NEAR: An artifact removal pipeline for human newborn EEG data.
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ABSTRACT:
SUBMITTER: Kumaravel VP
PROVIDER: S-EPMC8800139 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In simultaneous EEG-fMRI, the EEG recordings are severely contaminated by ballistocardiogram (BCG) artifacts, which are caused by cardiac pulsations. To reconstruct and remove the BCG artifacts, one promising method is to measure the artifacts in the absence of EEG signal by placing a group of electrodes (BCG electrodes) on a conductive layer (reference layer) insulated from the scalp. However, current BCG reference layer (BRL) methods either use a customized EEG cap composed of electrode pairs, or need to construct the custom reference layer through additional model-building experiments for each EEG-fMRI experiment. These requirements have limited the versatility and efficiency of BRL. The aim of this study is to propose a more practical and efficient BRL method and compare its performance with the most popular BCG removal method, the optimal basis sets (OBS) algorithm.By designing the reference layer as a permanent and reusable cap, the new BRL method is able to be used with a standard EEG cap, and no extra experiments and preparations are needed to use the BRL in an EEG-fMRI experiment.The BRL method effectively removed the BCG artifacts from both oscillatory and evoked potential scalp recordings and recovered the EEG signal.Compared to the OBS, this new BRL method improved the contrast-to-noise ratios of the alpha-wave, visual, and auditory evoked potential signals by 101%, 76%, and 75%, respectively, employing 160 BCG electrodes. Using only 20 BCG electrodes, the BRL improved the EEG signal by 74%/26%/41%, respectively.The proposed method can substantially improve the EEG signal quality compared with traditional methods.
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Project description:BackgroundArtifacts contained in EEG recordings hamper both, the visual interpretation by experts as well as the algorithmic processing and analysis (e.g. for Brain-Computer Interfaces (BCI) or for Mental State Monitoring). While hand-optimized selection of source components derived from Independent Component Analysis (ICA) to clean EEG data is widespread, the field could greatly profit from automated solutions based on Machine Learning methods. Existing ICA-based removal strategies depend on explicit recordings of an individual's artifacts or have not been shown to reliably identify muscle artifacts.MethodsWe propose an automatic method for the classification of general artifactual source components. They are estimated by TDSEP, an ICA method that takes temporal correlations into account. The linear classifier is based on an optimized feature subset determined by a Linear Programming Machine (LPM). The subset is composed of features from the frequency-, the spatial- and temporal domain. A subject independent classifier was trained on 640 TDSEP components (reaction time (RT) study, n = 12) that were hand labeled by experts as artifactual or brain sources and tested on 1080 new components of RT data of the same study. Generalization was tested on new data from two studies (auditory Event Related Potential (ERP) paradigm, n = 18; motor imagery BCI paradigm, n = 80) that used data with different channel setups and from new subjects.ResultsBased on six features only, the optimized linear classifier performed on level with the inter-expert disagreement (<10% Mean Squared Error (MSE)) on the RT data. On data of the auditory ERP study, the same pre-calculated classifier generalized well and achieved 15% MSE. On data of the motor imagery paradigm, we demonstrate that the discriminant information used for BCI is preserved when removing up to 60% of the most artifactual source components.ConclusionsWe propose a universal and efficient classifier of ICA components for the subject independent removal of artifacts from EEG data. Based on linear methods, it is applicable for different electrode placements and supports the introspection of results. Trained on expert ratings of large data sets, it is not restricted to the detection of eye- and muscle artifacts. Its performance and generalization ability is demonstrated on data of different EEG studies.
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Project description:We present an automated algorithm for unified rejection and repair of bad trials in magnetoencephalography (MEG) and electroencephalography (EEG) signals. Our method capitalizes on cross-validation in conjunction with a robust evaluation metric to estimate the optimal peak-to-peak threshold - a quantity commonly used for identifying bad trials in M/EEG. This approach is then extended to a more sophisticated algorithm which estimates this threshold for each sensor yielding trial-wise bad sensors. Depending on the number of bad sensors, the trial is then repaired by interpolation or by excluding it from subsequent analysis. All steps of the algorithm are fully automated thus lending itself to the name Autoreject. In order to assess the practical significance of the algorithm, we conducted extensive validation and comparisons with state-of-the-art methods on four public datasets containing MEG and EEG recordings from more than 200 subjects. The comparisons include purely qualitative efforts as well as quantitatively benchmarking against human supervised and semi-automated preprocessing pipelines. The algorithm allowed us to automate the preprocessing of MEG data from the Human Connectome Project (HCP) going up to the computation of the evoked responses. The automated nature of our method minimizes the burden of human inspection, hence supporting scalability and reliability demanded by data analysis in modern neuroscience.
