# VMTK

**URL:** https://discourse.slicer.org/c/community/vmtk/28.md?page=4

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

**Page:** 5

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## [Vmtkmarchingcubes error No Image](https://discourse.slicer.org/t/vmtkmarchingcubes-error-no-image/20789)

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**Author:** [@Lottep](https://discourse.slicer.org/u/Lottep)\
**Replies:** 4\
**Last updated:** [November 26, 2021, 5:40pm UTC](https://discourse.slicer.org/t/vmtkmarchingcubes-error-no-image/20789 "2021-11-26T17:40:00Z")

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Hello everyone, I am a new user of VMTK and I have finished multiple tutorials to get familiar with the software. Now I wanted to use VMTK for my own data, I have read in the dcm file and performed levelsetsegmentation.…

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## [vmtkimagefeatures](https://discourse.slicer.org/t/vmtkimagefeatures/20652)

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**Author:** [@biplabketan](https://discourse.slicer.org/u/biplabketan)\
**Replies:** 0\
**Last updated:** [November 17, 2021, 5:39am UTC](https://discourse.slicer.org/t/vmtkimagefeatures/20652 "2021-11-17T05:39:56Z")

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Please let me know the correct parameter settings for vmtkimagefeatures for coronary artery segmentation from dicom.

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## [Morphological changes analysis](https://discourse.slicer.org/t/morphological-changes-analysis/20624)

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**Author:** [@SPoloni](https://discourse.slicer.org/u/SPoloni)\
**Replies:** 5\
**Last updated:** [November 16, 2021, 9:20pm UTC](https://discourse.slicer.org/t/morphological-changes-analysis/20624 "2021-11-16T21:20:34Z")

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Hi all! I want to study the morphological changes on 2 models of the same vascular district acquired in time. After the registration and the computation of the distances between the two models, give a point on the centr…

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## [Extra or missing triangle with vmtksurfaceendclipper script](https://discourse.slicer.org/t/extra-or-missing-triangle-with-vmtksurfaceendclipper-script/20530)

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**Author:** [@Antoine\_Mathieu](https://discourse.slicer.org/u/Antoine_Mathieu)\
**Replies:** 3\
**Last updated:** [November 10, 2021, 4:52pm UTC](https://discourse.slicer.org/t/extra-or-missing-triangle-with-vmtksurfaceendclipper-script/20530 "2021-11-10T16:52:59Z")

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Dear all, I am using the vmtksurfaceendclipper script to clip the extremities of a segmentation and the output surface often contains either an extra or missing triangle part: vmtksurfaceendclipper -ifile "C:/temp/debu…

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## [Mean radius per branch + plot radius along branch](https://discourse.slicer.org/t/mean-radius-per-branch-plot-radius-along-branch/20399)

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**Author:** [@ames](https://discourse.slicer.org/u/ames)\
**Replies:** 2\
**Last updated:** [November 10, 2021, 3:23pm UTC](https://discourse.slicer.org/t/mean-radius-per-branch-plot-radius-along-branch/20399 "2021-11-10T15:23:09Z")

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Dear all, I am processing a surface model of the LIMA-LAD bypass in VMTK. I managed to split the domain in separate regions using VMTKBranchExtractor and VMTKBranchClipper, as shown in the figure. For each branch I want…

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## [Centerline bifurcations for multiple inlets](https://discourse.slicer.org/t/centerline-bifurcations-for-multiple-inlets/20444)

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**Author:** [@som1197](https://discourse.slicer.org/u/som1197)\
**Replies:** 10\
**Last updated:** [November 8, 2021, 10:40pm UTC](https://discourse.slicer.org/t/centerline-bifurcations-for-multiple-inlets/20444 "2021-11-08T22:40:33Z")

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Hello, I had some issues with the blanking array which is not generated correctly when multiple inlet branches are present. Consider the following example: I have 2 inputs coming from the left and right vertebral arter…

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## [Vmtkflowextensions](https://discourse.slicer.org/t/vmtkflowextensions/19656)

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**Author:** [@ames](https://discourse.slicer.org/u/ames)\
**Replies:** 1\
**Last updated:** [November 4, 2021, 9:10pm UTC](https://discourse.slicer.org/t/vmtkflowextensions/19656 "2021-11-04T21:10:04Z")

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I am using vmtkflowextensions to add short flow extensions to the inlet and outlets of my 3D model. In the attached screencapture it can be seen that the flow extension does not fit nicely to the domain. vmtksurfacer…

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## [Convert VTK model to STL while maintaining GroupIds](https://discourse.slicer.org/t/convert-vtk-model-to-stl-while-maintaining-groupids/20380)

