# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=312

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

**Page:** 313

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## [Volumetric Analysis of vertebral bodies](https://discourse.slicer.org/t/volumetric-analysis-of-vertebral-bodies/14455)

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**Author:** [@Siegmund\_Lang](https://discourse.slicer.org/u/Siegmund_Lang)\
**Replies:** 3\
**Last updated:** [November 10, 2020, 1:06pm UTC](https://discourse.slicer.org/t/volumetric-analysis-of-vertebral-bodies/14455 "2020-11-10T13:06:43Z")

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Dear 3DSlicer community, I am looking for a way to calculate the volume of vertebral bodies with a microsoft based software other than BrainLab. Do you know if there is a function in 3DSlicer to measure volume data (i…

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## [Extension manager icons look faded](https://discourse.slicer.org/t/extension-manager-icons-look-faded/14077)

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**Author:** [@Gaston](https://discourse.slicer.org/u/Gaston)\
**Replies:** 9\
**Last updated:** [November 10, 2020, 4:02am UTC](https://discourse.slicer.org/t/extension-manager-icons-look-faded/14077 "2020-11-10T04:02:31Z")

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When I open the extension manager the icons look washed out Mac osx catalina

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## [3D display pannel in Model mode is inactive](https://discourse.slicer.org/t/3d-display-pannel-in-model-mode-is-inactive/14501)

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**Author:** [@jarrik](https://discourse.slicer.org/u/jarrik)\
**Replies:** 2\
**Last updated:** [November 10, 2020, 1:09am UTC](https://discourse.slicer.org/t/3d-display-pannel-in-model-mode-is-inactive/14501 "2020-11-10T01:09:53Z")

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Operating system: Win 10 Slicer version: 4.11.0-2020-07-04 Expected behavior: Actual behavior: Hello! When I open 3D model with Model mode, some elements of 3D Display pannel stay inactive (Point Size and Line Width…

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## [BrainTissueExtension problem with installation](https://discourse.slicer.org/t/braintissueextension-problem-with-installation/14496)

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**Author:** [@Ester\_RG](https://discourse.slicer.org/u/Ester_RG)\
**Replies:** 1\
**Last updated:** [November 9, 2020, 8:52pm UTC](https://discourse.slicer.org/t/braintissueextension-problem-with-installation/14496 "2020-11-09T20:52:56Z")

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The problem I have is that when I try to install the BrainTissueExtension in Extension Wizard, it only recognizes one of the three modules it contains. The problem is that to make use of some of these modules depends on …

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## [Slices vs smooth transitions](https://discourse.slicer.org/t/slices-vs-smooth-transitions/14508)

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**Author:** [@11katie](https://discourse.slicer.org/u/11katie)\
**Replies:** 1\
**Last updated:** [November 9, 2020, 7:12pm UTC](https://discourse.slicer.org/t/slices-vs-smooth-transitions/14508 "2020-11-09T19:12:27Z")

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I am calculating volume of lesions on brain MRI data and for some scans that I upload into 3D slicer the slices appear in a smooth transition between them, creating hundreds of ‘slices’ making segmentation very difficult…

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## [Segment disapears when using segment margin-\> grow](https://discourse.slicer.org/t/segment-disapears-when-using-segment-margin-grow/14475)

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**Author:** [@l.znaniecki](https://discourse.slicer.org/u/l.znaniecki)\
**Replies:** 8\
**Last updated:** [November 8, 2020, 8:53pm UTC](https://discourse.slicer.org/t/segment-disapears-when-using-segment-margin-grow/14475 "2020-11-08T20:53:10Z")

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Problem report for Slicer 4.11.20200930 win-amd64: \[please describe expected and actual behavior\] Segment disapears when using segment margin-\> grow. This happens repeatedly on some segmentations of some CTs. I can’t fi…

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## [Bending 3D model](https://discourse.slicer.org/t/bending-3d-model/9340)

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**Author:** [@GL1984](https://discourse.slicer.org/u/GL1984)\
**Replies:** 5\
**Last updated:** [November 8, 2020, 8:38pm UTC](https://discourse.slicer.org/t/bending-3d-model/9340 "2020-11-08T20:38:19Z")

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Hello, I was wondering if I could use one of Slicer’s extension to bend a 3D model? Essentially I would like to contour a stabilising plate to the bone model ahead of surgery. I saw that there is an osteotomy planner m…

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## [Level tracing segmentation](https://discourse.slicer.org/t/level-tracing-segmentation/14490)

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**Author:** [@sahithi](https://discourse.slicer.org/u/sahithi)\
**Replies:** 1\
**Last updated:** [November 8, 2020, 3:20pm UTC](https://discourse.slicer.org/t/level-tracing-segmentation/14490 "2020-11-08T15:20:26Z")

