# \#segmentation

**URL:** https://discourse.slicer.org/tag/segmentation/8.md

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

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## [Mitral valve segmentation : echo or CT-scan?](https://discourse.slicer.org/t/mitral-valve-segmentation-echo-or-ct-scan/48173)

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**Author:** [@Giueva](https://discourse.slicer.org/u/Giueva)\
**Replies:** 3\
**Last updated:** [September 21, 2026, 1:32am UTC](https://discourse.slicer.org/t/mitral-valve-segmentation-echo-or-ct-scan/48173 "2026-09-21T01:32:32Z")

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Hello everyone, i am starting to use SlicerHeart from 3D Slicer. I want to segment the open and closed mitral valve (annulus, mitral leaflet, cordae and papillary muscle). I taught the best was from 3D echo images, but i…

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## [How does the Margin (grow/shrink) effect handle anisotropic voxel spacing?](https://discourse.slicer.org/t/how-does-the-margin-grow-shrink-effect-handle-anisotropic-voxel-spacing/48113)

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**Author:** [@Farah\_BH](https://discourse.slicer.org/u/Farah_BH)\
**Replies:** 1\
**Last updated:** [September 14, 2026, 10:10pm UTC](https://discourse.slicer.org/t/how-does-the-margin-grow-shrink-effect-handle-anisotropic-voxel-spacing/48113 "2026-09-14T22:10:31Z")

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Hello, I’m using the Margin effect in Segment Editor to isotropically expand a segment on CT data with anisotropic voxel spacing. When I request a 3.00 mm margin, the UI reports an actual expansion of 2.9 × 2.9 × 2.5 mm…

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## [How to extract 2D vessels quickly and accurately?](https://discourse.slicer.org/t/how-to-extract-2d-vessels-quickly-and-accurately/40039)

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**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 4\
**Last updated:** [September 11, 2026, 11:53am UTC](https://discourse.slicer.org/t/how-to-extract-2d-vessels-quickly-and-accurately/40039 "2026-09-11T11:53:04Z")

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Hello, I’m trying to segment out the left anterior descending coronary artery from a contrast enhanced XR image. The goal is to calculate the surface area of the vessel, and then compare this longitudinally within patie…

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## [Request for feedback on ToothAnalyserMicroCT extension PR](https://discourse.slicer.org/t/request-for-feedback-on-toothanalysermicroct-extension-pr/48077)

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**Author:** [@Lukon](https://discourse.slicer.org/u/Lukon)\
**Replies:** 2\
**Last updated:** [September 7, 2026, 3:01pm UTC](https://discourse.slicer.org/t/request-for-feedback-on-toothanalysermicroct-extension-pr/48077 "2026-09-07T15:01:21Z")

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Hi everyone, I hope this is the right place to ask for some guidance. I submitted a pull request to add our extension, ToothAnalyserMicroCT, to the Slicer Extensions Catalog: Pull Request #2342 ToothAnalyserMicroCT i…

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## [How to quickly recompile updated code based on the current build version](https://discourse.slicer.org/t/how-to-quickly-recompile-updated-code-based-on-the-current-build-version/48089)

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**Author:** [@zhuofalin](https://discourse.slicer.org/u/zhuofalin)\
**Replies:** 1\
**Last updated:** [September 7, 2026, 2:23pm UTC](https://discourse.slicer.org/t/how-to-quickly-recompile-updated-code-based-on-the-current-build-version/48089 "2026-09-07T14:23:19Z")

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Hello, I am very happy to be back in the Slicer community.:grinning\_face: I typically use an older version of the slicer for development, but thanks to the efforts of the developers, new features are constantly being a…

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## [Soft-tissue segmentation: advice needed](https://discourse.slicer.org/t/soft-tissue-segmentation-advice-needed/48060)

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**Author:** [@Toumia\_Bessedik](https://discourse.slicer.org/u/Toumia_Bessedik)\
**Replies:** 0\
**Last updated:** [September 3, 2026, 10:20pm UTC](https://discourse.slicer.org/t/soft-tissue-segmentation-advice-needed/48060 "2026-09-03T22:20:55Z")

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Hello, I would like to get your opinion on an approach I am currently using to refine the segmentation of soft tissues in a head MRI. I used TotalSegmentator (MR) to automatically segment the soft tissues, particularly…

