# \#visualization

**URL:** https://discourse.slicer.org/tag/visualization/56.md

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

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## [Image corruption when loading single DICOM CT slice as Scalar Volume](https://discourse.slicer.org/t/image-corruption-when-loading-single-dicom-ct-slice-as-scalar-volume/47388)

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**Author:** [@Martina\_Caro95](https://discourse.slicer.org/u/Martina_Caro95)\
**Replies:** 1\
**Last updated:** [June 20, 2026, 8:01pm UTC](https://discourse.slicer.org/t/image-corruption-when-loading-single-dicom-ct-slice-as-scalar-volume/47388 "2026-06-20T20:01:17Z")

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Hi everyone, I am currently working on building a retrospective clinical database, extracting body composition and radiomic data from thoracic CT scans specifically at the T4 level. Our historical workflow involved expo…

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## [Visualization of continuous uncertainty maps in 3D Slicer (volume appears uniform color)](https://discourse.slicer.org/t/visualization-of-continuous-uncertainty-maps-in-3d-slicer-volume-appears-uniform-color/46892)

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**Author:** [@Alexia\_Canosa\_Rojo](https://discourse.slicer.org/u/Alexia_Canosa_Rojo)\
**Replies:** 4\
**Last updated:** [May 2, 2026, 3:21pm UTC](https://discourse.slicer.org/t/visualization-of-continuous-uncertainty-maps-in-3d-slicer-volume-appears-uniform-color/46892 "2026-05-02T15:21:55Z")

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Hi, I am trying to visualize a continuous uncertainty map (entropy-based) generated from a deep learning segmentation model in 3D Slicer. The NIfTI file contains floating-point values (not binary), with a range approxi…

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## [Removal of Lightbox Mode](https://discourse.slicer.org/t/removal-of-lightbox-mode/45227)

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**Author:** [@dokay1](https://discourse.slicer.org/u/dokay1)\
**Replies:** 3\
**Last updated:** [December 21, 2025, 8:20pm UTC](https://discourse.slicer.org/t/removal-of-lightbox-mode/45227 "2025-12-21T20:20:00Z")

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I’ve just installed Version 5.10.0 to realize that Lightbox view was removed. While I understand that many don’t use it, it was the single most helpful image review setting. It allows one to review and compare thick sli…

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## [Issues visualizing results in DentalModelSeg (Slicer 5.8) – segmentation runs but no output appears](https://discourse.slicer.org/t/issues-visualizing-results-in-dentalmodelseg-slicer-5-8-segmentation-runs-but-no-output-appears/45405)

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**Author:** [@Brendy\_Villanueva](https://discourse.slicer.org/u/Brendy_Villanueva)\
**Replies:** 1\
**Last updated:** [December 11, 2025, 8:38pm UTC](https://discourse.slicer.org/t/issues-visualizing-results-in-dentalmodelseg-slicer-5-8-segmentation-runs-but-no-output-appears/45405 "2025-12-11T20:38:13Z")

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Hello everyone, I am trying to segment teeth from STL dental models using DentalModelSeg, but I am running into visualization issues, and I would really appreciate some guidance. I used: 3D Slicer version 5.8 Den…

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## [Only points showing in Mean Shape Visualization - Slicermorph](https://discourse.slicer.org/t/only-points-showing-in-mean-shape-visualization-slicermorph/45121)

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**Author:** [@emmm\_m](https://discourse.slicer.org/u/emmm_m)\
**Replies:** 8\
**Last updated:** [November 21, 2025, 3:26am UTC](https://discourse.slicer.org/t/only-points-showing-in-mean-shape-visualization-slicermorph/45121 "2025-11-21T03:26:33Z")

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I’m new to slicer so I apologize if this is a question driven by my ineptness. I am working on generating GPA/PCA visualizations, however when I try to generate a Mean shape visualization for the proximal and distal end …

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## [Image Orientation in SlicerIGTs Volume Reslice Driver](https://discourse.slicer.org/t/image-orientation-in-slicerigts-volume-reslice-driver/42526)

