# VMTK **URL:** https://discourse.slicer.org/c/community/vmtk/28.md?page=5 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 6 --- ## [VMTK Centerline extraction vs. CGAL mesh skeletonization](https://discourse.slicer.org/t/vmtk-centerline-extraction-vs-cgal-mesh-skeletonization/18063)
**Author:** [@Zemleroi](https://discourse.slicer.org/u/Zemleroi)\ **Replies:** 8\ **Last updated:** [June 12, 2021, 6:58am UTC](https://discourse.slicer.org/t/vmtk-centerline-extraction-vs-cgal-mesh-skeletonization/18063 "2021-06-12T06:58:11Z")
Hi, How does the vmtk centerline extraction method compare with CGAL’s Triangulated Surface Mesh Skeletonization? Does the method implemented in CGAL work less well on tubular geometry? --- ## [How to detect multiple vessels between two endpoints](https://discourse.slicer.org/t/how-to-detect-multiple-vessels-between-two-endpoints/17604)
**Author:** [@perecanals](https://discourse.slicer.org/u/perecanals)\ **Replies:** 1\ **Last updated:** [May 13, 2021, 2:19pm UTC](https://discourse.slicer.org/t/how-to-detect-multiple-vessels-between-two-endpoints/17604 "2021-05-13T14:19:48Z")
Hi, In the images I usually analyze, it is common to get vascular structures that have more than one path between endpoints (vessels that originate at one point and converge afterwards). As I understand it, the centerli… --- ## [Tips to circumvent not having pre-contrast injection images for the purpose of bone subtraction](https://discourse.slicer.org/t/tips-to-circumvent-not-having-pre-contrast-injection-images-for-the-purpose-of-bone-subtraction/17561)
**Author:** [@KyleVanBeek](https://discourse.slicer.org/u/KyleVanBeek)\ **Replies:** 1\ **Last updated:** [May 13, 2021, 1:54pm UTC](https://discourse.slicer.org/t/tips-to-circumvent-not-having-pre-contrast-injection-images-for-the-purpose-of-bone-subtraction/17561 "2021-05-13T13:54:54Z")
Hello, I have CTA brain data-sets for pre-operation and post operation of stroke patients and I want to segment the cerebral vessels to run some comparisons of geometry. I’ve been running into issues with other segmenta… --- ## [How to obtain the complete center lines using VMTK?](https://discourse.slicer.org/t/how-to-obtain-the-complete-center-lines-using-vmtk/14068)
**Author:** [@KaryLiang](https://discourse.slicer.org/u/KaryLiang)\ **Replies:** 12\ **Last updated:** [May 11, 2021, 11:54am UTC](https://discourse.slicer.org/t/how-to-obtain-the-complete-center-lines-using-vmtk/14068 "2021-05-11T11:54:59Z")
Hello, I’m trying to obtain center lines from airway using VMTK. After dilating the pixels of airway, i got most of the center line, including from the small airway, looks like this: my problem is, why the center lin… --- ## [Unable to run vmtksurfaceviewer](https://discourse.slicer.org/t/unable-to-run-vmtksurfaceviewer/17555)
**Author:** [@banderies](https://discourse.slicer.org/u/banderies)\ **Replies:** 1\ **Last updated:** [May 11, 2021, 4:12am UTC](https://discourse.slicer.org/t/unable-to-run-vmtksurfaceviewer/17555 "2021-05-11T04:12:02Z")
I installed VMTK using Anaconda as the website describes. When I try to run vmtksurfaceviewer, I get the following error: Unexpected error: \ Traceback (most recent call last): File “/home/… --- ## [Script to compute Voronoi diagrams/largest aorta diameter using VMTK](https://discourse.slicer.org/t/script-to-compute-voronoi-diagrams-largest-aorta-diameter-using-vmtk/17549)
