# Community **URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=33 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 34 --- ## [2021.03.16 Hangout](https://discourse.slicer.org/t/2021-03-16-hangout/16551)

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 4\ **Last updated:** [March 17, 2021, 11:24pm UTC](https://discourse.slicer.org/t/2021-03-16-hangout/16551 "2021-03-17T23:24:02Z")

**Author:** [@nahid](https://discourse.slicer.org/u/nahid)\ **Replies:** 2\ **Last updated:** [March 16, 2021, 5:24pm UTC](https://discourse.slicer.org/t/dtiprep-installation/1885 "2021-03-16T17:24:08Z")

Dear 3D Slicer experts I am pretty new in 3d Slicer. I want to use DTIPrep but it is not in the list of extensions to be installed. I have downloaded it separately but I don’t know how to install it. Any help appreciat… --- ## [Radiomics to creat image map](https://discourse.slicer.org/t/radiomics-to-creat-image-map/15760)

**Author:** [@Alsurayhi.H](https://discourse.slicer.org/u/Alsurayhi.H)\ **Replies:** 2\ **Last updated:** [March 11, 2021, 4:15pm UTC](https://discourse.slicer.org/t/radiomics-to-creat-image-map/15760 "2021-03-11T16:15:27Z")

Is it possible to create an image map based on specific features extracted using radiomics (for example GLCM feature)? --- ## [SlicerDMRI tractography measurements](https://discourse.slicer.org/t/slicerdmri-tractography-measurements/16468)

**Author:** [@amymanson](https://discourse.slicer.org/u/amymanson)\ **Replies:** 2\ **Last updated:** [March 11, 2021, 10:42am UTC](https://discourse.slicer.org/t/slicerdmri-tractography-measurements/16468 "2021-03-11T10:42:54Z")

Hi, I was wondering if anyone could clarify the meaning of one of the measurement results produced when running Diffusion-\>Quantify-\>Tractography Measurements on DTI data? The measurements produced are (among others) Nu… --- ## [2021.03.09 Hangout](https://discourse.slicer.org/t/2021-03-09-hangout/16433)

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 3\ **Last updated:** [March 9, 2021, 2:25pm UTC](https://discourse.slicer.org/t/2021-03-09-hangout/16433 "2021-03-09T14:25:12Z")

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 / VTK 9 Osteotomy … --- ## [Effect of background on radiomics features from filtered images](https://discourse.slicer.org/t/effect-of-background-on-radiomics-features-from-filtered-images/15688)

**Author:** [@mcastro](https://discourse.slicer.org/u/mcastro)\ **Replies:** 1\ **Last updated:** [March 9, 2021, 12:46pm UTC](https://discourse.slicer.org/t/effect-of-background-on-radiomics-features-from-filtered-images/15688 "2021-03-09T12:46:07Z")

I am studying the stability of radiomics features on a segmented whole organ at different time points. When masking the image using Mask Volume in Segment Editor, the user can set the background to any value, say 0. Fea… --- ## [Customizing the extraction features](https://discourse.slicer.org/t/customizing-the-extraction-features/15630)

**Author:** [@Aleja\_Ichina](https://discourse.slicer.org/u/Aleja_Ichina)\ **Replies:** 3\ **Last updated:** [March 9, 2021, 12:44pm UTC](https://discourse.slicer.org/t/customizing-the-extraction-features/15630 "2021-03-09T12:44:03Z")

Hi, I need help. I want to choose the features to extract but I have no idea how to do it. Can someone please help me? I tried to read the guide but I don’t understand where to edit. --- ## [How to make the segmentation](https://discourse.slicer.org/t/how-to-make-the-segmentation/15581)

**Author:** [@Aleja\_Ichina](https://discourse.slicer.org/u/Aleja_Ichina)\ **Replies:** 3\ **Last updated:** [March 9, 2021, 12:41pm UTC](https://discourse.slicer.org/t/how-to-make-the-segmentation/15581 "2021-03-09T12:41:48Z")

Hi, I have a question. How can I make the segmentation of my images? Has PyRadiomics this function? I don’t have idea please help me --- ## [How do extract GLRLM features from a .jpg image](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-jpg-image/15505)

