The effect of respiration variations on independent component analysis results of resting state functional connectivity

Modulation of Posterior Default Mode Network Activity During Interoceptive Attention and Relation to Mindfulness

Background

Interoceptive attention to internal sensory signals, such as the breath, is fundamental to mindfulness. However, interoceptive attention can be difficult to study, with many studies relying on subjective and retrospective measures. Response consistency is an established method for evaluating variability of attention on exteroceptive attention tasks, but it has rarely been applied to interoceptive attention tasks.

Methods

In this study, we measured consistency of response times on a breath-monitoring task with simultaneous electroencephalography in individuals across the life span (15-91 years of age, N = 324).

Results

We found that consistency on the breath-monitoring task was positively correlated with attentive performance on an exteroceptive inhibitory control task. Electroencephalography source reconstruction showed that on-task alpha band (8-12 Hz) activity was greater than that measured at rest. Low-consistency/longer breath responses were associated with elevated brain activity compared with high-consistency responses, particularly in posterior default mode network (pDMN) brain regions. pDMN activity was inversely linked with functional connectivity to the frontoparietal network and the cingulo-opercular network on task but not at rest, suggesting a role for these frontal networks in on-task regulation of pDMN activity. pDMN activity within the precuneus region was greater in participants who reported low subjective mindfulness and was adaptively modulated by task difficulty in an independent experiment.

Conclusions

Elevated pDMN alpha activity serves as an objective neural marker for low-consistency responding during interoceptive breath attention, scales with task difficulty, and is associated with low subjective mindfulness.

Functional alterations in overweight/obesity: focusing on the reward and executive control network

Overweight (OW) and obesity (OB) have become prevalent issues in the global public health arena. Serving as a prominent risk factor for various chronic diseases, overweight/obesity not only poses serious threats to people's physical and mental health but also imposes significant medical and economic burdens on society as a whole. In recent years, there has been a growing focus on basic scientific research dedicated to seeking the neural evidence underlying overweight/obesity, aiming to elucidate its causes and effects by revealing functional alterations in brain networks. Among them, dysfunction in the reward network (RN) and executive control network (ECN) during both resting state and task conditions is considered pivotal in neuroscience research on overweight/obesity. Their aberrations contribute to explaining why persons with overweight/obesity exhibit heightened sensitivity to food rewards and eating disinhibition. This review centers on the reward and executive control network by analyzing and organizing the resting-state and task-based fMRI studies of functional brain network alterations in overweight/obesity. Building upon this foundation, the authors further summarize a reward-inhibition dual-system model, with a view to establishing a theoretical framework for future exploration in this field.

Reproducibility and Sensitivity of Resting-State fMRI in Patients With Parkinson's Disease Using Cross Validation-Based Data Censoring

BACKGROUND

Uncontrollable body movements are typical symptoms of Parkinson's disease (PD), which results in inconsistent findings regarding resting-state functional connectivity (rsFC) networks, especially for group difference clusters. Systematically identifying the motion-associated data was highly demanded.

PURPOSE

To determine data censoring criteria using a quantitative cross validation-based data censoring (CVDC) method and to improve the detection of rsFC deficits in PD.

STUDY TYPE

Prospective.

SUBJECTS

Forty-one PD patients (68.63 ± 9.17 years, 44% female) and 20 healthy controls (66.83 ± 12.94 years, 55% female).

FIELD STRENGTH/SEQUENCE

3-T, T1-weighted gradient echo and EPI sequences.

ASSESSMENT

Clusters with significant differences between groups were found in three visual networks, default network, and right sensorimotor network. Five-fold cross-validation tests were performed using multiple motion exclusion criteria, and the selected criteria were determined based on cluster sizes, significance values, and Dice coefficients among the cross-validation tests. As a reference method, whole brain rsFC comparisons between groups were analyzed using a FMRIB Software Library (FSL) pipeline with default settings.