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**Author:** [@Khaleel\_Ur\_Rehman](https://discourse.slicer.org/u/Khaleel_Ur_Rehman)\
**Replies:** 1\
**Last updated:** [April 10, 2025, 6:23pm UTC](https://discourse.slicer.org/t/image-orientation-in-slicerigts-volume-reslice-driver/42526 "2025-04-10T18:23:29Z")

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Hi, @Sam\_Horvath, I am using volume reslice driver to visualize registration and tracking using an optical tracking system. The reslice driver is working good. As you might know that the driver has the generic Axial, Cor…

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## [Rotate Views Without Rotating Image](https://discourse.slicer.org/t/rotate-views-without-rotating-image/776)

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**Author:** [@\_jmichael](https://discourse.slicer.org/u/_jmichael)\
**Replies:** 6\
**Last updated:** [February 4, 2025, 11:03pm UTC](https://discourse.slicer.org/t/rotate-views-without-rotating-image/776 "2025-02-04T23:03:44Z")

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Hi all, I currently have a micro-CT of a phantom that, when loaded into Slicer, appears upside down (there are some file conversions going on before I get to Slicer, so this behaviour is probably correct from a software…

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## [How to implement CPR (curved planar reconstruction) from centerline?](https://discourse.slicer.org/t/how-to-implement-cpr-curved-planar-reconstruction-from-centerline/9456)

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**Author:** [@RayCui](https://discourse.slicer.org/u/RayCui)\
**Replies:** 22\
**Last updated:** [August 20, 2024, 10:09am UTC](https://discourse.slicer.org/t/how-to-implement-cpr-curved-planar-reconstruction-from-centerline/9456 "2024-08-20T10:09:53Z")

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I want to show the vessel in planar. Now I have a .csv file of centerline, that contains points of the veseel. How to reconstruction the vessel plannar from centerline file? How to import the csv file as a list of some…

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## [Lighting in 3D stereoscopic view](https://discourse.slicer.org/t/lighting-in-3d-stereoscopic-view/37769)

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**Author:** [@Laura\_A](https://discourse.slicer.org/u/Laura_A)\
**Replies:** 1\
**Last updated:** [August 8, 2024, 12:46pm UTC](https://discourse.slicer.org/t/lighting-in-3d-stereoscopic-view/37769 "2024-08-08T12:46:42Z")

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I am trying to apply the lighting of the 3D view a the left and right eye 3D stereoscopic views, but the lighting is only applied to the view in the 3D Slicer UI. Steps I follow: Load a model in 3D Slicer Create 3D st…

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## [Aspect ratio error when loading dicom](https://discourse.slicer.org/t/aspect-ratio-error-when-loading-dicom/35143)

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**Author:** [@juanslo](https://discourse.slicer.org/u/juanslo)\
**Replies:** 1\
**Last updated:** [March 27, 2024, 10:43pm UTC](https://discourse.slicer.org/t/aspect-ratio-error-when-loading-dicom/35143 "2024-03-27T22:43:10Z")

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I’ve recently had problems loading a .DCM file into 3D Slicer. The problem appears when viewing the file since two of the three planes appear outside their aspect ratio. These planes appear “clumped” or “crushed.” I have…

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## [3D Ultrasound Reconstruction with openIGTL (Verasonics & Polhemus)](https://discourse.slicer.org/t/3d-ultrasound-reconstruction-with-openigtl-verasonics-polhemus/32240)

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**Author:** [@ehdrmfdl3648](https://discourse.slicer.org/u/ehdrmfdl3648)\
**Replies:** 8\
**Last updated:** [February 22, 2024, 12:59am UTC](https://discourse.slicer.org/t/3d-ultrasound-reconstruction-with-openigtl-verasonics-polhemus/32240 "2024-02-22T00:59:34Z")

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US img: Verasonics 64 LE Position Sensor: Polhemus EMT Sensor Here’s what’s going on made Verasonics’ images available for import in Python. the values of the EMT sensor were imported into Python and a transform …

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## [WSL Slicer image overlay selector](https://discourse.slicer.org/t/wsl-slicer-image-overlay-selector/32132)