**Author:** [@banderies](https://discourse.slicer.org/u/banderies)\ **Replies:** 1\ **Last updated:** [May 11, 2021, 3:37am UTC](https://discourse.slicer.org/t/script-to-compute-voronoi-diagrams-largest-aorta-diameter-using-vmtk/17549 "2021-05-11T03:37:02Z")
I have a large number of aorta segmentations (nifti masks), and I would like to figure out how to load each one and compute the largest diameter (aneurysm). It looks as if computing a Voronoi diagram using VMTK is an ide… --- ## [Has Centerline from Extract centreline module be smoothed?](https://discourse.slicer.org/t/has-centerline-from-extract-centreline-module-be-smoothed/16986)
**Author:** [@Ge\_Tang](https://discourse.slicer.org/u/Ge_Tang)\ **Replies:** 1\ **Last updated:** [April 14, 2021, 5:28am UTC](https://discourse.slicer.org/t/has-centerline-from-extract-centreline-module-be-smoothed/16986 "2021-04-14T05:28:44Z")
I want to do the geometric analysis. The VMTK tutorial described that the centerline goes through a Laplacian smoothing filter first and then computes the derivatives and the related quantities (Geometric Analysis | vmtk… --- ## [Call script in conda](https://discourse.slicer.org/t/call-script-in-conda/16473)
**Author:** [@szhang](https://discourse.slicer.org/u/szhang)\ **Replies:** 2\ **Last updated:** [April 12, 2021, 9:50pm UTC](https://discourse.slicer.org/t/call-script-in-conda/16473 "2021-04-12T21:50:12Z")
How can I call the script correctly? Here’s how my Miniconda3 window looks like (base) PS C:\> conda activate foo (foo) PS C:\> vmtkimagereader vmtkimagereader : The term ‘vmtkimagereader’ is not recognized as the name… --- ## [Automatic endpoint selection outside of surface module](https://discourse.slicer.org/t/automatic-endpoint-selection-outside-of-surface-module/17037)
**Author:** [@perecanals](https://discourse.slicer.org/u/perecanals)\ **Replies:** 1\ **Last updated:** [April 12, 2021, 4:41pm UTC](https://discourse.slicer.org/t/automatic-endpoint-selection-outside-of-surface-module/17037 "2021-04-12T16:41:32Z")
Hi, I am trying to extract centerlines from vascular models using the automatic endpoint selection from the VMTK module in Slicer, and in some cases (I’d say in about 10-20% of cases) I come across an error which gets t… --- ## [Vmtk networkextraction algorithm](https://discourse.slicer.org/t/vmtk-networkextraction-algorithm/16611)
**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\ **Replies:** 7\ **Last updated:** [April 12, 2021, 8:54am UTC](https://discourse.slicer.org/t/vmtk-networkextraction-algorithm/16611 "2021-04-12T08:54:52Z")
Hi All, Could someone please let me know the name of the network extraction algorithm available in VMTK? --- ## [Merging Centrelines](https://discourse.slicer.org/t/merging-centrelines/16807)
**Author:** [@CJBright](https://discourse.slicer.org/u/CJBright)\ **Replies:** 1\ **Last updated:** [April 3, 2021, 2:42am UTC](https://discourse.slicer.org/t/merging-centrelines/16807 "2021-04-03T02:42:47Z")
Hi everyone, I used a programme to calculate the centrelines of a cardiovascular model I’ve been working on. I then used a Python script to save each branch individually. It starts at one end of the model and follows e… --- ## [Using VMTK in Python](https://discourse.slicer.org/t/using-vmtk-in-python/16479)
