# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=4

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

**Page:** 5

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## [Smallest specimen possible to image with Slicer Photogrammetry?](https://discourse.slicer.org/t/smallest-specimen-possible-to-image-with-slicer-photogrammetry/47522)

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**Author:** [@imfeldts001](https://discourse.slicer.org/u/imfeldts001)\
**Replies:** 5\
**Last updated:** [July 10, 2026, 5:38pm UTC](https://discourse.slicer.org/t/smallest-specimen-possible-to-image-with-slicer-photogrammetry/47522 "2026-07-10T17:38:57Z")

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Greetings! My students and I have begun a project using Slicer Photogrammetry to create 3D models of songbird skulls from natural history collection in the area. The platform has worked well for us with the largest spec…

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## [Pelvic screw planification ](https://discourse.slicer.org/t/pelvic-screw-planification/47578)

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**Author:** [@Emile\_Vandromme](https://discourse.slicer.org/u/Emile_Vandromme)\
**Replies:** 2\
**Last updated:** [July 8, 2026, 3:46pm UTC](https://discourse.slicer.org/t/pelvic-screw-planification/47578 "2026-07-08T15:46:40Z")

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Hi everyone, I’m an orthopedic trauma surgeon and I’m currently trying to use 3D Slicer for preoperative planning of trans-sacral and sacroiliac screw fixation. I’m looking for a way to simulate the screw trajectory di…

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## [Automated dental tools are not working but dental segmentator is working. ](https://discourse.slicer.org/t/automated-dental-tools-are-not-working-but-dental-segmentator-is-working/47577)

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**Author:** [@Sum123](https://discourse.slicer.org/u/Sum123)\
**Replies:** 0\
**Last updated:** [July 8, 2026, 11:08am UTC](https://discourse.slicer.org/t/automated-dental-tools-are-not-working-but-dental-segmentator-is-working/47577 "2026-07-08T11:08:25Z")

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The automated dental tools are not working, however, Dental segmentator is working well. I have downloaded the latest version, 5.12. I need to work on the following tools: ALI, AMASSS, V FACE, CLIC, AREG, AUTOCROP 3D…

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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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## [Overlay of coregistered brain MRI and CT](https://discourse.slicer.org/t/overlay-of-coregistered-brain-mri-and-ct/35465)

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**Author:** [@Kerezoudis](https://discourse.slicer.org/u/Kerezoudis)\
**Replies:** 2\
**Last updated:** [July 8, 2026, 8:53am UTC](https://discourse.slicer.org/t/overlay-of-coregistered-brain-mri-and-ct/35465 "2026-07-08T08:53:44Z")

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Operating system: MacOs Sonoma 14.4.1 Slicer version: 5.6.1 Expected behavior: I would like to overlay preoperative brain MRI with postoperative CT (after electrode placement) Actual behavior: images are not aligned. …

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## [Screen error - Black screen with double arrows when using ROI in Volume Rendering](https://discourse.slicer.org/t/screen-error-black-screen-with-double-arrows-when-using-roi-in-volume-rendering/47563)

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**Author:** [@Jknaub](https://discourse.slicer.org/u/Jknaub)\
**Replies:** 2\
**Last updated:** [July 7, 2026, 5:03pm UTC](https://discourse.slicer.org/t/screen-error-black-screen-with-double-arrows-when-using-roi-in-volume-rendering/47563 "2026-07-07T17:03:53Z")

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Operating system: Windows 11 Slicer version: 5.8.1, 5.10, and 5.12 Expected behavior: Moving ROI bounding box during volume rendering Actual behavior: The entire screen changes to a black background with double arrow…

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## [Nninteractive (slicer client) is stuck](https://discourse.slicer.org/t/nninteractive-slicer-client-is-stuck/47550)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 9\
**Last updated:** [July 7, 2026, 4:37pm UTC](https://discourse.slicer.org/t/nninteractive-slicer-client-is-stuck/47550 "2026-07-07T16:37:59Z")

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It doesn’t pass this stage during the module initialization. This is on ubuntu 24.04 Switch to module: “SlicerNNInteractive” QObject::setParent: Cannot set parent, new parent is in a different thread QObject::setP…

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## [I installed the Cochlear Automatic Segmentation extension successfully in 3D Slicer 5.8, ](https://discourse.slicer.org/t/i-installed-the-cochlear-automatic-segmentation-extension-successfully-in-3d-slicer-5-8/47562)

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**Author:** [@pasfri](https://discourse.slicer.org/u/pasfri)\
**Replies:** 0\
**Last updated:** [July 7, 2026, 1:39pm UTC](https://discourse.slicer.org/t/i-installed-the-cochlear-automatic-segmentation-extension-successfully-in-3d-slicer-5-8/47562 "2026-07-07T13:39:46Z")

