Fully automated three‐dimensional deep learning‐based magnetic resonance imaging segmentation of brain cavities in epilepsy surgery

OBJECTIVE: There are several clinical and research applications for determining the amount of brain tissue resected after epilepsy surgery; however, manual segmentation of postoperative magnetic resonance imaging (MRI) is imprecise and time-consuming. In this study, we developed and benchmarked ResectVol DL, a freely available deep learning-based tool that performs this task automatically. METHODS: To create ResectVol DL, we trained a UNet-like deep learning model using postoperative T1-weighted MRI from epilepsy surgery patients and evaluated it against manual delineations (ground truth). ResectVol DL was also compared with three automated methods (ResectVol 1.1.2, DeepResection, and Auto3DSeg) using Dice similarity coefficient (DSC), Pearson correlation coefficient, and relative volume difference from manual segmentation. To assess false-positive detections and generalizability beyond epilepsy, we additionally processed images from healthy controls (no resection) and brain tumor cases. RESULTS: The final epilepsy cohort comprised 120 patients (57 women, mean age at surgery = 31.5 ± 15.9 [SD] years), split into training (n = 72) and test (n = 48) sets. An additional 42 images (22 healthy controls and 20 brain tumor cases) were included to test for false positives and generalizability. Segmentation performance differed across methods (Friedman test, p < .001). ResectVol Dl achieved the highest median DSC (.925), significantly outperforming ResectVol 1.1.2, DeepResection, and Auto3DSeg after Bonferroni correction. Volume-based metrics were similar for Auto3DSeg and ResectVol DL (r = .988, relative difference = 8.4% vs. r = .985, 8.1%; no significant difference), yet Auto3DSeg produced three false-positive cavities in no-surgery controls (3/22, 95% confidence interval [CI] = 3%-35%), whereas none was observed for ResectVol DL and DeepResection (0/22, 95% CI = 0%-15%). SIGNIFICANCE: ResectVol DL provides accurate, fully automated segmentation of postoperative resection cavities, offering a robust and reproducible methodological tool for large-scale postoperative imaging studies in epilepsy surgery. ResectVol DL also provides volumetric information derived from region labeling, which may serve as potential input for predictive models associated with surgery outcome; however, this application has not yet been validated.