**Author:** [@Mohiuddin](https://discourse.slicer.org/u/Mohiuddin)\ **Replies:** 1\ **Last updated:** [March 9, 2021, 12:40pm UTC](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-jpg-image/15505 "2021-03-09T12:40:18Z")

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 understand about ‘mask’ input. Thus, can anybody help me by providing any sample … --- ## [Radiomics result validation](https://discourse.slicer.org/t/radiomics-result-validation/15181)

**Author:** [@vinartrulz](https://discourse.slicer.org/u/vinartrulz)\ **Replies:** 1\ **Last updated:** [March 9, 2021, 12:37pm UTC](https://discourse.slicer.org/t/radiomics-result-validation/15181 "2021-03-09T12:37:21Z")

Hello everyone. I am interested to know about the result validation strategy followed by libraries like pyradiomics. While looking through the unit test cases, I found the results are validated against golden data. How… --- ## [How to optimize the binwidth Value for MR images (Radiomics)](https://discourse.slicer.org/t/how-to-optimize-the-binwidth-value-for-mr-images-radiomics/15974)

**Author:** [@Ceylan](https://discourse.slicer.org/u/Ceylan)\ **Replies:** 1\ **Last updated:** [March 9, 2021, 12:23pm UTC](https://discourse.slicer.org/t/how-to-optimize-the-binwidth-value-for-mr-images-radiomics/15974 "2021-03-09T12:23:11Z")

Hello everyone, I’m trying to extract the radiomic features from MR images using Pyradiomics extension on 3DSlicer. I know that the default setting for the binwidth is 25. However, I am not sure which value is more sui… --- ## [FeatureExtractor values don't get along with reality value](https://discourse.slicer.org/t/featureextractor-values-dont-get-along-with-reality-value/15997)

**Author:** [@11117](https://discourse.slicer.org/u/11117)\ **Replies:** 1\ **Last updated:** [March 9, 2021, 12:22pm UTC](https://discourse.slicer.org/t/featureextractor-values-dont-get-along-with-reality-value/15997 "2021-03-09T12:22:09Z")

Hello everyone, I’m trying to understand my results that I get from pyradiomics - FeatureExtractor and I have two questions: I want to understand what values the extractor gets me, so I calculate manually the energy,… --- ## [Pyradiomics with masks extracted from DICOM dose cloud](https://discourse.slicer.org/t/pyradiomics-with-masks-extracted-from-dicom-dose-cloud/15965)

**Author:** [@Adam](https://discourse.slicer.org/u/Adam)\ **Replies:** 3\ **Last updated:** [March 9, 2021, 12:18pm UTC](https://discourse.slicer.org/t/pyradiomics-with-masks-extracted-from-dicom-dose-cloud/15965 "2021-03-09T12:18:58Z")

Operating system:Windows 10 Slicer version: 4.10.1 Hi, I have masks stored in numpy ndarray, and I am using pynrrd to write them to .nrrd format for use in pyradiomics. When I check the nrrd masks against the dicom im… --- ## [Automatic vessel endpoints detection](https://discourse.slicer.org/t/automatic-vessel-endpoints-detection/16435)

**Author:** [@fuentesdt](https://discourse.slicer.org/u/fuentesdt)\ **Replies:** 1\ **Last updated:** [March 8, 2021, 8:19pm UTC](https://discourse.slicer.org/t/automatic-vessel-endpoints-detection/16435 "2021-03-08T20:19:34Z")

i started off with the VMTK package directly before I was aware of this VMTK slicer extension. Endpoints seemed to need to be manually chosen in the interface released with the original vmtk packages. What algorithm are… --- ## [gap filling of breaks between vessels](https://discourse.slicer.org/t/gap-filling-of-breaks-between-vessels/16330)

**Author:** [@fuentesdt](https://discourse.slicer.org/u/fuentesdt)\ **Replies:** 1\ **Last updated:** [March 3, 2021, 3:27pm UTC](https://discourse.slicer.org/t/gap-filling-of-breaks-between-vessels/16330 "2021-03-03T15:27:13Z")

Hi, Is there any functionality in vmtk, slicer, or itk for gap filling? something like this tensor voting method: Risser, Laurent, Franck Plouraboué, and Xavier Descombes. “Gap filling of 3-D microvascular networks by te… --- ## [2021.03.02 Hangout](https://discourse.slicer.org/t/2021-03-02-hangout/16289)

