# VMTK

**URL:** https://discourse.slicer.org/c/community/vmtk/28.md?page=3

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

**Page:** 4

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## [Extract Centerlines cannot work with cyclical vessels?](https://discourse.slicer.org/t/extract-centerlines-cannot-work-with-cyclical-vessels/24758)

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**Author:** [@Doodads](https://discourse.slicer.org/u/Doodads)\
**Replies:** 1\
**Last updated:** [August 15, 2022, 7:37pm UTC](https://discourse.slicer.org/t/extract-centerlines-cannot-work-with-cyclical-vessels/24758 "2022-08-15T19:37:16Z")

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Hi, I used the Extract Centerlines tool on a Circle of Willis surface. The network is connected without an issue but the centerlines have a single vessel that it did not pass through (see image below). How do I adjust th…

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## [Funtion or Equation of centreline](https://discourse.slicer.org/t/funtion-or-equation-of-centreline/24640)

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**Author:** [@mann](https://discourse.slicer.org/u/mann)\
**Replies:** 3\
**Last updated:** [August 9, 2022, 8:57pm UTC](https://discourse.slicer.org/t/funtion-or-equation-of-centreline/24640 "2022-08-09T20:57:29Z")

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Hi All, I am using Extract centreline module for creating vessel centreline. Is their any way that I can get the function or equation that used to connect the control points ? Is there a way to edit/crop the centrelin…

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## [Clipping multiple branches with vmtkbranchclipper](https://discourse.slicer.org/t/clipping-multiple-branches-with-vmtkbranchclipper/24521)

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**Author:** [@susk](https://discourse.slicer.org/u/susk)\
**Replies:** 0\
**Last updated:** [July 27, 2022, 8:31am UTC](https://discourse.slicer.org/t/clipping-multiple-branches-with-vmtkbranchclipper/24521 "2022-07-27T08:31:23Z")

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Hi all, I am trying to clip more than one branch with vmtkBranchClipper in python. I’ve tried doing this both interactively and through supplying a GroupIds list. When I supply one GroupId, i.e. clip one branch, the cli…

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## [Lung Vessels Diameters using VMTK](https://discourse.slicer.org/t/lung-vessels-diameters-using-vmtk/24211)

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**Author:** [@Vir](https://discourse.slicer.org/u/Vir)\
**Replies:** 5\
**Last updated:** [July 14, 2022, 3:09pm UTC](https://discourse.slicer.org/t/lung-vessels-diameters-using-vmtk/24211 "2022-07-14T15:09:23Z")

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Hello I am working with lung vessels volumetric file (. img) which is a binary image . I want to extract the diameters of each vessels . Is there a way to extract these values using 3d slicer VMTK extension . Below is …

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## [Mean diameter for SlicerVMTK module](https://discourse.slicer.org/t/mean-diameter-for-slicervmtk-module/24224)

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**Author:** [@vyvyvyvy](https://discourse.slicer.org/u/vyvyvyvy)\
**Replies:** 3\
**Last updated:** [July 9, 2022, 3:16pm UTC](https://discourse.slicer.org/t/mean-diameter-for-slicervmtk-module/24224 "2022-07-09T15:16:24Z")

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How can I use the SlicerVMTK module, “cross-section analysis” to show the mean diameter? Right now, I seem to only see options for “min” and “max.” Is there a way to add the mean on my end?

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## [Calculating variability using vmtksurfacedistance](https://discourse.slicer.org/t/calculating-variability-using-vmtksurfacedistance/24101)

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**Author:** [@fsneden](https://discourse.slicer.org/u/fsneden)\
**Replies:** 0\
**Last updated:** [June 29, 2022, 12:52pm UTC](https://discourse.slicer.org/t/calculating-variability-using-vmtksurfacedistance/24101 "2022-06-29T12:52:39Z")

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I am trying to calculate intra-observer variability in a dataset. I am creating surface data from images, and using the vmtksurfacedistance script to calculate difference from an input image (my 2nd surface) and a refere…

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## [Hole due to vmtkbranchclipper](https://discourse.slicer.org/t/hole-due-to-vmtkbranchclipper/24069)

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**Author:** [@orxshi](https://discourse.slicer.org/u/orxshi)\
**Replies:** 1\
**Last updated:** [June 28, 2022, 4:28pm UTC](https://discourse.slicer.org/t/hole-due-to-vmtkbranchclipper/24069 "2022-06-28T16:28:51Z")

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I am following the tutorial of MappingAndPatching. After executing the commands for the following operations Centerlines extraction and branch splitting Bifurcation reference systems Surface splitting When I check out …

