# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=308

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

**Page:** 309

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## [Smooth object along only vertical axis](https://discourse.slicer.org/t/smooth-object-along-only-vertical-axis/14892)

<div class="topic-metadata">

**Author:** [@LuckyLuke](https://discourse.slicer.org/u/LuckyLuke)\
**Replies:** 15\
**Last updated:** [December 5, 2020, 7:24am UTC](https://discourse.slicer.org/t/smooth-object-along-only-vertical-axis/14892 "2020-12-05T07:24:45Z")

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I saw this post a month ago or so and I am wondering about the same thing: I have horizontal images in really nice resolution but they are spaced quite a lot 2mm! Now interest is to preserve the horizontal details but…

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## [How to include the aortic wall when i do auto segmentation using local threshold?](https://discourse.slicer.org/t/how-to-include-the-aortic-wall-when-i-do-auto-segmentation-using-local-threshold/14890)

<div class="topic-metadata">

**Author:** [@chendong9416](https://discourse.slicer.org/u/chendong9416)\
**Replies:** 2\
**Last updated:** [December 5, 2020, 5:53am UTC](https://discourse.slicer.org/t/how-to-include-the-aortic-wall-when-i-do-auto-segmentation-using-local-threshold/14890 "2020-12-05T05:53:54Z")

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this is a really importment step for centerline extration of aortic intramural hematoma!

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## [smoothing along only one axist](https://discourse.slicer.org/t/smoothing-along-only-one-axist/14893)

<div class="topic-metadata">

**Author:** [@LuckyLuke](https://discourse.slicer.org/u/LuckyLuke)\
**Replies:** 0\
**Last updated:** [December 5, 2020, 5:51am UTC](https://discourse.slicer.org/t/smoothing-along-only-one-axist/14893 "2020-12-05T05:51:26Z")

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As Murat has suggested I am trying to use smart filters but I have no idea which median or gaussian filter to choose in order to smooth object in one axis only. also have no idea where do I select the axis? muratmaga, …

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## [What does this second part of the code mean? Python](https://discourse.slicer.org/t/what-does-this-second-part-of-the-code-mean-python/14878)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 1\
**Last updated:** [December 4, 2020, 4:33pm UTC](https://discourse.slicer.org/t/what-does-this-second-part-of-the-code-mean-python/14878 "2020-12-04T16:33:17Z")

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Change spacing logging.info("change spacing") start = time.time() ijkToRas = vtk.vtkMatrix4x4() imagenode.GetIJKToRASMatrix(ijkToRas) for i in range(3): ijkToRas.SetElement(i, i, spacing\[i\]) …

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## [How can we make the vessel three-dimensional after finding the center line of the vessel?](https://discourse.slicer.org/t/how-can-we-make-the-vessel-three-dimensional-after-finding-the-center-line-of-the-vessel/14883)

<div class="topic-metadata">

**Author:** [@Faeezh\_Eydi](https://discourse.slicer.org/u/Faeezh_Eydi)\
**Replies:** 0\
**Last updated:** [December 4, 2020, 4:27pm UTC](https://discourse.slicer.org/t/how-can-we-make-the-vessel-three-dimensional-after-finding-the-center-line-of-the-vessel/14883 "2020-12-04T16:27:54Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [How to change this value in 3D slicer?](https://discourse.slicer.org/t/how-to-change-this-value-in-3d-slicer/14880)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 1\
**Last updated:** [December 4, 2020, 11:08am UTC](https://discourse.slicer.org/t/how-to-change-this-value-in-3d-slicer/14880 "2020-12-04T11:08:42Z")

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1.What is this? why this can not be changed, when click on it can not change it. what exact command controls this parameters because my script adds here -1 and -1 there. if i would know which command controls this, I …

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## [ROI to IJK coordinates with MATLAB bridge](https://discourse.slicer.org/t/roi-to-ijk-coordinates-with-matlab-bridge/14764)

<div class="topic-metadata">

**Author:** [@OscarD](https://discourse.slicer.org/u/OscarD)\
**Replies:** 1\
**Last updated:** [December 4, 2020, 9:06am UTC](https://discourse.slicer.org/t/roi-to-ijk-coordinates-with-matlab-bridge/14764 "2020-12-04T09:06:04Z")

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Operating system: Windows 10 Slicer version: 4.11.0 Expected behavior: Find IJK coordinates of ROI Actual behavior: I get negative or bigger than dimensions IJK coordinates Dear slicers, I am trying to get iMin, iMa…

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## [How to install modules offline](https://discourse.slicer.org/t/how-to-install-modules-offline/14868)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 3\
**Last updated:** [December 4, 2020, 7:03am UTC](https://discourse.slicer.org/t/how-to-install-modules-offline/14868 "2020-12-04T07:03:57Z")