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## [Segmentations Module - Opacity Issue](https://discourse.slicer.org/t/segmentations-module-opacity-issue/48044)

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**Author:** [@Malaquias\_Cerrillo](https://discourse.slicer.org/u/Malaquias_Cerrillo)\
**Replies:** 2\
**Last updated:** [September 3, 2026, 5:15pm UTC](https://discourse.slicer.org/t/segmentations-module-opacity-issue/48044 "2026-09-03T17:15:34Z")

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Hi everybody, i’m experiencing some trouble in the latest version 5.12.3 trying to shift the opacity of the different segmentations. However, I can shift the overall opacity of de segmentation node, does this happens to …

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## [New Extension: DRAI AI 3D Segmentation and Modelling Extension for 3D Slicer](https://discourse.slicer.org/t/new-extension-drai-ai-3d-segmentation-and-modelling-extension-for-3d-slicer/48031)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 0\
**Last updated:** [September 1, 2026, 4:12pm UTC](https://discourse.slicer.org/t/new-extension-drai-ai-3d-segmentation-and-modelling-extension-for-3d-slicer/48031 "2026-09-01T16:12:40Z")

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AI-powered segmentation for Spine/Pelvis (CT) and Aorta–Iliac–Femoral Arteries (CTA). Upload CT volumes directly from 3D Slicer to the DRAI server and receive high-quality, multi-label 3D segmentation masks and models w…

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## [Aligning STL anatomical models with MRI segmentations in 3D Slicer](https://discourse.slicer.org/t/aligning-stl-anatomical-models-with-mri-segmentations-in-3d-slicer/47983)

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**Author:** [@Toumia\_Bessedik](https://discourse.slicer.org/u/Toumia_Bessedik)\
**Replies:** 4\
**Last updated:** [August 27, 2026, 2:11pm UTC](https://discourse.slicer.org/t/aligning-stl-anatomical-models-with-mri-segmentations-in-3d-slicer/47983 "2026-08-27T14:11:01Z")

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Hi, I am working with an MRI of the head and I have existing STL models for several anatomical domains, including the skull, brain, soft tissue (ST), etc. I would like to use these STL models as references and align th…

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## [Question on Segmentation and Smoothing a Gecko Skull](https://discourse.slicer.org/t/question-on-segmentation-and-smoothing-a-gecko-skull/47990)

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**Author:** [@GBurkin](https://discourse.slicer.org/u/GBurkin)\
**Replies:** 2\
**Last updated:** [August 26, 2026, 6:51pm UTC](https://discourse.slicer.org/t/question-on-segmentation-and-smoothing-a-gecko-skull/47990 "2026-08-26T18:51:15Z")

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Hello, I’m working with CT scans of small geckos, and I’m working on segmenting their skulls and full skeletons. I have mostly taught myself how to segment via YouTube and help pages, but most of these are focused on hu…

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## [How to segment bad quality 4D MRI FLOW](https://discourse.slicer.org/t/how-to-segment-bad-quality-4d-mri-flow/47975)

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**Author:** [@VERRUCKT](https://discourse.slicer.org/u/VERRUCKT)\
**Replies:** 1\
**Last updated:** [August 26, 2026, 1:24pm UTC](https://discourse.slicer.org/t/how-to-segment-bad-quality-4d-mri-flow/47975 "2026-08-26T13:24:14Z")

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Hi everyone :slight\_smile: I’m working on aortic segmentation from 4D flow MRI. I’ve been using TotalSegmentator but results are poor, I assume mostly a domain issue, since it’s CT-trained, plus the low SNR of my data. …

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## [Bronchus segmentation loads but is not visible, while TotalSegmentator segmentation displays correctly](https://discourse.slicer.org/t/bronchus-segmentation-loads-but-is-not-visible-while-totalsegmentator-segmentation-displays-correctly/47886)

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**Author:** [@Tien\_Huynh](https://discourse.slicer.org/u/Tien_Huynh)\
**Replies:** 1\
**Last updated:** [August 23, 2026, 12:54pm UTC](https://discourse.slicer.org/t/bronchus-segmentation-loads-but-is-not-visible-while-totalsegmentator-segmentation-displays-correctly/47886 "2026-08-23T12:54:38Z")

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Hello, I am trying to compare two airway segmentations in 3D Slicer: a Bronchus segmentation generated by one algorithm and an airway segmentation generated by TotalSegmentator. The TotalSegmentator segmentation loads …

