Anatomy-Informed Deep Learning and Radiomics for Automated Neurofibroma Segmentation in Whole-Body MRI

Neurofibromatosis Type 1 is a genetic disorder characterized by the development of neurofibromas (NFs), which exhibit significant variability in size, morphology, and anatomical location. Accurate and automated segmentation of these tumors in whole-body magnetic resonance imaging (WB-MRI) is crucial to assess tumor burden and monitor disease progression. In this study, we present and analyze a fully automated pipeline for NF segmentation in fat-suppressed T2-weighted WB-MRI, consisting of three stages: anatomy segmentation, NF segmentation, and tumor candidate classification. In the first stage, we use the MRSegmentator model to generate an anatomy segmentation mask, extended with a high-risk zone for NFs. This mask is concatenated with the input image as anatomical context information for NF segmentation. The second stage employs an ensemble of 3D anisotropic anatomy-informed U-Nets to produce an NF segmentation confidence mask. In the final stage, tumor candidates are extracted from the confidence mask and classified based on radiomic features, distinguishing tumors from non-tumor regions and reducing false positives. We evaluate the proposed pipeline on three test sets representing different conditions: in-domain data (test set 1), varying imaging protocols and field strength (test set 2), and low tumor burden cases (test set 3). Experimental results show a 68% improvement in per-scan Dice Similarity Coefficient (DSC), a 21% increase in per-tumor DSC, and a two-fold improvement in F1 score for tumor detection in high tumor burden cases by integrating anatomy information. The method is integrated into the 3D Slicer platform for practical clinical use, with the code publicly accessible.