# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=26

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

**Page:** 27

---

## [Voxel-base registration?](https://discourse.slicer.org/t/voxel-base-registration/44617)

<div class="topic-metadata">

**Author:** [@Sule](https://discourse.slicer.org/u/Sule)\
**Replies:** 3\
**Last updated:** [September 29, 2025, 3:21pm UTC](https://discourse.slicer.org/t/voxel-base-registration/44617 "2025-09-29T15:21:55Z")

</div>

I’d like to make superimposition these 3D views but i couldnt do it whatever i tried. Can you help me please?

---

## [Issues with multiple labels and masks overlapping in Monailabel](https://discourse.slicer.org/t/issues-with-multiple-labels-and-masks-overlapping-in-monailabel/44448)

<div class="topic-metadata">

**Author:** [@koumeasa](https://discourse.slicer.org/u/koumeasa)\
**Replies:** 1\
**Last updated:** [September 29, 2025, 9:29am UTC](https://discourse.slicer.org/t/issues-with-multiple-labels-and-masks-overlapping-in-monailabel/44448 "2025-09-29T09:29:51Z")

</div>

Hey everyone, I’m labeling brain segments in MONAILabel. The masks / ROIs used as input for Monailabel are a subselection extracted by slicerio.extract\_segments() function from a 3DSlicer Segmentation node. I modified …

---

## [Fail to instantiate module "vtkvmtk"](https://discourse.slicer.org/t/fail-to-instantiate-module-vtkvmtk/35681)

<div class="topic-metadata">

**Author:** [@michaelli](https://discourse.slicer.org/u/michaelli)\
**Replies:** 1\
**Last updated:** [September 29, 2025, 2:29am UTC](https://discourse.slicer.org/t/fail-to-instantiate-module-vtkvmtk/35681 "2025-09-29T02:29:07Z")

</div>

I have installed the extension SlicerVMTK and restarted slicer 3d. This also happened to v5.7.0, v5.6.0, and v5.4.0 on Windows 10. So I installed the laterest version, v5.7.0-2024-04-19. But the error is the same. I ca…

---

## [Creating ROI box markups in image coordinates (rather than anatomical coordinates)](https://discourse.slicer.org/t/creating-roi-box-markups-in-image-coordinates-rather-than-anatomical-coordinates/43393)

<div class="topic-metadata">

**Author:** [@tvercaut](https://discourse.slicer.org/u/tvercaut)\
**Replies:** 12\
**Last updated:** [September 28, 2025, 4:20pm UTC](https://discourse.slicer.org/t/creating-roi-box-markups-in-image-coordinates-rather-than-anatomical-coordinates/43393 "2025-09-28T16:20:01Z")

</div>

Hi, I am interested in getting 3D box annotations in MRI data. ROI markups appear to be a good fit for this but the current behaviour is counterintuitive to users. In particular, they got confused by getting forced into…

---

## [Resampling a linear transformation](https://discourse.slicer.org/t/resampling-a-linear-transformation/42916)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [September 27, 2025, 8:13pm UTC](https://discourse.slicer.org/t/resampling-a-linear-transformation/42916 "2025-09-27T20:13:20Z")

</div>

In the recent versions of Slicer, I am having a hard time exporting a resampled volume from a linear transform. Hardening simply changes the image direction matrix, so does the crop volume (when the image is under a line…

---

## [Cant get rid of red window frame](https://discourse.slicer.org/t/cant-get-rid-of-red-window-frame/44606)

<div class="topic-metadata">

**Author:** [@Hannnonk](https://discourse.slicer.org/u/Hannnonk)\
**Replies:** 2\
**Last updated:** [September 27, 2025, 3:21pm UTC](https://discourse.slicer.org/t/cant-get-rid-of-red-window-frame/44606 "2025-09-27T15:21:42Z")

</div>

Even though it is turned off, I cant get rid of the red frame. Other windows are behaving normally. I have closed and reopened the program with no effect. thanks

