# VMTK

**URL:** https://discourse.slicer.org/c/community/vmtk/28.md?page=2

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

**Page:** 3

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## [Pypepad not opening after running "vmtk-exe.py" in Anaconda prompt](https://discourse.slicer.org/t/pypepad-not-opening-after-running-vmtk-exe-py-in-anaconda-prompt/31006)

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**Author:** [@jared](https://discourse.slicer.org/u/jared)\
**Replies:** 0\
**Last updated:** [August 6, 2023, 7:35am UTC](https://discourse.slicer.org/t/pypepad-not-opening-after-running-vmtk-exe-py-in-anaconda-prompt/31006 "2023-08-06T07:35:37Z")

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Hello, I’m new to using VMTK and I’ve unfortunately run into an issue with attempting to open the Pypepad using the Anaconda prompt. Every time I run the “vmtk-exe.py” line (as shown in the tutorials on the VMTK website…

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## [Smooth Capping Method in VMTK](https://discourse.slicer.org/t/smooth-capping-method-in-vmtk/30810)

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**Author:** [@iloliveira](https://discourse.slicer.org/u/iloliveira)\
**Replies:** 0\
**Last updated:** [July 26, 2023, 6:50pm UTC](https://discourse.slicer.org/t/smooth-capping-method-in-vmtk/30810 "2023-07-26T18:50:47Z")

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Hi all, I am trying to come up with a function to “cap” a clipped aneurysm sac surface with the goal to compute its “ostium” surface, i.e. the minimal surface that connects its 3D neck contour. Since I haven’t found any…

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## [Coordinate transformations? ](https://discourse.slicer.org/t/coordinate-transformations/30682)

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**Author:** [@Charlie\_Hayward](https://discourse.slicer.org/u/Charlie_Hayward)\
**Replies:** 1\
**Last updated:** [July 21, 2023, 2:11pm UTC](https://discourse.slicer.org/t/coordinate-transformations/30682 "2023-07-21T14:11:36Z")

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Hello, I am attempting to fully automate the vmtkcenterline function by specifying seed points like this: vmtkcenterlines -seedselector pointlist -sourcepoints 0 0 0 -targetpoints 1 1 1 2 2 2. To find the source and targ…

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## [TetGen: Stuck in final mesh improvement (vmtkmeshgenerator)](https://discourse.slicer.org/t/tetgen-stuck-in-final-mesh-improvement-vmtkmeshgenerator/30603)

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**Author:** [@Anewre](https://discourse.slicer.org/u/Anewre)\
**Replies:** 2\
**Last updated:** [July 14, 2023, 2:17pm UTC](https://discourse.slicer.org/t/tetgen-stuck-in-final-mesh-improvement-vmtkmeshgenerator/30603 "2023-07-14T14:17:57Z")

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Dear all, It seems this issue has been raised before, but since I was not successful in deriving a solution from previous Topics, I would like to bring it up once more. I am trying to mesh a complex vascular geometry u…

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## [CTA Vessel Segmentation](https://discourse.slicer.org/t/cta-vessel-segmentation/30568)

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**Author:** [@Dimitrios\_Rallios](https://discourse.slicer.org/u/Dimitrios_Rallios)\
**Replies:** 1\
**Last updated:** [July 14, 2023, 8:12am UTC](https://discourse.slicer.org/t/cta-vessel-segmentation/30568 "2023-07-14T08:12:24Z")

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I am trying to extract only the arteries from brain CT-Angiography. I tried a few things (Grow from seeds, vessel segmentation module etc. ) but nothing seems to work. Even if I could only get all the vessels would be a …

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## [VMTK extension fails to build for preview](https://discourse.slicer.org/t/vmtk-extension-fails-to-build-for-preview/30355)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 2\
**Last updated:** [July 4, 2023, 3:37pm UTC](https://discourse.slicer.org/t/vmtk-extension-fails-to-build-for-preview/30355 "2023-07-04T15:37:09Z")

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Hi, I draw to your attention that SlicerVMTK extension shows build failure on cdash for all OS. Thank you for considering.

