# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=38

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

**Page:** 39

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## [2020.07.28 Hangout - Early Posting for Project Week Brainstorming](https://discourse.slicer.org/t/2020-07-28-hangout-early-posting-for-project-week-brainstorming/12604)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 4\
**Last updated:** [July 28, 2020, 6:50pm UTC](https://discourse.slicer.org/t/2020-07-28-hangout-early-posting-for-project-week-brainstorming/12604 "2020-07-28T18:50:08Z")

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Hi all: This is an early announcement for the July 28th developer hangout at 10:00 AM EST until 11 AM EST. We will be brainstorming ideas for what a fully virtual January project week could look like. Anyone is welcom…

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## [Could use a model like \*.vtk or \*.obj as the input of SPHARM?](https://discourse.slicer.org/t/could-use-a-model-like-vtk-or-obj-as-the-input-of-spharm/12599)

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**Author:** [@Yoda0612](https://discourse.slicer.org/u/Yoda0612)\
**Replies:** 3\
**Last updated:** [July 27, 2020, 9:15pm UTC](https://discourse.slicer.org/t/could-use-a-model-like-vtk-or-obj-as-the-input-of-spharm/12599 "2020-07-27T21:15:51Z")

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I would like to obtain the spherical harmonic coefficients for a model. However, SPHARM ask me to input the binary image or vtk model with para model. I just have a model without para model. How could I obtain spheric…

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## [SlicerSALT 3.0 Release: Summary and Changelog](https://discourse.slicer.org/t/slicersalt-3-0-release-summary-and-changelog/12748)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 0\
**Last updated:** [July 27, 2020, 1:39pm UTC](https://discourse.slicer.org/t/slicersalt-3-0-release-summary-and-changelog/12748 "2020-07-27T13:39:16Z")

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The SlicerSALT team is proud to announce that version 3.0 is now available for download. This release introduces new features as well as bug fixes for better performance and stability. The development of SlicerSALT is su…

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## [Signal loss after epi correction](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723)

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**Author:** [@mali](https://discourse.slicer.org/u/mali)\
**Replies:** 5\
**Last updated:** [July 25, 2020, 8:06pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723 "2020-07-25T20:06:07Z")

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Dear Slicer community, I hope you can help me with an issue I am struggling with. Iam currently working on DTI scans using Slicer and the PNL Pipeline. After applying epi correction (epi.sh) I am getting images that loo…

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## [2020.07.21 Hangout](https://discourse.slicer.org/t/2020-07-21-hangout/12603)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [July 21, 2020, 1:31pm UTC](https://discourse.slicer.org/t/2020-07-21-hangout/12603 "2020-07-21T13:31:51Z")

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

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## [With Great Sadness, My Time on the Discourse Comes To An End](https://discourse.slicer.org/t/with-great-sadness-my-time-on-the-discourse-comes-to-an-end/12587)

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**Author:** [@vertebra](https://discourse.slicer.org/u/vertebra)\
**Replies:** 2\
**Last updated:** [July 16, 2020, 10:36pm UTC](https://discourse.slicer.org/t/with-great-sadness-my-time-on-the-discourse-comes-to-an-end/12587 "2020-07-16T22:36:16Z")

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I would like to give special thanks to Csaba Pinter(@cpinter) and Kyle Sunderland(@Sunderlankyl) for the help as well as Li Zhenzu(@timeanddoctor) for the educated reasoning. And more than anyone else on this entire plat…

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## [2020.07.14 Hangout](https://discourse.slicer.org/t/2020-07-14-hangout/12509)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 4\
**Last updated:** [July 14, 2020, 5:51am UTC](https://discourse.slicer.org/t/2020-07-14-hangout/12509 "2020-07-14T05:51:08Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Fe…

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## [Code stop extracting wavelet and gradient features (it used to do so)](https://discourse.slicer.org/t/code-stop-extracting-wavelet-and-gradient-features-it-used-to-do-so/12428)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 1\
**Last updated:** [July 8, 2020, 6:57pm UTC](https://discourse.slicer.org/t/code-stop-extracting-wavelet-and-gradient-features-it-used-to-do-so/12428 "2020-07-08T18:57:23Z")

