# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=22

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

**Page:** 23

---

## [2022.09.26 Weekly Meeting](https://discourse.slicer.org/t/2022-09-26-weekly-meeting/25441)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [September 27, 2022, 7:56pm UTC](https://discourse.slicer.org/t/2022-09-26-weekly-meeting/25441 "2022-09-27T19:56:27Z")

</div>

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

---

## [Features confounded by the volume or ROI](https://discourse.slicer.org/t/features-confounded-by-the-volume-or-roi/25413)

<div class="topic-metadata">

**Author:** [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Replies:** 1\
**Last updated:** [September 25, 2022, 1:21am UTC](https://discourse.slicer.org/t/features-confounded-by-the-volume-or-roi/25413 "2022-09-25T01:21:19Z")

</div>

Currently, I use 3D slicer (pyradiomics plug in) to analyze myocardium of the heart (left ventricle). I draw ROI on myocardium of each time frames (total 25 frames on the same imaging plane) throughout a cardiac cycle. H…

---

## [2022.09.20 Weekly Meeting](https://discourse.slicer.org/t/2022-09-20-weekly-meeting/25345)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [September 19, 2022, 10:03pm UTC](https://discourse.slicer.org/t/2022-09-20-weekly-meeting/25345 "2022-09-19T22:03:24Z")

</div>

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

---

## [How to improve the accuracy of ALPACA @slicerMorph?](https://discourse.slicer.org/t/how-to-improve-the-accuracy-of-alpaca-slicermorph/25262)

<div class="topic-metadata">

**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 5\
**Last updated:** [September 19, 2022, 3:40pm UTC](https://discourse.slicer.org/t/how-to-improve-the-accuracy-of-alpaca-slicermorph/25262 "2022-09-19T15:40:19Z")

</div>

Hi, the following experiment was performed in order to “validate” the accuracy of slicerMorph/ALPACA. 2 skull samples were measured on CT 9 landmarks were manually placed on each of the two samples experiment #…

---

## [Bone Reconstruction Planner](https://discourse.slicer.org/t/bone-reconstruction-planner/19289)

<div class="topic-metadata">

**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 11\
**Last updated:** [September 18, 2022, 6:39am UTC](https://discourse.slicer.org/t/bone-reconstruction-planner/19289 "2022-09-18T06:39:44Z")

</div>

Yesterday we did the first case of mandibular reconstruction with fibula free flap using 3D Slicer extension, bone reconstruction planner in Sri Lanka at the department of oral and maxillofacial surgery, faculty of the …

---

## [having difficulty saving a segmentation as nii.gz format](https://discourse.slicer.org/t/having-difficulty-saving-a-segmentation-as-nii-gz-format/25317)

<div class="topic-metadata">

**Author:** [@eleanor](https://discourse.slicer.org/u/eleanor)\
**Replies:** 0\
**Last updated:** [September 18, 2022, 5:08am UTC](https://discourse.slicer.org/t/having-difficulty-saving-a-segmentation-as-nii-gz-format/25317 "2022-09-18T05:08:35Z")

</div>

having difficulty saving a segmentation as nii.gz format

---

## [ProjectSemiLM producing file with same landmark coordinates for 78 surface landmarks](https://discourse.slicer.org/t/projectsemilm-producing-file-with-same-landmark-coordinates-for-78-surface-landmarks/25275)

<div class="topic-metadata">

**Author:** [@Corinthia\_Black](https://discourse.slicer.org/u/Corinthia_Black)\
**Replies:** 7\
**Last updated:** [September 15, 2022, 5:57pm UTC](https://discourse.slicer.org/t/projectsemilm-producing-file-with-same-landmark-coordinates-for-78-surface-landmarks/25275 "2022-09-15T17:57:48Z")

</div>

I am trying to produce surface landmarks on an extremely variable sclarite (hard bits of spiders/insects); however, when I run ProjectSemiLM, the data that is being generated seems to overwrite each line with the same in…

---

## [Fractal Dimension as feature](https://discourse.slicer.org/t/fractal-dimension-as-feature/25279)

<div class="topic-metadata">

**Author:** [@scat2801](https://discourse.slicer.org/u/scat2801)\
**Replies:** 0\
**Last updated:** [September 15, 2022, 11:32am UTC](https://discourse.slicer.org/t/fractal-dimension-as-feature/25279 "2022-09-15T11:32:27Z")

</div>

Does the package currently offer the option to include fractal dimension in its output?

