# Radiomics

**URL:** https://discourse.slicer.org/c/community/radiomics/23.md?page=3

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**Page:** 4

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## [Wrong message in extracting radiomics about 64-bit float](https://discourse.slicer.org/t/wrong-message-in-extracting-radiomics-about-64-bit-float/11669)

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**Author:** [@zhangqw](https://discourse.slicer.org/u/zhangqw)\
**Replies:** 6\
**Last updated:** [March 11, 2022, 8:53am UTC](https://discourse.slicer.org/t/wrong-message-in-extracting-radiomics-about-64-bit-float/11669 "2022-03-11T08:53:02Z")

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When I extracted from 3D segment, some could be extracted but some failed, the wrong messgae is as follows: \[2020-05-22 21:40:45\] E: radiomics.script: Feature extraction failed! Traceback (most recent call last): File…

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## [Missing IBSI fetaures in Pyradiomics.](https://discourse.slicer.org/t/missing-ibsi-fetaures-in-pyradiomics/22325)

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**Author:** [@JonasB](https://discourse.slicer.org/u/JonasB)\
**Replies:** 1\
**Last updated:** [March 5, 2022, 4:12pm UTC](https://discourse.slicer.org/t/missing-ibsi-fetaures-in-pyradiomics/22325 "2022-03-05T16:12:43Z")

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Dear Community. I noticed some Issues with missing features from the IBSI recommendation in Pyradiomics. I went through the feature definitions and compared them (IBSI: https://pubs.rsna.org/doi/full/10.1148/radiol.202…

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## [Scanner Comparision](https://discourse.slicer.org/t/scanner-comparision/22092)

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**Author:** [@Alan\_Haper](https://discourse.slicer.org/u/Alan_Haper)\
**Replies:** 0\
**Last updated:** [February 21, 2022, 5:15pm UTC](https://discourse.slicer.org/t/scanner-comparision/22092 "2022-02-21T17:15:48Z")

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Dear Community, I am new to pyradiomics and currently try to compare different scanners to each other. There is a difference in shape features even though the organs are about the same size in real world. (The nifti ima…

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## [Can I use lmaps generated from CIP to extract features with Pyradiomics?](https://discourse.slicer.org/t/can-i-use-lmaps-generated-from-cip-to-extract-features-with-pyradiomics/21785)

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**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 0\
**Last updated:** [February 3, 2022, 5:19pm UTC](https://discourse.slicer.org/t/can-i-use-lmaps-generated-from-cip-to-extract-features-with-pyradiomics/21785 "2022-02-03T17:19:48Z")

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I am new to pyradiomics. I have used CIPs Interactive lobe segmentation to get a lung label map(lmap.nrrd). and I’m using a ct.nrrd as my input volume, obtained from dicoms. I wanted to know if I can use this ct and lma…

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## [Brief Introduction. Help needed](https://discourse.slicer.org/t/brief-introduction-help-needed/21680)

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**Author:** [@dnevado](https://discourse.slicer.org/u/dnevado)\
**Replies:** 0\
**Last updated:** [January 28, 2022, 2:56pm UTC](https://discourse.slicer.org/t/brief-introduction-help-needed/21680 "2022-01-28T14:56:21Z")

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First, pleasure to be part of this discussion group. I am a newbie on this topic and struggling how to address on of the research someone has requested me to have a look. Objective is to analyze the likely progression of…

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## [Slicer radiomics-features](https://discourse.slicer.org/t/slicer-radiomics-features/21280)

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**Author:** [@MPhilip](https://discourse.slicer.org/u/MPhilip)\
**Replies:** 16\
**Last updated:** [January 28, 2022, 12:25pm UTC](https://discourse.slicer.org/t/slicer-radiomics-features/21280 "2022-01-28T12:25:17Z")

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Operating system:Windows 10 enterprise Slicer version:3D slicer 4.13.0-2021-12-15 Hi I was extracting features using the Slicer radiomics module from GTV of RTStruct. But when I see the table containing the features m…

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## [Radiomic features with identical values](https://discourse.slicer.org/t/radiomic-features-with-identical-values/18188)

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**Author:** [@Gergely\_Orsi](https://discourse.slicer.org/u/Gergely_Orsi)\
**Replies:** 3\
**Last updated:** [January 21, 2022, 10:21am UTC](https://discourse.slicer.org/t/radiomic-features-with-identical-values/18188 "2022-01-21T10:21:33Z")

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Dear Community Members, I do not have too much prior experience with pyradiomics, so sorry for the dull question. I have several features with identical values and I’d like to know if it’s ok, or not. Examples: In Gr…

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## [How radiomics calculate numbers](https://discourse.slicer.org/t/how-radiomics-calculate-numbers/19391)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 10:20am UTC](https://discourse.slicer.org/t/how-radiomics-calculate-numbers/19391 "2022-01-21T10:20:19Z")

