# \#vmtk-centerline

**URL:** https://discourse.slicer.org/tag/vmtk-centerline/329.md

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## [Automatic Extract Centerline with VMTK python (auto detect) from trachea segementation](https://discourse.slicer.org/t/automatic-extract-centerline-with-vmtk-python-auto-detect-from-trachea-segementation/46356)

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**Author:** [@hadrien\_calmet](https://discourse.slicer.org/u/hadrien_calmet)\
**Replies:** 0\
**Last updated:** [March 2, 2026, 11:09am UTC](https://discourse.slicer.org/t/automatic-extract-centerline-with-vmtk-python-auto-detect-from-trachea-segementation/46356 "2026-03-02T11:09:58Z")

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Hi everyone. Since several people seem to be working on this without a clear answer, I’m sharing my contribution in case it helps others in the community. Final main script: make\_clean\_centerlines\_zmax\_generic.py Cle…

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## [Generate segmentation node (binary label map) from centerline](https://discourse.slicer.org/t/generate-segmentation-node-binary-label-map-from-centerline/26166)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 5\
**Last updated:** [February 16, 2026, 1:03am UTC](https://discourse.slicer.org/t/generate-segmentation-node-binary-label-map-from-centerline/26166 "2026-02-16T01:03:58Z")

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Hi, I want to obtain a label map corresponding to centerline generated by VMTK. I would also like to get a different label for voxels belonging to different branches. I have generated centerline tree for a vessel label…

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## [Curvature, torsion from VMTK](https://discourse.slicer.org/t/curvature-torsion-from-vmtk/45652)

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**Author:** [@kuoi](https://discourse.slicer.org/u/kuoi)\
**Replies:** 0\
**Last updated:** [January 1, 2026, 5:24pm UTC](https://discourse.slicer.org/t/curvature-torsion-from-vmtk/45652 "2026-01-01T17:24:12Z")

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Hello, I am using the Extract Centerline module. I obtained one centerline and one table containing a single line with a pair of curvature and torsion values. I noticed that curvature and torsion are reported in the exp…

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## [VMTK generated centerline curves missing structure hierarchy](https://discourse.slicer.org/t/vmtk-generated-centerline-curves-missing-structure-hierarchy/36586)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 6\
**Last updated:** [April 29, 2025, 7:59am UTC](https://discourse.slicer.org/t/vmtk-generated-centerline-curves-missing-structure-hierarchy/36586 "2025-04-29T07:59:47Z")

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Hi, I am using the Extract Centerline module of VMTK extension to generate network and centerline curves for the network and centerline models. The problem is that the network curve generated is missing the hierarchical…

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## [VMTK Centerline Tree Model Implementation Problem](https://discourse.slicer.org/t/vmtk-centerline-tree-model-implementation-problem/41760)

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**Author:** [@yoonjh119](https://discourse.slicer.org/u/yoonjh119)\
**Replies:** 0\
**Last updated:** [February 18, 2025, 4:39pm UTC](https://discourse.slicer.org/t/vmtk-centerline-tree-model-implementation-problem/41760 "2025-02-18T16:39:04Z")

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Hello, I am implementing the centerline function of VMTK so that it can be executed with Python code. Recently, I have completed the implementation of the network model and am implementing the tree model. After loading t…

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## [Slicer vmtk centerline network model in coronary artery](https://discourse.slicer.org/t/slicer-vmtk-centerline-network-model-in-coronary-artery/41619)

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**Author:** [@yoonjh119](https://discourse.slicer.org/u/yoonjh119)\
**Replies:** 2\
**Last updated:** [February 13, 2025, 11:35am UTC](https://discourse.slicer.org/t/slicer-vmtk-centerline-network-model-in-coronary-artery/41619 "2025-02-13T11:35:39Z")

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I am extracting the centerline through a network model based on coronary artery segmentation including the aorta. When extracting the centerline, the centerline of the aorta-LM connection (red arrow) often deviates from …

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## [Extract centerline via python](https://discourse.slicer.org/t/extract-centerline-via-python/41631)

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**Author:** [@laurabc](https://discourse.slicer.org/u/laurabc)\
**Replies:** 0\
**Last updated:** [February 11, 2025, 3:32pm UTC](https://discourse.slicer.org/t/extract-centerline-via-python/41631 "2025-02-11T15:32:35Z")

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I’ve come across several posts about this module, but I haven’t been able to get it working with a Python script. I want to extract the centerline of the aortic root and obtain orthogonal planes across the centerline for…

