# Radiomics **URL:** https://discourse.slicer.org/c/community/radiomics/23.md?page=6 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 7 --- ## [Question regarding input as 3D image and setting voxelbased = False](https://discourse.slicer.org/t/question-regarding-input-as-3d-image-and-setting-voxelbased-false/12261)
**Author:** [@Haoxin\_Zheng](https://discourse.slicer.org/u/Haoxin_Zheng)\ **Replies:** 1\ **Last updated:** [June 30, 2020, 10:46am UTC](https://discourse.slicer.org/t/question-regarding-input-as-3d-image-and-setting-voxelbased-false/12261 "2020-06-30T10:46:38Z")
Hi, I think I just asked 2 related question but I wish I could get answers from your side both if possible. Im dealing with 2D MRI images. For each patient, the resolution in x-y direction is higher than the z directio… --- ## [Question regarding 3D extraction ](https://discourse.slicer.org/t/question-regarding-3d-extraction/12262)
**Author:** [@Haoxin\_Zheng](https://discourse.slicer.org/u/Haoxin_Zheng)\ **Replies:** 1\ **Last updated:** [June 30, 2020, 10:45am UTC](https://discourse.slicer.org/t/question-regarding-3d-extraction/12262 "2020-06-30T10:45:22Z")
Hi all, I recently tried to extract features from a stack of 2D images (which is 3D, e.g. shape (320x320x12)), by setting “voxelbased = True”. I’m confused why the returned value is not a dictionary like the case when I… --- ## [Image processing steps order when using the settings in the parameter file?](https://discourse.slicer.org/t/image-processing-steps-order-when-using-the-settings-in-the-parameter-file/11228)
**Author:** [@radio5](https://discourse.slicer.org/u/radio5)\ **Replies:** 3\ **Last updated:** [June 30, 2020, 10:32am UTC](https://discourse.slicer.org/t/image-processing-steps-order-when-using-the-settings-in-the-parameter-file/11228 "2020-06-30T10:32:32Z")
Hi! After I have cropped images to their tumour masks, I am aiming to: Resize all images to a specific image resolution Normalize image intensities Discretize images (Binning) However, I do not know what is the corre… --- ## [Compliance with IBSI](https://discourse.slicer.org/t/compliance-with-ibsi/12062)
**Author:** [@Bassam](https://discourse.slicer.org/u/Bassam)\ **Replies:** 2\ **Last updated:** [June 30, 2020, 10:28am UTC](https://discourse.slicer.org/t/compliance-with-ibsi/12062 "2020-06-30T10:28:05Z")
Hello team, I got a promising imaging biomarkers and I have to check their compliance with their reference values identified by IBSI. To do that, I have to specify the following settings in the parameter file (yaml file… --- ## [Possible issue with 2D extraction from DECT images](https://discourse.slicer.org/t/possible-issue-with-2d-extraction-from-dect-images/12238)
**Author:** [@sanlen](https://discourse.slicer.org/u/sanlen)\ **Replies:** 4\ **Last updated:** [June 29, 2020, 4:20pm UTC](https://discourse.slicer.org/t/possible-issue-with-2d-extraction-from-dect-images/12238 "2020-06-29T16:20:45Z")
Dear all, We are currently working on a project that involves obtaining pyradiomics features from dual-energy CT images which are in a normal DICOM format and can be loaded into 3DSlicer without any problems. We used th… --- ## [How to calculate 2D Radiomics features for each slice of a 3D volume with a 3D mask](https://discourse.slicer.org/t/how-to-calculate-2d-radiomics-features-for-each-slice-of-a-3d-volume-with-a-3d-mask/12163)
**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\ **Replies:** 2\ **Last updated:** [June 23, 2020, 12:06pm UTC](https://discourse.slicer.org/t/how-to-calculate-2d-radiomics-features-for-each-slice-of-a-3d-volume-with-a-3d-mask/12163 "2020-06-23T12:06:19Z")
Hi!!! I’m trying to calculate the radiomics features for each slice of a 3D volume with a 3D mask. I’ve been reading but nothing is very clear. I wonder if I will have to split the 3D volume and the 3D mask in 2D imag… --- ## [Input mask for .jpg files](https://discourse.slicer.org/t/input-mask-for-jpg-files/11984)