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After I downloaded the expansion modules separately, I followed the Slicer software on a computer without internet, and then installed the module. It failed. How can I install the module offline?I have downloaded the mod…

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## [Screen Capture features](https://discourse.slicer.org/t/screen-capture-features/14860)

<div class="topic-metadata">

**Author:** [@torquil](https://discourse.slicer.org/u/torquil)\
**Replies:** 2\
**Last updated:** [December 4, 2020, 6:06am UTC](https://discourse.slicer.org/t/screen-capture-features/14860 "2020-12-04T06:06:12Z")

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Hi! There are two features that I am missing from the Screen Capture module: Easily select to create a video in the reverse direction, i.e. “reverse yaw” og “reverse pitch”. Sometimes it is important for me to have cr…

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## [What does this part of code mean? python slicer](https://discourse.slicer.org/t/what-does-this-part-of-code-mean-python-slicer/14876)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 0\
**Last updated:** [December 4, 2020, 5:18am UTC](https://discourse.slicer.org/t/what-does-this-part-of-code-mean-python-slicer/14876 "2020-12-04T05:18:11Z")

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Can someone explain to me what does this part of code does: imagenode.SetOrigin(tuple(list(\[0,0,translation\]))) what does imagenode.setorigin does? Create image node start = time.time() imagenode = slicer.mrml…

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## [Using Slicer modules with Python interpreter or Jupyter Notebook (Help!)](https://discourse.slicer.org/t/using-slicer-modules-with-python-interpreter-or-jupyter-notebook-help/14861)

<div class="topic-metadata">

**Author:** [@perecanals](https://discourse.slicer.org/u/perecanals)\
**Replies:** 5\
**Last updated:** [December 4, 2020, 2:46am UTC](https://discourse.slicer.org/t/using-slicer-modules-with-python-interpreter-or-jupyter-notebook-help/14861 "2020-12-04T02:46:23Z")

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Hi, I am trying to automize Slicer functions that I regularly do manually using Python scripts and I have been facing some problems that have been slowing me down quite a bit. I have been reading through the forums and …

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## [How to show DICOM and the corresponding RT STRUCTURE?](https://discourse.slicer.org/t/how-to-show-dicom-and-the-corresponding-rt-structure/1562)

<div class="topic-metadata">

**Author:** [@glhfgg1024](https://discourse.slicer.org/u/glhfgg1024)\
**Replies:** 3\
**Last updated:** [December 3, 2020, 3:55am UTC](https://discourse.slicer.org/t/how-to-show-dicom-and-the-corresponding-rt-structure/1562 "2020-12-03T03:55:26Z")

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Hello everyone, I’m a newbie to Slicer. I have one DICOM directory where many .dcm files are there and another DICOM RT STRUCTURE directory where one .dcm file is there. I want to load the two directories into Slicer an…

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## [Error messages indicating 4 missing files](https://discourse.slicer.org/t/error-messages-indicating-4-missing-files/14839)

<div class="topic-metadata">

**Author:** [@Poul\_Andersson](https://discourse.slicer.org/u/Poul_Andersson)\
**Replies:** 4\
**Last updated:** [December 3, 2020, 10:33am UTC](https://discourse.slicer.org/t/error-messages-indicating-4-missing-files/14839 "2020-12-03T10:33:08Z")

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I have installed the module for the jupyter kernel to use 3DSlicer in notebooks but am now facing two problems: firstly, the 3DSlicer app keeps restarting automatically after proper exit; and secondly, I get the abo…

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## [How to measure left atrial wall thickness use CT Hounsfield Units](https://discourse.slicer.org/t/how-to-measure-left-atrial-wall-thickness-use-ct-hounsfield-units/14663)

<div class="topic-metadata">

**Author:** [@caiwei](https://discourse.slicer.org/u/caiwei)\
**Replies:** 1\
**Last updated:** [November 19, 2020, 3:21am UTC](https://discourse.slicer.org/t/how-to-measure-left-atrial-wall-thickness-use-ct-hounsfield-units/14663 "2020-11-19T03:21:59Z")

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I would like to know whether it is possible to use 3D Slicer to accurately measure the left atrial wall(myocardial) thickness which excludes the fat tissue use CT Hounsfield Units. The concrete method is showed in the be…

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## [NRRD vs NIFTI: which one to choose?](https://discourse.slicer.org/t/nrrd-vs-nifti-which-one-to-choose/7799)

<div class="topic-metadata">

**Author:** [@agirault](https://discourse.slicer.org/u/agirault)\
**Replies:** 14\
**Last updated:** [December 2, 2020, 11:58am UTC](https://discourse.slicer.org/t/nrrd-vs-nifti-which-one-to-choose/7799 "2020-12-02T11:58:23Z")

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This is a question for users of those two formats: if you had to set up a workflow where you need to store your medical images imported from DICOM in a single file, which would you choose between NRRD and NIFTI (or anoth…

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## [Showing grids in the viewer](https://discourse.slicer.org/t/showing-grids-in-the-viewer/5293)

<div class="topic-metadata">

**Author:** [@feng](https://discourse.slicer.org/u/feng)\
**Replies:** 6\
**Last updated:** [December 2, 2020, 2:41am UTC](https://discourse.slicer.org/t/showing-grids-in-the-viewer/5293 "2020-12-02T02:41:06Z")

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Is it possible to show grids in the viewer like this?