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I have this code which is an adaption of the examples offered and it use to extract all the features as described in the params.yaml . The code use to work well, now it is extracting less features than it has to. extrac…

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## [2020.07.07 Hangout](https://discourse.slicer.org/t/2020-07-07-hangout/12400)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [July 6, 2020, 6:26pm UTC](https://discourse.slicer.org/t/2020-07-07-hangout/12400 "2020-07-06T18:26:24Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Dis…

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## [Shape analysis interpretation](https://discourse.slicer.org/t/shape-analysis-interpretation/12193)

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**Author:** [@quentin\_devignes](https://discourse.slicer.org/u/quentin_devignes)\
**Replies:** 1\
**Last updated:** [July 6, 2020, 4:12pm UTC](https://discourse.slicer.org/t/shape-analysis-interpretation/12193 "2020-07-06T16:12:44Z")

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Dear SlicerSALT team, Currently using SPHARM-PDM analysis, I wonder what interpretation could be given when there are surface differences between two groups but no volume differences (assessed with 2 different methods)…

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## [Equation for medial axis from SPHARM-PDM](https://discourse.slicer.org/t/equation-for-medial-axis-from-spharm-pdm/12311)

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**Author:** [@christinah](https://discourse.slicer.org/u/christinah)\
**Replies:** 4\
**Last updated:** [July 6, 2020, 1:58pm UTC](https://discourse.slicer.org/t/equation-for-medial-axis-from-spharm-pdm/12311 "2020-07-06T13:58:59Z")

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Operating system: MacOS Catalina Slicer version: 4.10.2 Hi there, I’ve been using SPHARM-PDM and first want to say a really, truly huge thank you – both for the tool and for the extremely helpful Google slide tutorial…

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## [Multiple labels](https://discourse.slicer.org/t/multiple-labels/4505)

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**Author:** [@gpolier](https://discourse.slicer.org/u/gpolier)\
**Replies:** 0\
**Last updated:** [October 23, 2018, 3:05pm UTC](https://discourse.slicer.org/t/multiple-labels/4505 "2018-10-23T15:05:03Z")

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Operating system:MacOs Slicer version:1.0.0 Expected behavior:generate SPHARM from multiple labels Actual behavior: Hi, I would like to create one SPHARM-model from multiple lables (Hippocampus, 3 lables for head, b…

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## [2020.06.30 Hangout](https://discourse.slicer.org/t/2020-06-30-hangout/12286)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [June 30, 2020, 12:49pm UTC](https://discourse.slicer.org/t/2020-06-30-hangout/12286 "2020-06-30T12:49:21Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in New…

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## [Question regarding input as 3D image and setting voxelbased = False](https://discourse.slicer.org/t/question-regarding-input-as-3d-image-and-setting-voxelbased-false/12261)

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**Author:** [@Haoxin\_Zheng](https://discourse.slicer.org/u/Haoxin_Zheng)\
**Replies:** 1\
**Last updated:** [June 30, 2020, 10:46am UTC](https://discourse.slicer.org/t/question-regarding-input-as-3d-image-and-setting-voxelbased-false/12261 "2020-06-30T10:46:38Z")

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Hi, I think I just asked 2 related question but I wish I could get answers from your side both if possible. Im dealing with 2D MRI images. For each patient, the resolution in x-y direction is higher than the z directio…

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## [Question regarding 3D extraction ](https://discourse.slicer.org/t/question-regarding-3d-extraction/12262)

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**Author:** [@Haoxin\_Zheng](https://discourse.slicer.org/u/Haoxin_Zheng)\
**Replies:** 1\
**Last updated:** [June 30, 2020, 10:45am UTC](https://discourse.slicer.org/t/question-regarding-3d-extraction/12262 "2020-06-30T10:45:22Z")

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Hi all, I recently tried to extract features from a stack of 2D images (which is 3D, e.g. shape (320x320x12)), by setting “voxelbased = True”. I’m confused why the returned value is not a dictionary like the case when I…

