# Latest

**URL:** https://discourse.slicer.org/latest.md?page=40

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

**Page:** 41

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## [2025.09.02 Weekly Meeting](https://discourse.slicer.org/t/2025-09-02-weekly-meeting/44315)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [September 9, 2025, 1:55pm UTC](https://discourse.slicer.org/t/2025-09-02-weekly-meeting/44315 "2025-09-09T13:55:25Z")

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Today, we will be having our next weekly hangout at 10:00 AM ET until 11:00 AM ET. a Anyone is welcome to join at this link: https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Please post to this thread to p…

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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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## [vtkMRMLMarkupsLineNode view in slices only if intersecting the slice plans](https://discourse.slicer.org/t/vtkmrmlmarkupslinenode-view-in-slices-only-if-intersecting-the-slice-plans/44389)

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**Author:** [@sarafv](https://discourse.slicer.org/u/sarafv)\
**Replies:** 6\
**Last updated:** [September 9, 2025, 11:39am UTC](https://discourse.slicer.org/t/vtkmrmlmarkupslinenode-view-in-slices-only-if-intersecting-the-slice-plans/44389 "2025-09-09T11:39:18Z")

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Hi! There is a way to hide the control points of a vtkMRMLMarkupsLineNode in 2d views when the control points are not in the visible 2D Slices of Back/Foreground Volumes thanks! Sara

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## [Using Markups planes as a bone cut planning for navigation machine](https://discourse.slicer.org/t/using-markups-planes-as-a-bone-cut-planning-for-navigation-machine/44395)

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**Author:** [@Ben\_Fong](https://discourse.slicer.org/u/Ben_Fong)\
**Replies:** 1\
**Last updated:** [September 9, 2025, 2:29am UTC](https://discourse.slicer.org/t/using-markups-planes-as-a-bone-cut-planning-for-navigation-machine/44395 "2025-09-09T02:29:13Z")

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Hello, I am working on bone tumour surgery planning. I created planes in Markups for the bone cuts, and would like to convert them to models and then save them as STLs to import to the navigation machine. I have two que…

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## [Bones disappear at random frames (bug?)](https://discourse.slicer.org/t/bones-disappear-at-random-frames-bug/44261)

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**Author:** [@Lauren\_Swain](https://discourse.slicer.org/u/Lauren_Swain)\
**Replies:** 6\
**Last updated:** [September 8, 2025, 8:36pm UTC](https://discourse.slicer.org/t/bones-disappear-at-random-frames-bug/44261 "2025-09-08T20:36:31Z")

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Hello, I have just recently started trying to use SAM for image registration but I have run into an issue where the bone DRR will disappear (also from the world view) for random frames during my trial. When they disappe…

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## [Slicer stable cdash errors](https://discourse.slicer.org/t/slicer-stable-cdash-errors/44390)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [September 8, 2025, 3:40pm UTC](https://discourse.slicer.org/t/slicer-stable-cdash-errors/44390 "2025-09-08T15:40:12Z")

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Not sure if this is a concern but looks like both Mac and windows stable versions reporting an error and there is no Linux server (metroplex) listed for stable builds. No extensions are listed either. @jcfr @Sam\_Horvath …

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## [Scan naive rotation](https://discourse.slicer.org/t/scan-naive-rotation/44205)

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**Author:** [@Shirly\_Someck](https://discourse.slicer.org/u/Shirly_Someck)\
**Replies:** 7\
**Last updated:** [September 8, 2025, 3:32pm UTC](https://discourse.slicer.org/t/scan-naive-rotation/44205 "2025-09-08T15:32:34Z")

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Hi, I want to rotate a scan in a naive way, like this button in word for example, turn this: into: Shift didn’t work… Thanks in advance! Shirly

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## [qMRMLSubjectHierarchyTreeView::setCurrentItem proposal](https://discourse.slicer.org/t/qmrmlsubjecthierarchytreeview-setcurrentitem-proposal/44301)

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**Author:** [@aymeric.chataigner](https://discourse.slicer.org/u/aymeric.chataigner)\
**Replies:** 7\
**Last updated:** [September 8, 2025, 7:39am UTC](https://discourse.slicer.org/t/qmrmlsubjecthierarchytreeview-setcurrentitem-proposal/44301 "2025-09-08T07:39:31Z")

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Dear Slicer developers, I would like to get some feedback on a potential fix in qMRMLSubjectHierarchyTreeView: ENH: qMRMLSubjectHierarchyTreeView: call setCurrentIndex rather than … · Slicer/Slicer@1fdee41 · GitHub In …