---

## [Compounded Markup for osteotomy](https://discourse.slicer.org/t/compounded-markup-for-osteotomy/44607)

<div class="topic-metadata">

**Author:** [@Hans\_Peter](https://discourse.slicer.org/u/Hans_Peter)\
**Replies:** 2\
**Last updated:** [September 27, 2025, 3:12pm UTC](https://discourse.slicer.org/t/compounded-markup-for-osteotomy/44607 "2025-09-27T15:12:29Z")

</div>

I want to perform a repeatable osteotomy with a certain shape using Slicer. Essentially I need a modified plane Markup, where the section crossing the bone is not simply horizontal, but for ex. a Z-shape pattern. As I am…

---

## [Slicer script repository: module\_name.logic vs slicer.module\_name.widgetRepresentation().self().logic() vs slicer.modules.logic()](https://discourse.slicer.org/t/slicer-script-repository-module-name-logic-vs-slicer-module-name-widgetrepresentation-self-logic-vs-slicer-modules-logic/44454)

<div class="topic-metadata">

**Author:** [@tas47](https://discourse.slicer.org/u/tas47)\
**Replies:** 4\
**Last updated:** [September 26, 2025, 7:30pm UTC](https://discourse.slicer.org/t/slicer-script-repository-module-name-logic-vs-slicer-module-name-widgetrepresentation-self-logic-vs-slicer-modules-logic/44454 "2025-09-26T19:30:46Z")

</div>

Slicer API explanation: Hello all I have been trying to understand the Slicer API and I am having a lot of trouble understanding exactly how the ecosystem works. I want to specifically understand how the logic aspect …

---

## [Showing 2D contour (slice intersection) of segmentation in 3D viewport](https://discourse.slicer.org/t/showing-2d-contour-slice-intersection-of-segmentation-in-3d-viewport/44598)

<div class="topic-metadata">

**Author:** [@hfri](https://discourse.slicer.org/u/hfri)\
**Replies:** 2\
**Last updated:** [September 26, 2025, 7:26pm UTC](https://discourse.slicer.org/t/showing-2d-contour-slice-intersection-of-segmentation-in-3d-viewport/44598 "2025-09-26T19:26:26Z")

</div>

Dear forum, I would like to display my segmentations as 2D outlines in the 3D view port. I have the NIfTI segmentations, but currently, I can only show the outlines in the 2D views (red, yellow, green). In the 3D viewpo…

---

## [Exporting centreline ](https://discourse.slicer.org/t/exporting-centreline/44602)

<div class="topic-metadata">

**Author:** [@Caitlin\_Goldfinch](https://discourse.slicer.org/u/Caitlin_Goldfinch)\
**Replies:** 1\
**Last updated:** [September 26, 2025, 7:19pm UTC](https://discourse.slicer.org/t/exporting-centreline/44602 "2025-09-26T19:19:26Z")

</div>

I have created a centreline from a blood vessel segment. I want to export the centreline as an STL or OBJ file, so that I can import it into Fusion and use it as a path to extrude along. (Needing to 3d print this specifi…

---

## [Problem with bone texture extension 2025](https://discourse.slicer.org/t/problem-with-bone-texture-extension-2025/44601)

<div class="topic-metadata">

**Author:** [@Goose123](https://discourse.slicer.org/u/Goose123)\
**Replies:** 0\
**Last updated:** [September 26, 2025, 7:10pm UTC](https://discourse.slicer.org/t/problem-with-bone-texture-extension-2025/44601 "2025-09-26T19:10:26Z")

</div>

Hello! I have two problems with the “bone texture” extension: 1.) BM features result can’t be exported into a table (error: Please specify an output csv file) and BM feature maps can’t be exported as dwi files (exports…

---

## [SegmentMesher in Slicer 5.2 and 5.3 fail: Error: 'vtkmodules.vtkFiltersCore.vtkThreshold' object has no attribute 'ThresholdByUpper'](https://discourse.slicer.org/t/segmentmesher-in-slicer-5-2-and-5-3-fail-error-vtkmodules-vtkfilterscore-vtkthreshold-object-has-no-attribute-thresholdbyupper/27894)

