# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=157

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

**Page:** 158

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## [Slicer Linux X Windows remote display problem with Anaconda .bashrc setup](https://discourse.slicer.org/t/slicer-linux-x-windows-remote-display-problem-with-anaconda-bashrc-setup/30043)

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**Author:** [@NormandRobert](https://discourse.slicer.org/u/NormandRobert)\
**Replies:** 1\
**Last updated:** [June 16, 2023, 2:24pm UTC](https://discourse.slicer.org/t/slicer-linux-x-windows-remote-display-problem-with-anaconda-bashrc-setup/30043 "2023-06-16T14:24:28Z")

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Operating system: Ubuntu 22.04 remote and local Slicer version: 5.2.2 Expected behavior: Start Actual behavior: Window paint does not complete I have discovered that if the remote shell running Slicer has the anacon…

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## [Ascension 3DG connection issue](https://discourse.slicer.org/t/ascension-3dg-connection-issue/30051)

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**Author:** [@saeedeh\_lavasany](https://discourse.slicer.org/u/saeedeh_lavasany)\
**Replies:** 1\
**Last updated:** [June 16, 2023, 2:10pm UTC](https://discourse.slicer.org/t/ascension-3dg-connection-issue/30051 "2023-06-16T14:10:29Z")

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Hello . I’m doing pivot calibration, but at the first stage, I’m getting an unknown device type error while attaching the Ascension 3DG. The configuration is shown below. Is there anything more I should look into?

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## [Adjusting Opacity of Volume Rendering to Visualize Segmented Lesions](https://discourse.slicer.org/t/adjusting-opacity-of-volume-rendering-to-visualize-segmented-lesions/30056)

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**Author:** [@yanpfei](https://discourse.slicer.org/u/yanpfei)\
**Replies:** 2\
**Last updated:** [June 16, 2023, 1:55pm UTC](https://discourse.slicer.org/t/adjusting-opacity-of-volume-rendering-to-visualize-segmented-lesions/30056 "2023-06-16T13:55:27Z")

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I performed volume rendering on a volume from a CT scan. I segmented the lesions within the said volume. Now, I have displayed both parts of the content in a 3D window. However, the content of the volume rendering over…

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## [Segment cine MRI images](https://discourse.slicer.org/t/segment-cine-mri-images/30060)

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**Author:** [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Replies:** 1\
**Last updated:** [June 16, 2023, 1:37pm UTC](https://discourse.slicer.org/t/segment-cine-mri-images/30060 "2023-06-16T13:37:53Z")

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Hello, Currently, I have 25 cine MRI images (25 phases within a cardiac cycle). I want to load them to the 3D Slicer as independent pictures and draw contours on them to extract radiomics features and generate report fo…

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## [Creating Holes Based on Cordinates](https://discourse.slicer.org/t/creating-holes-based-on-cordinates/30070)

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**Author:** [@cnosyt](https://discourse.slicer.org/u/cnosyt)\
**Replies:** 0\
**Last updated:** [June 16, 2023, 1:02pm UTC](https://discourse.slicer.org/t/creating-holes-based-on-cordinates/30070 "2023-06-16T13:02:41Z")

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I am utilizing 3D slicer to eventually 3D print an abdominal wall based on a CT scan. I have a set of coordinates that indicate blood vessels which supply the underlying tissue at various locations. How does one create h…

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## [How to export a transformed CT scan and RT structure into DICOM format](https://discourse.slicer.org/t/how-to-export-a-transformed-ct-scan-and-rt-structure-into-dicom-format/29998)

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**Author:** [@Tiberiu](https://discourse.slicer.org/u/Tiberiu)\
**Replies:** 2\
**Last updated:** [June 16, 2023, 10:43am UTC](https://discourse.slicer.org/t/how-to-export-a-transformed-ct-scan-and-rt-structure-into-dicom-format/29998 "2023-06-16T10:43:36Z")

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Version: 5.2.2 OS : MacOS I read a scan and RT structures in dicom format in Slicer and successfully applied a rotation. I would like to export this into a new scan and structures in dicom format. Is that possible…

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## [Combining 3 ScalarVolume/DICOM Files into One?](https://discourse.slicer.org/t/combining-3-scalarvolume-dicom-files-into-one/29702)

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**Author:** [@ImotVoksim](https://discourse.slicer.org/u/ImotVoksim)\
**Replies:** 4\
**Last updated:** [June 16, 2023, 8:23am UTC](https://discourse.slicer.org/t/combining-3-scalarvolume-dicom-files-into-one/29702 "2023-06-16T08:23:00Z")

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Hello, I have an MRI scan whose sagittal, coronal, and transverse DICOM files are separated into 3 files. Or rather, each one of the files is high-dimensional only in one direction, and the other two directions are super…

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## [Where to find meniscus dicoms/nrrd](https://discourse.slicer.org/t/where-to-find-meniscus-dicoms-nrrd/30057)

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**Author:** [@Jacinta\_Ricardo](https://discourse.slicer.org/u/Jacinta_Ricardo)\
**Replies:** 0\
**Last updated:** [June 15, 2023, 6:27pm UTC](https://discourse.slicer.org/t/where-to-find-meniscus-dicoms-nrrd/30057 "2023-06-15T18:27:43Z")

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Hello, does anyone know where I can get DICOM/nrrd with CAT or MRI of the meniscus?