---

## [How can I use vmtk using python without 3D slicer GUI?](https://discourse.slicer.org/t/how-can-i-use-vmtk-using-python-without-3d-slicer-gui/20727)

<div class="topic-metadata">

**Author:** [@Amira\_Noaman](https://discourse.slicer.org/u/Amira_Noaman)\
**Replies:** 6\
**Last updated:** [September 15, 2022, 1:18am UTC](https://discourse.slicer.org/t/how-can-i-use-vmtk-using-python-without-3d-slicer-gui/20727 "2022-09-15T01:18:40Z")

</div>

Hello everyone, I’ve just started using vmtk package in python. (windows OS). I’m not willing to use the GUI provided by 3D slicer now, I’ll be building the complete project with python code, is it possible? and if yes…

---

## [Signed distance from mean shape and output csv/txt file for 400 subjects](https://discourse.slicer.org/t/signed-distance-from-mean-shape-and-output-csv-txt-file-for-400-subjects/23490)

<div class="topic-metadata">

**Author:** [@Khalid\_Saifullah](https://discourse.slicer.org/u/Khalid_Saifullah)\
**Replies:** 10\
**Last updated:** [September 12, 2022, 11:45pm UTC](https://discourse.slicer.org/t/signed-distance-from-mean-shape-and-output-csv-txt-file-for-400-subjects/23490 "2022-09-12T23:45:50Z")

</div>

Hi all! I am using SPHARM-PDM to generate shapes of subcortical structures. Using the output files “SubjectName\_pp\_surf\_SPHARM\_procalign.vtk”, I produced a mean vtk file with “Shape Variation Analyzer” module. My next …

---

## [2022.09.13 Weekly Meeting](https://discourse.slicer.org/t/2022-09-13-weekly-meeting/25222)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [September 12, 2022, 5:32pm UTC](https://discourse.slicer.org/t/2022-09-13-weekly-meeting/25222 "2022-09-12T17:32:41Z")

</div>

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

---

## [DICOM gray level normalization , 3 sigma normalization](https://discourse.slicer.org/t/dicom-gray-level-normalization-3-sigma-normalization/18518)

<div class="topic-metadata">

**Author:** [@hamdullaherk](https://discourse.slicer.org/u/hamdullaherk)\
**Replies:** 1\
**Last updated:** [July 13, 2021, 8:11pm UTC](https://discourse.slicer.org/t/dicom-gray-level-normalization-3-sigma-normalization/18518 "2021-07-13T20:11:21Z")

</div>

Hi, I am a radiologist who is interests in texture analysis and radomics. I am a beginner at 3Dslicer. Firstly I want to ask, how can I use 3sigma normalization technique in DICOM images. I don’t know how can ı do it? c…

---

## [2022.09.06 Weekly Meeting](https://discourse.slicer.org/t/2022-09-06-weekly-meeting/25123)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [September 6, 2022, 12:51pm UTC](https://discourse.slicer.org/t/2022-09-06-weekly-meeting/25123 "2022-09-06T12:51:57Z")

</div>

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

---

## [Add two surfaces to vtmkscripts.vmtkSurfaceViewer](https://discourse.slicer.org/t/add-two-surfaces-to-vtmkscripts-vmtksurfaceviewer/25014)

<div class="topic-metadata">

**Author:** [@carlosar](https://discourse.slicer.org/u/carlosar)\
**Replies:** 0\
**Last updated:** [August 30, 2022, 7:09pm UTC](https://discourse.slicer.org/t/add-two-surfaces-to-vtmkscripts-vmtksurfaceviewer/25014 "2022-08-30T19:09:48Z")

</div>

I’d like to compare the pre and post smoothed surface from the marching cubes script. Here is part of my code. I’m building my own pypes script, so I am trying to replicate what is found in this tutorial at the end: Prep…

---

## [Title: 2022.08.30 Weekly Meeting](https://discourse.slicer.org/t/title-2022-08-30-weekly-meeting/24930)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 3\
**Last updated:** [August 29, 2022, 3:57pm UTC](https://discourse.slicer.org/t/title-2022-08-30-weekly-meeting/24930 "2022-08-29T15:57:07Z")

</div>

Next Tuesday, we will be having our next weekly hangout at 10:00 AM ET until 11:00 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Extension dashboard s…