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## [Build error raised when building SlicerVMTK extension](https://discourse.slicer.org/t/build-error-raised-when-building-slicervmtk-extension/30384)

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**Author:** [@paul.w](https://discourse.slicer.org/u/paul.w)\
**Replies:** 2\
**Last updated:** [July 4, 2023, 3:37pm UTC](https://discourse.slicer.org/t/build-error-raised-when-building-slicervmtk-extension/30384 "2023-07-04T15:37:00Z")

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Build error raised when building SlicerVMTK extension SlicerExtension-VMTK within VS2022, the error code shows below: The Slicer 5.3.0 has been successfully built with Release, thus the environment should be okay, w…

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## [Pipeline centerline](https://discourse.slicer.org/t/pipeline-centerline/30236)

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**Author:** [@yangxw](https://discourse.slicer.org/u/yangxw)\
**Replies:** 0\
**Last updated:** [June 26, 2023, 2:56pm UTC](https://discourse.slicer.org/t/pipeline-centerline/30236 "2023-06-26T14:56:10Z")

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Hello author, I am new to VMTK, I want to extract the centerline of STL model (bronchus) by code, but I can’t do it by many methods, such as C++ and python, do you have an example of extracting the centerline of STL mode…

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## [vmtkmeshmergetimesteps UnboundLocalError](https://discourse.slicer.org/t/vmtkmeshmergetimesteps-unboundlocalerror/30113)

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**Author:** [@Krentos\_Iliakopoulos](https://discourse.slicer.org/u/Krentos_Iliakopoulos)\
**Replies:** 1\
**Last updated:** [June 20, 2023, 7:00pm UTC](https://discourse.slicer.org/t/vmtkmeshmergetimesteps-unboundlocalerror/30113 "2023-06-20T19:00:33Z")

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Hi, I try to trace particles using the tutorial Particle Tracing | vmtk - the Vascular Modelling Toolkit . Following the steps one by one, when i tried to execute vmtkmeshmergetimesteps like: vmtkmeshmergetimesteps -d…

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## [How to execute the MPR image by vmtkimagecurvedmpr？](https://discourse.slicer.org/t/how-to-execute-the-mpr-image-by-vmtkimagecurvedmpr/18551)

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**Author:** [@su2p](https://discourse.slicer.org/u/su2p)\
**Replies:** 5\
**Last updated:** [June 8, 2023, 7:55am UTC](https://discourse.slicer.org/t/how-to-execute-the-mpr-image-by-vmtkimagecurvedmpr/18551 "2023-06-08T07:55:50Z")

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I use this scripts to execute the MPR image, the input file format is vti, the output file format is vtp, the centerlines file is executed by other scrips of vmtk, but the output image size is 1k? Why output is so small? …

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## [Automatic SWI venography segmentation using VMTK](https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273)

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**Author:** [@OVSofia](https://discourse.slicer.org/u/OVSofia)\
**Replies:** 2\
**Last updated:** [May 22, 2023, 2:26pm UTC](https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273 "2023-05-22T14:26:42Z")

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Hello, Does anyone know how I could use VMTK to automatically segment vessels from SWI images? (particularly .nii format) I have been trying to get the vessel segmentation using vmtk (and vtk), but so far I can not do i…

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## [Regarding active scalars](https://discourse.slicer.org/t/regarding-active-scalars/29244)

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**Author:** [@Mudrika](https://discourse.slicer.org/u/Mudrika)\
**Replies:** 1\
**Last updated:** [May 10, 2023, 4:36am UTC](https://discourse.slicer.org/t/regarding-active-scalars/29244 "2023-05-10T04:36:40Z")

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Hello! Can anyone help me with how can I monitor what active scalars can be calculated for the centerline model in VMTK extension. I am getting only 3 options, but my interest lies in the calculation of curvature, torsi…