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## [Advice on cleaning up incredibly noisy segmentations](https://discourse.slicer.org/t/advice-on-cleaning-up-incredibly-noisy-segmentations/47837)

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**Author:** [@Chelonian](https://discourse.slicer.org/u/Chelonian)\
**Replies:** 6\
**Last updated:** [August 16, 2026, 6:37pm UTC](https://discourse.slicer.org/t/advice-on-cleaning-up-incredibly-noisy-segmentations/47837 "2026-08-16T18:37:54Z")

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I’m trying to segment the internals of some incredibly noisy CT scans. example of what I’m working with I’ve managed to segment the intestines but I’m not happy at all with the quality of the segments or the amount of…

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## [Request for Source Code or Alternatives Extension/Plugins Similar to " Colon CAD in 3D Slicer"](https://discourse.slicer.org/t/request-for-source-code-or-alternatives-extension-plugins-similar-to-colon-cad-in-3d-slicer/47846)

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**Author:** [@qn\_Huynh](https://discourse.slicer.org/u/qn_Huynh)\
**Replies:** 1\
**Last updated:** [August 10, 2026, 5:49pm UTC](https://discourse.slicer.org/t/request-for-source-code-or-alternatives-extension-plugins-similar-to-colon-cad-in-3d-slicer/47846 "2026-08-10T17:49:10Z")

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Request for Source Code or Alternatives Extension/Plugins Similar to " Colon CAD in 3D Slicer" I am very interested in the project developed by Xu and colleagues, entitled “An Open-Source Implementation of Colon CAD in …

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## [Level tracing tool is either an amnesiac or thinks I'm too stupid to segment on my own](https://discourse.slicer.org/t/level-tracing-tool-is-either-an-amnesiac-or-thinks-im-too-stupid-to-segment-on-my-own/47814)

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**Author:** [@Chelonian](https://discourse.slicer.org/u/Chelonian)\
**Replies:** 2\
**Last updated:** [August 8, 2026, 8:13am UTC](https://discourse.slicer.org/t/level-tracing-tool-is-either-an-amnesiac-or-thinks-im-too-stupid-to-segment-on-my-own/47814 "2026-08-08T08:13:36Z")

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Operating system: Windows 11 Pro Slicer version: 5.12.0 Expected behavior: Each level I trace using the “level tracing” tool is saved and placed into the 3d model of that segment Actual behavior: random sections (cons…

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## [A newcomer to 3D Slicer shares a cinematic interior fly-through of his own LAD and asks whether the rippled texture on the lumen wall is real anatomy or a segmentation/reconstruction artifact.](https://discourse.slicer.org/t/a-newcomer-to-3d-slicer-shares-a-cinematic-interior-fly-through-of-his-own-lad-and-asks-whether-the-rippled-texture-on-the-lumen-wall-is-real-anatomy-or-a-segmentation-reconstruction-artifact/47778)

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**Author:** [@Passerby](https://discourse.slicer.org/u/Passerby)\
**Replies:** 3\
**Last updated:** [August 3, 2026, 5:20pm UTC](https://discourse.slicer.org/t/a-newcomer-to-3d-slicer-shares-a-cinematic-interior-fly-through-of-his-own-lad-and-asks-whether-the-rippled-texture-on-the-lumen-wall-is-real-anatomy-or-a-segmentation-reconstruction-artifact/47778 "2026-08-03T17:20:26Z")

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Hi all, This is my first real project in 3D Slicer, and my first time using Guided Artery Segmentation, so I’d value a reality check from people who work with cardiac CTA. I’m a retired electrical engineer and commercia…

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## [Segmenting Occipital Bone on a Head CT](https://discourse.slicer.org/t/segmenting-occipital-bone-on-a-head-ct/47777)

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**Author:** [@Kate\_Sticha](https://discourse.slicer.org/u/Kate_Sticha)\
**Replies:** 1\
**Last updated:** [August 2, 2026, 11:49am UTC](https://discourse.slicer.org/t/segmenting-occipital-bone-on-a-head-ct/47777 "2026-08-02T11:49:51Z")

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Operating system: 3D slicer Slicer version: 5.8.1 Expected behavior: I am trying to segment the occipital bone of a Head CT. I set the initial threshold to 226-3071 in order to capture the skull bone. I think use the c…

