# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=27

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

**Page:** 28

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## [PyIGTL in Docker: Trouble with ](https://discourse.slicer.org/t/pyigtl-in-docker-trouble-with/44447)

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**Author:** [@Oskey999](https://discourse.slicer.org/u/Oskey999)\
**Replies:** 7\
**Last updated:** [September 19, 2025, 2:28am UTC](https://discourse.slicer.org/t/pyigtl-in-docker-trouble-with/44447 "2025-09-19T02:28:39Z")

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Hello, would this be the right place to post this? I am trying to run a python script that communicates with a 3d slicer extension using the pyigtl library. However, I am struggling to get the script to communicate wit…

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## [Codex ai coding implementation?](https://discourse.slicer.org/t/codex-ai-coding-implementation/44527)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [September 19, 2025, 1:56am UTC](https://discourse.slicer.org/t/codex-ai-coding-implementation/44527 "2025-09-19T01:56:10Z")

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been working on creating a personalized web app these days . personally i have zero coding skill or desire to learn coding . what i did is open Visual studio code . it has integrated chat GPT codex module . which can int…

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## [Create a series of slices for viewing ](https://discourse.slicer.org/t/create-a-series-of-slices-for-viewing/44526)

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**Author:** [@sophiasol](https://discourse.slicer.org/u/sophiasol)\
**Replies:** 1\
**Last updated:** [September 18, 2025, 5:52pm UTC](https://discourse.slicer.org/t/create-a-series-of-slices-for-viewing/44526 "2025-09-18T17:52:42Z")

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Hello! Sorry if this has been asked before, but I really don’t seem to be able to find how to extract a series of slices from a selected ROI for viewing purposes. For example, I want to have 1mm step 0,5mm thickness slic…

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## [Convert stl to DICOM file](https://discourse.slicer.org/t/convert-stl-to-dicom-file/14643)

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**Author:** [@archery](https://discourse.slicer.org/u/archery)\
**Replies:** 17\
**Last updated:** [November 2, 2023, 3:01am UTC](https://discourse.slicer.org/t/convert-stl-to-dicom-file/14643 "2023-11-02T03:01:08Z")

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Hello, I was using 4.10.2 to convert stl to DICOM. However, after update to 4.11.2 I could not fund functionality. Can anyone help me with this? Thank you, Amy

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## [How to create fixed 60°/90° wedge overlays for AHA17 segmentation on myocardium masks](https://discourse.slicer.org/t/how-to-create-fixed-60-90-wedge-overlays-for-aha17-segmentation-on-myocardium-masks/44511)

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**Author:** [@emisseria](https://discourse.slicer.org/u/emisseria)\
**Replies:** 0\
**Last updated:** [September 17, 2025, 9:21pm UTC](https://discourse.slicer.org/t/how-to-create-fixed-60-90-wedge-overlays-for-aha17-segmentation-on-myocardium-masks/44511 "2025-09-17T21:21:03Z")

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Hi all I already have a myocardium segmentation (label map) from short-axis cardiac MRI. What I need on one chosen slice, place a center point and draw radial wedge lines at fixed angles (basal/mid: 6×60°, apical: 4×90…

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## [transformed and hardend ROI not loading transformed](https://discourse.slicer.org/t/transformed-and-hardend-roi-not-loading-transformed/44506)

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**Author:** [@Tamara](https://discourse.slicer.org/u/Tamara)\
**Replies:** 3\
**Last updated:** [September 17, 2025, 8:04pm UTC](https://discourse.slicer.org/t/transformed-and-hardend-roi-not-loading-transformed/44506 "2025-09-17T20:04:37Z")

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Hello, I want to transform my ROI and slightly rotate it while the full image is loaded in preview mode. Then I want to just load the transformed ROI in full resolution in order to then just work on this part of the imag…

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## [How to handle errors reported by plugin Lung CT Segmenter？](https://discourse.slicer.org/t/how-to-handle-errors-reported-by-plugin-lung-ct-segmenter/44507)