**Author:** [@RafaelPalomar](https://discourse.slicer.org/u/RafaelPalomar)\ **Replies:** 4\ **Last updated:** [March 27, 2021, 6:36pm UTC](https://discourse.slicer.org/t/using-vmtk-in-python/16479 "2021-03-27T18:36:53Z")
Hello, I’m trying to use the functionality of VMTK in the python interpreter (Slicer stable 20210226, Linux. Slicer-VMTK extension installed from the extension manager). When trying to import vtkvmtk I ge the following … --- ## [Using VMTK Branch Extractor Programatically (Python)](https://discourse.slicer.org/t/using-vmtk-branch-extractor-programatically-python/16560)
**Author:** [@mjg](https://discourse.slicer.org/u/mjg)\ **Replies:** 1\ **Last updated:** [March 26, 2021, 3:34am UTC](https://discourse.slicer.org/t/using-vmtk-branch-extractor-programatically-python/16560 "2021-03-26T03:34:01Z")
How can I get a bifurcated centerline as two separate numpy arrays? I can view the two centerlines with the below code. How can I then get the red centerline as one numpy array, and the blue centerline as another numpy a… --- ## [set work directory in VMTK/Pypes?](https://discourse.slicer.org/t/set-work-directory-in-vmtk-pypes/16563)
**Author:** [@MPP](https://discourse.slicer.org/u/MPP)\ **Replies:** 1\ **Last updated:** [March 26, 2021, 3:30am UTC](https://discourse.slicer.org/t/set-work-directory-in-vmtk-pypes/16563 "2021-03-26T03:30:17Z")
Hi all, Is it possible to set a work directory and switch to this directory at the start of a text file containing a list of VMTK commands? I developed a vmtk for an older version of VMTK that I could still easily laun… --- ## [Centerline extraction from python](https://discourse.slicer.org/t/centerline-extraction-from-python/16728)
**Author:** [@Ge\_Tang](https://discourse.slicer.org/u/Ge_Tang)\ **Replies:** 2\ **Last updated:** [March 25, 2021, 5:14pm UTC](https://discourse.slicer.org/t/centerline-extraction-from-python/16728 "2021-03-25T17:14:01Z")
Operating system: Mac Slicer version:4.11 Expected behavior: The centerline model from GUI of slicer has a different number of points compared with the centerline model I get from the python script Actual behavior: T… --- ## [Automatic vessel endpoints detection](https://discourse.slicer.org/t/automatic-vessel-endpoints-detection/16435)
**Author:** [@fuentesdt](https://discourse.slicer.org/u/fuentesdt)\ **Replies:** 1\ **Last updated:** [March 8, 2021, 8:19pm UTC](https://discourse.slicer.org/t/automatic-vessel-endpoints-detection/16435 "2021-03-08T20:19:34Z")
i started off with the VMTK package directly before I was aware of this VMTK slicer extension. Endpoints seemed to need to be manually chosen in the interface released with the original vmtk packages. What algorithm are… --- ## [gap filling of breaks between vessels](https://discourse.slicer.org/t/gap-filling-of-breaks-between-vessels/16330)
**Author:** [@fuentesdt](https://discourse.slicer.org/u/fuentesdt)\ **Replies:** 1\ **Last updated:** [March 3, 2021, 3:27pm UTC](https://discourse.slicer.org/t/gap-filling-of-breaks-between-vessels/16330 "2021-03-03T15:27:13Z")
Hi, Is there any functionality in vmtk, slicer, or itk for gap filling? something like this tensor voting method: Risser, Laurent, Franck Plouraboué, and Xavier Descombes. “Gap filling of 3-D microvascular networks by te… --- ## [VMTK centrelines - stl format in ascii mode](https://discourse.slicer.org/t/vmtk-centrelines-stl-format-in-ascii-mode/16058)
**Author:** [@Dhaya](https://discourse.slicer.org/u/Dhaya)\ **Replies:** 4\ **Last updated:** [February 18, 2021, 12:37pm UTC](https://discourse.slicer.org/t/vmtk-centrelines-stl-format-in-ascii-mode/16058 "2021-02-18T12:37:18Z")
I am new to VTMK software nad have generated the centrelines in vtp format. vmtksurfacereader -ifile “E:/geometry/v3\_shortIliacExtendIMACAP\_V2\_vtmk.stl” --pipe vmtkcenterlines -seedselector openprofiles -ofile “C:/User… --- ## [Wrong face normals after Mesh conversion (OpenFOAM)](https://discourse.slicer.org/t/wrong-face-normals-after-mesh-conversion-openfoam/15738)
