# Community **URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=32 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 33 --- ## [More ROIs in one mask](https://discourse.slicer.org/t/more-rois-in-one-mask/17225)
**Author:** [@Giada\_Fiore](https://discourse.slicer.org/u/Giada_Fiore)\ **Replies:** 0\ **Last updated:** [April 21, 2021, 3:25pm UTC](https://discourse.slicer.org/t/more-rois-in-one-mask/17225 "2021-04-21T15:25:18Z")
Operating system: Windows 10 Slicer version: 4.10.2 Hi, I would like to extract the features from more ROIs, but I have only one mask that I have not created myself, so I load the image and its mask in .gz format. How … --- ## [IBSI configuration A-E parameter files](https://discourse.slicer.org/t/ibsi-configuration-a-e-parameter-files/17213)
**Author:** [@ivanzhovannik](https://discourse.slicer.org/u/ivanzhovannik)\ **Replies:** 0\ **Last updated:** [April 20, 2021, 3:04pm UTC](https://discourse.slicer.org/t/ibsi-configuration-a-e-parameter-files/17213 "2021-04-20T15:04:29Z")
Hi! I am trying to check if I understand the IBSI configurations https://ibsi.readthedocs.io/en/latest/05\_Reference\_data\_sets.htmlcorrectly by running their phantom through pyradiomics. However, I am constantly getting t… --- ## [2021.04.20 Hangout](https://discourse.slicer.org/t/2021-04-20-hangout/17181)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 2\ **Last updated:** [April 19, 2021, 5:52pm UTC](https://discourse.slicer.org/t/2021-04-20-hangout/17181 "2021-04-19T17:52:06Z")
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 Discourse subscrip… --- ## [2021.04.13 Hangout](https://discourse.slicer.org/t/2021-04-13-hangout/17045)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 7\ **Last updated:** [April 13, 2021, 3:44pm UTC](https://discourse.slicer.org/t/2021-04-13-hangout/17045 "2021-04-13T15:44:18Z")
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 PR-5349 - Pluggabl… --- ## [2021.03.30 Hangout](https://discourse.slicer.org/t/2021-03-30-hangout/16820)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 4\ **Last updated:** [April 19, 2021, 3:46pm UTC](https://discourse.slicer.org/t/2021-03-30-hangout/16820 "2021-04-19T15:46:44Z")
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 Website status Plu… --- ## [How to keep this setting as default](https://discourse.slicer.org/t/how-to-keep-this-setting-as-default/17168)
**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\ **Replies:** 0\ **Last updated:** [April 19, 2021, 12:37pm UTC](https://discourse.slicer.org/t/how-to-keep-this-setting-as-default/17168 "2021-04-19T12:37:16Z")
I used other extensions to change the background of the window. Problem is how to keep this setting as default, I tried to change the startup file, but it failed Anyone can help me?Thank you very much . --- ## [Help needed to segment CT spine vertebrae to stl](https://discourse.slicer.org/t/help-needed-to-segment-ct-spine-vertebrae-to-stl/17121)
**Author:** [@Hugo.altamirano](https://discourse.slicer.org/u/Hugo.altamirano)\ **Replies:** 1\ **Last updated:** [April 16, 2021, 4:03am UTC](https://discourse.slicer.org/t/help-needed-to-segment-ct-spine-vertebrae-to-stl/17121 "2021-04-16T04:03:16Z")
I’m new to annotation and am looking for help segmenting multi-level vertebrae in a CT scan to stl. Is there a guide or video to walk one through? Or can someone recommend a better tool? Thank you community in advance. --- ## [Different values of radiomics features between slicer radiomics and pyradiomics](https://discourse.slicer.org/t/different-values-of-radiomics-features-between-slicer-radiomics-and-pyradiomics/16956)
**Author:** [@Yasuhiro\_TAKEDA](https://discourse.slicer.org/u/Yasuhiro_TAKEDA)\ **Replies:** 2\ **Last updated:** [April 15, 2021, 1:03am UTC](https://discourse.slicer.org/t/different-values-of-radiomics-features-between-slicer-radiomics-and-pyradiomics/16956 "2021-04-15T01:03:21Z")
Hi I got different values of radiomics features between slicer radiomics (GUI) and pyradiomics (CUI). How could that happen? I read 5 MR images of brain, created 5 masks of tumor in 3d slicer, and performed radiomics … --- ## [Radiomics, image input volume](https://discourse.slicer.org/t/radiomics-image-input-volume/13329)
