# Radiomics

**URL:** https://discourse.slicer.org/c/community/radiomics/23.md?page=2

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**Page:** 3

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## [Wavelet transformed image with Pyradiomics looks similar to original Image](https://discourse.slicer.org/t/wavelet-transformed-image-with-pyradiomics-looks-similar-to-original-image/26612)

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**Author:** [@JonasB](https://discourse.slicer.org/u/JonasB)\
**Replies:** 0\
**Last updated:** [December 6, 2022, 6:58pm UTC](https://discourse.slicer.org/t/wavelet-transformed-image-with-pyradiomics-looks-similar-to-original-image/26612 "2022-12-06T18:58:05Z")

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Dear 3D Slicer community, I used pyradiomics for image transformation applied all filters. I noticed that the image transformed with the LLL Wavelet Kernel looks very similar to the original image. Am I overlooking so…

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## [Should CT images be windowed prior to feature extraction?](https://discourse.slicer.org/t/should-ct-images-be-windowed-prior-to-feature-extraction/26610)

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**Author:** [@Hansman](https://discourse.slicer.org/u/Hansman)\
**Replies:** 0\
**Last updated:** [December 6, 2022, 5:08pm UTC](https://discourse.slicer.org/t/should-ct-images-be-windowed-prior-to-feature-extraction/26610 "2022-12-06T17:08:21Z")

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We’ve had a bit of debate in our group about whether CT images should be windowed from 16 bit grayscale to 8 bit grayscale values prior to extracting features, and I can’t find anything about it in the documentation. Doe…

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## [Features extraction](https://discourse.slicer.org/t/features-extraction/11047)

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**Author:** [@Tonyale1975](https://discourse.slicer.org/u/Tonyale1975)\
**Replies:** 9\
**Last updated:** [November 2, 2022, 2:12pm UTC](https://discourse.slicer.org/t/features-extraction/11047 "2022-11-02T14:12:06Z")

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Good morning Pyradiomics community. Is it possible to extract characteristics from an image without informing the mask (region of interest)? that is, I want to extract characteristics from the whole image. Thanks.

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## [In the radiomics plugin in 3d slicer, is the Log kernel size filled in 3.5? And for CT images with layer thickness of 2-5mm, should  use 3.3.3 or 1.1.1 for resampling?](https://discourse.slicer.org/t/in-the-radiomics-plugin-in-3d-slicer-is-the-log-kernel-size-filled-in-3-5-and-for-ct-images-with-layer-thickness-of-2-5mm-should-use-3-3-3-or-1-1-1-for-resampling/25842)

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**Author:** [@chengdelu](https://discourse.slicer.org/u/chengdelu)\
**Replies:** 0\
**Last updated:** [October 22, 2022, 12:40pm UTC](https://discourse.slicer.org/t/in-the-radiomics-plugin-in-3d-slicer-is-the-log-kernel-size-filled-in-3-5-and-for-ct-images-with-layer-thickness-of-2-5mm-should-use-3-3-3-or-1-1-1-for-resampling/25842 "2022-10-22T12:40:51Z")

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In the radiomics plugin in 3d slicer, is the Log kernel size filled in 3.5? And for CT images with layer thickness of 2-5mm, should use 3.3.3 or 1.1.1 for resampling?

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## [In the radiomics plugin in 3d slicer, is the Log kernel size filled in 3,5,7? And for CT images with layer thickness of 2-5mm, should  use 3,3,3 or 1,1,1 for resampling?](https://discourse.slicer.org/t/in-the-radiomics-plugin-in-3d-slicer-is-the-log-kernel-size-filled-in-3-5-7-and-for-ct-images-with-layer-thickness-of-2-5mm-should-use-3-3-3-or-1-1-1-for-resampling/25840)

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**Author:** [@chengdelu](https://discourse.slicer.org/u/chengdelu)\
**Replies:** 0\
**Last updated:** [October 22, 2022, 11:45am UTC](https://discourse.slicer.org/t/in-the-radiomics-plugin-in-3d-slicer-is-the-log-kernel-size-filled-in-3-5-7-and-for-ct-images-with-layer-thickness-of-2-5mm-should-use-3-3-3-or-1-1-1-for-resampling/25840 "2022-10-22T11:45:36Z")

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In the radiomics plugin in 3d slicer, is the Log kernel size filled in 3,5,7? And for CT images with layer thickness of 2-5mm, should use 3,3,3 or 1,1,1 for resampling?

