Automatic localization of target point for subthalamic nucleus‐deep brain stimulation via hierarchical attention‐UNet based MRI segmentation

Abstract Background Deep brain stimulation of the subthalamic nucleus (STN‐DBS) is an effective treatment for patients with advanced Parkinson's disease, the outcome of this surgery is highly dependent on the accurate placement of the electrode in the optimal target of STN. Purpose In this study, we aim to develop a target localization pipeline for DBS surgery, considering that the heart of this matter is to achieve the STN and red nucleus segmentation, a deep learning‐based automatic segmentation approach is proposed to tackle this issue. Methods To address the problems of ambiguous boundaries and variable shape of the segmentation targets, the hierarchical attention mechanism with two different attention strategies is integrated into an encoder–decoder network for mining both semantics and fine‐grained details for segmentation. The hierarchical attention mechanism is utilized to suppress irrelevant regions in magnetic resonance (MR) images while build long‐range dependency among segmentation targets. Specifically, the attention gate (AG) is integrated into low‐level features to suppress irrelevant regions in an input image while highlighting the salient features useful for segmentation. Besides, the self‐attention involved in the transformer block is integrated into high‐level features to model the global context. Ninety‐nine brain magnetic resonance imaging (MRI) studies were collected from 99 patients with Parkinson's disease undergoing STN‐DBS surgery, among which 80 samples were randomly selected as the training datasets for deep learning training, and ground truths (segmentation masks) were manually generated by radiologists. Results We applied five‐fold cross‐validation on these data to train our model, the mean results on 19 test samples are used to conduct the comparison experiments, the Dice similarity coefficient (DSC), Jaccard (JA), sensitivity (SEN), and HD95 of the segmentation for STN are 88.20%, 80.32%, 90.13%, and 1.14 mm, respectively, outperforming the state‐of‐the‐art STN segmentation method with 2.82%, 4.52%, 2.56%, and 0.02 mm respectively. The source code and trained models of this work have been released in the URL below: https://github.com/liuruiqiang/HAUNet/tree/master . Conclusions In this study, we demonstrate the effectiveness of the hierarchical attention mechanism for building global dependency on high‐level semantic features and enhancing the fine‐grained details on low‐level features, the experimental results show that our method has considerable superiority for STN and red nucleus segmentation, which can provide accurate target localization for STN‐DBS.