# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=15

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

**Page:** 16

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## [Surface model turns black under transformation](https://discourse.slicer.org/t/surface-model-turns-black-under-transformation/46065)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 4\
**Last updated:** [February 5, 2026, 7:01pm UTC](https://discourse.slicer.org/t/surface-model-turns-black-under-transformation/46065 "2026-02-05T19:01:19Z")

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When I reflect a model node using a linear transform node that has a reflection, the visualization of it in 3D unexpectedly turns black. I gather from other posts and LLM consultation that this is because a transform wi…

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## [Medical Image Segmentation (CT) of Frog Organs using 3D Slicer](https://discourse.slicer.org/t/medical-image-segmentation-ct-of-frog-organs-using-3d-slicer/45615)

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**Author:** [@Fyn\_nari](https://discourse.slicer.org/u/Fyn_nari)\
**Replies:** 6\
**Last updated:** [February 5, 2026, 11:46am UTC](https://discourse.slicer.org/t/medical-image-segmentation-ct-of-frog-organs-using-3d-slicer/45615 "2026-02-05T11:46:29Z")

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I am working on a research project focused on environmental radioprotection. The goal is to develop voxelized phantoms of terrestrial species to study the radiological effects of pollutants. I have a CT-scan series of a …

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## [How to merge two views from different DICOMs?](https://discourse.slicer.org/t/how-to-merge-two-views-from-different-dicoms/46061)

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**Author:** [@mrrezaie](https://discourse.slicer.org/u/mrrezaie)\
**Replies:** 2\
**Last updated:** [February 5, 2026, 10:58am UTC](https://discourse.slicer.org/t/how-to-merge-two-views-from-different-dicoms/46061 "2026-02-05T10:58:16Z")

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Hello, I have two DICOMs (EOS bi-plane x-ray); they are orthogonal and synchronized. The program failed to load them as series, I imported each one separately as a volume. Now, I want to merge them, but only one view of…

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## [Draw tube scripting](https://discourse.slicer.org/t/draw-tube-scripting/44495)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 5\
**Last updated:** [February 5, 2026, 9:28am UTC](https://discourse.slicer.org/t/draw-tube-scripting/44495 "2026-02-05T09:28:06Z")

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Hi all, I am trying to automate the “Draw Tube” effect in Segment Editor using Python, but I am stuck at two points: How to pass an existing centerline to the effect programmatically (similar to setting "Radius" or "…

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## [Cropping a Cylindrical Volume (Jar) in a Circular ROI](https://discourse.slicer.org/t/cropping-a-cylindrical-volume-jar-in-a-circular-roi/42750)

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**Author:** [@sieunmiin96](https://discourse.slicer.org/u/sieunmiin96)\
**Replies:** 3\
**Last updated:** [February 5, 2026, 9:22am UTC](https://discourse.slicer.org/t/cropping-a-cylindrical-volume-jar-in-a-circular-roi/42750 "2026-02-05T09:22:35Z")

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Hi, I’m working with MR images of Fricke gel jars and trying to isolate each jar for analysis. I’m currently using the Crop Volume module in 3D Slicer, but it only lets me define a rectangular ROI. Since the jars are cy…

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## [Transform Source to Target 3D Model](https://discourse.slicer.org/t/transform-source-to-target-3d-model/45999)

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**Author:** [@md.walten](https://discourse.slicer.org/u/md.walten)\
**Replies:** 7\
**Last updated:** [February 3, 2026, 10:52pm UTC](https://discourse.slicer.org/t/transform-source-to-target-3d-model/45999 "2026-02-03T22:52:26Z")

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Hello I am doing a research study with human bones where every bone has a little bit of different area das is marked and I would like to transform a source model exactly to a target bone so I can see the difference betw…

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## [Lung segmentator not anymore in extensions. Any help?](https://discourse.slicer.org/t/lung-segmentator-not-anymore-in-extensions-any-help/46040)