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## [VMTK automatic cross-sectional analysis](https://discourse.slicer.org/t/vmtk-automatic-cross-sectional-analysis/28380)

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**Author:** [@SlicerPascal](https://discourse.slicer.org/u/SlicerPascal)\
**Replies:** 1\
**Last updated:** [May 7, 2023, 5:04pm UTC](https://discourse.slicer.org/t/vmtk-automatic-cross-sectional-analysis/28380 "2023-05-07T17:04:23Z")

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Operating system: Windows Slicer version: 5.2.1 I am using slicer and I have extracted the centerline network for an arterial model. Is it possible to automatically perform cross-sectional analysis for each of the cent…

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## [Geometric indices](https://discourse.slicer.org/t/geometric-indices/29191)

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**Author:** [@Mudrika](https://discourse.slicer.org/u/Mudrika)\
**Replies:** 0\
**Last updated:** [April 28, 2023, 4:23pm UTC](https://discourse.slicer.org/t/geometric-indices/29191 "2023-04-28T16:23:45Z")

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Hi! Can anyone help me with the active scalars that are available for calculation in the centreline model? For the first model, I tried, all parameters were visible (torsion, tortuosity, length and radius) but afterward…

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## [Curvature, torsion, tortuosity computation algorithms in VMTK](https://discourse.slicer.org/t/curvature-torsion-tortuosity-computation-algorithms-in-vmtk/29186)

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**Author:** [@Mudrika](https://discourse.slicer.org/u/Mudrika)\
**Replies:** 2\
**Last updated:** [April 28, 2023, 2:55pm UTC](https://discourse.slicer.org/t/curvature-torsion-tortuosity-computation-algorithms-in-vmtk/29186 "2023-04-28T14:55:34Z")

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Hello! I am trying to calculate the geometric indices such as curvature, torsion and tortuosity from the extracted centrelines in 3D slicer by using VMTK extension. Can anyone please tell me what are the mathematical de…

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## [How to change branch centerline](https://discourse.slicer.org/t/how-to-change-branch-centerline/18746)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 6\
**Last updated:** [April 18, 2023, 5:55pm UTC](https://discourse.slicer.org/t/how-to-change-branch-centerline/18746 "2023-04-18T17:55:08Z")

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hi,i have extract the centerline,but i find centerline bifurcation is not right.just like this,i want modify centerline bifurcation from fig 1 to fig2,is there any function can achieve?

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## [vmtkcenterlines not working with this geometry](https://discourse.slicer.org/t/vmtkcenterlines-not-working-with-this-geometry/28514)

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**Author:** [@amscosta](https://discourse.slicer.org/u/amscosta)\
**Replies:** 5\
**Last updated:** [March 24, 2023, 4:22am UTC](https://discourse.slicer.org/t/vmtkcenterlines-not-working-with-this-geometry/28514 "2023-03-24T04:22:46Z")

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Hello All, My question is very simple. When I try : vmtkcenterlines -ifile manifold\_shell.stl -ofile manifold\_centerlines.vtp After selecting source and target points graphically, The vmtk enters in a crash loop. Any…

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## [Extract centerline may crash slicer on tight arterial stenosis](https://discourse.slicer.org/t/extract-centerline-may-crash-slicer-on-tight-arterial-stenosis/19484)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 4\
**Last updated:** [March 18, 2023, 8:21am UTC](https://discourse.slicer.org/t/extract-centerline-may-crash-slicer-on-tight-arterial-stenosis/19484 "2023-03-18T08:21:04Z")

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First, this is reported for its technical aspects. Centerline extraction may not always produce a good one with default parameters and only two endpoints. I noticed that by decreasing ‘Decimation aggressiveness’, center…

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## [Error running VMTK Development version (vmtkcenterlines)](https://discourse.slicer.org/t/error-running-vmtk-development-version-vmtkcenterlines/28371)

