# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=31

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

**Page:** 32

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## [How to read .bimg file format?](https://discourse.slicer.org/t/how-to-read-bimg-file-format/17931)

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**Author:** [@sulaimanvesal](https://discourse.slicer.org/u/sulaimanvesal)\
**Replies:** 5\
**Last updated:** [August 11, 2025, 11:52am UTC](https://discourse.slicer.org/t/how-to-read-bimg-file-format/17931 "2025-08-11T11:52:36Z")

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Hi, I wanted to ask, if we can read .bimg file format in 3D slicer! I have received some raw ultrasound data stored in \*.bimg file format (I think, it’s a video frames). However, I looked all over the net to find some …

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## [Paint doesnt work. Just disappears from the region I paint.](https://discourse.slicer.org/t/paint-doesnt-work-just-disappears-from-the-region-i-paint/44009)

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**Author:** [@Ramya](https://discourse.slicer.org/u/Ramya)\
**Replies:** 3\
**Last updated:** [August 11, 2025, 6:36am UTC](https://discourse.slicer.org/t/paint-doesnt-work-just-disappears-from-the-region-i-paint/44009 "2025-08-11T06:36:51Z")

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Hi I am new to 3D slicer, I am trying to paint on my CT scan to do a segmentation. After I select the region to paint it doesn’t stay. May I know how to fix this issue.

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## [Latest slicer preview (r33816) does not launch in macos](https://discourse.slicer.org/t/latest-slicer-preview-r33816-does-not-launch-in-macos/43935)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 13\
**Last updated:** [August 9, 2025, 8:28pm UTC](https://discourse.slicer.org/t/latest-slicer-preview-r33816-does-not-launch-in-macos/43935 "2025-08-09T20:28:47Z")

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Tested on two different macs (imac and macbook pro) with Sequoia 15.5. After entering the security exception, Slicer icon continues to bounce for about a minute and then quits. When launched from the terminal window from…

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## [surfaceMarkups extension is failing to build on Preview](https://discourse.slicer.org/t/surfacemarkups-extension-is-failing-to-build-on-preview/44011)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [August 9, 2025, 8:28pm UTC](https://discourse.slicer.org/t/surfacemarkups-extension-is-failing-to-build-on-preview/44011 "2025-08-09T20:28:25Z")

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Seems across all the platforms. We do rely on that for a functionality in SlicerMorph, so I wanted to see if this is related to latest python changes. @cpinter

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## [TotalSegmentator error: \`returned non-zero exit status 1\`](https://discourse.slicer.org/t/totalsegmentator-error-returned-non-zero-exit-status-1/43932)

<div class="topic-metadata">

**Author:** [@era\_888](https://discourse.slicer.org/u/era_888)\
**Replies:** 3\
**Last updated:** [August 9, 2025, 7:40pm UTC](https://discourse.slicer.org/t/totalsegmentator-error-returned-non-zero-exit-status-1/43932 "2025-08-09T19:40:29Z")

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Failed to compute results. Command ‘\[‘E:/Slicer 5.8.1/bin/../bin\\PythonSlicer.EXE’, ‘E:\\Slicer 5.8.1\\lib\\Python\\Scripts\\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/msi/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-08-01\_17+24…

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## [Inverse ROI volume crop](https://discourse.slicer.org/t/inverse-roi-volume-crop/44032)

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**Author:** [@JaredAmudeo](https://discourse.slicer.org/u/JaredAmudeo)\
**Replies:** 1\
**Last updated:** [August 9, 2025, 4:39pm UTC](https://discourse.slicer.org/t/inverse-roi-volume-crop/44032 "2025-08-09T16:39:44Z")

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Hi! Is there a simple way to do a volume crop that selects everything outside the ROI, basically erasing everything inside?