**Author:** [@haontaler](https://discourse.slicer.org/u/haontaler)\ **Replies:** 3\ **Last updated:** [January 30, 2021, 5:58pm UTC](https://discourse.slicer.org/t/wrong-face-normals-after-mesh-conversion-openfoam/15738 "2021-01-30T17:58:30Z")
Hello everyone, I am not sure if this is the correct forum to post questions about VMTK mesh generation and conversion as it is not available in Slicer directly afaik. But I hope that you can still give me a hint to sol… --- ## [Mesh Parameterization](https://discourse.slicer.org/t/mesh-parameterization/15486)
**Author:** [@Shion\_Matsumoto](https://discourse.slicer.org/u/Shion_Matsumoto)\ **Replies:** 0\ **Last updated:** [January 12, 2021, 10:45pm UTC](https://discourse.slicer.org/t/mesh-parameterization/15486 "2021-01-12T22:45:25Z")
Hi, When parameterizing a mesh as in the Mapping and Patching tutorial, how is the orientation of the circumferential axis chosen? I would like to compare parameterized meshes of various vessels and would like it such … --- ## [VMTK Centerline Add-on for Blender](https://discourse.slicer.org/t/vmtk-centerline-add-on-for-blender/15405)
**Author:** [@ajorstad](https://discourse.slicer.org/u/ajorstad)\ **Replies:** 4\ **Last updated:** [January 8, 2021, 4:08pm UTC](https://discourse.slicer.org/t/vmtk-centerline-add-on-for-blender/15405 "2021-01-08T16:08:51Z")
My team has developed an add-on for Blender that loads centerlines generated by VMTK into Blender, and writes meshes from Blender so that they can be easily read by VMTK. The add-on has now been updated for the stable l… --- ## [Extract centerlines with radius variation for coronary stenosis](https://discourse.slicer.org/t/extract-centerlines-with-radius-variation-for-coronary-stenosis/15037)
**Author:** [@sajedaekram](https://discourse.slicer.org/u/sajedaekram)\ **Replies:** 0\ **Last updated:** [December 13, 2020, 5:32pm UTC](https://discourse.slicer.org/t/extract-centerlines-with-radius-variation-for-coronary-stenosis/15037 "2020-12-13T17:32:16Z")
Dear all, I would like to know about the vmtk for centerline extraction. Is it possible to extract centerlines with radius variation for coronary stenosis? I want to simulate blood flow for pressure loss in oneD simul… --- ## [vmtk-Annotation](https://discourse.slicer.org/t/vmtk-annotation/15027)
**Author:** [@safieh\_poor\_shaigan](https://discourse.slicer.org/u/safieh_poor_shaigan)\ **Replies:** 1\ **Last updated:** [December 12, 2020, 9:40pm UTC](https://discourse.slicer.org/t/vmtk-annotation/15027 "2020-12-12T21:40:18Z")
Hello How can Annotation be done in VMTK? For the Annotation of Vascular? Or Annotation the centerline path? Or For liver tissue… Annotation With the help of locational description and shape features, vessel annot… --- ## [vmtkparticletracer](https://discourse.slicer.org/t/vmtkparticletracer/14990)
**Author:** [@SPoloni](https://discourse.slicer.org/u/SPoloni)\ **Replies:** 1\ **Last updated:** [December 12, 2020, 5:48pm UTC](https://discourse.slicer.org/t/vmtkparticletracer/14990 "2020-12-12T17:48:17Z")
Hello! I have a problem with the command “vmtkparticletracer”. Putting as input the files (-ifile merge.vtu -sfile source.vtp) I obtain an empty output (traces.vtp). The command line is “vmtkparticletracer -ifile merge.… --- ## [Optical Coherence Tomography (OCT) images](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171)
