Methods for cleaning the BOLD fMRI signal

Available online 9 December 2016 http://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3Dihubhttp://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3DihubBlood oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI) has rapidly become a popular technique for the investigation of brain function in healthy individuals, patients as well as in animal studies. However, the BOLD signal arises from a complex mixture of neuronal, metabolic and vascular processes, being therefore an indirect measure of neuronal activity, which is further severely corrupted by multiple non-neuronal fluctuations of instrumental, physiological or subject-specific origin. This review aims to provide a comprehensive summary of existing methods for cleaning the BOLD fMRI signal. The description is given from a methodological point of view, focusing on the operation of the different techniques in addition to pointing out the advantages and limitations in their application. Since motion-related and physiological noise fluctuations are two of the main noise components of the signal, techniques targeting their removal are primarily addressed, including both data-driven approaches and using external recordings. Data-driven approaches, which are less specific in the assumed model and can simultaneously reduce multiple noise fluctuations, are mainly based on data decomposition techniques such as principal and independent component analysis. Importantly, the usefulness of strategies that benefit from the information available in the phase component of the signal, or in multiple signal echoes is also highlighted. The use of global signal regression for denoising is also addressed. Finally, practical recommendations regarding the optimization of the preprocessing pipeline for the purpose of denoising and future venues of research are indicated. Through the review, we summarize the importance of signal denoising as an essential step in the analysis pipeline of task-based and resting state fMRI studies.This work was supported by the Spanish Ministry of Economy and Competitiveness [Grant PSI 2013–42343 Neuroimagen Multimodal], the Severo Ochoa Programme for Centres/Units of Excellence in R & D [SEV-2015-490], and the research and writing of the paper were supported by the NIMH and NINDS Intramural Research Programs (ZICMH002888) of the NIH/HHS

Issues in the processing and analysis of functional NIRS imaging and a contrast with fMRI findings in a study of sensorimotor deactivation and connectivity

Includes abstract.~Includes bibliographical references.The first part of this thesis examines issues in the processing and analysis of continuous wave functional linear infrared spectroscopy (fNIRS) of the brain usung the DYNOT system. In the second part, the same sensorimotor experiment is carried out using functional magnetic resonance imaging (fMRI) and near infrared spectroscopy in eleven of the same subjects, to establish whether similar results can be obtained at the group level with each modality. Various techniques for motion artefact removal in fNIRS are compared. Imaging channels with negligible distance between source and detector are used to detect subject motion, and in data sets containing deliberate motion artefacts, independent component analysis and multiple-channel regression are found to improve the signal-to-noise ratio

Altered Relationship Between Heart Rate Variability and fMRI-Based Functional Connectivity in People With Epilepsy

Background: Disruptions in central autonomic processes in people with epilepsy have been studied through evaluation of heart rate variability (HRV). Decreased HRV appears in epilepsy compared to healthy controls, suggesting a shift in autonomic balance toward sympathetic dominance; recent studies have associated HRV changes with seizure severity and outcome of interventions. However, the processes underlying these autonomic changes remain unclear. We examined the nature of these changes by assessing alterations in whole-brain functional connectivity, and relating those alterations to HRV.Methods: We examined regional brain activity and functional organization in 28 drug-resistant epilepsy patients and 16 healthy controls using resting-state functional magnetic resonance imaging (fMRI). We employed an HRV state-dependent functional connectivity (FC) framework with low and high HRV states derived from the following four cardiac-related variables: 1. RR interval, 2. root mean square of successive differences (RMSSD), 4. low-frequency HRV (0.04–0.15 Hz; LF-HRV) and high-frequency HRV (0.15–0.40 Hz; HF-HRV). The effect of group (epilepsy vs. controls), HRV state (low vs. high) and the interactions of group and state were assessed using a mixed analysis of variance (ANOVA). We assessed FC within and between 7 large-scale functional networks consisting of cortical regions and 4 subcortical networks, the amygdala, hippocampus, basal ganglia and thalamus networks.Results: Consistent with previous studies, decreased RR interval (increased heart rate) and decreased HF-HRV appeared in people with epilepsy compared to healthy controls. For both groups, fluctuations in heart rate were positively correlated with BOLD activity in bilateral thalamus and regions of the cerebellum, and negatively correlated with BOLD activity in the insula, putamen, superior temporal gyrus and inferior frontal gyrus. Connectivity strength in patients between right thalamus and ventral attention network (mainly insula) increased in the high LF-HRV state compared to low LF-HRV; the opposite trend appeared in healthy controls. A similar pattern emerged for connectivity between the thalamus and basal ganglia.Conclusion: The findings suggest that resting connectivity patterns between the thalamus and other structures underlying HRV expression are modified in people with drug-resistant epilepsy compared to healthy controls

