# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=29

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

**Page:** 30

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## [Image and Mask origin mismatch](https://discourse.slicer.org/t/image-and-mask-origin-mismatch/19781)

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**Author:** [@Tanvi\_Vinay\_Kulkarni](https://discourse.slicer.org/u/Tanvi_Vinay_Kulkarni)\
**Replies:** 1\
**Last updated:** [September 21, 2021, 12:04pm UTC](https://discourse.slicer.org/t/image-and-mask-origin-mismatch/19781 "2021-09-21T12:04:21Z")

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While extracting pyradiomics features, my image and mask have the same spacing and size but the origins are off by a few millimeters. Feature extraction shows the below error Will increasing the tolerance in the sett…

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## [Can't start new Slicer](https://discourse.slicer.org/t/cant-start-new-slicer/19763)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 2\
**Last updated:** [September 20, 2021, 4:07pm UTC](https://discourse.slicer.org/t/cant-start-new-slicer/19763 "2021-09-20T16:07:58Z")

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Current version 4.13 0918 win7 64 what‘s wrong with my computer? The version 4.11 0226 can run normally.

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## [vtkvmtkCenterlineBranchExtractorfunction bug](https://discourse.slicer.org/t/vtkvmtkcenterlinebranchextractorfunction-bug/19761)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 0\
**Last updated:** [September 20, 2021, 2:44pm UTC](https://discourse.slicer.org/t/vtkvmtkcenterlinebranchextractorfunction-bug/19761 "2021-09-20T14:44:53Z")

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hi, i use vtkvmtkCenterlineBranchExtractor to calculate branch centerline,but i find there have bug that is the number of points is different the last offset value and i don’t use the function i can get the same numb…

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## [2021.09.14 Weekly Meeting](https://discourse.slicer.org/t/2021-09-14-weekly-meeting/19651)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [September 14, 2021, 4:46am UTC](https://discourse.slicer.org/t/2021-09-14-weekly-meeting/19651 "2021-09-14T04:46:35Z")

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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: Extension manager status Sl…

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## [Add CFD simulation Model in next VMTK Version?](https://discourse.slicer.org/t/add-cfd-simulation-model-in-next-vmtk-version/19602)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 2\
**Last updated:** [September 14, 2021, 2:53am UTC](https://discourse.slicer.org/t/add-cfd-simulation-model-in-next-vmtk-version/19602 "2021-09-14T02:53:20Z")

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hi,i find SimVascular CFD simulation tool from here https://simvascular.github.io/,the solver is svSolver,is there planning to add CFD model in next VMTK Version? thank you

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## [Build and release VMTK via GitHub Actions](https://discourse.slicer.org/t/build-and-release-vmtk-via-github-actions/19574)

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**Author:** [@rupertnash](https://discourse.slicer.org/u/rupertnash)\
**Replies:** 4\
**Last updated:** [September 10, 2021, 9:17am UTC](https://discourse.slicer.org/t/build-and-release-vmtk-via-github-actions/19574 "2021-09-10T09:17:29Z")

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For $reasons I need VMTK available for multiple versions of python. So I created a simple Github workflow to build VTK, ITK, and VMTK and bundle up the binaries. This is here: https://github.com/hemelb-codes/vmtk-build …

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## [Construction of a verticle plane for measurement of canine movement](https://discourse.slicer.org/t/construction-of-a-verticle-plane-for-measurement-of-canine-movement/19575)

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**Author:** [@Nikhil\_Jain](https://discourse.slicer.org/u/Nikhil_Jain)\
**Replies:** 1\
**Last updated:** [September 8, 2021, 3:01pm UTC](https://discourse.slicer.org/t/construction-of-a-verticle-plane-for-measurement-of-canine-movement/19575 "2021-09-08T15:01:55Z")

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Operating system:win 10 Slicer version:4.11 Expected behavior: Actual behavior: To measure the movement of canines on maxillary superimposed models, I want to project the two cusp points to the sagittal plane that is…

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## [Cannot obtain the center line.](https://discourse.slicer.org/t/cannot-obtain-the-center-line/18112)