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## [SlicerRT’s RTSTRUCT to Binary Mask Conversion Algorithm and Dice Coefficient Calculation](https://discourse.slicer.org/t/slicerrt-s-rtstruct-to-binary-mask-conversion-algorithm-and-dice-coefficient-calculation/44380)

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**Author:** [@azam](https://discourse.slicer.org/u/azam)\
**Replies:** 1\
**Last updated:** [September 7, 2025, 6:18pm UTC](https://discourse.slicer.org/t/slicerrt-s-rtstruct-to-binary-mask-conversion-algorithm-and-dice-coefficient-calculation/44380 "2025-09-07T18:18:35Z")

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Hello everyone, I need to calculate the Dice coefficient for my organs using Python code, independently from 3D Slicer. I have already written the code for calculating this coefficient and posted it at the following lin…

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## [Segment Editor:  clicking eye to toggle visibility should not select segment](https://discourse.slicer.org/t/segment-editor-clicking-eye-to-toggle-visibility-should-not-select-segment/20237)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 6\
**Last updated:** [September 6, 2025, 9:34pm UTC](https://discourse.slicer.org/t/segment-editor-clicking-eye-to-toggle-visibility-should-not-select-segment/20237 "2025-09-06T21:34:08Z")

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In a segmentation it is common to create multiple segments in the Segment Editor module. The current behaviour is that clicking eye displayed adjacent to an individual segment to toggle the visibility of that segment wi…

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## [Real-time collaborative segmentation #2](https://discourse.slicer.org/t/real-time-collaborative-segmentation-2/44373)

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**Author:** [@gregsharp.geo](https://discourse.slicer.org/u/gregsharp.geo)\
**Replies:** 4\
**Last updated:** [September 6, 2025, 6:34pm UTC](https://discourse.slicer.org/t/real-time-collaborative-segmentation-2/44373 "2025-09-06T18:34:56Z")

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Hello friends. Good to be back. I read the topic ( Adding near-real time collaborative manual segmentation ) with interest, and it partly answered my questions. But it seems maybe different use case, so I started a ne…

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## [Overlay text with masks in a dicomseg file](https://discourse.slicer.org/t/overlay-text-with-masks-in-a-dicomseg-file/40337)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 8\
**Last updated:** [September 5, 2025, 9:43pm UTC](https://discourse.slicer.org/t/overlay-text-with-masks-in-a-dicomseg-file/40337 "2025-09-05T21:43:24Z")

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Hi 3D Slicer Community, I was trying to implement a dicomseg file that can contain both segmentation masks and their corresponding texts. I can compute the exact location of all the texts. For instance, I have L1 and L2…

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## [Joint smooth in 2d](https://discourse.slicer.org/t/joint-smooth-in-2d/44369)

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**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 0\
**Last updated:** [September 5, 2025, 9:06pm UTC](https://discourse.slicer.org/t/joint-smooth-in-2d/44369 "2025-09-05T21:06:22Z")

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Hi, The joint smoothening tool historically works very well for me, but now I have a series of atlas segments that are very poorly sampled in Z. The X Y edges are also rather rough, and so I want to improve these by up…

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## [DICOM to Voxel(python) - Landmark Placement Issue for DL Dataset](https://discourse.slicer.org/t/dicom-to-voxel-python-landmark-placement-issue-for-dl-dataset/44366)

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**Author:** [@nik\_47](https://discourse.slicer.org/u/nik_47)\
**Replies:** 2\
**Last updated:** [September 5, 2025, 7:59pm UTC](https://discourse.slicer.org/t/dicom-to-voxel-python-landmark-placement-issue-for-dl-dataset/44366 "2025-09-05T19:59:57Z")

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Hey everyone! I’m currently working on a project to prepare a dataset for a deep learning model. The main goal is to train a neural network to detect specific landmarks on 3D MRIs. I’m using Slicer 3D to create landmark…

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## [how to improve the CenterLine extraction](https://discourse.slicer.org/t/how-to-improve-the-centerline-extraction/44365)

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**Author:** [@amscosta](https://discourse.slicer.org/u/amscosta)\
**Replies:** 1\
**Last updated:** [September 5, 2025, 6:22pm UTC](https://discourse.slicer.org/t/how-to-improve-the-centerline-extraction/44365 "2025-09-05T18:22:17Z")

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Hello, Need to extract the centerlines from a stl file. Please see the attached pictures. Really overwhelmed but the bunch of controls/options available. Could somebody with expertise give some guidelines/directions to …

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## [Bug Report ISO ASO Extension – Missing testWslAvailable and helper methods cause crash](https://discourse.slicer.org/t/bug-report-iso-aso-extension-missing-testwslavailable-and-helper-methods-cause-crash/44364)

