# \#pyradiomics

**URL:** https://discourse.slicer.org/tag/pyradiomics/186.md

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

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## [Pyradiomics GLRLM crashing at native 100um resolution vs 250um](https://discourse.slicer.org/t/pyradiomics-glrlm-crashing-at-native-100um-resolution-vs-250um/47500)

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**Author:** [@oviya](https://discourse.slicer.org/u/oviya)\
**Replies:** 2\
**Last updated:** [June 29, 2026, 7:25pm UTC](https://discourse.slicer.org/t/pyradiomics-glrlm-crashing-at-native-100um-resolution-vs-250um/47500 "2026-06-29T19:25:43Z")

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Hello everyone! My name is Oviya, I’m an undergrad hoping to get a bit of help. I have been trying extract features from MRI images via a compute cluster, and have been successful with downsampled (250um) images (41MB).…

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## [Problems related to features between theory of radiomics and pyradiomics ](https://discourse.slicer.org/t/problems-related-to-features-between-theory-of-radiomics-and-pyradiomics/45679)

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**Author:** [@Cidi-2810](https://discourse.slicer.org/u/Cidi-2810)\
**Replies:** 0\
**Last updated:** [January 5, 2026, 9:28pm UTC](https://discourse.slicer.org/t/problems-related-to-features-between-theory-of-radiomics-and-pyradiomics/45679 "2026-01-05T21:28:50Z")

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https://docs.google.com/spreadsheets/d/1DA15prfyoDq8dxiiPZnI\_mUPHrWa\_AMV/edit?usp=sharing&ouid=116590247353327979827&rtpof=true&sd=true (This is a link excel that my partner and me did the test with features, I just test…

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## [When I set voxelBased=True and calculate the featureclass of glcm,I meet some problems](https://discourse.slicer.org/t/when-i-set-voxelbased-true-and-calculate-the-featureclass-of-glcm-i-meet-some-problems/28418)

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**Author:** [@duckfen](https://discourse.slicer.org/u/duckfen)\
**Replies:** 0\
**Last updated:** [March 16, 2023, 1:28pm UTC](https://discourse.slicer.org/t/when-i-set-voxelbased-true-and-calculate-the-featureclass-of-glcm-i-meet-some-problems/28418 "2023-03-16T13:28:39Z")

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code: extractor = featureextractor.RadiomicsFeatureExtractor('.yaml') result = extractor.execute(image, mask, voxelBased=True) for key, val in six.iteritems(result): if isinstance(val, sitk.Image): shape = (s…

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## [Parallel Voxel Batch Processing](https://discourse.slicer.org/t/parallel-voxel-batch-processing/42802)

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**Author:** [@annapurna11](https://discourse.slicer.org/u/annapurna11)\
**Replies:** 0\
**Last updated:** [May 6, 2025, 12:05am UTC](https://discourse.slicer.org/t/parallel-voxel-batch-processing/42802 "2025-05-06T00:05:57Z")

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Hello! I am trying to perform voxel-based radiomic feature extraction (GLCM features) for a single 3D prostrate cancer image. I am trying to speed up and also parallelize feature extraction of voxels. But instead of work…

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## [DWI radiomic features looking awkward?](https://discourse.slicer.org/t/dwi-radiomic-features-looking-awkward/41782)

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**Author:** [@Fazilhan\_Altintas](https://discourse.slicer.org/u/Fazilhan_Altintas)\
**Replies:** 1\
**Last updated:** [February 19, 2025, 10:12pm UTC](https://discourse.slicer.org/t/dwi-radiomic-features-looking-awkward/41782 "2025-02-19T22:12:02Z")

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Hello Dear 3d Slicer Community, I was segmenting a lesion on mulitple mri sequances to extract radiomic features. After I did I realized something very weird. For example I drew a mask on DWI and then slapped it onto ad…

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## [Feature Extraction depending on image type and intensity range](https://discourse.slicer.org/t/feature-extraction-depending-on-image-type-and-intensity-range/38298)