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I installed the Cochlear Automatic Segmentation extension successfully in 3D Slicer 5.8, but it does not work. When I open the module, the output segmentation remains “None” and no segmentation is created after clicking …

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## [Crop segmentations with bounding box](https://discourse.slicer.org/t/crop-segmentations-with-bounding-box/47535)

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**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 2\
**Last updated:** [July 7, 2026, 2:40am UTC](https://discourse.slicer.org/t/crop-segmentations-with-bounding-box/47535 "2026-07-07T02:40:07Z")

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Are there any tools for cropping segments as readily as volumes? Ideally, similar to volume cropping, I’d like to render my segments in 3D and adjust a bounding box where all segment labels outside are deleted. Thanks

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## [Clip vessel module creates non-flat cuts with ridges](https://discourse.slicer.org/t/clip-vessel-module-creates-non-flat-cuts-with-ridges/47536)

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**Author:** [@Sanjib\_Gurung](https://discourse.slicer.org/u/Sanjib_Gurung)\
**Replies:** 1\
**Last updated:** [July 7, 2026, 12:50am UTC](https://discourse.slicer.org/t/clip-vessel-module-creates-non-flat-cuts-with-ridges/47536 "2026-07-07T00:50:06Z")

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Hi, I am trying to use 3D slicer to generate 3D models for CFD. I need to create flat ends to serve as inlets and outlets. In my current model, Clip vessel module is generating non-flat ends with ridges and need help sol…

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## [Using Cloud to run 3D Slicer](https://discourse.slicer.org/t/using-cloud-to-run-3d-slicer/47521)

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**Author:** [@Poupak\_Kermani](https://discourse.slicer.org/u/Poupak_Kermani)\
**Replies:** 3\
**Last updated:** [July 5, 2026, 5:20pm UTC](https://discourse.slicer.org/t/using-cloud-to-run-3d-slicer/47521 "2026-07-05T17:20:00Z")

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Hello, I do not have enough space in my laptop to run 3D Slicer. Could you please give me a step by step procedure on how to download and run 3D Slice using AWS Cloud service? Many Thanks

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## [C++ extension for 5.12 is not working (MacOS)](https://discourse.slicer.org/t/c-extension-for-5-12-is-not-working-macos/47542)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [July 4, 2026, 4:16pm UTC](https://discourse.slicer.org/t/c-extension-for-5-12-is-not-working-macos/47542 "2026-07-04T16:16:32Z")

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@ebrahim @Sam\_Horvath @lassoan this is urgent: I just downloaded 5.12 for my MacOS, and quite a few of the C++ extension are installed but non-functional for due to library mismatch. I need these extensions for my Slice…

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## [GUI panels from Slicer 5.12.0 shows over other software on Windows 11](https://discourse.slicer.org/t/gui-panels-from-slicer-5-12-0-shows-over-other-software-on-windows-11/47472)

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**Author:** [@Esteban\_Barreiro](https://discourse.slicer.org/u/Esteban_Barreiro)\
**Replies:** 4\
**Last updated:** [July 2, 2026, 7:23pm UTC](https://discourse.slicer.org/t/gui-panels-from-slicer-5-12-0-shows-over-other-software-on-windows-11/47472 "2026-07-02T19:23:38Z")

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Hello. I’m experiencing some GUI glitches in the Slicer 5.12.0 version. Some of the menus, from the Red, Green, Yellow viewers stay visible over every other software. I’m on Windows 11. In the attached image you can s…

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## [Scrambled image when setting Oppacity \< 1 in an stl image](https://discourse.slicer.org/t/scrambled-image-when-setting-oppacity-1-in-an-stl-image/47533)

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**Author:** [@Octavio](https://discourse.slicer.org/u/Octavio)\
**Replies:** 0\
**Last updated:** [July 2, 2026, 4:12pm UTC](https://discourse.slicer.org/t/scrambled-image-when-setting-oppacity-1-in-an-stl-image/47533 "2026-07-02T16:12:39Z")

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Operating system: Windows Slicer version: 5.12.0 and 5.13.0-2026-06-30 r34833 / d401fce Expected behavior: Display .stl surfaces when setting “Edit Properties”: Opacity \< 1.0 Actual behavior: Slicer fills the scr…

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## [2D slice draw/erase maps to adjacent slice in 3D instead of current](https://discourse.slicer.org/t/2d-slice-draw-erase-maps-to-adjacent-slice-in-3d-instead-of-current/47460)

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**Author:** [@falko76](https://discourse.slicer.org/u/falko76)\
**Replies:** 1\
**Last updated:** [July 2, 2026, 12:52pm UTC](https://discourse.slicer.org/t/2d-slice-draw-erase-maps-to-adjacent-slice-in-3d-instead-of-current/47460 "2026-07-02T12:52:24Z")

