# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=215

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

**Page:** 216

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## [Volume Rendering Problem](https://discourse.slicer.org/t/volume-rendering-problem/24110)

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**Author:** [@morganw3st](https://discourse.slicer.org/u/morganw3st)\
**Replies:** 4\
**Last updated:** [July 12, 2022, 12:01am UTC](https://discourse.slicer.org/t/volume-rendering-problem/24110 "2022-07-12T00:01:09Z")

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Hello, I have been having issues with Volume Rendering. When I render the scan, it looks fragmented and does not align with the other views. With that, the red, green, and yellow slices all look normal. I also only have …

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## [Use Julia with Slicer](https://discourse.slicer.org/t/use-julia-with-slicer/16765)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 7\
**Last updated:** [July 11, 2022, 8:45pm UTC](https://discourse.slicer.org/t/use-julia-with-slicer/16765 "2022-07-11T20:45:33Z")

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Hi, When building SlicerCAT I’m thinking about installing Julia (+miniconda) instead of Slicer’s Python while keeping Slicer+Python tight interaction. If someone has any thoughts please give an advice.

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## [How to solve the compilation problem of 3dslicer under the Linux system and arm64 architecture. Need help urgently!!!](https://discourse.slicer.org/t/how-to-solve-the-compilation-problem-of-3dslicer-under-the-linux-system-and-arm64-architecture-need-help-urgently/24251)

<div class="topic-metadata">

**Author:** [@wangyuyuyujun](https://discourse.slicer.org/u/wangyuyuyujun)\
**Replies:** 6\
**Last updated:** [July 11, 2022, 12:35pm UTC](https://discourse.slicer.org/t/how-to-solve-the-compilation-problem-of-3dslicer-under-the-linux-system-and-arm64-architecture-need-help-urgently/24251 "2022-07-11T12:35:10Z")

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I want to install 3dslicer-5.0.2. I have installed qt5-5.13.0 and other dependencies, so I began to build 3dslicer from the source code. But when I compiled, there was an error. I found that linux-amd64 was configured af…

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## [Slicer level tracing, itk::LevelTracingImageFilter](https://discourse.slicer.org/t/slicer-level-tracing-itk-leveltracingimagefilter/24269)

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**Author:** [@Eleonora\_Tiribilli](https://discourse.slicer.org/u/Eleonora_Tiribilli)\
**Replies:** 2\
**Last updated:** [July 11, 2022, 11:18am UTC](https://discourse.slicer.org/t/slicer-level-tracing-itk-leveltracingimagefilter/24269 "2022-07-11T11:18:01Z")

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Someone knows how the itk::LevelTracingImageFilter works? I found only the header file, with no explanation Slicer/itkLevelTracingImageFilter.h at main · Slicer/Slicer · GitHub

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## [Clear DICOM Images](https://discourse.slicer.org/t/clear-dicom-images/24268)

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**Author:** [@Tahara](https://discourse.slicer.org/u/Tahara)\
**Replies:** 0\
**Last updated:** [July 11, 2022, 10:28am UTC](https://discourse.slicer.org/t/clear-dicom-images/24268 "2022-07-11T10:28:27Z")

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Hello, Could anyone know about the voxel based cropping and how could I get clear images in case of NO voxel based cropping buttom? Thank you.

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## [segmentation of brain from CT ](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217)

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**Author:** [@iplneuro](https://discourse.slicer.org/u/iplneuro)\
**Replies:** 14\
**Last updated:** [July 9, 2022, 4:05pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217 "2022-07-09T16:05:37Z")

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Hi, I am just trying to segment brain from CT. Is there a way to segment brain from CT data or it is possible to segment brain from only MRI. Anyone can help me with this issue. Thanks in advance, Suba

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## [Fast Marching effect in 3D Slicer 5.0.1](https://discourse.slicer.org/t/fast-marching-effect-in-3d-slicer-5-0-1/24252)

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**Author:** [@Xray](https://discourse.slicer.org/u/Xray)\
**Replies:** 1\
**Last updated:** [July 9, 2022, 3:17pm UTC](https://discourse.slicer.org/t/fast-marching-effect-in-3d-slicer-5-0-1/24252 "2022-07-09T15:17:39Z")

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Hi, The attached picture is from 3D slicer version 4.9.0. It shows a fast marching effect. How to access that FAST MARCHING effect or Button in the 3D slicer version 5.0.1 or 5.0.2 ?