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 1\ **Last updated:** [March 2, 2021, 3:30pm UTC](https://discourse.slicer.org/t/2021-03-02-hangout/16289 "2021-03-02T15:30:31Z")

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 / VTK 9 macOS test… --- ## [Correlation analysis of shape parameters with a continuous variable](https://discourse.slicer.org/t/correlation-analysis-of-shape-parameters-with-a-continuous-variable/16252)

**Author:** [@Adarsh\_Ghosh](https://discourse.slicer.org/u/Adarsh_Ghosh)\ **Replies:** 0\ **Last updated:** [February 27, 2021, 4:12am UTC](https://discourse.slicer.org/t/correlation-analysis-of-shape-parameters-with-a-continuous-variable/16252 "2021-02-27T04:12:41Z")

Hello! I am new to shape analysis in general and I want to correlate a continuous pathological variable ( for example % of necrosis) with shape of a lesion ( I assume spherical topology). I assume Covariate Significanc… --- ## [How to calculate the average length and FA value of fiber bundles](https://discourse.slicer.org/t/how-to-calculate-the-average-length-and-fa-value-of-fiber-bundles/16225)

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\ **Replies:** 0\ **Last updated:** [February 26, 2021, 1:26am UTC](https://discourse.slicer.org/t/how-to-calculate-the-average-length-and-fa-value-of-fiber-bundles/16225 "2021-02-26T01:26:15Z")

How to calculate the average length and FA value of fiber bundles like this picture?For example, if I set a label or model and get the corresponding fiber bundle, how to calculate the average length and FA value of the f… --- ## [2021.02.23 Hangout](https://discourse.slicer.org/t/2021-02-23-hangout/16144)

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 1\ **Last updated:** [February 23, 2021, 3:11pm UTC](https://discourse.slicer.org/t/2021-02-23-hangout/16144 "2021-02-23T15:11:17Z")

**Author:** [@Sedra\_Mulki](https://discourse.slicer.org/u/Sedra_Mulki)\ **Replies:** 1\ **Last updated:** [February 21, 2021, 5:40am UTC](https://discourse.slicer.org/t/geometry-extraction/16113 "2021-02-21T05:40:43Z")

Hello Can I know which methods are available in 3D slicer to extract the geometry like marching cubes? --- ## [Frontal, parietal, temporal, ocipital cranial bones division](https://discourse.slicer.org/t/frontal-parietal-temporal-ocipital-cranial-bones-division/16083)

**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\ **Replies:** 0\ **Last updated:** [February 19, 2021, 1:35pm UTC](https://discourse.slicer.org/t/frontal-parietal-temporal-ocipital-cranial-bones-division/16083 "2021-02-19T13:35:51Z")

Hi: How can I do the division of the Frontal, parietal, temporal, and occipital bones from CT images (I have the cranial mesh)? Automatic or semiautomatic method using 3D Slicer? Sincerely, Gonzalo Rojas Costa --- ## [My life was saved](https://discourse.slicer.org/t/my-life-was-saved/16039)

**Author:** [@Klaus](https://discourse.slicer.org/u/Klaus)\ **Replies:** 3\ **Last updated:** [February 18, 2021, 7:15pm UTC](https://discourse.slicer.org/t/my-life-was-saved/16039 "2021-02-18T19:15:43Z")

Hi you all have literally saved my life. at least the software has! 8 years of misdiagnosis, ending up even finding a large portion of my many nerve injuries throughout my body from my CT scan Without this I would not… --- ## [VMTK centrelines - stl format in ascii mode](https://discourse.slicer.org/t/vmtk-centrelines-stl-format-in-ascii-mode/16058)

**Author:** [@Dhaya](https://discourse.slicer.org/u/Dhaya)\ **Replies:** 4\ **Last updated:** [February 18, 2021, 12:37pm UTC](https://discourse.slicer.org/t/vmtk-centrelines-stl-format-in-ascii-mode/16058 "2021-02-18T12:37:18Z")

