A Practical Roadmap to Implementing Deep Learning Segmentation in the Clinical Neuroimaging Research Workflow

Abstract

Thanks to the proliferation of open-source tools, we are seeing an exponential growth of machine-learning applications, and its integration has become more accessible, particularly for segmentation tools in neuroimaging. This article explores a generalized methodology that harnesses these tools and aims/enables to expedite and enhance the reproducibility of clinical research. Herein, critical considerations include hardware, software, neural network training strategies, and data labeling guidelines. More specifically, we advocate an iterative approach to model training and transfer learning, focusing on internal validation and outlier handling early in the labeling process and fine-tuning later. The iterative refinement process allows experts to intervene and improve model reliability while cutting down on their time spent in manual work. A seamless integration of the final model's predictions into clinical research is proposed to ensure standardized and reproducible results. In short, this article provides a comprehensive framework for accelerating research using machine-learning techniques for image segmentation.