# VMTK

**URL:** https://discourse.slicer.org/c/community/vmtk/28.md?page=1

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**Page:** 2

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## [Preparing a surface for meshing](https://discourse.slicer.org/t/preparing-a-surface-for-meshing/35794)

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**Author:** [@benzwick](https://discourse.slicer.org/u/benzwick)\
**Replies:** 6\
**Last updated:** [May 2, 2024, 4:53pm UTC](https://discourse.slicer.org/t/preparing-a-surface-for-meshing/35794 "2024-05-02T16:53:08Z")

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I am trying to prepare a surface mesh for use in a simulation. I need a surface with open ends that are perpendicular to the centerlines of the vessels. I have a segmentation that looks like this: I would like to cu…

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## [Mesh generation](https://discourse.slicer.org/t/mesh-generation/35559)

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**Author:** [@fil\_ita](https://discourse.slicer.org/u/fil_ita)\
**Replies:** 0\
**Last updated:** [April 17, 2024, 2:08pm UTC](https://discourse.slicer.org/t/mesh-generation/35559 "2024-04-17T14:08:25Z")

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Good morning, First of all I would like to thank your team for the development of such an amazing tool. I am trying to mesh a geometry that, although is not from a vascular scan, I believe it is suitable for VMTK. How…

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## [Centerline calculation warning (vmtkcenterlineviewer)](https://discourse.slicer.org/t/centerline-calculation-warning-vmtkcenterlineviewer/34573)

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**Author:** [@MicheleIng](https://discourse.slicer.org/u/MicheleIng)\
**Replies:** 3\
**Last updated:** [April 9, 2024, 3:36am UTC](https://discourse.slicer.org/t/centerline-calculation-warning-vmtkcenterlineviewer/34573 "2024-04-09T03:36:04Z")

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Once I import the stl file (the stl file is a vessel that has two bifurcations), vmtk doesn’t generate centerlines for me but it generates this warning message. Warning: In …\\vtkVmtk\\ComputationalGeometry\\vtkvmtkSteepe…

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## [Get the bifurcations points from a skeleton (network model)](https://discourse.slicer.org/t/get-the-bifurcations-points-from-a-skeleton-network-model/35292)

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**Author:** [@Antoine1](https://discourse.slicer.org/u/Antoine1)\
**Replies:** 0\
**Last updated:** [April 4, 2024, 3:51pm UTC](https://discourse.slicer.org/t/get-the-bifurcations-points-from-a-skeleton-network-model/35292 "2024-04-04T15:51:29Z")

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Hello everyone, I’m currently working on a project with vessels segmentation. So I already manage to get my vessels and from that I put it in 3D Slicer and used the VMTK modules “Extract Centerline” to get the Centerlin…

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## [Centerline smoothing by vmtkCenterlineSmoothing does not work](https://discourse.slicer.org/t/centerline-smoothing-by-vmtkcenterlinesmoothing-does-not-work/35200)

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**Author:** [@tomo-akiyama](https://discourse.slicer.org/u/tomo-akiyama)\
**Replies:** 4\
**Last updated:** [April 4, 2024, 1:44pm UTC](https://discourse.slicer.org/t/centerline-smoothing-by-vmtkcenterlinesmoothing-does-not-work/35200 "2024-04-04T13:44:20Z")

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Hello, everyone, I’m interested in smoothing the centerlines of the cerebral arteries. Following the parameters recommended by “Kjeldsberg et al. BioMedical Engineering OnLine (2021) Automated landmarking of bends in v…

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## [Regarding definition of mean curvature](https://discourse.slicer.org/t/regarding-definition-of-mean-curvature/32326)

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**Author:** [@Mudrika](https://discourse.slicer.org/u/Mudrika)\
**Replies:** 4\
**Last updated:** [April 3, 2024, 10:35pm UTC](https://discourse.slicer.org/t/regarding-definition-of-mean-curvature/32326 "2024-04-03T22:35:20Z")

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Hello everyone! I am extracting a centerline model for a geometry. By using the ‘markups’, I am drawing curves on the selected arteries and calculating geometric parameters like length and mean curvature. As we know, th…

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## [Colliding fronts under-segment where the vessel bends a lot](https://discourse.slicer.org/t/colliding-fronts-under-segment-where-the-vessel-bends-a-lot/16628)

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**Author:** [@Dave\_Fang](https://discourse.slicer.org/u/Dave_Fang)\
**Replies:** 5\
**Last updated:** [April 1, 2024, 3:52pm UTC](https://discourse.slicer.org/t/colliding-fronts-under-segment-where-the-vessel-bends-a-lot/16628 "2024-04-01T15:52:24Z")