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## [Curvature of the model](https://discourse.slicer.org/t/curvature-of-the-model/30028)

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**Author:** [@Muhammed\_Fatih\_Talu](https://discourse.slicer.org/u/Muhammed_Fatih_Talu)\
**Replies:** 2\
**Last updated:** [June 15, 2023, 7:21am UTC](https://discourse.slicer.org/t/curvature-of-the-model/30028 "2023-06-15T07:21:18Z")

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How can I generate Gauss and Mean Curvatures of the model? Is there any extention in Slicer which I can do this?

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## [Is DICOM to NIFTI a fully anonymised file in Slicer?](https://discourse.slicer.org/t/is-dicom-to-nifti-a-fully-anonymised-file-in-slicer/13347)

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**Author:** [@kt297](https://discourse.slicer.org/u/kt297)\
**Replies:** 5\
**Last updated:** [June 15, 2023, 4:52am UTC](https://discourse.slicer.org/t/is-dicom-to-nifti-a-fully-anonymised-file-in-slicer/13347 "2023-06-15T04:52:58Z")

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When saving a DICOM into NIFTI in slicer does the resultant NIFTI file fully anonymised to patient personal data?

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## [Looking for medialskeleton's instructions for use](https://discourse.slicer.org/t/looking-for-medialskeletons-instructions-for-use/30031)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 0\
**Last updated:** [June 14, 2023, 8:42am UTC](https://discourse.slicer.org/t/looking-for-medialskeletons-instructions-for-use/30031 "2023-06-14T08:42:41Z")

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Hi, I am looking for help with the medialskeletal extension. Is there a place where I could find some directions for use? Thanks for any cue.

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## [Philips4DUSDicomPatcher](https://discourse.slicer.org/t/philips4dusdicompatcher/30016)

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**Author:** [@Doaa\_Mahgoub](https://discourse.slicer.org/u/Doaa_Mahgoub)\
**Replies:** 4\
**Last updated:** [June 14, 2023, 3:53am UTC](https://discourse.slicer.org/t/philips4dusdicompatcher/30016 "2023-06-14T03:53:29Z")

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I can not find this module in the 3D slicer heart 5.2 version. I used to have it in the 4.11 version. Is there any way I can still use it on the 5.2? Otherwise, how can I download the 4.11 version?

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## [Saving as a single NRRD File](https://discourse.slicer.org/t/saving-as-a-single-nrrd-file/30017)

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**Author:** [@SuperArmySoldiers](https://discourse.slicer.org/u/SuperArmySoldiers)\
**Replies:** 1\
**Last updated:** [June 13, 2023, 5:22pm UTC](https://discourse.slicer.org/t/saving-as-a-single-nrrd-file/30017 "2023-06-13T17:22:45Z")

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Hey, I am new medical files etc. I am trying to convert my CT scan into an nrrd file to eventually 3D print. In the Slicer I am struggling to save the DICOM data to a single nrrd file. You can see on the attached imag…

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## [MRI intensity normalization](https://discourse.slicer.org/t/mri-intensity-normalization/4830)

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**Author:** [@TingtingYu](https://discourse.slicer.org/u/TingtingYu)\
**Replies:** 4\
**Last updated:** [June 13, 2023, 6:13am UTC](https://discourse.slicer.org/t/mri-intensity-normalization/4830 "2023-06-13T06:13:28Z")

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Hi, I am wondering how to apply “μ±3σ” normalization method in 3D slicer. I found a filter named “NormalizeImageFilter” which normalize an image by setting its mean to zero and variance to one. Can I modify this “Normal…

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## [Growing Region Segmentations](https://discourse.slicer.org/t/growing-region-segmentations/28605)

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**Author:** [@nysfour](https://discourse.slicer.org/u/nysfour)\
**Replies:** 17\
**Last updated:** [June 13, 2023, 5:13am UTC](https://discourse.slicer.org/t/growing-region-segmentations/28605 "2023-06-13T05:13:55Z")

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Is there a method for essentially ‘corralling’ a growing region segmentation? For example, if I want a dropped seed to expand throughout an anatomical region but I want to add a border so that the seed will not grow into…

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## [Segment comparison - DICE coefficient is wrong!](https://discourse.slicer.org/t/segment-comparison-dice-coefficient-is-wrong/30000)

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**Author:** [@Teddy](https://discourse.slicer.org/u/Teddy)\
**Replies:** 2\
**Last updated:** [June 13, 2023, 4:14am UTC](https://discourse.slicer.org/t/segment-comparison-dice-coefficient-is-wrong/30000 "2023-06-13T04:14:40Z")

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I used two same segments for comparison and calculate DICE using RTslicer module, but get the wrong result.

