# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=252

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

**Page:** 253

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## [Exporting Segmentations](https://discourse.slicer.org/t/exporting-segmentations/20469)

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**Author:** [@NaghmehAnsari](https://discourse.slicer.org/u/NaghmehAnsari)\
**Replies:** 1\
**Last updated:** [November 3, 2021, 4:26am UTC](https://discourse.slicer.org/t/exporting-segmentations/20469 "2021-11-03T04:26:53Z")

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Hello , I am trying to create a segment model consisting of a Ventricle and head model, two target points, and trajectories to targets and extract them into a merged file. I am receiving “the application has run out of…

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## [Segment Editor : Extra Effects — Fast Marching effect's URL dead](https://discourse.slicer.org/t/segment-editor-extra-effects-fast-marching-effects-url-dead/20446)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 4\
**Last updated:** [November 2, 2021, 9:54pm UTC](https://discourse.slicer.org/t/segment-editor-extra-effects-fast-marching-effects-url-dead/20446 "2021-11-02T21:54:01Z")

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The Fast Marching (extra) effect in the Segment Editor module has a link to http://www.spl.harvard.edu/publications/item/view/193 embedded as “The effect uses fast marching method”, but the link seems to be dead. Brow…

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## [Segment Editor : Extra Effects — Watershed effect should not recompute upon change of colour](https://discourse.slicer.org/t/segment-editor-extra-effects-watershed-effect-should-not-recompute-upon-change-of-colour/20447)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 3\
**Last updated:** [November 2, 2021, 8:26pm UTC](https://discourse.slicer.org/t/segment-editor-extra-effects-watershed-effect-should-not-recompute-upon-change-of-colour/20447 "2021-11-02T20:26:33Z")

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The Watershed (extra) effect in the Segment Editor module appeared to recompute upon a change of a segment’s colour (aka “color”), or possibly it was the segment’s Property type. This seemed to happen automatically when…

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## [Slicermarkupstomodel failing because of unauthenticated git protocol on port 9418 is no longer supported](https://discourse.slicer.org/t/slicermarkupstomodel-failing-because-of-unauthenticated-git-protocol-on-port-9418-is-no-longer-supported/20467)

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**Author:** [@Shazam\_L](https://discourse.slicer.org/u/Shazam_L)\
**Replies:** 2\
**Last updated:** [November 2, 2021, 8:02pm UTC](https://discourse.slicer.org/t/slicermarkupstomodel-failing-because-of-unauthenticated-git-protocol-on-port-9418-is-no-longer-supported/20467 "2021-11-02T20:02:51Z")

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Hello to whoever wants to help, I was building and got this error in the title. I was wondering how to solve this. Thanks, Shazam L

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## [Exporting planned trajectories from Slicer to Stealth System](https://discourse.slicer.org/t/exporting-planned-trajectories-from-slicer-to-stealth-system/20458)

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**Author:** [@punadkat13](https://discourse.slicer.org/u/punadkat13)\
**Replies:** 1\
**Last updated:** [November 2, 2021, 7:33pm UTC](https://discourse.slicer.org/t/exporting-planned-trajectories-from-slicer-to-stealth-system/20458 "2021-11-02T19:33:33Z")

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Hello Everyone, I was wondering if anyone has an already established workflow to importing planned trajectories on 3D slicer to the Stealth Navigation system. Once I have my trajectories set using Path explorer what’s t…

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## [Problem loading VolDICOM](https://discourse.slicer.org/t/problem-loading-voldicom/18640)

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**Author:** [@TKhienwad](https://discourse.slicer.org/u/TKhienwad)\
**Replies:** 14\
**Last updated:** [November 2, 2021, 2:04pm UTC](https://discourse.slicer.org/t/problem-loading-voldicom/18640 "2021-11-02T14:04:48Z")

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Hi all, I have a question regarding importing the VolDICOM format from echo images with 3D slicer. Does anyone know how to do that? Best,