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## [VMTK Extract Centerline with python console](https://discourse.slicer.org/t/vmtk-extract-centerline-with-python-console/31596)

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**Author:** [@wesselk](https://discourse.slicer.org/u/wesselk)\
**Replies:** 16\
**Last updated:** [December 28, 2024, 2:29pm UTC](https://discourse.slicer.org/t/vmtk-extract-centerline-with-python-console/31596 "2024-12-28T14:29:52Z")

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Hello, I am looking to utilize the vmtk module for the ‘Extract Centerline’ and ‘Cross-section Analysis’ features with a purely scripted method, similar to this issue which had a lot of great information. A brief summar…

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## [How to export centerline model as .vtp files in slicer](https://discourse.slicer.org/t/how-to-export-centerline-model-as-vtp-files-in-slicer/40871)

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**Author:** [@pc666nice](https://discourse.slicer.org/u/pc666nice)\
**Replies:** 0\
**Last updated:** [December 27, 2024, 2:56pm UTC](https://discourse.slicer.org/t/how-to-export-centerline-model-as-vtp-files-in-slicer/40871 "2024-12-27T14:56:46Z")

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Dear all: I used the python code that has been proposed by https://discourse.slicer.org/t/automatic-centerline/14829/23?u=pc666nice, but I can only generate the centerline curve, how I can generate centerline model and …

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## [Vmtk centerlines/network metrics](https://discourse.slicer.org/t/vmtk-centerlines-network-metrics/40362)

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**Author:** [@LB95](https://discourse.slicer.org/u/LB95)\
**Replies:** 0\
**Last updated:** [November 24, 2024, 11:59pm UTC](https://discourse.slicer.org/t/vmtk-centerlines-network-metrics/40362 "2024-11-24T23:59:17Z")

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Hi, I’ve been doing a lot of reading on these forums and managed to piece together a lot, however I’m still having some difficulty solving my problem. My aim is to extract the centerline of a vessel tree in order to com…

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## [What is the best way to segment renal arteries to an interlobar level?](https://discourse.slicer.org/t/what-is-the-best-way-to-segment-renal-arteries-to-an-interlobar-level/40209)

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**Author:** [@ntzvetkov](https://discourse.slicer.org/u/ntzvetkov)\
**Replies:** 7\
**Last updated:** [November 23, 2024, 7:47pm UTC](https://discourse.slicer.org/t/what-is-the-best-way-to-segment-renal-arteries-to-an-interlobar-level/40209 "2024-11-23T19:47:28Z")

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I’ve been struggling with the segmentation of the renal artery branches for so long. From what I have read VMTK would be a good tool to do a proper segmentation, but I just can’t figure out how to apply it. There is an m…

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## [How can I draw normal vectors of a centerline in the 3D slicer?](https://discourse.slicer.org/t/how-can-i-draw-normal-vectors-of-a-centerline-in-the-3d-slicer/37933)

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**Author:** [@mssm](https://discourse.slicer.org/u/mssm)\
**Replies:** 6\
**Last updated:** [August 19, 2024, 11:00pm UTC](https://discourse.slicer.org/t/how-can-i-draw-normal-vectors-of-a-centerline-in-the-3d-slicer/37933 "2024-08-19T23:00:54Z")

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Dear respected experts, Please teach me how to draw normal vectors in the 3D slicer. I want to draw the normal vectors of the centerline of blood vessels obtained by VMTK’s “Extract centerline” module to visualize the …

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## [Centerline extraction C++ having different result from the slicer](https://discourse.slicer.org/t/centerline-extraction-c-having-different-result-from-the-slicer/32370)

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**Author:** [@liy0na](https://discourse.slicer.org/u/liy0na)\
**Replies:** 2\
**Last updated:** [August 12, 2024, 12:47pm UTC](https://discourse.slicer.org/t/centerline-extraction-c-having-different-result-from-the-slicer/32370 "2024-08-12T12:47:56Z")

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Hello, I have an STL file containing a surface mesh. When I use the slicer I can easily extract the centerlines from it. However when I use the following C++ code. I am only getting 3 output points. vtkSmartPointe…

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## [VMTK - cross-sectional perimeter calculation](https://discourse.slicer.org/t/vmtk-cross-sectional-perimeter-calculation/37747)

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**Author:** [@JoGervCon](https://discourse.slicer.org/u/JoGervCon)\
**Replies:** 3\
**Last updated:** [August 8, 2024, 5:26pm UTC](https://discourse.slicer.org/t/vmtk-cross-sectional-perimeter-calculation/37747 "2024-08-08T17:26:11Z")

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Hi, I am using the VMTK extension to calculate the cross sectional area of arteries. Is there a function that can calculate the perimeter of the cross sectional area along the centerline?

