# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=166

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

**Page:** 167

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## [Error while exporting a model node as stl file](https://discourse.slicer.org/t/error-while-exporting-a-model-node-as-stl-file/29047)

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**Author:** [@Luca](https://discourse.slicer.org/u/Luca)\
**Replies:** 4\
**Last updated:** [April 25, 2023, 1:59pm UTC](https://discourse.slicer.org/t/error-while-exporting-a-model-node-as-stl-file/29047 "2023-04-25T13:59:05Z")

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Hello everyone, every time I try to export a model node (simple or complex) as stl file by using the GUI, I get the following error: Error: ERROR: In D:\\D\\S\\S-0-build\\VTK\\IO\\Geometry\\vtkSTLWriter.cxx, line 248 vtkSTL…

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## [Total Segmentator on 5.2.2 "scikit-learn" distribution not found](https://discourse.slicer.org/t/total-segmentator-on-5-2-2-scikit-learn-distribution-not-found/28727)

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**Author:** [@tsehrhardt](https://discourse.slicer.org/u/tsehrhardt)\
**Replies:** 22\
**Last updated:** [April 25, 2023, 12:44pm UTC](https://discourse.slicer.org/t/total-segmentator-on-5-2-2-scikit-learn-distribution-not-found/28727 "2023-04-25T12:44:29Z")

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After installing Slicer 5.2.2, Total Segmentator is no longer working. I read through the troubleshooting and uninstalled/reinstalled PyTorch and did a Force reinstall of Total Segmentator, but still can’t run it. I’m ju…

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## [Apply button for threshold computation](https://discourse.slicer.org/t/apply-button-for-threshold-computation/29106)

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**Author:** [@KSL](https://discourse.slicer.org/u/KSL)\
**Replies:** 1\
**Last updated:** [April 25, 2023, 11:21am UTC](https://discourse.slicer.org/t/apply-button-for-threshold-computation/29106 "2023-04-25T11:21:07Z")

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Hello friends, I am currently using Slicer 5.2.2. I want to segment tissues using threshold computation from Segment editor, but I couldn’t find the apply button. Can anyone suggest me how to fix this. Thanks in advance. …

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## [relative dose value in color legend/DVH](https://discourse.slicer.org/t/relative-dose-value-in-color-legend-dvh/29114)

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**Author:** [@VVCJ](https://discourse.slicer.org/u/VVCJ)\
**Replies:** 0\
**Last updated:** [April 25, 2023, 11:14am UTC](https://discourse.slicer.org/t/relative-dose-value-in-color-legend-dvh/29114 "2023-04-25T11:14:39Z")

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Hi all, I input the CT and RTDose data to review the dose distribution. By default, the color legend and DVH shows the absolute dose value (Gy) stored in RTDose.dcm. I was wondering if I could show the relative dose (%)…

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## [Parametric response mapping, chest CT](https://discourse.slicer.org/t/parametric-response-mapping-chest-ct/29111)

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**Author:** [@V\_LJ](https://discourse.slicer.org/u/V_LJ)\
**Replies:** 0\
**Last updated:** [April 25, 2023, 11:10am UTC](https://discourse.slicer.org/t/parametric-response-mapping-chest-ct/29111 "2023-04-25T11:10:32Z")

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Greetings Slicers, Is it possible to make a PRM (parametric response mapping) from an inspiratory and expiratory chest CT scan with 3DSlicer? I know, that i need an image registration between inspiratory and expiratory…

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## [Better GPU will benefit or not VR volume rendering](https://discourse.slicer.org/t/better-gpu-will-benefit-or-not-vr-volume-rendering/21008)

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**Author:** [@davide445](https://discourse.slicer.org/u/davide445)\
**Replies:** 64\
**Last updated:** [December 29, 2021, 9:49am UTC](https://discourse.slicer.org/t/better-gpu-will-benefit-or-not-vr-volume-rendering/21008 "2021-12-29T09:49:09Z")

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Was testing today VR view using a Vive Cosmos headset, a GTX 1070 GPU, Ryzen 2600X CPU and 64GB RAM. Works but it’s not really fluid, a bit of nauseating shutters. Tried to change various setting but didn’t find better…

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## [3D-2D CT-Fluoro registration](https://discourse.slicer.org/t/3d-2d-ct-fluoro-registration/29105)

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**Author:** [@BraveDistribution](https://discourse.slicer.org/u/BraveDistribution)\
**Replies:** 0\
**Last updated:** [April 25, 2023, 6:01am UTC](https://discourse.slicer.org/t/3d-2d-ct-fluoro-registration/29105 "2023-04-25T06:01:50Z")

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Hello community, I would like to perform 3D-2D registration (CT-fluoroscopy) on pelvis data from the GitHub repository GitHub - rg2/Regi2D3D-IPCAI2020: Code for the registration component of the IPCAI 2020 paper: "Autom…

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## [About CellPicker when markup by line](https://discourse.slicer.org/t/about-cellpicker-when-markup-by-line/29100)

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**Author:** [@dbtruong](https://discourse.slicer.org/u/dbtruong)\
**Replies:** 1\
**Last updated:** [April 25, 2023, 4:59am UTC](https://discourse.slicer.org/t/about-cellpicker-when-markup-by-line/29100 "2023-04-25T04:59:28Z")

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Hello everyone, vtkCellPicker will got a point in the world coordinates when click on surface. How to find the points isn’t on surface?

