# Radiomics

**URL:** https://discourse.slicer.org/c/community/radiomics/23.md?page=5

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**Page:** 6

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## [FeatureExtractor values don't get along with reality value](https://discourse.slicer.org/t/featureextractor-values-dont-get-along-with-reality-value/15997)

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**Author:** [@11117](https://discourse.slicer.org/u/11117)\
**Replies:** 1\
**Last updated:** [March 9, 2021, 12:22pm UTC](https://discourse.slicer.org/t/featureextractor-values-dont-get-along-with-reality-value/15997 "2021-03-09T12:22:09Z")

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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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## [Pyradiomics with masks extracted from DICOM dose cloud](https://discourse.slicer.org/t/pyradiomics-with-masks-extracted-from-dicom-dose-cloud/15965)

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**Author:** [@Adam](https://discourse.slicer.org/u/Adam)\
**Replies:** 3\
**Last updated:** [March 9, 2021, 12:18pm UTC](https://discourse.slicer.org/t/pyradiomics-with-masks-extracted-from-dicom-dose-cloud/15965 "2021-03-09T12:18:58Z")

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Operating system:Windows 10 Slicer version: 4.10.1 Hi, I have masks stored in numpy ndarray, and I am using pynrrd to write them to .nrrd format for use in pyradiomics. When I check the nrrd masks against the dicom im…

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## [Texture analysis on an image with cysts taken out](https://discourse.slicer.org/t/texture-analysis-on-an-image-with-cysts-taken-out/15098)

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**Author:** [@lekremer](https://discourse.slicer.org/u/lekremer)\
**Replies:** 1\
**Last updated:** [December 17, 2020, 12:49pm UTC](https://discourse.slicer.org/t/texture-analysis-on-an-image-with-cysts-taken-out/15098 "2020-12-17T12:49:20Z")

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Hello, I am looking at texture within a kidney, but removing all cysts to look only at healthy tissue. I was wondering how this would affect GLCM and other features, because there will now be pixels of 0 value within th…

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## [Higher order features on kidney segmentation ](https://discourse.slicer.org/t/higher-order-features-on-kidney-segmentation/15000)

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**Author:** [@lekremer](https://discourse.slicer.org/u/lekremer)\
**Replies:** 1\
**Last updated:** [December 17, 2020, 12:48pm UTC](https://discourse.slicer.org/t/higher-order-features-on-kidney-segmentation/15000 "2020-12-17T12:48:32Z")

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I am using pyradiomics to look at the texture of segmented kidney images with many cysts masked out, therefore the value being 0 anywhere in the kidney that we deem are cysts. How will this affect the GLCM and features t…

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## [Fixed Bin Width / Fixed Bin Count + Resegmentation](https://discourse.slicer.org/t/fixed-bin-width-fixed-bin-count-resegmentation/15038)

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**Author:** [@mcastro](https://discourse.slicer.org/u/mcastro)\
**Replies:** 0\
**Last updated:** [December 14, 2020, 1:00am UTC](https://discourse.slicer.org/t/fixed-bin-width-fixed-bin-count-resegmentation/15038 "2020-12-14T01:00:54Z")

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I am running 3D Slicer + Radiomics using Parameter Files. In my application, I need to compare a set of CT images that have the same minimum HU but varying maximum HU. Using resegmentation, I thought that I would be abl…

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## [How can I set absolute bound](https://discourse.slicer.org/t/how-can-i-set-absolute-bound/11263)

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**Author:** [@codecrazer](https://discourse.slicer.org/u/codecrazer)\
**Replies:** 5\
**Last updated:** [December 9, 2020, 4:01am UTC](https://discourse.slicer.org/t/how-can-i-set-absolute-bound/11263 "2020-12-09T04:01:11Z")

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Dear all, due to some of CT will have maximum Housefield units value more than 3000. Is it possible for me to absolute bound HU before binwith resampling in pyradiomics batch parameter file? Thanks for your help!

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## [Normalization question](https://discourse.slicer.org/t/normalization-question/14759)

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**Author:** [@mcastro](https://discourse.slicer.org/u/mcastro)\
**Replies:** 1\
**Last updated:** [November 26, 2020, 4:52pm UTC](https://discourse.slicer.org/t/normalization-question/14759 "2020-11-26T16:52:28Z")

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I am performing 3D organ-based radiomics analysis and I have a few questions about normalization. Let’s call: A the original image Bj the image where the organ was masked and the background was set to a value j Bk th…

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## [Voxel extraction , Calculation of GLSZM Failed](https://discourse.slicer.org/t/voxel-extraction-calculation-of-glszm-failed/14225)

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**Author:** [@Alessio\_Romita](https://discourse.slicer.org/u/Alessio_Romita)\
**Replies:** 2\
**Last updated:** [November 20, 2020, 4:32pm UTC](https://discourse.slicer.org/t/voxel-extraction-calculation-of-glszm-failed/14225 "2020-11-20T16:32:39Z")