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## [Question about the algorithm of the extract centerline module (VMTK)](https://discourse.slicer.org/t/question-about-the-algorithm-of-the-extract-centerline-module-vmtk/37495)

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**Author:** [@Seokjun\_Hwang](https://discourse.slicer.org/u/Seokjun_Hwang)\
**Replies:** 1\
**Last updated:** [July 22, 2024, 10:07pm UTC](https://discourse.slicer.org/t/question-about-the-algorithm-of-the-extract-centerline-module-vmtk/37495 "2024-07-22T22:07:19Z")

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Using the extract centerline module, I have obtained the centerline of the aorta, as shown in the picture. My research team members are interested in understanding and want to explain how this module generates the cent…

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## [VMTK - cross-sectional area and angle of bifurcation](https://discourse.slicer.org/t/vmtk-cross-sectional-area-and-angle-of-bifurcation/36818)

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**Author:** [@Patrick](https://discourse.slicer.org/u/Patrick)\
**Replies:** 0\
**Last updated:** [June 16, 2024, 6:05am UTC](https://discourse.slicer.org/t/vmtk-cross-sectional-area-and-angle-of-bifurcation/36818 "2024-06-16T06:05:17Z")

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Hi, I am using Slicer v 5.4.0 and currently trying to compute: cross-sectional area of a vessel angle of bifurcation I am using the cross-section analysis tool in VMTK but I am not sure if I am doing it correctly. I …

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## [Avoid creating multiple module widget instances from a python script](https://discourse.slicer.org/t/avoid-creating-multiple-module-widget-instances-from-a-python-script/36717)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 1\
**Last updated:** [June 12, 2024, 10:55am UTC](https://discourse.slicer.org/t/avoid-creating-multiple-module-widget-instances-from-a-python-script/36717 "2024-06-12T10:55:08Z")

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Hi, I am trying to generate centerlines for a batch of segmentation masks. I use a python script that uses the VMTK Extract Centerline widget. The issue is that for every new segmentation, Slicer opens a new Extract Cen…

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## [Binary segmentation mask to centerline polydata using a python script](https://discourse.slicer.org/t/binary-segmentation-mask-to-centerline-polydata-using-a-python-script/36523)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 4\
**Last updated:** [June 4, 2024, 10:53am UTC](https://discourse.slicer.org/t/binary-segmentation-mask-to-centerline-polydata-using-a-python-script/36523 "2024-06-04T10:53:12Z")

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Hi, I am working on Ubuntu 20.04.6 LTS with the ATM’22 dataset. I have the CT volumes and the binary segmenatation mask of the pulmonary airway as nifty (.nii.gz) files. To get the centerline of the pulmonary airway, I …

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## [Seeking Advice on Multi-Color Branching for Vascular Models](https://discourse.slicer.org/t/seeking-advice-on-multi-color-branching-for-vascular-models/36292)

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**Author:** [@petit223](https://discourse.slicer.org/u/petit223)\
**Replies:** 6\
**Last updated:** [May 29, 2024, 2:13pm UTC](https://discourse.slicer.org/t/seeking-advice-on-multi-color-branching-for-vascular-models/36292 "2024-05-29T14:13:31Z")

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Hello everyone, I am currently working on a project where I aim to color different branches of a vascular model with distinct colors. I start by selecting a main vessel and use the first branching point as an anchor. Fr…

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## [Broken centerline model with continuous voronoi diagram](https://discourse.slicer.org/t/broken-centerline-model-with-continuous-voronoi-diagram/35755)

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**Author:** [@ruili](https://discourse.slicer.org/u/ruili)\
**Replies:** 3\
**Last updated:** [April 27, 2024, 11:36am UTC](https://discourse.slicer.org/t/broken-centerline-model-with-continuous-voronoi-diagram/35755 "2024-04-27T11:36:08Z")

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Hello, I have been using the Extract Centerline module to extract the centerlines from some vessel segmentation. However, I have been struggling to get a fully connected centerline model even though the segmentation is …

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## [Slicer 3D view not displaying labels of markup curves properly](https://discourse.slicer.org/t/slicer-3d-view-not-displaying-labels-of-markup-curves-properly/34364)

