# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=36

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

**Page:** 37

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## [dMRI Extension Files -- Where do they end up?](https://discourse.slicer.org/t/dmri-extension-files-where-do-they-end-up/14246)

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**Author:** [@mgc26](https://discourse.slicer.org/u/mgc26)\
**Replies:** 6\
**Last updated:** [November 4, 2020, 2:00am UTC](https://discourse.slicer.org/t/dmri-extension-files-where-do-they-end-up/14246 "2020-11-04T02:00:15Z")

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I’ve been trying to complete the whitematteranalysis, but stuck on the last step as I cannot locate the SlicerDMRI extension files on my Ubuntu box. The step I’m stuck on: 8. Fiber tract diffusion measurements wm\_diff…

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## [Analysing bone porosity from CT scans using Radiomics](https://discourse.slicer.org/t/analysing-bone-porosity-from-ct-scans-using-radiomics/14412)

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**Author:** [@Varsha](https://discourse.slicer.org/u/Varsha)\
**Replies:** 0\
**Last updated:** [November 3, 2020, 8:00pm UTC](https://discourse.slicer.org/t/analysing-bone-porosity-from-ct-scans-using-radiomics/14412 "2020-11-03T20:00:55Z")

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How does one visualized porosities present on the Region of Interest from CT scans using Radiomics? Any help would be appreciated.

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## [Segment lung airway](https://discourse.slicer.org/t/segment-lung-airway/14398)

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**Author:** [@Alice](https://discourse.slicer.org/u/Alice)\
**Replies:** 0\
**Last updated:** [November 3, 2020, 8:07am UTC](https://discourse.slicer.org/t/segment-lung-airway/14398 "2020-11-03T08:07:40Z")

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when I run the module “segment lung airway”, there is some errors , and I failed to gain the airway. That can be seen in the picture. Does anyone know why?

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## [2020.11.03 Hangout](https://discourse.slicer.org/t/2020-11-03-hangout/14393)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [November 2, 2020, 9:18pm UTC](https://discourse.slicer.org/t/2020-11-03-hangout/14393 "2020-11-02T21:18:27Z")

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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…

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## [Project Week 34 Preparatory Videoconferences - Wk 4](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-4/14392)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [November 2, 2020, 9:16pm UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-4/14392 "2020-11-02T21:16:53Z")

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From the NA-MIC Project Week mailing list 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 ses…

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## [Great developer for SLICER \>\> Alex Vergara](https://discourse.slicer.org/t/great-developer-for-slicer-alex-vergara/14390)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 0\
**Last updated:** [November 2, 2020, 6:08pm UTC](https://discourse.slicer.org/t/great-developer-for-slicer-alex-vergara/14390 "2020-11-02T18:08:14Z")

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Hello, I was assigned to process some batches of data sets and it was so slow and time consuming. A developer I met on this website called " Alex\_Vergara " from France. Helped me so much! He offered his help and becaus…

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## [Setting up the segmentation volume for extract centerline module](https://discourse.slicer.org/t/setting-up-the-segmentation-volume-for-extract-centerline-module/14299)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 7\
**Last updated:** [November 1, 2020, 8:06pm UTC](https://discourse.slicer.org/t/setting-up-the-segmentation-volume-for-extract-centerline-module/14299 "2020-11-01T20:06:21Z")

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Hello Everyone, I have a segmentation volume shown in the image below, created after processing an image stack by pixel classification. I want to use this volume for creating a network model in the extract centerline m…

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## [Combination of methods in vmtkSurfaceCurvature](https://discourse.slicer.org/t/combination-of-methods-in-vmtksurfacecurvature/14226)

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**Author:** [@Jana\_Trdlicova](https://discourse.slicer.org/u/Jana_Trdlicova)\
**Replies:** 2\
**Last updated:** [October 30, 2020, 8:34am UTC](https://discourse.slicer.org/t/combination-of-methods-in-vmtksurfacecurvature/14226 "2020-10-30T08:34:24Z")

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Hi everyone, I have another problem with generating a ‘nice’ mesh of an aneurysm. I use the information about curvature (vmtkSurfaceCurvature) in vmtkMeshGenerator. There are 4 methods for computing the curvature, and I…