<div class="topic-metadata">

**Author:** [@Mat](https://discourse.slicer.org/u/Mat)\
**Replies:** 4\
**Last updated:** [September 26, 2025, 2:15pm UTC](https://discourse.slicer.org/t/segmentmesher-in-slicer-5-2-and-5-3-fail-error-vtkmodules-vtkfilterscore-vtkthreshold-object-has-no-attribute-thresholdbyupper/27894 "2025-09-26T14:15:23Z")

</div>

Operating system: Windows 11 Slicer version: 5.3 Expected behavior: complete successfully Actual behavior: fails I’m trying to create a volume mesh using segmentMesher and it keeps failing: Generating volumetric mes…

---

## [Extract centerlines irregularities](https://discourse.slicer.org/t/extract-centerlines-irregularities/44584)

<div class="topic-metadata">

**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 2\
**Last updated:** [September 25, 2025, 6:48pm UTC](https://discourse.slicer.org/t/extract-centerlines-irregularities/44584 "2025-09-25T18:48:33Z")

</div>

Hi everyone, I’m using the Extract Centerline module and I’m experiencing some irregularities in the extracted curve (see attached image). I’m not sure why this is happening. The problem becomes more evident when I use C…

---

## [Model to segment irregularities](https://discourse.slicer.org/t/model-to-segment-irregularities/44560)

<div class="topic-metadata">

**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 4\
**Last updated:** [September 25, 2025, 1:01pm UTC](https://discourse.slicer.org/t/model-to-segment-irregularities/44560 "2025-09-25T13:01:28Z")

</div>

Hi everyone, We’re trying to use the Segment Editor (Subtract) with shapeNodes (cylinders). Our current workflow is: Convert the shapeNode (model) into a segment. Apply the segment editor operations. The issue appea…

---

## [Pytomography Extension output](https://discourse.slicer.org/t/pytomography-extension-output/44583)

<div class="topic-metadata">

**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 0\
**Last updated:** [September 25, 2025, 12:56pm UTC](https://discourse.slicer.org/t/pytomography-extension-output/44583 "2025-09-25T12:56:54Z")

</div>

Dear Luke, Sorry interrupted. Recently, I did simulation NEMA phantom of I131 used SIMIND. But what I reached is, there is problem with my projection data. As comparing with example given from you (first picture), I …

---

## [SegmentGeometry compactness bug?](https://discourse.slicer.org/t/segmentgeometry-compactness-bug/44577)

<div class="topic-metadata">

**Author:** [@cliftong](https://discourse.slicer.org/u/cliftong)\
**Replies:** 2\
**Last updated:** [September 25, 2025, 5:45am UTC](https://discourse.slicer.org/t/segmentgeometry-compactness-bug/44577 "2025-09-25T05:45:52Z")

</div>

Hi @jmhuie ! I have a weird behavior happening with SegmentGeometry that I’m hoping you can help me understand. We are calculating the cross-sectional area and properties of a segment with slices aligned with the green …

---

## [Applying Transform Changes number of stacks on the file](https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478)

<div class="topic-metadata">

**Author:** [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Replies:** 2\
**Last updated:** [September 24, 2025, 12:37pm UTC](https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478 "2025-09-24T12:37:08Z")

</div>

Dear Colleagues, I am registering the Fixed.tiff image to the Moving.tiff image using the Elastix module within 3D Slicer. Both images are 512 × 512 × 381. The registration works well, and after I apply the transform, e…

---

## [Need help with analyzing segmentations from 2 different MRIs :( ](https://discourse.slicer.org/t/need-help-with-analyzing-segmentations-from-2-different-mris/44567)

<div class="topic-metadata">

**Author:** [@Mc\_Konni](https://discourse.slicer.org/u/Mc_Konni)\
**Replies:** 1\
**Last updated:** [September 24, 2025, 11:05am UTC](https://discourse.slicer.org/t/need-help-with-analyzing-segmentations-from-2-different-mris/44567 "2025-09-24T11:05:42Z")