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Hi all, I got some basic questions about radiomics. Say I have input image A and a lablemap B as input region, I got first-order features like mean, min, max using Radiomics. I assume Radiomics first generate an array u…

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## [Image type input to pyRadiommics](https://discourse.slicer.org/t/image-type-input-to-pyradiommics/17893)

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**Author:** [@11117](https://discourse.slicer.org/u/11117)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 10:07am UTC](https://discourse.slicer.org/t/image-type-input-to-pyradiommics/17893 "2022-01-21T10:07:49Z")

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Hi, pyRadiommics knows how to handle float input? (nrrd file with float arrays) or it will convert it to int? or there is a any problem with very high float variable? Tnx

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## [Feature Extraction](https://discourse.slicer.org/t/feature-extraction/17706)

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**Author:** [@HAFSA](https://discourse.slicer.org/u/HAFSA)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 10:05am UTC](https://discourse.slicer.org/t/feature-extraction/17706 "2022-01-21T10:05:04Z")

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Hey: I want to extract the radiomic features of 2D Slices. But it fails when the mask with only background is found or no tumor area. You can say blank slices .On the other hand I want to extract the feature of all slic…

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## [Help in deep understanding pyRadiomics](https://discourse.slicer.org/t/help-in-deep-understanding-pyradiomics/16269)

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**Author:** [@11117](https://discourse.slicer.org/u/11117)\
**Replies:** 3\
**Last updated:** [January 21, 2022, 10:01am UTC](https://discourse.slicer.org/t/help-in-deep-understanding-pyradiomics/16269 "2022-01-21T10:01:12Z")

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Hello everyone, I’m trying to understand my results that I get from pyradiomics - FeatureExtractor and I have two questions: I want to understand what values the extractor gets me, so I calculate manually the energy, …

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## [Extract multiple labels from one image without reloading image and mask data? ](https://discourse.slicer.org/t/extract-multiple-labels-from-one-image-without-reloading-image-and-mask-data/21468)

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**Author:** [@Sebastian\_Nagel](https://discourse.slicer.org/u/Sebastian_Nagel)\
**Replies:** 3\
**Last updated:** [January 19, 2022, 8:40pm UTC](https://discourse.slicer.org/t/extract-multiple-labels-from-one-image-without-reloading-image-and-mask-data/21468 "2022-01-19T20:40:17Z")

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Dear Community, we performed a CT segmentation for which we placed multiple labels into one dataset. Now when we start extracting the features using either the command line or a Jupyter notebook, the image and mask dat…

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## [Radiomics warning Size in specified 2D dimension (0) is greater than 1, cannot calculate 2D shape](https://discourse.slicer.org/t/radiomics-warning-size-in-specified-2d-dimension-0-is-greater-than-1-cannot-calculate-2d-shape/21424)

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**Author:** [@zandarina](https://discourse.slicer.org/u/zandarina)\
**Replies:** 2\
**Last updated:** [January 18, 2022, 12:38pm UTC](https://discourse.slicer.org/t/radiomics-warning-size-in-specified-2d-dimension-0-is-greater-than-1-cannot-calculate-2d-shape/21424 "2022-01-18T12:38:39Z")

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Dear all, I am trying to compute the radiomics and I get this warning: Size in specified 2D dimension (0) is greater than 1, cannot calculate 2D shape result = extractor.execute(image, mask) and the image size is: (…

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## [Pyradiomics (GLCM) calculation](https://discourse.slicer.org/t/pyradiomics-glcm-calculation/21154)

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**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\
**Replies:** 2\
**Last updated:** [January 14, 2022, 7:34pm UTC](https://discourse.slicer.org/t/pyradiomics-glcm-calculation/21154 "2022-01-14T19:34:47Z")

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Hi developers, I am working on implementing a past study on radiomics. The extract from the published report includes the definition of the GLCM radiomic features as follows in their matlab software: “Neighbouring voxe…

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## [Feature extraction from anisotropic 3D VOIs: should we apply Force2D potion?](https://discourse.slicer.org/t/feature-extraction-from-anisotropic-3d-vois-should-we-apply-force2d-potion/21285)

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**Author:** [@Eugene](https://discourse.slicer.org/u/Eugene)\
**Replies:** 5\
**Last updated:** [January 12, 2022, 2:03am UTC](https://discourse.slicer.org/t/feature-extraction-from-anisotropic-3d-vois-should-we-apply-force2d-potion/21285 "2022-01-12T02:03:54Z")

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Greetings expert team. Much obliged for your great invention and maintanance of pyradiomics! I’m currently working on some MRI T2WI data, consecutively delineating 2D ROIs in each slice on the coronal plane. I noticed t…

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## [Pyradiomics LoG filter voxel or physical space?](https://discourse.slicer.org/t/pyradiomics-log-filter-voxel-or-physical-space/19944)

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**Author:** [@GVK](https://discourse.slicer.org/u/GVK)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 12:20pm UTC](https://discourse.slicer.org/t/pyradiomics-log-filter-voxel-or-physical-space/19944 "2022-01-11T12:20:52Z")

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Operating system:na Slicer version:na Expected behavior:na Actual behavior:na In pyradiomics default settings, are the settings of the LoG filter defined in voxel space or in physical space?