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**Author:** [@MartinMD89](https://discourse.slicer.org/u/MartinMD89)\
**Replies:** 1\
**Last updated:** [February 3, 2026, 10:30am UTC](https://discourse.slicer.org/t/lung-segmentator-not-anymore-in-extensions-any-help/46040 "2026-02-03T10:30:42Z")

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Hi everyone, paediatric surgeon here. We are planning to perform an operation on a with CPAM and I wanted to create s segmentation of the lungs and the lesion. Some time ago, i used this lung segmentator extension. Now …

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## [Dental Segmentator not working with M1 Mac](https://discourse.slicer.org/t/dental-segmentator-not-working-with-m1-mac/46041)

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**Author:** [@nguyetun](https://discourse.slicer.org/u/nguyetun)\
**Replies:** 0\
**Last updated:** [February 3, 2026, 4:04am UTC](https://discourse.slicer.org/t/dental-segmentator-not-working-with-m1-mac/46041 "2026-02-03T04:04:48Z")

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I’ve downloaded Slicer 5.11 and the Dental Segmentator isn’t working. I’ve attached the error message.

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## [Saving parameter preset in ANTs extension changes initialization value](https://discourse.slicer.org/t/saving-parameter-preset-in-ants-extension-changes-initialization-value/45993)

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**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 8\
**Last updated:** [February 3, 2026, 12:40am UTC](https://discourse.slicer.org/t/saving-parameter-preset-in-ants-extension-changes-initialization-value/45993 "2026-02-03T00:40:14Z")

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In the General ANTs 3D slicer extension I noticed something rather odd. I can take one of the default parameter presets, say “QuickSyn”, change nothing, and click “save as preset”. The new .json preset saves in the cor…

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## [📢 New 3D Slicer Extensions: KonfAI & IMPACT-Synth Reliable AI Synthetic CT and Segmentation with Integrated QA](https://discourse.slicer.org/t/new-3d-slicer-extensions-konfai-impact-synth-reliable-ai-synthetic-ct-and-segmentation-with-integrated-qa/46032)

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**Author:** [@vboussot](https://discourse.slicer.org/u/vboussot)\
**Replies:** 0\
**Last updated:** [February 2, 2026, 2:55pm UTC](https://discourse.slicer.org/t/new-3d-slicer-extensions-konfai-impact-synth-reliable-ai-synthetic-ct-and-segmentation-with-integrated-qa/46032 "2026-02-02T14:55:13Z")

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Dear All, We are happy to announce the release of two new open-source 3D Slicer extensions, KonfAI and IMPACT-Synth, which provide graphical interfaces to run AI tasks (such as segmentation and synthetic CT generation) …

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## [How to improve surface model quality when visualizing brain ROI masks in 3D Slicer](https://discourse.slicer.org/t/how-to-improve-surface-model-quality-when-visualizing-brain-roi-masks-in-3d-slicer/45985)

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**Author:** [@younghoo](https://discourse.slicer.org/u/younghoo)\
**Replies:** 5\
**Last updated:** [February 1, 2026, 2:24pm UTC](https://discourse.slicer.org/t/how-to-improve-surface-model-quality-when-visualizing-brain-roi-masks-in-3d-slicer/45985 "2026-02-01T14:24:41Z")

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Dear experts, I am trying to visualize a set of white matter tract masks in 3D using 3D Slicer. My current workflow involves loading the masks as segmentations and then using the “Export visible segments to models” tool…

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## [Segmenting cortical and cancellous bone from spinal ct scan](https://discourse.slicer.org/t/segmenting-cortical-and-cancellous-bone-from-spinal-ct-scan/46001)

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**Author:** [@Jamielynn\_Lu](https://discourse.slicer.org/u/Jamielynn_Lu)\
**Replies:** 3\
**Last updated:** [January 31, 2026, 12:21pm UTC](https://discourse.slicer.org/t/segmenting-cortical-and-cancellous-bone-from-spinal-ct-scan/46001 "2026-01-31T12:21:23Z")

