaver-cli.exe' returned non-zero exit status 3221226505](https://discourse.slicer.org/t/segmentmesher-error-command-cleaver-cli-exe-returned-non-zero-exit-status-3221226505/31172)

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**Author:** [@Mehdi\_Khamesi](https://discourse.slicer.org/u/Mehdi_Khamesi)\
**Replies:** 7\
**Last updated:** [August 20, 2023, 6:39pm UTC](https://discourse.slicer.org/t/segmentmesher-error-command-cleaver-cli-exe-returned-non-zero-exit-status-3221226505/31172 "2023-08-20T18:39:01Z")

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Operating system: Windows 10 Slicer version: 5.2.2 Expected behavior: Creating volumetric mesh Actual behavior: Error: Command ‘cleaver-cli.exe’ returned non-zero exit status 3221226505 Hello everyone, I have a Segm…

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## [Error of cleaver while using segmentmesher](https://discourse.slicer.org/t/error-of-cleaver-while-using-segmentmesher/16128)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 6\
**Last updated:** [February 22, 2021, 10:42pm UTC](https://discourse.slicer.org/t/error-of-cleaver-while-using-segmentmesher/16128 "2021-02-22T22:42:38Z")

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Hello all, I am trying to mesh my model using segmentmesher (cleaver). When the resolution of model is high, I can do meshing without any problems; however, when I decrease the resolution of my segmentations, I get an e…

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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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## [How to export segments as \*multimaterial\* model in SegmentMesher extension?](https://discourse.slicer.org/t/how-to-export-segments-as-multimaterial-model-in-segmentmesher-extension/25598)

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**Author:** [@SlicerGroupie](https://discourse.slicer.org/u/SlicerGroupie)\
**Replies:** 1\
**Last updated:** [October 7, 2022, 7:21pm UTC](https://discourse.slicer.org/t/how-to-export-segments-as-multimaterial-model-in-segmentmesher-extension/25598 "2022-10-07T19:21:42Z")

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Hello, We have 4 segments of the cerebrum. When we export them as a model, it works, but it exports as a single material model (where the four segments get fused into one large mesh). But we want to export it as a mult…

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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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## [Segmentation from point cloud](https://discourse.slicer.org/t/segmentation-from-point-cloud/22843)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 1\
**Last updated:** [April 6, 2022, 5:24am UTC](https://discourse.slicer.org/t/segmentation-from-point-cloud/22843 "2022-04-06T05:24:32Z")

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Dear Andras, I have .vtk a surface mesh, which I generated using pyvista using cloud of points. I could not see .vtk in slicer but I can see in paraview and I convert it into vtp and now ican see the file in slicer. I …

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## [Smoothening of a volumetric mesh created by SegmentMesher and changed by applying DVF](https://discourse.slicer.org/t/smoothening-of-a-volumetric-mesh-created-by-segmentmesher-and-changed-by-applying-dvf/22757)

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**Author:** [@BraveDistribution](https://discourse.slicer.org/u/BraveDistribution)\
**Replies:** 3\
**Last updated:** [March 31, 2022, 2:00pm UTC](https://discourse.slicer.org/t/smoothening-of-a-volumetric-mesh-created-by-segmentmesher-and-changed-by-applying-dvf/22757 "2022-03-31T14:00:50Z")

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Hello, I face a problem that after transforming mesh created by SegmentMesher with transform obtained by elastix registration, mesh is heavily deformed and yielding weird outliers, see following image: The registrat…

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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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## [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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## [Problem with volumetric mesh](https://discourse.slicer.org/t/problem-with-volumetric-mesh/18881)

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**Author:** [@rcapozza](https://discourse.slicer.org/u/rcapozza)\
**Replies:** 5\
**Last updated:** [July 23, 2021, 5:03pm UTC](https://discourse.slicer.org/t/problem-with-volumetric-mesh/18881 "2021-07-23T17:03:50Z")

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Hi guys. I’ve a series of ct-scans images of a central part of human tibia, this was obtained with a Stratec pQCT machine and exported in jpg format, named accordingly, for perform later import in Slicer software. Once …