**Author:** [@KLH](https://discourse.slicer.org/u/KLH)\ **Replies:** 2\ **Last updated:** [April 14, 2021, 11:32am UTC](https://discourse.slicer.org/t/radiomics-image-input-volume/13329 "2021-04-14T11:32:40Z")
Operating system: Windows 10 Slicer version:4.10.2 Expected behavior: Able to choose a different image input volume Actual behavior:Can only select one image input volume (first one loaded maybe) Im new to slicer and… --- ## [cannot open .nhdr file on Slicer](https://discourse.slicer.org/t/cannot-open-nhdr-file-on-slicer/16579)
**Author:** [@Tamires\_Zanao](https://discourse.slicer.org/u/Tamires_Zanao)\ **Replies:** 1\ **Last updated:** [April 14, 2021, 6:16am UTC](https://discourse.slicer.org/t/cannot-open-nhdr-file-on-slicer/16579 "2021-04-14T06:16:32Z")
Hi everyone! I am trying to proceed with dwi QC, but I cannot open my axis aligned .nhdr dwi image on Slicer. I checked with unu head and the information of the image itself looks fine. I can also open/visualize my previ… --- ## [Has Centerline from Extract centreline module be smoothed?](https://discourse.slicer.org/t/has-centerline-from-extract-centreline-module-be-smoothed/16986)
**Author:** [@Ge\_Tang](https://discourse.slicer.org/u/Ge_Tang)\ **Replies:** 1\ **Last updated:** [April 14, 2021, 5:28am UTC](https://discourse.slicer.org/t/has-centerline-from-extract-centreline-module-be-smoothed/16986 "2021-04-14T05:28:44Z")
I want to do the geometric analysis. The VMTK tutorial described that the centerline goes through a Laplacian smoothing filter first and then computes the derivatives and the related quantities (Geometric Analysis | vmtk… --- ## [Convert JPG to nrrd](https://discourse.slicer.org/t/convert-jpg-to-nrrd/17047)
**Author:** [@Tonyale1975](https://discourse.slicer.org/u/Tonyale1975)\ **Replies:** 2\ **Last updated:** [April 14, 2021, 1:15am UTC](https://discourse.slicer.org/t/convert-jpg-to-nrrd/17047 "2021-04-14T01:15:00Z")
Dear PyRadiomics / 3DSlicer community, I imagine that the subject has already been discussed before. But, I couldn’t find the reference. I need to extract radiomic characteristics from .jpg images, is it possible? I t… --- ## [Call script in conda](https://discourse.slicer.org/t/call-script-in-conda/16473)
**Author:** [@szhang](https://discourse.slicer.org/u/szhang)\ **Replies:** 2\ **Last updated:** [April 12, 2021, 9:50pm UTC](https://discourse.slicer.org/t/call-script-in-conda/16473 "2021-04-12T21:50:12Z")
How can I call the script correctly? Here’s how my Miniconda3 window looks like (base) PS C:\> conda activate foo (foo) PS C:\> vmtkimagereader vmtkimagereader : The term ‘vmtkimagereader’ is not recognized as the name… --- ## [Project Week 35 preparation meetings start May 18 - mark your calendar!](https://discourse.slicer.org/t/project-week-35-preparation-meetings-start-may-18-mark-your-calendar/17044)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 0\ **Last updated:** [April 12, 2021, 6:37pm UTC](https://discourse.slicer.org/t/project-week-35-preparation-meetings-start-may-18-mark-your-calendar/17044 "2021-04-12T18:37:25Z")
Dear members of the Project Week community, After the success of the first online project week last December, we are renewing the experience for Project Week 35 (June 28-July 2, 2021). Weekly preparation meetings will s… --- ## [Automatic endpoint selection outside of surface module](https://discourse.slicer.org/t/automatic-endpoint-selection-outside-of-surface-module/17037)
**Author:** [@perecanals](https://discourse.slicer.org/u/perecanals)\ **Replies:** 1\ **Last updated:** [April 12, 2021, 4:41pm UTC](https://discourse.slicer.org/t/automatic-endpoint-selection-outside-of-surface-module/17037 "2021-04-12T16:41:32Z")
Hi, I am trying to extract centerlines from vascular models using the automatic endpoint selection from the VMTK module in Slicer, and in some cases (I’d say in about 10-20% of cases) I come across an error which gets t… --- ## [Query on interpretation](https://discourse.slicer.org/t/query-on-interpretation/16639)