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## [Unable to run PlaceSemiLMPatches due to missing function?](https://discourse.slicer.org/t/unable-to-run-placesemilmpatches-due-to-missing-function/29048)

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**Author:** [@Maria\_Feiler](https://discourse.slicer.org/u/Maria_Feiler)\
**Replies:** 8\
**Last updated:** [April 25, 2023, 4:13am UTC](https://discourse.slicer.org/t/unable-to-run-placesemilmpatches-due-to-missing-function/29048 "2023-04-25T04:13:27Z")

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@muratmaga There seems to be an issue concerning the PlaceSemiLMPatches module in SlicerMorph. I have organized my files as described in the help files, but I receive the following errors when trying to place my patches …

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## [Installation of new Slicer version without loss of settings and modules](https://discourse.slicer.org/t/installation-of-new-slicer-version-without-loss-of-settings-and-modules/29056)

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**Author:** [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Replies:** 2\
**Last updated:** [April 24, 2023, 6:36pm UTC](https://discourse.slicer.org/t/installation-of-new-slicer-version-without-loss-of-settings-and-modules/29056 "2023-04-24T18:36:32Z")

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Hello, I am currently running Slicer 5.1.0 for Windows and want to update to the latest 3D Slicer version. However, I want to keep the way I have organised Slicer currently and the extensions/ modules I have downloaded.…

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## [Matching Voxels After Registration](https://discourse.slicer.org/t/matching-voxels-after-registration/29089)

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**Author:** [@yonnif](https://discourse.slicer.org/u/yonnif)\
**Replies:** 0\
**Last updated:** [April 24, 2023, 1:44pm UTC](https://discourse.slicer.org/t/matching-voxels-after-registration/29089 "2023-04-24T13:44:25Z")

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Hi, I have two registered CT images that I’m trying to register to an MRI image. The CT images have matching matrices but they are different to the MRI image. After successfully registering one of them with ANTs, the r…

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## [Exporting/Saving Transformed DICOM Volumes](https://discourse.slicer.org/t/exporting-saving-transformed-dicom-volumes/29087)

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**Author:** [@18ilyasa](https://discourse.slicer.org/u/18ilyasa)\
**Replies:** 3\
**Last updated:** [April 24, 2023, 1:09pm UTC](https://discourse.slicer.org/t/exporting-saving-transformed-dicom-volumes/29087 "2023-04-24T13:09:07Z")

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Hi, I’m pretty green to Slicer, so apologies if this is a naive question. I’ve applied a transform to a DICOM volume, hardened it and then saved the file (both as a nrrd and as a new dicom folder). When I open these fil…

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## [How can I see the name of the current viewed slide?](https://discourse.slicer.org/t/how-can-i-see-the-name-of-the-current-viewed-slide/29086)

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**Author:** [@Roro1](https://discourse.slicer.org/u/Roro1)\
**Replies:** 0\
**Last updated:** [April 24, 2023, 9:29am UTC](https://discourse.slicer.org/t/how-can-i-see-the-name-of-the-current-viewed-slide/29086 "2023-04-24T09:29:33Z")

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Hello everyone, in our project we have to perform 3D and 2D analysis of a bone sample. The fact is that we would like to select a particular area in our 3d model in order to perform further imagej-2d analysis in exactly…

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## [Plot data with Markers and without Line](https://discourse.slicer.org/t/plot-data-with-markers-and-without-line/29071)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 5\
**Last updated:** [April 24, 2023, 8:32am UTC](https://discourse.slicer.org/t/plot-data-with-markers-and-without-line/29071 "2023-04-24T08:32:09Z")

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Hi, It seems I can’t show markers. I loaded the sample data: # Get a volume from SampleData and compute its histogram import SampleData import numpy as np volumeNode = SampleData.SampleDataLogic().downloadMRHead() his…

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## [Cropping a particular region in 3D slicer](https://discourse.slicer.org/t/cropping-a-particular-region-in-3d-slicer/29061)

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**Author:** [@Roro1](https://discourse.slicer.org/u/Roro1)\
**Replies:** 2\
**Last updated:** [April 24, 2023, 7:23am UTC](https://discourse.slicer.org/t/cropping-a-particular-region-in-3d-slicer/29061 "2023-04-24T07:23:32Z")

