# Radiomics

**URL:** https://discourse.slicer.org/c/community/radiomics/23.md?page=4

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**Page:** 5

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## [Extract features using segment generated labelmap](https://discourse.slicer.org/t/extract-features-using-segment-generated-labelmap/19188)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 3\
**Last updated:** [August 17, 2021, 8:02pm UTC](https://discourse.slicer.org/t/extract-features-using-segment-generated-labelmap/19188 "2021-08-17T20:02:11Z")

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Hi all, In Slicer, I have segment done on CT images, but registration for CT and MRI is not good (these two are too far away). So I manually transform MRI to align with CT and harden the transform. Then, generate labelm…

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## [Radiomics error - No module named ‘pywt’](https://discourse.slicer.org/t/radiomics-error-no-module-named-pywt/19128)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 8\
**Last updated:** [August 12, 2021, 7:11pm UTC](https://discourse.slicer.org/t/radiomics-error-no-module-named-pywt/19128 "2021-08-12T19:11:22Z")

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Another question: I am trying to from radiomics import getFeatureClasses, but got the error " No module named ‘pywt’ ". I fixed the problem using the code mentioned here Slicer Radiomics error - #3 by fedorov , and @fed…

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## [Voxel-based feature extraction](https://discourse.slicer.org/t/voxel-based-feature-extraction/19060)

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**Author:** [@Sovan\_Mukherjee](https://discourse.slicer.org/u/Sovan_Mukherjee)\
**Replies:** 1\
**Last updated:** [August 4, 2021, 10:54pm UTC](https://discourse.slicer.org/t/voxel-based-feature-extraction/19060 "2021-08-04T22:54:41Z")

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Hi, I am trying to do a voxel-based feature extraction based on a CT pancreas mask. After setting Voxelbased = True, I extracted 88 features. It created 88 nifti images for individual features. While looking at the imag…

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## [Slicer Dicom to NRRD](https://discourse.slicer.org/t/slicer-dicom-to-nrrd/18629)

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**Author:** [@SyedaFatima123](https://discourse.slicer.org/u/SyedaFatima123)\
**Replies:** 12\
**Last updated:** [July 15, 2021, 3:25pm UTC](https://discourse.slicer.org/t/slicer-dicom-to-nrrd/18629 "2021-07-15T15:25:30Z")

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Hello I need urgent help . I have a dataset of caner patients, every patient with an ID has a folder with 28 dcm MRI images . I am using slicer to convert it to NRRD format but I want to ask is there any way I can conver…

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## [Normalize Pyradiomics features by the number of pixels (Volume)](https://discourse.slicer.org/t/normalize-pyradiomics-features-by-the-number-of-pixels-volume/18617)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 0\
**Last updated:** [July 10, 2021, 2:17pm UTC](https://discourse.slicer.org/t/normalize-pyradiomics-features-by-the-number-of-pixels-volume/18617 "2021-07-10T14:17:06Z")

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Hey guys, I am extracting radiomics from several different volume ROIS. I am afraid the ROI volume affects my evaluation, since many radiomic features are not divided by the number of pixels. I did even read an article …

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## [How to change Feature Filters in 3D Slicer?](https://discourse.slicer.org/t/how-to-change-feature-filters-in-3d-slicer/18281)

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**Author:** [@Mostafa2020](https://discourse.slicer.org/u/Mostafa2020)\
**Replies:** 0\
**Last updated:** [June 22, 2021, 7:20pm UTC](https://discourse.slicer.org/t/how-to-change-feature-filters-in-3d-slicer/18281 "2021-06-22T19:20:01Z")

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Hi all, Is there any way to change Feature Filters in 3D Slicer for the Radiomics module? Is “Wavelet-based features” the only option, or can we also consider other filter classes like square, square root, etc.? Thanks…

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## [Similarity of feature classes between 3D Slicer and PyRadiomics](https://discourse.slicer.org/t/similarity-of-feature-classes-between-3d-slicer-and-pyradiomics/18232)

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**Author:** [@Mostafa2020](https://discourse.slicer.org/u/Mostafa2020)\
**Replies:** 0\
**Last updated:** [June 20, 2021, 4:17am UTC](https://discourse.slicer.org/t/similarity-of-feature-classes-between-3d-slicer-and-pyradiomics/18232 "2021-06-20T04:17:11Z")

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Hi all, I am trying to extract features from a medical image; I wondered if a more expanded library of functions for feature classes is available and usable with Pyradiomics that is not available in 3D Slicer. Thanks.