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Hello everyone, I have a doubt regarding level tracing segmentation. Is level tracing segmentaion kind of thresholding segmentation(semi automatic) or not? If it is diffrent from thresholding, can somebody please tell …

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## [Help with lung fibrosis measurement](https://discourse.slicer.org/t/help-with-lung-fibrosis-measurement/14489)

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**Author:** [@Dave](https://discourse.slicer.org/u/Dave)\
**Replies:** 0\
**Last updated:** [November 8, 2020, 2:44pm UTC](https://discourse.slicer.org/t/help-with-lung-fibrosis-measurement/14489 "2020-11-08T14:44:03Z")

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Hi, I am currently working on measuring lung fibrosis lesions in mice models using µCT, at diferent time-lapses. We are following an approach based on segmenting the fibrotic volume, and then extracting Hounsfield-Units…

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## [Help with Segmentation of MRI](https://discourse.slicer.org/t/help-with-segmentation-of-mri/14485)

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**Author:** [@ssk](https://discourse.slicer.org/u/ssk)\
**Replies:** 1\
**Last updated:** [November 8, 2020, 11:05am UTC](https://discourse.slicer.org/t/help-with-segmentation-of-mri/14485 "2020-11-08T11:05:48Z")

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I am new to segmenting MRI’s and learning to do so for a project. How do I quantify volumes/areas, etc from an MRI image? Tissue in question is extraorbital muscles (as circled in image). I wish to isolate it on multipl…

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## [Ruler does not work properly](https://discourse.slicer.org/t/ruler-does-not-work-properly/14482)

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**Author:** [@iboeth](https://discourse.slicer.org/u/iboeth)\
**Replies:** 4\
**Last updated:** [November 7, 2020, 9:45pm UTC](https://discourse.slicer.org/t/ruler-does-not-work-properly/14482 "2020-11-07T21:45:32Z")

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Operating system: MacOSCatalina Version 10.15.7 Slicer version: 14.11.20200930 Expected behavior: Actual behavior: Using the ruler shows no measure of my ROI. What am I doing wrong?

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## [Save reformatted MRI planes](https://discourse.slicer.org/t/save-reformatted-mri-planes/14480)

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**Author:** [@susana.amoros](https://discourse.slicer.org/u/susana.amoros)\
**Replies:** 0\
**Last updated:** [November 7, 2020, 8:15pm UTC](https://discourse.slicer.org/t/save-reformatted-mri-planes/14480 "2020-11-07T20:15:13Z")

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Operating system: macOS Sierra v10.12.6 Slicer version: 4.10.2 I need a guided step-by-step tutorial (or python code) on how to save a volume using reformatted axes. I have reformatted an atlas to match a home-made or…

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## [How to overlap CT images](https://discourse.slicer.org/t/how-to-overlap-ct-images/14478)

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**Author:** [@Anonymous1](https://discourse.slicer.org/u/Anonymous1)\
**Replies:** 0\
**Last updated:** [November 7, 2020, 8:14pm UTC](https://discourse.slicer.org/t/how-to-overlap-ct-images/14478 "2020-11-07T20:14:44Z")

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Hi!! Does anyone know how to overlap different CT images? Thank you

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## [No images shown in slice viewers in latest preview release (Slicer-4.13.0)](https://discourse.slicer.org/t/no-images-shown-in-slice-viewers-in-latest-preview-release-slicer-4-13-0/13899)

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**Author:** [@am\_49](https://discourse.slicer.org/u/am_49)\
**Replies:** 7\
**Last updated:** [November 6, 2020, 10:27pm UTC](https://discourse.slicer.org/t/no-images-shown-in-slice-viewers-in-latest-preview-release-slicer-4-13-0/13899 "2020-11-06T22:27:02Z")

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Problem report for Slicer 4.13.0-2020-10-05 win-amd64: \[please describe expected and actual behavior\] I am running Windows 10 on ASUS AiO desktop (Intel Core i5, RAM 16 GB, NVIDIA GeForce GTX 1050, updated drivers and a…

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## [Layout change doesn't work](https://discourse.slicer.org/t/layout-change-doesnt-work/14451)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 7\
**Last updated:** [November 6, 2020, 9:25pm UTC](https://discourse.slicer.org/t/layout-change-doesnt-work/14451 "2020-11-06T21:25:51Z")

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I add this line slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView) on the end of the createUserInterface function on the ScrewStep.py module of the Pedicle Screw Simulator Extension and…

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## [Registration of CT brain segmentation template into head phantom in 3D Slicer](https://discourse.slicer.org/t/registration-of-ct-brain-segmentation-template-into-head-phantom-in-3d-slicer/14458)