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## [Resolving gap between centerline and control point in centerline extraction](https://discourse.slicer.org/t/resolving-gap-between-centerline-and-control-point-in-centerline-extraction/23584)

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**Author:** [@kvmontez](https://discourse.slicer.org/u/kvmontez)\
**Replies:** 1\
**Last updated:** [May 25, 2022, 12:09pm UTC](https://discourse.slicer.org/t/resolving-gap-between-centerline-and-control-point-in-centerline-extraction/23584 "2022-05-25T12:09:16Z")

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Hi! I’ve been working with the centerline extraction feature to create a centerline network in the built-in CTACardio data in 3D Slicer 5.1.0-2022-05-23. However, when the centerline is generated, there is a gap between…

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## [Reconstruct Mesh from a custom centerline](https://discourse.slicer.org/t/reconstruct-mesh-from-a-custom-centerline/22006)

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**Author:** [@\_11](https://discourse.slicer.org/u/_11)\
**Replies:** 6\
**Last updated:** [May 19, 2022, 8:04am UTC](https://discourse.slicer.org/t/reconstruct-mesh-from-a-custom-centerline/22006 "2022-05-19T08:04:13Z")

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Hi, Thanks for the very valuable repository. I am wondering if it is possible to generate the tubular mesh based on a synthetically generated centerline with bifurcation? So what I have is a graph/tree structure with n…

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## [vmtksurfaceconnector](https://discourse.slicer.org/t/vmtksurfaceconnector/23453)

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**Author:** [@Benny\_Loretoni](https://discourse.slicer.org/u/Benny_Loretoni)\
**Replies:** 0\
**Last updated:** [May 17, 2022, 11:22am UTC](https://discourse.slicer.org/t/vmtksurfaceconnector/23453 "2022-05-17T11:22:26Z")

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I’m not able to run vmtksurfaceconnector due to the fact that more options of our command are “unknown” such as: -keepfirstsurface -keepsecondsurface –preventmanyonsameside did someone had the same problem? how to so…

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## [ running vmtklevelsetsegmentation results in fallback error](https://discourse.slicer.org/t/running-vmtklevelsetsegmentation-results-in-fallback-error/23215)

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**Author:** [@alice-hsu](https://discourse.slicer.org/u/alice-hsu)\
**Replies:** 0\
**Last updated:** [May 1, 2022, 12:01pm UTC](https://discourse.slicer.org/t/running-vmtklevelsetsegmentation-results-in-fallback-error/23215 "2022-05-01T12:01:58Z")

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When I try to run vmtklevelsetsegmentation, I receive a black screen and fallback errors, which I believe is due to depreciation of OpenGL on Mac OS 12. Not sure if this is the right direction, but I would appreciate any…

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## [Creating smooth flow extensions](https://discourse.slicer.org/t/creating-smooth-flow-extensions/23197)

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**Author:** [@JuliaW](https://discourse.slicer.org/u/JuliaW)\
**Replies:** 1\
**Last updated:** [April 29, 2022, 4:38pm UTC](https://discourse.slicer.org/t/creating-smooth-flow-extensions/23197 "2022-04-29T16:38:02Z")

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Dear vmtk community, Currently, I am preparing a segmented aorta for flow analysis. Using vmtk I have cut open the surface and added flow extensions. However, at opening of the aorta, the transition between the flow e…

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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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## [Boundary point of a cross-section ](https://discourse.slicer.org/t/boundary-point-of-a-cross-section/22719)

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**Author:** [@Dongwei1](https://discourse.slicer.org/u/Dongwei1)\
**Replies:** 2\
**Last updated:** [March 31, 2022, 11:32am UTC](https://discourse.slicer.org/t/boundary-point-of-a-cross-section/22719 "2022-03-31T11:32:03Z")

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Hi all, I am currently using vmtk to compute the centerline and cross-section of the vessel. I do aware that vmtkcenterlinesections can help me calculate the area of the cross-section perpendicular to the centerline, bu…

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## [Problem in computing centerline](https://discourse.slicer.org/t/problem-in-computing-centerline/22603)

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**Author:** [@A\_Khabarkhaan](https://discourse.slicer.org/u/A_Khabarkhaan)\
**Replies:** 4\
**Last updated:** [March 21, 2022, 3:23am UTC](https://discourse.slicer.org/t/problem-in-computing-centerline/22603 "2022-03-21T03:23:38Z")

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Hi I’m trying to create centerline of a shape (the sample cerebral aneurysm in the site and others) I face to the below warning: Warning: in …\\Common\\DataModel\\vtkPolyData.cxx, line 982 vtkPolyData (0000024c243cd6b0):…

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## [How to generate Vascular stent?](https://discourse.slicer.org/t/how-to-generate-vascular-stent/22430)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 2\
**Last updated:** [March 15, 2022, 3:23am UTC](https://discourse.slicer.org/t/how-to-generate-vascular-stent/22430 "2022-03-15T03:23:56Z")

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hi,i want generate Virtual Vascular Stent in VTK，i can generate simple Vascular Stent,like this i want make simple Vascular Stent more truely，like this result： can anyone know how to do it? thank you!!

