# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=1

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

**Page:** 2

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## [Spect Ct Reconstruction ](https://discourse.slicer.org/t/spect-ct-reconstruction/48001)

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**Author:** [@JuanIgnacioElutchanz](https://discourse.slicer.org/u/JuanIgnacioElutchanz)\
**Replies:** 3\
**Last updated:** [August 30, 2026, 3:47pm UTC](https://discourse.slicer.org/t/spect-ct-reconstruction/48001 "2026-08-30T15:47:13Z")

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Hello everyone, I need some help in terms of spect reconstruction in 3dSlicer. I’m student of Nuclear Medicine in Uruguay, I’m currently working on a research project to present at the Uruguayan Con…

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## [Load Failed over multiple formats (TIFF, NRRD)](https://discourse.slicer.org/t/load-failed-over-multiple-formats-tiff-nrrd/48018)

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**Author:** [@asims](https://discourse.slicer.org/u/asims)\
**Replies:** 4\
**Last updated:** [August 30, 2026, 5:30am UTC](https://discourse.slicer.org/t/load-failed-over-multiple-formats-tiff-nrrd/48018 "2026-08-30T05:30:07Z")

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Hi I have an image stack to load which was provided to me as a series of TIFF files. These can be successfully opened in 3rd party tools such as ImageJ (Fiji) and GIMP. However there is a warning message about the descr…

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## [Adjusting position of markups text](https://discourse.slicer.org/t/adjusting-position-of-markups-text/48014)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 2\
**Last updated:** [August 30, 2026, 1:08am UTC](https://discourse.slicer.org/t/adjusting-position-of-markups-text/48014 "2026-08-30T01:08:14Z")

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I use markups quite often to illustrate CT findings. It would be very helpful if the text within markups could be easily repositioned. At present, it can be difficult to read when the text overlaps with anatomical struct…

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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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## [Extension Manager does not launch on Win 11 (Slicer 5.12.3)](https://discourse.slicer.org/t/extension-manager-does-not-launch-on-win-11-slicer-5-12-3/47935)

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**Author:** [@dumichgh](https://discourse.slicer.org/u/dumichgh)\
**Replies:** 3\
**Last updated:** [August 24, 2026, 12:37pm UTC](https://discourse.slicer.org/t/extension-manager-does-not-launch-on-win-11-slicer-5-12-3/47935 "2026-08-24T12:37:25Z")

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Problem report for 3D Slicer 5.12.3 win-amd64: \[please describe expected and actual behavior\] Extension manager does not launch on Windows 11 system after 30min Log: \[DEBUG\]\[Qt\] 19.08.2026 17:14:18 \[\] (unknown:0) - S…

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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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## [TotalSegmentator Extension failed to install req. package](https://discourse.slicer.org/t/totalsegmentator-extension-failed-to-install-req-package/47939)

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**Author:** [@dumichgh](https://discourse.slicer.org/u/dumichgh)\
**Replies:** 2\
**Last updated:** [August 21, 2026, 1:44pm UTC](https://discourse.slicer.org/t/totalsegmentator-extension-failed-to-install-req-package/47939 "2026-08-21T13:44:25Z")

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Problem report for Slicer 5.6.2 win-amd64: When trying to run a TotalSeg got an “error” and process halted : Failed to install required packages. Command ‘\[‘C:/Users/XXXX/AppData/Local/slicer.org/Slicer 5.6.2/bin/../b…

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## [Error using OpenDose 3D ](https://discourse.slicer.org/t/error-using-opendose-3d/46768)

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**Author:** [@Oscar\_Azula](https://discourse.slicer.org/u/Oscar_Azula)\
**Replies:** 1\
**Last updated:** [August 21, 2026, 7:48am UTC](https://discourse.slicer.org/t/error-using-opendose-3d/46768 "2026-08-21T07:48:11Z")

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Hello, I am working with patient images from a Lu-177 therapy study in 3D Slicer. After segmenting the organs and integrating the Absorbed dose rate, I am getting a mass of 0 for all segmented organs. I would apprecia…

