# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=6

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

**Page:** 7

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## [How to measure area of visceral and subcutaneous visceral fat on a single CT image (L3 level)?](https://discourse.slicer.org/t/how-to-measure-area-of-visceral-and-subcutaneous-visceral-fat-on-a-single-ct-image-l3-level/47262)

<div class="topic-metadata">

**Author:** [@Alexandre\_Bezerra](https://discourse.slicer.org/u/Alexandre_Bezerra)\
**Replies:** 1\
**Last updated:** [June 7, 2026, 12:00pm UTC](https://discourse.slicer.org/t/how-to-measure-area-of-visceral-and-subcutaneous-visceral-fat-on-a-single-ct-image-l3-level/47262 "2026-06-07T12:00:15Z")

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Hello! is there an automatic or simple way to measure the area visceral and subcutaneous fat on a single CT slice? I am able to calculate the volume of fat on all slices of an exam, but can´t seem to find a way to select…

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## [NDI Polaris Lyra + 3D Slicer OpenIGTLink: How to Keep Registration Valid After Moving the Phantom?](https://discourse.slicer.org/t/ndi-polaris-lyra-3d-slicer-openigtlink-how-to-keep-registration-valid-after-moving-the-phantom/47234)

<div class="topic-metadata">

**Author:** [@AdamDomafoldi](https://discourse.slicer.org/u/AdamDomafoldi)\
**Replies:** 4\
**Last updated:** [June 6, 2026, 5:14pm UTC](https://discourse.slicer.org/t/ndi-polaris-lyra-3d-slicer-openigtlink-how-to-keep-registration-valid-after-moving-the-phantom/47234 "2026-06-06T17:14:57Z")

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Hello, I have been experimenting with the NDI Polaris Lyra and Slicer OpenIGTLink. I have read all the documentation and, after numerous attempts, I think I have some parts working, but I would like to ask for help. Wh…

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## [3D rendering makes whole screen glitch](https://discourse.slicer.org/t/3d-rendering-makes-whole-screen-glitch/46520)

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**Author:** [@naomic2](https://discourse.slicer.org/u/naomic2)\
**Replies:** 3\
**Last updated:** [June 5, 2026, 4:31pm UTC](https://discourse.slicer.org/t/3d-rendering-makes-whole-screen-glitch/46520 "2026-06-05T16:31:22Z")

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When I’m in Segmentation Editor and I press “Show 3D” the screen glitches between something like this image and normal. When I have all of my segments deselected with Show 3D on, the screen is also normal. I’m not rea…

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## [Reimplementation of 3D slicer CPR using pure VTK](https://discourse.slicer.org/t/reimplementation-of-3d-slicer-cpr-using-pure-vtk/46316)

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**Author:** [@S-Linh](https://discourse.slicer.org/u/S-Linh)\
**Replies:** 6\
**Last updated:** [June 5, 2026, 4:10pm UTC](https://discourse.slicer.org/t/reimplementation-of-3d-slicer-cpr-using-pure-vtk/46316 "2026-06-05T16:10:02Z")

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Hello everyone, I’m trying to develop 3d Slicer Curve Planar Reformation in my own PACS Viewer, specifically OHIF: I’m looking to use VTK Wasm to implement this. My question is: Since Slicer’s CPR extension is made …

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## [AMASSS issues - No nnUNET models found](https://discourse.slicer.org/t/amasss-issues-no-nnunet-models-found/47246)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 0\
**Last updated:** [June 5, 2026, 12:37pm UTC](https://discourse.slicer.org/t/amasss-issues-no-nnunet-models-found/47246 "2026-06-05T12:37:25Z")

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Dear All, I tried using AMASSS after fresh installation of both 3D Slicer stable version and latest preview release. No Conflicting extensions. (fresh install) However both version give the same error. I have run thi…

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## [Clarification on L3 SMA calculations and Pixel Spacing](https://discourse.slicer.org/t/clarification-on-l3-sma-calculations-and-pixel-spacing/47219)

