Automated Brain Metastases Segmentation With a Deep Dive Into False-positive Detection

Abstract

Purpose: The clinical management of brain metastases after stereotactic radiosurgery (SRS) is difficult, because a physician must review follow-up magnetic resonance imaging (MRI) scans to determine treatment outcome, which is often labor intensive. The purpose of this study was to develop an automated framework to contour brain metastases in MRI to help treatment planning for SRS and understand its limitations. Methods and Materials: Two self-adaptive nnU-Net models trained on postcontrast 3-dimensional T1-weighted MRI scans from patients who underwent SRS were analyzed. Performance was evaluated by computing positive predictive value (PPV), sensitivity, and Dice similarity coefficient (DSC). The training and testing sets included 3482 metastases on 845 patient MRI scans and 930 metastases on 206 patient MRI scans, respectively. Results: In the per-patient analysis, PPV was 90.1% ± 17.7%, sensitivity 88.4% ± 18.0%, DSC 82.2% ± 9.5%, and false positive (FP) 0.4 ± 1.0. For large metastases (≥6 mm), the per-patient PPV was 95.6% ± 17.5%, sensitivity 94.5% ± 18.1%, DSC 86.8% ± 7.5%, and FP 0.1 ± 0.4. The quality of autosegmented true-positive (TP) contours was also assessed by 2 physicians using a 5-point scale for clinical acceptability. Seventy-five percent of contours were assigned scores of 4 or 5, which shows that contours could be used as-is in clinical application, and the remaining 25% were assigned a score of 3, which means they needed minor editing only. Notably, a deep dive into FPs indicated that 9% were TP metastases not identified on the original radiology review, but identified on subsequent follow-up imaging (early detection). Fifty-four percent were real metastases (TP) that were identified but purposefully not contoured for target treatment, mainly because the patient underwent whole-brain radiation therapy before/after SRS treatment. Conclusions: These findings show that our tool can help radiologists and radiation oncologists detect and contour tumors from MRI, make precise decisions about suspicious lesions, and potentially find lesions at early stages.