# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=24

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

**Page:** 25

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## [Reconstruct Mesh from a custom centerline](https://discourse.slicer.org/t/reconstruct-mesh-from-a-custom-centerline/22006)

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**Author:** [@\_11](https://discourse.slicer.org/u/_11)\
**Replies:** 6\
**Last updated:** [May 19, 2022, 8:04am UTC](https://discourse.slicer.org/t/reconstruct-mesh-from-a-custom-centerline/22006 "2022-05-19T08:04:13Z")

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Hi, Thanks for the very valuable repository. I am wondering if it is possible to generate the tubular mesh based on a synthetically generated centerline with bifurcation? So what I have is a graph/tree structure with n…

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## [What is the ideal bin width for PET radiomics?](https://discourse.slicer.org/t/what-is-the-ideal-bin-width-for-pet-radiomics/10558)

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**Author:** [@Nora](https://discourse.slicer.org/u/Nora)\
**Replies:** 4\
**Last updated:** [May 19, 2022, 2:41am UTC](https://discourse.slicer.org/t/what-is-the-ideal-bin-width-for-pet-radiomics/10558 "2022-05-19T02:41:54Z")

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Hi all, I’m trying to extract the radiomic features from PET images using Pyradiomics extension on 3DSlicer. The default settings for the binwidth is 25, however, that’s can’t calculate some features like the GLCMs. …

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## [2d image segmentation radiomic feature generator ](https://discourse.slicer.org/t/2d-image-segmentation-radiomic-feature-generator/23457)

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**Author:** [@Manju\_Manju](https://discourse.slicer.org/u/Manju_Manju)\
**Replies:** 0\
**Last updated:** [May 17, 2022, 1:47pm UTC](https://discourse.slicer.org/t/2d-image-segmentation-radiomic-feature-generator/23457 "2022-05-17T13:47:21Z")

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Sir Im trying segmentation on 2d images but im not able to get the output table of radiomic feature generator.can you please guide me

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## [vmtksurfaceconnector](https://discourse.slicer.org/t/vmtksurfaceconnector/23453)

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**Author:** [@Benny\_Loretoni](https://discourse.slicer.org/u/Benny_Loretoni)\
**Replies:** 0\
**Last updated:** [May 17, 2022, 11:22am UTC](https://discourse.slicer.org/t/vmtksurfaceconnector/23453 "2022-05-17T11:22:26Z")

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I’m not able to run vmtksurfaceconnector due to the fact that more options of our command are “unknown” such as: -keepfirstsurface -keepsecondsurface –preventmanyonsameside did someone had the same problem? how to so…

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## [2022.05.03 - No weekly meeting](https://discourse.slicer.org/t/2022-05-03-no-weekly-meeting/23260)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [May 3, 2022, 12:21pm UTC](https://discourse.slicer.org/t/2022-05-03-no-weekly-meeting/23260 "2022-05-03T12:21:42Z")

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Hi all, There will be no developer meeting today, as we will be having the first project week Prep meeting. Scheduling of the developer meeting during the Project Week Prep period will be discussed at that time. See p…

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## [Project Week Prep meeting starts today!](https://discourse.slicer.org/t/project-week-prep-meeting-starts-today/23259)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [May 3, 2022, 12:19pm UTC](https://discourse.slicer.org/t/project-week-prep-meeting-starts-today/23259 "2022-05-03T12:19:07Z")

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Dear members of the Project Week community, We are happy to announce the beginning of preparation meetings for the next project week (June 27- July 1st, 2022). Weekly meetings will start on May 3rd, 2022 (10 am Boston t…

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## [Total number of radiomics features](https://discourse.slicer.org/t/total-number-of-radiomics-features/17947)

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**Author:** [@Chenglin\_Zhu](https://discourse.slicer.org/u/Chenglin_Zhu)\
**Replies:** 4\
**Last updated:** [May 3, 2022, 7:42am UTC](https://discourse.slicer.org/t/total-number-of-radiomics-features/17947 "2022-05-03T07:42:44Z")

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Hello Slicer Community! In Radiomics of Slicer, the maximum number of radiomic features is 130, which is mostly consistent with the number of features specified in the documentation of Pyradiomics (Radiomic Features — p…

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## [Reproducibility of Radiomics Results with Pyradiomics and Parenchymal Analysis](https://discourse.slicer.org/t/reproducibility-of-radiomics-results-with-pyradiomics-and-parenchymal-analysis/22933)