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## [JSON file contents questions](https://discourse.slicer.org/t/json-file-contents-questions/14832)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [December 1, 2020, 6:41pm UTC](https://discourse.slicer.org/t/json-file-contents-questions/14832 "2020-12-01T18:41:08Z")

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We discussed this here, but as far as I can it is not implemented for the latest stable. Also, what is the purpose of the “orientation” tag?

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## [How to set or customize keyboard shortcuts in Slicer?](https://discourse.slicer.org/t/how-to-set-or-customize-keyboard-shortcuts-in-slicer/14814)

<div class="topic-metadata">

**Author:** [@Aitekk](https://discourse.slicer.org/u/Aitekk)\
**Replies:** 2\
**Last updated:** [December 1, 2020, 6:46am UTC](https://discourse.slicer.org/t/how-to-set-or-customize-keyboard-shortcuts-in-slicer/14814 "2020-12-01T06:46:30Z")

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I have some problems about using Slicer. First, how to set or customize keyboard shortcuts in Slicer? This will make slicer more in line with my habits. In addition, I found that when there are many segments in the scene…

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## [How to convert model node (points) to Volume node?](https://discourse.slicer.org/t/how-to-convert-model-node-points-to-volume-node/14816)

<div class="topic-metadata">

**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 0\
**Last updated:** [November 30, 2020, 1:13pm UTC](https://discourse.slicer.org/t/how-to-convert-model-node-points-to-volume-node/14816 "2020-11-30T13:13:33Z")

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Hello Dear Developers and Users I have a model that contains 48425 points or cells. These points are the result of sampling of pulmonary vessels in CT images by the Chest Imaging Platform (which are known as particles s…

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## [Slicer 4.10.2 vs Slicer 4.11.2 volumes rendering](https://discourse.slicer.org/t/slicer-4-10-2-vs-slicer-4-11-2-volumes-rendering/14807)

<div class="topic-metadata">

**Author:** [@a10227](https://discourse.slicer.org/u/a10227)\
**Replies:** 2\
**Last updated:** [November 29, 2020, 10:41pm UTC](https://discourse.slicer.org/t/slicer-4-10-2-vs-slicer-4-11-2-volumes-rendering/14807 "2020-11-29T22:41:02Z")

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Good day, I had Slicer 4.10.2 version on my PC. After a while, I noticed that for some images the uploading time is too slow, so I installed the latest stable version 4.11.2. In the latest version, I have no problem wit…

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## [How can I use 3DSlicer by python?](https://discourse.slicer.org/t/how-can-i-use-3dslicer-by-python/14808)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.slicer.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [November 29, 2020, 7:00pm UTC](https://discourse.slicer.org/t/how-can-i-use-3dslicer-by-python/14808 "2020-11-29T19:00:59Z")

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Thanks for all developer for 3D slicer. Currently, I want to use the semi-automatic segmentation method of 3D slicer in python. Can I install 3D slicer by pip install slicer? Which module of 3D slicer is designed for s…

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## [Downloading Slicer on Mac](https://discourse.slicer.org/t/downloading-slicer-on-mac/14805)

<div class="topic-metadata">

**Author:** [@Marcos\_Martinez](https://discourse.slicer.org/u/Marcos_Martinez)\
**Replies:** 1\
**Last updated:** [November 29, 2020, 3:56am UTC](https://discourse.slicer.org/t/downloading-slicer-on-mac/14805 "2020-11-29T03:56:35Z")

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I am trying to download Slicer 4.11.20200930 on my MacBook Air, but I am encountering this pop-up provided on the image I uploaded. I downloaded Slicer on my iMac 2015 with ease; however, I am having complications on my …

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## [Can't get axial, sagital, and coronal MRI slices to display together like in tutorial](https://discourse.slicer.org/t/cant-get-axial-sagital-and-coronal-mri-slices-to-display-together-like-in-tutorial/14796)

<div class="topic-metadata">

**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 8\
**Last updated:** [November 29, 2020, 3:55am UTC](https://discourse.slicer.org/t/cant-get-axial-sagital-and-coronal-mri-slices-to-display-together-like-in-tutorial/14796 "2020-11-29T03:55:20Z")