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**Author:** [@merckins](https://discourse.slicer.org/u/merckins)\
**Replies:** 2\
**Last updated:** [June 4, 2026, 7:31am UTC](https://discourse.slicer.org/t/clarification-on-l3-sma-calculations-and-pixel-spacing/47219 "2026-06-04T07:31:29Z")

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Hello, I’m working on calculating CT L3 SMA, but some aspects are still unclear to me. I may be overlooking something, so I would really appreciate any feedback. I have original CT volumes with differing pixel spacings…

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## [Decrease file sizes](https://discourse.slicer.org/t/decrease-file-sizes/47224)

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**Author:** [@FabricioFO](https://discourse.slicer.org/u/FabricioFO)\
**Replies:** 2\
**Last updated:** [June 4, 2026, 12:21am UTC](https://discourse.slicer.org/t/decrease-file-sizes/47224 "2026-06-04T00:21:52Z")

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Hello, everyone. I’m trying to upload my ctscans, but the filles are really big, the resolution is too high. I wanna know how do you solve this kind of problem, How do you reduce file sizes without losing quality?

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## [Micro CT larvae with soft tissue](https://discourse.slicer.org/t/micro-ct-larvae-with-soft-tissue/47220)

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**Author:** [@Rin\_2529](https://discourse.slicer.org/u/Rin_2529)\
**Replies:** 4\
**Last updated:** [June 3, 2026, 11:27pm UTC](https://discourse.slicer.org/t/micro-ct-larvae-with-soft-tissue/47220 "2026-06-03T23:27:49Z")

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Hi everyone, I am working with micro-CT scans of mosquito larvae (~3.97 µm voxel size) and I am trying to generate rendered anatomical visualizations similar to the figures in this paper: https://www.nature.com/article…

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## [Invisible wall limiting segmentation](https://discourse.slicer.org/t/invisible-wall-limiting-segmentation/46973)

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**Author:** [@FabricioFO](https://discourse.slicer.org/u/FabricioFO)\
**Replies:** 4\
**Last updated:** [June 3, 2026, 8:46pm UTC](https://discourse.slicer.org/t/invisible-wall-limiting-segmentation/46973 "2026-06-03T20:46:07Z")

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Example Hello, everyone. I’m facing the same problem as in the video: I try to segment a specific region and it doesn’t work, it seems like there’s an invisible wall preventing me from segmenting that region even with…

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## [Mensure tooth torque](https://discourse.slicer.org/t/mensure-tooth-torque/47140)

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**Author:** [@Kevin\_Nguyen](https://discourse.slicer.org/u/Kevin_Nguyen)\
**Replies:** 2\
**Last updated:** [June 3, 2026, 5:52am UTC](https://discourse.slicer.org/t/mensure-tooth-torque/47140 "2026-06-03T05:52:56Z")

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Hello! I’m a dentist currently working on a project where I’m measuring tooth torque, specifically the angle of the root. I’m looking for some guidance regarding which tools and measurement methods would be most appropr…

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## [Division of the brain into individual parts](https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214)

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**Author:** [@Tedy](https://discourse.slicer.org/u/Tedy)\
**Replies:** 2\
**Last updated:** [June 2, 2026, 7:24pm UTC](https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214 "2026-06-02T19:24:37Z")

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Hi, can someone please help me cut out the brain parts from an MRI? I had a brain tumor and I want to make 3D models of the parts of my brain that were compressed by the tumor. It will help me come to terms with the dia…

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## [How can I calculate dose-mass histograms and the impact of lung expansion](https://discourse.slicer.org/t/how-can-i-calculate-dose-mass-histograms-and-the-impact-of-lung-expansion/46997)

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**Author:** [@zahra\_Tabasi](https://discourse.slicer.org/u/zahra_Tabasi)\
**Replies:** 2\
**Last updated:** [June 2, 2026, 11:56am UTC](https://discourse.slicer.org/t/how-can-i-calculate-dose-mass-histograms-and-the-impact-of-lung-expansion/46997 "2026-06-02T11:56:56Z")

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Hello everyone, I am currently working on a research project involving unilateral left-sided breast cancer patients undergoing radiotherapy. My study compares Free Breathing (FB) and Deep Inspiration Breath Hold (DIBH) …

