Deep attentive spatio-temporal feature learning for automatic resting-state fMRI denoising

Resting-state functional magnetic resonance imaging (rs-fMRI) is a non-invasive functional neuroimaging modality that has been widely used to investigate functional connectomes in the brain. Since noise and artifacts generated by non-neuronal physiological activities are predominant in raw rs-fMRI data, effective noise removal is one of the most important preprocessing steps prior to any subsequent analysis. For rs-fMRI denoising, a common trend is to decompose rs-fMRI data into multiple components and then regress out noise-related components. Therefore, various machine learning techniques have been used in such analyses with predefined procedures and manually engineered features. However, the lack of a universal definition of a noise-related source or artifact complicates manual feature engineering. Manual feature selection can result in the failure to capture unknown types of noise. Furthermore, the possibility that the hand-crafted features will only work for the broader population (e.g., healthy adults) but not for “outliers” (e.g., infants or subjects that belong to a disease cohort) is quite high. In practice, we have limited knowledge of which features should be extracted; thus, multi-classifier assembly must be implemented to improve performance, although this process is quite time-consuming. However, in real rs-fMRI applications, fast and accurate automatic identification of noise-related components on different datasets is critical. To solve this problem, we propose a novel, automatic, and end-to-end deep learning framework dedicated to noise-related component identification via a faster and more effective multi-layer feature extraction strategy that learns deeply embedded spatio-temporal features of the components. In this study, we achieved remarkable performance on various rs-fMRI datasets, including multiple adult rs-fMRI datasets from different rs-fMRI studies and an infant rs-fMRI dataset, which is quite heterogeneous and differs from that of adults. Our proposed framework also dramatically increases the noise detection speed owing to its inherent ability for deep learning (< 1s for single-component classification). It can be easily integrated into any preprocessing pipeline, even those that do not use standard procedures but depend on alternative toolboxes.