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**Author:** [@IVarha](https://discourse.slicer.org/u/IVarha)\
**Replies:** 5\
**Last updated:** [October 10, 2023, 10:54am UTC](https://discourse.slicer.org/t/wsl-slicer-image-overlay-selector/32132 "2023-10-10T10:54:06Z")

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I am trying to select overlay between images on WSL, hovewer the selector does not work for me Operating system: Windows / WSL Fedora /WSL ubuntu Slicer version: 5.4 Expected behavior: I am able to overlay two imag…

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## [Update 3D Visualization programmatically](https://discourse.slicer.org/t/update-3d-visualization-programmatically/30158)

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**Author:** [@marm](https://discourse.slicer.org/u/marm)\
**Replies:** 21\
**Last updated:** [September 1, 2023, 12:19pm UTC](https://discourse.slicer.org/t/update-3d-visualization-programmatically/30158 "2023-09-01T12:19:40Z")

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Hi, First of all, thank you for your effort in developing 3DSlicer as it is a great platform. I am developing a 3DSlicer module for surgical tool navigation. I want to update the 3D visualization of a model every time …

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## [Multiple tractography file selection for visualization and 2D vs 3D visualization toggles](https://discourse.slicer.org/t/multiple-tractography-file-selection-for-visualization-and-2d-vs-3d-visualization-toggles/30314)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 3\
**Last updated:** [June 30, 2023, 3:33pm UTC](https://discourse.slicer.org/t/multiple-tractography-file-selection-for-visualization-and-2d-vs-3d-visualization-toggles/30314 "2023-06-30T15:33:43Z")

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Hi, when having multiple bundle data loaded onto Slicer, is there a way to select multiple files at the same time and to change the visualization type (under Diffusion/Tractography/Tractography Display) to Tubes instead…

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## [How to visualize a 3D skeleton image](https://discourse.slicer.org/t/how-to-visualize-a-3d-skeleton-image/29155)

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**Author:** [@Peidi\_Xu](https://discourse.slicer.org/u/Peidi_Xu)\
**Replies:** 1\
**Last updated:** [April 26, 2023, 9:39pm UTC](https://discourse.slicer.org/t/how-to-visualize-a-3d-skeleton-image/29155 "2023-04-26T21:39:16Z")

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I have a simple 3D binary in .nii.gz form, where voxel value 1 means foreground and 0 means background. So it is a skeleton because every foreground voxel has a thickness of one, e.g., it is the output after running skim…

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## [Remove CT table from volume rendering](https://discourse.slicer.org/t/remove-ct-table-from-volume-rendering/28872)

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**Author:** [@Jonathan\_Millard](https://discourse.slicer.org/u/Jonathan_Millard)\
**Replies:** 13\
**Last updated:** [April 15, 2023, 4:16pm UTC](https://discourse.slicer.org/t/remove-ct-table-from-volume-rendering/28872 "2023-04-15T16:16:31Z")

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Hello all, I am attempting to visualize the skeletal elements of a CT scan (DICOM), along with taking screenshots suitable for publication. I am using the volume rendering module CT-AAA2 preset and it looks lovely; howe…

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## [Volume Reslice for Calibrated Ultrasound Images](https://discourse.slicer.org/t/volume-reslice-for-calibrated-ultrasound-images/11546)

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**Author:** [@Winona\_Richey](https://discourse.slicer.org/u/Winona_Richey)\
**Replies:** 4\
**Last updated:** [February 15, 2023, 4:19am UTC](https://discourse.slicer.org/t/volume-reslice-for-calibrated-ultrasound-images/11546 "2023-02-15T04:19:33Z")

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Operating system: Windows 7 and MacOS 10.14.6 Slicer version: 4.10.1 Expected behavior: 1. Set the incoming tracked image as the driver for the corresponding 2D viewer. 2. Find the appropriate mode from the Mode list …

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## [Special Issue of Frontiers in Virtual Reality journal - Medical Simulation and Visualization](https://discourse.slicer.org/t/special-issue-of-frontiers-in-virtual-reality-journal-medical-simulation-and-visualization/24966)