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## [Multiple sessions of Slicer are launched in a loop](https://discourse.slicer.org/t/multiple-sessions-of-slicer-are-launched-in-a-loop/20454)

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**Author:** [@lb123](https://discourse.slicer.org/u/lb123)\
**Replies:** 1\
**Last updated:** [November 2, 2021, 12:39pm UTC](https://discourse.slicer.org/t/multiple-sessions-of-slicer-are-launched-in-a-loop/20454 "2021-11-02T12:39:08Z")

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Hi, I built Slicer 4.13.0 in Ubuntu 20.04.3 LTS. It worked properly and I was able to use Slicer. Then I built SlicerIGT following these steps: $ git clone https://github.com/SlicerIGT/SlicerIGT.git $ mkdir SlicerIGT-…

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## [Dicom segmentation object Q/R](https://discourse.slicer.org/t/dicom-segmentation-object-q-r/12762)

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**Author:** [@Krishna\_Nanda](https://discourse.slicer.org/u/Krishna_Nanda)\
**Replies:** 2\
**Last updated:** [November 2, 2021, 12:22pm UTC](https://discourse.slicer.org/t/dicom-segmentation-object-q-r/12762 "2021-11-02T12:22:52Z")

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Hello, We have setup the 3D Slicer dicom browser to be able to Q/R into a vendor software. The query shows all the series, including a dicom segmentation object (modality SEG). The retrieve is successful in pulling all …

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## [Segment statistics for each slice of segmented volume](https://discourse.slicer.org/t/segment-statistics-for-each-slice-of-segmented-volume/20421)

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**Author:** [@Michel\_Atieh](https://discourse.slicer.org/u/Michel_Atieh)\
**Replies:** 9\
**Last updated:** [November 1, 2021, 9:07pm UTC](https://discourse.slicer.org/t/segment-statistics-for-each-slice-of-segmented-volume/20421 "2021-11-01T21:07:05Z")

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Hello, to calculate the radiation dose received by the fetus during a CT exam, I need to know the mean Hounsfield Unit for each slice of my segmented volume (the uterus). However, I am only able to obtain statistics for…

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## [veterinary dog bone model](https://discourse.slicer.org/t/veterinary-dog-bone-model/20432)

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**Author:** [@rameshvet2000](https://discourse.slicer.org/u/rameshvet2000)\
**Replies:** 1\
**Last updated:** [November 1, 2021, 8:50pm UTC](https://discourse.slicer.org/t/veterinary-dog-bone-model/20432 "2021-11-01T20:50:11Z")

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veterinary dog bone model creation from dicom file from ct scan

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## [Calculating Second Moment of Area from Segment](https://discourse.slicer.org/t/calculating-second-moment-of-area-from-segment/16459)

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**Author:** [@jmhuie](https://discourse.slicer.org/u/jmhuie)\
**Replies:** 4\
**Last updated:** [November 1, 2021, 7:36pm UTC](https://discourse.slicer.org/t/calculating-second-moment-of-area-from-segment/16459 "2021-11-01T19:36:51Z")

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In the SlicerMorph workshop yesterday, @muratmaga and I briefly talked about the steps needed to measure second moment of area from a long bone image stack/volume. Currently I do this using ImageJ with BoneJ, but it’d be…

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## [Team needed to develop a Magnetic Ressonance segmentation of the spinal column](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189)

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**Author:** [@Ricardoneuro](https://discourse.slicer.org/u/Ricardoneuro)\
**Replies:** 4\
**Last updated:** [October 31, 2021, 8:13pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189 "2021-10-31T20:13:49Z")

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I have been using a very efficient column volumetric magnetic resonance protocol for the past 5 years. I’m looking for a group of people interested in a segmentation protocol that can extract and segment bone tissue from…

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## [Perform gamma analysis with slicerRT using python scripting](https://discourse.slicer.org/t/perform-gamma-analysis-with-slicerrt-using-python-scripting/20423)