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## [Intensity Resampling in SlicerRadiomicc](https://discourse.slicer.org/t/intensity-resampling-in-slicerradiomicc/17134)

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**Author:** [@Giada\_Fiore](https://discourse.slicer.org/u/Giada_Fiore)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 12:14pm UTC](https://discourse.slicer.org/t/intensity-resampling-in-slicerradiomicc/17134 "2022-01-11T12:14:28Z")

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Hi, I’m working with CT images in Slicer Radiomics, but I have a doubt: is intensity resampling absolute or relative to ROI? I have set a fixed bin length. Thank you!

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## [Classification of features radiomics](https://discourse.slicer.org/t/classification-of-features-radiomics/17077)

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**Author:** [@Tonyale1975](https://discourse.slicer.org/u/Tonyale1975)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 12:09pm UTC](https://discourse.slicer.org/t/classification-of-features-radiomics/17077 "2022-01-11T12:09:06Z")

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Dear PyRadiomics / 3DSlicer community, I have been extracting radiomic features with PyRadiomics. But, when I try to carry out a classification using machine learning techniques, usually the different classifiers class…

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## [Syntax parameter file](https://discourse.slicer.org/t/syntax-parameter-file/16907)

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**Author:** [@Marion](https://discourse.slicer.org/u/Marion)\
**Replies:** 6\
**Last updated:** [January 11, 2022, 12:06pm UTC](https://discourse.slicer.org/t/syntax-parameter-file/16907 "2022-01-11T12:06:02Z")

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Operating system: macOS High Sierra (10.13.6) Slicer version: 4.11.20200930 Expected behavior: Actual behavior: Hi everyone, I have a problem with the syntax of the parameter file for the Radiomics module. I attach …

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## [number of extracted features](https://discourse.slicer.org/t/number-of-extracted-features/21002)

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**Author:** [@mina](https://discourse.slicer.org/u/mina)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 11:32am UTC](https://discourse.slicer.org/t/number-of-extracted-features/21002 "2022-01-11T11:32:14Z")

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Operating system:IOS Slicer version:.11.20210226 r29738 hello, I have a question about the extracted features by Radiomics extension. when I resample a MRI sequence, for some sapcing -dimensions it extracts 140 featu…

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## [Changing pyradiomics json Params file](https://discourse.slicer.org/t/changing-pyradiomics-json-params-file/21075)

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**Author:** [@Valentina\_Nepi](https://discourse.slicer.org/u/Valentina_Nepi)\
**Replies:** 3\
**Last updated:** [January 11, 2022, 11:31am UTC](https://discourse.slicer.org/t/changing-pyradiomics-json-params-file/21075 "2022-01-11T11:31:29Z")

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Is it possible to change this file? I’ve tried to use a params file.yaml converted in json but it doesn’t work. Any suggestions? Thanks

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## [Pyradiomics in 3D Slicer - install via Extension Manager?](https://discourse.slicer.org/t/pyradiomics-in-3d-slicer-install-via-extension-manager/21394)

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**Author:** [@Gordon\_Cowell](https://discourse.slicer.org/u/Gordon_Cowell)\
**Replies:** 2\
**Last updated:** [January 11, 2022, 1:07am UTC](https://discourse.slicer.org/t/pyradiomics-in-3d-slicer-install-via-extension-manager/21394 "2022-01-11T01:07:43Z")

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Hi, I’m needing to switch from using Slicer 3D on my MacBook to a newer Windows version to help workflow on a project. However, the Radiomics extension doesn’t now work when you try to install in via the Slicer 3D exten…

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## [Using ImageJ segmentations with Pyradiomics](https://discourse.slicer.org/t/using-imagej-segmentations-with-pyradiomics/20835)

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**Author:** [@Sari\_Khalil](https://discourse.slicer.org/u/Sari_Khalil)\
**Replies:** 5\
**Last updated:** [December 5, 2021, 3:35pm UTC](https://discourse.slicer.org/t/using-imagej-segmentations-with-pyradiomics/20835 "2021-12-05T15:35:36Z")

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Hello, I want to convert a deck of segmentations of multiple slices in a CT image made using ImageJ into usable input for pyRadiomics. For example, in the attached screenshot, you can see that I have 3 segmentations,…