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**Author:** [@MichelODU](https://discourse.slicer.org/u/MichelODU)\
**Replies:** 0\
**Last updated:** [August 28, 2022, 9:19pm UTC](https://discourse.slicer.org/t/special-issue-of-frontiers-in-virtual-reality-journal-medical-simulation-and-visualization/24966 "2022-08-28T21:19:42Z")

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Dear members of the Slicer Community, this post is to announce a Special Issue of Frontiers in Virtual Reality journal - Medical Simulation and Visualization, which I believe could align with much of the work that build…

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## [Error to visualize polydata in slicer 4.10.2](https://discourse.slicer.org/t/error-to-visualize-polydata-in-slicer-4-10-2/23327)

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**Author:** [@hehongwei120](https://discourse.slicer.org/u/hehongwei120)\
**Replies:** 1\
**Last updated:** [May 8, 2022, 4:30am UTC](https://discourse.slicer.org/t/error-to-visualize-polydata-in-slicer-4-10-2/23327 "2022-05-08T04:30:04Z")

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Operating system: ubuntu 18.04 Slicer version: 4.10.2 Expected behavior: the same as slicer 4.13.0 or paraview Actual behavior: error visualize I use the same polydata.stl,but different visualize in slicer 4.10.…

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## [I want to achieve real-time positioning tracking and visualization of the scalpel, but I don't know how to track the position of the scalpel in real time and achieve visualization](https://discourse.slicer.org/t/i-want-to-achieve-real-time-positioning-tracking-and-visualization-of-the-scalpel-but-i-dont-know-how-to-track-the-position-of-the-scalpel-in-real-time-and-achieve-visualization/23132)

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**Author:** [@wanghao1](https://discourse.slicer.org/u/wanghao1)\
**Replies:** 2\
**Last updated:** [April 28, 2022, 2:44am UTC](https://discourse.slicer.org/t/i-want-to-achieve-real-time-positioning-tracking-and-visualization-of-the-scalpel-but-i-dont-know-how-to-track-the-position-of-the-scalpel-in-real-time-and-achieve-visualization/23132 "2022-04-28T02:44:54Z")

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I want to achieve real-time positioning tracking and visualization of the scalpel, but I don’t know how to track the position of the scalpel in real time and achieve visualization

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## [Model visualization](https://discourse.slicer.org/t/model-visualization/21469)

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**Author:** [@Luca](https://discourse.slicer.org/u/Luca)\
**Replies:** 1\
**Last updated:** [January 16, 2022, 9:28pm UTC](https://discourse.slicer.org/t/model-visualization/21469 "2022-01-16T21:28:59Z")

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Dear community, I imported a model by python scripting with the following lines: inputModel = slicer.util.loadModel(model\_path) inputModel.SetDisplayVisibility(1) inputModel.GetDisplayNode().SetOpacity(0.25) inputMo…

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## [Visualize the difference between two meshes](https://discourse.slicer.org/t/visualize-the-difference-between-two-meshes/20729)

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**Author:** [@suranga](https://discourse.slicer.org/u/suranga)\
**Replies:** 1\
**Last updated:** [November 23, 2021, 7:07am UTC](https://discourse.slicer.org/t/visualize-the-difference-between-two-meshes/20729 "2021-11-23T07:07:31Z")

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I have two volumetric liver meshes in .vtk format (i.e. ground-truth and predicted versions) and I want to plot the error i.e., for example, the difference between the ground-truth and the predicted liver meshes on the p…

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## [Exporting 2 volumes as a stack of image files (PNG).](https://discourse.slicer.org/t/exporting-2-volumes-as-a-stack-of-image-files-png/20187)

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**Author:** [@neuralnet](https://discourse.slicer.org/u/neuralnet)\
**Replies:** 2\
**Last updated:** [November 12, 2021, 10:25pm UTC](https://discourse.slicer.org/t/exporting-2-volumes-as-a-stack-of-image-files-png/20187 "2021-11-12T22:25:15Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: N/A Actual behavior: N/A Hi all, I am very new to slicer and to medical imaging in general, so I apologize if this question is very obvious. I …