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## [How Can I convert the levelsets segment results(can use marchingcube get surface) to volume mask?](https://discourse.slicer.org/t/how-can-i-convert-the-levelsets-segment-results-can-use-marchingcube-get-surface-to-volume-mask/22304)

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**Author:** [@gang\_fang](https://discourse.slicer.org/u/gang_fang)\
**Replies:** 1\
**Last updated:** [March 11, 2022, 6:40am UTC](https://discourse.slicer.org/t/how-can-i-convert-the-levelsets-segment-results-can-use-marchingcube-get-surface-to-volume-mask/22304 "2022-03-11T06:40:48Z")

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Hi, I have used the fastmarching to get the levelset surface, but I want to use the segmentation mask. How can I convert ? any advice? Best, gang

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## [Improving segmentation procedure](https://discourse.slicer.org/t/improving-segmentation-procedure/22236)

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**Author:** [@fsneden](https://discourse.slicer.org/u/fsneden)\
**Replies:** 0\
**Last updated:** [March 1, 2022, 3:02pm UTC](https://discourse.slicer.org/t/improving-segmentation-procedure/22236 "2022-03-01T15:02:06Z")

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Trying to improve the segmentation of carotid arteries with time-of-flight (TOF) MR images, and I sometimes get a lot of artefact within the segmentation. This looks to be fatty tissue within the neck. I am using these i…

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## [Internalerror in findedge() TetGen Problem](https://discourse.slicer.org/t/internalerror-in-findedge-tetgen-problem/22193)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 0\
**Last updated:** [February 26, 2022, 11:01am UTC](https://discourse.slicer.org/t/internalerror-in-findedge-tetgen-problem/22193 "2022-02-26T11:01:28Z")

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Hello everyone, I’m having trouble using the command “vmtkmeshgenerator” to obtain internal tetrahedral mesh, in particular starting with this command: vmtk vmtkmeshgenerator -ifile sup3.vtp -skipremeshing 1 -volumeele…

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## [support vtk 9.0.3?](https://discourse.slicer.org/t/support-vtk-9-0-3/18635)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 5\
**Last updated:** [February 24, 2022, 8:57am UTC](https://discourse.slicer.org/t/support-vtk-9-0-3/18635 "2022-02-24T08:57:57Z")

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hi,i want use vmtk 1.4.0 with vtk 9.0.3,but there have some different between 8.1.0 and 9.0.3.can you share the latest vmtk version source code that supports vtk 9.0.3? thank you

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## [How can I get centerlines of .stl file when there is a bifurcation?](https://discourse.slicer.org/t/how-can-i-get-centerlines-of-stl-file-when-there-is-a-bifurcation/21934)

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**Author:** [@SuHong\_Park](https://discourse.slicer.org/u/SuHong_Park)\
**Replies:** 4\
**Last updated:** [February 13, 2022, 2:04am UTC](https://discourse.slicer.org/t/how-can-i-get-centerlines-of-stl-file-when-there-is-a-bifurcation/21934 "2022-02-13T02:04:06Z")

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Hi, I’m just downloaded 3d slicer to get center line of a vessel(.stl file). Since I’m new to 3d slicer and vmtk, I prepared a small part of my research domain with a bifurcation. But, the result didn’t turned out so w…

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## [vmtkcenterlines openprofiles issue](https://discourse.slicer.org/t/vmtkcenterlines-openprofiles-issue/21906)

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**Author:** [@hemjo](https://discourse.slicer.org/u/hemjo)\
**Replies:** 5\
**Last updated:** [February 12, 2022, 5:28am UTC](https://discourse.slicer.org/t/vmtkcenterlines-openprofiles-issue/21906 "2022-02-12T05:28:12Z")

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I am trying to use vmtkcenterlines, but even on the test data aorta-surface-open-ends.stl when I run vmtksurfacereader -ifile aorta-surface-open-ends.stl --pipe vmtkcenterlines -seedselector openprofiles -endpoints 1 -o…

