# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=35

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

**Page:** 36

---

## [How can I set absolute bound](https://discourse.slicer.org/t/how-can-i-set-absolute-bound/11263)

<div class="topic-metadata">

**Author:** [@codecrazer](https://discourse.slicer.org/u/codecrazer)\
**Replies:** 5\
**Last updated:** [December 9, 2020, 4:01am UTC](https://discourse.slicer.org/t/how-can-i-set-absolute-bound/11263 "2020-12-09T04:01:11Z")

</div>

Dear all, due to some of CT will have maximum Housefield units value more than 3000. Is it possible for me to absolute bound HU before binwith resampling in pyradiomics batch parameter file? Thanks for your help!

---

## [Optical Coherence Tomography (OCT) images](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171)

<div class="topic-metadata">

**Author:** [@syedf](https://discourse.slicer.org/u/syedf)\
**Replies:** 6\
**Last updated:** [December 8, 2020, 2:23am UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171 "2020-12-08T02:23:26Z")

</div>

Hello, I was wondering if VMTK can segment OCT .dcm images. I’ve used VMTK before for MRI/CT dicoms, but when I try it for the OCT file, I get no output. The PypePad executes, but stops after a while. Command: vmtklev…

---

## [2020.12.08 Hangout](https://discourse.slicer.org/t/2020-12-08-hangout/14932)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [December 8, 2020, 3:02am UTC](https://discourse.slicer.org/t/2020-12-08-hangout/14932 "2020-12-08T03:02:30Z")

</div>

Tomorrow, we will be having our next weekly hangout at 11 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 and VTK 9 Progress Feel free to po…

---

## [Project Week 34 Preparatory Videoconferences - Wk 9](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-9/14931)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [December 8, 2020, 3:01am UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-9/14931 "2020-12-08T03:01:30Z")

</div>

From the NA-MIC Project Week mailing list Dear members of the Project Week community, Tomorrow (Tue Dec 8, 10am Boston time) we’ll have our last preparation meeting for Project Week #34. Here’s the link to the zoom ses…

---

## [2020.12.01 Hangout](https://discourse.slicer.org/t/2020-12-01-hangout/14822)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [December 1, 2020, 12:09am UTC](https://discourse.slicer.org/t/2020-12-01-hangout/14822 "2020-12-01T00:09:45Z")

</div>

Tomorrow, we will be having our next weekly hangout at 11:00 AM , immediately after the project week call (https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-8/14821) Anyone is welcome to joi…

---

## [Project Week 34 Preparatory Videoconferences - Wk 8](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-8/14821)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [November 30, 2020, 11:08pm UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-8/14821 "2020-11-30T23:08:34Z")

</div>

From the NA-MIC Project Week mailing list Dear members of the Project Week community, Tomorrow (Tue Dec 1, 10am Boston time) we’ll have our next preparation meeting for Project Week #34. Here’s the link to the zoom ses…

---

## [Normalization question](https://discourse.slicer.org/t/normalization-question/14759)

<div class="topic-metadata">

**Author:** [@mcastro](https://discourse.slicer.org/u/mcastro)\
**Replies:** 1\
**Last updated:** [November 26, 2020, 4:52pm UTC](https://discourse.slicer.org/t/normalization-question/14759 "2020-11-26T16:52:28Z")

</div>

I am performing 3D organ-based radiomics analysis and I have a few questions about normalization. Let’s call: A the original image Bj the image where the organ was masked and the background was set to a value j Bk th…

---

## [Vmtkcenterlines -seedselector pointlist problem](https://discourse.slicer.org/t/vmtkcenterlines-seedselector-pointlist-problem/14744)

<div class="topic-metadata">

**Author:** [@Haim\_Ezer](https://discourse.slicer.org/u/Haim_Ezer)\
**Replies:** 2\
**Last updated:** [November 26, 2020, 5:47am UTC](https://discourse.slicer.org/t/vmtkcenterlines-seedselector-pointlist-problem/14744 "2020-11-26T05:47:12Z")

</div>

Hello, Luca, Everyone, vmtkcenterlines.py -ifile “Case1.vtk” -seedselector pointlist -sourcepoints 0.00571137 -0.01748690 -0.02422070 -targetpoints 0.00571797 -0.00042939 -0.02172360 But what I get is this: Traceback …

---

## [How to add color to my surface in VMTK](https://discourse.slicer.org/t/how-to-add-color-to-my-surface-in-vmtk/14767)

<div class="topic-metadata">

**Author:** [@13552060266](https://discourse.slicer.org/u/13552060266)\
**Replies:** 1\
**Last updated:** [November 25, 2020, 8:19pm UTC](https://discourse.slicer.org/t/how-to-add-color-to-my-surface-in-vmtk/14767 "2020-11-25T20:19:26Z")

</div>

Operating system:VMTK Slicer version:1.4 Expected behavior: Actual behavior: I want to add color to my surface in VMTK. Does anyone know how to do it? It’s better to write the pypepad command. I’m very impressed.