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## [Project Week 34 Preparatory Videoconferences - Wk 3](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-3/14255)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 26, 2020, 5:36pm UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-3/14255 "2020-10-26T17:36:33Z")

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\[From the NA-MIC Project Week mailing list\] Dear members of the Project Week community, Tomorrow (Tue Oct 26, 10am Boston time) we’ll have our third preparation meeting for Project Week #34. Here’s the link to the zoom…

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## [2020.10.27 Hangout](https://discourse.slicer.org/t/2020-10-27-hangout/14254)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 26, 2020, 5:35pm UTC](https://discourse.slicer.org/t/2020-10-27-hangout/14254 "2020-10-26T17:35:15Z")

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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…

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## [How vmtkboundaryreferencesystems works?](https://discourse.slicer.org/t/how-vmtkboundaryreferencesystems-works/14082)

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**Author:** [@Jana\_Trdlicova](https://discourse.slicer.org/u/Jana_Trdlicova)\
**Replies:** 2\
**Last updated:** [October 24, 2020, 8:09am UTC](https://discourse.slicer.org/t/how-vmtkboundaryreferencesystems-works/14082 "2020-10-24T08:09:20Z")

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Hi all, I am trying to implement a non-interactive clipping and meshing of an aneurysm geometry and I have problems with understanding what vmtkboundaryreferencesystems does. More specifically, I need to control that my…

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## [Contribute to 3D Slicer, without writing code! Letters of support needed!](https://discourse.slicer.org/t/contribute-to-3d-slicer-without-writing-code-letters-of-support-needed/14175)

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**Author:** [@aylward](https://discourse.slicer.org/u/aylward)\
**Replies:** 0\
**Last updated:** [October 20, 2020, 10:16pm UTC](https://discourse.slicer.org/t/contribute-to-3d-slicer-without-writing-code-letters-of-support-needed/14175 "2020-10-20T22:16:59Z")

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Want to contribute to open-source 3D Slicer and point-of-care ultrasound research without writing code? Please send us a letter of support for our grant NIH proposal! The proposal is for the renewal of the grant that fu…

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## [Project Week 34 Preparatory Videoconferences - Wk 2](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-2/14147)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 20, 2020, 12:05am UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences-wk-2/14147 "2020-10-20T00:05:58Z")

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\[From the NA-MIC Project Week mailing list\] Dear members of the Project Week community, Tomorrow (Tue Oct 20, 10am Boston time) we’ll have our second preparation meeting for Project Week #34. Here’s the link to the zoo…

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## [2020.10.20 Hangout](https://discourse.slicer.org/t/2020-10-20-hangout/14146)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 20, 2020, 12:03am UTC](https://discourse.slicer.org/t/2020-10-20-hangout/14146 "2020-10-20T00:03:48Z")

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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…

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## [FDR or Multiple Comparison Corection in Covariate Significance Testing](https://discourse.slicer.org/t/fdr-or-multiple-comparison-corection-in-covariate-significance-testing/13953)

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**Author:** [@iPsych](https://discourse.slicer.org/u/iPsych)\
**Replies:** 1\
**Last updated:** [October 13, 2020, 1:40pm UTC](https://discourse.slicer.org/t/fdr-or-multiple-comparison-corection-in-covariate-significance-testing/13953 "2020-10-13T13:40:41Z")

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Hi, Does the Covariate Significance Testing include any FDR or Multiple Comparison Correction method in its pipeline? I read carefully the documentation, but found no information about it. If not, is there any recommen…

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## [2020.10.13 Hangout](https://discourse.slicer.org/t/2020-10-13-hangout/14005)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 12, 2020, 6:16pm UTC](https://discourse.slicer.org/t/2020-10-13-hangout/14005 "2020-10-12T18:16:34Z")

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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 Fee…

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## [Project Week 34 Preparatory Videoconferences](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences/14004)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 12, 2020, 6:13pm UTC](https://discourse.slicer.org/t/project-week-34-preparatory-videoconferences/14004 "2020-10-12T18:13:21Z")

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\[Shared from the NA-MIC Project Week Mailing List\] Project Week#34 will be held Dec 14-18, 2020 on the internet . Please look here for additional details: https://projectweek.na-mic.org/PW34\_2020\_Virtual/ Due to the C…

