Artifacts
Research Papers
EEG-LLAMAS: A low-latency neurofeedback platform for artifact reduction in EEG-fMRI
Simultaneous EEG-fMRI is a powerful multimodal technique for imaging the brain, but its use in neurofeedback experiments has been limited by EEG noise caused by the MRI environment. Neurofeedback studies typically require analysis of EEG in real time, but EEG acquired inside the scanner is heavily contaminated with ballistocardiogram (BCG) artifact, a high-amplitude artifact locked to the cardiac cycle. Although techniques for removing BCG artifacts do exist, they are either not suited to real-time, low-latency applications, such as neurofeedback, or have limited efficacy. We propose and validate a new open-source artifact removal software called EEG-LLAMAS (Low Latency Artifact Mitigation Acquisition Software), which adapts and advances existing artifact removal techniques for low-latency experiments. We first used simulations to validate LLAMAS in data with known ground truth. We found that LLAMAS performed better than the best publicly-available real-time BCG removal technique, optimal basis sets (OBS), in terms of its ability to recover EEG waveforms, power spectra, and slow wave phase. To determine whether LLAMAS would be effective in practice, we then used it to conduct real-time EEG-fMRI recordings in healthy adults, using a steady state visual evoked potential (SSVEP) task. We found that LLAMAS was able to recover the SSVEP in real time, and recovered the power spectra collected outside the scanner better than OBS. We also measured the latency of LLAMAS during live recordings, and found that it introduced a lag of less than 50 ms on average. The low latency of LLAMAS, coupled with its improved artifact reduction, can thus be effectively used for EEG-fMRI neurofeedback. A limitation of the method is its use of a reference layer, a piece of EEG equipment which is not commercially available, but can be assembled in-house. This platform enables closed-loop experiments which previously would have been prohibitively difficult, such as those that target short-duration EEG events, and is shared openly with the neuroscience community.
View Full Paper →The impact of real-time fMRI denoising on online evaluation of brain activity and functional connectivity
Objective. Comprehensive denoising is imperative in functional magnetic resonance imaging (fMRI) analysis to reliably evaluate neural activity from the blood oxygenation level dependent signal. In real-time fMRI, however, only a minimal denoising process has been applied and the impact of insufficient denoising on online brain activity estimation has not been assessed comprehensively. This study evaluated the noise reduction performance of online fMRI processes in a real-time estimation of regional brain activity and functional connectivity.Approach.We performed a series of real-time processing simulations of online fMRI processing, including slice-timing correction, motion correction, spatial smoothing, signal scaling, and noise regression with high-pass filtering, motion parameters, motion derivatives, global signal, white matter/ventricle average signals, and physiological noise models with image-based retrospective correction of physiological motion effects (RETROICOR) and respiration volume per time (RVT).Main results.All the processing was completed in less than 400 ms for whole-brain voxels. Most processing had a benefit for noise reduction except for RVT that did not work due to the limitation of the online peak detection. The global signal regression, white matter/ventricle signal regression, and RETROICOR had a distinctive noise reduction effect, depending on the target signal, and could not substitute for each other. Global signal regression could eliminate the noise-associated bias in the mean dynamic functional connectivity across time.Significance.The results indicate that extensive real-time denoising is possible and highly recommended for real-time fMRI applications.
View Full Paper →Unified Retrospective EEG Motion Educated Artefact Suppression for EEG-fMRI to Suppress Magnetic Field Gradient Artefacts During Motion
The data quality of simultaneously acquired electroencephalography and functional magnetic resonance imaging (EEG-fMRI) can be strongly affected by motion. Recent work has shown that the quality of fMRI data can be improved by using a Moiré-Phase-Tracker (MPT)-camera system for prospective motion correction. The use of the head position acquired by the MPT-camera-system has also been shown to correct motion-induced voltages, ballistocardiogram (BCG) and gradient artefact residuals separately. In this work we show the concept of an integrated framework based on the general linear model to provide a unified motion informed model of in-MRI artefacts. This model (retrospective EEG motion educated gradient artefact suppression, REEG-MEGAS) is capable of correcting voltage-induced, BCG and gradient artefact residuals of EEG data acquired simultaneously with prospective motion corrected fMRI. In our results, we have verified that applying REEG-MEGAS correction to EEG data acquired during subject motion improves the data quality in terms of motion induced voltages and also GA residuals in comparison to standard Artefact Averaging Subtraction and Retrospective EEG Motion Artefact Suppression. Besides that, we provide preliminary evidence that although adding more regressors to a model may slightly affect the power of physiological signals such as the alpha-rhythm, its application may increase the overall quality of a dataset, particularly when strongly affected by motion. This was verified by analysing the EEG traces, power spectra density and the topographic distribution from two healthy subjects. We also have verified that the correction by REEG-MEGAS improves higher frequency artefact correction by decreasing the power of Gradient Artefact harmonics. Our method showed promising results for decreasing the power of artefacts for frequencies up to 250 Hz. Additionally, REEG-MEGAS is a hybrid framework that can be implemented for real time prospective motion correction of EEG and fMRI data. Among other EEG-fMRI applications, the approach described here may benefit applications such as EEG-fMRI neurofeedback and brain computer interface, which strongly rely on the prospective acquisition and application of motion artefact removal.
