STNAGNN: Spatiotemporal Node Attention Graph Neural Network for Task-based fMRI Analysis

Task-based fMRI uses actions or stimuli to trigger task-specific brain responses and measures them using BOLD contrast. Despite the significant task-induced spatiotemporal brain activation fluctuations, most studies on task-based fMRI ignore the task context information aligned with fMRI and consider task-based fMRI a coherent sequence. In this paper, we show that using the task structures as data-driven guidance is effective for spatiotemporal analysis. We propose STNAGNN, a GNN-based spatiotemporal architecture, and validate its performance in an autism classification task. The trained model is also interpreted for identifying autism-related spatiotemporal brain biomarkers.

Efficient Annotation for Medical Image Analysis: A One-Pass Selective Annotation Approach

Annotating biomedical images for supervised learning is a complex and labor-intensive task due to data diversity and its intricate nature. In this paper, we propose an innovative method, the efficient one-pass selective annotation (EPOSA), that significantly reduces the annotation burden while maintaining robust model performance. Our approach employs a variational autoencoder (VAE) to extract salient features from unannotated images, which are subsequently clustered using the DBSCAN algorithm. This process groups similar images together, forming distinct clusters. We then use a two-stage sample selection algorithm, called representative selection (RepSel), to form a selected dataset. The first stage is a Markov Chain Monte Carlo (MCMC) sampling technique to select representative samples from each cluster for annotations. This selection process is the second stage, which is guided by the principle of maximizing intra-cluster mutual information and minimizing inter-cluster mutual information. This ensures a diverse set of features for model training and minimizes outlier inclusion. The selected samples are used to train a VGG-16 network for image classification. Experimental results on the Med-MNIST dataset demonstrate that our proposed EPOSA outperforms random selection and other state-of-the-art methods under the same annotation budget, presenting a promising direction for efficient and effective annotation in medical image analysis.

Rapid Brain Meninges Surface Reconstruction with Layer Topology Guarantee

The meninges, located between the skull and brain, are composed of three membrane layers: the pia, the arachnoid, and the dura. Reconstruction of these layers can aid in studying volume differences between patients with neurodegenerative diseases and normal aging subjects. In this work, we use convolutional neural networks (CNNs) to reconstruct surfaces representing meningeal layer boundaries from magnetic resonance (MR) images. We first use the CNNs to predict the signed distance functions (SDFs) representing these surfaces while preserving their anatomical ordering. The marching cubes algorithm is then used to generate continuous surface representations; both the subarachnoid space (SAS) and the intracranial volume (ICV) are computed from these surfaces. The proposed method is compared to a state-of-the-art deformable model-based reconstruction method, and we show that our method can reconstruct smoother and more accurate surfaces using less computation time. Finally, we conduct experiments with volumetric analysis on both subjects with multiple sclerosis and healthy controls. For healthy and MS subjects, ICVs and SAS volumes are found to be significantly correlated to sex (p<0.01) and age (p<0.03) changes, respectively.