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**Author:** [@Lorenzo\_Civilla](https://discourse.slicer.org/u/Lorenzo_Civilla)\
**Replies:** 0\
**Last updated:** [March 14, 2023, 11:40am UTC](https://discourse.slicer.org/t/error-running-vmtk-development-version-vmtkcenterlines/28371 "2023-03-14T11:40:23Z")

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Dear all, I installed VMTK Development version on a VirtualMachine running Ubuntu 22.04.2. There I installed the latest versions of the dependencies of Git, Pyhton3, CMake and g++. The problem I have occurs when I run v…

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## [Exceptions when trying to compute center lines using vtkvmtkPolyDataCenterlines](https://discourse.slicer.org/t/exceptions-when-trying-to-compute-center-lines-using-vtkvmtkpolydatacenterlines/28071)

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**Author:** [@rmacule](https://discourse.slicer.org/u/rmacule)\
**Replies:** 0\
**Last updated:** [February 27, 2023, 4:51pm UTC](https://discourse.slicer.org/t/exceptions-when-trying-to-compute-center-lines-using-vtkvmtkpolydatacenterlines/28071 "2023-02-27T16:51:04Z")

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If I use the following code I get exceptions when calling the vtkvmtkPolyDataCenterlines-\>update() method: // Read file vtkSmartPointer\<vtkXMLImageDataReader\> reader = vtkSmartPointer\<vtkXMLImageDataReader\>::New(); …

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## [ Crash using ‘vtk vmtk Threshold Segmentation Level Set Image Filter’](https://discourse.slicer.org/t/crash-using-vtk-vmtk-threshold-segmentation-level-set-image-filter/28070)

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**Author:** [@rmacule](https://discourse.slicer.org/u/rmacule)\
**Replies:** 0\
**Last updated:** [February 27, 2023, 4:50pm UTC](https://discourse.slicer.org/t/crash-using-vtk-vmtk-threshold-segmentation-level-set-image-filter/28070 "2023-02-27T16:50:55Z")

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If I use the attached vti file and the following code I get an exception. I would really appreciate any suggestions and/or guidance on how to resolve this :slight\_smile: vtkSmartPointer\<vtkXMLImageDataReader\> reader = v…

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## [Problem with using 【CMakeLists】 to run 【VMTK c++】 code](https://discourse.slicer.org/t/problem-with-using-cmakelists-to-run-vmtk-c-code/27936)

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**Author:** [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Replies:** 4\
**Last updated:** [February 22, 2023, 12:58pm UTC](https://discourse.slicer.org/t/problem-with-using-cmakelists-to-run-vmtk-c-code/27936 "2023-02-22T12:58:28Z")

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Dear All, In my project, I am to run a VMTK c++ code using CMake. My setup are 【linux mint】+ 【gcc】+【visual studio code】+【cmake】, and first serveral lines of code are at the very bottom: The problem I have is with CMak…

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## [Centerline model has duplicate points](https://discourse.slicer.org/t/centerline-model-has-duplicate-points/27545)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 0\
**Last updated:** [January 30, 2023, 9:51pm UTC](https://discourse.slicer.org/t/centerline-model-has-duplicate-points/27545 "2023-01-30T21:51:36Z")

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Centerline model has duplicate points Centerline models from ‘Extract centerline’ often, if not always, have duplicate points. I don’t know since when, this is apparent when using ‘Cross-section analysis’. At the duplic…

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## [vmtkbranchclipper running for a day and still no result.](https://discourse.slicer.org/t/vmtkbranchclipper-running-for-a-day-and-still-no-result/27303)

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**Author:** [@Fotos\_Stylianou](https://discourse.slicer.org/u/Fotos_Stylianou)\
**Replies:** 9\
**Last updated:** [January 20, 2023, 11:55am UTC](https://discourse.slicer.org/t/vmtkbranchclipper-running-for-a-day-and-still-no-result/27303 "2023-01-20T11:55:41Z")