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## [3D Slicer crashes when using the Smoother during segmentation](https://discourse.slicer.org/t/3d-slicer-crashes-when-using-the-smoother-during-segmentation/47193)

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**Author:** [@Camilla](https://discourse.slicer.org/u/Camilla)\
**Replies:** 2\
**Last updated:** [June 2, 2026, 2:09am UTC](https://discourse.slicer.org/t/3d-slicer-crashes-when-using-the-smoother-during-segmentation/47193 "2026-06-02T02:09:19Z")

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3D Slicer crashes when using the Smoother during segmentation. The program is ‘thinking’ for a really long time and ultimately end up not responding and I have to start over. Any suggestions on why that happens? I’m t…

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## [Slicer 5.11.0 crashes immediately when switching to nnInteractive module](https://discourse.slicer.org/t/slicer-5-11-0-crashes-immediately-when-switching-to-nninteractive-module/47098)

<div class="topic-metadata">

**Author:** [@aabrown100-git](https://discourse.slicer.org/u/aabrown100-git)\
**Replies:** 6\
**Last updated:** [June 1, 2026, 6:59am UTC](https://discourse.slicer.org/t/slicer-5-11-0-crashes-immediately-when-switching-to-nninteractive-module/47098 "2026-06-01T06:59:15Z")

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Using Slicer 5.11.0 on 2026 Macbook pro, M5 Pro chip. After installing the nnInteractive extension and restarting Slicer, when I switch to the nnInteractive module, it tries to install some dependencies. Almost immediat…

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## [Why won't my mrml file open in 3D slicer, or my stl file become visible?](https://discourse.slicer.org/t/why-wont-my-mrml-file-open-in-3d-slicer-or-my-stl-file-become-visible/47172)

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**Author:** [@Emerson](https://discourse.slicer.org/u/Emerson)\
**Replies:** 1\
**Last updated:** [May 29, 2026, 2:34pm UTC](https://discourse.slicer.org/t/why-wont-my-mrml-file-open-in-3d-slicer-or-my-stl-file-become-visible/47172 "2026-05-29T14:34:17Z")

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I was trying to open an mrml file I have saved, and while it opened the app it did not open the file or show up anywhere. I tried again with the stl file and while it showed up under ‘data’ (which is farther than I got w…

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## [3D Slicer Virtual Reality Experience with Meta Quest 3](https://discourse.slicer.org/t/3d-slicer-virtual-reality-experience-with-meta-quest-3/44542)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 6\
**Last updated:** [May 29, 2026, 1:27pm UTC](https://discourse.slicer.org/t/3d-slicer-virtual-reality-experience-with-meta-quest-3/44542 "2026-05-29T13:27:35Z")

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I’m writing to share my initial experience using the 3D Slicer VR extension with a Meta Quest 3 on Windows 11 and to ask for some guidance. My Setup: Headset: Meta Quest 3 PC OS: Windows 11 Connection Methods T…

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## [Exporting DICOM perfusion/cine as NIfTI gives only 1 dynamic (but Slicer shows 150 frames)](https://discourse.slicer.org/t/exporting-dicom-perfusion-cine-as-nifti-gives-only-1-dynamic-but-slicer-shows-150-frames/47163)

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**Author:** [@Demy](https://discourse.slicer.org/u/Demy)\
**Replies:** 0\
**Last updated:** [May 28, 2026, 7:37pm UTC](https://discourse.slicer.org/t/exporting-dicom-perfusion-cine-as-nifti-gives-only-1-dynamic-but-slicer-shows-150-frames/47163 "2026-05-28T19:37:10Z")

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Hi everyone, I am loading a DICOM perfusion/cine MRI dataset into 3D Slicer. In the DICOM browser, the series summary shows: Modality: MR Size: 180 × 208 Count: 150 frames So Slicer correctly detects that t…

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## [Animator module not exporting in any format](https://discourse.slicer.org/t/animator-module-not-exporting-in-any-format/47153)

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**Author:** [@Atticus](https://discourse.slicer.org/u/Atticus)\
**Replies:** 6\
**Last updated:** [May 28, 2026, 4:41pm UTC](https://discourse.slicer.org/t/animator-module-not-exporting-in-any-format/47153 "2026-05-28T16:41:54Z")

