Deep Learning for Gradient and BCG Artifacts Removal in EEG During Simultaneous fMRI

Abstract: Simultaneous EEG-fMRI recording combines high temporal and spatial resolution for tracking neural activity. However, its usefulness is greatly limited by artifacts from magnetic resonance (MR), especially gradient artifacts (GA) and ballistocardiogram (BCG) artifacts, which interfere with the EEG signal. To address this issue, we used a denoising autoencoder (DAR), a deep learning framework designed to reduce MR-related artifacts in EEG recordings. Using paired data that includes both artifact-contaminated and MR-corrected EEG from the CWL EEG-fMRI dataset, DAR uses a 1D convolutional autoencoder to learn a direct mapping from noisy to clear signal segments. Compared to traditional artifact removal methods like principal component analysis (PCA), independent component analysis (ICA), average artifact subtraction (AAS), and wavelet thresholding, DAR shows better performance. It achieves a root-mean-squared error (RMSE) of 0.0218 $\pm$ 0.0152, a structural similarity index (SSIM) of 0.8885 $\pm$ 0.0913, and a signal-to-noise ratio (SNR) gain of 14.63 dB. Statistical analysis with paired t-tests confirms that these improvements are significant (p<0.001; Cohen's d>1.2). A leave-one-subject-out (LOSO) cross-validation protocol shows that the model generalizes well, yielding an average RMSE of 0.0635 $\pm$ 0.0110 and an SSIM of 0.6658 $\pm$ 0.0880 across unseen subjects. Additionally, saliency-based visualizations demonstrate that DAR highlights areas with dense artifacts, which makes its decisions easier to interpret. Overall, these results position DAR as a potential and understandable solution for real-time EEG artifact removal in simultaneous EEG-fMRI applications.