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**Author:** [@Esther](https://discourse.slicer.org/u/Esther)\
**Replies:** 0\
**Last updated:** [September 17, 2025, 2:11pm UTC](https://discourse.slicer.org/t/how-to-handle-errors-reported-by-plugin-lung-ct-segmenter/44507 "2025-09-17T14:11:59Z")

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Hey guys, I’d like to ask how to handle this error？

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## [I can't find any extensions in the latest version of 3D slicer](https://discourse.slicer.org/t/i-cant-find-any-extensions-in-the-latest-version-of-3d-slicer/44491)

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**Author:** [@researchtomliu](https://discourse.slicer.org/u/researchtomliu)\
**Replies:** 5\
**Last updated:** [September 17, 2025, 1:33am UTC](https://discourse.slicer.org/t/i-cant-find-any-extensions-in-the-latest-version-of-3d-slicer/44491 "2025-09-17T01:33:21Z")

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Today, I’ve downloaded the latest version of 3D Slicer (5.9.0-2025-09-14). When I installed it, I couldn’t find any extensions in the “Extension Manager”. How can I solve this issue? Thanks a lot.

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## [Identifying problematic landmarks in large landmark dataset](https://discourse.slicer.org/t/identifying-problematic-landmarks-in-large-landmark-dataset/44498)

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**Author:** [@christyhipsley](https://discourse.slicer.org/u/christyhipsley)\
**Replies:** 1\
**Last updated:** [September 16, 2025, 4:13pm UTC](https://discourse.slicer.org/t/identifying-problematic-landmarks-in-large-landmark-dataset/44498 "2025-09-16T16:13:13Z")

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I’m seeking advice on how to identify potentially problematic landmarks in a large (1531 landmarks on 101 specimens) dataset, where I suspect some landmarks may have fallen through the surface of the 3D objects. The land…

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## [Segment paint did not remain. just disappear](https://discourse.slicer.org/t/segment-paint-did-not-remain-just-disappear/44497)

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**Author:** [@omfs\_snudh](https://discourse.slicer.org/u/omfs_snudh)\
**Replies:** 0\
**Last updated:** [September 16, 2025, 12:50pm UTC](https://discourse.slicer.org/t/segment-paint-did-not-remain-just-disappear/44497 "2025-09-16T12:50:03Z")

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Operating system: Window Slicer version: 5.81 I just used segment editor based on my DICOM files. But, segment paint has disappeared right after when I touch. I checked “everwhere” and unchecked “intensity range”…

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## [Measuring an irregular 3D image surface area](https://discourse.slicer.org/t/measuring-an-irregular-3d-image-surface-area/44487)

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**Author:** [@highlook](https://discourse.slicer.org/u/highlook)\
**Replies:** 3\
**Last updated:** [September 16, 2025, 12:11pm UTC](https://discourse.slicer.org/t/measuring-an-irregular-3d-image-surface-area/44487 "2025-09-16T12:11:53Z")

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Hello everyone. After segmenting brain tumors from contrast-enhanced brain MRI images using the BrainLab application, I can export the resulting 3D tumor image as a DICOM file. My goal is to calculate the surface area of…

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## [Use of 3D slicer for creating surface meshes of wood from micro tomograph imagery](https://discourse.slicer.org/t/use-of-3d-slicer-for-creating-surface-meshes-of-wood-from-micro-tomograph-imagery/44361)

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**Author:** [@franco\_otaola](https://discourse.slicer.org/u/franco_otaola)\
**Replies:** 6\
**Last updated:** [September 15, 2025, 2:57pm UTC](https://discourse.slicer.org/t/use-of-3d-slicer-for-creating-surface-meshes-of-wood-from-micro-tomograph-imagery/44361 "2025-09-15T14:57:01Z")

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Hello, I am not a current user of slicer3D but I am looking for a software to transform the output of a college doing microtomograph to, ideally a surface mesh of different sections of a scan of wood. the scans are gen…

