This is a matlab demo showing how to construct radiomic matrix and extract radiomic features using different strategies/parameter settings for PET/CT scanned NPC images.
Citation:
[1] Lv W, Yuan Q et al (2018) Robustness versus disease differentiation when varying parameter settings in radiomics features: application to nasopharyngeal PET/CT. European Radiology 28:3245-3254
[2] Lu L, Lv W, Jiang J et al (2016) Robustness of radiomic features in [11C]choline and [18F]FDG PET/CT imaging of nasopharyngeal carcinoma: impact of segmentation and discretization. Mol Imaging Biol 18:935-945
Author: Wenbing Lv, Lijun Lu ljlubme@gmail.com Southern Medical University
History:
Creation: 2017.11
This matlab code contains 3 demos:
-
“demo_FeaExtr”: matlab codes to load PET images, segmentation mask and extract radiomic features under different parameter settings, i.e. symmetry, averaging strategy and distance for GLCM, averaging strategy for GLRLM, neighborhood extent for GLSZM and window size for NGTDM.
-
"demo_ICC":matlab codes to calculate the intra-class correlation coeffcient of feature extracted under different parameter settings.
-
"demo_AUC":matlab codes to calculate the AUC, Sensitivity and Specificity after logistic regression with leave-one-out cross validation.
Ackonwledgements:
- Martin Vallières: https://github.com/mvallieres/radiomics
- Wei's GLRLM toolbox: Xunkai Wei, Gray Level Run Length Matrix Toolbox v1.0, Software,Beijing Aeronautical Technology Research Center, 2007. http://www.mathworks.com/matlabcentral/fileexchange/17482-gray-level-run-length-matrix-toolbox
- Q. Li: http://www.mathworks.com/matlabcentral/fileexchange/23377-ellipsoid-fitting
- CERR development team: http://www.cerr.info/
- Dirk-Jan Kroon (imresize3D.m): http://www.mathworks.com/matlabcentral/fileexchange/21451-multimodality-non-rigid-demon-algorithm-image-registration/content//functions/imresize3d.m
- David Reshef and Yakir Reshef: MINE version 1.0.1d http://www.exploredata.net/
- DREES development team: http://www.cerr.info/drees
- Enric Junqué de Fortuny (fastAUC.cpp): http://www.mathworks.com/matlabcentral/fileexchange/41258-faster-roc-auc
- François Beauducel (roundsd.m): http://www.mathworks.com/matlabcentral/fileexchange/26212-round-with-significant-digits
- Jos van der Geest (herrorbar.m): http://www.mathworks.com/matlabcentral/fileexchange/3963-herrorbar