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Hello I am trying to find the best way to differentiate between cancellous and cortical bone in my vertebrae for a FEA. I am having a hard time thresholding to create the different bone textures as my scan isn’t the best…

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## [3D Volume Reconstruction from 2D Ultrasound Slices](https://discourse.slicer.org/t/3d-volume-reconstruction-from-2d-ultrasound-slices/43658)

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**Author:** [@martina\_paccini](https://discourse.slicer.org/u/martina_paccini)\
**Replies:** 5\
**Last updated:** [January 31, 2026, 1:31am UTC](https://discourse.slicer.org/t/3d-volume-reconstruction-from-2d-ultrasound-slices/43658 "2026-01-31T01:31:46Z")

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Operating system: Windows Slicer version: 5.8.1 Expected behavior: volume reconstruction and rendering Actual behavior: crash Hi everyone, I’m quite new to 3D Slicer and this community. I’m trying to reconstruct a 3…

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## [Changing precision](https://discourse.slicer.org/t/changing-precision/45987)

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**Author:** [@dpvaldes](https://discourse.slicer.org/u/dpvaldes)\
**Replies:** 7\
**Last updated:** [January 30, 2026, 1:29pm UTC](https://discourse.slicer.org/t/changing-precision/45987 "2026-01-30T13:29:38Z")

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Is there any way I can change the precision of my voxel signal? Not just for displaying the values but actually changing precision. I have voxels with very small values (10\*\*(-7)) and I want them rounded to 3 decimals. …

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## [Customizing Slicer 3d toolbar](https://discourse.slicer.org/t/customizing-slicer-3d-toolbar/13545)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 7\
**Last updated:** [January 30, 2026, 6:15am UTC](https://discourse.slicer.org/t/customizing-slicer-3d-toolbar/13545 "2026-01-30T06:15:04Z")

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How to customize slicer in-built toolbar? I want to hide some in=built buttons in toolbar and add custom buttons into it?

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## ["Color Scalar Bar" reworked and upgraded, now it’s called "Color Legend"](https://discourse.slicer.org/t/color-scalar-bar-reworked-and-upgraded-now-it-s-called-color-legend/21567)

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**Author:** [@Mik](https://discourse.slicer.org/u/Mik)\
**Replies:** 15\
**Last updated:** [January 30, 2026, 5:19am UTC](https://discourse.slicer.org/t/color-scalar-bar-reworked-and-upgraded-now-it-s-called-color-legend/21567 "2026-01-30T05:19:41Z")

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Starting from version 30530 build 2022-01-15 “Color Scalar Bar” section from “Colors” module was replaced with “Color Legend” section. The “Color Legend” section has been also added to the “Volume”, “Model” and “Markups…

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## [Landmark to .ply misalignment when reloaded for editing](https://discourse.slicer.org/t/landmark-to-ply-misalignment-when-reloaded-for-editing/45995)

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**Author:** [@emmm\_m](https://discourse.slicer.org/u/emmm_m)\
**Replies:** 5\
**Last updated:** [January 30, 2026, 3:38am UTC](https://discourse.slicer.org/t/landmark-to-ply-misalignment-when-reloaded-for-editing/45995 "2026-01-30T03:38:48Z")

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When I reload a saved markup file to it’s original .ply file to adjust a point which was incorrectly placed, the points appear entirely offset from the orientation of the scan. It appears as though the points are at abou…

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## [Bone Thickness Mapping not functioning](https://discourse.slicer.org/t/bone-thickness-mapping-not-functioning/29453)

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**Author:** [@damiazlkflee](https://discourse.slicer.org/u/damiazlkflee)\
**Replies:** 2\
**Last updated:** [January 29, 2026, 7:17pm UTC](https://discourse.slicer.org/t/bone-thickness-mapping-not-functioning/29453 "2026-01-29T19:17:17Z")