</div>

Hi Guys, i am completely new to 3D Slicer, i have tried to solve the following issue for a couple of days and im honestly about to give up. Heres my issue: Im conducting research with ULF MR Imaging and have segmentate…

---

## [Loading DeCA module](https://discourse.slicer.org/t/loading-deca-module/43237)

<div class="topic-metadata">

**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 36\
**Last updated:** [September 23, 2025, 9:21am UTC](https://discourse.slicer.org/t/loading-deca-module/43237 "2025-09-23T09:21:54Z")

</div>

Hi, I think that this one is for Muratmaga. I am interested in the DeCA module, since I understood that it was able to create a template out of a series of segmented skulls, a function which would be very usefull for my…

---

## [OpenDose3D to analyse monte carlo simulations results](https://discourse.slicer.org/t/opendose3d-to-analyse-monte-carlo-simulations-results/44080)

<div class="topic-metadata">

**Author:** [@imbeatriz](https://discourse.slicer.org/u/imbeatriz)\
**Replies:** 6\
**Last updated:** [September 22, 2025, 1:34pm UTC](https://discourse.slicer.org/t/opendose3d-to-analyse-monte-carlo-simulations-results/44080 "2025-09-22T13:34:52Z")

</div>

Hi everyone, I am trying to use OpenDose3D to analyse the results of dose images from monte carlo simulations which are in the format .mhd. From what I understood by the documentation, OpenDose3D is only able to perfor…

---

## [TotalSegmentator Licensed Tasks Not Appearing in 3D Slicer Interface](https://discourse.slicer.org/t/totalsegmentator-licensed-tasks-not-appearing-in-3d-slicer-interface/43523)

<div class="topic-metadata">

**Author:** [@Guilherme\_Augusto](https://discourse.slicer.org/u/Guilherme_Augusto)\
**Replies:** 2\
**Last updated:** [September 22, 2025, 1:59am UTC](https://discourse.slicer.org/t/totalsegmentator-licensed-tasks-not-appearing-in-3d-slicer-interface/43523 "2025-09-22T01:59:54Z")

</div>

TotalSegmentator Licensed Tasks Not Appearing in 3D Slicer Interface Problem Description I have TotalSegmentator v2.10.0 installed and working via Python API in 3D Slicer 5.7.0, but licensed tasks like thigh\_shoulder\_…

---

## [New Extension: MassVision](https://discourse.slicer.org/t/new-extension-massvision/44540)

<div class="topic-metadata">

**Author:** [@Amoon](https://discourse.slicer.org/u/Amoon)\
**Replies:** 0\
**Last updated:** [September 21, 2025, 2:28am UTC](https://discourse.slicer.org/t/new-extension-massvision/44540 "2025-09-21T02:28:12Z")

</div>

:rocket: Happy to announce the official release of MassVision extension v 1.0, now available through the 3D Slicer Extension Manager (compatible with the latest stable release, v5.8.1). :light\_bulb: MassVision is an end…

---

## [Read GE .vol files](https://discourse.slicer.org/t/read-ge-vol-files/44539)

<div class="topic-metadata">

**Author:** [@Sharmeen\_Khan](https://discourse.slicer.org/u/Sharmeen_Khan)\
**Replies:** 2\
**Last updated:** [September 20, 2025, 10:43pm UTC](https://discourse.slicer.org/t/read-ge-vol-files/44539 "2025-09-20T22:43:37Z")

</div>

I have ge .vol files which i need to read in python for which i tried third-party software which would be able to convert it into a suitable format like dicom, like 3d slicer, dicomatic etc. but 3d slicer with extension …

---

## [How to edit segmentations in total segmentator](https://discourse.slicer.org/t/how-to-edit-segmentations-in-total-segmentator/35498)

<div class="topic-metadata">

**Author:** [@jake14](https://discourse.slicer.org/u/jake14)\
**Replies:** 7\
**Last updated:** [September 20, 2025, 10:27pm UTC](https://discourse.slicer.org/t/how-to-edit-segmentations-in-total-segmentator/35498 "2025-09-20T22:27:09Z")