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Project description:Electroencephalograms (EEGs) recorded simultaneously with functional magnetic resonance imaging (fMRI) are corrupted by large repetitive artifacts generated by the switched MR gradients. Several methods have been proposed to remove these distortions by subtraction of averaged artifact templates from the ongoing EEG. Here, we present a modification of this approach which accounts for head movements to improve the extracted template. Using the fMRI analysis package statistical parametric mapping (SPM; FIL London) the head displacement is determined at each half fMRI-volume. The basic idea is to apply a moving average algorithm for template extraction but to include only epochs that were obtained at the same head position as the artefact to be removed. This approach was derived from phantom EEG measurements demonstrating substantial variations of the artefact waveform in response to movements of the phantom in the MRI magnet. To further reduce the residual noise, we applied a resampling algorithm which aligns the EEG samples in a strict adaptive manner to the fMRI timing. Finally, we propose a new algorithm to suppress residual artifacts such as those occasionally observed in case of brief strong movements, which are not reflected by the movement indicator because of the limited temporal resolution of the fMRI sequence. On the basis of EEG recordings of six subjects these measures combined reduce the residual artefact activity quantified in terms of the spectral power at the gradient repetition rate and its harmonics by roughly 20 to 50% (depending on the amount of movement) predominantly in frequencies beyond 30 Hz.
| S-EPMC6870712 | biostudies-literature
Project description:Artifact Subspace Reconstruction (ASR) is an adaptive method for the online or offline correction of artifacts comprising multichannel electroencephalography (EEG) recordings. It repeatedly computes a principal component analysis (PCA) on covariance matrices to detect artifacts based on their statistical properties in the component subspace. We adapted the existing ASR implementation by using Riemannian geometry for covariance matrix processing. EEG data that were recorded on smartphone in both outdoors and indoors conditions were used for evaluation (N = 27). A direct comparison between the original ASR and Riemannian ASR (rASR) was conducted for three performance measures: reduction of eye-blinks (sensitivity), improvement of visual-evoked potentials (VEPs) (specificity), and computation time (efficiency). Compared to ASR, our rASR algorithm performed favorably on all three measures. We conclude that rASR is suitable for the offline and online correction of multichannel EEG data acquired in laboratory and in field conditions.
| S-EPMC6499032 | biostudies-literature
Project description:Concurrent single-pulse TMS-EEG (spTMS-EEG) is an emerging noninvasive tool for probing causal brain dynamics in humans. However, in addition to the common artifacts in standard EEG data, spTMS-EEG data suffer from enormous stimulation-induced artifacts, posing significant challenges to the extraction of neural information. Typically, neural signals are analyzed after a manual time-intensive and often subjective process of artifact rejection. Here we describe a fully automated algorithm for spTMS-EEG artifact rejection. A key step of this algorithm is to decompose the spTMS-EEG data into statistically independent components (ICs), and then train a pattern classifier to automatically identify artifact components based on knowledge of the spatio-temporal profile of both neural and artefactual activities. The autocleaned and hand-cleaned data yield qualitatively similar group evoked potential waveforms. The algorithm achieves a 95% IC classification accuracy referenced to expert artifact rejection performance, and does so across a large number of spTMS-EEG data sets (n?=?90 stimulation sites), retains high accuracy across stimulation sites/subjects/populations/montages, and outperforms current automated algorithms. Moreover, the algorithm was superior to the artifact rejection performance of relatively novice individuals, who would be the likely users of spTMS-EEG as the technique becomes more broadly disseminated. In summary, our algorithm provides an automated, fast, objective, and accurate method for cleaning spTMS-EEG data, which can increase the utility of TMS-EEG in both clinical and basic neuroscience settings.
