PREP Pipeline

Tool: PREP pipeline
Authors: Nima Bigdely-Shamlo, Tim Mullen, Christian Kothe(Intheon), Kyung-Min Su and Kay Robbins (UTSA)
Software Language(s): MATLAB 2014 or later
Software Type: command line / EEGLAB plugin with GUI


What it does: PREP does automated early-stage preprocessing of EEG.  Specifically, PREP removes line noise, computes a robust (artifact-independent) average reference, and identifies bad channels. PREP also produces an extensive report about signal quality.

Why is this important? EEG is very susceptible to artifacts and manual-based removal is time-consuming and highly subjective. Unfortunately, end-results are strongly influenced by this step. PREP standardizes and automates several baseline processing steps. We have demonstrated the effectiveness of this processing in large-scale analysis.  SANDR uses PREP to produce its “level 2” processed data.

Principal publication:

Bigdely-Shamlo N, Mullen T, Kothe C, Su K-M and Robbins KA (2015)
The PREP pipeline: standardized preprocessing for large-scale EEG analysis
Neuroinform. 9:16. doi: 10.3389/fninf.2015.00016.

Recent publications that have used PREP in analysis:

Bigdely-Shamlo, N., Touryan, T., A. Ojeda, C. Kothe, T. Mullen, and K. Robbins, K., 2019. Automated EEG mega-analysis I: Spectral and amplitude characteristics across studies, Neuroimage. 2019 Nov 23:116361.

Bigdely-Shamlo, N., Touryan, J., Ojeda, A., Kothe, C., Mullen, T., and Robbins, K., 2019. Automated EEG mega-analysis II: Cognitive aspects of event related features, Neuroimage. 2019 Sep 4:116054.

Robbins, K., Touryan, J. Mullen, T., Kothe, C. Bigdely-Shamlo, N., 2020. How sensitive are EEG results to preprocessing methods: A benchmarking study, IEEE Transactions on Neural Engineering and Rehabilitation. doi: 10.1109/TNSRE.2020.2980223.