sEEGnal: an automated EEG preprocessing pipeline evaluated against expert-driven preprocessing

Electroencephalography (EEG) preprocessing is a critical yet time-consuming step that often relies on expert-driven, semi-automatic pipelines, limiting scalability and reproducibility across large datasets. In this work, we present sEEGnal, a fully automated and modular pipeline for EEG preprocessing designed to produce outputs comparable to expert-driven preprocessing while ensuring consistency and computational efficiency. The pipeline integrates three main modules: data standardisation following the EEG extension of the Brain Imaging Data Structure (BIDS), bad channel detection, and artefact identification, combining physiologically grounded criteria with independent component analysis and ICLabel-based classification.

Performance was evaluated against manual preprocessing performed by EEG experts at two complementary levels: preprocessing metadata (bad channels, artefact duration, and rejected components) and EEG-derived measures. In addition, test–retest analyses were conducted to assess the stability of the pipeline across repeated recordings.

Results show that sEEGnal achieves performance comparable to expert-driven preprocessing while preserving key neurophysiological features. Furthermore, the pipeline demonstrates reduced variability and increased consistency compared to human experts. These findings support sEEGnal as a robust and scalable solution for automated EEG preprocessing in both research and large-scale applications.