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**Author:** [@hajarzuber](https://discourse.slicer.org/u/hajarzuber)\
**Replies:** 1\
**Last updated:** [November 6, 2020, 4:26pm UTC](https://discourse.slicer.org/t/registration-of-ct-brain-segmentation-template-into-head-phantom-in-3d-slicer/14458 "2020-11-06T16:26:34Z")

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Hi, I am developing a head phantom made of wood (all HU represent soft tissue), thus the image in CT shows only homogenous grayscale with no bone. However, I need to delineate OAR (parotid gland, lens and brain) for meas…

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## [Python debugging in Pycharm](https://discourse.slicer.org/t/python-debugging-in-pycharm/14461)

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**Author:** [@Masteling](https://discourse.slicer.org/u/Masteling)\
**Replies:** 1\
**Last updated:** [November 6, 2020, 4:03pm UTC](https://discourse.slicer.org/t/python-debugging-in-pycharm/14461 "2020-11-06T16:03:50Z")

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I have followed the steps suggested here: Documentation/Nightly/Extensions/DebuggingTools - Slicer Wiki And I am able to connect Slicer and Pycharm, however, after the connection is established this error occurs: An…

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## [MRTrix vs. Slicer color information](https://discourse.slicer.org/t/mrtrix-vs-slicer-color-information/14334)

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**Author:** [@jaredsullivan](https://discourse.slicer.org/u/jaredsullivan)\
**Replies:** 1\
**Last updated:** [November 5, 2020, 11:36pm UTC](https://discourse.slicer.org/t/mrtrix-vs-slicer-color-information/14334 "2020-11-05T23:36:23Z")

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Hello, I am having trouble using Slicer to view a directionally-encoded color track density imaging (DEC-TDI) map created in MRtrix (documentation: https://mrtrix.readthedocs.io/en/latest/reference/commands/tckmap.html)…

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## [DICOM browser hangs](https://discourse.slicer.org/t/dicom-browser-hangs/14452)

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**Author:** [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Replies:** 1\
**Last updated:** [November 5, 2020, 9:35pm UTC](https://discourse.slicer.org/t/dicom-browser-hangs/14452 "2020-11-05T21:35:37Z")

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Why I am getting ‘‘Not Responding’’ error in windows with the stable release?

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## [CT image registration](https://discourse.slicer.org/t/ct-image-registration/14430)

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**Author:** [@sahithi](https://discourse.slicer.org/u/sahithi)\
**Replies:** 1\
**Last updated:** [November 5, 2020, 6:49pm UTC](https://discourse.slicer.org/t/ct-image-registration/14430 "2020-11-05T18:49:09Z")

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Operating system:windows 10 Slicer version:4.10.2 Hello Everyone, while i was trying to register two CT abdomen scans using general registration(brains) - geometry align, in the output image i am getting lines at th…

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## [Pedicle Screw Simulator bugs](https://discourse.slicer.org/t/pedicle-screw-simulator-bugs/14446)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 2\
**Last updated:** [November 5, 2020, 6:17pm UTC](https://discourse.slicer.org/t/pedicle-screw-simulator-bugs/14446 "2020-11-05T18:17:18Z")

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Hi. I found some bugs on the PedicleScrewSimulator extension. The ones I’d like to be solved the most are number 6 and 7 because they affect funcionality, the other ones refer to the GUI 1- In step “5. Place Screws”: lo…

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## [Quantification of Porosity from micro CT scans](https://discourse.slicer.org/t/quantification-of-porosity-from-micro-ct-scans/10698)

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**Author:** [@gretaa](https://discourse.slicer.org/u/gretaa)\
**Replies:** 3\
**Last updated:** [November 5, 2020, 4:55pm UTC](https://discourse.slicer.org/t/quantification-of-porosity-from-micro-ct-scans/10698 "2020-11-05T16:55:33Z")

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Operating system: Mac OS Catalina Slicer version: 4.10.2 Expected behavior: Actual behavior: Hi guys, I have a bmp dataset of micro CT scans (1.3 mm diameter, 600 nm = 1 pixel resolution). I would like to quantify …

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## [Problem running Slicer on CentOS8](https://discourse.slicer.org/t/problem-running-slicer-on-centos8/14413)

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**Author:** [@Yuting\_Deng](https://discourse.slicer.org/u/Yuting_Deng)\
**Replies:** 5\
**Last updated:** [November 5, 2020, 5:18am UTC](https://discourse.slicer.org/t/problem-running-slicer-on-centos8/14413 "2020-11-05T05:18:33Z")