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hi， guys, I use colliding fronts to initialize the segementaion on 3D DSA of intracranial blood vessels. But I found there was serious under-seg where the vessel bends a lot, Anyone else know the solution to the pro…

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## [Trimming normal to boundary](https://discourse.slicer.org/t/trimming-normal-to-boundary/34791)

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**Author:** [@Beth\_Thompson](https://discourse.slicer.org/u/Beth_Thompson)\
**Replies:** 2\
**Last updated:** [March 8, 2024, 8:49pm UTC](https://discourse.slicer.org/t/trimming-normal-to-boundary/34791 "2024-03-08T20:49:08Z")

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Hi, I have a 3D model of a pulmonary artery generated in SimVascular. I am trying to add extensions to it, but first I need to clip the ends to open it. I would like to trim the ends just the tiniest bit to open them, a…

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## [Automatic centerline](https://discourse.slicer.org/t/automatic-centerline/14829)

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**Author:** [@Daniele\_Morbidelli](https://discourse.slicer.org/u/Daniele_Morbidelli)\
**Replies:** 31\
**Last updated:** [February 29, 2024, 7:33pm UTC](https://discourse.slicer.org/t/automatic-centerline/14829 "2024-02-29T19:33:11Z")

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Hi All, is there a way to generate the centerline automatically? In my case I have a geometry with always one input and 4 outputs.

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## [Colliding fronts output near a side branch](https://discourse.slicer.org/t/colliding-fronts-output-near-a-side-branch/34416)

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**Author:** [@ckolluru](https://discourse.slicer.org/u/ckolluru)\
**Replies:** 0\
**Last updated:** [February 20, 2024, 5:58am UTC](https://discourse.slicer.org/t/colliding-fronts-output-near-a-side-branch/34416 "2024-02-20T05:58:33Z")

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I’m trying to add seed points before and after a bifurcation to run colliding fronts with VMTK. Let’s say the parent vessel branches into two, branch 1 and branch 2. I add one seed point in the parent vessel and one in …

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## [Using vmtk scripts within Slicer with vmtk-extension](https://discourse.slicer.org/t/using-vmtk-scripts-within-slicer-with-vmtk-extension/24757)

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**Author:** [@Doodads](https://discourse.slicer.org/u/Doodads)\
**Replies:** 2\
**Last updated:** [February 9, 2024, 7:35pm UTC](https://discourse.slicer.org/t/using-vmtk-scripts-within-slicer-with-vmtk-extension/24757 "2024-02-09T19:35:15Z")

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Hi, I have a vessel modelling workflow written in python which makes use of vmtk to convert a surface file (.vtk) to a mesh file (.vtu). I would like to migrate the workflow to use the Slicer environment as well as repla…

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## [Problem displaying 2 surfaces together in one window, in Python way](https://discourse.slicer.org/t/problem-displaying-2-surfaces-together-in-one-window-in-python-way/34159)

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**Author:** [@guozhi0302](https://discourse.slicer.org/u/guozhi0302)\
**Replies:** 1\
**Last updated:** [February 7, 2024, 1:53pm UTC](https://discourse.slicer.org/t/problem-displaying-2-surfaces-together-in-one-window-in-python-way/34159 "2024-02-07T13:53:20Z")

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The official tutorial Computing Centerlines has demonstrated displaying multiple surfaces (or centerlines) in one window with Pype commands. vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines --pipe vmtkrenderer --…

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## [Problem of vtkvmtkMergeCenterlines](https://discourse.slicer.org/t/problem-of-vtkvmtkmergecenterlines/34095)

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**Author:** [@chuanqiWen](https://discourse.slicer.org/u/chuanqiWen)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 3:22pm UTC](https://discourse.slicer.org/t/problem-of-vtkvmtkmergecenterlines/34095 "2024-02-01T15:22:54Z")

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Taking the result of vtkvmtkCenterlineBranchExtractor as input to vtkvmtkMergeCenterlines, the final result obtained is empty

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## [branch splitting in vmtk](https://discourse.slicer.org/t/branch-splitting-in-vmtk/34018)

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**Author:** [@MicheleIng](https://discourse.slicer.org/u/MicheleIng)\
**Replies:** 4\
**Last updated:** [January 29, 2024, 4:44pm UTC](https://discourse.slicer.org/t/branch-splitting-in-vmtk/34018 "2024-01-29T16:44:56Z")

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Hi! I am fairly new to both 3d slicer and vmtk. Is it possible to do the branch splitting in vmtk (link) with 3d slicer? I want to create those spheres and know the coordinates of the nodes as in the picture.