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## [Transparent background in screen capture module](https://discourse.slicer.org/t/transparent-background-in-screen-capture-module/44013)

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**Author:** [@JaredAmudeo](https://discourse.slicer.org/u/JaredAmudeo)\
**Replies:** 2\
**Last updated:** [August 9, 2025, 9:08am UTC](https://discourse.slicer.org/t/transparent-background-in-screen-capture-module/44013 "2025-08-09T09:08:05Z")

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Hi! Could someone help me? I’m trying to make a simple rotation video in 3D view, but no matter what background color or video format I choose, the video appears with a background, not the transparent background as ma…

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## [Slicer ignoring command line path with accents](https://discourse.slicer.org/t/slicer-ignoring-command-line-path-with-accents/24569)

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**Author:** [@Ale](https://discourse.slicer.org/u/Ale)\
**Replies:** 2\
**Last updated:** [August 8, 2025, 6:17pm UTC](https://discourse.slicer.org/t/slicer-ignoring-command-line-path-with-accents/24569 "2025-08-08T18:17:10Z")

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Hi all, I’m getting this error when trying to load a file in command line: Slicer /home/mark/Docs/GMM\_Cráneos\_Armadillos/Models/cvi\_24.ply Then, the error below shows strange characters where the “á” was in the path. …

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## [VMTK, Centerline Extraction](https://discourse.slicer.org/t/vmtk-centerline-extraction/44027)

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**Author:** [@Paria.M](https://discourse.slicer.org/u/Paria.M)\
**Replies:** 3\
**Last updated:** [August 8, 2025, 5:05pm UTC](https://discourse.slicer.org/t/vmtk-centerline-extraction/44027 "2025-08-08T17:05:53Z")

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Hi everyone, I want to extract the centerline using VMTK. When I select the Endpoints, the extracted centerline does not cross the points properly, and its far from the Endpoints! Can anyone help me to see what is the p…

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## [Error while installing pytorch](https://discourse.slicer.org/t/error-while-installing-pytorch/26956)

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**Author:** [@Anish\_Raj](https://discourse.slicer.org/u/Anish_Raj)\
**Replies:** 22\
**Last updated:** [August 8, 2025, 3:21pm UTC](https://discourse.slicer.org/t/error-while-installing-pytorch/26956 "2025-08-08T15:21:15Z")

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Hii, I am having trouble applying the module in slicer 5.2.1. When i press apply, it says pytorch will be installed using light-the-torch. After few seconds, i get the error: failed to compute results, no module named t…

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## [Is there a way to use Slicer Virtual Reality with standalone VR headsets like the Magic Leap 2 or Lynx R1?](https://discourse.slicer.org/t/is-there-a-way-to-use-slicer-virtual-reality-with-standalone-vr-headsets-like-the-magic-leap-2-or-lynx-r1/44026)

<div class="topic-metadata">

**Author:** [@tech\_curious](https://discourse.slicer.org/u/tech_curious)\
**Replies:** 0\
**Last updated:** [August 8, 2025, 3:11pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-use-slicer-virtual-reality-with-standalone-vr-headsets-like-the-magic-leap-2-or-lynx-r1/44026 "2025-08-08T15:11:28Z")

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I’m exploring ways to visualize 3D Slicer models in AR using either the Magic Leap 2 or Lynx R1, but I’m unsure about compatibility as they both support OpenXR but with the runtime locally on the device. Is it possible t…

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## [Compare 2 models](https://discourse.slicer.org/t/compare-2-models/44014)

<div class="topic-metadata">

**Author:** [@michaelli](https://discourse.slicer.org/u/michaelli)\
**Replies:** 4\
**Last updated:** [August 8, 2025, 2:14am UTC](https://discourse.slicer.org/t/compare-2-models/44014 "2025-08-08T02:14:46Z")

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I want to compare two models in two 3D views, so that I can rotate the camera independently for each 3D view. But all the models show in all views, how can I load the first model into the first 3d view window and the se…

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## [Margin Tool Erases Segmentation](https://discourse.slicer.org/t/margin-tool-erases-segmentation/43973)

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**Author:** [@jr2637](https://discourse.slicer.org/u/jr2637)\
**Replies:** 4\
**Last updated:** [August 7, 2025, 3:36pm UTC](https://discourse.slicer.org/t/margin-tool-erases-segmentation/43973 "2025-08-07T15:36:07Z")

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Hi, I am trying to grow my segment using the margin tool, but when I attempt to do so, the segment erases. How can I fix this? Thank you!