I am new to VTMK software nad have generated the centrelines in vtp format. vmtksurfacereader -ifile “E:/geometry/v3\_shortIliacExtendIMACAP\_V2\_vtmk.stl” --pipe vmtkcenterlines -seedselector openprofiles -ofile “C:/User… --- ## [Blurb for Slicer Download page](https://discourse.slicer.org/t/blurb-for-slicer-download-page/16040)

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\ **Replies:** 5\ **Last updated:** [February 17, 2021, 7:57pm UTC](https://discourse.slicer.org/t/blurb-for-slicer-download-page/16040 "2021-02-17T19:57:58Z")

Often new users of Slicer are confused about what version of Slicer to use, and also how the stable and preview versions differ from each other. It also doesn’t help that the current preview has red “unstable” text next… --- ## [Covariate Significance Testing - multiple covariate testing problem(s)](https://discourse.slicer.org/t/covariate-significance-testing-multiple-covariate-testing-problem-s/16036)

**Author:** [@ikhsannk](https://discourse.slicer.org/u/ikhsannk)\ **Replies:** 0\ **Last updated:** [February 17, 2021, 5:29pm UTC](https://discourse.slicer.org/t/covariate-significance-testing-multiple-covariate-testing-problem-s/16036 "2021-02-17T17:29:48Z")

Hello, my name is Ikhsan and I have some questions regarding multiple covariate testing on the Covariate Significance Testing module. Before that, I have followed the tutorial using the example dataset (bump\*\*.vtk) prov… --- ## [2021.02.16 Hangout](https://discourse.slicer.org/t/2021-02-16-hangout/16002)

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 6\ **Last updated:** [February 16, 2021, 6:56pm UTC](https://discourse.slicer.org/t/2021-02-16-hangout/16002 "2021-02-16T18:56:18Z")

**Author:** [@ikhsannk](https://discourse.slicer.org/u/ikhsannk)\ **Replies:** 4\ **Last updated:** [February 16, 2021, 3:45pm UTC](https://discourse.slicer.org/t/spharm-pdm-alignment/15943 "2021-02-16T15:45:56Z")

Hello, Beatriz, Martin, and others. My name is Ikhsan and I would like to ask a few things regarding SPHARM-PDM. Firstly, I have looked at the tutorial and worked on the hippocampus example dataset. It functions properl… --- ## [3D slicer is an fantastic and powerful tool for radiotherapy](https://discourse.slicer.org/t/3d-slicer-is-an-fantastic-and-powerful-tool-for-radiotherapy/15924)

**Author:** [@hao](https://discourse.slicer.org/u/hao)\ **Replies:** 0\ **Last updated:** [February 9, 2021, 9:10pm UTC](https://discourse.slicer.org/t/3d-slicer-is-an-fantastic-and-powerful-tool-for-radiotherapy/15924 "2021-02-09T21:10:45Z")

I am new user of 3D slicer. at first I search on internet for a simple Dicom viewer but when I tried the 3D slicer, I realize that it is far more than an image viewer. I work in a radiotherapy department in which image … --- ## [2021.02.09 Hangout](https://discourse.slicer.org/t/2021-02-09-hangout/15911)

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 0\ **Last updated:** [February 8, 2021, 11:05pm UTC](https://discourse.slicer.org/t/2021-02-09-hangout/15911 "2021-02-08T23:05:13Z")

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 / VTK 9 Feel free… --- ## [Problems with the SPHARM-PDM on Slicer-4.8.0-linux-amd64 (Command-Line Tool, the step GenParaMesh)](https://discourse.slicer.org/t/problems-with-the-spharm-pdm-on-slicer-4-8-0-linux-amd64-command-line-tool-the-step-genparamesh/15877)

**Author:** [@Daisy\_Xiong](https://discourse.slicer.org/u/Daisy_Xiong)\ **Replies:** 0\ **Last updated:** [February 7, 2021, 4:31am UTC](https://discourse.slicer.org/t/problems-with-the-spharm-pdm-on-slicer-4-8-0-linux-amd64-command-line-tool-the-step-genparamesh/15877 "2021-02-07T04:31:43Z")

Hello, everyone, I tried to utilize the software Slicer(Slicer-4.8.0-linux-amd64) and the method SPHARM-PDM to get the some SPHARM Mesh ( such as the output files \*para.vtk and \*SPHARM\_Ellalign.vtk). If I use the main … [Previous page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=32) [Next page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=34)