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**Author:** [@ames](https://discourse.slicer.org/u/ames)\
**Replies:** 2\
**Last updated:** [October 27, 2021, 4:42pm UTC](https://discourse.slicer.org/t/convert-vtk-model-to-stl-while-maintaining-groupids/20380 "2021-10-27T16:42:19Z")

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Dear all, I am processing a surface model of the LIMA-LAD bypass in VMTK. I managed to split the domain in separate regions using VMTKBranchExtractor and VMTKBranchClipper, as shown in the figure. In the VTK file format…

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## [vmtkcenterlinesections doesn't work sometime](https://discourse.slicer.org/t/vmtkcenterlinesections-doesnt-work-sometime/18729)

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**Author:** [@Dongwei](https://discourse.slicer.org/u/Dongwei)\
**Replies:** 3\
**Last updated:** [October 22, 2021, 5:56am UTC](https://discourse.slicer.org/t/vmtkcenterlinesections-doesnt-work-sometime/18729 "2021-10-22T05:56:41Z")

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Hi, I am using vmtkcenterlinesections to calculate the cross-sectional area of my vessel. But sometimes the function brokes for certain vessel geometry… It says ‘executing vmtkcenterlinesections’, then directly exit wit…

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## [VMTK compatibility in mac m1](https://discourse.slicer.org/t/vmtk-compatibility-in-mac-m1/19683)

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**Author:** [@Weiqiang\_Liu](https://discourse.slicer.org/u/Weiqiang_Liu)\
**Replies:** 2\
**Last updated:** [September 21, 2021, 9:43pm UTC](https://discourse.slicer.org/t/vmtk-compatibility-in-mac-m1/19683 "2021-09-21T21:43:49Z")

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I use 3D slicer extension VMTK to extract the centerline and do diameter analysis. I use my own STL file and follow the guidelines in youtube. But I got: Failed to compute results: VMTK library is not found. I also trie…

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## [vtkvmtkCenterlineBranchExtractorfunction bug](https://discourse.slicer.org/t/vtkvmtkcenterlinebranchextractorfunction-bug/19761)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 0\
**Last updated:** [September 20, 2021, 2:44pm UTC](https://discourse.slicer.org/t/vtkvmtkcenterlinebranchextractorfunction-bug/19761 "2021-09-20T14:44:53Z")

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hi, i use vtkvmtkCenterlineBranchExtractor to calculate branch centerline,but i find there have bug that is the number of points is different the last offset value and i don’t use the function i can get the same numb…

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## [Add CFD simulation Model in next VMTK Version?](https://discourse.slicer.org/t/add-cfd-simulation-model-in-next-vmtk-version/19602)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 2\
**Last updated:** [September 14, 2021, 2:53am UTC](https://discourse.slicer.org/t/add-cfd-simulation-model-in-next-vmtk-version/19602 "2021-09-14T02:53:20Z")

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hi,i find SimVascular CFD simulation tool from here https://simvascular.github.io/,the solver is svSolver,is there planning to add CFD model in next VMTK Version? thank you

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## [Build and release VMTK via GitHub Actions](https://discourse.slicer.org/t/build-and-release-vmtk-via-github-actions/19574)

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**Author:** [@rupertnash](https://discourse.slicer.org/u/rupertnash)\
**Replies:** 4\
**Last updated:** [September 10, 2021, 9:17am UTC](https://discourse.slicer.org/t/build-and-release-vmtk-via-github-actions/19574 "2021-09-10T09:17:29Z")

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For $reasons I need VMTK available for multiple versions of python. So I created a simple Github workflow to build VTK, ITK, and VMTK and bundle up the binaries. This is here: https://github.com/hemelb-codes/vmtk-build …

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## [Cannot obtain the center line.](https://discourse.slicer.org/t/cannot-obtain-the-center-line/18112)

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**Author:** [@zhang-qiang-github](https://discourse.slicer.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:11pm UTC](https://discourse.slicer.org/t/cannot-obtain-the-center-line/18112 "2021-09-07T19:11:07Z")

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I have two arteries, like: I can obtain the centerline for one artery, but fail for the other one. It failed to obtain the centerline between the two red point. The runni…

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## [Mapping and Patching result have inanition](https://discourse.slicer.org/t/mapping-and-patching-result-have-inanition/18988)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 2\
**Last updated:** [August 31, 2021, 1:17am UTC](https://discourse.slicer.org/t/mapping-and-patching-result-have-inanition/18988 "2021-08-31T01:17:05Z")

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hi,i follow the example of An example: WSS and OSI along a branching vascular district from here:http://www.vmtk.org/tutorials/MappingAndPatching.html,i set params -longitudinalpatchsize 0.5 -circularpatches 12,but the r…

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## [Failed to load VMTK libraries in Vesselness Filtering](https://discourse.slicer.org/t/failed-to-load-vmtk-libraries-in-vesselness-filtering/19367)