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## [Image processing steps order when using the settings in the parameter file?](https://discourse.slicer.org/t/image-processing-steps-order-when-using-the-settings-in-the-parameter-file/11228)

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**Author:** [@radio5](https://discourse.slicer.org/u/radio5)\
**Replies:** 3\
**Last updated:** [June 30, 2020, 10:32am UTC](https://discourse.slicer.org/t/image-processing-steps-order-when-using-the-settings-in-the-parameter-file/11228 "2020-06-30T10:32:32Z")

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Hi! After I have cropped images to their tumour masks, I am aiming to: Resize all images to a specific image resolution Normalize image intensities Discretize images (Binning) However, I do not know what is the corre…

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## [Compliance with IBSI](https://discourse.slicer.org/t/compliance-with-ibsi/12062)

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**Author:** [@Bassam](https://discourse.slicer.org/u/Bassam)\
**Replies:** 2\
**Last updated:** [June 30, 2020, 10:28am UTC](https://discourse.slicer.org/t/compliance-with-ibsi/12062 "2020-06-30T10:28:05Z")

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Hello team, I got a promising imaging biomarkers and I have to check their compliance with their reference values identified by IBSI. To do that, I have to specify the following settings in the parameter file (yaml file…

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## [Possible issue with 2D extraction from DECT images](https://discourse.slicer.org/t/possible-issue-with-2d-extraction-from-dect-images/12238)

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**Author:** [@sanlen](https://discourse.slicer.org/u/sanlen)\
**Replies:** 4\
**Last updated:** [June 29, 2020, 4:20pm UTC](https://discourse.slicer.org/t/possible-issue-with-2d-extraction-from-dect-images/12238 "2020-06-29T16:20:45Z")

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Dear all, We are currently working on a project that involves obtaining pyradiomics features from dual-energy CT images which are in a normal DICOM format and can be loaded into 3DSlicer without any problems. We used th…

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## [2020.06.23 Hangout](https://discourse.slicer.org/t/2020-06-23-hangout/12168)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [June 23, 2020, 2:36pm UTC](https://discourse.slicer.org/t/2020-06-23-hangout/12168 "2020-06-23T14:36:10Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Fe…

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## [How to calculate 2D Radiomics features for each slice of a 3D volume with a 3D mask](https://discourse.slicer.org/t/how-to-calculate-2d-radiomics-features-for-each-slice-of-a-3d-volume-with-a-3d-mask/12163)

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**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\
**Replies:** 2\
**Last updated:** [June 23, 2020, 12:06pm UTC](https://discourse.slicer.org/t/how-to-calculate-2d-radiomics-features-for-each-slice-of-a-3d-volume-with-a-3d-mask/12163 "2020-06-23T12:06:19Z")

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Hi!!! I’m trying to calculate the radiomics features for each slice of a 3D volume with a 3D mask. I’ve been reading but nothing is very clear. I wonder if I will have to split the 3D volume and the 3D mask in 2D imag…

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## [Input mask for .jpg files](https://discourse.slicer.org/t/input-mask-for-jpg-files/11984)

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**Author:** [@Khalifa1997](https://discourse.slicer.org/u/Khalifa1997)\
**Replies:** 1\
**Last updated:** [June 23, 2020, 9:57am UTC](https://discourse.slicer.org/t/input-mask-for-jpg-files/11984 "2020-06-23T09:57:04Z")

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Hey there, I hope you guys are good, currently I am working on .jpg images, however I’d like to use radiomics.featureextractor.RadiomicsFeatureExtractor() the problem I am having however, is with the .execute is that wh…

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## [2020.06.16 Hangout](https://discourse.slicer.org/t/2020-06-16-hangout/12047)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 5\
**Last updated:** [June 19, 2020, 3:58am UTC](https://discourse.slicer.org/t/2020-06-16-hangout/12047 "2020-06-19T03:58:07Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Fe…

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## [dMRI Scalar Maps & Meausrements](https://discourse.slicer.org/t/dmri-scalar-maps-meausrements/11933)