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**Author:** [@zhang-qiang-github](https://discourse.slicer.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:11pm UTC](https://discourse.slicer.org/t/cannot-obtain-the-center-line/18112 "2021-09-07T19:11:07Z")

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I have two arteries, like: I can obtain the centerline for one artery, but fail for the other one. It failed to obtain the centerline between the two red point. The runni…

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## [Convert points markups to open curves](https://discourse.slicer.org/t/convert-points-markups-to-open-curves/19547)

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**Author:** [@Ale](https://discourse.slicer.org/u/Ale)\
**Replies:** 3\
**Last updated:** [September 7, 2021, 6:24pm UTC](https://discourse.slicer.org/t/convert-points-markups-to-open-curves/19547 "2021-09-07T18:24:15Z")

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Hi all, I’m using Slicer and Slicermorph to place landmarks and semilandmarks (open curves) into mammalian skulls. I’m testing ALPACA to transfer point configuration to others skulls. I have two open curves describing zy…

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## [2021.09.07 Weekly Meeting](https://discourse.slicer.org/t/2021-09-07-weekly-meeting/19548)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [September 7, 2021, 2:52pm UTC](https://discourse.slicer.org/t/2021-09-07-weekly-meeting/19548 "2021-09-07T14:52:35Z")

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Today, we had our weekly hangout at 10:00 AM ET until 11 AM ET (https://bit.ly/slicer-googlemeet-hosted-by-kitware ) Notes: Discussed status of extensions manager transition: Will deploy a “legacy bridge” allowing ol…

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## [Recommendations for segmenting internal cavities ](https://discourse.slicer.org/t/recommendations-for-segmenting-internal-cavities/19505)

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**Author:** [@Ale](https://discourse.slicer.org/u/Ale)\
**Replies:** 1\
**Last updated:** [September 3, 2021, 9:32pm UTC](https://discourse.slicer.org/t/recommendations-for-segmenting-internal-cavities/19505 "2021-09-03T21:32:19Z")

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Hi, I’m working with a microCT of bone osteoderms. I need to segment internal cavities and external compact bone. I started with threshold tool to segment compact bone and went successful. But the internal cavities is a …

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## [Can't change the model's color](https://discourse.slicer.org/t/cant-change-the-models-color/19398)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 3\
**Last updated:** [August 31, 2021, 4:09am UTC](https://discourse.slicer.org/t/cant-change-the-models-color/19398 "2021-08-31T04:09:44Z")

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4.11 win64 As is shown in this video when I assign the color to the parent file，then I can’t change the color of sub models. Is this a Bug? Maybe the file,Segmentation-models,shoud’t have the color attributes …

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## [Mapping and Patching result have inanition](https://discourse.slicer.org/t/mapping-and-patching-result-have-inanition/18988)

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**Author:** [@junqiangchen](https://discourse.slicer.org/u/junqiangchen)\
**Replies:** 2\
**Last updated:** [August 31, 2021, 1:17am UTC](https://discourse.slicer.org/t/mapping-and-patching-result-have-inanition/18988 "2021-08-31T01:17:05Z")

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hi,i follow the example of An example: WSS and OSI along a branching vascular district from here:http://www.vmtk.org/tutorials/MappingAndPatching.html,i set params -longitudinalpatchsize 0.5 -circularpatches 12,but the r…

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## [2021.08.31 Weekly Meeting](https://discourse.slicer.org/t/2021-08-31-weekly-meeting/19413)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 3\
**Last updated:** [August 30, 2021, 7:19pm UTC](https://discourse.slicer.org/t/2021-08-31-weekly-meeting/19413 "2021-08-30T19:19:58Z")

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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: Extension manager status Bu…

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## [Failed to load VMTK libraries in Vesselness Filtering](https://discourse.slicer.org/t/failed-to-load-vmtk-libraries-in-vesselness-filtering/19367)

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**Author:** [@simone](https://discourse.slicer.org/u/simone)\
**Replies:** 1\
**Last updated:** [August 27, 2021, 1:36am UTC](https://discourse.slicer.org/t/failed-to-load-vmtk-libraries-in-vesselness-filtering/19367 "2021-08-27T01:36:29Z")