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## [No module named vtkmodules.vtkCommonCore](https://discourse.slicer.org/t/no-module-named-vtkmodules-vtkcommoncore/21854)

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**Author:** [@n\_h](https://discourse.slicer.org/u/n_h)\
**Replies:** 7\
**Last updated:** [February 9, 2022, 11:43am UTC](https://discourse.slicer.org/t/no-module-named-vtkmodules-vtkcommoncore/21854 "2022-02-09T11:43:13Z")

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Hey, I have recently got in touch with vmtk but I have still some issues making it work from python scripts. I would like to used it to implement an automatic segmentation and meshing workflow. I have set up an Ubuntu …

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## [vmtkcenterlinegeometry - can't view output file](https://discourse.slicer.org/t/vmtkcenterlinegeometry-cant-view-output-file/21544)

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**Author:** [@fsneden](https://discourse.slicer.org/u/fsneden)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 9:19am UTC](https://discourse.slicer.org/t/vmtkcenterlinegeometry-cant-view-output-file/21544 "2022-01-21T09:19:39Z")

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Hi, Have used vmtkcenterline geometry to calculate tortuousity of a carotid artery. Output runs fine; the file is written under .vtp extension as in tutorial. However, I want numbers that relate to tortuousity, curvatur…

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## [add flow extension to irregularly shaped outlet](https://discourse.slicer.org/t/add-flow-extension-to-irregularly-shaped-outlet/21445)

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**Author:** [@susk](https://discourse.slicer.org/u/susk)\
**Replies:** 0\
**Last updated:** [January 13, 2022, 1:58pm UTC](https://discourse.slicer.org/t/add-flow-extension-to-irregularly-shaped-outlet/21445 "2022-01-13T13:58:34Z")

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I am trying to add a flow extension to an outlet using vmtkflowextensions. However, the outlet has a very irregular shape due to the presence of plaque, and the added flow extension does not fit the outlet very well: …

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## [Only 1 DICOM image imported using vmtkimageviewer](https://discourse.slicer.org/t/only-1-dicom-image-imported-using-vmtkimageviewer/21110)

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**Author:** [@fsneden](https://discourse.slicer.org/u/fsneden)\
**Replies:** 0\
**Last updated:** [December 17, 2021, 12:23pm UTC](https://discourse.slicer.org/t/only-1-dicom-image-imported-using-vmtkimageviewer/21110 "2021-12-17T12:23:15Z")

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I have tried reading an image set and have run into a couple problems. First, I found that it wouldn’t read until I moved the folder to much earlier in the file path. I’ve now corrected this. However, once the images hav…

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## [vmtkcenterlines script profileidlist points order](https://discourse.slicer.org/t/vmtkcenterlines-script-profileidlist-points-order/20667)

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**Author:** [@scarpma](https://discourse.slicer.org/u/scarpma)\
**Replies:** 8\
**Last updated:** [December 16, 2021, 1:44pm UTC](https://discourse.slicer.org/t/vmtkcenterlines-script-profileidlist-points-order/20667 "2021-12-16T13:44:56Z")

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Hello everyone, I am currently trying to automatize the extraction of centerlines in my python script, using vmtk. From the command line one can specify the id of the source and target points by setting seedselector to…

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## [converting dicom dataset into vtp file](https://discourse.slicer.org/t/converting-dicom-dataset-into-vtp-file/20867)

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**Author:** [@khater](https://discourse.slicer.org/u/khater)\
**Replies:** 2\
**Last updated:** [December 3, 2021, 3:22pm UTC](https://discourse.slicer.org/t/converting-dicom-dataset-into-vtp-file/20867 "2021-12-03T15:22:38Z")

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i just started using vmtk on python ( windows operating system) and i want to use the vmtkcenterlines but the problem is that vmtkcenterlines uses .vtp file and i didn’t find any tutorial to help converting dicom files i…

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## [Parameter settings for Levelset segmentation in coronary artery segmentation](https://discourse.slicer.org/t/parameter-settings-for-levelset-segmentation-in-coronary-artery-segmentation/20651)

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**Author:** [@biplabketan](https://discourse.slicer.org/u/biplabketan)\
**Replies:** 1\
**Last updated:** [November 29, 2021, 11:35pm UTC](https://discourse.slicer.org/t/parameter-settings-for-levelset-segmentation-in-coronary-artery-segmentation/20651 "2021-11-29T23:35:53Z")

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Please let me know the correct parameter settings for levelset segmentation for coronary artery segmentation. Also, how the number of iterations can be selected? What is the significance of it and what is the convergence…

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