---

## [Special Issue of Frontiers in Virtual Reality journal - Medical Simulation and Visualization](https://discourse.slicer.org/t/special-issue-of-frontiers-in-virtual-reality-journal-medical-simulation-and-visualization/24966)

<div class="topic-metadata">

**Author:** [@MichelODU](https://discourse.slicer.org/u/MichelODU)\
**Replies:** 0\
**Last updated:** [August 28, 2022, 9:19pm UTC](https://discourse.slicer.org/t/special-issue-of-frontiers-in-virtual-reality-journal-medical-simulation-and-visualization/24966 "2022-08-28T21:19:42Z")

</div>

Dear members of the Slicer Community, this post is to announce a Special Issue of Frontiers in Virtual Reality journal - Medical Simulation and Visualization, which I believe could align with much of the work that build…

---

## [SPHARM flip option](https://discourse.slicer.org/t/spharm-flip-option/16681)

<div class="topic-metadata">

**Author:** [@ikhsannk](https://discourse.slicer.org/u/ikhsannk)\
**Replies:** 2\
**Last updated:** [August 22, 2022, 4:05pm UTC](https://discourse.slicer.org/t/spharm-flip-option/16681 "2022-08-22T16:05:37Z")

</div>

Hello Bea @bpaniagua , Martin @styner and everyone. I have a simple question regarding SPHARM, is there a way to manually flip the output SPHARM file within SlicerSALT? I am aware that there are ‘flip template’ and ‘…

---

## [2022.08.23 Weekly Meeting](https://discourse.slicer.org/t/2022-08-23-weekly-meeting/24868)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [August 22, 2022, 2:58pm UTC](https://discourse.slicer.org/t/2022-08-23-weekly-meeting/24868 "2022-08-22T14:58:36Z")

</div>

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

---

## [Model to Model Distance Parameters](https://discourse.slicer.org/t/model-to-model-distance-parameters/6543)

<div class="topic-metadata">

**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 11\
**Last updated:** [August 19, 2022, 12:47pm UTC](https://discourse.slicer.org/t/model-to-model-distance-parameters/6543 "2022-08-19T12:47:42Z")

</div>

What are the differences between the parameters in model to model distance? By that I mean, what’s the differences between absolute closest point, signed closest point, and closest point? How do these differences effect …

---

## [2022.08.16 Weekly Meeting](https://discourse.slicer.org/t/2022-08-16-weekly-meeting/24730)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [August 16, 2022, 11:20pm UTC](https://discourse.slicer.org/t/2022-08-16-weekly-meeting/24730 "2022-08-16T23:20:15Z")

</div>

Next Tuesday, we will be having our next weekly hangout at 10:00 AM ET until 11:00 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Extension dashboard s…

---

## [Extract Centerlines cannot work with cyclical vessels?](https://discourse.slicer.org/t/extract-centerlines-cannot-work-with-cyclical-vessels/24758)

<div class="topic-metadata">

**Author:** [@Doodads](https://discourse.slicer.org/u/Doodads)\
**Replies:** 1\
**Last updated:** [August 15, 2022, 7:37pm UTC](https://discourse.slicer.org/t/extract-centerlines-cannot-work-with-cyclical-vessels/24758 "2022-08-15T19:37:16Z")

</div>

Hi, I used the Extract Centerlines tool on a Circle of Willis surface. The network is connected without an issue but the centerlines have a single vessel that it did not pass through (see image below). How do I adjust th…

---

## [Funtion or Equation of centreline](https://discourse.slicer.org/t/funtion-or-equation-of-centreline/24640)

<div class="topic-metadata">

**Author:** [@mann](https://discourse.slicer.org/u/mann)\
**Replies:** 3\
**Last updated:** [August 9, 2022, 8:57pm UTC](https://discourse.slicer.org/t/funtion-or-equation-of-centreline/24640 "2022-08-09T20:57:29Z")

</div>

Hi All, I am using Extract centreline module for creating vessel centreline. Is their any way that I can get the function or equation that used to connect the control points ? Is there a way to edit/crop the centrelin…

---

## [2022.08.09 Weekly Meeting](https://discourse.slicer.org/t/2022-08-09-weekly-meeting/24658)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [August 9, 2022, 1:02pm UTC](https://discourse.slicer.org/t/2022-08-09-weekly-meeting/24658 "2022-08-09T13:02:19Z")