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I have used the Animator module in the past to produce short animations of volumes rotating, being cropped to ROIs or changing their colors. I have not been able to export animations today, in any format or resolution, …

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## [Why aren't we building the extensions in parallel?](https://discourse.slicer.org/t/why-arent-we-building-the-extensions-in-parallel/47155)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 10\
**Last updated:** [May 28, 2026, 12:14am UTC](https://discourse.slicer.org/t/why-arent-we-building-the-extensions-in-parallel/47155 "2026-05-28T00:14:14Z")

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When I look at the dashboard for extension and sort them by time, there is a clear pattern. Extensions are build sequentially by the operating system. Is there are reason we are doing that? Can’t they be parallelized? L…

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## [how to segment intact lumen and vessel wall in 3d slicer?](https://discourse.slicer.org/t/how-to-segment-intact-lumen-and-vessel-wall-in-3d-slicer/2531)

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**Author:** [@Bio\_Medical](https://discourse.slicer.org/u/Bio_Medical)\
**Replies:** 4\
**Last updated:** [May 27, 2026, 7:09pm UTC](https://discourse.slicer.org/t/how-to-segment-intact-lumen-and-vessel-wall-in-3d-slicer/2531 "2026-05-27T19:09:54Z")

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I want to create lumen and plaque inside an arterial wall(similar to the structure in attached file).So it will be a hollow wall and lumen inside it(fixed,no spaces between them).How can i do it in slicer?

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## [Volume rendering broken in latest Linux previews?](https://discourse.slicer.org/t/volume-rendering-broken-in-latest-linux-previews/46974)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 32\
**Last updated:** [May 27, 2026, 1:28pm UTC](https://discourse.slicer.org/t/volume-rendering-broken-in-latest-linux-previews/46974 "2026-05-27T13:28:43Z")

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I am using the preview build from May 5th on Ubuntu, and I can’t get the MRHead (or any of the baked data) to render. When I drag and drop volume object to the 3D viewer, application fails catastrophically, without any e…

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## [Obscuring Bone Removal for 3D Viz of Cardiac CTA](https://discourse.slicer.org/t/obscuring-bone-removal-for-3d-viz-of-cardiac-cta/47095)

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**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 1\
**Last updated:** [May 26, 2026, 11:46am UTC](https://discourse.slicer.org/t/obscuring-bone-removal-for-3d-viz-of-cardiac-cta/47095 "2026-05-26T11:46:08Z")

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Basically trying to automatically mask the spine and ribs. Or Mask everything but the spine and ribs. Thresholding is not good. Need to retain all heart calcium and blood.. TotalSegmentator does not completely segment …

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## [PlusToolkit with GE Ultrasound using AppAPI + OpenIGTLink](https://discourse.slicer.org/t/plustoolkit-with-ge-ultrasound-using-appapi-openigtlink/47133)

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**Author:** [@nicxo99](https://discourse.slicer.org/u/nicxo99)\
**Replies:** 0\
**Last updated:** [May 24, 2026, 8:34am UTC](https://discourse.slicer.org/t/plustoolkit-with-ge-ultrasound-using-appapi-openigtlink/47133 "2026-05-24T08:34:32Z")

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Hello! I am trying to connect a GE ultrasound machine to the Plus framework for free-hand calibration (fCal). I am using Slicer to check that the data is valid. I wrote a small program in C++ that sends image data using…

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## [On end capping in slicer vs a commercial software ( Treatment Planning System)](https://discourse.slicer.org/t/on-end-capping-in-slicer-vs-a-commercial-software-treatment-planning-system/47118)

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**Author:** [@G\_Tom](https://discourse.slicer.org/u/G_Tom)\
**Replies:** 2\
**Last updated:** [May 22, 2026, 10:32pm UTC](https://discourse.slicer.org/t/on-end-capping-in-slicer-vs-a-commercial-software-treatment-planning-system/47118 "2026-05-22T22:32:56Z")