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**Author:** [@Cedric\_Belanger](https://discourse.slicer.org/u/Cedric_Belanger)\
**Replies:** 1\
**Last updated:** [October 31, 2021, 12:32pm UTC](https://discourse.slicer.org/t/perform-gamma-analysis-with-slicerrt-using-python-scripting/20423 "2021-10-31T12:32:15Z")

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Hello, I am quite new to the slicer community. I would like to know how to perform a 3D gamma analysis using python scripting with slicerRT dose comparison tool. Are there any tutorials on this? Any insights would be m…

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## [Can’t cut away unwanted tissue](https://discourse.slicer.org/t/can-t-cut-away-unwanted-tissue/20417)

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**Author:** [@mdear](https://discourse.slicer.org/u/mdear)\
**Replies:** 2\
**Last updated:** [October 30, 2021, 11:51pm UTC](https://discourse.slicer.org/t/can-t-cut-away-unwanted-tissue/20417 "2021-10-30T23:51:51Z")

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Newbie question. I pull in DICOM data, go to data module and drag the data series into the 3D window. I then go to the segmentation editor and select threshold tool and select all voxels. I then select the box to allow …

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## [Perfusion MRI-3DSlicer](https://discourse.slicer.org/t/perfusion-mri-3dslicer/17790)

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**Author:** [@SantosCNEURO](https://discourse.slicer.org/u/SantosCNEURO)\
**Replies:** 3\
**Last updated:** [October 30, 2021, 11:27pm UTC](https://discourse.slicer.org/t/perfusion-mri-3dslicer/17790 "2021-10-30T23:27:37Z")

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Hi everyone, my name is Yusniel Santos Rodríguez, I am a Cuban neuroscientist and currently I work on issues related to the pre-surgical planning of brain tumors. Recently i have turned my attention to MRI perfusion imag…

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## [How to update Slicer's Python version from 3.6.7 to 3.7?](https://discourse.slicer.org/t/how-to-update-slicers-python-version-from-3-6-7-to-3-7/20409)

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**Author:** [@andieku](https://discourse.slicer.org/u/andieku)\
**Replies:** 3\
**Last updated:** [October 29, 2021, 10:39pm UTC](https://discourse.slicer.org/t/how-to-update-slicers-python-version-from-3-6-7-to-3-7/20409 "2021-10-29T22:39:52Z")

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Hi, is there a way to upgrade my Slicer’s (v. 4.11) Python version from 3.6.7 to 3.7 (or newer) without updating the slicer itself? I would like to use skimage’s skimage.segmentation.expand\_labels() function and it requi…

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## [Sandbox extension needed for mandible reconstruction extension and it is not available](https://discourse.slicer.org/t/sandbox-extension-needed-for-mandible-reconstruction-extension-and-it-is-not-available/20413)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 5\
**Last updated:** [October 29, 2021, 10:18pm UTC](https://discourse.slicer.org/t/sandbox-extension-needed-for-mandible-reconstruction-extension-and-it-is-not-available/20413 "2021-10-29T22:18:23Z")

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Hi. Users are telling me that they cannot finish surgical planning because they cannot make boolean operations because the CombineModels module is not found, because the extension manager cannot install Sandbox extension…

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## [How to update Python version from 3.67 to 3.8](https://discourse.slicer.org/t/how-to-update-python-version-from-3-67-to-3-8/16650)

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**Author:** [@full\_stack\_master](https://discourse.slicer.org/u/full_stack_master)\
**Replies:** 4\
**Last updated:** [October 29, 2021, 3:55pm UTC](https://discourse.slicer.org/t/how-to-update-python-version-from-3-67-to-3-8/16650 "2021-10-29T15:55:45Z")

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I want to update My slicer’s Python version from 3.6.7 to 3.8 because I am going to use Torch package As you know, this package is working on Python 3.8 Can you help me?