---

## [2020.11.24 Hangout](https://discourse.slicer.org/t/2020-11-24-hangout/14750)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [November 24, 2020, 4:09pm UTC](https://discourse.slicer.org/t/2020-11-24-hangout/14750 "2020-11-24T16:09:03Z")

</div>

Hi all: Tomorrow, we will be having our next weekly hangout at 11 AM, immediately after the Project Week prep call . We will be using the same Zoom link as the PW call: this link Agenda: Slicer 5/ VTK 9 progress F…

---

## [Where can I get the trial VMTKLab?](https://discourse.slicer.org/t/where-can-i-get-the-trial-vmtklab/14658)

<div class="topic-metadata">

**Author:** [@Yang\_Yu](https://discourse.slicer.org/u/Yang_Yu)\
**Replies:** 3\
**Last updated:** [November 24, 2020, 7:36am UTC](https://discourse.slicer.org/t/where-can-i-get-the-trial-vmtklab/14658 "2020-11-24T07:36:14Z")

</div>

I want to play with VMTKLab to see whether it can satisfy my need,. Where can I have a try version?

---

## [Project Week 34 Preparatory Videoconferences - Wk 7](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-7/14749)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [November 23, 2020, 9:03pm UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-7/14749 "2020-11-23T21:03:53Z")

</div>

From the NA-MIC Project Week mailing list Dear members of the Project Week community, Tomorrow (Tue Nov 24, 10am Boston time) we’ll have our next preparation meeting for Project Week #34. Here’s the link to the zoom se…

---

## [Voxel extraction , Calculation of GLSZM Failed](https://discourse.slicer.org/t/voxel-extraction-calculation-of-glszm-failed/14225)

<div class="topic-metadata">

**Author:** [@Alessio\_Romita](https://discourse.slicer.org/u/Alessio_Romita)\
**Replies:** 2\
**Last updated:** [November 20, 2020, 4:32pm UTC](https://discourse.slicer.org/t/voxel-extraction-calculation-of-glszm-failed/14225 "2020-11-20T16:32:39Z")

</div>

Hi everyone , I’m trying to calculate the value of Glszm feature using voxel based extraction. But I got this erro :IndexError: Calculation of GLSZM Failed. The setting used are : voxelSetting: kernelRadius: 2 mask…

---

## [Tracking how the values in GLCM, GLSZM matrices are populated](https://discourse.slicer.org/t/tracking-how-the-values-in-glcm-glszm-matrices-are-populated/13808)

<div class="topic-metadata">

**Author:** [@Ankita\_Singh](https://discourse.slicer.org/u/Ankita_Singh)\
**Replies:** 6\
**Last updated:** [November 18, 2020, 6:56pm UTC](https://discourse.slicer.org/t/tracking-how-the-values-in-glcm-glszm-matrices-are-populated/13808 "2020-11-18T18:56:31Z")

</div>

Hello, I am interested in understanding how the values in GLCM and GLSZM are computed for each gray level. I know that there are C++ functions calculate\_glcm and calculate\_glszm that compute these matrices. Using these …

---

## [Display image/mask pair after mask correction?](https://discourse.slicer.org/t/display-image-mask-pair-after-mask-correction/14649)

<div class="topic-metadata">

**Author:** [@Cody\_Keller](https://discourse.slicer.org/u/Cody_Keller)\
**Replies:** 1\
**Last updated:** [November 18, 2020, 6:48pm UTC](https://discourse.slicer.org/t/display-image-mask-pair-after-mask-correction/14649 "2020-11-18T18:48:23Z")

</div>

Operating system: Windows10 64-bit Slicer version: 4.11.0 Hello, I’ve been working through some bugs in feature extraction with a data set of image/mask pairs that are pretty heterogenous in terms of size and file typ…

---

## [Output in different order ar eat execution](https://discourse.slicer.org/t/output-in-different-order-ar-eat-execution/12447)

<div class="topic-metadata">

**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 4\
**Last updated:** [November 18, 2020, 5:21pm UTC](https://discourse.slicer.org/t/output-in-different-order-ar-eat-execution/12447 "2020-11-18T17:21:51Z")

</div>

The output (features extracted and values) come in a random order every time I execute (in this Post). It use to work well but I do not know what happened that it is now random. Any thoughts?