STATISTICAL TESTS

Group difference clusters were calculated using nonparametric permutation statistics of FSL-randomize. The family-wise error was corrected. Demographic information was evaluated using independent sample t-tests and Pearson's Chi-squared tests. The level of statistical significance was set at P < 0.05.

RESULTS

With the FSL processing pipeline, the mean Dice coefficient of the network clusters was 0.411, indicating a low reproducibility. With the proposed CVDC method, motion exclusion criteria were determined as frame-wise displacement >0.55 mm. Group-difference clusters showed a mean P-value of 0.01 and a 72% higher mean Dice coefficient compared to the FSL pipeline. Furthermore, the CVDC method was capable of detecting subtle rsFC deficits in the medial sensorimotor network and auditory network that were unobservable using the conventional pipeline.

DATA CONCLUSION

The CVDC method may provide superior sensitivity and improved reproducibility for detecting rsFC deficits in PD.

LEVEL OF EVIDENCE

1 TECHNICAL EFFICACY: Stage 2.

"Brain-breath" interactions: respiration-timing-dependent impact on functional brain networks and beyond

Breathing is a natural daily action that one cannot do without, and it sensitively and intensely changes under various situations. What if this essential act of breathing can impact our overall well-being? Recent studies have demonstrated that breathing oscillations couple with higher brain functions, i.e., perception, motor actions, and cognition. Moreover, the timing of breathing, a phase transition from exhalation to inhalation, modulates specific cortical activity and accuracy in cognitive tasks. To determine possible respiratory roles in attentional and memory processes and functional neural networks, we discussed how breathing interacts with the brain that are measured by electrophysiology and functional neuroimaging: (i) respiration-dependent modulation of mental health and cognition; (ii) respiratory rhythm generation and respiratory pontomedullary networks in the brainstem; (iii) respiration-dependent effects on specific brainstem regions and functional neural networks (e.g., glutamatergic PreBötzinger complex neurons, GABAergic parafacial neurons, adrenergic C1 neurons, parabrachial nucleus, locus coeruleus, temporoparietal junction, default-mode network, ventral attention network, and cingulo-opercular salience network); and (iv) a potential application of breathing manipulation in mental health care. These outlines and considerations of "brain-breath" interactions lead to a better understanding of the interoceptive and cognitive mechanisms that underlie brain-body interactions in health conditions and in stress-related and neuropsychiatric disorders.

From Lung to Brain: Respiration Modulates Neural and Mental Activity

Respiration protocols have been developed to manipulate mental states, including their use for therapeutic purposes. In this systematic review, we discuss evidence that respiration may play a fundamental role in coordinating neural activity, behavior, and emotion. The main findings are: (1) respiration affects the neural activity of a wide variety of regions in the brain; (2) respiration modulates different frequency ranges in the brain's dynamics; (3) different respiration protocols (spontaneous, hyperventilation, slow or resonance respiration) yield different neural and mental effects; and (4) the effects of respiration on the brain are related to concurrent modulation of biochemical (oxygen delivery, pH) and physiological (cerebral blood flow, heart rate variability) variables. We conclude that respiration may be an integral rhythm of the brain's neural activity. This provides an intimate connection of respiration with neuro-mental features like emotion. A respiratory-neuro-mental connection holds the promise for a brain-based therapeutic usage of respiration in mental disorders.

Estimating and mitigating the effects of systemic low frequency oscillations (sLFO) on resting state networks in awake non-human primates using time lag dependent methodology

AIM

Resting-state fMRI (rs-fMRI) is often used to infer regional brain interactions from the degree of temporal correlation between spontaneous low-frequency fluctuations, thought to reflect local changes in the BOLD signal due to neuronal activity. One complication in the analysis and interpretation of rs-fMRI data is the existence of non-neuronal low frequency physiological noise (systemic low frequency oscillations; sLFOs) which occurs within the same low frequency band as the signal used to compute functional connectivity. Here, we demonstrate the use of a time lag mapping technique to estimate and mitigate the effects of the sLFO signal on resting state functional connectivity of awake squirrel monkeys.

