A Parkinson’s disease-related nuclei segmentation network based on CNN-Transformer interleaved encoder with feature fusion

Automatic segmentation of Parkinson’s disease (PD) related deep gray matter (DGM) nuclei based on brain magnetic resonance imaging (MRI) is significant in assisting the diagnosis of PD. However, due to the degenerative-induced changes in appearance, low tissue contrast, and tiny DGM nuclei size in elders’ brain MRI images, many existing segmentation models are limited in the application. To address these challenges, this paper proposes a PD-related DGM nuclei segmentation network to provide precise prior knowledge for aiding diagnosis PD. The encoder of network is designed as an alternating encoding structure where the convolutional neural network (CNN) captures spatial and depth texture features, while the Transformer complements global position information between DGM nuclei. Moreover, we propose a cascaded channel-spatial-wise block to fuse features extracted by the CNN and Transformer, thereby achieving more precise DGM nuclei segmentation. The decoder incorporates a symmetrical boundary attention module, leveraging the symmetrical structures of bilateral nuclei regions by constructing signed distance maps for symmetric differences, which optimizes segmentation boundaries. Furthermore, we employ a dynamic adaptive region of interests weighted Dice loss to enhance sensitivity towards smaller structures, thereby improving segmentation accuracy. In qualitative analysis, our method achieved optimal average values for PD-related DGM nuclei (DSC: 0.854, IOU: 0.750, HD95: 1.691 mm, ASD: 0.195 mm). Experiments conducted on multi-center clinical datasets and public datasets demonstrate the good generalizability of the proposed method. Furthermore, a volumetric analysis of segmentation results reveals significant differences between HCs and PDs. Our method holds promise for assisting clinicians in the rapid and accurate diagnosis of PD, offering a practical method for the imaging analysis of neurodegenerative diseases.