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**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\
**Replies:** 4\
**Last updated:** [June 9, 2020, 4:53pm UTC](https://discourse.slicer.org/t/dmri-scalar-maps-meausrements/11933 "2020-06-09T16:53:26Z")

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Hi everyone, I could not find this info when going through the documentation, but I was wondering if there were definitions or more info about how the following are calculated using dMRI: -Relative Anisotropy -Determi…

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## [2020.06.09 Hangout](https://discourse.slicer.org/t/2020-06-09-hangout/11939)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [June 9, 2020, 2:15am UTC](https://discourse.slicer.org/t/2020-06-09-hangout/11939 "2020-06-09T02:15:09Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Fe…

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## [Can I calculate the feature "Ellipsoidity" of one 3D segmentation](https://discourse.slicer.org/t/can-i-calculate-the-feature-ellipsoidity-of-one-3d-segmentation/11750)

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**Author:** [@yanpfei](https://discourse.slicer.org/u/yanpfei)\
**Replies:** 4\
**Last updated:** [June 7, 2020, 11:33am UTC](https://discourse.slicer.org/t/can-i-calculate-the-feature-ellipsoidity-of-one-3d-segmentation/11750 "2020-06-07T11:33:49Z")

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I am using pyRadiomics to analyzed 3D segmentation of tumors. I noticed the feature " Sphericity" and it is very useful for tumor analysis. Besides this feauture, I want to calculate the " Ellipsoidity" of a tumor. Whe…

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## [2020.06.02 Hangout](https://discourse.slicer.org/t/2020-06-02-hangout/11820)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 2\
**Last updated:** [June 2, 2020, 3:51pm UTC](https://discourse.slicer.org/t/2020-06-02-hangout/11820 "2020-06-02T15:51:33Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Buil…

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## [Volume confounded variables](https://discourse.slicer.org/t/volume-confounded-variables/10526)

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**Author:** [@Martin\_Bzr](https://discourse.slicer.org/u/Martin_Bzr)\
**Replies:** 9\
**Last updated:** [May 26, 2020, 8:32pm UTC](https://discourse.slicer.org/t/volume-confounded-variables/10526 "2020-05-26T20:32:47Z")

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Hi, Thank you for this great toolbox ! As I understood from the docs the ‘\_firstorder\_Energy’ feature is volume confounded. What about ‘\_ngtdm\_Coarseness’ ? I’m looking at relationships between features and and the s…

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## [2020.05.26 Hangout](https://discourse.slicer.org/t/2020-05-26-hangout/11700)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [May 26, 2020, 1:57pm UTC](https://discourse.slicer.org/t/2020-05-26-hangout/11700 "2020-05-26T13:57:07Z")

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Tomorrow, we will be having our weekly hangout at 10:00 AM EST until 11 AM EST. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress check-in Fe…

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## [Default settings for defying GLCM, RLM](https://discourse.slicer.org/t/default-settings-for-defying-glcm-rlm/11629)

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**Author:** [@Bassam](https://discourse.slicer.org/u/Bassam)\
**Replies:** 2\
**Last updated:** [May 23, 2020, 8:49pm UTC](https://discourse.slicer.org/t/default-settings-for-defying-glcm-rlm/11629 "2020-05-23T20:49:41Z")

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Hi team. Kindly, I am quite a little bit confused about the default settings used for defying the gray level co-occurrence matrix (GLCM) and run length matrix as well (RLM). Does the GLCM, by default, study the occurre…

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## [Multiple VOI in pyradiomics](https://discourse.slicer.org/t/multiple-voi-in-pyradiomics/11482)

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**Author:** [@codecrazer](https://discourse.slicer.org/u/codecrazer)\
**Replies:** 3\
**Last updated:** [May 23, 2020, 2:15pm UTC](https://discourse.slicer.org/t/multiple-voi-in-pyradiomics/11482 "2020-05-23T14:15:28Z")

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If there were multiple VOIs and the pipeline extraction were used, but only Image and Mask were specified. The label column were not used. What will happen?

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