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## [SlicerRT built from source cannot start](https://discourse.slicer.org/t/slicerrt-built-from-source-cannot-start/43792)

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**Author:** [@ferhue](https://discourse.slicer.org/u/ferhue)\
**Replies:** 42\
**Last updated:** [August 7, 2025, 2:06pm UTC](https://discourse.slicer.org/t/slicerrt-built-from-source-cannot-start/43792 "2025-08-07T14:06:57Z")

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I’ve built Slicer and then SlicerRT from source several times in the past. I followed the online instructions. In the same computer, I recently updated (via git pull) the Slicer and SlicerRT repositories to master, and …

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## [WebAssembly version](https://discourse.slicer.org/t/webassembly-version/43997)

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**Author:** [@Taron\_Holikyan](https://discourse.slicer.org/u/Taron_Holikyan)\
**Replies:** 1\
**Last updated:** [August 7, 2025, 12:37pm UTC](https://discourse.slicer.org/t/webassembly-version/43997 "2025-08-07T12:37:53Z")

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Hi, I want to know if this library has a WebAssembly version that works with Three.js. If not, would I need to create it myself? And if a WebAssembly version doesn’t exist, how difficult would it be to make one?

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## [Help Needed – Integrating Brodmann Area Overlay & MNI Space Registration Module into Custom Application](https://discourse.slicer.org/t/help-needed-integrating-brodmann-area-overlay-mni-space-registration-module-into-custom-application/44001)

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**Author:** [@salim](https://discourse.slicer.org/u/salim)\
**Replies:** 0\
**Last updated:** [August 7, 2025, 12:36pm UTC](https://discourse.slicer.org/t/help-needed-integrating-brodmann-area-overlay-mni-space-registration-module-into-custom-application/44001 "2025-08-07T12:36:52Z")

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Hi Dear Community, I have developed a module in 3D Slicer for Brodmann Area overlay and MNI space registration. The module builds successfully, but I’m facing an issue integrating it into my custom Slicer-based applicat…

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## [Add all nodes to custom module gui](https://discourse.slicer.org/t/add-all-nodes-to-custom-module-gui/24660)

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**Author:** [@rhodesdante](https://discourse.slicer.org/u/rhodesdante)\
**Replies:** 3\
**Last updated:** [August 7, 2025, 7:41am UTC](https://discourse.slicer.org/t/add-all-nodes-to-custom-module-gui/24660 "2025-08-07T07:41:19Z")

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I would like to enable the user of a custom python module to look at all the volume nodes at once, rather than selecting them using a qMRMLComboBox to select them individually. In addition, I would like to allow them to …

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## [Renaming Segments forces color selection as well](https://discourse.slicer.org/t/renaming-segments-forces-color-selection-as-well/43970)

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**Author:** [@tsehrhardt](https://discourse.slicer.org/u/tsehrhardt)\
**Replies:** 9\
**Last updated:** [August 6, 2025, 2:41pm UTC](https://discourse.slicer.org/t/renaming-segments-forces-color-selection-as-well/43970 "2025-08-06T14:41:08Z")

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I used to be able to double-click a segment name in Segment Editor to change ONLY the name. Now when double-clicking, the box to change color and name both pop up, but requires me to select a color as well or else it wil…

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## [MRI-CT Spine Registration Data](https://discourse.slicer.org/t/mri-ct-spine-registration-data/43985)