Identifying Respiration-Related Aliasing Artifacts in the Rodent Resting-State fMRI

Resting-state functional magnetic resonance imaging (rs-fMRI) combined with optogenetics and electrophysiological/calcium recordings in animal models is becoming a popular platform to investigate brain dynamics under specific neurological states. Physiological noise originating from the cardiac and respiration signal is the dominant interference in human rs-fMRI and extensive efforts have been made to reduce these artifacts from the human data. In animal fMRI studies, physiological noise sources including the respiratory and cardiorespiratory artifacts to the rs-fMRI signal fluctuation have typically been less investigated. In this article, we demonstrate evidence of aliasing effects into the low-frequency rs-fMRI signal fluctuation mainly due to respiration-induced B0 offsets in anesthetized rats. This aliased signal was examined by systematically altering the fMRI sampling rate, i.e., the time of repetition (TR), in free-breathing conditions and by adjusting the rate of ventilation. Anesthetized rats under ventilation showed a significantly narrower frequency bandwidth of the aliasing effect than free-breathing animals. It was found that the aliasing effect could be further reduced in ventilated animals with a muscle relaxant. This work elucidates the respiration-related aliasing effects on the rs-fMRI signal fluctuation from anesthetized rats, indicating non-negligible physiological noise needed to be taken care of in both awake and anesthetized animal rs-fMRI studies

Towards a better understanding of the impact of heart rate on the BOLD signal: a new method for physiological noise correction and its applications

Functional magnetic resonance imaging (fMRI) based on blood oxygenation level-dependent (BOLD) contrast allows non-invasive examination of brain activity and is widely used in the neuroimaging field. The BOLD contrast mechanism reflects hemodynamic changes resulting from a complex interplay of blood flow, blood volume, and oxygen consumption. Heart rate (HR) variations are the most intriguing and less understood physiological processes affecting the BOLD signal, as they are the result of a wide variety of interacting factors. The use of the response function that best models HR-induced signal changes, called cardiac response function (CRF), is an effective method to reduce HR noise in fMRI. However, current models of physiological noise correction based on CRF, i.e. canonical and individual, either do not take into account variations in HR between subjects, and are thus inadequate for cohorts with varying HR, or require time-consuming quality control of individual physiological recordings and derived CRFs. By analyzing a large cohort of healthy individuals, the results presented in this thesis show that different HRs influence the BOLD signal and their corresponding spectra differently. A further finding is that HR plays an essential role in determining the shape of the CRF. Slower HRs produce a smoothed CRF with a single well-defined maximum, while faster HRs cause a second maximum. Taking advantage of this dependence of the CRF on HR, a novel method is proposed to model HR-induced fluctuations in the BOLD signal more accurately than current approaches of physiological noise correction. This method, called HR-based CRF, consists of two CRFs: one for HRs below 68 bpm and one for HRs above this value. HR-based CRFs can be directly applied to the fMRI data without the time-consuming task of deriving a CRF for each subject while accounting for inter-subject variability in HR response

fMRI BOLD Correlates of EEG Independent Components: Spatial Correspondence With the Default Mode Network