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Hello, I got through the DICOM tutorial, but have hit a wall when loading in my own MRI data. In the tutorial, the series loads in and the 3 slices appear in the 3D viewer together, however when I load in my series, it …

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## [NRRD or SEG.NRRD to PNG](https://discourse.slicer.org/t/nrrd-or-seg-nrrd-to-png/14459)

<div class="topic-metadata">

**Author:** [@LuckyLuke](https://discourse.slicer.org/u/LuckyLuke)\
**Replies:** 5\
**Last updated:** [November 28, 2020, 8:16pm UTC](https://discourse.slicer.org/t/nrrd-or-seg-nrrd-to-png/14459 "2020-11-28T20:16:33Z")

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So I have a request from somene to export his DICOM and NRRD files 5 of them into a set of PNG images. Images are to be numbered and saved without losing any info, in other words either a lossless compression format or …

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## [Extension manager consistenly doesn't load on first try](https://discourse.slicer.org/t/extension-manager-consistenly-doesnt-load-on-first-try/14800)

<div class="topic-metadata">

**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 5\
**Last updated:** [November 28, 2020, 7:01pm UTC](https://discourse.slicer.org/t/extension-manager-consistenly-doesnt-load-on-first-try/14800 "2020-11-28T19:01:29Z")

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After a fresh boot of slicer, my extension manager opens to a blank page. I need to close the extension manager and then re-open it to get it to work. This is consistently reproducible. Logs and screenshot of fresh boot …

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## [Cannot install EAMapReader-Slicer-4.11 extension ](https://discourse.slicer.org/t/cannot-install-eamapreader-slicer-4-11-extension/14795)

<div class="topic-metadata">

**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 1\
**Last updated:** [November 28, 2020, 4:58pm UTC](https://discourse.slicer.org/t/cannot-install-eamapreader-slicer-4-11-extension/14795 "2020-11-28T16:58:10Z")

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Problem report for Slicer 4.11.20200930 macosx-amd64 I am trying to install the following extension: https://github.com/stephan1312/SlicerEAMapReader#readme Expected Behavior: In the extension manager select “Install …

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## [How to adjust the thickness](https://discourse.slicer.org/t/how-to-adjust-the-thickness/14734)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 3\
**Last updated:** [November 28, 2020, 2:59pm UTC](https://discourse.slicer.org/t/how-to-adjust-the-thickness/14734 "2020-11-28T14:59:52Z")

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I got a guide plate, this model is very thin, is there a way to adjust its thickness? I plan to make a guide plate for hematoma puncture and add a tube to this model.

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## [All yellow displacement field. MMI value](https://discourse.slicer.org/t/all-yellow-displacement-field-mmi-value/14793)

<div class="topic-metadata">

**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 0\
**Last updated:** [November 27, 2020, 6:42pm UTC](https://discourse.slicer.org/t/all-yellow-displacement-field-mmi-value/14793 "2020-11-27T18:42:55Z")

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Operating system: MacOS 10.14 Slicer version: 4.11.20200930 Hi all, I’m registering CT and MRI images of pelvis and completely new to Slicer . To get the MMI value, to be able to compare the registrations, I found in …

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## [Segmentation is cropped to minimum extent](https://discourse.slicer.org/t/segmentation-is-cropped-to-minimum-extent/14788)

<div class="topic-metadata">

**Author:** [@ButuiHu](https://discourse.slicer.org/u/ButuiHu)\
**Replies:** 5\
**Last updated:** [November 27, 2020, 4:54am UTC](https://discourse.slicer.org/t/segmentation-is-cropped-to-minimum-extent/14788 "2020-11-27T04:54:27Z")

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step to reproduce: create segmentation in segmen editor using the MRHead from sample data. export segmentation to labelmap save MRHead, Segmentation, and the labelmap (as Segmentation-label.nrrd) to file. load MRHead a…

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## [Build slicer error,need your help](https://discourse.slicer.org/t/build-slicer-error-need-your-help/7207)

<div class="topic-metadata">

**Author:** [@zhaobingshuai](https://discourse.slicer.org/u/zhaobingshuai)\
**Replies:** 4\
**Last updated:** [November 27, 2020, 3:13am UTC](https://discourse.slicer.org/t/build-slicer-error-need-your-help/7207 "2020-11-27T03:13:47Z")

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hello, when i build slicer, i enter \<ccmake -DCMAKE\_BUILD\_TYPE:STRING=Release DQt5\_DIR:PATH=/home/zbs/package/Qt/5.12.2/gcc\_64/lib/cmake/Qt5/Qt5Config.cmake …/Slicer\> i meet errors as follows, maybe the reason is i ins…

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