**Author:** [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\ **Replies:** 4\ **Last updated:** [April 12, 2021, 9:02am UTC](https://discourse.slicer.org/t/query-on-interpretation/16639 "2021-04-12T09:02:26Z")
Hi… I am working on a 2 groups of patients with different therapies in brain cancer. I carried out T2 MRI texture analysis for different ROI. In selected 10 features for heterogeneity (uniformity, TE, entropy, variance,… --- ## [Vmtk networkextraction algorithm](https://discourse.slicer.org/t/vmtk-networkextraction-algorithm/16611)
**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\ **Replies:** 7\ **Last updated:** [April 12, 2021, 8:54am UTC](https://discourse.slicer.org/t/vmtk-networkextraction-algorithm/16611 "2021-04-12T08:54:52Z")
Hi All, Could someone please let me know the name of the network extraction algorithm available in VMTK? --- ## [Related to basics of pyradiomics](https://discourse.slicer.org/t/related-to-basics-of-pyradiomics/16984)
**Author:** [@Shalini](https://discourse.slicer.org/u/Shalini)\ **Replies:** 1\ **Last updated:** [April 12, 2021, 8:40am UTC](https://discourse.slicer.org/t/related-to-basics-of-pyradiomics/16984 "2021-04-12T08:40:20Z")
Hi All, I am very new to this study … Can anyone guide me how to proceed with learning feature extraction using pyradiomics… and how to understand the documentation better --- ## [Features value (mean and variance)](https://discourse.slicer.org/t/features-value-mean-and-variance/15850)
**Author:** [@Aleja\_Ichina](https://discourse.slicer.org/u/Aleja_Ichina)\ **Replies:** 6\ **Last updated:** [April 12, 2021, 8:33am UTC](https://discourse.slicer.org/t/features-value-mean-and-variance/15850 "2021-04-12T08:33:30Z")
Hi, Sorry, I have a question, why mean value and variance value are big. For example, I’m working with DICOM abdomen images and I segmented these in 3D slicer and I converted to .nrrd but when I apply pyradiomics the me… --- ## [Total energy of image](https://discourse.slicer.org/t/total-energy-of-image/16660)
**Author:** [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\ **Replies:** 1\ **Last updated:** [April 12, 2021, 8:16am UTC](https://discourse.slicer.org/t/total-energy-of-image/16660 "2021-04-12T08:16:45Z")
Hi… I am working on a 2 groups of patients with different therapies in brain cancer. I carried out T2 MRI texture analysis for different ROI. In selected 10 features for heterogeneity (uniformity, TE, entropy, variance,… --- ## [I got shape results (such as MajorAxisLength, LeastriAxisLength) through Radiomics analysis. Can I visualize it on model with 3Dslicer?](https://discourse.slicer.org/t/i-got-shape-results-such-as-majoraxislength-leastriaxislength-through-radiomics-analysis-can-i-visualize-it-on-model-with-3dslicer/16817)
**Author:** [@jinzhi\_lin](https://discourse.slicer.org/u/jinzhi_lin)\ **Replies:** 2\ **Last updated:** [April 12, 2021, 8:08am UTC](https://discourse.slicer.org/t/i-got-shape-results-such-as-majoraxislength-leastriaxislength-through-radiomics-analysis-can-i-visualize-it-on-model-with-3dslicer/16817 "2021-04-12T08:08:55Z")
I got shape results (such as MajorAxisLength, LeastriAxisLength) through Radiomics analysis. Can I visualize it on model with 3Dslicer? --- ## [2021.04.06 Hangout](https://discourse.slicer.org/t/2021-04-06-hangout/16953)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 2\ **Last updated:** [April 6, 2021, 11:49pm UTC](https://discourse.slicer.org/t/2021-04-06-hangout/16953 "2021-04-06T23:49:09Z")
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 Feel free to post… --- ## [Is there a way to make the bone flap we made into a lattice pattern](https://discourse.slicer.org/t/is-there-a-way-to-make-the-bone-flap-we-made-into-a-lattice-pattern/16939)
**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\ **Replies:** 2\ **Last updated:** [April 4, 2021, 3:56pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-make-the-bone-flap-we-made-into-a-lattice-pattern/16939 "2021-04-04T15:56:22Z")
Is there a way to make the bone flap we made into a lattice pattern, or similar to this pattern, just like this picture… --- ## [Merging Centrelines](https://discourse.slicer.org/t/merging-centrelines/16807)