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Hi everyone , I’m trying to calculate the value of Glszm feature using voxel based extraction. But I got this erro :IndexError: Calculation of GLSZM Failed. The setting used are : voxelSetting: kernelRadius: 2 mask…

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## [Tracking how the values in GLCM, GLSZM matrices are populated](https://discourse.slicer.org/t/tracking-how-the-values-in-glcm-glszm-matrices-are-populated/13808)

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**Author:** [@Ankita\_Singh](https://discourse.slicer.org/u/Ankita_Singh)\
**Replies:** 6\
**Last updated:** [November 18, 2020, 6:56pm UTC](https://discourse.slicer.org/t/tracking-how-the-values-in-glcm-glszm-matrices-are-populated/13808 "2020-11-18T18:56:31Z")

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Hello, I am interested in understanding how the values in GLCM and GLSZM are computed for each gray level. I know that there are C++ functions calculate\_glcm and calculate\_glszm that compute these matrices. Using these …

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## [Display image/mask pair after mask correction?](https://discourse.slicer.org/t/display-image-mask-pair-after-mask-correction/14649)

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**Author:** [@Cody\_Keller](https://discourse.slicer.org/u/Cody_Keller)\
**Replies:** 1\
**Last updated:** [November 18, 2020, 6:48pm UTC](https://discourse.slicer.org/t/display-image-mask-pair-after-mask-correction/14649 "2020-11-18T18:48:23Z")

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Operating system: Windows10 64-bit Slicer version: 4.11.0 Hello, I’ve been working through some bugs in feature extraction with a data set of image/mask pairs that are pretty heterogenous in terms of size and file typ…

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## [Output in different order ar eat execution](https://discourse.slicer.org/t/output-in-different-order-ar-eat-execution/12447)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 4\
**Last updated:** [November 18, 2020, 5:21pm UTC](https://discourse.slicer.org/t/output-in-different-order-ar-eat-execution/12447 "2020-11-18T17:21:51Z")

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The output (features extracted and values) come in a random order every time I execute (in this Post). It use to work well but I do not know what happened that it is now random. Any thoughts?

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## [Slicer Radiomics error ](https://discourse.slicer.org/t/slicer-radiomics-error/14279)

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**Author:** [@ngillingham](https://discourse.slicer.org/u/ngillingham)\
**Replies:** 4\
**Last updated:** [November 10, 2020, 7:47pm UTC](https://discourse.slicer.org/t/slicer-radiomics-error/14279 "2020-11-10T19:47:00Z")

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Hello, I’ve run into the following error with both nightly and stable releases of Slicer, on a Mac. Same error when I tried at work, on Windows, with both nightly and stable release, although I’m not able to poke around …

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## [LBP and KNN i need help](https://discourse.slicer.org/t/lbp-and-knn-i-need-help/14525)

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**Author:** [@Jhonatan\_Ferreira](https://discourse.slicer.org/u/Jhonatan_Ferreira)\
**Replies:** 0\
**Last updated:** [November 10, 2020, 7:18pm UTC](https://discourse.slicer.org/t/lbp-and-knn-i-need-help/14525 "2020-11-10T19:18:55Z")

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hello, I need help with LBP and KNN to do machine learning anyone can help me ??

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## [Analysing bone porosity from CT scans using Radiomics](https://discourse.slicer.org/t/analysing-bone-porosity-from-ct-scans-using-radiomics/14412)

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**Author:** [@Varsha](https://discourse.slicer.org/u/Varsha)\
**Replies:** 0\
**Last updated:** [November 3, 2020, 8:00pm UTC](https://discourse.slicer.org/t/analysing-bone-porosity-from-ct-scans-using-radiomics/14412 "2020-11-03T20:00:55Z")

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How does one visualized porosities present on the Region of Interest from CT scans using Radiomics? Any help would be appreciated.

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## [multimodal radiomics](https://discourse.slicer.org/t/multimodal-radiomics/13908)

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**Author:** [@icetin](https://discourse.slicer.org/u/icetin)\
**Replies:** 1\
**Last updated:** [October 10, 2020, 1:44pm UTC](https://discourse.slicer.org/t/multimodal-radiomics/13908 "2020-10-10T13:44:05Z")

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Hi! Is it possible to extract radiomics features on pairs of images using pyradiomics? i.e. features based on the joint histogram, or a way to manage the data so pyradiomics knows that they are two views of the same thi…

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## [Using png file with radiomics](https://discourse.slicer.org/t/using-png-file-with-radiomics/13891)