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## [multimodal radiomics](https://discourse.slicer.org/t/multimodal-radiomics/13908)

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**Author:** [@icetin](https://discourse.slicer.org/u/icetin)\
**Replies:** 1\
**Last updated:** [October 10, 2020, 1:44pm UTC](https://discourse.slicer.org/t/multimodal-radiomics/13908 "2020-10-10T13:44:05Z")

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Hi! Is it possible to extract radiomics features on pairs of images using pyradiomics? i.e. features based on the joint histogram, or a way to manage the data so pyradiomics knows that they are two views of the same thi…

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## [Using png file with radiomics](https://discourse.slicer.org/t/using-png-file-with-radiomics/13891)

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**Author:** [@cucphuong](https://discourse.slicer.org/u/cucphuong)\
**Replies:** 2\
**Last updated:** [October 10, 2020, 1:40pm UTC](https://discourse.slicer.org/t/using-png-file-with-radiomics/13891 "2020-10-10T13:40:44Z")

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Hello everyone, I am working with radiomics and want to use RadiomicsGLCM to extract feature. I want to extract glcm from brain tumor which will be segmented by mask. Here is my code: img = sitk.ReadImage(path) mask =…

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## [Use segmentation for radiomics](https://discourse.slicer.org/t/use-segmentation-for-radiomics/13969)

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**Author:** [@Mgi](https://discourse.slicer.org/u/Mgi)\
**Replies:** 0\
**Last updated:** [October 9, 2020, 8:16pm UTC](https://discourse.slicer.org/t/use-segmentation-for-radiomics/13969 "2020-10-09T20:16:43Z")

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Hi @fedorov I want to convert the nrrd file obtained from the segmentation on PET-Indic to DICOM to save them on the PACS. After I’ll use them for Radiomics. What is the better way?

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## [Trying to do tractography from DICOM DTI](https://discourse.slicer.org/t/trying-to-do-tractography-from-dicom-dti/13964)

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**Author:** [@Cerebellum](https://discourse.slicer.org/u/Cerebellum)\
**Replies:** 1\
**Last updated:** [October 9, 2020, 8:22pm UTC](https://discourse.slicer.org/t/trying-to-do-tractography-from-dicom-dti/13964 "2020-10-09T20:22:29Z")

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Hello! Recently I found an old disk from the place I used to work with where I saved my own brain MRI (I used to do tractography with FiberTrak in a Philips station for neuroanatomy teaching purposes). In that disk I ha…

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## [Incongruence with some feautures](https://discourse.slicer.org/t/incongruence-with-some-feautures/13864)

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**Author:** [@Nicolas\_Destefanis](https://discourse.slicer.org/u/Nicolas_Destefanis)\
**Replies:** 2\
**Last updated:** [October 6, 2020, 1:22pm UTC](https://discourse.slicer.org/t/incongruence-with-some-feautures/13864 "2020-10-06T13:22:40Z")

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I am currently working on my MSc thesis in Mathematics, and I’m fairly new with PyRadiomics. I’m having some issues when extracting some features. I was comparing their output with the ones extracted using another softwa…

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## [Validity of Radiomics Fractional Bin Width](https://discourse.slicer.org/t/validity-of-radiomics-fractional-bin-width/13877)

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**Author:** [@furMan](https://discourse.slicer.org/u/furMan)\
**Replies:** 1\
**Last updated:** [October 6, 2020, 2:06am UTC](https://discourse.slicer.org/t/validity-of-radiomics-fractional-bin-width/13877 "2020-10-06T02:06:08Z")

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Operating system: Windows 10 Slicer version:4.10.2 Expected behavior: Actual behavior: I’m analyzing MR images, and am normalizing the images using the following method: Subtract the mean of the non-zero intensitie…

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## [2020.10.06 Hangout w/ Project Week Discussion](https://discourse.slicer.org/t/2020-10-06-hangout-w-project-week-discussion/13872)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [October 5, 2020, 8:56pm UTC](https://discourse.slicer.org/t/2020-10-06-hangout-w-project-week-discussion/13872 "2020-10-05T20:56:01Z")

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Title: 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 (10:00 - 10:30): We …

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## [Calculation of lung airway data](https://discourse.slicer.org/t/calculation-of-lung-airway-data/13862)

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**Author:** [@1119](https://discourse.slicer.org/u/1119)\
**Replies:** 0\
**Last updated:** [October 5, 2020, 6:50am UTC](https://discourse.slicer.org/t/calculation-of-lung-airway-data/13862 "2020-10-05T06:50:33Z")

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In CIP, there is the airwayinspector module, which can manually mark some problems in calculating the lung airway. Is there any more automatic method to batch process the data? Thank you very much for your answer.