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Hi, I am using Slicer 4.11.20210226 on macOS 11.5. I am trying to use Vesselness Filtering but I get the error above. This is the full log: \[DEBUG\]\[Qt\] 26.08.2021 11:07:13 \[\] (unknown:0) - Session start time …: 2021-08-…

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## [Use segmentation from Segment Editor as initialization for Level Set Segmentation](https://discourse.slicer.org/t/use-segmentation-from-segment-editor-as-initialization-for-level-set-segmentation/19329)

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**Author:** [@tossin](https://discourse.slicer.org/u/tossin)\
**Replies:** 2\
**Last updated:** [August 25, 2021, 3:08pm UTC](https://discourse.slicer.org/t/use-segmentation-from-segment-editor-as-initialization-for-level-set-segmentation/19329 "2021-08-25T15:08:54Z")

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From what I can tell, the Level Set Segmentation panel from the Slicer VMTK Extension only allows initialization from scratch using colliding fronts or fast marching. However, I’d like to be able to use Level Set Segmen…

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## [2021.08.24 Weekly Meeting](https://discourse.slicer.org/t/2021-08-24-weekly-meeting/19327)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [August 23, 2021, 6:37pm UTC](https://discourse.slicer.org/t/2021-08-24-weekly-meeting/19327 "2021-08-23T18:37:53Z")

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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: Extension manager transitio…

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## [How do extract GLRLM features from a single .jpg image](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-single-jpg-image/15473)

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**Author:** [@Mohiuddin](https://discourse.slicer.org/u/Mohiuddin)\
**Replies:** 1\
**Last updated:** [March 9, 2021, 12:39pm UTC](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-single-jpg-image/15473 "2021-03-09T12:39:30Z")

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Operating system: Windows Slicer version: Expected behavior: Actual behavior: I am a learner and want to generate Gray Level Run Length Matrix features for a .jpg image. I am reading an image via opencv but could not…

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## [Extract features using segment generated labelmap](https://discourse.slicer.org/t/extract-features-using-segment-generated-labelmap/19188)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 3\
**Last updated:** [August 17, 2021, 8:02pm UTC](https://discourse.slicer.org/t/extract-features-using-segment-generated-labelmap/19188 "2021-08-17T20:02:11Z")

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Hi all, In Slicer, I have segment done on CT images, but registration for CT and MRI is not good (these two are too far away). So I manually transform MRI to align with CT and harden the transform. Then, generate labelm…

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## [Title: 2021.08.17 Weekly Meeting](https://discourse.slicer.org/t/title-2021-08-17-weekly-meeting/19219)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [August 17, 2021, 12:33am UTC](https://discourse.slicer.org/t/title-2021-08-17-weekly-meeting/19219 "2021-08-17T00:33:57Z")

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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: Extension manager switch ov…

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## [Radiomics error - No module named ‘pywt’](https://discourse.slicer.org/t/radiomics-error-no-module-named-pywt/19128)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 8\
**Last updated:** [August 12, 2021, 7:11pm UTC](https://discourse.slicer.org/t/radiomics-error-no-module-named-pywt/19128 "2021-08-12T19:11:22Z")

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Another question: I am trying to from radiomics import getFeatureClasses, but got the error " No module named ‘pywt’ ". I fixed the problem using the code mentioned here Slicer Radiomics error - #3 by fedorov , and @fed…

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## [Is there a way to segment stenotic coronary arteries?](https://discourse.slicer.org/t/is-there-a-way-to-segment-stenotic-coronary-arteries/19142)

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**Author:** [@Mattia\_Chiesa](https://discourse.slicer.org/u/Mattia_Chiesa)\
**Replies:** 3\
**Last updated:** [August 11, 2021, 1:44pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-segment-stenotic-coronary-arteries/19142 "2021-08-11T13:44:28Z")

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Dear all, I’d like to automatically segment the three main coronaries (LCA (LDA+LCX) and RCA) feeding DICOM of stenotic patients into 3D slicer. I followed these 2 VMTK tutorials: https://www.youtube.com/watch?v=yi07m…

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## [What should be included in CMakeLists.txt to start a VMTK C++ project?](https://discourse.slicer.org/t/what-should-be-included-in-cmakelists-txt-to-start-a-vmtk-c-project/18734)