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## [Segment comparison module (Dice and Hausdorff) - but with markup points](https://discourse.slicer.org/t/segment-comparison-module-dice-and-hausdorff-but-with-markup-points/20358)

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**Author:** [@mk.kassai](https://discourse.slicer.org/u/mk.kassai)\
**Replies:** 3\
**Last updated:** [October 29, 2021, 2:14pm UTC](https://discourse.slicer.org/t/segment-comparison-module-dice-and-hausdorff-but-with-markup-points/20358 "2021-10-29T14:14:33Z")

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Hi, I want to evaluate segmentation by comparing them to markup points. I would be interested in the Dice metrics; however, the only module I found with Dice is the segment comparison which works only with segments. I…

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## [How to run MS Lesion Simulator module ?](https://discourse.slicer.org/t/how-to-run-ms-lesion-simulator-module/20335)

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**Author:** [@MouSah](https://discourse.slicer.org/u/MouSah)\
**Replies:** 5\
**Last updated:** [October 29, 2021, 12:20pm UTC](https://discourse.slicer.org/t/how-to-run-ms-lesion-simulator-module/20335 "2021-10-29T12:20:21Z")

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Operating system: Windows Slicer version: 3D Slicer 4.5.0-1 Expected behavior: Actual behavior: I didn’t found the MS Lesion Simulator module in my 3D installed slicer. May be this is due to the slicer version. Could…

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## [How to distinguish between translation, scaling and reduction by DIR](https://discourse.slicer.org/t/how-to-distinguish-between-translation-scaling-and-reduction-by-dir/20412)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 0\
**Last updated:** [October 29, 2021, 10:59am UTC](https://discourse.slicer.org/t/how-to-distinguish-between-translation-scaling-and-reduction-by-dir/20412 "2021-10-29T10:59:30Z")

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I want to distinguish between translation, enlargement, and reduction by DIR for each contour. When I asked about this before, I was told that there is a tool called bounding box that can be used to determine scaling, a…

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## [Labelmap volume rendering preset (default) is not available from preset dropdown](https://discourse.slicer.org/t/labelmap-volume-rendering-preset-default-is-not-available-from-preset-dropdown/20375)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 8\
**Last updated:** [October 29, 2021, 4:52am UTC](https://discourse.slicer.org/t/labelmap-volume-rendering-preset-default-is-not-available-from-preset-dropdown/20375 "2021-10-29T04:52:10Z")

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If I create a volume from the Simple Region Growing Segmentation module, then I suppose it is a binary labelmap. It can be viewed in 3D through the Volume Rendering module. By default this comes up with a kind of colo…

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## [New physician-annotated .dcm files not loading](https://discourse.slicer.org/t/new-physician-annotated-dcm-files-not-loading/20359)

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**Author:** [@BoneArtist](https://discourse.slicer.org/u/BoneArtist)\
**Replies:** 3\
**Last updated:** [October 29, 2021, 2:11am UTC](https://discourse.slicer.org/t/new-physician-annotated-dcm-files-not-loading/20359 "2021-10-29T02:11:25Z")

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The original .dcm files work fine, but my client recently annotated new versions of the study with color demarcations. Although these new versions are also .dcm files, they will not load as a scalar volume. The original…

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## [Text node: new lines not restored](https://discourse.slicer.org/t/text-node-new-lines-not-restored/20404)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 1\
**Last updated:** [October 29, 2021, 12:34am UTC](https://discourse.slicer.org/t/text-node-new-lines-not-restored/20404 "2021-10-29T00:34:06Z")

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New lines are not restored when opening a saved scene. If the scene project file has the following : \<Text id="vtkMRMLTextNode2" name="Text\_1" hideFromEditors="false" selectable="true" selected="false" userTags="" te…

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## [Error Using nVIDIA AIAA - Prostate Model ](https://discourse.slicer.org/t/error-using-nvidia-aiaa-prostate-model/20367)