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## [How to view a thrombosis with the 3D Slicer?](https://discourse.slicer.org/t/how-to-view-a-thrombosis-with-the-3d-slicer/33295)

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**Author:** [@Benny\_Zamir](https://discourse.slicer.org/u/Benny_Zamir)\
**Replies:** 1\
**Last updated:** [December 8, 2023, 8:05am UTC](https://discourse.slicer.org/t/how-to-view-a-thrombosis-with-the-3d-slicer/33295 "2023-12-08T08:05:34Z")

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Hi I would like to know how to view a thrombosis with the 3D Slicer?

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## [Why the Vessel Segmentation module does not exist?](https://discourse.slicer.org/t/why-the-vessel-segmentation-module-does-not-exist/33208)

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**Author:** [@Benny\_Zamir](https://discourse.slicer.org/u/Benny_Zamir)\
**Replies:** 0\
**Last updated:** [December 4, 2023, 6:45pm UTC](https://discourse.slicer.org/t/why-the-vessel-segmentation-module-does-not-exist/33208 "2023-12-04T18:45:40Z")

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Hi I would like to know Why the Vessel Segmentation module does not exist in my 3D Slicer? I have the VMTK module and I use 3D Slicer for Windows.

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## [What is your diagnosis?](https://discourse.slicer.org/t/what-is-your-diagnosis/33182)

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**Author:** [@Benny\_Zamir](https://discourse.slicer.org/u/Benny_Zamir)\
**Replies:** 1\
**Last updated:** [December 3, 2023, 2:07am UTC](https://discourse.slicer.org/t/what-is-your-diagnosis/33182 "2023-12-03T02:07:21Z")

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Vascular 3D

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## [Atypical proposal of a new module](https://discourse.slicer.org/t/atypical-proposal-of-a-new-module/32838)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [November 30, 2023, 7:31pm UTC](https://discourse.slicer.org/t/atypical-proposal-of-a-new-module/32838 "2023-11-30T19:31:10Z")

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Hi, I’ve pushed this module, ‘Centerline disassembly’, on my gitlab repository. It breaks down a centerline model into groups that can be identified by the VMTK libraries, namely bifurcations, branches and individual ce…

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## [how to remove flow extensions from a model](https://discourse.slicer.org/t/how-to-remove-flow-extensions-from-a-model/32865)

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**Author:** [@federica.chieffallo](https://discourse.slicer.org/u/federica.chieffallo)\
**Replies:** 0\
**Last updated:** [November 16, 2023, 5:02pm UTC](https://discourse.slicer.org/t/how-to-remove-flow-extensions-from-a-model/32865 "2023-11-16T17:02:57Z")

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Hi! How can I remove flow extension from a model in vmtk? Thank you for your kind help

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## [Cross-section analysis ImportError on Mac](https://discourse.slicer.org/t/cross-section-analysis-importerror-on-mac/32849)

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**Author:** [@urethralking](https://discourse.slicer.org/u/urethralking)\
**Replies:** 3\
**Last updated:** [November 16, 2023, 1:06pm UTC](https://discourse.slicer.org/t/cross-section-analysis-importerror-on-mac/32849 "2023-11-16T13:06:23Z")

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Hi everyone, I installed Slicer VMTK using the extensions module on my Mac M1 and successfully extracted a centerline of a urethra using the module. However, when I try to use Cross-section Analysis, I keep getting the f…

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## [HELP VMTK on Mac M1](https://discourse.slicer.org/t/help-vmtk-on-mac-m1/32525)

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**Author:** [@FabioTraina](https://discourse.slicer.org/u/FabioTraina)\
**Replies:** 1\
**Last updated:** [November 5, 2023, 11:06am UTC](https://discourse.slicer.org/t/help-vmtk-on-mac-m1/32525 "2023-11-05T11:06:30Z")

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Hi everyone, I need help installing vmtk on my m1 mac. How should I do it?

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## [aneurysm removal and reconstruct the parent vessel](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304)

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**Author:** [@Tingchenccmu](https://discourse.slicer.org/u/Tingchenccmu)\
**Replies:** 10\
**Last updated:** [October 27, 2023, 6:04pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304 "2023-10-27T18:04:09Z")

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I want to perform digital aneurysm removal and reconstruct the parent vessel according to the tutorials. But I can’t find the three Python scripts because I find there is no path of vmtk/vmtkApps/CerebralAneurysms/Parent…

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## [Separating centerline metrics](https://discourse.slicer.org/t/separating-centerline-metrics/19173)

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**Author:** [@som1197](https://discourse.slicer.org/u/som1197)\
**Replies:** 10\
**Last updated:** [October 27, 2023, 12:07pm UTC](https://discourse.slicer.org/t/separating-centerline-metrics/19173 "2023-10-27T12:07:22Z")

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Hello, I want to isolate parameters such as Tortuosity, Curvature, Torsion, Length, Radius etc. for the centerlines. The current vmtk version groups these centerlines based on Centerline Ids, Group Ids etc. But it stil…