</div>

Next Tuesday, we will be having our next weekly hangout at 10:00 AM ET until 11:00 AM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Extension dashboard s…

---

## [Group analysis with SPHARM-PDM](https://discourse.slicer.org/t/group-analysis-with-spharm-pdm/885)

<div class="topic-metadata">

**Author:** [@laurapascal](https://discourse.slicer.org/u/laurapascal)\
**Replies:** 11\
**Last updated:** [August 8, 2022, 8:47am UTC](https://discourse.slicer.org/t/group-analysis-with-spharm-pdm/885 "2022-08-08T08:47:25Z")

</div>

Interesting questions form Panos about group analysis with SPHARM-PDM tool: I am trying to compare regional differences in hippocampal structure between three groups (2 diseased groups, and one healthy control group), …

---

## [How to get the 3D map with PET and MR in Slicer](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 6\
**Last updated:** [August 3, 2022, 1:39pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591 "2022-08-03T13:39:02Z")

</div>

How to use slicer get the result like the above picture,it used PET-CT.

---

## [2022.08.02 Weekly Meeting](https://discourse.slicer.org/t/2022-08-02-weekly-meeting/24594)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [August 1, 2022, 4:50pm UTC](https://discourse.slicer.org/t/2022-08-02-weekly-meeting/24594 "2022-08-01T16:50:53Z")

</div>

Tomorrow, we will be having our next weekly hangout at 10 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 :tada: Exte…

---

## [Load DSI Studio (\*.trk.gz) or TrackVis (\*.trk) tracks in Slicer](https://discourse.slicer.org/t/load-dsi-studio-trk-gz-or-trackvis-trk-tracks-in-slicer/1356)

<div class="topic-metadata">

**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 16\
**Last updated:** [July 28, 2022, 11:05am UTC](https://discourse.slicer.org/t/load-dsi-studio-trk-gz-or-trackvis-trk-tracks-in-slicer/1356 "2022-07-28T11:05:13Z")

</div>

Does anyone have experience converting and then loading fibertrack generated by these software into 3D Slicer ? Is there any recommended pathway to export tracts and import them into Slicer ? We are thinking of these …

---

## [Clipping multiple branches with vmtkbranchclipper](https://discourse.slicer.org/t/clipping-multiple-branches-with-vmtkbranchclipper/24521)

<div class="topic-metadata">

**Author:** [@susk](https://discourse.slicer.org/u/susk)\
**Replies:** 0\
**Last updated:** [July 27, 2022, 8:31am UTC](https://discourse.slicer.org/t/clipping-multiple-branches-with-vmtkbranchclipper/24521 "2022-07-27T08:31:23Z")

</div>

Hi all, I am trying to clip more than one branch with vmtkBranchClipper in python. I’ve tried doing this both interactively and through supplying a GroupIds list. When I supply one GroupId, i.e. clip one branch, the cli…

---

## [pyradiomics w/ fixed bin width: bin number varies significantly across derived images](https://discourse.slicer.org/t/pyradiomics-w-fixed-bin-width-bin-number-varies-significantly-across-derived-images/24498)

<div class="topic-metadata">

**Author:** [@stef](https://discourse.slicer.org/u/stef)\
**Replies:** 0\
**Last updated:** [July 26, 2022, 2:14pm UTC](https://discourse.slicer.org/t/pyradiomics-w-fixed-bin-width-bin-number-varies-significantly-across-derived-images/24498 "2022-07-26T14:14:51Z")

</div>

Hi all, When using the fixed bin width setting, the median number of bins per patient varies a lot across the different derived images and the original image. I know this can be in part addressed by selecting a differen…

---

## [Why is SlicerRadiomics only partly functional?](https://discourse.slicer.org/t/why-is-slicerradiomics-only-partly-functional/24449)

<div class="topic-metadata">

**Author:** [@harad](https://discourse.slicer.org/u/harad)\
**Replies:** 3\
**Last updated:** [July 22, 2022, 1:54pm UTC](https://discourse.slicer.org/t/why-is-slicerradiomics-only-partly-functional/24449 "2022-07-22T13:54:12Z")

</div>

Hi everyone, I wonder why the GUI of Slicer radiomics has a massively trimmed functionality in comparison to the standalone Pyradiomics. Thereby, only LoG, Wavelet and Original image types can be activated. That leaves s…

[Previous page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=21)

[Next page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=23)