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**Author:** [@fabien-prog](https://discourse.slicer.org/u/fabien-prog)\
**Replies:** 0\
**Last updated:** [September 5, 2025, 4:58pm UTC](https://discourse.slicer.org/t/bug-report-iso-aso-extension-missing-testwslavailable-and-helper-methods-cause-crash/44364 "2025-09-05T16:58:05Z")

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Hi everyone, I ran into an issue trying to use the ISO ASO extension (Automated Dental Tools) in 3D Slicer 5.8.1 on Windows 11 with WSL2 + Ubuntu 24.04. Problem When launching ISO ASO and clicking Run, the module gets …

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## [Can’t visualize my liver segmentation in 3D after cropping (Scalar Range shows 0–2 but nothing displays)](https://discourse.slicer.org/t/can-t-visualize-my-liver-segmentation-in-3d-after-cropping-scalar-range-shows-0-2-but-nothing-displays/44355)

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**Author:** [@era\_888](https://discourse.slicer.org/u/era_888)\
**Replies:** 1\
**Last updated:** [September 5, 2025, 10:34am UTC](https://discourse.slicer.org/t/can-t-visualize-my-liver-segmentation-in-3d-after-cropping-scalar-range-shows-0-2-but-nothing-displays/44355 "2025-09-05T10:34:36Z")

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Hello everyone. I am working on a liver surgery simulation project. I have: Pre-operative MRI resampled to isotropic (preop\_n4\_iso) Liver segmentation exported as labelmap (liver\_full\_seg) What I did: Resamp…

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## [Questions regarding technique to making lung model including an comparison](https://discourse.slicer.org/t/questions-regarding-technique-to-making-lung-model-including-an-comparison/44316)

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**Author:** [@jamesgyh](https://discourse.slicer.org/u/jamesgyh)\
**Replies:** 3\
**Last updated:** [September 5, 2025, 6:37am UTC](https://discourse.slicer.org/t/questions-regarding-technique-to-making-lung-model-including-an-comparison/44316 "2025-09-05T06:37:02Z")

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here is the model from Stanford. According to them, they use 3d Slicer to build such a detailed bronchi model. However, what I build for now is like this which is roughly one level bronchi smaller than the standford mod…

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## [Using SlicerIGT viewpoint in Virtual Reality](https://discourse.slicer.org/t/using-slicerigt-viewpoint-in-virtual-reality/44353)

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**Author:** [@tech\_curious](https://discourse.slicer.org/u/tech_curious)\
**Replies:** 0\
**Last updated:** [September 5, 2025, 6:04am UTC](https://discourse.slicer.org/t/using-slicerigt-viewpoint-in-virtual-reality/44353 "2025-09-05T06:04:09Z")

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Hello, I have been experimenting with an IGT setup in Slicer which I want to visualize with a virtual reality headset. Now I am trying to match the VR view to the actual perspective on the phantom and tool by also tracki…

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## [Resamping for CT with different voxel, can I still compare CTs of two patients with different voxel sizes/number of voxel per axis](https://discourse.slicer.org/t/resamping-for-ct-with-different-voxel-can-i-still-compare-cts-of-two-patients-with-different-voxel-sizes-number-of-voxel-per-axis/44295)

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**Author:** [@CS1](https://discourse.slicer.org/u/CS1)\
**Replies:** 3\
**Last updated:** [September 4, 2025, 10:20am UTC](https://discourse.slicer.org/t/resamping-for-ct-with-different-voxel-can-i-still-compare-cts-of-two-patients-with-different-voxel-sizes-number-of-voxel-per-axis/44295 "2025-09-04T10:20:07Z")

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Hi there, as I was trying to train my nnunet model, I was having quite some issues with broadcasting due to images having different sizes/voxels/pixels. As I was looking into this, I realised different CTs of my patients…

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## [How to Package a Custom Slicer Application for Distribution](https://discourse.slicer.org/t/how-to-package-a-custom-slicer-application-for-distribution/44298)

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**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 6\
**Last updated:** [September 4, 2025, 9:07am UTC](https://discourse.slicer.org/t/how-to-package-a-custom-slicer-application-for-distribution/44298 "2025-09-04T09:07:06Z")

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I have built a custom Slicer application using the Kitware SlicerCustomAppTemplate. I have also integrated 5 custom scripted modules successfully. Now, I would like to package the application so that it can be distribut…

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## [Slicer for Ubuntu arm64](https://discourse.slicer.org/t/slicer-for-ubuntu-arm64/6459)

