TY - JOUR T1 - Development and Practical Implementation of a Deep Learning–Based Pipeline for Automated Pre- and Postoperative Glioma Segmentation JF - American Journal of Neuroradiology JO - Am. J. Neuroradiol. SP - 24 LP - 32 DO - 10.3174/ajnr.A7363 VL - 43 IS - 1 AU - E. Lotan AU - B. Zhang AU - S. Dogra AU - W.D. Wang AU - D. Carbone AU - G. Fatterpekar AU - E.K. Oermann AU - Y.W. Lui Y1 - 2022/01/01 UR - http://www.ajnr.org/content/43/1/24.abstract N2 - BACKGROUND AND PURPOSE: Quantitative volumetric segmentation of gliomas has important implications for diagnosis, treatment, and prognosis. We present a deep-learning model that accommodates automated preoperative and postoperative glioma segmentation with a pipeline for clinical implementation. Developed and engineered in concert, the work seeks to accelerate clinical realization of such tools.MATERIALS AND METHODS: A deep learning model, autoencoder regularization–cascaded anisotropic, was developed, trained, and tested fusing key elements of autoencoder regularization with a cascaded anisotropic convolutional neural network. We constructed a dataset consisting of 437 cases with 40 cases reserved as a held-out test and the remainder split 80:20 for training and validation. We performed data augmentation and hyperparameter optimization and used a mean Dice score to evaluate against baseline models. To facilitate clinical adoption, we developed the model with an end-to-end pipeline including routing, preprocessing, and end-user interaction.RESULTS: The autoencoder regularization–cascaded anisotropic model achieved median and mean Dice scores of 0.88/0.83 (SD, 0.09), 0.89/0.84 (SD, 0.08), and 0.81/0.72 (SD, 0.1) for whole-tumor, tumor core/resection cavity, and enhancing tumor subregions, respectively, including both preoperative and postoperative follow-up cases. The overall total processing time per case was ∼10 minutes, including data routing (∼1 minute), preprocessing (∼6 minute), segmentation (∼1–2 minute), and postprocessing (∼1 minute). Implementation challenges were discussed.CONCLUSIONS: We show the feasibility and advantages of building a coordinated model with a clinical pipeline for the rapid and accurate deep learning segmentation of both preoperative and postoperative gliomas. The ability of the model to accommodate cases of postoperative glioma is clinically important for follow-up. An end-to-end approach, such as used here, may lead us toward successful clinical translation of tools for quantitative volume measures for glioma.ARautoencoder regularizationBraTSBrain Tumor SegmentationCAcascaded anisotropicCNNconvolutional neural networkDLdeep learningETenhancing tumorHGGhigh-grade gliomaLGGlow-grade gliomaNCnecrotic coreRCresection cavityT1ceT1 postcontrastTCtumor coreWTwhole tumor ER -