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## [Opendose 3D cannot generate integratation of absorbed dose rate table](https://discourse.slicer.org/t/opendose-3d-cannot-generate-integratation-of-absorbed-dose-rate-table/47822)

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**Author:** [@jghtt](https://discourse.slicer.org/u/jghtt)\
**Replies:** 1\
**Last updated:** [August 21, 2026, 7:41am UTC](https://discourse.slicer.org/t/opendose-3d-cannot-generate-integratation-of-absorbed-dose-rate-table/47822 "2026-08-21T07:41:17Z")

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Hello, When I used the extension of Opendose 3D, I have got the absorbed dose rate table,but it is not valid in clicking integrate absorbed dose rate. Did anyone got same problem and how to solve it. Thanks.

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## [Fat Segmentation (SAT, VAT)](https://discourse.slicer.org/t/fat-segmentation-sat-vat/47940)

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**Author:** [@Sahar\_KARIMI](https://discourse.slicer.org/u/Sahar_KARIMI)\
**Replies:** 0\
**Last updated:** [August 20, 2026, 7:05pm UTC](https://discourse.slicer.org/t/fat-segmentation-sat-vat/47940 "2026-08-20T19:05:35Z")

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Hello, I am doing Fat segmentation for Subcutaneous Adipose Tissue (SAT) and Visceral Adipose Tissue(VAT) with 3D-slicer using Thresholding and Grow from seeds modules. HU for both are considered between -190 to -30. H…

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## [Echo Volume Render depth coloring not working](https://discourse.slicer.org/t/echo-volume-render-depth-coloring-not-working/47196)

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**Author:** [@aabrown100-git](https://discourse.slicer.org/u/aabrown100-git)\
**Replies:** 9\
**Last updated:** [August 20, 2026, 5:55pm UTC](https://discourse.slicer.org/t/echo-volume-render-depth-coloring-not-working/47196 "2026-08-20T17:55:03Z")

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My volume rendering of a 3D echo image does not show depth dependent coloring, like in this demo video: https://www.youtube.com/watch?v=hzxzUILNhnA&list=PLIFpHI5hhxkszTWJTaWDM-eGTR8zBubSA&index=14. I tried adjusting t…

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## [Cannot install any extension updates](https://discourse.slicer.org/t/cannot-install-any-extension-updates/47912)

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**Author:** [@RushAR3DLab](https://discourse.slicer.org/u/RushAR3DLab)\
**Replies:** 8\
**Last updated:** [August 19, 2026, 7:13pm UTC](https://discourse.slicer.org/t/cannot-install-any-extension-updates/47912 "2026-08-19T19:13:39Z")

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hi, I upgraded today from 3d Slicer v 5.8 to 5.12 (latest stable version), because I had been experiencing the same issue already with v 5.8. When I launch Extension Manager it cannot download the files for updates. The …

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## [3D Slicer Freezes When Enabling Markups ROI Interaction Handles](https://discourse.slicer.org/t/3d-slicer-freezes-when-enabling-markups-roi-interaction-handles/47905)

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**Author:** [@vedat\_ozturk](https://discourse.slicer.org/u/vedat_ozturk)\
**Replies:** 3\
**Last updated:** [August 19, 2026, 6:48pm UTC](https://discourse.slicer.org/t/3d-slicer-freezes-when-enabling-markups-roi-interaction-handles/47905 "2026-08-19T18:48:43Z")

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Problem report for 3D Slicer 5.12.3 win-amd64: \[please describe expected and actual behavior\] Dear 3D Slicer Team, I would greatly appreciate your help with a persistent and highly reproducible 3D rendering/freezing is…

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## [How can I generate an inflated cortical surface/map in 3D Slicer](https://discourse.slicer.org/t/how-can-i-generate-an-inflated-cortical-surface-map-in-3d-slicer/47906)