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**Author:** [@adamrankin](https://discourse.slicer.org/u/adamrankin)\
**Replies:** 59\
**Last updated:** [September 3, 2025, 3:21pm UTC](https://discourse.slicer.org/t/slicer-for-ubuntu-arm64/6459 "2025-09-03T15:21:02Z")

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Notes on compilation efforts for compiling Slicer for arm64: Problem: VTK does not compile. Solution: Set VTK\_OPENGL\_HAS\_EGL and VTK\_OPENGL\_HAS\_ES In \<SlicerDir\>/SuperBuild/External\_VTK.cmake remove section that has -…

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## [Tumor segmentation-spine](https://discourse.slicer.org/t/tumor-segmentation-spine/44332)

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**Author:** [@sabnis93](https://discourse.slicer.org/u/sabnis93)\
**Replies:** 0\
**Last updated:** [September 3, 2025, 2:26pm UTC](https://discourse.slicer.org/t/tumor-segmentation-spine/44332 "2025-09-03T14:26:46Z")

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Hello all, I am trying to segment and calculate tumor volume for spine neurofibromas in mice models. I acquired T2 TurboRARE images for axial, coronal and sagittal orientations separately. I am seeing tumors in few slic…

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## [Failed to Install PyTorch Offline](https://discourse.slicer.org/t/failed-to-install-pytorch-offline/44331)

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**Author:** [@bulala](https://discourse.slicer.org/u/bulala)\
**Replies:** 0\
**Last updated:** [September 3, 2025, 2:26pm UTC](https://discourse.slicer.org/t/failed-to-install-pytorch-offline/44331 "2025-09-03T14:26:44Z")

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I‘m trying to install Pytorch for 3D Slicer 5.8.1 on a computer that has no internet access.Although I have already installed PyTorch, a “PyTorch not installed” prompt appears when I try to activate the TotalSegmentator …

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## [List of cmake variables that I can set on a Slicer build?](https://discourse.slicer.org/t/list-of-cmake-variables-that-i-can-set-on-a-slicer-build/37093)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 1\
**Last updated:** [September 3, 2025, 12:16pm UTC](https://discourse.slicer.org/t/list-of-cmake-variables-that-i-can-set-on-a-slicer-build/37093 "2025-09-03T12:16:52Z")

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Actually, I’m trying to build the stable release to test changes on stable release extensions that I’m also going to build. I can point the Slicer code folder to branch 5.6 but cmake configuration log still says the rele…

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## [How to convert a custom 3D Slicer plugin with ParameterNodes into a CLI-friendly module?](https://discourse.slicer.org/t/how-to-convert-a-custom-3d-slicer-plugin-with-parameternodes-into-a-cli-friendly-module/44217)

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**Author:** [@khyatisethia](https://discourse.slicer.org/u/khyatisethia)\
**Replies:** 2\
**Last updated:** [September 3, 2025, 11:47am UTC](https://discourse.slicer.org/t/how-to-convert-a-custom-3d-slicer-plugin-with-parameternodes-into-a-cli-friendly-module/44217 "2025-09-03T11:47:54Z")

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Hi everyone, I’ve been working on a custom plugin for 3D Slicer, and I’ve run into a design issue that makes it hard to reuse the logic outside of the GUI. Right now, my ModuleWidget class is tightly coupled to the Sli…

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## [Nrrd vs vtp model coordinate systems in Python](https://discourse.slicer.org/t/nrrd-vs-vtp-model-coordinate-systems-in-python/44323)

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**Author:** [@elisedl1](https://discourse.slicer.org/u/elisedl1)\
**Replies:** 1\
**Last updated:** [September 3, 2025, 4:07am UTC](https://discourse.slicer.org/t/nrrd-vs-vtp-model-coordinate-systems-in-python/44323 "2025-09-03T04:07:24Z")

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Hello, My model (.vtp) and image (.nrrd) align in slicer correctly. I am trying to use the model and image information in Python, but they do not visually align when plotted; they are in different coordinate systems (wo…

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## [Automatic organ dimensions measurement ](https://discourse.slicer.org/t/automatic-organ-dimensions-measurement/44306)

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**Author:** [@bexsero](https://discourse.slicer.org/u/bexsero)\
**Replies:** 3\
**Last updated:** [September 2, 2025, 4:55pm UTC](https://discourse.slicer.org/t/automatic-organ-dimensions-measurement/44306 "2025-09-02T16:55:38Z")

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Hi. I’m new to 3d slicer. I was wondering if there is a tool that can automatically measure the dimensions of segmented organ. I know of SlicerRadiomics, but it’s unavailable in newest stable version. I’m kindly asking …

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