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## [New Colorize Volume module](https://discourse.slicer.org/t/new-colorize-volume-module/32254)

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**Author:** [@jaimigray](https://discourse.slicer.org/u/jaimigray)\
**Replies:** 18\
**Last updated:** [July 31, 2026, 2:45pm UTC](https://discourse.slicer.org/t/new-colorize-volume-module/32254 "2026-07-31T14:45:36Z")

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Just added to 3D Slicer 5.5 is the new Colorize Volume module! I tried it on a fully segmented rattlesnake skull with really nice results comparable to the expensive proprietary software VGStudio Max. I played around wit…

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## [Problem using MEMOS extension](https://discourse.slicer.org/t/problem-using-memos-extension/34456)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 25\
**Last updated:** [July 29, 2026, 5:00pm UTC](https://discourse.slicer.org/t/problem-using-memos-extension/34456 "2026-07-29T17:00:51Z")

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Dear Murat, very excited to use this tool for tests but I seem to be stuck. Most likely a problem with my environment but any suggestion or help appreciated. I installed a fresh version of slicer (5.6.1) on windows 11.…

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## [Grow from seeds error - minimum 2 visible segments required](https://discourse.slicer.org/t/grow-from-seeds-error-minimum-2-visible-segments-required/33279)

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**Author:** [@JamesM](https://discourse.slicer.org/u/JamesM)\
**Replies:** 24\
**Last updated:** [July 28, 2026, 10:06pm UTC](https://discourse.slicer.org/t/grow-from-seeds-error-minimum-2-visible-segments-required/33279 "2026-07-28T22:06:48Z")

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Hello! I am measuring tumor volume, segmenting the inside and background separately and using the “grow from seed” function. However, when I try to use “grow from seed” again after filling in the completed volume where t…

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## [How to see VAT and SAT crossection area at L3 level](https://discourse.slicer.org/t/how-to-see-vat-and-sat-crossection-area-at-l3-level/47756)

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**Author:** [@Vishal\_91](https://discourse.slicer.org/u/Vishal_91)\
**Replies:** 0\
**Last updated:** [July 28, 2026, 1:10pm UTC](https://discourse.slicer.org/t/how-to-see-vat-and-sat-crossection-area-at-l3-level/47756 "2026-07-28T13:10:32Z")

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How to calculate VAT and SAT crossection area at L3 level? VAT/SAT ratio also required. Please someone help me, i need it for research purpose. Extensions are not working in my laptop

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## [How to segment ligaments on 3D T1w MRI images?](https://discourse.slicer.org/t/how-to-segment-ligaments-on-3d-t1w-mri-images/47705)

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**Author:** [@LuuTrinh](https://discourse.slicer.org/u/LuuTrinh)\
**Replies:** 0\
**Last updated:** [July 21, 2026, 2:38pm UTC](https://discourse.slicer.org/t/how-to-segment-ligaments-on-3d-t1w-mri-images/47705 "2026-07-21T14:38:12Z")

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Hi everyone, I am working on segmenting ligaments using 3D T1-weighted (T1w) MRI data in 3D Slicer, and I would appreciate some advice on the best workflow/tools for this task.

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## [Segment tooth enamel and pulp from TotalSegmentator tooth-by-tooth](https://discourse.slicer.org/t/segment-tooth-enamel-and-pulp-from-totalsegmentator-tooth-by-tooth/47637)

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**Author:** [@r\_vorup](https://discourse.slicer.org/u/r_vorup)\
**Replies:** 4\
**Last updated:** [July 19, 2026, 6:11pm UTC](https://discourse.slicer.org/t/segment-tooth-enamel-and-pulp-from-totalsegmentator-tooth-by-tooth/47637 "2026-07-19T18:11:58Z")

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Hello all, I have used the TotalSegmentator to segment a CBCT scan of upper and lower jaw, and have gotten each tooth in an individual segment. I now want to split each tooth into dentine and enamel, for them to be 3D p…

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## [Segment Not working](https://discourse.slicer.org/t/segment-not-working/47659)

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**Author:** [@Reza\_ashtiani](https://discourse.slicer.org/u/Reza_ashtiani)\
**Replies:** 0\
**Last updated:** [July 17, 2026, 3:25pm UTC](https://discourse.slicer.org/t/segment-not-working/47659 "2026-07-17T15:25:39Z")