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CT scan, using Watershed or Grow from Seeds from SegmentEditorExtraEffects. Detecting a bone OK and clicking apply. Segment mapping is done and visually in 2d and 3d it looks fine, but erasing or drawing in 2d affects n…

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## [Automate bone segmentation from MRI](https://discourse.slicer.org/t/automate-bone-segmentation-from-mri/21530)

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**Author:** [@Sezen](https://discourse.slicer.org/u/Sezen)\
**Replies:** 5\
**Last updated:** [July 2, 2026, 9:10am UTC](https://discourse.slicer.org/t/automate-bone-segmentation-from-mri/21530 "2026-07-02T09:10:49Z")

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Operating system:Windows 11 I am doing a project on whether it is possible to automate the segmentation of bone from specifically MRI scans however I am new to the software. Can anyone point me in the right direction or…

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## [.vgl to 3D Slicer](https://discourse.slicer.org/t/vgl-to-3d-slicer/37475)

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**Author:** [@Mach\_3\_Turbo](https://discourse.slicer.org/u/Mach_3_Turbo)\
**Replies:** 14\
**Last updated:** [July 1, 2026, 2:40pm UTC](https://discourse.slicer.org/t/vgl-to-3d-slicer/37475 "2026-07-01T14:40:13Z")

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Hi, Maybe my question is very beginner, so I apologize for that. I would like to say that I totally don’t understand any specialized terms connected with CT scanning and X-ray. I just want to measure distances inside a …

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## [Using 3D slicer to make a bone model from MRI](https://discourse.slicer.org/t/using-3d-slicer-to-make-a-bone-model-from-mri/2403)

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**Author:** [@NAHL](https://discourse.slicer.org/u/NAHL)\
**Replies:** 3\
**Last updated:** [July 1, 2026, 9:29am UTC](https://discourse.slicer.org/t/using-3d-slicer-to-make-a-bone-model-from-mri/2403 "2026-07-01T09:29:00Z")

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Operating system: Windows 10 Slicer version: 4.8.0 I’m trying to make a bone model from MRI data using slicer. The idea is to colour each slice and then slicer constructs a 3d model. I’m quite new to the program. I’ve …

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## [Pyradiomics GLRLM crashing at native 100um resolution vs 250um](https://discourse.slicer.org/t/pyradiomics-glrlm-crashing-at-native-100um-resolution-vs-250um/47500)

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**Author:** [@oviya](https://discourse.slicer.org/u/oviya)\
**Replies:** 2\
**Last updated:** [June 29, 2026, 7:25pm UTC](https://discourse.slicer.org/t/pyradiomics-glrlm-crashing-at-native-100um-resolution-vs-250um/47500 "2026-06-29T19:25:43Z")

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Hello everyone! My name is Oviya, I’m an undergrad hoping to get a bit of help. I have been trying extract features from MRI images via a compute cluster, and have been successful with downsampled (250um) images (41MB).…

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## [Surface Registration Help](https://discourse.slicer.org/t/surface-registration-help/47499)

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**Author:** [@cgroth](https://discourse.slicer.org/u/cgroth)\
**Replies:** 1\
**Last updated:** [June 29, 2026, 5:38pm UTC](https://discourse.slicer.org/t/surface-registration-help/47499 "2026-06-29T17:38:26Z")

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New to 3D Slicer, so be gentle. Trying to do some comparisons of planned vs achieved tooth movements and I’m struggling to find the surface registration tool within SlicerCMF. What am I missing? Thanks!

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## [Beginner to Slicer, SOFA, etc - Advice?](https://discourse.slicer.org/t/beginner-to-slicer-sofa-etc-advice/47469)

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**Author:** [@KarimA](https://discourse.slicer.org/u/KarimA)\
**Replies:** 1\
**Last updated:** [June 27, 2026, 12:49pm UTC](https://discourse.slicer.org/t/beginner-to-slicer-sofa-etc-advice/47469 "2026-06-27T12:49:38Z")

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Hello everyone, I’m a computer engineering undergrad (senior) new to 3DSlicer and related medical software. I have recently become interested in surgical robotics and have been working on a few research projects regardi…

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## [Volume reconstruction feature missing in v.5.12](https://discourse.slicer.org/t/volume-reconstruction-feature-missing-in-v-5-12/47475)

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**Author:** [@Olivier](https://discourse.slicer.org/u/Olivier)\
**Replies:** 0\
**Last updated:** [June 27, 2026, 9:38am UTC](https://discourse.slicer.org/t/volume-reconstruction-feature-missing-in-v-5-12/47475 "2026-06-27T09:38:24Z")

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After updating to v 5.12, VolumeReconstruction is in the module list but when I click on it I get: VolumeReconstruction module is not loaded Any suggestion other than downgrading to 5.10?