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**Author:** [@chuawm](https://discourse.slicer.org/u/chuawm)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:40am UTC](https://discourse.slicer.org/t/reproducibility-of-radiomics-results-with-pyradiomics-and-parenchymal-analysis/22933 "2022-05-03T07:40:55Z")

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Hi there, I am trying to see if the Radiomics module analysis for the lung segmentation I performed using CIP is consistent with that derived from Parenchymal Analysis. This is partly because the Parenchymal Analysis is…

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## [features extract with .png image](https://discourse.slicer.org/t/features-extract-with-png-image/23049)

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**Author:** [@JY\_C](https://discourse.slicer.org/u/JY_C)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:34am UTC](https://discourse.slicer.org/t/features-extract-with-png-image/23049 "2022-05-03T07:34:35Z")

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I want to extract features with HE image, and I save the tiles with .png file. Here is my code: image = sitk.ReadImage(‘test.png’) # dim=(1024, 1024, 3) mask\_arr = np.ones(image.GetSize()\[::-1\]) mask = sitk.GetImageFr…

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## [Many 0 and 1 appear in the extracted features](https://discourse.slicer.org/t/many-0-and-1-appear-in-the-extracted-features/23172)

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**Author:** [@lrc\_09](https://discourse.slicer.org/u/lrc_09)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:24am UTC](https://discourse.slicer.org/t/many-0-and-1-appear-in-the-extracted-features/23172 "2022-05-03T07:24:43Z")

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Hi, I used Radiomics module to extract PET image features. I set resampled voxel size to 1,1,1 and bin width to 64 based on the literatures , and the result shows that there are many 0 and 1 in GLCM, GLDM, GLRLM, GLSZM …

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## [image artifacts and example data files](https://discourse.slicer.org/t/image-artifacts-and-example-data-files/23233)

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**Author:** [@ZUSV5EHlK7](https://discourse.slicer.org/u/ZUSV5EHlK7)\
**Replies:** 1\
**Last updated:** [May 2, 2022, 4:41pm UTC](https://discourse.slicer.org/t/image-artifacts-and-example-data-files/23233 "2022-05-02T16:41:05Z")

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For my master thesis I am researching ways to reduce image artifacts in direct volume rendering. Perhaps you know some conventional approaches that are used in slicing. Furthermore I am searching some example data sets…

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## [About CT slices](https://discourse.slicer.org/t/about-ct-slices/23236)

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**Author:** [@zhiyuan](https://discourse.slicer.org/u/zhiyuan)\
**Replies:** 2\
**Last updated:** [May 2, 2022, 2:23pm UTC](https://discourse.slicer.org/t/about-ct-slices/23236 "2022-05-02T14:23:42Z")

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I have a question, that is, medical CT images are slice images, and the shooting interval is uncertain. How does slicer software fit these slice images into three-dimensional models, and there will be an interval between…

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## [ running vmtklevelsetsegmentation results in fallback error](https://discourse.slicer.org/t/running-vmtklevelsetsegmentation-results-in-fallback-error/23215)

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**Author:** [@alice-hsu](https://discourse.slicer.org/u/alice-hsu)\
**Replies:** 0\
**Last updated:** [May 1, 2022, 12:01pm UTC](https://discourse.slicer.org/t/running-vmtklevelsetsegmentation-results-in-fallback-error/23215 "2022-05-01T12:01:58Z")

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When I try to run vmtklevelsetsegmentation, I receive a black screen and fallback errors, which I believe is due to depreciation of OpenGL on Mac OS 12. Not sure if this is the right direction, but I would appreciate any…

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## [Creating smooth flow extensions](https://discourse.slicer.org/t/creating-smooth-flow-extensions/23197)

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**Author:** [@JuliaW](https://discourse.slicer.org/u/JuliaW)\
**Replies:** 1\
**Last updated:** [April 29, 2022, 4:38pm UTC](https://discourse.slicer.org/t/creating-smooth-flow-extensions/23197 "2022-04-29T16:38:02Z")

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Dear vmtk community, Currently, I am preparing a segmented aorta for flow analysis. Using vmtk I have cut open the surface and added flow extensions. However, at opening of the aorta, the transition between the flow e…