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Dear friends I am new on program. When I want to segment my CBCT, it simply doesn’t work. I’m using CUDA. The first step — loading the DICOM file — works fine, but the dental segmentation process doesn’t proceed be…

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## [Muscle Segmentation without Organ](https://discourse.slicer.org/t/muscle-segmentation-without-organ/40695)

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**Author:** [@kwonheokju](https://discourse.slicer.org/u/kwonheokju)\
**Replies:** 1\
**Last updated:** [July 14, 2026, 3:58pm UTC](https://discourse.slicer.org/t/muscle-segmentation-without-organ/40695 "2026-07-14T15:58:12Z")

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Hi, I’m a student who uses a 3D Slicer. I’m splitting certain muscles. But it takes too long to split this up. I’ve tried Volume Rendering, but it doesn’t seem to fix it here. And even if it does, it’s difficult. Set…

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## [Write 3D model to CT images](https://discourse.slicer.org/t/write-3d-model-to-ct-images/47587)

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**Author:** [@KarelPenicka](https://discourse.slicer.org/u/KarelPenicka)\
**Replies:** 3\
**Last updated:** [July 13, 2026, 11:13am UTC](https://discourse.slicer.org/t/write-3d-model-to-ct-images/47587 "2026-07-13T11:13:03Z")

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Hello gentlemen. I have a 3D model of a mirrored healthy femur proximally aligned to the operated femur. In the 3D slicer I can see the difference and how they are superimposed. But I would like to write the 3D model int…

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## [Converting Radial Artery from DICOM ( CT files) and Segmentation using slicer manually and using slicer AI 3d segmentation for simulation](https://discourse.slicer.org/t/converting-radial-artery-from-dicom-ct-files-and-segmentation-using-slicer-manually-and-using-slicer-ai-3d-segmentation-for-simulation/47603)

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**Author:** [@Chandana](https://discourse.slicer.org/u/Chandana)\
**Replies:** 0\
**Last updated:** [July 13, 2026, 3:22am UTC](https://discourse.slicer.org/t/converting-radial-artery-from-dicom-ct-files-and-segmentation-using-slicer-manually-and-using-slicer-ai-3d-segmentation-for-simulation/47603 "2026-07-13T03:22:57Z")

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Operating system: Windows 11 Slicer version: 5.9 Expected behavior: clear radial artery stl Actual behavior: unclear lump with bone

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## [issue with automated dental tools ](https://discourse.slicer.org/t/issue-with-automated-dental-tools/47576)

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**Author:** [@deepak\_R](https://discourse.slicer.org/u/deepak_R)\
**Replies:** 0\
**Last updated:** [July 8, 2026, 11:07am UTC](https://discourse.slicer.org/t/issue-with-automated-dental-tools/47576 "2026-07-08T11:07:49Z")

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Hello everyone, I am using 3D Slicer 5.12.0 (also tested with 5.10.0) and the latest AutomatedDentalTools extension from the Extension Manager. I am trying to run ALI on Carestream CBCT DICOM data. The volume loads co…

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## [Workflow for segmenting many lesions as separate segments?](https://discourse.slicer.org/t/workflow-for-segmenting-many-lesions-as-separate-segments/47094)

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**Author:** [@zhousy5310](https://discourse.slicer.org/u/zhousy5310)\
**Replies:** 5\
**Last updated:** [July 8, 2026, 8:56am UTC](https://discourse.slicer.org/t/workflow-for-segmenting-many-lesions-as-separate-segments/47094 "2026-07-08T08:56:49Z")

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Hi all, I’m currently working on NF1 cases using Slicer, and trying to find a better workflow. The main difficulty is not segmenting one lesion, but handling many separate lesions efficiently while keeping them as diff…

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## [STL Tooth Segmentation](https://discourse.slicer.org/t/stl-tooth-segmentation/47526)

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**Author:** [@cgroth](https://discourse.slicer.org/u/cgroth)\
**Replies:** 1\
**Last updated:** [July 2, 2026, 7:20pm UTC](https://discourse.slicer.org/t/stl-tooth-segmentation/47526 "2026-07-02T19:20:29Z")

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Hey all I’ve got the registration figured out but now I am trying to figure out how to make each tooth an individual segment/shell. After that, I need to add a point that is approximately 8mm from the CEJ and use that …

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