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## [How to save .seg.nrrd with script?](https://discourse.slicer.org/t/how-to-save-seg-nrrd-with-script/4614)

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**Author:** [@kayarre](https://discourse.slicer.org/u/kayarre)\
**Replies:** 4\
**Last updated:** [June 13, 2023, 3:19am UTC](https://discourse.slicer.org/t/how-to-save-seg-nrrd-with-script/4614 "2023-06-13T03:19:42Z")

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Hi, I am trying to save a segmentation node using the slicer.util.SaveNode where the node is a vtkMRMLSegmentationNode but I get this weird error even though it appears to save the segmentation. it might be a bug somewh…

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## [Linear measurement](https://discourse.slicer.org/t/linear-measurement/29981)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 5\
**Last updated:** [June 12, 2023, 7:51pm UTC](https://discourse.slicer.org/t/linear-measurement/29981 "2023-06-12T19:51:30Z")

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is there a way to measure without placing a line in markup ? if not available I guess it would be a good idea to be able to measure without it thanks

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## [Loosing 4th dimension after segmentation ](https://discourse.slicer.org/t/loosing-4th-dimension-after-segmentation/29881)

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**Author:** [@chopraamhk](https://discourse.slicer.org/u/chopraamhk)\
**Replies:** 4\
**Last updated:** [June 12, 2023, 2:13pm UTC](https://discourse.slicer.org/t/loosing-4th-dimension-after-segmentation/29881 "2023-06-12T14:13:58Z")

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Hi, My original nifti file is having 4dimensions , i.e., ( 196, 240, 100, 1). I have done segmentation in 3d slicer using 2 labels, and after saving the segmented file, it is giving me output as 3d. My new dimensions ar…

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## [How to fix the y-axis of a plot module chart?](https://discourse.slicer.org/t/how-to-fix-the-y-axis-of-a-plot-module-chart/29958)

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**Author:** [@David.Xu](https://discourse.slicer.org/u/David.Xu)\
**Replies:** 3\
**Last updated:** [June 11, 2023, 1:56pm UTC](https://discourse.slicer.org/t/how-to-fix-the-y-axis-of-a-plot-module-chart/29958 "2023-06-11T13:56:54Z")

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How can I fix the y-axis coordinates from 0 to 2?

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## [How to open .mat file in 3D Slicer](https://discourse.slicer.org/t/how-to-open-mat-file-in-3d-slicer/29960)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 1\
**Last updated:** [June 10, 2023, 8:31pm UTC](https://discourse.slicer.org/t/how-to-open-mat-file-in-3d-slicer/29960 "2023-06-10T20:31:45Z")

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Dear All, I have the file attached (you can download it thru the link). the unit in every voxel is supposed Gray (Gy). Anyone can help me how to open it in 3D Slicer so that when I put the cursor on my image’s voxel, t…

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## [Align multiple DICOM images](https://discourse.slicer.org/t/align-multiple-dicom-images/29964)

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**Author:** [@kristinbindas](https://discourse.slicer.org/u/kristinbindas)\
**Replies:** 0\
**Last updated:** [June 10, 2023, 4:21pm UTC](https://discourse.slicer.org/t/align-multiple-dicom-images/29964 "2023-06-10T16:21:10Z")

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Hi there! I have been using slicer to import multiple DICOM files to compare the shapes of bones across multiple patients. I have been trying to see if Slicer aligns all DICOM images so that they are all in the same dire…

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## [Removing "Closed Surface" from seg.nrrd image header Line: Segmentation\_ContainedRepresentationNames](https://discourse.slicer.org/t/removing-closed-surface-from-seg-nrrd-image-header-line-segmentation-containedrepresentationnames/28987)

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**Author:** [@Joshua\_Binswanger](https://discourse.slicer.org/u/Joshua_Binswanger)\
**Replies:** 1\
**Last updated:** [June 9, 2023, 10:51pm UTC](https://discourse.slicer.org/t/removing-closed-surface-from-seg-nrrd-image-header-line-segmentation-containedrepresentationnames/28987 "2023-06-09T22:51:13Z")