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## [Grey Level Image looking Blue (or other color)](https://discourse.slicer.org/t/grey-level-image-looking-blue-or-other-color/18095)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 4\
**Last updated:** [June 15, 2021, 9:13pm UTC](https://discourse.slicer.org/t/grey-level-image-looking-blue-or-other-color/18095 "2021-06-15T21:13:09Z")

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Hey guys recurrently I get into this situation. I have a gray scale medical image, but when I load the image inside 3D slicer… the image appears BLUE! Take a look. It is like this: But appears like this: Could’n…

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## [How to render a volume by vector?](https://discourse.slicer.org/t/how-to-render-a-volume-by-vector/17526)

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**Author:** [@Raykie](https://discourse.slicer.org/u/Raykie)\
**Replies:** 6\
**Last updated:** [May 28, 2021, 8:33am UTC](https://discourse.slicer.org/t/how-to-render-a-volume-by-vector/17526 "2021-05-28T08:33:09Z")

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Generally, the volume rendering works based on the intensity of a voxel. What if I need to do it based on a vector (k1, k2)? Thanks!

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## [ALive research project](https://discourse.slicer.org/t/alive-research-project/12467)

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**Author:** [@RafaelPalomar](https://discourse.slicer.org/u/RafaelPalomar)\
**Replies:** 0\
**Last updated:** [July 9, 2020, 4:54pm UTC](https://discourse.slicer.org/t/alive-research-project/12467 "2020-07-09T16:54:49Z")

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ALive Project https://alive-research.no Dear Slicer community, I would like to call your attention to the ALive project that will start in Autumn 2020. In ALive, we are planning to research new methods for computati…

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## [Display different images and models in different views](https://discourse.slicer.org/t/display-different-images-and-models-in-different-views/11442)

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**Author:** [@kristjanq](https://discourse.slicer.org/u/kristjanq)\
**Replies:** 6\
**Last updated:** [May 7, 2020, 10:14pm UTC](https://discourse.slicer.org/t/display-different-images-and-models-in-different-views/11442 "2020-05-07T22:14:29Z")

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Dear Slicer community, I am trying to build a training phantom for Interventional Cardiologists making use of tracked Ultrasound using PlusToolkit from @lassoan et al, as part of my master thesis. To give a big picture:…

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## [Slicer in CentOS 7.6](https://discourse.slicer.org/t/slicer-in-centos-7-6/10025)

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**Author:** [@muntahi398](https://discourse.slicer.org/u/muntahi398)\
**Replies:** 3\
**Last updated:** [January 30, 2020, 3:31pm UTC](https://discourse.slicer.org/t/slicer-in-centos-7-6/10025 "2020-01-30T15:31:11Z")

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Operating system: CentOS 7.6 Slicer version: 4.11.0 Expected behavior: Actual behavior: Data is not shown Dear people, In a server computer running CentOS 7.6, I installed Slicer1.11.0 and downloaded sample model of…

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## [Show 2D slices based on needle tip location in Slicer 4](https://discourse.slicer.org/t/show-2d-slices-based-on-needle-tip-location-in-slicer-4/9836)

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**Author:** [@gjackson](https://discourse.slicer.org/u/gjackson)\
**Replies:** 9\
**Last updated:** [January 20, 2020, 12:45pm UTC](https://discourse.slicer.org/t/show-2d-slices-based-on-needle-tip-location-in-slicer-4/9836 "2020-01-20T12:45:05Z")

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Hi all, I’m using OpenIGTLinkIF to stream tracking data from an NDI Aurora tracking system into Slicer. (I work at NDI.) I’m tracking a needle, and in Slicer 3.x was able to have the relevant 2D slices show based on the…

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## [Get Mesh Cell and Modify](https://discourse.slicer.org/t/get-mesh-cell-and-modify/9459)

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**Author:** [@lausiv](https://discourse.slicer.org/u/lausiv)\
**Replies:** 9\
**Last updated:** [December 20, 2019, 8:39pm UTC](https://discourse.slicer.org/t/get-mesh-cell-and-modify/9459 "2019-12-20T20:39:36Z")

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for mesh cell 1 …, end of mesh \<== executing all of the mesh Get each mesh cell(below first picture) of all the mesh cells in the volume Modify each cell value(color) referral script code^^ modelNode = slicer…

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