METHODS

Twelve squirrel monkeys (6 male/6 female) were acclimated to awake scanning procedures; whole-brain fMRI images were acquired with a 9.4 Tesla scanner. Rs-fMRI data was preprocessed using an in-house pipeline and sLFOs were detected using a seed regressor generated by averaging BOLD signal across all voxels in the brain, which was then refined recursively within a time window of -16-12 s. The refined regressor was then used to estimate the voxel-wise sLFOs; these regressors were subsequently included in the general linear model to remove these moving hemodynamic components from the rs-fMRI data using general linear model filtering. Group level independent component analysis (ICA) with dual regression was used to detect resting-state networks and compare networks before and after sLFO denoising.

RESULTS

Results show sLFOs constitute ~64% of the low frequency fMRI signal in squirrel monkey gray matter; they arrive earlier in regions in proximity to the middle cerebral arteries (e.g., somatosensory cortex) and later in regions close to draining vessels (e.g., cerebellum). Dual regression results showed that the physiological noise was significantly reduced after removing sLFOs and the extent of reduction was determined by the brain region contained in the resting-state network.

CONCLUSION

These results highlight the need to estimate and remove sLFOs from fMRI data before further analysis.

An orderly sequence of autonomic and neural events at transient arousal changes

Resting-state functional magnetic resonance imaging (rsfMRI) allows the study of functional brain connectivity based on spatially structured variations in neuronal activity. Proper evaluation of connectivity requires removal of non-neural contributions to the fMRI signal, in particular hemodynamic changes associated with autonomic variability. Regression analysis based on autonomic indicator signals has been used for this purpose, but may be inadequate if neuronal and autonomic activities covary. To investigate this potential co-variation, we performed rsfMRI experiments while concurrently acquiring electroencephalography (EEG) and autonomic indicator signals, including heart rate, respiratory depth, and peripheral vascular tone. We identified a recurrent and systematic spatiotemporal pattern of fMRI (named as fMRI cascade), which features brief signal reductions in salience and default-mode networks and the thalamus, followed by a biphasic global change with a sensory-motor dominance. This fMRI cascade, which was mostly observed during eyes-closed condition, was accompanied by large EEG and autonomic changes indicative of arousal modulations. Importantly, the removal of the fMRI cascade dynamics from rsfMRI diminished its correlations with various signals. These results suggest that the rsfMRI correlations with various physiological and neural signals are not independent but arise, at least partly, from the fMRI cascades and associated neural and physiological changes at arousal modulations.

Unsupervised physiological noise correction of functional magnetic resonance imaging data using phase and magnitude information (PREPAIR)

Of the sources of noise affecting blood oxygen level-dependent functional magnetic resonance imaging (fMRI), respiration and cardiac fluctuations are responsible for the largest part of the variance, particularly at high and ultrahigh field. Existing approaches to removing physiological noise either use external recordings, which can be unwieldy and unreliable, or attempt to identify physiological noise from the magnitude fMRI data. Data-driven approaches are limited by sensitivity, temporal aliasing, and the need for user interaction. In the light of the sensitivity of the phase of the MR signal to local changes in the field stemming from physiological processes, we have developed an unsupervised physiological noise correction method using the information carried in the phase and the magnitude of echo-planar imaging data. Our technique, Physiological Regressor Estimation from Phase and mAgnItude, sub-tR (PREPAIR) derives time series signals sampled at the slice TR from both phase and magnitude images. It allows physiological noise to be captured without aliasing, and efficiently removes other sources of signal fluctuations not related to physiology, prior to regressor estimation. We demonstrate that the physiological signal time courses identified with PREPAIR agree well with those from external devices and retrieve challenging cardiac dynamics. The removal of physiological noise was as effective as that achieved with the most used approach based on external recordings, RETROICOR. In comparison with widely used recording-free physiological noise correction tools-PESTICA and FIX, both performed in unsupervised mode-PREPAIR removed significantly more respiratory and cardiac noise than PESTICA, and achieved a larger increase in temporal signal-to-noise-ratio at both 3 and 7 T.