**Author:** [@Khalifa1997](https://discourse.slicer.org/u/Khalifa1997)\ **Replies:** 1\ **Last updated:** [June 23, 2020, 9:57am UTC](https://discourse.slicer.org/t/input-mask-for-jpg-files/11984 "2020-06-23T09:57:04Z")
Hey there, I hope you guys are good, currently I am working on .jpg images, however I’d like to use radiomics.featureextractor.RadiomicsFeatureExtractor() the problem I am having however, is with the .execute is that wh… --- ## [Can I calculate the feature "Ellipsoidity" of one 3D segmentation](https://discourse.slicer.org/t/can-i-calculate-the-feature-ellipsoidity-of-one-3d-segmentation/11750)
**Author:** [@yanpfei](https://discourse.slicer.org/u/yanpfei)\ **Replies:** 4\ **Last updated:** [June 7, 2020, 11:33am UTC](https://discourse.slicer.org/t/can-i-calculate-the-feature-ellipsoidity-of-one-3d-segmentation/11750 "2020-06-07T11:33:49Z")
I am using pyRadiomics to analyzed 3D segmentation of tumors. I noticed the feature " Sphericity" and it is very useful for tumor analysis. Besides this feauture, I want to calculate the " Ellipsoidity" of a tumor. Whe… --- ## [Volume confounded variables](https://discourse.slicer.org/t/volume-confounded-variables/10526)
**Author:** [@Martin\_Bzr](https://discourse.slicer.org/u/Martin_Bzr)\ **Replies:** 9\ **Last updated:** [May 26, 2020, 8:32pm UTC](https://discourse.slicer.org/t/volume-confounded-variables/10526 "2020-05-26T20:32:47Z")
Hi, Thank you for this great toolbox ! As I understood from the docs the ‘\_firstorder\_Energy’ feature is volume confounded. What about ‘\_ngtdm\_Coarseness’ ? I’m looking at relationships between features and and the s… --- ## [Default settings for defying GLCM, RLM](https://discourse.slicer.org/t/default-settings-for-defying-glcm-rlm/11629)
**Author:** [@Bassam](https://discourse.slicer.org/u/Bassam)\ **Replies:** 2\ **Last updated:** [May 23, 2020, 8:49pm UTC](https://discourse.slicer.org/t/default-settings-for-defying-glcm-rlm/11629 "2020-05-23T20:49:41Z")
Hi team. Kindly, I am quite a little bit confused about the default settings used for defying the gray level co-occurrence matrix (GLCM) and run length matrix as well (RLM). Does the GLCM, by default, study the occurre… --- ## [Multiple VOI in pyradiomics](https://discourse.slicer.org/t/multiple-voi-in-pyradiomics/11482)
**Author:** [@codecrazer](https://discourse.slicer.org/u/codecrazer)\ **Replies:** 3\ **Last updated:** [May 23, 2020, 2:15pm UTC](https://discourse.slicer.org/t/multiple-voi-in-pyradiomics/11482 "2020-05-23T14:15:28Z")
If there were multiple VOIs and the pipeline extraction were used, but only Image and Mask were specified. The label column were not used. What will happen? --- ## [Force2D parameter when input is a 3D VOI](https://discourse.slicer.org/t/force2d-parameter-when-input-is-a-3d-voi/11467)
**Author:** [@radio5](https://discourse.slicer.org/u/radio5)\ **Replies:** 2\ **Last updated:** [May 14, 2020, 2:34pm UTC](https://discourse.slicer.org/t/force2d-parameter-when-input-is-a-3d-voi/11467 "2020-05-14T14:34:42Z")
Hi! I am using pyRadiomics v3.0. I have a VOI of an organ, which was created by consecutively delineating 2D ROIs on the axial plane, i.e., in each slice. I want to characterise the whole volume using radiomic features. … --- ## [Authorization to cite articles !!](https://discourse.slicer.org/t/authorization-to-cite-articles/11259)
**Author:** [@Tonyale1975](https://discourse.slicer.org/u/Tonyale1975)\ **Replies:** 1\ **Last updated:** [April 27, 2020, 4:09pm UTC](https://discourse.slicer.org/t/authorization-to-cite-articles/11259 "2020-04-27T16:09:28Z")
Dr. Joost, I am writing an article for publication in a biomedical engineering congress in Brazil, and I intend to quote and reference part (a) of figure 1 of the article: Computational Radiomics System to Decode the Ra… --- ## [Radiomics doesn't work on macOS Catalina](https://discourse.slicer.org/t/radiomics-doesnt-work-on-macos-catalina/11079)