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Hi all, I am new here! As the title says, I have been using the vmtkbranchclipper on a tracheobronchial tree to generate the branches but the command is running forever. The command I am using is this “~/vmtk\_Py36/vm…

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## [Picking centerline endpoints via command line](https://discourse.slicer.org/t/picking-centerline-endpoints-via-command-line/26358)

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**Author:** [@nlbrown62](https://discourse.slicer.org/u/nlbrown62)\
**Replies:** 3\
**Last updated:** [November 22, 2022, 4:44pm UTC](https://discourse.slicer.org/t/picking-centerline-endpoints-via-command-line/26358 "2022-11-22T16:44:51Z")

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Hello, I have been using centerline and network extraction in VMTK through the Python interface. For centerlines, I have been using the pickpoint GUI to set the start and endpoints for vessels, and I want to switch to s…

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## [Error creating a module](https://discourse.slicer.org/t/error-creating-a-module/25712)

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**Author:** [@LuisaDantas](https://discourse.slicer.org/u/LuisaDantas)\
**Replies:** 15\
**Last updated:** [November 8, 2022, 2:48pm UTC](https://discourse.slicer.org/t/error-creating-a-module/25712 "2022-11-08T14:48:46Z")

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Hey, I’m following PerkLab’s Slicer bootcamp tutorial on how to create a Module for 3D Slicer. But when I try to run the code to see the changes it returns this error: ModuleNotFoundError: No module named 'vtkmodules.v…

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## [Installing VMTK with VSCode](https://discourse.slicer.org/t/installing-vmtk-with-vscode/25740)

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**Author:** [@Malalvarez](https://discourse.slicer.org/u/Malalvarez)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 4:05pm UTC](https://discourse.slicer.org/t/installing-vmtk-with-vscode/25740 "2022-10-19T16:05:09Z")

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Hi, i am new at this, and trying to install VMTK and use it with Python 3.9 in Visual Studio Code. Is that possible? Or only from Anaconda is possible?

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## [Is it possible to run CFD simulation in Slicer?](https://discourse.slicer.org/t/is-it-possible-to-run-cfd-simulation-in-slicer/25500)

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**Author:** [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Replies:** 10\
**Last updated:** [October 17, 2022, 3:16am UTC](https://discourse.slicer.org/t/is-it-possible-to-run-cfd-simulation-in-slicer/25500 "2022-10-17T03:16:01Z")

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now i can use vmtk to build vascular mesh and extract centerline is it possible to run CFD simulation with the data vmtk generated and show simulation in the sequence module?

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## [How can I use vmtk using python without 3D slicer GUI?](https://discourse.slicer.org/t/how-can-i-use-vmtk-using-python-without-3d-slicer-gui/20727)

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**Author:** [@Amira\_Noaman](https://discourse.slicer.org/u/Amira_Noaman)\
**Replies:** 6\
**Last updated:** [September 15, 2022, 1:18am UTC](https://discourse.slicer.org/t/how-can-i-use-vmtk-using-python-without-3d-slicer-gui/20727 "2022-09-15T01:18:40Z")

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Hello everyone, I’ve just started using vmtk package in python. (windows OS). I’m not willing to use the GUI provided by 3D slicer now, I’ll be building the complete project with python code, is it possible? and if yes…

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## [Add two surfaces to vtmkscripts.vmtkSurfaceViewer](https://discourse.slicer.org/t/add-two-surfaces-to-vtmkscripts-vmtksurfaceviewer/25014)

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**Author:** [@carlosar](https://discourse.slicer.org/u/carlosar)\
**Replies:** 0\
**Last updated:** [August 30, 2022, 7:09pm UTC](https://discourse.slicer.org/t/add-two-surfaces-to-vtmkscripts-vmtksurfaceviewer/25014 "2022-08-30T19:09:48Z")

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I’d like to compare the pre and post smoothed surface from the marching cubes script. Here is part of my code. I’m building my own pypes script, so I am trying to replicate what is found in this tutorial at the end: Prep…

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