Resting-state Functional Connectivity During Controlled Respiratory Cycles Using Functional Magnetic Resonance Imaging

Introduction

This study aimed to assess the effect of controlled mouth breathing during the resting state using functional magnetic resonance imaging (fMRI).

Methods

Eleven subjects participated in this experiment in which the controlled "Nose" and "Mouth" breathings of 6 s respiratory cycle were performed with a visual cue at 3T MRI. Voxel-wise seed-to-voxel maps and whole-brain region of interest (ROI)-to-ROI connectome maps were analyzed in both "Nose>Mouth" and "Mouth>Nose" contrasts.

Results

As a result, there were more connection pairs in the "Mouth" breathing condition, i.e., 14 seeds and 14 connecting pairs in the "Mouth>Nose" contrast, compared to 7 seeds and 4 connecting pairs in the "Nose>Mouth" contrast (false discovery rate [FDR] of P<0.05).

Conclusion

The present study demonstrated that mouth breathing with controlled respiratory cycles could significantly induce alterations in functional connectivity in the resting-state network, suggesting that it can differently affect resting brain function; in particular, the brain can hardly rest during mouth breathing, as opposed to conventional nasal breathing.

Mode decomposition-based time-varying phase synchronization for fMRI

Recently, there has been significant interest in measuring time-varying functional connectivity (TVC) between different brain regions using resting-state functional magnetic resonance imaging (rs-fMRI) data. One way to assess the relationship between signals from different brain regions is to measure their phase synchronization (PS) across time. However, this requires the a priori choice of type and cut-off frequencies for the bandpass filter needed to perform the analysis. Here we explore alternative approaches based on the use of various mode decomposition (MD) techniques that provide a more data driven solution to this issue. These techniques allow for the data driven decomposition of signals jointly into narrow-band components at different frequencies, thus fulfilling the requirements needed to measure PS. We explore several variants of MD, including empirical mode decomposition (EMD), bivariate EMD (BEMD), noise-assisted multivariate EMD (na-MEMD), and introduce the use of multivariate variational mode decomposition (MVMD) in the context of estimating time-varying PS. We contrast the approaches using a series of simulations and application to rs-fMRI data. Our results show that MVMD outperforms other evaluated MD approaches, and further suggests that this approach can be used as a tool to reliably investigate time-varying PS in rs-fMRI data.

fMRI studies evaluating central respiratory control in humans

A plethora of neural centers in the central nervous system control the fundamental respiratory pattern. This control is ensured by neurons that act as pacemakers, modulating activity through chemical control driven by changes in the O2/CO2 balance. Most of the respiratory neural centers are located in the brainstem, but difficult to localize on magnetic resonance imaging (MRI) due to their small size, lack of visually-detectable borders with neighboring areas, and significant physiological noise hampering detection of its activity with functional MRI (fMRI). Yet, several approaches make it possible to study the normal response to different abnormal stimuli or conditions such as CO2 inhalation, induced hypercapnia, volitional apnea, induced hypoxia etc. This review provides a comprehensive overview of the majority of available studies on central respiratory control in humans.

Application of graph theory across multiple frequency bands in drug-naïve obsessive-compulsive disorder with no comorbidity

Recently, graph theoretical analysis based on resting-state functional magnetic resonance imaging has provided a means of investigating the complex brain connectome in obsessive-compulsive disorder (OCD) patients. However, these studies have been restricted to spontaneous blood oxygen level-dependent (BOLD) signals with frequency bands between 0.01 and 0.08 Hz, and the parameters from graph theory across multiple frequency bands have seldom been studied. Here, we calculated global metrics (small-worldness, global efficiency and modularity) and nodal metrics (degree centrality, betweenness centrality, nodal clustering coefficient and shortest path) at four different frequency bands (slow-2 (0.199-0.25 Hz), slow-3 (0.074-0.198 Hz), slow-4 (0.027-0.073 Hz) and slow-5 (0.01-0.027 Hz), from 0.01 to 0.25 Hz) in seventy-three OCD patients and ninety healthy controls. The analyses were also calculated in traditional low-frequency bands (0.01-0.08 Hz) for reference. For the global metrics, the OCD patients showed increased small-worldness and modularity only in the slow-3 band. For the local metrics, we observed a frequency-dependent characteristic, with the main significant differences in regions including the right precentral gyrus, occipital region, right anterior cingulum cortex and fusiform cortex. Our results suggested frequency-specific abnormalities of the brain connectome in OCD and the future studies may need to consider different frequency bands when measuring spontaneous activity in the brain.