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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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## [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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## [Applying different Wavelet Filters](https://discourse.slicer.org/t/applying-different-wavelet-filters/25029)

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**Author:** [@Ella1](https://discourse.slicer.org/u/Ella1)\
**Replies:** 0\
**Last updated:** [August 31, 2022, 2:50pm UTC](https://discourse.slicer.org/t/applying-different-wavelet-filters/25029 "2022-08-31T14:50:06Z")

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Operating system: Windows 10 Slicer version: 5.0.3 Expected behavior: Applying different Wavelet (db, coeif, …) and expect to see some differences Actual behavior: Do not see any differences between values after and b…

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## [Ask the easily install pyradiomic pip or conda at mac os monterey](https://discourse.slicer.org/t/ask-the-easily-install-pyradiomic-pip-or-conda-at-mac-os-monterey/25477)

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**Author:** [@taehyeongkim9010](https://discourse.slicer.org/u/taehyeongkim9010)\
**Replies:** 1\
**Last updated:** [September 29, 2022, 12:22pm UTC](https://discourse.slicer.org/t/ask-the-easily-install-pyradiomic-pip-or-conda-at-mac-os-monterey/25477 "2022-09-29T12:22:25Z")

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Can you suggest about the easily install pyradiomic pip or conda at mac os monterey Just a simple person who wanna study…

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## [Features confounded by the volume or ROI](https://discourse.slicer.org/t/features-confounded-by-the-volume-or-roi/25413)

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**Author:** [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Replies:** 1\
**Last updated:** [September 25, 2022, 1:21am UTC](https://discourse.slicer.org/t/features-confounded-by-the-volume-or-roi/25413 "2022-09-25T01:21:19Z")

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Currently, I use 3D slicer (pyradiomics plug in) to analyze myocardium of the heart (left ventricle). I draw ROI on myocardium of each time frames (total 25 frames on the same imaging plane) throughout a cardiac cycle. H…

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## [Fractal Dimension as feature](https://discourse.slicer.org/t/fractal-dimension-as-feature/25279)

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**Author:** [@scat2801](https://discourse.slicer.org/u/scat2801)\
**Replies:** 0\
**Last updated:** [September 15, 2022, 11:32am UTC](https://discourse.slicer.org/t/fractal-dimension-as-feature/25279 "2022-09-15T11:32:27Z")

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Does the package currently offer the option to include fractal dimension in its output?

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## [DICOM gray level normalization , 3 sigma normalization](https://discourse.slicer.org/t/dicom-gray-level-normalization-3-sigma-normalization/18518)

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**Author:** [@hamdullaherk](https://discourse.slicer.org/u/hamdullaherk)\
**Replies:** 1\
**Last updated:** [July 13, 2021, 8:11pm UTC](https://discourse.slicer.org/t/dicom-gray-level-normalization-3-sigma-normalization/18518 "2021-07-13T20:11:21Z")

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Hi, I am a radiologist who is interests in texture analysis and radomics. I am a beginner at 3Dslicer. Firstly I want to ask, how can I use 3sigma normalization technique in DICOM images. I don’t know how can ı do it? c…

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## [Why is SlicerRadiomics only partly functional?](https://discourse.slicer.org/t/why-is-slicerradiomics-only-partly-functional/24449)

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**Author:** [@harad](https://discourse.slicer.org/u/harad)\
**Replies:** 3\
**Last updated:** [July 22, 2022, 1:54pm UTC](https://discourse.slicer.org/t/why-is-slicerradiomics-only-partly-functional/24449 "2022-07-22T13:54:12Z")

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Hi everyone, I wonder why the GUI of Slicer radiomics has a massively trimmed functionality in comparison to the standalone Pyradiomics. Thereby, only LoG, Wavelet and Original image types can be activated. That leaves s…

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## [Feature Error in python](https://discourse.slicer.org/t/feature-error-in-python/24428)

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**Author:** [@Van\_Tran\_Sang\_Huynh](https://discourse.slicer.org/u/Van_Tran_Sang_Huynh)\
**Replies:** 1\
**Last updated:** [July 21, 2022, 5:23pm UTC](https://discourse.slicer.org/t/feature-error-in-python/24428 "2022-07-21T17:23:36Z")

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I use python pyrradiomics to extract features for .nrrd images. And I got an error… how can i fix it. Please help!!! Respect Sang I use code And error…

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## [Texture features](https://discourse.slicer.org/t/texture-features/23985)

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**Author:** [@Chiara](https://discourse.slicer.org/u/Chiara)\
**Replies:** 1\
**Last updated:** [June 21, 2022, 4:37pm UTC](https://discourse.slicer.org/t/texture-features/23985 "2022-06-21T16:37:48Z")

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Hello, we are students. We would like to ask for help on texture features (GLCM e GLRLM), are they dimensionless quantities? If yes, can you explain how they are calculated? thanks to those who will answer!