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## [2022.04.25 Weekly Meeting](https://discourse.slicer.org/t/2022-04-25-weekly-meeting/23119)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [April 25, 2022, 10:03pm UTC](https://discourse.slicer.org/t/2022-04-25-weekly-meeting/23119 "2022-04-25T22:03:00Z")

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Tomorrow, we will be having our next weekly hangout at 10:00 AM ET until 11 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Please po…

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## [Pyradiomics extension](https://discourse.slicer.org/t/pyradiomics-extension/23089)

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**Author:** [@Ywatana29](https://discourse.slicer.org/u/Ywatana29)\
**Replies:** 2\
**Last updated:** [April 23, 2022, 6:32pm UTC](https://discourse.slicer.org/t/pyradiomics-extension/23089 "2022-04-23T18:32:51Z")

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I have noticed the following message at Radiomics. Is it correct. It must be because I cannot find Slicer Radiomics in the extension manager currently. Pending resolution of packaging issues, SlicerRadiomics is not curr…

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## [Title: 2022.04.19 Weekly Meeting](https://discourse.slicer.org/t/title-2022-04-19-weekly-meeting/23005)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [April 19, 2022, 12:59pm UTC](https://discourse.slicer.org/t/title-2022-04-19-weekly-meeting/23005 "2022-04-19T12:59:03Z")

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Tomorrow, we will be having our next weekly hangout at 10:00 AM ET until 11 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Please po…

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## [ITK Examples Hackathon 2022](https://discourse.slicer.org/t/itk-examples-hackathon-2022/22967)

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**Author:** [@tom.birdsong](https://discourse.slicer.org/u/tom.birdsong)\
**Replies:** 0\
**Last updated:** [April 14, 2022, 4:14pm UTC](https://discourse.slicer.org/t/itk-examples-hackathon-2022/22967 "2022-04-14T16:14:09Z")

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The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Documentation for the toolkit ranges from the ITK Software Guide textbook…

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## [myvmtkmeshDlabeling](https://discourse.slicer.org/t/myvmtkmeshdlabeling/22959)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 2\
**Last updated:** [April 14, 2022, 5:51pm UTC](https://discourse.slicer.org/t/myvmtkmeshdlabeling/22959 "2022-04-14T17:51:20Z")

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I’m working with macOS operating system on mac with M1 processor. I’m having problems in order to obtain a meshDxx.vtu (starting from 2 files meshR.vtu and Dxx.mhd) which associates the values of the tensor built in Dxx…

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## [Problem with myvmtkmeshDlabeling](https://discourse.slicer.org/t/problem-with-myvmtkmeshdlabeling/22953)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 0\
**Last updated:** [April 13, 2022, 10:09pm UTC](https://discourse.slicer.org/t/problem-with-myvmtkmeshdlabeling/22953 "2022-04-13T22:09:08Z")

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I’m working with macOS operating system on mac with M1 processor. I’m having problems in order to obtain a meshDxx.vtu (starting from 2 files meshR.vtu and Dxx.mhd) which associates the values of the tensor built in Dxx…

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## [slicerMorph - ALPACA registration error in open3d](https://discourse.slicer.org/t/slicermorph-alpaca-registration-error-in-open3d/22908)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 5\
**Last updated:** [April 13, 2022, 1:53pm UTC](https://discourse.slicer.org/t/slicermorph-alpaca-registration-error-in-open3d/22908 "2022-04-13T13:53:04Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 r29738 / 7a593c8 Expected behavior: I am trying to redo an example of the SlicerMORPH workshop (S\_2020/README.md at master · SlicerMorph/S\_2020 · GitHub). Dat…

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## [How to find a default colorbar unit or calibrate in mm](https://discourse.slicer.org/t/how-to-find-a-default-colorbar-unit-or-calibrate-in-mm/22501)

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**Author:** [@Lexus\_H](https://discourse.slicer.org/u/Lexus_H)\
**Replies:** 24\
**Last updated:** [April 12, 2022, 3:03am UTC](https://discourse.slicer.org/t/how-to-find-a-default-colorbar-unit-or-calibrate-in-mm/22501 "2022-04-12T03:03:12Z")

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Hi, I have been able to colormap surface difference with ranges from -5 to 0 then differences from model 1 to model 2 ranging from 3mm to 9mm so I am wondering if the color bar ranges or values are based on mm or whatev…

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## [2022.04.12 Weekly Meeting](https://discourse.slicer.org/t/2022-04-12-weekly-meeting/22914)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [April 11, 2022, 8:43pm UTC](https://discourse.slicer.org/t/2022-04-12-weekly-meeting/22914 "2022-04-11T20:43:29Z")

