Machine reasoning for segmentation of the kidneys on CT images: improving CNN performance by incorporating anatomical knowledge in post-processing

Abstract

Purpose: Convolutional Neural Networks (CNN) are frequently used for organ segmentation in medical imaging. Many CNNs, however, struggle for acceptance into clinical practice because of mis-segmentations that are obvious to radiologists or other experts. We propose using a Cognitive AI framework that applies anatomical knowledge and machine reasoning to check and improve CNN segmentations and avoid obvious mis-segmentations. Methods: We used the open-source SimpleMind framework that allows post-processing and machine reasoning to be applied to CNN segmentation results. Within this framework, a 3D-UNet CNN was trained on 212 contrast-enhanced kidney CT scans. From an anatomical knowledge base, SimpleMind derived the following Cognitive AI post-processing steps: (1) identification of the abdomen, (2) segmentation of the spine by searching for bone in the posterior region of the abdomen, (3) CNN output separation into right and left kidneys using the spine as reference, (4) refinement of individual kidney segmentations using thresholds of volume, HU, and voxel count, which are designed to eliminate disconnected false positives, (5) morphological opening to reduce connected false positives bordering the kidneys’ segmentations. On a test set of 53 scans, using reference annotations, Dice Coefficient (DC), Hausdorff Distance (HD) and Average Symmetric Surface Distances (ASSD) were computed and compared for the CNN and post-processed outputs. Results: Post-processing with Cognitive AI reduced the kidney segmentation HD from 46.4±55.8 mm to 30.7±17.6 mm, with the decrease in variance being statistically significant (p = 0.0296). DC and ASSD metrics were also improved. Conclusions: This initial work demonstrates that the incorporation of anatomical knowledge using Cognitive AI techniques can improve the segmentation accuracy of CNNs. The CNN provides very good overall kidney segmentation performance, and in cases where segmentation errors occur the post processing was able to improve performance.