---

## [How to access/get to the scale space particles system?](https://discourse.slicer.org/t/how-to-access-get-to-the-scale-space-particles-system/13675)

<div class="topic-metadata">

**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 6\
**Last updated:** [November 18, 2020, 2:12pm UTC](https://discourse.slicer.org/t/how-to-access-get-to-the-scale-space-particles-system/13675 "2020-11-18T14:12:04Z")

</div>

Hello Dear Developers and Users Excuse me for asking this question again. I asked this question in 3Dslicer Support but did not receive any answer or guidance. How can I access the scale space particles ? I found out …

---

## [2020.11.16 Hangout - 10 am start time](https://discourse.slicer.org/t/2020-11-16-hangout-10-am-start-time/14652)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [November 17, 2020, 3:14pm UTC](https://discourse.slicer.org/t/2020-11-16-hangout-10-am-start-time/14652 "2020-11-17T15:14:15Z")

</div>

Hi all: Tomorrow, we will be having our next weekly hangout at 10 AM, immediately after the Project Week prep call . We will be using the same Zoom link as the PW call: this link Agenda: Slicer 5/ VTK 9 progress Py…

---

## [Project Week 34 Preparatory Videoconferences - Wk 6 \*9 am start time\*](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-6-9-am-start-time/14651)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [November 17, 2020, 12:45am UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-6-9-am-start-time/14651 "2020-11-17T00:45:53Z")

</div>

From the NA-MIC Project Week mailing list Dear members of the Project Week community, Tomorrow (Tue Nov 17, 9am Boston time) we’ll have our next preparation meeting for Project Week #34. Here’s the link to the zoom ses…

---

## [Airway parameter calculation](https://discourse.slicer.org/t/airway-parameter-calculation/14623)

<div class="topic-metadata">

**Author:** [@1119](https://discourse.slicer.org/u/1119)\
**Replies:** 1\
**Last updated:** [November 16, 2020, 1:43am UTC](https://discourse.slicer.org/t/airway-parameter-calculation/14623 "2020-11-16T01:43:13Z")

</div>

In the CIP module, select the airwayinspector to calculate the relevant parameters. After selecting the location, the calculation result cannot be generated

---

## [Error when generate centerline wih my own fbx.](https://discourse.slicer.org/t/error-when-generate-centerline-wih-my-own-fbx/14564)

<div class="topic-metadata">

**Author:** [@Yang\_Yu](https://discourse.slicer.org/u/Yang_Yu)\
**Replies:** 2\
**Last updated:** [November 13, 2020, 1:15am UTC](https://discourse.slicer.org/t/error-when-generate-centerline-wih-my-own-fbx/14564 "2020-11-13T01:15:33Z")

</div>

I converted the fbx to obj, then used the ParaView software to convert obj to vtp file, then used VMTK like above, but no matter which fbx I chose, the above error always occured . Why is that?

---

## [How does vmtksurfacecenterlineprojection work](https://discourse.slicer.org/t/how-does-vmtksurfacecenterlineprojection-work/14513)

<div class="topic-metadata">

**Author:** [@Nadun\_19](https://discourse.slicer.org/u/Nadun_19)\
**Replies:** 1\
**Last updated:** [November 13, 2020, 12:28am UTC](https://discourse.slicer.org/t/how-does-vmtksurfacecenterlineprojection-work/14513 "2020-11-13T00:28:52Z")

</div>

Hi I was wondering how the vmtksurfacecenterlineprojection function actually carries out the centerline projection to a surface. Thanks Nadun

---

## [Group comparison with shape regression ](https://discourse.slicer.org/t/group-comparison-with-shape-regression/14561)

<div class="topic-metadata">

**Author:** [@orangekic](https://discourse.slicer.org/u/orangekic)\
**Replies:** 0\
**Last updated:** [November 12, 2020, 12:35pm UTC](https://discourse.slicer.org/t/group-comparison-with-shape-regression/14561 "2020-11-12T12:35:59Z")

</div>

I want to perform a statistical group comparison with shape regression. Is there any tutorial regarding this analysis? Which module should I use (“GROUP” or “Shape Regression”)? Thank you very much.