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## [Slicer 5.12.0 Extension Manager](https://discourse.slicer.org/t/slicer-5-12-0-extension-manager/47474)

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**Author:** [@kareem\_abdelaziz](https://discourse.slicer.org/u/kareem_abdelaziz)\
**Replies:** 0\
**Last updated:** [June 26, 2026, 9:47pm UTC](https://discourse.slicer.org/t/slicer-5-12-0-extension-manager/47474 "2026-06-26T21:47:10Z")

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Slicer version 5.12.0 extension manager not working , do i need ot manually install extensions from source ? I saw that the VR module openxr backend now support Passthorugh camera for the Meta Quest 3 and wanted to try …

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## [Two SlicerMorph and MorphoDepot packaged extensions for todays Stable 5.12 build](https://discourse.slicer.org/t/two-slicermorph-and-morphodepot-packaged-extensions-for-todays-stable-5-12-build/47467)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [June 25, 2026, 7:14pm UTC](https://discourse.slicer.org/t/two-slicermorph-and-morphodepot-packaged-extensions-for-todays-stable-5-12-build/47467 "2026-06-25T19:14:04Z")

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On a clean Slicer 5.12.0 (revision 34621) Linux install, installing SlicerMorph or MorphoDepot via the Extensions Manager (installExtensionFromServer) fails with “Failed to retrieve metadata for … extension”. The other e…

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## [Extension manager hangs and crashes Slicer 5.10 today](https://discourse.slicer.org/t/extension-manager-hangs-and-crashes-slicer-5-10-today/47452)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [June 25, 2026, 6:14pm UTC](https://discourse.slicer.org/t/extension-manager-hangs-and-crashes-slicer-5-10-today/47452 "2026-06-25T18:14:52Z")

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I am using Slicer 5.10 on Windows, and wanted to add the model to model distance extension today. However, when I open the Extension Manager, I get a blank window and spinning waiting cursor for an indefinite period, ap…

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## [How to fix the cracking the window when I changed the opacity from the segmentation result?](https://discourse.slicer.org/t/how-to-fix-the-cracking-the-window-when-i-changed-the-opacity-from-the-segmentation-result/47415)

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**Author:** [@wnsdn0497](https://discourse.slicer.org/u/wnsdn0497)\
**Replies:** 2\
**Last updated:** [June 23, 2026, 3:13pm UTC](https://discourse.slicer.org/t/how-to-fix-the-cracking-the-window-when-i-changed-the-opacity-from-the-segmentation-result/47415 "2026-06-23T15:13:48Z")

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Hi, I am writing to fix the issue that I am encountering suddenly. All of sudden, the 3D slicer browser is cracked like below when I turned the opacity from 1.00 to somewhere. Is there anyone who faces the same issu…

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## [Visualizing 3D bounding boxes in Slicer Markups (Fiducials vs Lines) + JSON format question](https://discourse.slicer.org/t/visualizing-3d-bounding-boxes-in-slicer-markups-fiducials-vs-lines-json-format-question/47419)

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**Author:** [@khorlint](https://discourse.slicer.org/u/khorlint)\
**Replies:** 1\
**Last updated:** [June 22, 2026, 10:30pm UTC](https://discourse.slicer.org/t/visualizing-3d-bounding-boxes-in-slicer-markups-fiducials-vs-lines-json-format-question/47419 "2026-06-22T22:30:00Z")

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Description: I am working with 3D Slicer markups to debug an interactive model that uses prompt-based inputs (3D bounding boxes). My goal is to ensure that the voxel → world coordinate transformation is correct and that…

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## [Lattice structure segmentation](https://discourse.slicer.org/t/lattice-structure-segmentation/47417)

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**Author:** [@Tasrif-Ul\_Anwar](https://discourse.slicer.org/u/Tasrif-Ul_Anwar)\
**Replies:** 1\
**Last updated:** [June 22, 2026, 10:17pm UTC](https://discourse.slicer.org/t/lattice-structure-segmentation/47417 "2026-06-22T22:17:48Z")

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We are working with a 3D-printed TPMS lattice structure (fig b) that was tested under compression (we have 4 scans at different loading). I am currently segmenting the sample so that we can compare the deformation of ind…

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## [Measuring diameter of mouse lung airway](https://discourse.slicer.org/t/measuring-diameter-of-mouse-lung-airway/47396)

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**Author:** [@ljuno](https://discourse.slicer.org/u/ljuno)\
**Replies:** 5\
**Last updated:** [June 22, 2026, 4:31pm UTC](https://discourse.slicer.org/t/measuring-diameter-of-mouse-lung-airway/47396 "2026-06-22T16:31:37Z")

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Hi all, I have created this segmentation of part of the airways of a mouse lung. The images were generated from lightsheet microscopy and I used various tools to segment them - thresholding, painting, etc. I eventually …

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