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Removing or giving the option to bypass “Closed Surface” Representation of Segmentations in the image header of seg.nrrd files on the line “Segmentation\_ContainedRepresentationNames” The Corresponding Line in the Header…

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## [Model Maker module not producing a model](https://discourse.slicer.org/t/model-maker-module-not-producing-a-model/29946)

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**Author:** [@devjklein](https://discourse.slicer.org/u/devjklein)\
**Replies:** 1\
**Last updated:** [June 9, 2023, 9:11pm UTC](https://discourse.slicer.org/t/model-maker-module-not-producing-a-model/29946 "2023-06-09T21:11:45Z")

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Hi all, I am on version 5.2.2 on Windows 11 and trying to run Model Maker on a dataset that I segmented. In IO I pick my segmentation, I created a new ModelHierachy, and I click apply. The module runs, but no 3D surface …

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## [Create histogram widget in the GUI](https://discourse.slicer.org/t/create-histogram-widget-in-the-gui/29919)

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**Author:** [@tux](https://discourse.slicer.org/u/tux)\
**Replies:** 4\
**Last updated:** [June 9, 2023, 2:21pm UTC](https://discourse.slicer.org/t/create-histogram-widget-in-the-gui/29919 "2023-06-09T14:21:22Z")

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Os : Ubuntu 20.04.6 Slicer version : 5.2.2 Hello ! I am currently searching how to create an histogram but as a widget inside my module GUI like the one in the volume module : I already have one in the “visualisat…

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## [Repost in support (sorry) python function vs main / crash in function but not in main](https://discourse.slicer.org/t/repost-in-support-sorry-python-function-vs-main-crash-in-function-but-not-in-main/29915)

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**Author:** [@Nicolas\_Tempier](https://discourse.slicer.org/u/Nicolas_Tempier)\
**Replies:** 3\
**Last updated:** [June 9, 2023, 1:43pm UTC](https://discourse.slicer.org/t/repost-in-support-sorry-python-function-vs-main-crash-in-function-but-not-in-main/29915 "2023-06-09T13:43:12Z")

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Hello everyone, first of all, sorry for the repost, i posted this issue in development section instead of support … i have a little problem understanding why my code crashes when i use it as a function. i want to disp…

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## [Grow from seeds stopped working.....](https://discourse.slicer.org/t/grow-from-seeds-stopped-working/29922)

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**Author:** [@ahmsam](https://discourse.slicer.org/u/ahmsam)\
**Replies:** 3\
**Last updated:** [June 9, 2023, 11:24am UTC](https://discourse.slicer.org/t/grow-from-seeds-stopped-working/29922 "2023-06-09T11:24:00Z")

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Operating system: windows Slicer version:5.2.2 Expected behavior:3D area Actual behavior: only selected areas appears after initialization. Hello every one, I did grow from seeds many times successfully, however, som…

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## [Slicer Heart - annulus angles in valve quantification](https://discourse.slicer.org/t/slicer-heart-annulus-angles-in-valve-quantification/29940)

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**Author:** [@RGhosh](https://discourse.slicer.org/u/RGhosh)\
**Replies:** 1\
**Last updated:** [June 9, 2023, 11:18am UTC](https://discourse.slicer.org/t/slicer-heart-annulus-angles-in-valve-quantification/29940 "2023-06-09T11:18:26Z")

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Operating system: Windows 10 Slicer version: 5.2.1 In the SlicerHeart Valve Quantification module - there are several measurements made regarding annulus angles (bending angle, etc). How do we find out how these angles…

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## [Exist a plug-in for orthognathic surgery?](https://discourse.slicer.org/t/exist-a-plug-in-for-orthognathic-surgery/29938)

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**Author:** [@francesca\_flore](https://discourse.slicer.org/u/francesca_flore)\
**Replies:** 0\
**Last updated:** [June 9, 2023, 10:24am UTC](https://discourse.slicer.org/t/exist-a-plug-in-for-orthognathic-surgery/29938 "2023-06-09T10:24:17Z")

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Hi all! Is there a plug-in for orthognathic surgical planning? With the reference standards of the skull. Thanks!

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## [Create 1 volume from 3 volumes](https://discourse.slicer.org/t/create-1-volume-from-3-volumes/29869)

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**Author:** [@KarelPenicka](https://discourse.slicer.org/u/KarelPenicka)\
**Replies:** 2\
**Last updated:** [June 8, 2023, 7:28pm UTC](https://discourse.slicer.org/t/create-1-volume-from-3-volumes/29869 "2023-06-08T19:28:57Z")

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Hi guys. I got from hospital Axial, Koronal and Sagital Series.Each of these series have resolution 0,15 x 0,1 5x 2 mm. I want to take from eaxh series only one view (one with higher resolution ) and create new serie. I…

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