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**Author:** [@AMM](https://discourse.slicer.org/u/AMM)\
**Replies:** 0\
**Last updated:** [September 9, 2024, 6:55pm UTC](https://discourse.slicer.org/t/feature-extraction-depending-on-image-type-and-intensity-range/38298 "2024-09-09T18:55:06Z")

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Hi, I’m extracting features from MRI images. I do an initial feature extraction, followed by selection and binary classification with various machine learning models. My images are originally int16, the intensity acros…

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## [Automated PyRadiomics Feature work with DICOM(input image volume) and DICOM RT structure (input regions)](https://discourse.slicer.org/t/automated-pyradiomics-feature-work-with-dicom-input-image-volume-and-dicom-rt-structure-input-regions/36806)

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**Author:** [@youngchanseo](https://discourse.slicer.org/u/youngchanseo)\
**Replies:** 1\
**Last updated:** [June 17, 2024, 8:42am UTC](https://discourse.slicer.org/t/automated-pyradiomics-feature-work-with-dicom-input-image-volume-and-dicom-rt-structure-input-regions/36806 "2024-06-17T08:42:34Z")

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Hello. I have already installed pyradiomics and Slicer RT via extension manager. In the DICOM RT structure file, there are contour data for regions of interest (ROIs) \[1\]) of the tumor shape. In the DICOM file, I have…

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## [Voxel-based radiomic feature extraction](https://discourse.slicer.org/t/voxel-based-radiomic-feature-extraction/18901)

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**Author:** [@smcch](https://discourse.slicer.org/u/smcch)\
**Replies:** 12\
**Last updated:** [June 3, 2024, 12:00pm UTC](https://discourse.slicer.org/t/voxel-based-radiomic-feature-extraction/18901 "2024-06-03T12:00:33Z")

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Hi everyone, I am doing radiomic feature extraction using voxel-based mode. Although I can get the feature maps (.nrrd files), I can’t find a way to get each voxel’s values (radiomic feature). I need those values in a .c…

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## [Can you run PyRadiomics on multiple scans with labels within Slicer?](https://discourse.slicer.org/t/can-you-run-pyradiomics-on-multiple-scans-with-labels-within-slicer/35913)

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**Author:** [@Numan\_Kutaiba](https://discourse.slicer.org/u/Numan_Kutaiba)\
**Replies:** 2\
**Last updated:** [May 5, 2024, 1:32am UTC](https://discourse.slicer.org/t/can-you-run-pyradiomics-on-multiple-scans-with-labels-within-slicer/35913 "2024-05-05T01:32:54Z")

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Hi, I have used Slicer to extract radiomics features from CT scans with segmentation masks (for liver and spleen); one scan and mask at a time. I want to know if I could do the same for a whole folder of multiple scans…

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## [Cannot find Slicer Radiomics in extensions library](https://discourse.slicer.org/t/cannot-find-slicer-radiomics-in-extensions-library/35749)

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**Author:** [@Celina\_Hallal](https://discourse.slicer.org/u/Celina_Hallal)\
**Replies:** 1\
**Last updated:** [April 26, 2024, 2:49pm UTC](https://discourse.slicer.org/t/cannot-find-slicer-radiomics-in-extensions-library/35749 "2024-04-26T14:49:23Z")

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I’m trying to install Radiomics extension, but I can’t find it. Tried to install from file also, with no success. I’m currently using v5.7-2024-04-22 in a MacOS. Thanks in advance!

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## [How to select best parameter setting? (bin width)](https://discourse.slicer.org/t/how-to-select-best-parameter-setting-bin-width/21877)

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**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 2\
**Last updated:** [April 6, 2024, 2:44am UTC](https://discourse.slicer.org/t/how-to-select-best-parameter-setting-bin-width/21877 "2024-04-06T02:44:40Z")

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I am new to pyradiomics. I want to extract feature from a ct scan of lungs. I want to know what the best parameter settings are to extract my feature. Every time I use a different binwidth I get different results. I just…

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## [Error installing PyRadiomics](https://discourse.slicer.org/t/error-installing-pyradiomics/35105)