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## [Automatic segmentation best for entire the mandible including dentition, trabecular and cortical bone](https://discourse.slicer.org/t/automatic-segmentation-best-for-entire-the-mandible-including-dentition-trabecular-and-cortical-bone/13805)

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**Author:** [@Lexus\_H](https://discourse.slicer.org/u/Lexus_H)\
**Replies:** 1\
**Last updated:** [October 2, 2020, 8:48am UTC](https://discourse.slicer.org/t/automatic-segmentation-best-for-entire-the-mandible-including-dentition-trabecular-and-cortical-bone/13805 "2020-10-02T08:48:10Z")

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How do I automatically segment all of the teeth, cortical and trabecular bone in the mandible? Is it better to use ITK-SNAP or Slicer? Is colorbar in an increment of 1cmm? I mean for a range Is there a way to crop col…

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## [GLCM extraction error on .png image](https://discourse.slicer.org/t/glcm-extraction-error-on-png-image/13566)

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**Author:** [@Shibashis\_Sahu](https://discourse.slicer.org/u/Shibashis_Sahu)\
**Replies:** 1\
**Last updated:** [September 30, 2020, 11:38am UTC](https://discourse.slicer.org/t/glcm-extraction-error-on-png-image/13566 "2020-09-30T11:38:29Z")

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Operating system: Windows 10 Slicer version: Expected behavior: Actual behavior: HI, I am new to pyradiomics and getting an error while extracting using GLCM, here is my code: ig = sitk.ReadImage(’./PAC\_14\_DN0.png’…

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## [Can radiomics in 3dslicer output many results of different patients in a CSV?](https://discourse.slicer.org/t/can-radiomics-in-3dslicer-output-many-results-of-different-patients-in-a-csv/13500)

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**Author:** [@Jeff\_W](https://discourse.slicer.org/u/Jeff_W)\
**Replies:** 2\
**Last updated:** [September 30, 2020, 1:42pm UTC](https://discourse.slicer.org/t/can-radiomics-in-3dslicer-output-many-results-of-different-patients-in-a-csv/13500 "2020-09-30T13:42:28Z")

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Can radiomics in 3dslicer output many results of different patients in a CSV?Can radiomics in 3dslicer output many results of different patients in a CSV?Can radiomics in 3dslicer output many results of different patient…

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## [install pyradiomics via conda](https://discourse.slicer.org/t/install-pyradiomics-via-conda/13661)

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**Author:** [@YinYunchao](https://discourse.slicer.org/u/YinYunchao)\
**Replies:** 1\
**Last updated:** [September 30, 2020, 11:34am UTC](https://discourse.slicer.org/t/install-pyradiomics-via-conda/13661 "2020-09-30T11:34:31Z")

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Hi there, I was trying to install pyradiomics by the command line ‘conda install -c radiomics pyradiomics’. However, it reported: pyradiomics -\> python\[version=’\>=2.7,\<2.8.0a0|\>=3.7,\<3.8.0a0|\>=3.6,\<3.7.0a0|\>=3.5,\<3.6.…

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## [Standardized yaml. or json file for image preprocessing?](https://discourse.slicer.org/t/standardized-yaml-or-json-file-for-image-preprocessing/12986)

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**Author:** [@aileeno](https://discourse.slicer.org/u/aileeno)\
**Replies:** 3\
**Last updated:** [September 30, 2020, 11:41am UTC](https://discourse.slicer.org/t/standardized-yaml-or-json-file-for-image-preprocessing/12986 "2020-09-30T11:41:39Z")

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Hi there, I’m wondering if there is a standardized yaml.-file or JSON which can be used for image preprocessing prior to running pyRadiomics extension. We have data from \> 16 CT scanners and were told that this would mi…

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