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Operating system: Windows 10 Slicer version: 5.2.2 Expected behavior: Bone thickness map Extension complete execute Actual behavior: did not execute I used the bone thickness map extension on my mesh in 3Dslicer vers…

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## [BoneThicknessMapping does not work](https://discourse.slicer.org/t/bonethicknessmapping-does-not-work/30738)

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**Author:** [@Yanglab](https://discourse.slicer.org/u/Yanglab)\
**Replies:** 1\
**Last updated:** [January 29, 2026, 7:15pm UTC](https://discourse.slicer.org/t/bonethicknessmapping-does-not-work/30738 "2026-01-29T19:15:45Z")

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Hi guys, I’m try to use bone thickness mapping on my own data and demo data (Predentalsurgery). But none of them worked. The status kept showing Initializing execution, and the process was permanantly 0%. When I check…

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## [Segment overlap versus 3D view](https://discourse.slicer.org/t/segment-overlap-versus-3d-view/45984)

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**Author:** [@Hannnonk](https://discourse.slicer.org/u/Hannnonk)\
**Replies:** 3\
**Last updated:** [January 29, 2026, 5:38pm UTC](https://discourse.slicer.org/t/segment-overlap-versus-3d-view/45984 "2026-01-29T17:38:04Z")

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Two segments. 3D view when segments overlap, and larger segment (segment 1) is 50% transparent: 3D view when smaller segment is subtracted from larger segment (segment 1). Larger segment is 50% transparent: Why …

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## [Missing menu items from Slicer Application macOS Ventura](https://discourse.slicer.org/t/missing-menu-items-from-slicer-application-macos-ventura/45983)

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**Author:** [@juliangallaun](https://discourse.slicer.org/u/juliangallaun)\
**Replies:** 2\
**Last updated:** [January 29, 2026, 2:09pm UTC](https://discourse.slicer.org/t/missing-menu-items-from-slicer-application-macos-ventura/45983 "2026-01-29T14:09:41Z")

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Hi, I seem to have the same problem as in a previous topic (Missing menu items from Slicer Application Main Window link), the Slicer’s Main Application menu seems to be missing (File, Edit, View and Help). see below I …

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## [Slice, resample and export along an oblique plane](https://discourse.slicer.org/t/slice-resample-and-export-along-an-oblique-plane/45967)

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**Author:** [@N-Van](https://discourse.slicer.org/u/N-Van)\
**Replies:** 5\
**Last updated:** [January 28, 2026, 5:43pm UTC](https://discourse.slicer.org/t/slice-resample-and-export-along-an-oblique-plane/45967 "2026-01-28T17:43:44Z")

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Hi, new here. I’m processing CT scan data and I need to extract a resampled, arbitrarily oriented, cross section of my volume. I need a slice that doesn’t show artifacts/stripes, and I need it with the same resolution a…

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## [Alpaca template selection K-means](https://discourse.slicer.org/t/alpaca-template-selection-k-means/45963)

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**Author:** [@Stephan\_Collins](https://discourse.slicer.org/u/Stephan_Collins)\
**Replies:** 1\
**Last updated:** [January 28, 2026, 3:52pm UTC](https://discourse.slicer.org/t/alpaca-template-selection-k-means/45963 "2026-01-28T15:52:21Z")

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Dear all, there’s something I did not understand in the ALPACA workflow. The plos one paper clearly explains the benefits of doing K means clustering and choosing templates that best match subgroups of data relative to …

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## [Landmark registration overlay not showing up](https://discourse.slicer.org/t/landmark-registration-overlay-not-showing-up/45965)

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**Author:** [@RHB](https://discourse.slicer.org/u/RHB)\
**Replies:** 2\
**Last updated:** [January 28, 2026, 3:25pm UTC](https://discourse.slicer.org/t/landmark-registration-overlay-not-showing-up/45965 "2026-01-28T15:25:02Z")