</div>

Used total segmentor for one case and there was an incorrect segmentation done where it has a gap in a structure I am intersted in. Is there an easy was to correct and edit the segmentation that is not accurate? every ot…

---

## [Extract center line from CT empty snail shell](https://discourse.slicer.org/t/extract-center-line-from-ct-empty-snail-shell/44456)

<div class="topic-metadata">

**Author:** [@kuoi](https://discourse.slicer.org/u/kuoi)\
**Replies:** 32\
**Last updated:** [September 19, 2025, 4:53pm UTC](https://discourse.slicer.org/t/extract-center-line-from-ct-empty-snail-shell/44456 "2025-09-19T16:53:25Z")

</div>

Hello, I know there is a post about extracting a centerline from a solid 3D model. However, my case is more complicated: it is an empty shell with an internal cavity. What I actually want to do is extract a centerline fr…

---

## [New lightbox (contact image) mode in screen capture module](https://discourse.slicer.org/t/new-lightbox-contact-image-mode-in-screen-capture-module/10840)

<div class="topic-metadata">

**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 7\
**Last updated:** [September 19, 2025, 4:28pm UTC](https://discourse.slicer.org/t/new-lightbox-contact-image-mode-in-screen-capture-module/10840 "2025-09-19T16:28:54Z")

</div>

A new “lightbox image” output type has been added in latest Slicer Preview Release. In this mode captured images are exported as a large grid of images: Images can be exported from any views, with any animation mode,…

---

## [​Where is “Relax Polygons” in the latest Slicer version? Any alternatives?](https://discourse.slicer.org/t/where-is-relax-polygons-in-the-latest-slicer-version-any-alternatives/44525)

<div class="topic-metadata">

**Author:** [@DDD](https://discourse.slicer.org/u/DDD)\
**Replies:** 5\
**Last updated:** [September 19, 2025, 3:45pm UTC](https://discourse.slicer.org/t/where-is-relax-polygons-in-the-latest-slicer-version-any-alternatives/44525 "2025-09-19T15:45:56Z")

</div>

​Hi everyone, I’m using the latest version of 3D Slicer (version 5.6.2), and I can’t seem to find the “Relax Polygons” option in the “Surface Toolbox” module anymore. In previous versions, I used “Relax Polygons” regul…

---

## [Interest to create Flatpak for 3D Slicer, have issue with GUISupportQtOpenGL not found](https://discourse.slicer.org/t/interest-to-create-flatpak-for-3d-slicer-have-issue-with-guisupportqtopengl-not-found/16532)

<div class="topic-metadata">

**Author:** [@Andythe\_great](https://discourse.slicer.org/u/Andythe_great)\
**Replies:** 40\
**Last updated:** [September 19, 2025, 9:27am UTC](https://discourse.slicer.org/t/interest-to-create-flatpak-for-3d-slicer-have-issue-with-guisupportqtopengl-not-found/16532 "2025-09-19T09:27:38Z")

</div>

Hello, I want to create Flatpak for 3D Slicer. Flatpak is a packaging and distributing desktop software on Linux. https://www.flatpak.org/ I would like it to be submit to Flathub, an app store for Flatpak apps. Many …

---

## [Trouble with opening 3D Slicer](https://discourse.slicer.org/t/trouble-with-opening-3d-slicer/44528)

<div class="topic-metadata">

**Author:** [@binhyc11](https://discourse.slicer.org/u/binhyc11)\
**Replies:** 1\
**Last updated:** [September 19, 2025, 5:54am UTC](https://discourse.slicer.org/t/trouble-with-opening-3d-slicer/44528 "2025-09-19T05:54:57Z")

</div>

I got myself in trouble with opening the application on Windows 11 v24H2. Context: Our lab was moving so I had to unplug my desktop for a month. Couple of days before when I clicked on the 3D Slicer icon, I saw the app …

---

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

<div class="topic-metadata">

**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")

</div>

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…

[Previous page](https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=25)

[Next page](https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=27)