Deep Feature Stability Analysis Using CT Images of a Physical Phantom across Scanner Manufacturers, Cartridges, Pixel Sizes, and Slice Thickness

Image acquisition parameters for computed tomography scans such as slice thickness and field of view may vary depending on tumor size and site. Recent studies have shown that some radiomics features were dependent on voxel size (= pixel size × slice thickness), and with proper normalization, this voxel size dependency could be reduced. Deep features from a convolutional neural network (CNN) have shown great promise in characterizing cancers. However, how do these deep features vary with changes in imaging acquisition parameters? To analyze the variability of deep features, a physical radiomics phantom with 10 different material cartridges was scanned on 8 different scanners. We assessed scans from 3 different cartridges (rubber, dense cork, and normal cork). Deep features from the penultimate layer of the CNN before (pre-rectified linear unit) and after (post-rectified linear unit) applying the rectified linear unit activation function were extracted from a pre-trained CNN using transfer learning. We studied both the interscanner and intrascanner dependency of deep features and also the deep features' dependency over the 3 cartridges. We found some deep features were dependent on pixel size and that, with appropriate normalization, this dependency could be reduced. False discovery rate was applied for multiple comparisons, to mitigate potentially optimistic results. We also used stable deep features for prognostic analysis on 1 non–small cell lung cancer data set.