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## [ pyradiomics with DICOM data](https://discourse.slicer.org/t/pyradiomics-with-dicom-data/22636)

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**Author:** [@Geor\_F](https://discourse.slicer.org/u/Geor_F)\
**Replies:** 14\
**Last updated:** [June 13, 2022, 2:27pm UTC](https://discourse.slicer.org/t/pyradiomics-with-dicom-data/22636 "2022-06-13T14:27:38Z")

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Hello, I would like to use pyradiomics with DICOM data, in the guideline it says “The script will accept as input a directory with a single DICOM image study for the input image, and the file name pointing to a DICOM S…

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## [Feature extraction in 2D image](https://discourse.slicer.org/t/feature-extraction-in-2d-image/23828)

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**Author:** [@Rohini\_Gaikar](https://discourse.slicer.org/u/Rohini_Gaikar)\
**Replies:** 1\
**Last updated:** [June 12, 2022, 1:20am UTC](https://discourse.slicer.org/t/feature-extraction-in-2d-image/23828 "2022-06-12T01:20:04Z")

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I have image and mask in float64. When I try to cast mask in INT32vit gives me error. sitk\_mask = sitk.Cast(sitk\_mask, sitk.sitkInt32) Error is as: sitk::ERROR: Filter does not support casting from casting 64-bit flo…

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## [N4ITK filter Question](https://discourse.slicer.org/t/n4itk-filter-question/23802)

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**Author:** [@Josefa\_Garcia](https://discourse.slicer.org/u/Josefa_Garcia)\
**Replies:** 0\
**Last updated:** [June 9, 2022, 9:12pm UTC](https://discourse.slicer.org/t/n4itk-filter-question/23802 "2022-06-09T21:12:14Z")

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Hi everyone, I’m in the pre-processing imaging step of radiomics workflow, and I was wondering if the N4ITK filter is enough to correct intensity inhomogeneities and noise on MRI brain images. Thanks!

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## [Mask of dicom image](https://discourse.slicer.org/t/mask-of-dicom-image/23684)

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**Author:** [@Van\_Tran\_Sang\_Huynh](https://discourse.slicer.org/u/Van_Tran_Sang_Huynh)\
**Replies:** 2\
**Last updated:** [June 5, 2022, 1:33pm UTC](https://discourse.slicer.org/t/mask-of-dicom-image/23684 "2022-06-05T13:33:39Z")

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I use python pyradiomics for feature extraction. I have imported the DICOM image but about the masking part i still don’t know if i did it right or not. If my masking part is wrong, please tell me how to correct and mask…

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## [How to run Pyradiomics](https://discourse.slicer.org/t/how-to-run-pyradiomics/23047)

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**Author:** [@Van\_Tran\_Sang\_Huynh](https://discourse.slicer.org/u/Van_Tran_Sang_Huynh)\
**Replies:** 11\
**Last updated:** [May 31, 2022, 11:29am UTC](https://discourse.slicer.org/t/how-to-run-pyradiomics/23047 "2022-05-31T11:29:23Z")

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Hi. I am a student, I am practicing using pyrradiomics for feature extraction. I have installed pyradiomics in python 3.6 (64bit), but I don’t know how to run Pyradiomics, please help. Thank you

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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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## [2d image segmentation radiomic feature generator ](https://discourse.slicer.org/t/2d-image-segmentation-radiomic-feature-generator/23457)

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**Author:** [@Manju\_Manju](https://discourse.slicer.org/u/Manju_Manju)\
**Replies:** 0\
**Last updated:** [May 17, 2022, 1:47pm UTC](https://discourse.slicer.org/t/2d-image-segmentation-radiomic-feature-generator/23457 "2022-05-17T13:47:21Z")

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Sir Im trying segmentation on 2d images but im not able to get the output table of radiomic feature generator.can you please guide me

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## [Total number of radiomics features](https://discourse.slicer.org/t/total-number-of-radiomics-features/17947)