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## [Volumetric mesh from CT file?](https://discourse.slicer.org/t/volumetric-mesh-from-ct-file/21611)

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**Author:** [@Vasko](https://discourse.slicer.org/u/Vasko)\
**Replies:** 6\
**Last updated:** [July 8, 2022, 11:58pm UTC](https://discourse.slicer.org/t/volumetric-mesh-from-ct-file/21611 "2022-07-08T23:58:04Z")

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Hello, I’ve recently discovered the 3D Slicer and it’s possibilities. I’m beginning to work on project for analysis of occlusal stress distribution in cantilever dental bridges. Our starting point is CT file of the jaws…

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## [Renaming segments based on .txt file](https://discourse.slicer.org/t/renaming-segments-based-on-txt-file/24198)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 8\
**Last updated:** [July 8, 2022, 6:36pm UTC](https://discourse.slicer.org/t/renaming-segments-based-on-txt-file/24198 "2022-07-08T18:36:15Z")

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Dear all, I’m new to Slicer which I learning and finding fantastic, steep learning curve though. So I hope this is not too obvious but I have a lot of segments which are numbered and I would like to rename them based on…

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## [Feedback about TransformManager](https://discourse.slicer.org/t/feedback-about-transformmanager/24243)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 0\
**Last updated:** [July 8, 2022, 3:01pm UTC](https://discourse.slicer.org/t/feedback-about-transformmanager/24243 "2022-07-08T15:01:12Z")

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This is a module that let’s define a linear transformNode with: till n (currently 8) different relative rotations and a 3D translation axis of rotation, angle and pivot point Also allows to visualize the transform inf…

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## [Unable to create 3 model from MRI](https://discourse.slicer.org/t/unable-to-create-3-model-from-mri/24242)

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**Author:** [@bharath\_bhat](https://discourse.slicer.org/u/bharath_bhat)\
**Replies:** 0\
**Last updated:** [July 8, 2022, 2:56pm UTC](https://discourse.slicer.org/t/unable-to-create-3-model-from-mri/24242 "2022-07-08T14:56:29Z")

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I am ubale to create 3D models from MRI. The model does not get smoothed or wraped after drawing the body parts in each slice. KIndly help.

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## [How to change the  icon\[SlicerEditCut.png\]](https://discourse.slicer.org/t/how-to-change-the-icon-slicereditcut-png/24241)

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**Author:** [@csm1044690543](https://discourse.slicer.org/u/csm1044690543)\
**Replies:** 0\
**Last updated:** [July 8, 2022, 2:56pm UTC](https://discourse.slicer.org/t/how-to-change-the-icon-slicereditcut-png/24241 "2022-07-08T14:56:27Z")

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Which method can be modified， thanks Scissors icon or Scissors size

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## [Error message: \`vtkMRMLStorableNode::UpdateScene failed: Failed to read node\`](https://discourse.slicer.org/t/error-message-vtkmrmlstorablenode-updatescene-failed-failed-to-read-node/24225)

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**Author:** [@sandigeeup](https://discourse.slicer.org/u/sandigeeup)\
**Replies:** 3\
**Last updated:** [July 8, 2022, 9:21am UTC](https://discourse.slicer.org/t/error-message-vtkmrmlstorablenode-updatescene-failed-failed-to-read-node/24225 "2022-07-08T09:21:14Z")

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Error: Loading C:/Users/sandi/OneDrive/Desktop/Slicer - Canine Liver/Tumour cases/2022-07-06-Tumour case 1mrml.mrml - ERROR: In D:\\D\\S\\S-0\\Libs\\MRML\\Core\\vtkMRMLStorableNode.cxx, line 322 vtkMRMLScalarVolumeNode (000001…

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## [Difference between .py and .ipynb code execution](https://discourse.slicer.org/t/difference-between-py-and-ipynb-code-execution/24215)

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**Author:** [@rbaheti](https://discourse.slicer.org/u/rbaheti)\
**Replies:** 7\
**Last updated:** [July 8, 2022, 2:49am UTC](https://discourse.slicer.org/t/difference-between-py-and-ipynb-code-execution/24215 "2022-07-08T02:49:16Z")

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Hi, I’ve been executing sitk commands using Jupyter Notebook (.ipynb) and it’s been working perfectly. As a next step I’ve to execute the python code on Matlab using pyrunfile() command. This requires the code to have a…

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## [Problem importing JPEG series ](https://discourse.slicer.org/t/problem-importing-jpeg-series/24233)

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**Author:** [@marco1](https://discourse.slicer.org/u/marco1)\
**Replies:** 6\
**Last updated:** [July 7, 2022, 10:13pm UTC](https://discourse.slicer.org/t/problem-importing-jpeg-series/24233 "2022-07-07T22:13:13Z")

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Hi, I’m currently importing JPEG series of brain MRIs for a volumetric tumor analysis. I’m having no problems importing axial sequences, but importing sagittal or coronal sequences always ends up with the sequences in t…