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**Author:** [@elisedl1](https://discourse.slicer.org/u/elisedl1)\
**Replies:** 0\
**Last updated:** [August 6, 2025, 2:05pm UTC](https://discourse.slicer.org/t/mri-ct-spine-registration-data/43985 "2025-08-06T14:05:23Z")

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Hi all, It seems as though the SpineWeb Dataset is no longer accessible via its online link (http://spineweb.cigitalimaginggroup.ca/spineweb/index.php?n=Main.Datasets). Would anyone know of any other MRI-CT spine data …

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## [Method on how to remove black background from Brain MRI images](https://discourse.slicer.org/t/method-on-how-to-remove-black-background-from-brain-mri-images/31459)

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**Author:** [@Alvi\_Rahman](https://discourse.slicer.org/u/Alvi_Rahman)\
**Replies:** 1\
**Last updated:** [August 6, 2025, 6:22am UTC](https://discourse.slicer.org/t/method-on-how-to-remove-black-background-from-brain-mri-images/31459 "2025-08-06T06:22:11Z")

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My aim is to remove the black ground from each brain MRI slice. I want to achieve this using Python. I have given my code below: import os import numpy as np import SimpleITK as sitk from PIL import Image from skimage.…

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## [Segmenting arteries and pelvic bone in pelvic CT](https://discourse.slicer.org/t/segmenting-arteries-and-pelvic-bone-in-pelvic-ct/43975)

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**Author:** [@Alanlau434](https://discourse.slicer.org/u/Alanlau434)\
**Replies:** 0\
**Last updated:** [August 5, 2025, 3:40pm UTC](https://discourse.slicer.org/t/segmenting-arteries-and-pelvic-bone-in-pelvic-ct/43975 "2025-08-05T15:40:50Z")

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Hello guys, I’m a novice to 3D slicer, doing a project on pelvic exenteration and I need to isolate pelvic arteries and bones (inc lumbar spine). Is there a way to segment and put the two together on the same 3D plane? T…

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## [I am unable to use 3D slicer through leaddbs](https://discourse.slicer.org/t/i-am-unable-to-use-3d-slicer-through-leaddbs/43974)

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**Author:** [@Reem](https://discourse.slicer.org/u/Reem)\
**Replies:** 0\
**Last updated:** [August 5, 2025, 3:40pm UTC](https://discourse.slicer.org/t/i-am-unable-to-use-3d-slicer-through-leaddbs/43974 "2025-08-05T15:40:47Z")

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Hello, I am trying to view images from leaddbs software through 3D slicer, but I am getting an error that the slicer path is not defined in Matlab. Can you please advise on how to set the path for slicer in leaddbs throu…

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## [CMake Error during PlusLib SuperBuild: "The source does not match..."](https://discourse.slicer.org/t/cmake-error-during-pluslib-superbuild-the-source-does-not-match/43972)

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**Author:** [@Jaeseong](https://discourse.slicer.org/u/Jaeseong)\
**Replies:** 0\
**Last updated:** [August 5, 2025, 3:40pm UTC](https://discourse.slicer.org/t/cmake-error-during-pluslib-superbuild-the-source-does-not-match/43972 "2025-08-05T15:40:36Z")

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Hi everyone, I’m encountering an error during the building of Pluslib, which is a dependency for Slicer on Ubuntu. My goal is to acquire ultrasound images from a Windows machine using the PLUS server. I followed the in…

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## [Scissors Not Working](https://discourse.slicer.org/t/scissors-not-working/21835)

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**Author:** [@Sandy1](https://discourse.slicer.org/u/Sandy1)\
**Replies:** 14\
**Last updated:** [August 5, 2025, 2:39pm UTC](https://discourse.slicer.org/t/scissors-not-working/21835 "2025-08-05T14:39:47Z")

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I am in the segment editor, and I am attempting to remove jewelry and bone from my image. I have selected the erase inside option. Nothing happens once I’ve circled the areas with the scissors that I want to remove. Plea…