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I have exported a structure which is a simple sphere from Eclipse to slicer via DICOM export/import I noticed some difference at the “end caps” in slicer. I compare the result with a commercial software, Varian Eclipse.…

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## [Slicermorph- Segment Endocranium Taking Too Long](https://discourse.slicer.org/t/slicermorph-segment-endocranium-taking-too-long/47093)

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**Author:** [@PitaChib](https://discourse.slicer.org/u/PitaChib)\
**Replies:** 4\
**Last updated:** [May 21, 2026, 11:15pm UTC](https://discourse.slicer.org/t/slicermorph-segment-endocranium-taking-too-long/47093 "2026-05-21T23:15:02Z")

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Hi all, I’ve been doing rodent endocast with wrap solidify for a bit with success, but I’ve always been curious to try out segment endocranium feature automatically. Before I thought my computer was not good enough, but …

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## [SwissSkullStripper is having trouble with multiple splices, and so am I](https://discourse.slicer.org/t/swissskullstripper-is-having-trouble-with-multiple-splices-and-so-am-i/47111)

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**Author:** [@HomerHaddock](https://discourse.slicer.org/u/HomerHaddock)\
**Replies:** 0\
**Last updated:** [May 21, 2026, 8:30pm UTC](https://discourse.slicer.org/t/swissskullstripper-is-having-trouble-with-multiple-splices-and-so-am-i/47111 "2026-05-21T20:30:45Z")

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I am having trouble with getting a CT scan exported. The scan has one splice for X, Y, and Z where it gets the most quality. To show my problem I used the scan best used on the horizontal plane (It has the most imaging…

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## [Qt6 build: close scene and discard modifications is ignored](https://discourse.slicer.org/t/qt6-build-close-scene-and-discard-modifications-is-ignored/47108)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 0\
**Last updated:** [May 21, 2026, 5:10pm UTC](https://discourse.slicer.org/t/qt6-build-close-scene-and-discard-modifications-is-ignored/47108 "2026-05-21T17:10:34Z")

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I am experimenting with using Slicer built with Qt6 on Arch Linux on a daily basis. When a scene is closed, the SaveBeforeClosingScene appears. When the Close scene (discard modifications) button is clicked, the scene i…

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## [How to use the extension SlicerHeart](https://discourse.slicer.org/t/how-to-use-the-extension-slicerheart/45964)

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**Author:** [@hoangdinhau](https://discourse.slicer.org/u/hoangdinhau)\
**Replies:** 1\
**Last updated:** [May 20, 2026, 12:47pm UTC](https://discourse.slicer.org/t/how-to-use-the-extension-slicerheart/45964 "2026-05-20T12:47:47Z")

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Hello everyone, Who can help me how to use the extention SlicerHeart: we have MRI and 512 slices CT Thank you

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## [Improved python package installation: slicer.packaging](https://discourse.slicer.org/t/improved-python-package-installation-slicer-packaging/47088)

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**Author:** [@ebrahim](https://discourse.slicer.org/u/ebrahim)\
**Replies:** 0\
**Last updated:** [May 19, 2026, 3:58pm UTC](https://discourse.slicer.org/t/improved-python-package-installation-slicer-packaging/47088 "2026-05-19T15:58:35Z")

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An improved python package installation experience is now available out of the box for extension developers: slicer.packaging. This feature was merged about a month ago and is available in the preview version of Slicer. …

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## [Displace the axes idependently of the plane + navigate in time (4D-flow MRI dataset) + coding preset in python](https://discourse.slicer.org/t/displace-the-axes-idependently-of-the-plane-navigate-in-time-4d-flow-mri-dataset-coding-preset-in-python/47080)

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**Author:** [@jceb](https://discourse.slicer.org/u/jceb)\
**Replies:** 0\
**Last updated:** [May 19, 2026, 12:33pm UTC](https://discourse.slicer.org/t/displace-the-axes-idependently-of-the-plane-navigate-in-time-4d-flow-mri-dataset-coding-preset-in-python/47080 "2026-05-19T12:33:20Z")

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Dear 3D Slicer community First many thanks to developers and maintainers of this incredible software. I am working with 4D flow MRI datasets and have the following questions (if needed I can post separate questions) …

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