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Hi everyone, in our project we have to create a 3D section of a rat bone (I’ve put the corresponding picture in the post). In this project, we also have to determine if the hole (also present in the linked picture) is…

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## [Developer's mode edit button no action in Linux](https://discourse.slicer.org/t/developers-mode-edit-button-no-action-in-linux/29072)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [April 23, 2023, 9:34pm UTC](https://discourse.slicer.org/t/developers-mode-edit-button-no-action-in-linux/29072 "2023-04-23T21:34:36Z")

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After enabling the developer mode, I expect the edit button would open the source code of the active module in a text editor. In Linux, this doesn’t seem to do anything, even though there are multiple registered edit…

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## [Exporting Transformations from Sequence in 3D Slicer](https://discourse.slicer.org/t/exporting-transformations-from-sequence-in-3d-slicer/28868)

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**Author:** [@AliciaPose](https://discourse.slicer.org/u/AliciaPose)\
**Replies:** 7\
**Last updated:** [April 23, 2023, 12:52pm UTC](https://discourse.slicer.org/t/exporting-transformations-from-sequence-in-3d-slicer/28868 "2023-04-23T12:52:36Z")

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Hi everyone, I have a sequence in 3D Slicer that reproduces the movement of some 3D models by modifying their associated transforms. The sequence was originally recorded using a tracking system that navigated 4 differen…

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## [The Total Segmentator](https://discourse.slicer.org/t/the-total-segmentator/29068)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 0\
**Last updated:** [April 23, 2023, 12:22pm UTC](https://discourse.slicer.org/t/the-total-segmentator/29068 "2023-04-23T12:22:05Z")

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It’s exciting to try to experience the Total Segmentator in Slicer,but it seemed that little problem occured. Slicer 5.2.2,using the CTA-cardio example data, the result is as follows: Restart Slicer time and time ag…

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## [Quantifying the bone to muscle ratio](https://discourse.slicer.org/t/quantifying-the-bone-to-muscle-ratio/29062)

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**Author:** [@Saeed\_Anwar](https://discourse.slicer.org/u/Saeed_Anwar)\
**Replies:** 0\
**Last updated:** [April 22, 2023, 8:30pm UTC](https://discourse.slicer.org/t/quantifying-the-bone-to-muscle-ratio/29062 "2023-04-22T20:30:06Z")

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Operating system: Windows 10 Slicer version: 5.0.3 Expected behavior: Actual behavior: I want to assess the bone to muscle ratio, both in terms of volume and mass, from whole body µCT scan images. Can anybody suggest…

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## [Lung segmentation](https://discourse.slicer.org/t/lung-segmentation/15324)

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**Author:** [@sergiGB](https://discourse.slicer.org/u/sergiGB)\
**Replies:** 23\
**Last updated:** [April 22, 2023, 5:26pm UTC](https://discourse.slicer.org/t/lung-segmentation/15324 "2023-04-22T17:26:59Z")

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how can I know oxygen lung´s saturation ? first I have to segment the lung but I dont know what to do after, thanks s much

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## [Slicer crash without any message when try to run my own module](https://discourse.slicer.org/t/slicer-crash-without-any-message-when-try-to-run-my-own-module/29058)

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**Author:** [@Lorenzo\_Lasagni](https://discourse.slicer.org/u/Lorenzo_Lasagni)\
**Replies:** 0\
**Last updated:** [April 22, 2023, 1:41pm UTC](https://discourse.slicer.org/t/slicer-crash-without-any-message-when-try-to-run-my-own-module/29058 "2023-04-22T13:41:24Z")

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Problem report for Slicer 4.11.20210226 win-amd64: \[please describe expected and actual behavior\] Me and a colleague of mine have write a new module for slicer, but since he sent me last version it crash when i press th…

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## [Centerline Extraction on Bronchoscopy](https://discourse.slicer.org/t/centerline-extraction-on-bronchoscopy/28900)

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**Author:** [@Komal](https://discourse.slicer.org/u/Komal)\
**Replies:** 7\
**Last updated:** [April 21, 2023, 9:24pm UTC](https://discourse.slicer.org/t/centerline-extraction-on-bronchoscopy/28900 "2023-04-21T21:24:04Z")

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Hi, Please can you help me to get centerline extraction on bronchoscopy using python ,VMTK and which algorithm I need to use .Please send me the source code of the same.