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**Author:** [@simone](https://discourse.slicer.org/u/simone)\
**Replies:** 1\
**Last updated:** [August 27, 2021, 1:36am UTC](https://discourse.slicer.org/t/failed-to-load-vmtk-libraries-in-vesselness-filtering/19367 "2021-08-27T01:36:29Z")

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Hi, I am using Slicer 4.11.20210226 on macOS 11.5. I am trying to use Vesselness Filtering but I get the error above. This is the full log: \[DEBUG\]\[Qt\] 26.08.2021 11:07:13 \[\] (unknown:0) - Session start time …: 2021-08-…

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## [Use segmentation from Segment Editor as initialization for Level Set Segmentation](https://discourse.slicer.org/t/use-segmentation-from-segment-editor-as-initialization-for-level-set-segmentation/19329)

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**Author:** [@tossin](https://discourse.slicer.org/u/tossin)\
**Replies:** 2\
**Last updated:** [August 25, 2021, 3:08pm UTC](https://discourse.slicer.org/t/use-segmentation-from-segment-editor-as-initialization-for-level-set-segmentation/19329 "2021-08-25T15:08:54Z")

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From what I can tell, the Level Set Segmentation panel from the Slicer VMTK Extension only allows initialization from scratch using colliding fronts or fast marching. However, I’d like to be able to use Level Set Segmen…

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## [Is there a way to segment stenotic coronary arteries?](https://discourse.slicer.org/t/is-there-a-way-to-segment-stenotic-coronary-arteries/19142)

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**Author:** [@Mattia\_Chiesa](https://discourse.slicer.org/u/Mattia_Chiesa)\
**Replies:** 3\
**Last updated:** [August 11, 2021, 1:44pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-segment-stenotic-coronary-arteries/19142 "2021-08-11T13:44:28Z")

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Dear all, I’d like to automatically segment the three main coronaries (LCA (LDA+LCX) and RCA) feeding DICOM of stenotic patients into 3D slicer. I followed these 2 VMTK tutorials: https://www.youtube.com/watch?v=yi07m…

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## [What should be included in CMakeLists.txt to start a VMTK C++ project?](https://discourse.slicer.org/t/what-should-be-included-in-cmakelists-txt-to-start-a-vmtk-c-project/18734)

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**Author:** [@frankiole](https://discourse.slicer.org/u/frankiole)\
**Replies:** 1\
**Last updated:** [August 10, 2021, 9:01pm UTC](https://discourse.slicer.org/t/what-should-be-included-in-cmakelists-txt-to-start-a-vmtk-c-project/18734 "2021-08-10T21:01:14Z")

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Hi, I am trying to implement VMTK functions in my C++ code. I am able to run my program using both ITK and VTK libraries, however I cannot access VMTK libraries. I’ve already built VMTK, and I’m tweaking my CMakeLists.t…

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## [AbcissaMetric does not write](https://discourse.slicer.org/t/abcissametric-does-not-write/19012)

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**Author:** [@cborras](https://discourse.slicer.org/u/cborras)\
**Replies:** 0\
**Last updated:** [August 1, 2021, 11:40am UTC](https://discourse.slicer.org/t/abcissametric-does-not-write/19012 "2021-08-01T11:40:50Z")

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Operating system: Windows 10 Hi everybody! I am working on aortas and I am using this command for the writing of the angular and abcissa coordinates: #vmtkbranchmetrics -ifile aorta\_clipped.vtp -centerlinesfile Ht\_Lum\_…

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## [How to use VMTKLab CFD model in my project?](https://discourse.slicer.org/t/how-to-use-vmtklab-cfd-model-in-my-project/18848)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 6\
**Last updated:** [July 28, 2021, 7:01pm UTC](https://discourse.slicer.org/t/how-to-use-vmtklab-cfd-model-in-my-project/18848 "2021-07-28T19:01:11Z")

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hi,i want simulation CFD in my project,i find the VMTKLab is suitable,but i don’t know how to use it just like vmtk library?

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## [vmtkMeshGenerator error](https://discourse.slicer.org/t/vmtkmeshgenerator-error/18889)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 2\
**Last updated:** [July 27, 2021, 9:18am UTC](https://discourse.slicer.org/t/vmtkmeshgenerator-error/18889 "2021-07-27T09:18:08Z")

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hi,i use vmtkMeshGenerator to get volume meshing,follow this example:http://www.vmtk.org/tutorials/MeshGeneration.html,but i get the error that is TetGen command line options: pq1.414000q10.000000q165.000000YsT1.000000e-…

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## [Conda install not working due to incompatibilities](https://discourse.slicer.org/t/conda-install-not-working-due-to-incompatibilities/18865)