**Author:** [@Andrea\_Barucci1](https://discourse.slicer.org/u/Andrea_Barucci1)\ **Replies:** 1\ **Last updated:** [April 12, 2020, 4:08pm UTC](https://discourse.slicer.org/t/radiomics-doesnt-work-on-macos-catalina/11079 "2020-04-12T16:08:14Z")
Dear all, I apologise if this question has already found an answer. I have not been able to find the solution to this problem. Despite the version of 3D Slicer I’m trying to run I always face the same error when tryin… --- ## [Coundn't not enable correctMask](https://discourse.slicer.org/t/coundnt-not-enable-correctmask/11009)
**Author:** [@codecrazer](https://discourse.slicer.org/u/codecrazer)\ **Replies:** 1\ **Last updated:** [April 8, 2020, 5:28am UTC](https://discourse.slicer.org/t/coundnt-not-enable-correctmask/11009 "2020-04-08T05:28:45Z")
I have encountered the problem of image/mask mismatch, after searching on the website, it said that just add correctMask: true, the problem will be solved. However, after I add it, the problem did’t resolved. Thanks for … --- ## [Slice by slice radiomics feature extraction](https://discourse.slicer.org/t/slice-by-slice-radiomics-feature-extraction/10964)
**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\ **Replies:** 0\ **Last updated:** [April 1, 2020, 9:22pm UTC](https://discourse.slicer.org/t/slice-by-slice-radiomics-feature-extraction/10964 "2020-04-01T21:22:36Z")
Hi developers, Is there a way to do radiomics feature extraction slice by slice from a 3D volume? best Tenzin --- ## [PET/CT DICOM data for radiomics](https://discourse.slicer.org/t/pet-ct-dicom-data-for-radiomics/10745)
**Author:** [@Nora](https://discourse.slicer.org/u/Nora)\ **Replies:** 2\ **Last updated:** [March 19, 2020, 3:21pm UTC](https://discourse.slicer.org/t/pet-ct-dicom-data-for-radiomics/10745 "2020-03-19T15:21:44Z")
Hi all, When I pull the PET/CT DICOM data from the PACS. I’m getting 5 different groups of series files. 3 for PET data, namely, PT HD AC, PT NC and PTQC400. 2 for CT: WB slandered and CTAC 3.75 Thick. Which ones sh… --- ## [Voxel-based extraction depends on mask](https://discourse.slicer.org/t/voxel-based-extraction-depends-on-mask/10709)
**Author:** [@geraghbj](https://discourse.slicer.org/u/geraghbj)\ **Replies:** 5\ **Last updated:** [March 17, 2020, 5:50pm UTC](https://discourse.slicer.org/t/voxel-based-extraction-depends-on-mask/10709 "2020-03-17T17:50:36Z")
I have a case where there are multiple ROIs representing multiple lesions from a brain metastasis patient. Running a voxel-based extraction on two of these ROIs independently provides different answers than when I extrac… --- ## [Issue with 2D extraction and resampling](https://discourse.slicer.org/t/issue-with-2d-extraction-and-resampling/9910)
**Author:** [@rcuocolo](https://discourse.slicer.org/u/rcuocolo)\ **Replies:** 2\ **Last updated:** [January 28, 2020, 11:31am UTC](https://discourse.slicer.org/t/issue-with-2d-extraction-and-resampling/9910 "2020-01-28T11:31:50Z")
Hello, I am havong an issue on PyRadiomics 2.2.0 using the terminal (Ubuntu 18.04) for batch extraction. I have images and masks in .nii.gz format, both with 1x1x3 mm voxels. I have drawn bidimensional ROIs on ITKSnap w… --- ## [Hi,50% ROI volume](https://discourse.slicer.org/t/hi-50-roi-volume/9498)
**Author:** [@nanjiqie](https://discourse.slicer.org/u/nanjiqie)\ **Replies:** 1\ **Last updated:** [December 14, 2019, 7:41pm UTC](https://discourse.slicer.org/t/hi-50-roi-volume/9498 "2019-12-14T19:41:51Z")
Hi, I haved got a ROI.However,I can not got 50% ROI volume.How can I get it?Thank you. --- ## [Correct image and mask using command line](https://discourse.slicer.org/t/correct-image-and-mask-using-command-line/9386)
**Author:** [@Bassam](https://discourse.slicer.org/u/Bassam)\ **Replies:** 3\ **Last updated:** [December 10, 2019, 6:39am UTC](https://discourse.slicer.org/t/correct-image-and-mask-using-command-line/9386 "2019-12-10T06:39:17Z")
Hi pyradiomics team, kindly I imported DICOM images into 3D slicer and did segmentation and extract the features properly using 3D slicer, then I saved the image and the mask into file. now I wanna make sure that the sa… [Previous page](https://discourse.slicer.org/c/community/radiomics/23.md?page=5)