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**Author:** [@miral](https://discourse.slicer.org/u/miral)\
**Replies:** 0\
**Last updated:** [August 17, 2026, 2:41pm UTC](https://discourse.slicer.org/t/how-can-i-generate-an-inflated-cortical-surface-map-in-3d-slicer/47906 "2026-08-17T14:41:09Z")

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Hi everyone, I am working with rhesus macaque MRI data in 3D Slicer and am trying to generate an inflated cortical surface for visualization and cortical mapping. I currently have a 3D cortical surface/model in .vtk fo…

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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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## [Protocol for RTK CT Reconstruction from Bruker Skyscan?](https://discourse.slicer.org/t/protocol-for-rtk-ct-reconstruction-from-bruker-skyscan/47894)

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**Author:** [@raranda22](https://discourse.slicer.org/u/raranda22)\
**Replies:** 1\
**Last updated:** [August 15, 2026, 11:51pm UTC](https://discourse.slicer.org/t/protocol-for-rtk-ct-reconstruction-from-bruker-skyscan/47894 "2026-08-15T23:51:55Z")

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Hello, I’m wondering if anyone would be willing to share instructions on how to use RTK for CT reconstructions, assuming output from Bruker Skyscan (CT scanner)? I have access to Morphocloud, so I’m able to use GPU and/o…

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## [Analyzer Results in report Extended analysis (Table 2) all results are zero (0).](https://discourse.slicer.org/t/analyzer-results-in-report-extended-analysis-table-2-all-results-are-zero-0/47870)

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**Author:** [@yilinguo256](https://discourse.slicer.org/u/yilinguo256)\
**Replies:** 1\
**Last updated:** [August 15, 2026, 11:46pm UTC](https://discourse.slicer.org/t/analyzer-results-in-report-extended-analysis-table-2-all-results-are-zero-0/47870 "2026-08-15T23:46:32Z")

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@rbumm How to solve this problem? Thanks!

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## [TotalSegmentator failed to install required packages](https://discourse.slicer.org/t/totalsegmentator-failed-to-install-required-packages/47606)

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**Author:** [@johny723](https://discourse.slicer.org/u/johny723)\
**Replies:** 8\
**Last updated:** [August 15, 2026, 9:33pm UTC](https://discourse.slicer.org/t/totalsegmentator-failed-to-install-required-packages/47606 "2026-08-15T21:33:40Z")

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I keep having a similar issue - how do I fix this? Thanks!

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## [Working with 4D flow MRI data](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214)

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**Author:** [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Replies:** 13\
**Last updated:** [August 14, 2026, 3:45pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214 "2026-08-14T15:45:12Z")

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I’ve never worked with 4D flow MRI data (head) before and am wondering if it is possible to perform flow analysis in 3D Slicer. I’ve also attempted to segment the brain vessels but cannot capture any vessels apart from t…

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## [Installing extension in user's folder in Linux](https://discourse.slicer.org/t/installing-extension-in-users-folder-in-linux/34805)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 26\
**Last updated:** [August 13, 2026, 7:58pm UTC](https://discourse.slicer.org/t/installing-extension-in-users-folder-in-linux/34805 "2026-08-13T19:58:31Z")

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In a project we might need to mount the Slicer installation tree in a read only network share, with the assumption that all user configs and extensions can be installed under user’s own folder, perhaps something like /ho…

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## [Setting segment opacity to \< 1.0 hides segments](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 12\
**Last updated:** [August 12, 2026, 1:24pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800 "2026-08-12T13:24:28Z")

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If the opacity of a segment is reduced from the default 1.0, either for the whole segmentation or for the selected segment, the 3D representation does not persist. It appears again if set to 1.0. This is seen in Linux b…

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## [LungCTAnalyzer extension for lung CT segmentation and analysis for COVID-19 assessment](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 52\
**Last updated:** [August 12, 2026, 7:29am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006 "2026-08-12T07:29:32Z")