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## [Interactively change the nodes of mesh](https://discourse.slicer.org/t/interactively-change-the-nodes-of-mesh/18361)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 8\
**Last updated:** [June 29, 2021, 2:33pm UTC](https://discourse.slicer.org/t/interactively-change-the-nodes-of-mesh/18361 "2021-06-29T14:33:51Z")

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Hello all, Consider a mesh that is created with the segmentmesher module. For some reason, I want to change the locations of a few nodes in the created volumetric mesh to make my mesh more smooth. How can I do it? Is it…

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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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## [Get cell indices in exported mesh corresponding to each segment](https://discourse.slicer.org/t/get-cell-indices-in-exported-mesh-corresponding-to-each-segment/15437)

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**Author:** [@Elijah\_Alexson](https://discourse.slicer.org/u/Elijah_Alexson)\
**Replies:** 14\
**Last updated:** [January 13, 2021, 7:00pm UTC](https://discourse.slicer.org/t/get-cell-indices-in-exported-mesh-corresponding-to-each-segment/15437 "2021-01-13T19:00:14Z")

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Dear 3D Slicer Team, I have generated a volumetric heart mesh and now need to extract certain geometry information, that is I want to export indices of nodes on the epicardium, indices of nodes on the left ventricular s…

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## [Problem in using segmentmesher](https://discourse.slicer.org/t/problem-in-using-segmentmesher/14261)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 11\
**Last updated:** [October 28, 2020, 1:37am UTC](https://discourse.slicer.org/t/problem-in-using-segmentmesher/14261 "2020-10-28T01:37:41Z")

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Hello, I encountered a problem while using segmentmesher. I used slicer 4.10.1 in the past and now I am moving to the newest stable version. I found that the segmentmesher in the previous version needs considerably less…

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## [Meshing a model with different parts](https://discourse.slicer.org/t/meshing-a-model-with-different-parts/14168)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 14\
**Last updated:** [October 24, 2020, 1:18am UTC](https://discourse.slicer.org/t/meshing-a-model-with-different-parts/14168 "2020-10-24T01:18:15Z")

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Hello all, Considering a segmented model that includes different parts (bones, ligaments, etc.). In FEM, we may need to have a fine mesh for some parts of the model and a coarse mesh for other parts (for example fine me…

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## [Element sizes in segmentmesher](https://discourse.slicer.org/t/element-sizes-in-segmentmesher/14083)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 0\
**Last updated:** [October 16, 2020, 5:14pm UTC](https://discourse.slicer.org/t/element-sizes-in-segmentmesher/14083 "2020-10-16T17:14:01Z")

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Hello all, I am using the segmentmesher to create a volumetric mesh. However, the generated meshes do not look fine to me; at some parts the mesh is coarse and at some parts, it is very fine. I tried to play with segmen…

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## [Segment-Meshing multiple segments](https://discourse.slicer.org/t/segment-meshing-multiple-segments/13595)

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**Author:** [@Shajia\_Ali](https://discourse.slicer.org/u/Shajia_Ali)\
**Replies:** 10\
**Last updated:** [September 30, 2020, 8:04am UTC](https://discourse.slicer.org/t/segment-meshing-multiple-segments/13595 "2020-09-30T08:04:52Z")

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Hi, I discovered segment-mesher quite recently and my goal is to create a mesh of a nutshell and the vascular bundles within it. My attempt is to have two meshes. One for the shell (with holes) and one only for the vasc…

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## [Error when using segmentmesher](https://discourse.slicer.org/t/error-when-using-segmentmesher/10509)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 4\
**Last updated:** [March 5, 2020, 4:29pm UTC](https://discourse.slicer.org/t/error-when-using-segmentmesher/10509 "2020-03-05T16:29:36Z")

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Hello all, I got the following error when I want to mesh my segmentations in segmentmesher: ./config/NA-MIC/Extensions-28797/SegmentMesher/lib/Slicer-4.11/qt-scripted-modules/SegmentMesher.py", line 296, in onApplyButt…