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I was having the same problems opening Slicer 4.11 with CentOS8. I have followed the methods mentioned above and made sure that all the missing libraries have been installed, but I still keep having the following errors: …

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## [Mac osX 10.15.7. Can't load volumes](https://discourse.slicer.org/t/mac-osx-10-15-7-cant-load-volumes/14396)

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**Author:** [@axlander](https://discourse.slicer.org/u/axlander)\
**Replies:** 7\
**Last updated:** [November 4, 2020, 10:51pm UTC](https://discourse.slicer.org/t/mac-osx-10-15-7-cant-load-volumes/14396 "2020-11-04T22:51:04Z")

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I downloaded and installed slicer 4.11 in my Applications folder. Slicer starts normally but I can’t load volumes (.nii) or load dcm files. After starting, the following warnings appear. When loading module “DICOM” ,…

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## [How to customize SubjectHierarchyTreeView?](https://discourse.slicer.org/t/how-to-customize-subjecthierarchytreeview/14358)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 8\
**Last updated:** [November 4, 2020, 10:13pm UTC](https://discourse.slicer.org/t/how-to-customize-subjecthierarchytreeview/14358 "2020-11-04T22:13:22Z")

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Hi! I want to customize a SubjectHierarchyTreeView Widget in a module. Things to change: Filter Model nodes: made self.uit.SubjectHierarchyTreeView.nodeTypes = \[“vtkMRMLModelNode”\] Change header text: “Node”…

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## [slicerradiomics error](https://discourse.slicer.org/t/slicerradiomics-error/14258)

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**Author:** [@firatoz](https://discourse.slicer.org/u/firatoz)\
**Replies:** 12\
**Last updated:** [November 4, 2020, 9:29pm UTC](https://discourse.slicer.org/t/slicerradiomics-error/14258 "2020-11-04T21:29:24Z")

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When using Slicer Radiomics in 4.13 version I get this error: RadiomicsCLI standard error: Traceback (most recent call last): File “C:/Users/Yi�it/AppData/Roaming/NA-MIC/Extensions-29434/SlicerRadiomics/lib/Slicer-4.1…

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## [SEEGA extension not working with Slicer stable release](https://discourse.slicer.org/t/seega-extension-not-working-with-slicer-stable-release/14431)

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**Author:** [@BushraR](https://discourse.slicer.org/u/BushraR)\
**Replies:** 3\
**Last updated:** [November 4, 2020, 6:37pm UTC](https://discourse.slicer.org/t/seega-extension-not-working-with-slicer-stable-release/14431 "2020-11-04T18:37:12Z")

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Hello, I am new to this community. I am using SEEGA extension with the slicer stable release 4.11. It seems that author of that extension doesn’t read this forum and I have already seen someone else reporting the error …

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## [Manipulating objects script doesn't work](https://discourse.slicer.org/t/manipulating-objects-script-doesnt-work/14432)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 1\
**Last updated:** [November 4, 2020, 5:31pm UTC](https://discourse.slicer.org/t/manipulating-objects-script-doesnt-work/14432 "2020-11-04T17:31:58Z")

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The script is this one. The drawn circle should be updated in relation to the two fiducials position but after is created it doesn’t update with a modification to the position of the fiducials. I added this line logging.…

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## [Can't load one of volumes into neither elastic nor BRAINS registration](https://discourse.slicer.org/t/cant-load-one-of-volumes-into-neither-elastic-nor-brains-registration/14417)

<div class="topic-metadata">

**Author:** [@l.znaniecki](https://discourse.slicer.org/u/l.znaniecki)\
**Replies:** 2\
**Last updated:** [November 4, 2020, 2:39pm UTC](https://discourse.slicer.org/t/cant-load-one-of-volumes-into-neither-elastic-nor-brains-registration/14417 "2020-11-04T14:39:01Z")

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HI, Slicer 4.11.0 form 12.9.2020 Module: elastics / BRAINS registration. I have two series from the same examination (contrast & non-contrast) as two volumes. The problem is - in both registration modules the non-con…

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## [How can I find a voxel value from a CT](https://discourse.slicer.org/t/how-can-i-find-a-voxel-value-from-a-ct/14427)

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**Author:** [@Giovanni\_Cunha](https://discourse.slicer.org/u/Giovanni_Cunha)\
**Replies:** 0\
**Last updated:** [November 4, 2020, 1:26pm UTC](https://discourse.slicer.org/t/how-can-i-find-a-voxel-value-from-a-ct/14427 "2020-11-04T13:26:46Z")

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Dear community I need to find the voxel used in each CT from my sample to standardize. To discover kVp, mA/s and slice thickness I have been used the option “dicom metadata” in the option Dicom (DCM). But cant find the…

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