Goal: We aimed to identify electroencephalographic (EEG) signal fluctuations within independent components (ICs) that correlate to spontaneous blood oxygenation level dependent (BOLD) activity in regions of the default mode network (DMN) during eyes-closed resting state.Methods: We analyzed simultaneously acquired EEG and functional magnetic resonance imaging (fMRI) eyes-closed resting state data in a convenience sample of 30 participants. IC analysis (ICA) was used to decompose the EEG time-series and common ICs were identified using data-driven IC clustering across subjects. The IC time courses were filtered into seven frequency bands, convolved with a hemeodynamic response function (HRF) and used to model spontaneous fMRI signal fluctuations across the brain. In parallel, group ICA analysis was used to decompose the fMRI signal into ICs from which the DMN was identified. Frequency and IC cluster associated hemeodynamic correlation maps obtained from the regression analysis were spatially correlated with the DMN. To investigate the reliability of our findings, the analyses were repeated with data collected from the same subjects 1 year later.Results: Our results indicate a relationship between power fluctuations in the delta, theta, beta and gamma frequency range and the DMN in different EEG ICs in our sample as shown by small to moderate spatial correlations at the first measurement (0.234 < |r| < 0.346, p < 0.0001). Furthermore, activity within an EEG component commonly identified as eye movements correlates with BOLD activity within regions of the DMN. In addition, we demonstrate that correlations between EEG ICs and the BOLD signal during rest are in part stable across time.Discussion: We show that ICA source separated EEG signals can be used to investigate electrophysiological correlates of the DMN. The relationship between the eye movement component and the DMN points to a behavioral association between DMN activity and the level of eye movement or the presence of neuronal activity in this component. Previous findings of an association between frontal midline theta activity and the DMN were replicated

Simultaneous EEG and fMRI at high fields

The work described in this thesis involves an investigation of the implementation and application of simultaneous EEG and fMRI. The two techniques arc complementary, with EEG providing excellent temporal resolution and fMRI having good spatial resolution. Combined EEG/fMRI thus forms a powerful tool for neuroscience studies. In initial work, methods for improving the removal of the gradient and pulse artefacts, which are induced in EEG traces recorded during concurrent MRI, have been developed. Subsequently, the effects of the EEG hardware on MR images were investigated. This involved acquiring a series of scans to identify the sources of B0- and B1 inhomogeneities and the extent to which these affect EPI data. The adverse effects on data quality of combining EEG and fMRI increase with field strength. Consequently, EEG-fMRI at 7T is particularly challenging, although a number of advantages make its implementation desirable. Safety tests were performed which showed the presence of the EEG system caused a negligible increase in RF heating effects during scanning at 7T. After elimination of a number of noise sources, the first simultaneous EEG-fMRI experiments at 7T using commercially available equipment were performed. Concurrent EEG/fMRI at 3T was then used to investigate the correlation between the BOLD (blood oxygenation level dependent) response measured during visual stimulation and both the preceding alpha power and the strength of the driven, electrical response. In considering the correlation of the range of variation of the alpha power and BOLD response, a trend emerged which allowed tentative conclusions to be drawn. Variation of the BOLD and driven response with the frequency of visual stimulation relative to a subject's individual alpha frequency (IAF) was also investigated. A significant increase in the driven response, accompanied by a decrease in the BOLD response was observed in visual cortex when it was driven at the IAF