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**Author:** [@UnknownIta](https://discourse.slicer.org/u/UnknownIta)\
**Replies:** 3\
**Last updated:** [March 27, 2024, 5:12pm UTC](https://discourse.slicer.org/t/error-installing-pyradiomics/35105 "2024-03-27T17:12:47Z")

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I’m trying to download Radiomics but I ran into this error. Can anyone explain to me how I can solve this? Thank you in advance Install target: install C:\\Users\\AppData\\Local\\Temp\\pip-install-2mkjrouf\\simpleitk af1blh…

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## [Pyradiomics doesn't calculate features for all VOIs](https://discourse.slicer.org/t/pyradiomics-doesnt-calculate-features-for-all-vois/34454)

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**Author:** [@Dhartez](https://discourse.slicer.org/u/Dhartez)\
**Replies:** 0\
**Last updated:** [February 21, 2024, 4:08pm UTC](https://discourse.slicer.org/t/pyradiomics-doesnt-calculate-features-for-all-vois/34454 "2024-02-21T16:08:16Z")

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Hi all, I am having a little issue with pyradiomics in Slicer. Briefly, this is to extract features from CNN generated segmentations of two brain structures (bilaterally, so 4 segmentations / VOIs in total) on MRI. Whe…

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## [Slicer v. 5.6.0. Radiomics-module error while extracting features?](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280)

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**Author:** [@Magnus](https://discourse.slicer.org/u/Magnus)\
**Replies:** 5\
**Last updated:** [December 7, 2023, 2:26pm UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280 "2023-12-07T14:26:05Z")

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Hello, Updated slicer to the latest version (5.6.0). Now I get an error while trying to extract radiomic features using the Radiomics module. See following error message. What can I do? \[2023-12-07 09:15:38\] I: radiomi…

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## [How do I know what bin length I should be using?](https://discourse.slicer.org/t/how-do-i-know-what-bin-length-i-should-be-using/33164)

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**Author:** [@WilliamSchalley](https://discourse.slicer.org/u/WilliamSchalley)\
**Replies:** 0\
**Last updated:** [December 1, 2023, 4:50pm UTC](https://discourse.slicer.org/t/how-do-i-know-what-bin-length-i-should-be-using/33164 "2023-12-01T16:50:52Z")

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I am trying to incorporate radiomics into some MRI lung images and wondering if anyone has advice on what bin length I should be using? Or how do I find the best bin length to use? Any and all feedback is appreciated!

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## [DICOM to NRRD conversion in command line (for PyRadiomics)](https://discourse.slicer.org/t/dicom-to-nrrd-conversion-in-command-line-for-pyradiomics/32306)

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**Author:** [@marcin.jakalski](https://discourse.slicer.org/u/marcin.jakalski)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 5:50pm UTC](https://discourse.slicer.org/t/dicom-to-nrrd-conversion-in-command-line-for-pyradiomics/32306 "2023-10-18T17:50:25Z")

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Hello! I would like to recreate some of the functionality of 3D Slicer in command line for batch analysis of several hundred of patients’ images. I have a set of DICOM images along with their segmentations. For these I w…

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## [subregion analysis pyradiomics](https://discourse.slicer.org/t/subregion-analysis-pyradiomics/30758)

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**Author:** [@EdiKEM](https://discourse.slicer.org/u/EdiKEM)\
**Replies:** 0\
**Last updated:** [July 24, 2023, 11:42am UTC](https://discourse.slicer.org/t/subregion-analysis-pyradiomics/30758 "2023-07-24T11:42:57Z")

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Dear community, I have MRI dataset that has been outlined in clinical radiotherapy software to produce RTSS. I have converted the image and contours to NRRD format using the BatchStrutureSetConversion script. I am keen …

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## [About convert jpg to nrrd](https://discourse.slicer.org/t/about-convert-jpg-to-nrrd/30702)