Behavioral and physiological monitoring for awake neurovascular coupling experiments: a how-to guide

Significance: Functional brain imaging in awake animal models is a popular and powerful technique that allows the investigation of neurovascular coupling (NVC) under physiological conditions. However, ubiquitous facial and body motions (fidgeting) are prime drivers of spontaneous fluctuations in neural and hemodynamic signals. During periods without movement, animals can rapidly transition into sleep, and the hemodynamic signals tied to arousal state changes can be several times larger than sensory-evoked responses. Given the outsized influence of facial and body motions and arousal signals in neural and hemodynamic signals, it is imperative to detect and monitor these events in experiments with un-anesthetized animals. Aim: To cover the importance of monitoring behavioral state in imaging experiments using un-anesthetized rodents, and describe how to incorporate detailed behavioral and physiological measurements in imaging experiments. Approach: We review the effects of movements and sleep-related signals (heart rate, respiration rate, electromyography, intracranial pressure, whisking, and other body movements) on brain hemodynamics and electrophysiological signals, with a focus on head-fixed experimental setup. We summarize the measurement methods currently used in animal models for detection of those behaviors and arousal changes. We then provide a guide on how to incorporate this measurements with functional brain imaging and electrophysiology measurements. Results: We provide a how-to guide on monitoring and interpreting a variety of physiological signals and their applications to NVC experiments in awake behaving mice. Conclusion: This guide facilitates the application of neuroimaging in awake animal models and provides neuroscientists with a standard approach for monitoring behavior and other associated physiological parameters in head-fixed animals.

A comprehensive investigation of physiologic noise modeling in resting state fMRI; time shifted cardiac noise in EPI and its removal without external physiologic signal measures

Hemodynamic cardiac and respiratory-cycle fluctuations are a source of unwanted non-neuronal signal components, often called physiologic noise, in resting state (rs-) fMRI studies. Here, we use image-based retrospective correction of physiological motion (RETROICOR) with externally measured physiologic signals to investigate cardiac and respiratory hemodynamic phase functions reflected in rs-fMRI data. We find that the cardiac phase function is time shifted locally, while the respiratory phase function is described as single, fixed phase form across the brain. In light of these findings, we propose an update to Physiologic EStimation by Temporal ICA (PESTICA), our publically available software package that estimates physiologic signals when external physiologic measures are not available. This update incorporates: 1) auto-selection of slicewise physiologic regressors and generation of physiologic fixed phase regressors with total slices/TR sampling rate, 2) Fourier series expansion of the cardiac fixed phase regressor to account for time delayed cardiac noise 3) removal of cardiac and respiratory noise in imaging data. We compare the efficacy of the updated method to RETROICOR.

Deep Attentive Spatio-Temporal Feature Learning for Automatic Resting-State fMRI Denoising