**Author:** [@syedf](https://discourse.slicer.org/u/syedf)\ **Replies:** 6\ **Last updated:** [December 8, 2020, 2:23am UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171 "2020-12-08T02:23:26Z")
Hello, I was wondering if VMTK can segment OCT .dcm images. I’ve used VMTK before for MRI/CT dicoms, but when I try it for the OCT file, I get no output. The PypePad executes, but stops after a while. Command: vmtklev… --- ## [Vmtkcenterlines -seedselector pointlist problem](https://discourse.slicer.org/t/vmtkcenterlines-seedselector-pointlist-problem/14744)
**Author:** [@Haim\_Ezer](https://discourse.slicer.org/u/Haim_Ezer)\ **Replies:** 2\ **Last updated:** [November 26, 2020, 5:47am UTC](https://discourse.slicer.org/t/vmtkcenterlines-seedselector-pointlist-problem/14744 "2020-11-26T05:47:12Z")
Hello, Luca, Everyone, vmtkcenterlines.py -ifile “Case1.vtk” -seedselector pointlist -sourcepoints 0.00571137 -0.01748690 -0.02422070 -targetpoints 0.00571797 -0.00042939 -0.02172360 But what I get is this: Traceback … --- ## [How to add color to my surface in VMTK](https://discourse.slicer.org/t/how-to-add-color-to-my-surface-in-vmtk/14767)
**Author:** [@13552060266](https://discourse.slicer.org/u/13552060266)\ **Replies:** 1\ **Last updated:** [November 25, 2020, 8:19pm UTC](https://discourse.slicer.org/t/how-to-add-color-to-my-surface-in-vmtk/14767 "2020-11-25T20:19:26Z")
Operating system:VMTK Slicer version:1.4 Expected behavior: Actual behavior: I want to add color to my surface in VMTK. Does anyone know how to do it? It’s better to write the pypepad command. I’m very impressed. --- ## [Where can I get the trial VMTKLab?](https://discourse.slicer.org/t/where-can-i-get-the-trial-vmtklab/14658)
**Author:** [@Yang\_Yu](https://discourse.slicer.org/u/Yang_Yu)\ **Replies:** 3\ **Last updated:** [November 24, 2020, 7:36am UTC](https://discourse.slicer.org/t/where-can-i-get-the-trial-vmtklab/14658 "2020-11-24T07:36:14Z")
I want to play with VMTKLab to see whether it can satisfy my need,. Where can I have a try version? --- ## [Error when generate centerline wih my own fbx.](https://discourse.slicer.org/t/error-when-generate-centerline-wih-my-own-fbx/14564)
**Author:** [@Yang\_Yu](https://discourse.slicer.org/u/Yang_Yu)\ **Replies:** 2\ **Last updated:** [November 13, 2020, 1:15am UTC](https://discourse.slicer.org/t/error-when-generate-centerline-wih-my-own-fbx/14564 "2020-11-13T01:15:33Z")
I converted the fbx to obj, then used the ParaView software to convert obj to vtp file, then used VMTK like above, but no matter which fbx I chose, the above error always occured . Why is that? --- ## [How does vmtksurfacecenterlineprojection work](https://discourse.slicer.org/t/how-does-vmtksurfacecenterlineprojection-work/14513)
**Author:** [@Nadun\_19](https://discourse.slicer.org/u/Nadun_19)\ **Replies:** 1\ **Last updated:** [November 13, 2020, 12:28am UTC](https://discourse.slicer.org/t/how-does-vmtksurfacecenterlineprojection-work/14513 "2020-11-13T00:28:52Z")
Hi I was wondering how the vmtksurfacecenterlineprojection function actually carries out the centerline projection to a surface. Thanks Nadun [Previous page](https://discourse.slicer.org/c/community/vmtk/28.md?page=4) [Next page](https://discourse.slicer.org/c/community/vmtk/28.md?page=6)