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## [create a scripted segment editor effect by extension wizard  ](https://discourse.slicer.org/t/create-a-scripted-segment-editor-effect-by-extension-wizard/44409)

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**Author:** [@LeonHaoWI](https://discourse.slicer.org/u/LeonHaoWI)\
**Replies:** 4\
**Last updated:** [September 15, 2025, 2:18pm UTC](https://discourse.slicer.org/t/create-a-scripted-segment-editor-effect-by-extension-wizard/44409 "2025-09-15T14:18:07Z")

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I’m new to slicer development, try to create a scripted module base on segment editor effect, I’m using 5.9 version, and try to create a skeleton by using extension wizard, no information is shown in error log window, b…

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## [Automated Atlas Alignment](https://discourse.slicer.org/t/automated-atlas-alignment/44476)

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**Author:** [@diseaseprogression](https://discourse.slicer.org/u/diseaseprogression)\
**Replies:** 1\
**Last updated:** [September 15, 2025, 5:06am UTC](https://discourse.slicer.org/t/automated-atlas-alignment/44476 "2025-09-15T05:06:09Z")

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Hi everyone, I am trying to use the OpenAnatomy Atlas extension on Slicer with various MRI scans but am struggling with aligning the atlas with the scans. For some scans, it is automatically aligned, but for others they …

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## [DBS electrode reconstruction](https://discourse.slicer.org/t/dbs-electrode-reconstruction/1872)

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**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\
**Replies:** 9\
**Last updated:** [September 14, 2025, 7:48am UTC](https://discourse.slicer.org/t/dbs-electrode-reconstruction/1872 "2025-09-14T07:48:56Z")

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## [TotalSegmentator No Output](https://discourse.slicer.org/t/totalsegmentator-no-output/44433)

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**Author:** [@aceegreene](https://discourse.slicer.org/u/aceegreene)\
**Replies:** 7\
**Last updated:** [September 13, 2025, 7:29pm UTC](https://discourse.slicer.org/t/totalsegmentator-no-output/44433 "2025-09-13T19:29:25Z")

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Hi everyone - I am trying to use totalsegmentator to segment an MRI image I have and seem to not be getting any results. There seem to be no errors in the module itself or in the Python console but once the processing i…

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## [Mirroring landmarks prior to GPA](https://discourse.slicer.org/t/mirroring-landmarks-prior-to-gpa/44457)

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**Author:** [@macorreia42](https://discourse.slicer.org/u/macorreia42)\
**Replies:** 2\
**Last updated:** [September 12, 2025, 2:57pm UTC](https://discourse.slicer.org/t/mirroring-landmarks-prior-to-gpa/44457 "2025-09-12T14:57:56Z")

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Dear Support, I have a number of incomplete mandibles on which I have placed landmarks prior to GM analyses. For each one, I only placed landmarks on the most complete side, so some .mrk.json have landmarks on a left ma…

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## [Slicer Morph GPA | Interactive 3D vizualization | Cannot warp around PCs](https://discourse.slicer.org/t/slicer-morph-gpa-interactive-3d-vizualization-cannot-warp-around-pcs/44416)

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**Author:** [@macorreia42](https://discourse.slicer.org/u/macorreia42)\
**Replies:** 7\
**Last updated:** [September 12, 2025, 10:54am UTC](https://discourse.slicer.org/t/slicer-morph-gpa-interactive-3d-vizualization-cannot-warp-around-pcs/44416 "2025-09-12T10:54:07Z")

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Operating system: Windows 11 Home Slicer version: 5.8.1 r33241 / 11eaf62 Expected behavior: reference model warps around PCs Actual behavior: Critical error TypeError: unsupported operand type(s) for -: ‘str’ and ‘int…

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## [How to perform myocardial segmentation based on AHA 17-segment](https://discourse.slicer.org/t/how-to-perform-myocardial-segmentation-based-on-aha-17-segment/44446)