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**Author:** [@mario.boccia1992](https://discourse.slicer.org/u/mario.boccia1992)\
**Replies:** 2\
**Last updated:** [October 28, 2021, 12:31pm UTC](https://discourse.slicer.org/t/error-using-nvidia-aiaa-prostate-model/20367 "2021-10-28T12:31:17Z")

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Dear all, Unfortunately I’m facing issue using nVIDIA AIAA module: prostate MRI segmentation. Running the AI I get this error: " Traceback (most recent call last): File “C:/Users/M/AppData/Local/NA-MIC/Slicer 4.11.20…

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## [Build Plus Toolkit in Ubuntu 20.04.3 LTS](https://discourse.slicer.org/t/build-plus-toolkit-in-ubuntu-20-04-3-lts/20389)

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**Author:** [@lb123](https://discourse.slicer.org/u/lb123)\
**Replies:** 1\
**Last updated:** [October 28, 2021, 2:05am UTC](https://discourse.slicer.org/t/build-plus-toolkit-in-ubuntu-20-04-3-lts/20389 "2021-10-28T02:05:48Z")

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Hi, I’m trying to build Plus Toolkit 2.8 in Ubuntu 20.04.3 LTS. I have followed the information of this page PlusBuild/BuildInstructionsLinux.md at master · PlusToolkit/PlusBuild · GitHub The only thing I did in a dif…

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## [Bonetexture in 3D Slicer won’t compute/display feature maps](https://discourse.slicer.org/t/bonetexture-in-3d-slicer-won-t-compute-display-feature-maps/8758)

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**Author:** [@11128](https://discourse.slicer.org/u/11128)\
**Replies:** 11\
**Last updated:** [October 27, 2021, 1:11pm UTC](https://discourse.slicer.org/t/bonetexture-in-3d-slicer-won-t-compute-display-feature-maps/8758 "2021-10-27T13:11:36Z")

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I can’t get the extension to compute or display feature maps. I am able to get the actual feature set (numerical output for the features). Please help. I had tried many times to follow the tutorial (Documentation/Nightl…

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## [Simple Color vs Terminology Color usage](https://discourse.slicer.org/t/simple-color-vs-terminology-color-usage/20271)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 18\
**Last updated:** [October 27, 2021, 8:04am UTC](https://discourse.slicer.org/t/simple-color-vs-terminology-color-usage/20271 "2021-10-27T08:04:56Z")

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I have found it confusing that 2 similar looking color objects bring up different options. First, there is the color selector in a node table such as in this table in the Markups module, but also used in the Segment Edi…

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## [Automate Dental Splint Generation Pt. 2](https://discourse.slicer.org/t/automate-dental-splint-generation-pt-2/20348)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 3\
**Last updated:** [October 26, 2021, 8:56pm UTC](https://discourse.slicer.org/t/automate-dental-splint-generation-pt-2/20348 "2021-10-26T20:56:19Z")

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Hello, I am following up on my previous post hoping to get some advise on the use of segmentation effects programmatically. I am currently running a smoothing operation (gaussian), two subtractions, and an additional s…

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## [Synthetic CT from MRI - editing MRI segments to Hounsfield Units](https://discourse.slicer.org/t/synthetic-ct-from-mri-editing-mri-segments-to-hounsfield-units/20351)

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**Author:** [@Harsforn](https://discourse.slicer.org/u/Harsforn)\
**Replies:** 6\
**Last updated:** [October 26, 2021, 8:50pm UTC](https://discourse.slicer.org/t/synthetic-ct-from-mri-editing-mri-segments-to-hounsfield-units/20351 "2021-10-26T20:50:38Z")

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Hi all, I’m trying to generate a synthetic CT from an MRI for use in an MRI-only radiotherapy treatment planning approach (with SlicerRT). I’ve segmented out bone, air, tissue, and a mock tumour from the MRI - is there…

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