Electroenchephalography (EEG) recordings collected with developmental populations present particular challenges from a data processing perspective. These EEGs have a high degree of artifact contamination and often short recording lengths. As both sample sizes and EEG channel densities increase, traditional processing approaches like manual data rejection are becoming unsustainable. Moreover, such subjective approaches preclude standardized metrics of data quality, despite the heightened importance of such measures for EEGs with high rates of initial artifact contamination. There is presently a paucity of automated resources for processing these EEG data and no consistent reporting of data quality measures. To address these challenges, we propose the Harvard Automated Processing Pipeline for EEG (HAPPE) as a standardized, automated pipeline compatible with EEG recordings of variable lengths and artifact contamination levels, including high-artifact and short EEG recordings from young children or those with neurodevelopmental disorders. HAPPE processes event-related and resting-state EEG data from raw files through a series of filtering, artifact rejection, and re-referencing steps to processed EEG suitable for time-frequency-domain analyses. HAPPE also includes a post-processing report of data quality metrics to facilitate the evaluation and reporting of data quality in a standardized manner. Here, we describe each processing step in HAPPE, perform an example analysis with EEG files we have made freely available, and show that HAPPE outperforms seven alternative, widely-used processing approaches. HAPPE removes more artifact than all alternative approaches while simultaneously preserving greater or equivalent amounts of EEG signal in almost all instances. We also provide distributions of HAPPE's data quality metrics in an 867 file dataset as a reference distribution and in support of HAPPE's performance across EEG data with variable artifact contamination and recording lengths. HAPPE software is freely available under the terms of the GNU General Public License at https://github.com/lcnhappe/happe.

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The Harvard Automated Processing Pipeline for Electroencephalography (HAPPE): Standardized Processing Software for Developmental and High-Artifact Data

Brain activities commonly recorded using the electroencephalogram (EEG) are contaminated with ocular artifacts. These activities can be suppressed using a robust independent component analysis (ICA) tool, but its efficiency relies on manual intervention to accurately identify the independent artifactual components. In this paper, we present a new unsupervised, robust, and computationally fast statistical algorithm that uses modified multiscale sample entropy (mMSE) and Kurtosis to automatically identify the independent eye blink artifactual components, and subsequently denoise these components using biorthogonal wavelet decomposition. A 95% two-sided confidence interval of the mean is used to determine the threshold for Kurtosis and mMSE to identify the blink related components in the ICA decomposed data. The algorithm preserves the persistent neural activity in the independent components and removes only the artifactual activity. Results have shown improved performance in the reconstructed EEG signals using the proposed unsupervised algorithm in terms of mutual information, correlation coefficient, and spectral coherence in comparison with conventional zeroing-ICA and wavelet enhanced ICA artifact removal techniques. The algorithm achieves an average sensitivity of 90% and an average specificity of 98%, with average execution time for the datasets ( $N = 7$ ) of 0.06 s ( ${\rm SD} = 0.021$ ) compared to the conventional wICA requiring 0.1078 s ( ${\rm SD} = 0.004$ ). The proposed algorithm neither requires manual identification for artifactual components nor additional electrooculographic channel. The algorithm was tested for 12 channels, but might be useful for dense EEG systems.

Unsupervised Eye Blink Artifact Denoising of EEG Data with Modified Multiscale Sample Entropy, Kurtosis, and Wavelet-ICA

This paper presents a method to reduce artifacts from scalp EEG recordings to facilitate seizure diagnosis/detection for epilepsy patients. The proposed method is primarily based on stationary wavelet transform and takes the spectral band of seizure activities (i.e., 0.5–29 Hz) into account to separate artifacts from seizures. Different artifact templates have been simulated to mimic the most commonly appeared artifacts in real EEG recordings. The algorithm is applied on three sets of synthesized data including fully simulated, semi-simulated, and real data to evaluate both the artifact removal performance and seizure detection performance. The EEG features responsible for the detection of seizures from nonseizure epochs have been found to be easily distinguishable after artifacts are removed, and consequently, the false alarms in seizure detection are reduced. Results from an extensive experiment with these datasets prove the efficacy of the proposed algorithm, which makes it possible to use it for artifact removal in epilepsy diagnosis as well as other applications regarding neuroscience studies.

A Wavelet-Based Artifact Reduction From Scalp EEG for Epileptic Seizure Detection

Artifacts-matched blind source separation and wavelet transform for multichannel EEG denoising

Neural activities recorded using electroencephalography (EEG) are mostly contaminated with eye blink (EB) artifact. This results in undesired activation of brain–computer interface (BCI) systems. Hence, removal of EB artifact is an important issue in EEG signal analysis. Of late, several artifact removal methods have been reported in the literature and they are based on independent component analysis (ICA), thresholding, wavelet transformation, etc. These methods are computationally expensive and result in information loss which makes them unsuitable for online BCI system development. To address the above problems, we have investigated sparsity-based EB artifact removal methods. Two sparsity-based techniques namely morphological component analysis (MCA) and K-SVD-based artifact removal method have been evaluated in our work. MCA-based algorithm exploits the morphological characteristics of EEG and EB using predefined Dirac and discrete cosine transform (DCT) dictionaries. Next, in K-SVD-based algorithm an overcomplete dictionary is learned from the EEG data itself and is designed to model EB characteristics. To substantiate the efficacy of the two algorithms, we have carried out our experiments with both synthetic and real EEG data. We observe that the K-SVD algorithm, which uses a learned dictionary, delivers superior performance for suppressing EB artifacts when compared to MCA technique. Finally, the results of both the techniques are compared with the recent state-of-the-art FORCe method. We demonstrate that the proposed sparsity-based algorithms perform equal to the state-of-the-art technique. It is shown that without using any computationally expensive algorithms, only with the use of over-complete dictionaries the proposed sparsity-based algorithms eliminate EB artifacts accurately from the EEG signals.

Removal of Eye Blink Artifacts From EEG Signals Using Sparsity

The goal of this paper is to describe a robust artifact removal (RAR) method, an automatic sequential procedure which is capable of removing short-duration, high-amplitude artifacts from long-term neonatal EEG recordings. Such artifacts are mainly caused by movement activity, and have an adverse effect on the automatic processing of long-term sleep recordings. The artifacts are removed sequentially in short-term signals using independent component analysis (ICA) transformation and wavelet denoising. In order to gain robustness of the RAR method, the whole EEG recording is processed multiple times. The resulting tentative reconstructions are then combined. We show results in a data set of signals from ten healthy newborns. Those results prove, both qualitatively and quantitatively, that the RAR method is capable of automatically rejecting the mentioned artifacts without changes in overall signal properties such as the spectrum. The method is shown to perform better than either the wavelet-enhanced ICA or the simple artifact rejection method without the combination procedure.

Robust removal of short-duration artifacts in long neonatal EEG recordings using wavelet-enhanced ICA and adaptive combining of tentative reconstructions

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Robust removal of short-duration artifacts in long neonatal EEG recordings using wavelet-enhanced ICA and adaptive combining of tentative reconstructions