Image Phenotyping using the SlicerRadiomics Extension - 3D Slicer Tutorial

This video tutorial is an introduction to performing Image Phenotyping using the SlicerRadiomics Extension in 3D Slicer. An MR Image of a brain tumor patient is chosen, from which the tumor is segmented. Following that, first order features and glcm features are extracted from the segmented tumor using the SlicerRadiomics extension and stored in a CSV file.
This video is based upon "An Introduction to Image Phenotyping", a 3D Slicer tutorial by Sonia Pujol, Ph.D., Assistant Professor of Radiology Brigham and Women’s Hospital at Harvard Medical School.
Link to that tutorial: spujol.github....
3D Slicer is a free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research.
3D Slicer Website: www.slicer.org/
SlicerRadiomics is an extension for 3D Slicer that encapsulates pyradiomics library, which in turn implements calculation of a variety of radiomics features.
SlicerRadiomics webpage: www.radiomics.i...
Pyradiomics webpage: www.radiomics.i...
This video is taken as part of an assignment for the Medical Imaging course taken by Dr. Subrahmanyam Gorthi, from the Department of Electrical Engineering at the Indian Institute of Technology (IIT), Tirupati.

[@manjumanju5406]

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

[@tomaskorinek9838]

Hello, such a great video. I have made Segmentation set from my whole RT Structure set. Why are there no feature results when I use radiomics as you? Clicking on "Apply", waiting a few seconds and then ther is only a row containing "image type, feature class, feature name, and then contour names". No other rows. Could you pretty please help me? Would you guess where is the problem?

[@prabhatreddy1359]

Thanks for the comment! I faced a similar problem too (watch from 7:50). I'm not sure about where the problem is, but I think it has something with the naming convention of the file. I managed to get around that problem by saving the segmentation as an 'nrrd' file, renaming it, and running the Radiomics extension on this renamed segmentation (watch from 8:05). Have you tried this approach?

[@tomaskorinek9838]

@@prabhatreddy1359 Hello, thanks for your answer! I am really appriciating that! Unfortunately, I have a strange problem. I have a Structure set (from dicom RS file) as Segmentation. It contains 20 structures. When I save it with representation "binary labelmap", it has .seg.nrrd ending, when I use "closed surface", iit has .seg.vtm ending. When I go to file with segmentation.seg.nrrd file and change it to segmentation-seg.nrrd and load it, nothing happend. still the same problem. No feature results. I have tried to calculate only with one structure, but it make also nothing. Sorry for long reading but I am really desperate. :D