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**Author:** [@frankiole](https://discourse.slicer.org/u/frankiole)\
**Replies:** 1\
**Last updated:** [August 10, 2021, 9:01pm UTC](https://discourse.slicer.org/t/what-should-be-included-in-cmakelists-txt-to-start-a-vmtk-c-project/18734 "2021-08-10T21:01:14Z")

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Hi, I am trying to implement VMTK functions in my C++ code. I am able to run my program using both ITK and VTK libraries, however I cannot access VMTK libraries. I’ve already built VMTK, and I’m tweaking my CMakeLists.t…

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## [2021.08.10 Weekly Meeting](https://discourse.slicer.org/t/2021-08-10-weekly-meeting/19126)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 2\
**Last updated:** [August 10, 2021, 3:08pm UTC](https://discourse.slicer.org/t/2021-08-10-weekly-meeting/19126 "2021-08-10T15:08:34Z")

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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 / Extension manage…

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## [Looking for 3D Slicer Workshop](https://discourse.slicer.org/t/looking-for-3d-slicer-workshop/19115)

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**Author:** [@HAFIZAL](https://discourse.slicer.org/u/HAFIZAL)\
**Replies:** 3\
**Last updated:** [August 10, 2021, 5:52am UTC](https://discourse.slicer.org/t/looking-for-3d-slicer-workshop/19115 "2021-08-10T05:52:41Z")

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Hi there, I wonder is there any 3D slicer workshop that I can attend to improve my knowledge and skills in this software? Thank you.

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## [Voxel-based feature extraction](https://discourse.slicer.org/t/voxel-based-feature-extraction/19060)

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**Author:** [@Sovan\_Mukherjee](https://discourse.slicer.org/u/Sovan_Mukherjee)\
**Replies:** 1\
**Last updated:** [August 4, 2021, 10:54pm UTC](https://discourse.slicer.org/t/voxel-based-feature-extraction/19060 "2021-08-04T22:54:41Z")

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Hi, I am trying to do a voxel-based feature extraction based on a CT pancreas mask. After setting Voxelbased = True, I extracted 88 features. It created 88 nifti images for individual features. While looking at the imag…

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## [2021.07.13 Hangout](https://discourse.slicer.org/t/2021-07-13-hangout/18648)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [August 3, 2021, 2:02pm UTC](https://discourse.slicer.org/t/2021-07-13-hangout/18648 "2021-08-03T14:02:14Z")

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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 Extension manager …

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## [2021.08.03 Weekly Meeting](https://discourse.slicer.org/t/2021-08-03-weekly-meeting/19033)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [August 3, 2021, 12:29pm UTC](https://discourse.slicer.org/t/2021-08-03-weekly-meeting/19033 "2021-08-03T12:29:52Z")

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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 Extension manager a…

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## [AbcissaMetric does not write](https://discourse.slicer.org/t/abcissametric-does-not-write/19012)

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**Author:** [@cborras](https://discourse.slicer.org/u/cborras)\
**Replies:** 0\
**Last updated:** [August 1, 2021, 11:40am UTC](https://discourse.slicer.org/t/abcissametric-does-not-write/19012 "2021-08-01T11:40:50Z")

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Operating system: Windows 10 Hi everybody! I am working on aortas and I am using this command for the writing of the angular and abcissa coordinates: #vmtkbranchmetrics -ifile aorta\_clipped.vtp -centerlinesfile Ht\_Lum\_…

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## [Some questions about SPHARM-PDM, alignment, and registration](https://discourse.slicer.org/t/some-questions-about-spharm-pdm-alignment-and-registration/10499)

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**Author:** [@keven](https://discourse.slicer.org/u/keven)\
**Replies:** 5\
**Last updated:** [July 29, 2021, 8:21am UTC](https://discourse.slicer.org/t/some-questions-about-spharm-pdm-alignment-and-registration/10499 "2021-07-29T08:21:57Z")

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Dear experts : Recently，I read a paper, Clinical application of SPHARM-PDM to quantify temporomandibular joint osteoarthritis, which was published in the Computerized Medical Imaging and Graphics in 2011. This is a bri…

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