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**Author:** [@Matt8268](https://discourse.slicer.org/u/Matt8268)\
**Replies:** 1\
**Last updated:** [July 21, 2023, 2:15pm UTC](https://discourse.slicer.org/t/about-convert-jpg-to-nrrd/30702 "2023-07-21T14:15:45Z")

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Dear PyRadiomics / 3DSlicer community, When importing JPEG images into 3D Slicer and converting them to the NRRD format, they may not be recognized by the Radiomics module. However, by converting them to a scalar volume…

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## [Help in setting up a script for CT image feature extraction with input as .npy files](https://discourse.slicer.org/t/help-in-setting-up-a-script-for-ct-image-feature-extraction-with-input-as-npy-files/30208)

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**Author:** [@Silke77](https://discourse.slicer.org/u/Silke77)\
**Replies:** 0\
**Last updated:** [June 24, 2023, 2:10pm UTC](https://discourse.slicer.org/t/help-in-setting-up-a-script-for-ct-image-feature-extraction-with-input-as-npy-files/30208 "2023-06-24T14:10:35Z")

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Dear all, is here someone i can talk to, who can help me with the start of uploading my data (.npy) in pyradiomics and extract features? the data is pre segmented CT images, which need to be loaded in python and i want …

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## [Radiomics stability analysis](https://discourse.slicer.org/t/radiomics-stability-analysis/22682)

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**Author:** [@JonasB](https://discourse.slicer.org/u/JonasB)\
**Replies:** 1\
**Last updated:** [March 19, 2023, 7:15pm UTC](https://discourse.slicer.org/t/radiomics-stability-analysis/22682 "2023-03-19T19:15:41Z")

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Hi, I am currently searching for a good method to test for radiomics feature stability. Unfortionetly, I do not have the opportunity to do a test-retesting as I am working with retrospective data. Is there any good me…

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## [Error in feature extraction for single voxel](https://discourse.slicer.org/t/error-in-feature-extraction-for-single-voxel/26927)

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**Author:** [@Satvik](https://discourse.slicer.org/u/Satvik)\
**Replies:** 0\
**Last updated:** [December 26, 2022, 3:09pm UTC](https://discourse.slicer.org/t/error-in-feature-extraction-for-single-voxel/26927 "2022-12-26T15:09:18Z")

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Can anyone suggest how to resolve this error in PyRadiomics? “mask only contains 1 segmented voxel! Cannot extract features for a single voxel.” Are there any parameters that can be adjusted in settings to resolve this…

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## [How to get the number of bins in pyradiomics?](https://discourse.slicer.org/t/how-to-get-the-number-of-bins-in-pyradiomics/25783)

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**Author:** [@Martha](https://discourse.slicer.org/u/Martha)\
**Replies:** 0\
**Last updated:** [October 19, 2022, 9:18pm UTC](https://discourse.slicer.org/t/how-to-get-the-number-of-bins-in-pyradiomics/25783 "2022-10-19T21:18:42Z")

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Hello, I‘m using pyradiomics and a constant binwith of default 25. How can I get the number of resulting bins? Thank you for your help.

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## [Default pyradiomics settings for PET and CT](https://discourse.slicer.org/t/default-pyradiomics-settings-for-pet-and-ct/25623)

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**Author:** [@mmay](https://discourse.slicer.org/u/mmay)\
**Replies:** 0\
**Last updated:** [October 10, 2022, 5:03am UTC](https://discourse.slicer.org/t/default-pyradiomics-settings-for-pet-and-ct/25623 "2022-10-10T05:03:07Z")

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Can the default pyradiomics settings be used indistinctly for PET, CT and MRI studies, without modifying any parameters? Thank you for your help!