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Hi, I have 2 2D oct slices that I want to register mutually, these are not 3D volume, just retinal 2D slice and previously I tried to do Landmark registration using these, it worked. Now after that I am trying to do the…

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## [Slicer 5.10 qMRMLSubjectHierarchyComboBox turned to 'None' but no issue with 5.8.1](https://discourse.slicer.org/t/slicer-5-10-qmrmlsubjecthierarchycombobox-turned-to-none-but-no-issue-with-5-8-1/45203)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 8\
**Last updated:** [January 28, 2026, 3:00pm UTC](https://discourse.slicer.org/t/slicer-5-10-qmrmlsubjecthierarchycombobox-turned-to-none-but-no-issue-with-5-8-1/45203 "2026-01-28T15:00:19Z")

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Dear all, In a new Extension I recently made SlicerOrbitSurgerySim (installable in Extension Manager in Slicer 5.10), when I run a function called onInitialRegistrationPushButton from the plateRegistration module, the n…

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## [NNInteractive fails to export segmentations](https://discourse.slicer.org/t/nninteractive-fails-to-export-segmentations/45968)

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**Author:** [@doreenpa](https://discourse.slicer.org/u/doreenpa)\
**Replies:** 4\
**Last updated:** [January 28, 2026, 9:59am UTC](https://discourse.slicer.org/t/nninteractive-fails-to-export-segmentations/45968 "2026-01-28T09:59:19Z")

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I am working with NNInteractive module in 3D slicer on 3D NRRD files (I converted from DICOM via 3D slicer itself). The module worked smoothly and nicely generated volume segmentations, but once I tried to export them th…

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## [Tools for planning segmentectomy of a lung](https://discourse.slicer.org/t/tools-for-planning-segmentectomy-of-a-lung/36629)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 4\
**Last updated:** [January 28, 2026, 6:02am UTC](https://discourse.slicer.org/t/tools-for-planning-segmentectomy-of-a-lung/36629 "2026-01-28T06:02:09Z")

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Open to hear your ideas @rbumm would you suggest any workflow or slicer extensions for this task? Segmentation wise, is it possible to separate lobe’s segments individualy with some tools that may or may not be integra…

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## [3d view in volume rendering](https://discourse.slicer.org/t/3d-view-in-volume-rendering/45716)

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**Author:** [@alex\_He](https://discourse.slicer.org/u/alex_He)\
**Replies:** 17\
**Last updated:** [January 28, 2026, 5:10am UTC](https://discourse.slicer.org/t/3d-view-in-volume-rendering/45716 "2026-01-28T05:10:43Z")

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I wander is all dicom volume series can have a 3d view display in volume rendering? I find a few volumes cannot display in 3d view

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## [Recovering or creating a large nonlinear inverse transform from an ANTs registration](https://discourse.slicer.org/t/recovering-or-creating-a-large-nonlinear-inverse-transform-from-an-ants-registration/45712)

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**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 17\
**Last updated:** [January 27, 2026, 3:38am UTC](https://discourse.slicer.org/t/recovering-or-creating-a-large-nonlinear-inverse-transform-from-an-ants-registration/45712 "2026-01-27T03:38:01Z")

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I need to invert a nonlinear transform generated with the standard 3D Slicer ANTs extension, so it can be applied back to the fixed image to make it more like the moving, but it is becoming clear I do not understand how …

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## [nnInteractive module no longer segments properly](https://discourse.slicer.org/t/nninteractive-module-no-longer-segments-properly/45914)

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**Author:** [@lukejprose](https://discourse.slicer.org/u/lukejprose)\
**Replies:** 11\
**Last updated:** [January 27, 2026, 3:33am UTC](https://discourse.slicer.org/t/nninteractive-module-no-longer-segments-properly/45914 "2026-01-27T03:33:09Z")

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I have been using the nnInteractive module through MorphoCloud to segment CT scans of fish skulls, with a good bit of success. Now, however, the nnInteractive module no longer functions properly. The Configuration tab sa…

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