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Tomorrow, we will be having our next weekly hangout at 10:00 AM ET until 11 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Please po…

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## [I can't achieve five lobe segmentation with interactive lobe segmentation in CIP, can someone help me?](https://discourse.slicer.org/t/i-cant-achieve-five-lobe-segmentation-with-interactive-lobe-segmentation-in-cip-can-someone-help-me/13113)

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**Author:** [@ava\_yektaeian](https://discourse.slicer.org/u/ava_yektaeian)\
**Replies:** 9\
**Last updated:** [April 10, 2022, 6:19pm UTC](https://discourse.slicer.org/t/i-cant-achieve-five-lobe-segmentation-with-interactive-lobe-segmentation-in-cip-can-someone-help-me/13113 "2022-04-10T18:19:10Z")

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I completely follow the the interactive lobe segmentation in slicer but most of the time I can’t achieve the lobe segmentation can some one give tips?

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## [Dental models superimposition](https://discourse.slicer.org/t/dental-models-superimposition/6374)

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**Author:** [@sara](https://discourse.slicer.org/u/sara)\
**Replies:** 2\
**Last updated:** [April 9, 2022, 6:29pm UTC](https://discourse.slicer.org/t/dental-models-superimposition/6374 "2022-04-09T18:29:05Z")

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Operating system: Slicer version: Slicer 3D CMF 4.0 Expected behavior: Actual behavior: I used model to model distance to superimpose dental models. How does the software superimpose them? Are there multiple landmark…

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## [2022.04.05 Weekly Meeting](https://discourse.slicer.org/t/2022-04-05-weekly-meeting/22833)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [April 5, 2022, 11:16am UTC](https://discourse.slicer.org/t/2022-04-05-weekly-meeting/22833 "2022-04-05T11:16:36Z")

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Today we will be having our next weekly hangout at 10:00 AM ET until 11 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Please post t…

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## [Boundary point of a cross-section ](https://discourse.slicer.org/t/boundary-point-of-a-cross-section/22719)

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**Author:** [@Dongwei1](https://discourse.slicer.org/u/Dongwei1)\
**Replies:** 2\
**Last updated:** [March 31, 2022, 11:32am UTC](https://discourse.slicer.org/t/boundary-point-of-a-cross-section/22719 "2022-03-31T11:32:03Z")

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Hi all, I am currently using vmtk to compute the centerline and cross-section of the vessel. I do aware that vmtkcenterlinesections can help me calculate the area of the cross-section perpendicular to the centerline, bu…

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## [2022.03.29 Weekly Meeting](https://discourse.slicer.org/t/2022-03-29-weekly-meeting/22737)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [March 28, 2022, 8:42pm UTC](https://discourse.slicer.org/t/2022-03-29-weekly-meeting/22737 "2022-03-28T20:42:18Z")

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Tomorrow, we will be having our next weekly hangout at 10:00 AM ET until 11 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 extensions finaliza…

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## [SPHARM-PDM: Different morphology from a model maker and SPHARM](https://discourse.slicer.org/t/spharm-pdm-different-morphology-from-a-model-maker-and-spharm/22711)

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**Author:** [@Bryan\_Jung](https://discourse.slicer.org/u/Bryan_Jung)\
**Replies:** 2\
**Last updated:** [March 28, 2022, 5:01pm UTC](https://discourse.slicer.org/t/spharm-pdm-different-morphology-from-a-model-maker-and-spharm/22711 "2022-03-28T17:01:38Z")

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Dear Slicer community, I am teaching myself how to use SPHARM-PDM for my future research projects. I have been using publicly available CBCT images. Recently, I successfully segmented a TMJ from a CBCT file using ITK-Sn…

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## [DTI Statistics for a specific ROI of a fiber?](https://discourse.slicer.org/t/dti-statistics-for-a-specific-roi-of-a-fiber/10385)

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**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\
**Replies:** 4\
**Last updated:** [March 28, 2022, 8:35am UTC](https://discourse.slicer.org/t/dti-statistics-for-a-specific-roi-of-a-fiber/10385 "2022-03-28T08:35:47Z")

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Hi all, I generated my fiber tracts using interactive markup. I would like to generate statistics based on a specific region of these tracts. Is there a way I can do this? Many thanks,

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