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**Author:** [@zhaoshihai](https://discourse.slicer.org/u/zhaoshihai)\
**Replies:** 0\
**Last updated:** [September 11, 2025, 2:10pm UTC](https://discourse.slicer.org/t/how-to-perform-myocardial-segmentation-based-on-aha-17-segment/44446 "2025-09-11T14:10:40Z")

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Hi everyone, I’m trying to calculate cardiac ADC values using 3D Slicer (v5.8.1), both globally and based on the AHA 17-segment model. However, I’m unsure how to perform myocardial segmentation. I’ve installed the Slice…

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## [New extension: ModalityConverter - bringing AI medical image-to-image translation to 3D Slicer](https://discourse.slicer.org/t/new-extension-modalityconverter-bringing-ai-medical-image-to-image-translation-to-3d-slicer/44405)

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**Author:** [@ciro.raggio](https://discourse.slicer.org/u/ciro.raggio)\
**Replies:** 9\
**Last updated:** [September 11, 2025, 1:12pm UTC](https://discourse.slicer.org/t/new-extension-modalityconverter-bringing-ai-medical-image-to-image-translation-to-3d-slicer/44405 "2025-09-11T13:12:28Z")

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ModalityConverter is officially available in the 3D Slicer Extensions Index, under the Image Synthesis category (from version 5.9.0)! The extension makes medical image-to-image translation AI models freely and easily ac…

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## [Change transform display spacing less than 1 mm](https://discourse.slicer.org/t/change-transform-display-spacing-less-than-1-mm/44440)

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**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 3\
**Last updated:** [September 10, 2025, 10:25pm UTC](https://discourse.slicer.org/t/change-transform-display-spacing-less-than-1-mm/44440 "2025-09-10T22:25:37Z")

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Hi, I applied a transform to a small rodent volume, but the various arrow and grid options seem far too large for visualizing the transform. The key seems to be lowering the “spacing” under the “advanced” menu, but it …

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## [Creating macOS Installer for Custom Slicer App](https://discourse.slicer.org/t/creating-macos-installer-for-custom-slicer-app/44432)

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**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 0\
**Last updated:** [September 10, 2025, 2:00pm UTC](https://discourse.slicer.org/t/creating-macos-installer-for-custom-slicer-app/44432 "2025-09-10T14:00:00Z")

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I have built and packaged my custom Slicer application on a Windows machine using Visual Studio. Now I want to create a macOS installer for the same custom application. Is it possible to generate a macOS package directl…

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## [Sandbox extension and Slicer version 5.8.1](https://discourse.slicer.org/t/sandbox-extension-and-slicer-version-5-8-1/44410)

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**Author:** [@patpaul](https://discourse.slicer.org/u/patpaul)\
**Replies:** 2\
**Last updated:** [September 10, 2025, 7:33am UTC](https://discourse.slicer.org/t/sandbox-extension-and-slicer-version-5-8-1/44410 "2025-09-10T07:33:54Z")

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Hi all, a little new to slicer. I am trying to create a plane using my three point fiducial list but slicer version 5.8.1 doesn’t have the feature. I installed sandbox and slicerigt extension but I can’t find it in the s…

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## [Request for Academic License – “Appendicular Bones” TotalSegmentator Module](https://discourse.slicer.org/t/request-for-academic-license-appendicular-bones-totalsegmentator-module/44086)

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**Author:** [@JuanCarlos](https://discourse.slicer.org/u/JuanCarlos)\
**Replies:** 2\
**Last updated:** [September 9, 2025, 5:31pm UTC](https://discourse.slicer.org/t/request-for-academic-license-appendicular-bones-totalsegmentator-module/44086 "2025-09-09T17:31:41Z")

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Dear 3D Slicer Community, My name is Juan Carlos Conesa Gallego and I am currently completing my Bachelor’s Thesis in Biomedical Engineering at the Polytechnic University of Cartagena (UPCT), Spain. The project is title…