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## [Extract preprocessed image and mask from Pyradiomics](https://discourse.slicer.org/t/extract-preprocessed-image-and-mask-from-pyradiomics/22654)

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**Author:** [@JonasB](https://discourse.slicer.org/u/JonasB)\
**Replies:** 4\
**Last updated:** [October 6, 2022, 9:50am UTC](https://discourse.slicer.org/t/extract-preprocessed-image-and-mask-from-pyradiomics/22654 "2022-10-06T09:50:08Z")

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Dear community, I was wondering if it is possible to extract the images and masks on which the feature calculation is based with Pyradiomics in command-line batch mode. I would like to make some comparisons on different…

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## [Pyradiomics, Brain MRI: How to Interpolate and remove outliers? ](https://discourse.slicer.org/t/pyradiomics-brain-mri-how-to-interpolate-and-remove-outliers/24683)

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**Author:** [@someOne](https://discourse.slicer.org/u/someOne)\
**Replies:** 0\
**Last updated:** [August 9, 2022, 6:39am UTC](https://discourse.slicer.org/t/pyradiomics-brain-mri-how-to-interpolate-and-remove-outliers/24683 "2022-08-09T06:39:36Z")

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Hello Team I was trying to extract features from brain MRI images using pyradiomics. According to this article (Page4) https://rdcu.be/cTh2N Two essential steps before the feature extraction are Interpolation to isot…

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## [pyradiomics w/ fixed bin width: bin number varies significantly across derived images](https://discourse.slicer.org/t/pyradiomics-w-fixed-bin-width-bin-number-varies-significantly-across-derived-images/24498)

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**Author:** [@stef](https://discourse.slicer.org/u/stef)\
**Replies:** 0\
**Last updated:** [July 26, 2022, 2:14pm UTC](https://discourse.slicer.org/t/pyradiomics-w-fixed-bin-width-bin-number-varies-significantly-across-derived-images/24498 "2022-07-26T14:14:51Z")

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Hi all, When using the fixed bin width setting, the median number of bins per patient varies a lot across the different derived images and the original image. I know this can be in part addressed by selecting a differen…

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## [What is the ideal bin width for PET radiomics?](https://discourse.slicer.org/t/what-is-the-ideal-bin-width-for-pet-radiomics/10558)

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**Author:** [@Nora](https://discourse.slicer.org/u/Nora)\
**Replies:** 4\
**Last updated:** [May 19, 2022, 2:41am UTC](https://discourse.slicer.org/t/what-is-the-ideal-bin-width-for-pet-radiomics/10558 "2022-05-19T02:41:54Z")

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Hi all, I’m trying to extract the radiomic features from PET images using Pyradiomics extension on 3DSlicer. The default settings for the binwidth is 25, however, that’s can’t calculate some features like the GLCMs. …

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## [PyRadiomics for 2D images (png or nrrd)](https://discourse.slicer.org/t/pyradiomics-for-2d-images-png-or-nrrd/6357)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 13\
**Last updated:** [May 17, 2022, 1:04pm UTC](https://discourse.slicer.org/t/pyradiomics-for-2d-images-png-or-nrrd/6357 "2022-05-17T13:04:11Z")

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Hi everyone, I am trying to extract radiomic features from 2D images (PNG or Nrrd) but I start to get a series of errors saying basically “3D array expected”. When I do that directly on slicer it works well. I’m using …

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## [Wavelet features with "flat region"?](https://discourse.slicer.org/t/wavelet-features-with-flat-region/22644)

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**Author:** [@Helo](https://discourse.slicer.org/u/Helo)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:46am UTC](https://discourse.slicer.org/t/wavelet-features-with-flat-region/22644 "2022-05-03T07:46:15Z")

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Hi everyone! I am doing a feature extraction and one of the problems I am having is some “flat regions” in the wavelet features of some events (not all dataset and not always the same features), like: …

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## [Many 0 and 1 appear in the extracted features](https://discourse.slicer.org/t/many-0-and-1-appear-in-the-extracted-features/23172)

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**Author:** [@lrc\_09](https://discourse.slicer.org/u/lrc_09)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:24am UTC](https://discourse.slicer.org/t/many-0-and-1-appear-in-the-extracted-features/23172 "2022-05-03T07:24:43Z")

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Hi, I used Radiomics module to extract PET image features. I set resampled voxel size to 1,1,1 and bin width to 64 based on the literatures , and the result shows that there are many 0 and 1 in GLCM, GLDM, GLRLM, GLSZM …

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