**Author:** [@CJBright](https://discourse.slicer.org/u/CJBright)\ **Replies:** 1\ **Last updated:** [April 3, 2021, 2:42am UTC](https://discourse.slicer.org/t/merging-centrelines/16807 "2021-04-03T02:42:47Z")
Hi everyone, I used a programme to calculate the centrelines of a cardiovascular model I’ve been working on. I then used a Python script to save each branch individually. It starts at one end of the model and follows e… --- ## [Feature class (Image original, Mask original, Image interpolated, Mask interpolated)](https://discourse.slicer.org/t/feature-class-image-original-mask-original-image-interpolated-mask-interpolated/15806)
**Author:** [@Yasuhiro\_TAKEDA](https://discourse.slicer.org/u/Yasuhiro_TAKEDA)\ **Replies:** 3\ **Last updated:** [March 30, 2021, 2:56am UTC](https://discourse.slicer.org/t/feature-class-image-original-mask-original-image-interpolated-mask-interpolated/15806 "2021-03-30T02:56:49Z")
Hi I have a question about feature class in diagnostic, such as Image original, Mask original, Image interpolated, and Mask interpolated. What do they mean exactly? As in the figure above, the values of spacing, si… --- ## [Using VMTK in Python](https://discourse.slicer.org/t/using-vmtk-in-python/16479)
**Author:** [@RafaelPalomar](https://discourse.slicer.org/u/RafaelPalomar)\ **Replies:** 4\ **Last updated:** [March 27, 2021, 6:36pm UTC](https://discourse.slicer.org/t/using-vmtk-in-python/16479 "2021-03-27T18:36:53Z")
Hello, I’m trying to use the functionality of VMTK in the python interpreter (Slicer stable 20210226, Linux. Slicer-VMTK extension installed from the extension manager). When trying to import vtkvmtk I ge the following … --- ## [Using VMTK Branch Extractor Programatically (Python)](https://discourse.slicer.org/t/using-vmtk-branch-extractor-programatically-python/16560)
**Author:** [@mjg](https://discourse.slicer.org/u/mjg)\ **Replies:** 1\ **Last updated:** [March 26, 2021, 3:34am UTC](https://discourse.slicer.org/t/using-vmtk-branch-extractor-programatically-python/16560 "2021-03-26T03:34:01Z")
How can I get a bifurcated centerline as two separate numpy arrays? I can view the two centerlines with the below code. How can I then get the red centerline as one numpy array, and the blue centerline as another numpy a… --- ## [set work directory in VMTK/Pypes?](https://discourse.slicer.org/t/set-work-directory-in-vmtk-pypes/16563)
**Author:** [@MPP](https://discourse.slicer.org/u/MPP)\ **Replies:** 1\ **Last updated:** [March 26, 2021, 3:30am UTC](https://discourse.slicer.org/t/set-work-directory-in-vmtk-pypes/16563 "2021-03-26T03:30:17Z")
Hi all, Is it possible to set a work directory and switch to this directory at the start of a text file containing a list of VMTK commands? I developed a vmtk for an older version of VMTK that I could still easily laun… --- ## [Centerline extraction from python](https://discourse.slicer.org/t/centerline-extraction-from-python/16728)
**Author:** [@Ge\_Tang](https://discourse.slicer.org/u/Ge_Tang)\ **Replies:** 2\ **Last updated:** [March 25, 2021, 5:14pm UTC](https://discourse.slicer.org/t/centerline-extraction-from-python/16728 "2021-03-25T17:14:01Z")
Operating system: Mac Slicer version:4.11 Expected behavior: The centerline model from GUI of slicer has a different number of points compared with the centerline model I get from the python script Actual behavior: T… --- ## [2021.03.23 Hangout](https://discourse.slicer.org/t/2021-03-23-hangout/16692)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 2\ **Last updated:** [March 23, 2021, 2:49pm UTC](https://discourse.slicer.org/t/2021-03-23-hangout/16692 "2021-03-23T14:49:18Z")
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 Width issue w/ Li… [Previous page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=31) [Next page](https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=33)