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New extension is added for lung CT segmentation and analysis for COVID-19 assessment. It is developed by Prof. Rudolf Bumm (@rbumm), a clinician in KSGR (Chur, Switzerland; with some help from Slicer core developers to p…

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## [3D Slicer cannot be installed in Windows 11](https://discourse.slicer.org/t/3d-slicer-cannot-be-installed-in-windows-11/47861)

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**Author:** [@Abdoelabassi](https://discourse.slicer.org/u/Abdoelabassi)\
**Replies:** 1\
**Last updated:** [August 12, 2026, 3:17am UTC](https://discourse.slicer.org/t/3d-slicer-cannot-be-installed-in-windows-11/47861 "2026-08-12T03:17:56Z")

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I downloaded the installer, but the integrity check of Win11 has failed. Common causes include an incomplete download (which is unlikely, because the download was healthy and complete) and damaged media.

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## [AI-Powered Automatic Segmentation Assistant for 3D Slicer](https://discourse.slicer.org/t/ai-powered-automatic-segmentation-assistant-for-3d-slicer/47860)

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**Author:** [@AIOmarRehan](https://discourse.slicer.org/u/AIOmarRehan)\
**Replies:** 1\
**Last updated:** [August 11, 2026, 3:08pm UTC](https://discourse.slicer.org/t/ai-powered-automatic-segmentation-assistant-for-3d-slicer/47860 "2026-08-11T15:08:02Z")

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Hi everyone, I’m interested in contributing to 3D Slicer by developing an AI-Powered Automatic Segmentation Assistant. The idea is to provide a user-friendly workflow for applying modern AI segmentation models to medic…

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## [Tomografo EAGLE EDGE ](https://discourse.slicer.org/t/tomografo-eagle-edge/47862)

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**Author:** [@AMILCAR](https://discourse.slicer.org/u/AMILCAR)\
**Replies:** 1\
**Last updated:** [August 11, 2026, 3:05pm UTC](https://discourse.slicer.org/t/tomografo-eagle-edge/47862 "2026-08-11T15:05:04Z")

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Good morning. The radiology center has a Brazilian EAGLE EDGE CT scanner, and the slicer cannot read these DCM files. How can I solve this problem? Thank you very much for your help.

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## [How can I manually assign colors to structures in my 3D Model?](https://discourse.slicer.org/t/how-can-i-manually-assign-colors-to-structures-in-my-3d-model/47827)

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**Author:** [@Nonso](https://discourse.slicer.org/u/Nonso)\
**Replies:** 3\
**Last updated:** [August 11, 2026, 2:02pm UTC](https://discourse.slicer.org/t/how-can-i-manually-assign-colors-to-structures-in-my-3d-model/47827 "2026-08-11T14:02:38Z")

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Operating system: Windows 11 Pro Slicer version: 5.10.0 Expected behavior: Actual behavior: I imported a segmented model in .nrrd format, from MIB. After creating a model in 3D Slicer, using the model maker, most of t…

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## [Segmentation clipping as a node](https://discourse.slicer.org/t/segmentation-clipping-as-a-node/47852)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [August 10, 2026, 7:24pm UTC](https://discourse.slicer.org/t/segmentation-clipping-as-a-node/47852 "2026-08-10T19:24:13Z")

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im a big fan of clipping , however it is too far hidden and so many step to toggle back and forth. i think making it a module vs a node would be great addition . if two clipping can work as boundaries rather than just c…

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## [Slicer crashes after multiple slicer.mmrlScene.Clear(0)](https://discourse.slicer.org/t/slicer-crashes-after-multiple-slicer-mmrlscene-clear-0/47801)

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**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 2\
**Last updated:** [August 10, 2026, 2:25pm UTC](https://discourse.slicer.org/t/slicer-crashes-after-multiple-slicer-mmrlscene-clear-0/47801 "2026-08-10T14:25:51Z")

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When processing numerous studies with a Clear(0) after each, I eventually get a fatal exception crash. Work flow is define convenience functions in the python console, (load mrb, process, save, Clear, repeat). Of cours…

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