| S-EPMC6866546 | biostudies-literature
Project description:The appreciation for the need to record electroencephalographic (EEG) signals from humans while walking has been steadily growing in recent years, particularly in relation to understanding gait disturbances. Movement artefacts (MA) in EEG signals originate from mechanical forces applied to the scalp electrodes, inducing small electrode movements relative to the scalp which, in turn, cause the recorded voltage to change irrespectively of cortical activity. These mechanical forces, and thus MA, may have various sources (e.g., ground reaction forces, head movements, etc.) that are inherent to daily activities, notably walking. In this paper we introduce a systematic, integrated methodology for removing MA from EEG signals recorded during treadmill (TM) and over-ground (OG) walking, as well as quantify the prevalence of MA in different locomotion settings. In our experiments, participants performed walking trials at various speeds both OG and on a TM while wearing a 32-channel EEG cap and a 3-axis accelerometer, placed on the forehead. Data preprocessing included separating the EEG signals into statistically independent additive components using independent component analysis (ICA). We observed an increase in electro-physiological signals (e.g., neck EMG activations for stabilizing the head during heel-strikes) as the walking speed increased. These artefact independent-components (ICs), while not originating from electrode movement, still exhibit a similar spectral pattern to the MA ICs-a peak at the stepping frequency. MA was identified and quantified in each component using a novel method that utilizes the participant's stepping frequency, derived from a forehead-mounted accelerometer. We then benchmarked the EEG data by applying newly established metrics to quantify the success of our method in cleaning the data. The results indicate that our approach can be successfully applied to EEG data recorded during TM and OG walking, and is offered as a unified methodology for MA removal from EEG collected during gait trials.
| S-EPMC5955591 | biostudies-literature
Project description:BackgroundIn concurrent EEG/fMRI recordings, EEG data are impaired by the fMRI gradient artifacts which exceed the EEG signal by several orders of magnitude. While several algorithms exist to correct the EEG data, these algorithms lack the flexibility to either leave out or add new steps. The here presented open-source MATLAB toolbox FACET is a modular toolbox for the fast and flexible correction and evaluation of imaging artifacts from concurrently recorded EEG datasets. It consists of an Analysis, a Correction and an Evaluation framework allowing the user to choose from different artifact correction methods with various pre- and post-processing steps to form flexible combinations. The quality of the chosen correction approach can then be evaluated and compared to different settings.ResultsFACET was evaluated on a dataset provided with the FMRIB plugin for EEGLAB using two different correction approaches: Averaged Artifact Subtraction (AAS, Allen et al., NeuroImage 12(2):230-239, 2000) and the FMRI Artifact Slice Template Removal (FASTR, Niazy et al., NeuroImage 28(3):720-737, 2005). Evaluation of the obtained results were compared to the FASTR algorithm implemented in the EEGLAB plugin FMRIB. No differences were found between the FACET implementation of FASTR and the original algorithm across all gradient artifact relevant performance indices.ConclusionThe FACET toolbox not only provides facilities for all three modalities: data analysis, artifact correction as well as evaluation and documentation of the results but it also offers an easily extendable framework for development and evaluation of new approaches.
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Project description:Alternating current stimulation is a promising method for the study and treatment of various visual neurological dysfunctions as well as progressive understanding of the healthy brain. Unfortunately, due to the current stimulation artifact, problems remain in the context of analysis of the electroencephalography (EEG) signal recorded during ongoing stimulation. To address this problem, we propose the use of a simple moving average subtraction as a method for artifact elimination. This method involves the creation of a template of the stimulation artifact from EEG signal recorded during non-invasive electrical stimulation with a sinusoidal alternating current. The present report describes results of the effects of a simple moving average filtration that varies based on averaging parameters; in particular, we varied the number of sinusoidal periods per segment of the recorded signal and the number of segments used to construct an artifact template. Given the ongoing lack of a mathematical model that allows for the prediction of the "hidden" EEG signal with the alternating current stimulation artifact, we propose performing an earlier simulation that is based on the addition of artificial stimulation artifact to the known EEG signal. This solution allows for the optimization of filtering parameters with detailed knowledge about the accuracy of artifact removal. The algorithm, designed in the MATLAB environment, has been tested on data recorded from two volunteers subjected to sinusoidal transorbital alternating current stimulation. Analysis of the percentage difference between the original and filtered signal in time and frequency domain highlights the advantage of 1-period filtration.
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Project description:With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency.
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