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## [Centerline computation problem - straight lines](https://discourse.slicer.org/t/centerline-computation-problem-straight-lines/32397)

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**Author:** [@smoudour](https://discourse.slicer.org/u/smoudour)\
**Replies:** 0\
**Last updated:** [October 24, 2023, 2:39pm UTC](https://discourse.slicer.org/t/centerline-computation-problem-straight-lines/32397 "2023-10-24T14:39:42Z")

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Hi all. I have been working with 3D slicer for a few months now. I am trying to isolate coronary arteries from CCTA scans, get the centerlines and quantify some geometric features I need for further analysis. As far, I…

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## [ How to run VMTK script in PypePad](https://discourse.slicer.org/t/how-to-run-vmtk-script-in-pypepad/32395)

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**Author:** [@Tingchenccmu](https://discourse.slicer.org/u/Tingchenccmu)\
**Replies:** 0\
**Last updated:** [October 24, 2023, 12:35pm UTC](https://discourse.slicer.org/t/how-to-run-vmtk-script-in-pypepad/32395 "2023-10-24T12:35:56Z")

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I want to perform digital aneurysm removal and reconstruct the parent vessel according to the tutorials. And the three python scripts are in my path. But there is something wrong when I run this code “python patchandinte…

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## [Discrepancy between image coordinates and seed points centerline extraction](https://discourse.slicer.org/t/discrepancy-between-image-coordinates-and-seed-points-centerline-extraction/31504)

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**Author:** [@IlvaHou55](https://discourse.slicer.org/u/IlvaHou55)\
**Replies:** 5\
**Last updated:** [September 4, 2023, 2:11pm UTC](https://discourse.slicer.org/t/discrepancy-between-image-coordinates-and-seed-points-centerline-extraction/31504 "2023-09-04T14:11:36Z")

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Hello, I am using VMTK to extract the hepatic arteries from contrast-enhanced CT scans. After centerline extraction I need to make the connection between the outlets of the centerlines and the original image. While I wa…

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## [Measure Diameter using centerline length and surface](https://discourse.slicer.org/t/measure-diameter-using-centerline-length-and-surface/31382)

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**Author:** [@cams2b](https://discourse.slicer.org/u/cams2b)\
**Replies:** 1\
**Last updated:** [August 26, 2023, 6:25pm UTC](https://discourse.slicer.org/t/measure-diameter-using-centerline-length-and-surface/31382 "2023-08-26T18:25:29Z")

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I am trying to extract the radius at each point on the centerline from my tubular mesh. I am using the vmtk script vmtkDistanceToCenterlines and setting the variable EvaluateCenterlineRadius = True. I was expecting this…

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## [Is there a corresponding python script for cross-sectional analysis to achieve fully automatic analysis](https://discourse.slicer.org/t/is-there-a-corresponding-python-script-for-cross-sectional-analysis-to-achieve-fully-automatic-analysis/31359)

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**Author:** [@Tao\_Wang](https://discourse.slicer.org/u/Tao_Wang)\
**Replies:** 0\
**Last updated:** [August 25, 2023, 1:26pm UTC](https://discourse.slicer.org/t/is-there-a-corresponding-python-script-for-cross-sectional-analysis-to-achieve-fully-automatic-analysis/31359 "2023-08-25T13:26:45Z")

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I have already used a python script to extract the mesh and centerline. Is there a corresponding python script for cross-sectional analysis to achieve fully automatic analysis? I would appreciate any answer

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## [RFC : can this module have a place in SlicerVMTK?](https://discourse.slicer.org/t/rfc-can-this-module-have-a-place-in-slicervmtk/31117)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 2\
**Last updated:** [August 13, 2023, 3:22pm UTC](https://discourse.slicer.org/t/rfc-can-this-module-have-a-place-in-slicervmtk/31117 "2023-08-13T15:22:20Z")

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Hi all, I’m wondering if this module, Arterial calcification pre-processor, may be moved to SlicerVMTK. It grows an input diseased arterial lumen segment to isolate dense calcifications in the wall within a calculated …

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## [RFC : is there interest in this custom module - Guided vein segmentation](https://discourse.slicer.org/t/rfc-is-there-interest-in-this-custom-module-guided-vein-segmentation/31002)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [August 7, 2023, 1:52pm UTC](https://discourse.slicer.org/t/rfc-is-there-interest-in-this-custom-module-guided-vein-segmentation/31002 "2023-08-07T13:52:13Z")

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Hi all, I am contemplating merging this module, Guided vein segmentation, in SlicerVMTK, so that it become easily available. Beforehand, I wish to know if other users find it worthwhile as an addition to SlicerVMTK. I…

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