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**Author:** [@Chenglin\_Zhu](https://discourse.slicer.org/u/Chenglin_Zhu)\
**Replies:** 4\
**Last updated:** [May 3, 2022, 7:42am UTC](https://discourse.slicer.org/t/total-number-of-radiomics-features/17947 "2022-05-03T07:42:44Z")

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Hello Slicer Community! In Radiomics of Slicer, the maximum number of radiomic features is 130, which is mostly consistent with the number of features specified in the documentation of Pyradiomics (Radiomic Features — p…

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## [Reproducibility of Radiomics Results with Pyradiomics and Parenchymal Analysis](https://discourse.slicer.org/t/reproducibility-of-radiomics-results-with-pyradiomics-and-parenchymal-analysis/22933)

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**Author:** [@chuawm](https://discourse.slicer.org/u/chuawm)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:40am UTC](https://discourse.slicer.org/t/reproducibility-of-radiomics-results-with-pyradiomics-and-parenchymal-analysis/22933 "2022-05-03T07:40:55Z")

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Hi there, I am trying to see if the Radiomics module analysis for the lung segmentation I performed using CIP is consistent with that derived from Parenchymal Analysis. This is partly because the Parenchymal Analysis is…

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## [features extract with .png image](https://discourse.slicer.org/t/features-extract-with-png-image/23049)

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**Author:** [@JY\_C](https://discourse.slicer.org/u/JY_C)\
**Replies:** 1\
**Last updated:** [May 3, 2022, 7:34am UTC](https://discourse.slicer.org/t/features-extract-with-png-image/23049 "2022-05-03T07:34:35Z")

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I want to extract features with HE image, and I save the tiles with .png file. Here is my code: image = sitk.ReadImage(‘test.png’) # dim=(1024, 1024, 3) mask\_arr = np.ones(image.GetSize()\[::-1\]) mask = sitk.GetImageFr…

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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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## [Pyradiomics extension](https://discourse.slicer.org/t/pyradiomics-extension/23089)

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**Author:** [@Ywatana29](https://discourse.slicer.org/u/Ywatana29)\
**Replies:** 2\
**Last updated:** [April 23, 2022, 6:32pm UTC](https://discourse.slicer.org/t/pyradiomics-extension/23089 "2022-04-23T18:32:51Z")

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I have noticed the following message at Radiomics. Is it correct. It must be because I cannot find Slicer Radiomics in the extension manager currently. Pending resolution of packaging issues, SlicerRadiomics is not curr…

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## [IBSI & pyRadiomic](https://discourse.slicer.org/t/ibsi-pyradiomic/18137)

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**Author:** [@Chenglin\_Zhu](https://discourse.slicer.org/u/Chenglin_Zhu)\
**Replies:** 3\
**Last updated:** [March 23, 2022, 2:16pm UTC](https://discourse.slicer.org/t/ibsi-pyradiomic/18137 "2022-03-23T14:16:52Z")

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Dear community, Are there any tutorials on setting the pyRadiomic to adhere to the IBSI? I wish to follow the IBSI standardization yet I am not willing to give up the convenience of pyRadiomic. If not, is there any reco…

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## [Creation of Mask files for the given images](https://discourse.slicer.org/t/creation-of-mask-files-for-the-given-images/22584)

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**Author:** [@Praful\_Kumar](https://discourse.slicer.org/u/Praful_Kumar)\
**Replies:** 0\
**Last updated:** [March 18, 2022, 2:10pm UTC](https://discourse.slicer.org/t/creation-of-mask-files-for-the-given-images/22584 "2022-03-18T14:10:10Z")

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I have with me a dataset for brain tumour detection REMBRANDT - The Cancer Imaging Archive (TCIA) Public Access - Cancer Imaging Archive Wiki. I want to extract radiomic features by using pyradiomics library. However, …

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## [Discontinuous ROI for radiomics](https://discourse.slicer.org/t/discontinuous-roi-for-radiomics/22483)

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**Author:** [@Amir\_Zolal](https://discourse.slicer.org/u/Amir_Zolal)\
**Replies:** 0\
**Last updated:** [March 13, 2022, 12:59pm UTC](https://discourse.slicer.org/t/discontinuous-roi-for-radiomics/22483 "2022-03-13T12:59:00Z")

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Hello, this is rather a general question regarding the functioning of the algorithm. I have some ROIs that I use to extract image pixel intensity from images and would like to re-use these ROIs in feature detection. How…

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