Simultaneous EEG-fMRI at ultra-high field for the study of human brain function

Scalp electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) have highly complementary domains, and their combination has been actively sought within neuroscience research. The important gains in fMRI sensitivity achieved with higher field strengths open exciting perspectives for combined EEG-fMRI; however, simultaneous acquisitions are subject to highly undesirable interactions between the two modalities, which can strongly compromise data quality and subject safety, and most of these interactions are increased at higher fields. The work described in this thesis was centered on the development of simultaneous EEG-fMRI in humans at 7T, covering aspects of subject safety, signal quality assessment, and quality improvement. Additionally, given the potential value of high-field EEG-fMRI to study the neuronal correlates of so-called negative BOLD responses, an initial fMRI study was dedicated to these phenomena. The initial fMRI study aimed to characterize positive (PBR) and negative BOLD responses (NBR) to visual checkerboard stimulation of varying contrast and duration, focusing on NBRs occurring in visual and in auditory cortical regions. Results showed that visual PBRs and both visual and auditory NBRs significantly depend on stimulus contrast and duration, suggesting a dynamic system of visual-auditory interactions, sensitive to stimulus contrast and duration. The neuronal correlates of these interactions could not be addressed in higher detail with fMRI alone, yet could potentially be clarified in future work with combined EEG-fMRI. Moving on to simultaneous EEG-fMRI implementation, the first stage comprised an assessment of potential safety concerns at 7T. The safety tests comprised numerical simulations of RF power distribution and real temperature measurements on a phantom during acquisition. Overall, no significant safety concerns were found for the setup tested. A characterization of artifacts induced on MRI data due to the presence of EEG components was then performed. With the introduction of the EEG system, functional and anatomical images exhibited general losses in spatial SNR, with a smaller loss in temporal SNR in fMRI data. B0 and B1 field mapping pointed towards RF pulse disruption as the major degradation mechanism affecting MRI data. The main part of this work focused on EEG artifacts induced by MRI. The first step focused on optimizing signal transmission between the EEG cap and amplifiers, to minimize artifact contamination at this important stage. Along this line, adequate cable shortening and bundling effectively reduced environment noise in EEG recordings. Simultaneous acquisitions were then performed on humans using the optimized setup. On average, EEG data exhibited clear alpha modulation and average visual evoked potentials (VEP), with concomitant BOLD signal changes. In the second step, a novel approach for head motion artifact detection was developed, based on a simple modification of the EEG cap, and simultaneous acquisitions were performed in volunteers undergoing visual checkerboard stimulation. After gradient artifact correction, EEG signal variance was found to be largely dominated by pulse artifacts, but contributions from spontaneous motion were still comparable to those of neuronal activity. Using a combination of pulse artifact correction, motion artifact correction and ICA denoising, strong improvements in data quality could be obtained, especially at a single-trial level

EEG-fMRI signatures of spontaneous brain activity in healthy volunteers and epilepsy patients

Background: Functional magnetic resonance imaging (fMRI) provides maps of haemodynamic activity with uniform resolution across the brain. Simultaneous recording of electroencephalography (EEG) during fMRI (EEG-fMRI) was developed to localize spontaneously occurring epileptiform discharges. In focal epilepsy, it can identify candidate brain regions for surgical removal as a treatment option in medically refractory epilepsy; and in generalized epilepsy syndromes reveals those involved during the EEG changes. In healthy subjects, EEG-fMRI has linked spontaneous ongoing EEG activity with fMRI resting state networks. Methods: After method refinements, patients with medically refractory focal epilepsy and those with generalized epilepsy were studied with EEG-fMRI and group analyses performed to identify typical sets of brain regions involved in the epileptic process. Findings: In individual patients with refractory focal epilepsy, EEG-fMRI can produce activity maps including the seizure onset zone and propagated epileptic activity. Clinically, these can be confirmatory of results from alternative diagnostic techniques, or alternatively serve to generate a hypothesis on the potential epileptic focus, but under certain conditions may also be of negative predictive value with respect to surgical treatment success. At the group level in patients with temporal lobe epilepsy and complex partial seizures as well as in patients with generalized epilepsy and absence seizures, altered resting state network activity during EEG changes were found in default mode brain regions fitting well the ictal semiology, because these are known to reduce their activity during states of reduced consciousness. In (1) lateralized temporal lobe epilepsies, (2) an unselected mix of focal epilepsies, and (3) generalized epilepsies, activity increases occurred in typical brain regions suggesting an associated “hub function”, namely ipsilateral to the presumed cortical focus in the hippocampus; in an area near the frontal piriform cortex; and bilaterally in the thalamus, respectively. These findings argue for a network rather than a zone concept of epilepsy