View Full Paper →Just a very expensive breathing training? Risk of respiratory artefacts in functional connectivity-based real-time fMRI neurofeedback
Real-time functional magnetic resonance imaging neurofeedback (rtfMRI NFB) is a promising method for targeted regulation of pathological brain processes in mental disorders. But most NFB approaches so far have used relatively restricted regional activation as a target, which might not address the complexity of the underlying network changes. Aiming towards advancing novel treatment tools for disorders like schizophrenia, we developed a large-scale network functional connectivity-based rtfMRI NFB approach targeting dorsolateral prefrontal cortex and anterior cingulate cortex connectivity with the striatum. In a double-blind randomized yoke-controlled single-session feasibility study with N = 38 healthy controls, we identified strong associations between our connectivity estimates and physiological parameters reflecting the rate and regularity of breathing. These undesired artefacts are especially detrimental in rtfMRI NFB, where the same data serves as an online feedback signal and offline analysis target. To evaluate ways to control for the identified respiratory artefacts, we compared model-based physiological nuisance regression and global signal regression (GSR) and found that GSR was the most effective method in our data. Our results strongly emphasize the need to control for physiological artefacts in connectivity-based rtfMRI NFB approaches and suggest that GSR might be a useful method for online data correction for respiratory artefacts.
View Full Paper →Cognitive Behavior Classification From Scalp EEG Signals
Electroencephalography (EEG) has become increasingly valuable outside of its traditional use in neurology. EEG is now used for neuropsychiatric diagnosis, neurological evaluation of traumatic brain injury, neurotherapy, gaming, neurofeedback, mindfulness, and cognitive enhancement training. The trend to increase the number of EEG electrodes, the development of novel analytical methods, and the availability of large data sets has created a data analysis challenge to find the "signal of interest" that conveys the most information about ongoing cognitive effort. Accordingly, we compare three common types of neural synchrony measures that are applied to EEG-power analysis, phase locking, and phase-amplitude coupling to assess which analytical measure provides the best separation between EEG signals that were recorded, while healthy subjects performed eight cognitive tasks-Hopkins Verbal Learning Test and its delayed version, Stroop Test, Symbol Digit Modality Test, Controlled Oral Word Association Test, Trail Marking Test, Digit Span Test, and Benton Visual Retention Test. We find that of the three analytical methods, phase-amplitude coupling, specifically theta (4-7 Hz)-high gamma (70-90 Hz) obtained from frontal and parietal EEG electrodes provides both the largest separation between the EEG during cognitive tasks and also the highest classification accuracy between pairs of tasks. We also find that phase-locking analysis provides the most distinct clustering of tasks based on their utilization of long-term memory. Finally, we show that phase-amplitude coupling is the least sensitive to contamination by intense jaw-clenching muscle artifact.
View Full Paper →Real-time fMRI processing with physiological noise correction - Comparison with off-line analysis
BACKGROUND: While applications of real-time functional magnetic resonance imaging (rtfMRI) are growing rapidly, there are still limitations in real-time data processing compared to off-line analysis. NEW METHODS: We developed a proof-of-concept real-time fMRI processing (rtfMRIp) system utilizing a personal computer (PC) with a dedicated graphic processing unit (GPU) to demonstrate that it is now possible to perform intensive whole-brain fMRI data processing in real-time. The rtfMRIp performs slice-timing correction, motion correction, spatial smoothing, signal scaling, and general linear model (GLM) analysis with multiple noise regressors including physiological noise modeled with cardiac (RETROICOR) and respiration volume per time (RVT). RESULTS: The whole-brain data analysis with more than 100,000voxels and more than 250volumes is completed in less than 300ms, much faster than the time required to acquire the fMRI volume. Real-time processing implementation cannot be identical to off-line analysis when time-course information is used, such as in slice-timing correction, signal scaling, and GLM. We verified that reduced slice-timing correction for real-time analysis had comparable output with off-line analysis. The real-time GLM analysis, however, showed over-fitting when the number of sampled volumes was small. COMPARISON WITH EXISTING METHODS: Our system implemented real-time RETROICOR and RVT physiological noise corrections for the first time and it is capable of processing these steps on all available data at a given time, without need for recursive algorithms. CONCLUSIONS: Comprehensive data processing in rtfMRI is possible with a PC, while the number of samples should be considered in real-time GLM.
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