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**Author:** [@cucphuong](https://discourse.slicer.org/u/cucphuong)\
**Replies:** 2\
**Last updated:** [October 10, 2020, 1:40pm UTC](https://discourse.slicer.org/t/using-png-file-with-radiomics/13891 "2020-10-10T13:40:44Z")

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Hello everyone, I am working with radiomics and want to use RadiomicsGLCM to extract feature. I want to extract glcm from brain tumor which will be segmented by mask. Here is my code: img = sitk.ReadImage(path) mask =…

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## [Use segmentation for radiomics](https://discourse.slicer.org/t/use-segmentation-for-radiomics/13969)

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**Author:** [@Mgi](https://discourse.slicer.org/u/Mgi)\
**Replies:** 0\
**Last updated:** [October 9, 2020, 8:16pm UTC](https://discourse.slicer.org/t/use-segmentation-for-radiomics/13969 "2020-10-09T20:16:43Z")

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Hi @fedorov I want to convert the nrrd file obtained from the segmentation on PET-Indic to DICOM to save them on the PACS. After I’ll use them for Radiomics. What is the better way?

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## [Incongruence with some feautures](https://discourse.slicer.org/t/incongruence-with-some-feautures/13864)

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**Author:** [@Nicolas\_Destefanis](https://discourse.slicer.org/u/Nicolas_Destefanis)\
**Replies:** 2\
**Last updated:** [October 6, 2020, 1:22pm UTC](https://discourse.slicer.org/t/incongruence-with-some-feautures/13864 "2020-10-06T13:22:40Z")

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I am currently working on my MSc thesis in Mathematics, and I’m fairly new with PyRadiomics. I’m having some issues when extracting some features. I was comparing their output with the ones extracted using another softwa…

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## [Validity of Radiomics Fractional Bin Width](https://discourse.slicer.org/t/validity-of-radiomics-fractional-bin-width/13877)

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**Author:** [@furMan](https://discourse.slicer.org/u/furMan)\
**Replies:** 1\
**Last updated:** [October 6, 2020, 2:06am UTC](https://discourse.slicer.org/t/validity-of-radiomics-fractional-bin-width/13877 "2020-10-06T02:06:08Z")

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Operating system: Windows 10 Slicer version:4.10.2 Expected behavior: Actual behavior: I’m analyzing MR images, and am normalizing the images using the following method: Subtract the mean of the non-zero intensitie…

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## [GLCM extraction error on .png image](https://discourse.slicer.org/t/glcm-extraction-error-on-png-image/13566)

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**Author:** [@Shibashis\_Sahu](https://discourse.slicer.org/u/Shibashis_Sahu)\
**Replies:** 1\
**Last updated:** [September 30, 2020, 11:38am UTC](https://discourse.slicer.org/t/glcm-extraction-error-on-png-image/13566 "2020-09-30T11:38:29Z")

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Operating system: Windows 10 Slicer version: Expected behavior: Actual behavior: HI, I am new to pyradiomics and getting an error while extracting using GLCM, here is my code: ig = sitk.ReadImage(’./PAC\_14\_DN0.png’…

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## [Can radiomics in 3dslicer output many results of different patients in a CSV?](https://discourse.slicer.org/t/can-radiomics-in-3dslicer-output-many-results-of-different-patients-in-a-csv/13500)

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**Author:** [@Jeff\_W](https://discourse.slicer.org/u/Jeff_W)\
**Replies:** 2\
**Last updated:** [September 30, 2020, 1:42pm UTC](https://discourse.slicer.org/t/can-radiomics-in-3dslicer-output-many-results-of-different-patients-in-a-csv/13500 "2020-09-30T13:42:28Z")

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Can radiomics in 3dslicer output many results of different patients in a CSV?Can radiomics in 3dslicer output many results of different patients in a CSV?Can radiomics in 3dslicer output many results of different patient…

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## [install pyradiomics via conda](https://discourse.slicer.org/t/install-pyradiomics-via-conda/13661)

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**Author:** [@YinYunchao](https://discourse.slicer.org/u/YinYunchao)\
**Replies:** 1\
**Last updated:** [September 30, 2020, 11:34am UTC](https://discourse.slicer.org/t/install-pyradiomics-via-conda/13661 "2020-09-30T11:34:31Z")

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Hi there, I was trying to install pyradiomics by the command line ‘conda install -c radiomics pyradiomics’. However, it reported: pyradiomics -\> python\[version=’\>=2.7,\<2.8.0a0|\>=3.7,\<3.8.0a0|\>=3.6,\<3.7.0a0|\>=3.5,\<3.6.…

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## [Standardized yaml. or json file for image preprocessing?](https://discourse.slicer.org/t/standardized-yaml-or-json-file-for-image-preprocessing/12986)

