# aneurysm removal and reconstruct the parent vessel

**URL:** <https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304>\
**Category:** VMTK\
**Tags:** extensions-manager, python\
**Created:** [October 18, 2023, 3:48pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304 "2023-10-18T15:48:22Z")\
**Posts on this page:** 11\
**Page:** 1

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**Author:** ![Tingchenccmu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tingchenccmu/32/67994_2.png) [@Tingchenccmu](https://discourse.slicer.org/u/Tingchenccmu)\
**Post date:** [October 18, 2023, 3:48pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/1 "2023-10-18T15:48:22Z")

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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/ParentVesselReconstructions. Do you know why?

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**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [October 19, 2023, 1:17am UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/2 "2023-10-19T01:17:03Z")

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> [@Tingchenccmu](#):
>
> vmtk/vmtkApps/CerebralAneurysms

Does this help?

> <https://github.com/vmtk/vmtk/tree/master/vmtkApps/CerebralAneurysms/ParentVesselReconstruction>
>
> //github.com/vmtk/vmtk/tree/master/vmtkApps/CerebralAneurysms/ParentVesselReconstruction

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<div class="post-metadata">

**Author:** ![Tingchenccmu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tingchenccmu/32/67994_2.png) [@Tingchenccmu](https://discourse.slicer.org/u/Tingchenccmu)\
**Post date:** [October 24, 2023, 5:32am UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/3 "2023-10-24T05:32:09Z")

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Thanks so much! It does work. 😁

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**Author:** ![hamedtopic](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hamedtopic/32/521_2.png) [@hamedtopic](https://discourse.slicer.org/u/hamedtopic)\
**Post date:** [October 25, 2023, 9:45pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/4 "2023-10-25T21:45:13Z")

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Are you working on brain aneurysms?

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**Author:** ![hamedtopic](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hamedtopic/32/521_2.png) [@hamedtopic](https://discourse.slicer.org/u/hamedtopic)\
**Post date:** [October 25, 2023, 9:46pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/5 "2023-10-25T21:46:10Z")

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is it available for us to remove the aneurysm right from the extension in Slicer?

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**Author:** ![hamedtopic](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hamedtopic/32/521_2.png) [@hamedtopic](https://discourse.slicer.org/u/hamedtopic)\
**Post date:** [October 25, 2023, 9:58pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/6 "2023-10-25T21:58:58Z")

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how about aneurysm removal?

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 25, 2023, 11:48pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/7 "2023-10-25T23:48:41Z")

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What do you mean by “aneurysm removal”? Removing of aneurysms from the segmentation? You can do that using the Segment Editor module’s Scissors tool.

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**Author:** ![hamedtopic](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hamedtopic/32/521_2.png) [@hamedtopic](https://discourse.slicer.org/u/hamedtopic)\
**Post date:** [October 26, 2023, 2:42am UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/8 "2023-10-26T02:42:45Z")

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I mean this: [Parent vessel reconstruction | vmtk - the Vascular Modelling Toolkit](http://www.vmtk.org/tutorials/ParentVesselReconstruction.html)  
though it is just for saccular aneurysm.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 26, 2023, 3:16am UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/9 "2023-10-26T03:16:46Z")

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The simplest is to cut off the aneurysm sack using Scissors effect and then use Smoothing effect’s brush mode to touch up. This should be quite quick and easy.

If you want to automate it (which may pay off if you need to process hundreds of images and the script works flawlessly) then I would recommend to run the referenced Pypes scripts by copying the contents into Slicer’s Python interpreter (or maybe put it into a Slicer module for your convenience).

Making the Pypes scripts work as they are may be an option, too. I always just use those scripts as examples, so I don’t know if you can still run the via the command line.

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<div class="post-metadata">

**Author:** ![Tingchenccmu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tingchenccmu/32/67994_2.png) [@Tingchenccmu](https://discourse.slicer.org/u/Tingchenccmu)\
**Post date:** [October 27, 2023, 12:09pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/10 "2023-10-27T12:09:02Z")

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Hello! I think we have met the same problem. I also want to perform digital aneurysm removal and reconstruct the parent vessel according to the tutorials. But there is something wrong when I run this code “python patchandinterpolatecenterlines.py directoryPath id1 lateral” in PypePad during the Centerlines interpolation step. It shows that no module named ‘vmtk.python’. You know it is so confusing when errors happen according to the tutorials. If you have the answer, please let me know and thanks a lot.

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**Author:** ![hamedtopic](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hamedtopic/32/521_2.png) [@hamedtopic](https://discourse.slicer.org/u/hamedtopic)\
**Post date:** [October 27, 2023, 6:04pm UTC](https://discourse.slicer.org/t/aneurysm-removal-and-reconstruct-the-parent-vessel/32304/11 "2023-10-27T18:04:09Z")

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Thanks, Andras, the question is that how accurate the centerline will be by manually removing the aneurysm. But since the code is just for the saccular aneurysms, it may make sense that one does it manually.