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## [Lung CT Analyzer is not showing extended analysis results](https://discourse.slicer.org/t/lung-ct-analyzer-is-not-showing-extended-analysis-results/42010)

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**Author:** [@LukasR](https://discourse.slicer.org/u/LukasR)\
**Replies:** 5\
**Last updated:** [September 9, 2025, 4:17pm UTC](https://discourse.slicer.org/t/lung-ct-analyzer-is-not-showing-extended-analysis-results/42010 "2025-09-09T16:17:21Z")

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Hello, while using the extension Lung CT Analyzer I came across one problem. After I select “compute results” It’s not showing Lung CT analysis extended results neither in 3D Slicer nor PDF report. There are just zeros.…

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## [PlaceLandmarkGrid doesn't produce the grid](https://discourse.slicer.org/t/placelandmarkgrid-doesnt-produce-the-grid/44396)

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**Author:** [@kuoi](https://discourse.slicer.org/u/kuoi)\
**Replies:** 18\
**Last updated:** [September 9, 2025, 2:47pm UTC](https://discourse.slicer.org/t/placelandmarkgrid-doesnt-produce-the-grid/44396 "2025-09-09T14:47:58Z")

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Hello I am using PlaceLandmarkGrid in Slicer Morph on Linux, version c944db9 (2025-06-26) I tried to generate semi-landmarks on a grid from existing points, but instead of obtaining a grid containing the semi-landmar…

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## [SlicerMorph CreateSemiLMPatches gaps between 2 triangle regions](https://discourse.slicer.org/t/slicermorph-createsemilmpatches-gaps-between-2-triangle-regions/44407)

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**Author:** [@kuoi](https://discourse.slicer.org/u/kuoi)\
**Replies:** 1\
**Last updated:** [September 9, 2025, 2:41pm UTC](https://discourse.slicer.org/t/slicermorph-createsemilmpatches-gaps-between-2-triangle-regions/44407 "2025-09-09T14:41:43Z")

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Hello, I am new to 3D Slicer and SlicerMorph. I want to use the CreateSemiLMPatches module in the SlicerMorph extension to map semi-landmarks on a surface. However, after following tutorial 1 and tutorial 2, I still cann…

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## [Make clipping to be separate module](https://discourse.slicer.org/t/make-clipping-to-be-separate-module/44266)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 4\
**Last updated:** [September 9, 2025, 1:41pm UTC](https://discourse.slicer.org/t/make-clipping-to-be-separate-module/44266 "2025-09-09T13:41:35Z")

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@pieper @lassoan @chir.set i posted earlier about clipping to be separate module or be much more accessible . its an amazing feature that’s so hard to use . since i accidently discovered it i use it all the time . togg…

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## [Is it possible to create a new segment from a fiducial point cloud?](https://discourse.slicer.org/t/is-it-possible-to-create-a-new-segment-from-a-fiducial-point-cloud/44408)

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**Author:** [@maria\_m](https://discourse.slicer.org/u/maria_m)\
**Replies:** 1\
**Last updated:** [September 9, 2025, 1:27pm UTC](https://discourse.slicer.org/t/is-it-possible-to-create-a-new-segment-from-a-fiducial-point-cloud/44408 "2025-09-09T13:27:56Z")

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I am using 3D Slicer for my master’s thesis. My project involves working with 4 slices in the axial plane of a brain MRI. In each slice, I use the segmentation tool to select the cerebral cortex, and then with a Python s…

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## [Gut segmentation](https://discourse.slicer.org/t/gut-segmentation/44406)

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**Author:** [@gomsh](https://discourse.slicer.org/u/gomsh)\
**Replies:** 0\
**Last updated:** [September 9, 2025, 1:14pm UTC](https://discourse.slicer.org/t/gut-segmentation/44406 "2025-09-09T13:14:57Z")

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Operating system: Windows 11 Slicer version:5.0.3 Hi everyone Newbie here - does anyone know of a good way of segmenting the intestines/gut from mouse MRI scans? Thanks Ana

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