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## [complex value for shape feature elongation and flatness which involves two PCA components ](https://discourse.slicer.org/t/complex-value-for-shape-feature-elongation-and-flatness-which-involves-two-pca-components/20601)

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**Author:** [@gyy](https://discourse.slicer.org/u/gyy)\
**Replies:** 0\
**Last updated:** [November 12, 2021, 1:37pm UTC](https://discourse.slicer.org/t/complex-value-for-shape-feature-elongation-and-flatness-which-involves-two-pca-components/20601 "2021-11-12T13:37:44Z")

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Operating system: OS Slicer version: not about slicer Expected behavior: Actual behavior: I extracted from some dcm slices and corresponding masks via pyradiomics package, the puzzle is that I got some complex values…

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## [Radiomics for entire image- not only on segmentation](https://discourse.slicer.org/t/radiomics-for-entire-image-not-only-on-segmentation/13344)

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**Author:** [@KLH](https://discourse.slicer.org/u/KLH)\
**Replies:** 2\
**Last updated:** [November 11, 2021, 6:11am UTC](https://discourse.slicer.org/t/radiomics-for-entire-image-not-only-on-segmentation/13344 "2021-11-11T06:11:22Z")

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Operating system:Windows 10 Slicer version:4.10.2 Expected behavior: Features extracted from whole image Actual behavior: Need segmentation I am using radiomics to analyze grayscale confocal microscopy images and I d…

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## [sitk error. Input for "LabelStatisticsImageFilter" does not match the primary input's size](https://discourse.slicer.org/t/sitk-error-input-for-labelstatisticsimagefilter-does-not-match-the-primary-inputs-size/20326)

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**Author:** [@Fabio\_Nunes](https://discourse.slicer.org/u/Fabio_Nunes)\
**Replies:** 1\
**Last updated:** [October 26, 2021, 3:03am UTC](https://discourse.slicer.org/t/sitk-error-input-for-labelstatisticsimagefilter-does-not-match-the-primary-inputs-size/20326 "2021-10-26T03:03:29Z")

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Hello dear members, I’ve been working with pyradiomics to try to analyse a segment of pericardial fat. I will replicate the code bellow. Unfortunatly I cannot attach the files here as the upload option does not allow fo…

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## [Pyradiomics feature extraction for bin-width 255](https://discourse.slicer.org/t/pyradiomics-feature-extraction-for-bin-width-255/20347)

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**Author:** [@Sovan\_Mukherjee](https://discourse.slicer.org/u/Sovan_Mukherjee)\
**Replies:** 0\
**Last updated:** [October 25, 2021, 11:01pm UTC](https://discourse.slicer.org/t/pyradiomics-feature-extraction-for-bin-width-255/20347 "2021-10-25T23:01:15Z")

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Hi, I was extracting radiomics features from a CT dataset using PyRadiomics at various bin-widths for a comparison study (25, 32, 255 etc). I was comparing individual gray level features between bin-width 25 and 255. M…

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## [brain white matter tissue probability map as mask - behaviour of pyradiomics](https://discourse.slicer.org/t/brain-white-matter-tissue-probability-map-as-mask-behaviour-of-pyradiomics/19969)

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**Author:** [@nhaliasos](https://discourse.slicer.org/u/nhaliasos)\
**Replies:** 0\
**Last updated:** [October 2, 2021, 2:16pm UTC](https://discourse.slicer.org/t/brain-white-matter-tissue-probability-map-as-mask-behaviour-of-pyradiomics/19969 "2021-10-02T14:16:54Z")

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greetings to community, i have a doubt: when i use spm12 to produce a brain white matter segmentation from a T1 MRI scan the image produced by spm has various intensities from 0 to 1 especially at the edges between the…

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## [Image and Mask origin mismatch](https://discourse.slicer.org/t/image-and-mask-origin-mismatch/19781)

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**Author:** [@Tanvi\_Vinay\_Kulkarni](https://discourse.slicer.org/u/Tanvi_Vinay_Kulkarni)\
**Replies:** 1\
**Last updated:** [September 21, 2021, 12:04pm UTC](https://discourse.slicer.org/t/image-and-mask-origin-mismatch/19781 "2021-09-21T12:04:21Z")

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While extracting pyradiomics features, my image and mask have the same spacing and size but the origins are off by a few millimeters. Feature extraction shows the below error Will increasing the tolerance in the sett…

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## [How do extract GLRLM features from a single .jpg image](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-single-jpg-image/15473)

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**Author:** [@Mohiuddin](https://discourse.slicer.org/u/Mohiuddin)\
**Replies:** 1\
**Last updated:** [March 9, 2021, 12:39pm UTC](https://discourse.slicer.org/t/how-do-extract-glrlm-features-from-a-single-jpg-image/15473 "2021-03-09T12:39:30Z")

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Operating system: Windows Slicer version: Expected behavior: Actual behavior: 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…

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