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**Author:** [@perecanals](https://discourse.slicer.org/u/perecanals)\
**Replies:** 2\
**Last updated:** [July 22, 2021, 9:51am UTC](https://discourse.slicer.org/t/conda-install-not-working-due-to-incompatibilities/18865 "2021-07-22T09:51:42Z")

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Hi, OS: Linux (Ubuntu 20.04.2) I was trying to install VMTK via conda in an already created environment (Python 3.7.10) and I get the following error: Found conflicts! Looking for incompatible packages. This can take …

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## [How to calculate surface length with centerline project into surface](https://discourse.slicer.org/t/how-to-calculate-surface-length-with-centerline-project-into-surface/18747)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 8\
**Last updated:** [July 21, 2021, 11:51am UTC](https://discourse.slicer.org/t/how-to-calculate-surface-length-with-centerline-project-into-surface/18747 "2021-07-21T11:51:18Z")

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hi,i have centerline and centerlinesection,i want to calculate surfce line length,like this,green line is centerline and blue line is surface line,how to get this blue line?

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## [Help installing SlicerVMTK Extension](https://discourse.slicer.org/t/help-installing-slicervmtk-extension/17711)

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**Author:** [@KyleVanBeek](https://discourse.slicer.org/u/KyleVanBeek)\
**Replies:** 2\
**Last updated:** [July 18, 2021, 3:06am UTC](https://discourse.slicer.org/t/help-installing-slicervmtk-extension/17711 "2021-07-18T03:06:54Z")

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Hello, I am looking for a straightforward tutorial for downloading the SlicerVMTK extension as I do not have a computer science background. All tutorials found online involve the usage of python and while it may be a s…

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## [How to avoid the holes caused by branch splitting, or repair it](https://discourse.slicer.org/t/how-to-avoid-the-holes-caused-by-branch-splitting-or-repair-it/18582)

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**Author:** [@JunjieWu](https://discourse.slicer.org/u/JunjieWu)\
**Replies:** 5\
**Last updated:** [July 15, 2021, 2:57am UTC](https://discourse.slicer.org/t/how-to-avoid-the-holes-caused-by-branch-splitting-or-repair-it/18582 "2021-07-15T02:57:27Z")

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I have something trouble in branch splitting of vascular bifurcation. Holes are created at the junction of the dividing lines, and i can’t use vmtksurfacecapper to fix it. How can i avoid it, or repair it ? vmtkbranchcl…

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## [how to generate multiple mesh files with different time steps](https://discourse.slicer.org/t/how-to-generate-multiple-mesh-files-with-different-time-steps/18596)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 3\
**Last updated:** [July 12, 2021, 1:32am UTC](https://discourse.slicer.org/t/how-to-generate-multiple-mesh-files-with-different-time-steps/18596 "2021-07-12T01:32:58Z")

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Hi, than you for sharing the PARTICLE TRACING example with vmtk,i have problem that how to generate different timestep meshs,can anyone share some example code or tools how to use it generate different timestep meshes? …

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## [Method Requires VTK Object Error](https://discourse.slicer.org/t/method-requires-vtk-object-error/18386)

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**Author:** [@Bastien\_Saunois](https://discourse.slicer.org/u/Bastien_Saunois)\
**Replies:** 3\
**Last updated:** [July 8, 2021, 10:18am UTC](https://discourse.slicer.org/t/method-requires-vtk-object-error/18386 "2021-07-08T10:18:52Z")

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I am implementing the extract Network algorithm, but I get an issue with this line : networkExtraction.SetInputData(surfacePolyData) I get this error : method requires a VTK object I saw on some forums that it could …

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## [Import issue of vmtk libraries](https://discourse.slicer.org/t/import-issue-of-vmtk-libraries/18321)

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**Author:** [@Bastien\_Saunois](https://discourse.slicer.org/u/Bastien_Saunois)\
**Replies:** 5\
**Last updated:** [June 28, 2021, 8:45am UTC](https://discourse.slicer.org/t/import-issue-of-vmtk-libraries/18321 "2021-06-28T08:45:54Z")

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I am trying to re-use the ExtractCenterline.py code. In the script there are 2 imports that interest me : import vtkvmtkComputationalGeometryPython as vtkvmtkComputationalGeometry import vtkvmtkMiscPyt…

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## [Where is the code for computation of centerline?](https://discourse.slicer.org/t/where-is-the-code-for-computation-of-centerline/18183)

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**Author:** [@Bastien\_Saunois](https://discourse.slicer.org/u/Bastien_Saunois)\
**Replies:** 4\
**Last updated:** [June 18, 2021, 8:19am UTC](https://discourse.slicer.org/t/where-is-the-code-for-computation-of-centerline/18183 "2021-06-18T08:19:11Z")

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Hi, I am trying to use VMTK to compute the centerline of a hollowed cylinder with Python. But I can’t find the code responsible of computing the centerline. Could someone guide me to this certain code? I would appreci…

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