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## [Add SFORM\_Permissive mode for nifti files](https://discourse.slicer.org/t/add-sform-permissive-mode-for-nifti-files/29049)

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**Author:** [@Alexander\_Kagan](https://discourse.slicer.org/u/Alexander_Kagan)\
**Replies:** 2\
**Last updated:** [April 21, 2023, 6:47pm UTC](https://discourse.slicer.org/t/add-sform-permissive-mode-for-nifti-files/29049 "2023-04-21T18:47:42Z")

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I currently have an issue with opening a large number of nifti ct scans from the dataset i’m working on (totalsegmentator dataset). it throws an error: “itk only supports orthonormal direction cosines. no orthonormal def…

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## [How to show Orthopeadic hip and shoulder Deformities on 3D prints](https://discourse.slicer.org/t/how-to-show-orthopeadic-hip-and-shoulder-deformities-on-3d-prints/28884)

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**Author:** [@MorganB](https://discourse.slicer.org/u/MorganB)\
**Replies:** 5\
**Last updated:** [April 21, 2023, 2:20pm UTC](https://discourse.slicer.org/t/how-to-show-orthopeadic-hip-and-shoulder-deformities-on-3d-prints/28884 "2023-04-21T14:20:07Z")

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Currently I work for Orthopaedic Surgery and we use 3D models for pre-operative planning. We have noticed that slicer smooths over bone deformities. The recons (ROI) show lots of boney landmarks and deformities. However,…

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## [Maxilla segmentation - Ai driven?](https://discourse.slicer.org/t/maxilla-segmentation-ai-driven/28556)

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**Author:** [@Gergo\_Dr\_Balazs](https://discourse.slicer.org/u/Gergo_Dr_Balazs)\
**Replies:** 5\
**Last updated:** [April 20, 2023, 8:14pm UTC](https://discourse.slicer.org/t/maxilla-segmentation-ai-driven/28556 "2023-04-20T20:14:19Z")

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Dear 3D Slicer Community, I am writing to you with great admiration and respect for your hard work in creating such an amazing platform. I am a second-year orthodontic resident from Hungary with a strong interest in 3D …

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## [Slicer Elastix Error Code: 4294967294](https://discourse.slicer.org/t/slicer-elastix-error-code-4294967294/25574)

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**Author:** [@oliverhalaseh](https://discourse.slicer.org/u/oliverhalaseh)\
**Replies:** 2\
**Last updated:** [April 20, 2023, 4:49pm UTC](https://discourse.slicer.org/t/slicer-elastix-error-code-4294967294/25574 "2023-04-20T16:49:18Z")

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Dear All, I started work on SlicerSegmentationRecipes/VesselSegmentationBySubtraction at master · lassoan/SlicerSegmentationRecipes · GitHub I tried to run the Elastix module, but I keep getting the same error : Error…

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## [Finding the Jacobian of a 3D image transform](https://discourse.slicer.org/t/finding-the-jacobian-of-a-3d-image-transform/29018)

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**Author:** [@Akor](https://discourse.slicer.org/u/Akor)\
**Replies:** 3\
**Last updated:** [April 20, 2023, 4:41pm UTC](https://discourse.slicer.org/t/finding-the-jacobian-of-a-3d-image-transform/29018 "2023-04-20T16:41:36Z")

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Hi, so I have two 3D CT images that I’d like to register. The first being the fixed image and the second the moving image, using elastix in 3D slicer. Is there a way to have elastix output the Jacobian of the image trans…

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## [Are G and Y channels infered?](https://discourse.slicer.org/t/are-g-and-y-channels-infered/29027)

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**Author:** [@Ilias\_P](https://discourse.slicer.org/u/Ilias_P)\
**Replies:** 1\
**Last updated:** [April 20, 2023, 11:50am UTC](https://discourse.slicer.org/t/are-g-and-y-channels-infered/29027 "2023-04-20T11:50:58Z")

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I have some nii.gz files which, when I open using imajeJ , or any python library such as SimpleITK or Monai I get a stack of MRI images, as if taken from top to bottom. That being said, when I open the same file with sli…

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## [Extract pixel values from reformatted red slice](https://discourse.slicer.org/t/extract-pixel-values-from-reformatted-red-slice/29004)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 3\
**Last updated:** [April 20, 2023, 11:45am UTC](https://discourse.slicer.org/t/extract-pixel-values-from-reformatted-red-slice/29004 "2023-04-20T11:45:48Z")

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Hi, We want to extract pixel values from reformatted red slice to obtain a perpendicular view. To do that, we use endoscopy module in the following way: # Get curve info curveNode = slicer.util.getNode(curveNa…

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## [PET / SPECT Maximum Intensity Projection](https://discourse.slicer.org/t/pet-spect-maximum-intensity-projection/28143)

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**Author:** [@Jan\_Lennart](https://discourse.slicer.org/u/Jan_Lennart)\
**Replies:** 1\
**Last updated:** [April 20, 2023, 6:29am UTC](https://discourse.slicer.org/t/pet-spect-maximum-intensity-projection/28143 "2023-04-20T06:29:40Z")

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Hi Slicer Community, Can someone guide me to a tutorial or the appropriate manual on creating a 2d MIP of SPECT or PET scans? Thanks, Jan

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