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## [Saving a select view as a DICOM file](https://discourse.slicer.org/t/saving-a-select-view-as-a-dicom-file/24227)

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**Author:** [@beginl22](https://discourse.slicer.org/u/beginl22)\
**Replies:** 10\
**Last updated:** [July 7, 2022, 8:44pm UTC](https://discourse.slicer.org/t/saving-a-select-view-as-a-dicom-file/24227 "2022-07-07T20:44:04Z")

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I am working with CT scans of metatarsals and I am looking at the anterior to posterior configuration (cross section of diaphysis). But when I go to save the view as a DICOM, it just ends up saving a DICOM file of the in…

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## [Installing openslide-python](https://discourse.slicer.org/t/installing-openslide-python/24187)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 9\
**Last updated:** [July 7, 2022, 8:15pm UTC](https://discourse.slicer.org/t/installing-openslide-python/24187 "2022-07-07T20:15:51Z")

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I’m trying to install openslide-python via pip\_install to support reading NRRD files with @MONAI. I am getting the following error with Slicer 5.0.2 on Linux: \>\>\> pip\_install('openslide-python') Collecting openslide-pyt…

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## [Import file dicom in Python Pyradiomics](https://discourse.slicer.org/t/import-file-dicom-in-python-pyradiomics/24197)

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**Author:** [@Van\_Tran\_Sang\_Huynh](https://discourse.slicer.org/u/Van_Tran_Sang_Huynh)\
**Replies:** 3\
**Last updated:** [July 7, 2022, 7:45pm UTC](https://discourse.slicer.org/t/import-file-dicom-in-python-pyradiomics/24197 "2022-07-07T19:45:02Z")

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Hello, I want to import 1 patient CT dicom image file (about 100+ images) into python pyrradiomics for feature extraction. How can I use the code? hope the helping. Thank. Sang

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## [Toggle fiducial marker at move slices](https://discourse.slicer.org/t/toggle-fiducial-marker-at-move-slices/24222)

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**Author:** [@hmaguilera](https://discourse.slicer.org/u/hmaguilera)\
**Replies:** 0\
**Last updated:** [July 7, 2022, 2:36pm UTC](https://discourse.slicer.org/t/toggle-fiducial-marker-at-move-slices/24222 "2022-07-07T14:36:53Z")

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Hi, I was helping a collegue with 3D slicer today, where we were using a 3D echocardiographic volume and fiducial markers. He installed it today, and was not able to toggle a fiducial marker and then let all slices mer…

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## [QT designer python code generation, and nodule auto-naming](https://discourse.slicer.org/t/qt-designer-python-code-generation-and-nodule-auto-naming/24186)

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**Author:** [@Kevin.Kn](https://discourse.slicer.org/u/Kevin.Kn)\
**Replies:** 7\
**Last updated:** [July 7, 2022, 3:02am UTC](https://discourse.slicer.org/t/qt-designer-python-code-generation-and-nodule-auto-naming/24186 "2022-07-07T03:02:00Z")

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I have been messing around with creating my own extensions, and was wondering if it was possible at all for code to be generated from the Qt Designer in a python environment. I see this previous post and that the design…

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## [Save transformed data](https://discourse.slicer.org/t/save-transformed-data/2151)

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**Author:** [@Nathan](https://discourse.slicer.org/u/Nathan)\
**Replies:** 24\
**Last updated:** [July 7, 2022, 12:41am UTC](https://discourse.slicer.org/t/save-transformed-data/2151 "2022-07-07T00:41:17Z")

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Operating system: windows Slicer version: 4.8.1 Hello, I have ~50 sets of images that I have registered to a brain template. Would it be possible to save them after regridding to a common matrix? I would like to open …

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## [Converting .nrrd file to .stl (using python)](https://discourse.slicer.org/t/converting-nrrd-file-to-stl-using-python/24166)

<div class="topic-metadata">

**Author:** [@rbaheti](https://discourse.slicer.org/u/rbaheti)\
**Replies:** 9\
**Last updated:** [July 6, 2022, 1:05am UTC](https://discourse.slicer.org/t/converting-nrrd-file-to-stl-using-python/24166 "2022-07-06T01:05:06Z")

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Is there a way to convert .nrrd file to a .stl file on python? The nrrd file is binary (every voxel has a value of either 0 or 255).