---

## [Model alignment ](https://discourse.slicer.org/t/model-alignment/14527)

<div class="topic-metadata">

**Author:** [@had\_al-a](https://discourse.slicer.org/u/had_al-a)\
**Replies:** 5\
**Last updated:** [November 11, 2020, 11:22am UTC](https://discourse.slicer.org/t/model-alignment/14527 "2020-11-11T11:22:14Z")

</div>

I’m an orthodontic postgraduate student. I’m trying to superimpose “align” 2 models and do some 3d measurements. Every time I use the CMF, I chose the points for alignment and then change their radius for ROI and choose …

---

## [Slicer Radiomics error ](https://discourse.slicer.org/t/slicer-radiomics-error/14279)

<div class="topic-metadata">

**Author:** [@ngillingham](https://discourse.slicer.org/u/ngillingham)\
**Replies:** 4\
**Last updated:** [November 10, 2020, 7:47pm UTC](https://discourse.slicer.org/t/slicer-radiomics-error/14279 "2020-11-10T19:47:00Z")

</div>

Hello, I’ve run into the following error with both nightly and stable releases of Slicer, on a Mac. Same error when I tried at work, on Windows, with both nightly and stable release, although I’m not able to poke around …

---

## [LBP and KNN i need help](https://discourse.slicer.org/t/lbp-and-knn-i-need-help/14525)

<div class="topic-metadata">

**Author:** [@Jhonatan\_Ferreira](https://discourse.slicer.org/u/Jhonatan_Ferreira)\
**Replies:** 0\
**Last updated:** [November 10, 2020, 7:18pm UTC](https://discourse.slicer.org/t/lbp-and-knn-i-need-help/14525 "2020-11-10T19:18:55Z")

</div>

hello, I need help with LBP and KNN to do machine learning anyone can help me ??

---

## [Project Week 34 Preparatory Videoconferences - Wk 5](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-5/14514)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [November 10, 2020, 12:49am UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-5/14514 "2020-11-10T00:49:43Z")

</div>

Dear members of the Project Week community, Tomorrow (Tue Nov 3, 10am Boston time) we’ll have our next preparation meeting for Project Week #34. Here’s the link to the zoom session, which will remain the same for all ot…

---

## [ROI Registration Non-Functional](https://discourse.slicer.org/t/roi-registration-non-functional/14509)

<div class="topic-metadata">

**Author:** [@ahopf](https://discourse.slicer.org/u/ahopf)\
**Replies:** 0\
**Last updated:** [November 9, 2020, 5:02pm UTC](https://discourse.slicer.org/t/roi-registration-non-functional/14509 "2020-11-09T17:02:04Z")

</div>

I am trying to use ROI registration (within the surface registration module) to register two .ply models based on an overlapping section of the models after fiducial registration (which gave close pre-alignment). I ha…

---

## [Module "Airway Inspector" just can be uesd in the red slice](https://discourse.slicer.org/t/module-airway-inspector-just-can-be-uesd-in-the-red-slice/14422)

<div class="topic-metadata">

**Author:** [@Alice](https://discourse.slicer.org/u/Alice)\
**Replies:** 0\
**Last updated:** [November 4, 2020, 11:19am UTC](https://discourse.slicer.org/t/module-airway-inspector-just-can-be-uesd-in-the-red-slice/14422 "2020-11-04T11:19:34Z")

</div>

When I used the module “Airway Inspector” ,I suddenly found that the module “Airway Inspector” just can be uesd in the red slice,and in yellow slice and green one,the window of airway is completely black,and the related …

---

## [Coronary centerline extraction problem ](https://discourse.slicer.org/t/coronary-centerline-extraction-problem/14415)

<div class="topic-metadata">

**Author:** [@yuyang](https://discourse.slicer.org/u/yuyang)\
**Replies:** 1\
**Last updated:** [November 4, 2020, 4:49am UTC](https://discourse.slicer.org/t/coronary-centerline-extraction-problem/14415 "2020-11-04T04:49:23Z")

</div>

Hi all， I am working on extraction cardiovascular centerline from CT images using VMTK following the instructions of https://www.slicer.org/wiki/Modules:VMTK\_in\_3D\_Slicer\_Tutorial:\_Coronary\_Artery\_Centerline\_Extraction. …

[Previous page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=34)

[Next page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=36)