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## [All radiomic features show blank after renaming a segmentation](https://discourse.slicer.org/t/all-radiomic-features-show-blank-after-renaming-a-segmentation/17652)

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**Author:** [@xackey](https://discourse.slicer.org/u/xackey)\
**Replies:** 2\
**Last updated:** [June 16, 2021, 3:28am UTC](https://discourse.slicer.org/t/all-radiomic-features-show-blank-after-renaming-a-segmentation/17652 "2021-06-16T03:28:12Z")

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In slicer radiomics, I find an issue below. Step 1. Make a segmentation by segmentation editor. Step 2. If change name of the segmentation, all radiomic features show blank and cannot be calculated (there is no problem…

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## [Can SlicerRadiomics perform Feature selection for 2D imaging?](https://discourse.slicer.org/t/can-slicerradiomics-perform-feature-selection-for-2d-imaging/11903)

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**Author:** [@LinJP123](https://discourse.slicer.org/u/LinJP123)\
**Replies:** 8\
**Last updated:** [June 5, 2021, 6:43pm UTC](https://discourse.slicer.org/t/can-slicerradiomics-perform-feature-selection-for-2d-imaging/11903 "2021-06-05T18:43:03Z")

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Operating system:window 10 Slicer version: 4.10.2 Expected behavior: Actual behavior: Can the SlicerRadiomics perform Feature selection for 2D imaging? And how to set?

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## [Error after building ](https://discourse.slicer.org/t/error-after-building/17445)

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**Author:** [@MarioGQ](https://discourse.slicer.org/u/MarioGQ)\
**Replies:** 1\
**Last updated:** [May 21, 2021, 6:36pm UTC](https://discourse.slicer.org/t/error-after-building/17445 "2021-05-21T18:36:53Z")

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Hi everyone. I keep receiving this error when i try to open Slicer environmenr after building it QWindowsEGLContext: ANGLE only partially supports OpenGL ES \> 3.0 QWindowsEGLContext: Failed to create context, eglError:…

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## [Resampling grey levels on imaging sets](https://discourse.slicer.org/t/resampling-grey-levels-on-imaging-sets/17468)

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**Author:** [@mdpy](https://discourse.slicer.org/u/mdpy)\
**Replies:** 0\
**Last updated:** [May 5, 2021, 12:29pm UTC](https://discourse.slicer.org/t/resampling-grey-levels-on-imaging-sets/17468 "2021-05-05T12:29:52Z")

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I finally have sorted all my raw imaging and labels (only took 3 months of coding!). Since then, I’ve been running some feature extractions on approximately 200 image sets. However after getting the basic’s running I th…

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## [R6034 Error using 3dSlicer](https://discourse.slicer.org/t/r6034-error-using-3dslicer/17300)

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**Author:** [@MarioGQ](https://discourse.slicer.org/u/MarioGQ)\
**Replies:** 0\
**Last updated:** [April 24, 2021, 11:00pm UTC](https://discourse.slicer.org/t/r6034-error-using-3dslicer/17300 "2021-04-24T23:00:51Z")

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Hi everyone. I am having trouble trying to use 3D Slicer to work with pyradiomics, specifically i get the Runtime Error R6034 (An application has made attemp to load the C runtime library incorrectly. Please contact the …

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## [More ROIs in one mask](https://discourse.slicer.org/t/more-rois-in-one-mask/17225)

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**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")

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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 …

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## [IBSI configuration A-E parameter files](https://discourse.slicer.org/t/ibsi-configuration-a-e-parameter-files/17213)

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**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")

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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…

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## [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)

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**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")

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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 …

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## [Radiomics, image input volume](https://discourse.slicer.org/t/radiomics-image-input-volume/13329)

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**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")

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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…

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## [Convert JPG to nrrd](https://discourse.slicer.org/t/convert-jpg-to-nrrd/17047)

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**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")

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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…

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## [Query on interpretation](https://discourse.slicer.org/t/query-on-interpretation/16639)

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**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")

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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,…

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## [Related to basics of pyradiomics](https://discourse.slicer.org/t/related-to-basics-of-pyradiomics/16984)

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**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")

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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

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## [Features value (mean and variance)](https://discourse.slicer.org/t/features-value-mean-and-variance/15850)

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**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")

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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…

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## [Total energy of image](https://discourse.slicer.org/t/total-energy-of-image/16660)

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**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")

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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,…

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## [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)

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**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")

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I got shape results (such as MajorAxisLength, LeastriAxisLength) through Radiomics analysis. Can I visualize it on model with 3Dslicer?

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## [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)

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**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")

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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…

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## [Radiomics to creat image map](https://discourse.slicer.org/t/radiomics-to-creat-image-map/15760)

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**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")

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Is it possible to create an image map based on specific features extracted using radiomics (for example GLCM feature)?

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

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**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")

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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…

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## [Customizing the extraction features](https://discourse.slicer.org/t/customizing-the-extraction-features/15630)

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**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")

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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.

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## [How to make the segmentation](https://discourse.slicer.org/t/how-to-make-the-segmentation/15581)

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**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")

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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

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## [How do extract GLRLM features from a .jpg image](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-jpg-image/15505)

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**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")

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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 …

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## [Radiomics result validation](https://discourse.slicer.org/t/radiomics-result-validation/15181)

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**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")

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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…

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## [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)

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**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")

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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…

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