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## [A problem of showing up the segmentation when loading](https://discourse.slicer.org/t/a-problem-of-showing-up-the-segmentation-when-loading/24183)

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**Author:** [@zkzk96871](https://discourse.slicer.org/u/zkzk96871)\
**Replies:** 4\
**Last updated:** [July 6, 2022, 1:19pm UTC](https://discourse.slicer.org/t/a-problem-of-showing-up-the-segmentation-when-loading/24183 "2022-07-06T13:19:59Z")

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I loaded a nii label file segemented by others and i met a problem. As the image shows, teeth are segmented well in the 3D view, but in the three views the segmentations are gone. And I don’t know how to make it show …

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## [Can not select input volume of MR scan](https://discourse.slicer.org/t/can-not-select-input-volume-of-mr-scan/24181)

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**Author:** [@francesca\_flore](https://discourse.slicer.org/u/francesca_flore)\
**Replies:** 6\
**Last updated:** [July 6, 2022, 6:51am UTC](https://discourse.slicer.org/t/can-not-select-input-volume-of-mr-scan/24181 "2022-07-06T06:51:19Z")

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I can not select input volume of MR scan in all the modules. Only CT scans and not MR scans are displayed in the drop-down menu to select a volume.

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## [Creating Samsung DICOM Volume Render](https://discourse.slicer.org/t/creating-samsung-dicom-volume-render/24195)

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**Author:** [@FlowDynamic](https://discourse.slicer.org/u/FlowDynamic)\
**Replies:** 1\
**Last updated:** [July 6, 2022, 4:05am UTC](https://discourse.slicer.org/t/creating-samsung-dicom-volume-render/24195 "2022-07-06T04:05:15Z")

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Hi everyone. I used to use 3D Slicer for Voluson GE Volume files, and now I work with two devices: Samsung HS40 and HS60. When I drag and drop any file into 3D Slicer, the software joins everything into axial axis; sag…

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## [Segment smooting performance issue using a M1 Apple Silicon Mac](https://discourse.slicer.org/t/segment-smooting-performance-issue-using-a-m1-apple-silicon-mac/24175)

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**Author:** [@lodumont](https://discourse.slicer.org/u/lodumont)\
**Replies:** 1\
**Last updated:** [July 5, 2022, 9:50pm UTC](https://discourse.slicer.org/t/segment-smooting-performance-issue-using-a-m1-apple-silicon-mac/24175 "2022-07-05T21:50:50Z")

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I am using Slicer 5.0.2 on a Mac Studio with a M1 Max chip (10 cores, 64 GB memory) in order to segment the volumes of archaeological finds (in that case a Bronze Age sword hilt). I am working with a 5.84 GB nrrd file wi…

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## [How to import the corresponding NII label after importing NII data](https://discourse.slicer.org/t/how-to-import-the-corresponding-nii-label-after-importing-nii-data/24149)

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**Author:** [@zkzk96871](https://discourse.slicer.org/u/zkzk96871)\
**Replies:** 2\
**Last updated:** [July 5, 2022, 12:14pm UTC](https://discourse.slicer.org/t/how-to-import-the-corresponding-nii-label-after-importing-nii-data/24149 "2022-07-05T12:14:42Z")

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How to import the corresponding NII label(multiple labels) after importing NII data, so that they overlap with each other (consistent with the function segment edit)? Please help me! thx

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## [Vesselness with no contrast](https://discourse.slicer.org/t/vesselness-with-no-contrast/24179)

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**Author:** [@KateDelb](https://discourse.slicer.org/u/KateDelb)\
**Replies:** 1\
**Last updated:** [July 5, 2022, 12:02pm UTC](https://discourse.slicer.org/t/vesselness-with-no-contrast/24179 "2022-07-05T12:02:23Z")

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Dear, I am currently using the vesselness filter to extract vessels from MRI images. However, this filter automatically assumes that the vessels are highlighted compared to the background, however my vessels are darker …

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## [how to smooth a model in order to meshing](https://discourse.slicer.org/t/how-to-smooth-a-model-in-order-to-meshing/24009)

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**Author:** [@1191620](https://discourse.slicer.org/u/1191620)\
**Replies:** 3\
**Last updated:** [July 5, 2022, 11:35am UTC](https://discourse.slicer.org/t/how-to-smooth-a-model-in-order-to-meshing/24009 "2022-07-05T11:35:45Z")

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Hello i have segmented a brain model in to gray matter , white matter and CSF and now I want to export it as a stl file to IA\_FEmesh in order to meshing, but my model need to smooth as much as possible. Unfortunately th…

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## [My clipping plane moves when shift is pressed](https://discourse.slicer.org/t/my-clipping-plane-moves-when-shift-is-pressed/24173)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 1\
**Last updated:** [July 4, 2022, 10:34pm UTC](https://discourse.slicer.org/t/my-clipping-plane-moves-when-shift-is-pressed/24173 "2022-07-04T22:34:34Z")

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For my module i am moving my mouse on the surface of a 3D model while holding shift (to get the surface coordinates) But when I define a clipping plane on my model the clipping plane is moved/updated then doing this. I…

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