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**Author:** [@ruili](https://discourse.slicer.org/u/ruili)\
**Replies:** 5\
**Last updated:** [April 26, 2024, 4:16pm UTC](https://discourse.slicer.org/t/slicer-3d-view-not-displaying-labels-of-markup-curves-properly/34364 "2024-04-26T16:16:40Z")

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Hello, I am writing to report what seems to be a bug with the labelling of centerline curves or markup curves in general in the 3D view. The details of this bug can be found in a previous discussion here. But to summari…

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## [VMTK Inlet and Outlet Point Creation](https://discourse.slicer.org/t/vmtk-inlet-and-outlet-point-creation/35338)

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**Author:** [@THartman](https://discourse.slicer.org/u/THartman)\
**Replies:** 6\
**Last updated:** [April 10, 2024, 10:09pm UTC](https://discourse.slicer.org/t/vmtk-inlet-and-outlet-point-creation/35338 "2024-04-10T22:09:08Z")

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I’m currently building an extension that uses VMTK to extract the centerlines of vessel trees in the lungs, and am looking to speed it up by adding some preprocessing to determine the inlet and outlet points of the blood…

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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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## [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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## [Application crashes when extracting centerline](https://discourse.slicer.org/t/application-crashes-when-extracting-centerline/34751)

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**Author:** [@Paula\_Feldman](https://discourse.slicer.org/u/Paula_Feldman)\
**Replies:** 2\
**Last updated:** [March 7, 2024, 12:33pm UTC](https://discourse.slicer.org/t/application-crashes-when-extracting-centerline/34751 "2024-03-07T12:33:09Z")

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Unfortunatelly the forum won´t allow me to upload the mesh. i´ve analyzed it and found no clue as to why it fails, with some meshes it works smoothly I´m using the latest slicer stable release

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## [Exporting to as GLTF changes names](https://discourse.slicer.org/t/exporting-to-as-gltf-changes-names/34623)

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**Author:** [@MuckYu](https://discourse.slicer.org/u/MuckYu)\
**Replies:** 0\
**Last updated:** [February 29, 2024, 6:34pm UTC](https://discourse.slicer.org/t/exporting-to-as-gltf-changes-names/34623 "2024-02-29T18:34:22Z")

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I am trying to export the centerline from a scene with a python script. OBJ/STL etc. don’t export the centerline at all. So I have to use GLTF - which works fine so far. The problem here is that it exports the whole s…

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## [Extract centerline curves in two disconnected branches](https://discourse.slicer.org/t/extract-centerline-curves-in-two-disconnected-branches/34135)

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**Author:** [@ruili](https://discourse.slicer.org/u/ruili)\
**Replies:** 6\
**Last updated:** [February 16, 2024, 12:13pm UTC](https://discourse.slicer.org/t/extract-centerline-curves-in-two-disconnected-branches/34135 "2024-02-16T12:13:26Z")

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Hi! I have been using the ExtractCenterline module in 3D slicer to extract centerlines in a vessel structure. The original segmentation that I have has a small part of a large vessel, from which multiple branches of smal…

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## [VMTK Extract Centerline extracts centerline curves with both a curve and a straight line](https://discourse.slicer.org/t/vmtk-extract-centerline-extracts-centerline-curves-with-both-a-curve-and-a-straight-line/33954)

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**Author:** [@ruili](https://discourse.slicer.org/u/ruili)\
**Replies:** 2\
**Last updated:** [January 25, 2024, 4:17pm UTC](https://discourse.slicer.org/t/vmtk-extract-centerline-extracts-centerline-curves-with-both-a-curve-and-a-straight-line/33954 "2024-01-25T16:17:26Z")

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Hello! I have been using the Extract Centerline module from the SlicerVMTK extension to extract the centerline of a vessel struction. The extracted ‘Centerline Model’ is relatively accurate, however, the ‘Centerline Curv…

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## [VMTK automatic centerline and export control points as XYZ coordinates](https://discourse.slicer.org/t/vmtk-automatic-centerline-and-export-control-points-as-xyz-coordinates/33841)

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**Author:** [@RD\_morph](https://discourse.slicer.org/u/RD_morph)\
**Replies:** 0\
**Last updated:** [January 17, 2024, 7:52pm UTC](https://discourse.slicer.org/t/vmtk-automatic-centerline-and-export-control-points-as-xyz-coordinates/33841 "2024-01-17T19:52:06Z")

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Operating system: Windows 10 Slicer version: 5.6.1 Expected behavior: Use the ExtractCenterline.py code to automatically generate centerlines for existing models and export XYZ control points of centerlines Actual beh…

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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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