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**Author:** [@aileeno](https://discourse.slicer.org/u/aileeno)\
**Replies:** 3\
**Last updated:** [September 30, 2020, 11:41am UTC](https://discourse.slicer.org/t/standardized-yaml-or-json-file-for-image-preprocessing/12986 "2020-09-30T11:41:39Z")

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Hi there, I’m wondering if there is a standardized yaml.-file or JSON which can be used for image preprocessing prior to running pyRadiomics extension. We have data from \> 16 CT scanners and were told that this would mi…

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## [GLSZM feature map in 3D Slicer](https://discourse.slicer.org/t/glszm-feature-map-in-3d-slicer/13463)

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**Author:** [@Matt5](https://discourse.slicer.org/u/Matt5)\
**Replies:** 2\
**Last updated:** [September 13, 2020, 2:44am UTC](https://discourse.slicer.org/t/glszm-feature-map-in-3d-slicer/13463 "2020-09-13T02:44:29Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Is there a GLSZM feature map tool available in 3D Slicer?

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## [What was the mother wavelet function used for computing the wavelet features by SlicerRadiomic?](https://discourse.slicer.org/t/what-was-the-mother-wavelet-function-used-for-computing-the-wavelet-features-by-slicerradiomic/13071)

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**Author:** [@danceward](https://discourse.slicer.org/u/danceward)\
**Replies:** 1\
**Last updated:** [August 28, 2020, 2:19am UTC](https://discourse.slicer.org/t/what-was-the-mother-wavelet-function-used-for-computing-the-wavelet-features-by-slicerradiomic/13071 "2020-08-28T02:19:16Z")

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Hello, I am doing some work about radiomic feature extraction from chest CT by SlicerRadiomic, and I want to know what was the mother wavelet function used for computing the wavelet features? Thanks!

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## [2D Shape features for multiple ROIs in single image](https://discourse.slicer.org/t/2d-shape-features-for-multiple-rois-in-single-image/12911)

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**Author:** [@kalyani7195](https://discourse.slicer.org/u/kalyani7195)\
**Replies:** 2\
**Last updated:** [August 10, 2020, 5:15am UTC](https://discourse.slicer.org/t/2d-shape-features-for-multiple-rois-in-single-image/12911 "2020-08-10T05:15:09Z")

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Hello Pyradiomics team, I am currently working on Mammograms from INBreast dataset and each mammogram has multiple calcifications. The mask is white(65535) for ROIs i.e. calcifications and black for the rest of the area…

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## [PET normalisation before Radiomics](https://discourse.slicer.org/t/pet-normalisation-before-radiomics/12765)

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**Author:** [@Nora](https://discourse.slicer.org/u/Nora)\
**Replies:** 1\
**Last updated:** [July 31, 2020, 4:48am UTC](https://discourse.slicer.org/t/pet-normalisation-before-radiomics/12765 "2020-07-31T04:48:39Z")

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Hello All, I’ve been trying to calculate the bin width for fixed bin numbers. However, some PET data range were fluctuating. Example the minimum SUV = 3274.76, and the maximum = 14063.3. I looked to pyradiomics recomme…

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## [Slicer Radiomics](https://discourse.slicer.org/t/slicer-radiomics/12791)

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**Author:** [@mcastro](https://discourse.slicer.org/u/mcastro)\
**Replies:** 2\
**Last updated:** [July 31, 2020, 4:43am UTC](https://discourse.slicer.org/t/slicer-radiomics/12791 "2020-07-31T04:43:01Z")

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Operating system: Windiows Slicer version: 4.10.2 Expected behavior: Actual behavior: I am using Slicer Radiomics with a parameter file. The possible settings depends on the PyRadiomics version used within Slicer Rad…

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## [cannot import name 'featureextractor' from 'radiomics'](https://discourse.slicer.org/t/cannot-import-name-featureextractor-from-radiomics/12768)

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**Author:** [@hanna](https://discourse.slicer.org/u/hanna)\
**Replies:** 1\
**Last updated:** [July 29, 2020, 1:19pm UTC](https://discourse.slicer.org/t/cannot-import-name-featureextractor-from-radiomics/12768 "2020-07-29T13:19:34Z")

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I have installed the python 3.7 and the radiomics. when I ran the .py file there is an error"cannot import name ‘featureextractor’ from ‘radiomics’ ". What can I do to resolve the problem?

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## [Code stop extracting wavelet and gradient features (it used to do so)](https://discourse.slicer.org/t/code-stop-extracting-wavelet-and-gradient-features-it-used-to-do-so/12428)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 1\
**Last updated:** [July 8, 2020, 6:57pm UTC](https://discourse.slicer.org/t/code-stop-extracting-wavelet-and-gradient-features-it-used-to-do-so/12428 "2020-07-08T18:57:23Z")

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I have this code which is an adaption of the examples offered and it use to extract all the features as described in the params.yaml . The code use to work well, now it is extracting less features than it has to. extrac…

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