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## [hi i want i small CT Knee scan file for 3d slicer and i couldn t find one ](https://discourse.slicer.org/t/hi-i-want-i-small-ct-knee-scan-file-for-3d-slicer-and-i-couldn-t-find-one/43763)

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**Author:** [@wsymjlal781](https://discourse.slicer.org/u/wsymjlal781)\
**Replies:** 2\
**Last updated:** [August 5, 2025, 1:32pm UTC](https://discourse.slicer.org/t/hi-i-want-i-small-ct-knee-scan-file-for-3d-slicer-and-i-couldn-t-find-one/43763 "2025-08-05T13:32:27Z")

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hi i want i small CT Knee scan file for 3d slicer and i couldn t find one

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## [DVH variations after Deformable Registration](https://discourse.slicer.org/t/dvh-variations-after-deformable-registration/43936)

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**Author:** [@azam](https://discourse.slicer.org/u/azam)\
**Replies:** 3\
**Last updated:** [August 5, 2025, 11:39am UTC](https://discourse.slicer.org/t/dvh-variations-after-deformable-registration/43936 "2025-08-05T11:39:57Z")

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Hi everyone, I would like to register two DICOM CT images (CT FB, CT DIBH) that I exported from the treatment planning system, and then apply the resulting transformation matrix to the DICOM RT dose and RT structure dat…

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## [Combining registered volumes from different perspectives for improved resolution](https://discourse.slicer.org/t/combining-registered-volumes-from-different-perspectives-for-improved-resolution/43960)

<div class="topic-metadata">

**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 2\
**Last updated:** [August 4, 2025, 11:01pm UTC](https://discourse.slicer.org/t/combining-registered-volumes-from-different-perspectives-for-improved-resolution/43960 "2025-08-04T23:01:35Z")

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Say I have two MR volumes of the same brain; one coronal and one sagittal. The axial z resolution is ~5x poorer volume. I imagine there must be some way (after registering the volumes) to create a new “average” volume …

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## [Clipping a model via scripting](https://discourse.slicer.org/t/clipping-a-model-via-scripting/43963)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 0\
**Last updated:** [August 4, 2025, 10:19pm UTC](https://discourse.slicer.org/t/clipping-a-model-via-scripting/43963 "2025-08-04T22:19:56Z")

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Hi all, I am trying to clipping a model via scripting: if not clipModelsNode: clipModelsNode = slicer.mrmlScene.AddNewNodeByClass( 'vtkMRMLClipModelsNode', 'ClipModels') # Get model node to clip modelNode …

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## [Threshold segmentation not captures the areas I intended](https://discourse.slicer.org/t/threshold-segmentation-not-captures-the-areas-i-intended/43921)

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**Author:** [@mina.dehghan](https://discourse.slicer.org/u/mina.dehghan)\
**Replies:** 1\
**Last updated:** [August 4, 2025, 3:04pm UTC](https://discourse.slicer.org/t/threshold-segmentation-not-captures-the-areas-i-intended/43921 "2025-08-04T15:04:50Z")

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Hello, I have a cubic shape of Al and Zn (High difference in density). Within the cubic there are some voids that I’m not able to capture them using the threshold segmentation for volume measurements. Is there a way I c…

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## [How to export centerline generated by the VMTK?](https://discourse.slicer.org/t/how-to-export-centerline-generated-by-the-vmtk/22735)

<div class="topic-metadata">

**Author:** [@canadan](https://discourse.slicer.org/u/canadan)\
**Replies:** 6\
**Last updated:** [August 4, 2025, 12:48pm UTC](https://discourse.slicer.org/t/how-to-export-centerline-generated-by-the-vmtk/22735 "2025-08-04T12:48:54Z")

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Operating system: Linux Slicer version:4.11.20210226 r29738 / 7a593c8 Expected behavior: Actual behavior: Following a recent online tutorial, I was able to generate a centerline of a segemented aorta. I would like to…

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