# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=28

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

**Page:** 29

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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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## [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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## [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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## [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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## [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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## [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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## [Can MONAI Auto3dSeg use metal (MPS) on M series processors running MacOS?](https://discourse.slicer.org/t/can-monai-auto3dseg-use-metal-mps-on-m-series-processors-running-macos/44305)

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**Author:** [@GeneRisi](https://discourse.slicer.org/u/GeneRisi)\
**Replies:** 4\
**Last updated:** [September 2, 2025, 4:47pm UTC](https://discourse.slicer.org/t/can-monai-auto3dseg-use-metal-mps-on-m-series-processors-running-macos/44305 "2025-09-02T16:47:15Z")

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I am running Auto3dSeg on my MacBook Pro with M3 Pro and wondering whether there is something I need to do to enable use of MTL for inferencing? Thank you. Gene Risi

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## [Hide slice rectangles in 3D view](https://discourse.slicer.org/t/hide-slice-rectangles-in-3d-view/42912)

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**Author:** [@spichardo](https://discourse.slicer.org/u/spichardo)\
**Replies:** 8\
**Last updated:** [September 2, 2025, 3:50pm UTC](https://discourse.slicer.org/t/hide-slice-rectangles-in-3d-view/42912 "2025-09-02T15:50:57Z")

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Operating system: macOS 15.4.1 Slicer version: 5.8.1 Expected behavior: Old versions of 3DSlicer didn’t show these rectangles, they are in the way for illustration purposes Actual behavior: The “new” rectangles are sh…

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## [Create new vector volume](https://discourse.slicer.org/t/create-new-vector-volume/9297)

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**Author:** [@sthirumal](https://discourse.slicer.org/u/sthirumal)\
**Replies:** 7\
**Last updated:** [September 2, 2025, 3:46pm UTC](https://discourse.slicer.org/t/create-new-vector-volume/9297 "2025-09-02T15:46:13Z")

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Operating system: Windows 10 Slicer version: 4.10.1 I am trying to create a new vector volume (since I need a colour image) and am wondering how to go about coding this.

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## [Data file information](https://discourse.slicer.org/t/data-file-information/44274)

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**Author:** [@michaelli](https://discourse.slicer.org/u/michaelli)\
**Replies:** 8\
**Last updated:** [September 2, 2025, 1:43pm UTC](https://discourse.slicer.org/t/data-file-information/44274 "2025-09-02T13:43:41Z")

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I load a bunch of data files into Slicer 3D, including DICOM, STL and others, how can I get the file path and file name information? I cannot see the file information from data structure. I ask this because I have files …

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## [Questions regarding filling between bronchis of small spaces and reason of bad result display here](https://discourse.slicer.org/t/questions-regarding-filling-between-bronchis-of-small-spaces-and-reason-of-bad-result-display-here/44082)

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**Author:** [@jamesgyh](https://discourse.slicer.org/u/jamesgyh)\
**Replies:** 2\
**Last updated:** [September 2, 2025, 1:36pm UTC](https://discourse.slicer.org/t/questions-regarding-filling-between-bronchis-of-small-spaces-and-reason-of-bad-result-display-here/44082 "2025-09-02T13:36:07Z")

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Here is the result of my bronchi after using the LungCT segmentation. May I ask how can I manually connect the small spaces and also make the model display better? This is 0.5mm thickness and I have no idea why the su…

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## [SlicerAstro extension](https://discourse.slicer.org/t/slicerastro-extension/44307)

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**Author:** [@AJO\_VICTOR](https://discourse.slicer.org/u/AJO_VICTOR)\
**Replies:** 1\
**Last updated:** [September 2, 2025, 11:15am UTC](https://discourse.slicer.org/t/slicerastro-extension/44307 "2025-09-02T11:15:52Z")

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I cant find any extension named “slicerastro“ extension inside extension manager.Can somebody help?

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## [Batch Processing with SlicerLungCTAnalyzer](https://discourse.slicer.org/t/batch-processing-with-slicerlungctanalyzer/42768)

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**Author:** [@omegayen](https://discourse.slicer.org/u/omegayen)\
**Replies:** 2\
**Last updated:** [September 2, 2025, 11:08am UTC](https://discourse.slicer.org/t/batch-processing-with-slicerlungctanalyzer/42768 "2025-09-02T11:08:46Z")

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Hi @rbumm thanks for your work. I am working with SlicerLungCTAnalyzer and having difficulty with batch processing with both the segmenter and analyzer. I reviewed the instructions here Batch processing with Lung CT Seg…

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## [Changing the voxel size (resolution) and saving a new volume.](https://discourse.slicer.org/t/changing-the-voxel-size-resolution-and-saving-a-new-volume/44260)

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**Author:** [@Chanrury\_s](https://discourse.slicer.org/u/Chanrury_s)\
**Replies:** 3\
**Last updated:** [September 1, 2025, 4:30pm UTC](https://discourse.slicer.org/t/changing-the-voxel-size-resolution-and-saving-a-new-volume/44260 "2025-09-01T16:30:34Z")

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Hello. I work with CT scans of jaw bones and teeth. The original volume was recorded with the spacing parameter = 0.2 mm. For me, this is a fairly thick slice and I was looking for ways to improve the quality of segment…

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## [SlicerRT not visible in modules after installation](https://discourse.slicer.org/t/slicerrt-not-visible-in-modules-after-installation/44185)

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**Author:** [@Mahrukh\_Tariq](https://discourse.slicer.org/u/Mahrukh_Tariq)\
**Replies:** 11\
**Last updated:** [September 1, 2025, 3:25pm UTC](https://discourse.slicer.org/t/slicerrt-not-visible-in-modules-after-installation/44185 "2025-09-01T15:25:10Z")

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Hi. Can you please help to resolve the issue I‘m facing with SlicerRT extension not being visible in the Modules even after it has been installed and visible in Extensions Manager. 3D Slicer version 5.8.1

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## [The size and position of the bounding box](https://discourse.slicer.org/t/the-size-and-position-of-the-bounding-box/44289)

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**Author:** [@Konstantin](https://discourse.slicer.org/u/Konstantin)\
**Replies:** 1\
**Last updated:** [September 1, 2025, 9:14am UTC](https://discourse.slicer.org/t/the-size-and-position-of-the-bounding-box/44289 "2025-09-01T09:14:38Z")

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Hello. How can I make the position and dimensions of the bounding box like the 3D model?

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