Resting-state functional magnetic resonance imaging (rs-fMRI) is a non-invasive functional neuroimaging modality that has been widely used to investigate functional connectomes in the brain. Since noise and artifacts generated by non-neuronal physiological activities are predominant in raw rs-fMRI data, effective noise removal is one of the most important preprocessing steps prior to any subsequent analysis. For rs-fMRI denoising, a common trend is to decompose rs-fMRI data into multiple components and then regress out noise-related components. Therefore, various machine learning techniques have been used in such analyses with predefined procedures and manually engineered features. However, the lack of a universal definition of a noise-related source or artifact complicates manual feature engineering. Manual feature selection can result in the failure to capture unknown types of noise. Furthermore, the possibility that the hand-crafted features will only work for the broader population (e.g., healthy adults) but not for "outliers" (e.g., infants or subjects that belong to a disease cohort) is quite high. In practice, we have limited knowledge of which features should be extracted; thus, multi-classifier assembly must be implemented to improve performance, although this process is quite time-consuming. However, in real rs-fMRI applications, fast and accurate automatic identification of noise-related components on different datasets is critical. To solve this problem, we propose a novel, automatic, and end-to-end deep learning framework dedicated to noise-related component identification via a faster and more effective multi-layer feature extraction strategy that learns deeply embedded spatio-temporal features of the components. In this study, we achieved remarkable performance on various rs-fMRI datasets, including multiple adult rs-fMRI datasets from different rs-fMRI studies and an infant rs-fMRI dataset, which is quite heterogeneous and differs from that of adults. Our proposed framework also dramatically increases the noise detection speed owing to its inherent ability for deep learning (< 1s for single-component classification). It can be easily integrated into any preprocessing pipeline, even those that do not use standard procedures but depend on alternative toolboxes.

Resting-State Correlations of Fatigue Following Military Deployment

OBJECTIVE

Persistent fatigue is common among military servicemembers returning from deployment, especially those with a history of mild traumatic brain injury (mTBI). The purpose of this study was to characterize fatigue following deployment using the Multidimensional Fatigue Inventory (MFI), a multidimensional self-report instrument. The study was developed to test the hypothesis that if fatigue involves disrupted effort/reward processing, this should manifest as altered basal ganglia functional connectivity as observed in other amotivational states.

METHODS

Twenty-eight current and former servicemembers were recruited and completed the MFI. All 28 participants had a history of at least one mTBI during deployment. Twenty-six participants underwent resting-state functional MRI. To test the hypothesis that fatigue was associated with basal ganglia functional connectivity, the investigators measured correlations between MFI subscale scores and the functional connectivity of the left and right caudate, the putamen, and the globus pallidus with the rest of the brain, adjusting for the presence of depression.

RESULTS

The investigators found a significant correlation between functional connectivity of the left putamen and bilateral superior frontal gyri and mental fatigue scores. No correlations with the other MFI subscales survived multiple comparisons correction.

CONCLUSIONS

This exploratory study suggests that mental fatigue in military servicemembers with a history of deployment with at least one mTBI may be related to increased striatal-prefrontal functional connectivity, independent of depression. A finding of effort/reward mismatch may guide future treatment approaches.

A multi-measure approach for assessing the performance of fMRI preprocessing strategies in resting-state functional connectivity

It is well established that head motion and physiological processes (e.g. cardiac and breathing activity) should be taken into consideration when analyzing and interpreting results in fMRI studies. However, even though recent studies aimed to evaluate the performance of different preprocessing pipelines there is still no consensus on the optimal strategy. This is partly due to the fact that the quality control (QC) metrics used to evaluate differences in performance across pipelines have often yielded contradictory results. Furthermore, preprocessing techniques based on physiological recordings or data decomposition techniques (e.g. aCompCor) have not been comprehensively examined. Here, to address the aforementioned issues, we propose a framework that summarizes the scores from eight previously proposed and novel QC metrics to a reduced set of two QC metrics that reflect the signal-to-noise ratio and the reduction in motion artifacts and biases in the preprocessed fMRI data. Using this framework, we evaluate the performance of three commonly used practices on the quality of data: 1) Removal of nuisance regressors from fMRI data, 2) discarding motion-contaminated volumes (i.e., scrubbing) before regression, and 3) low-pass filtering the data and the nuisance regressors before their removal. Using resting-state fMRI data from the Human Connectome Project, we show that the scores of the examined QC metrics improve the most when the global signal (GS) and about 17% of principal components from white matter (WM) are removed from the data. Finally, we observe a small further improvement with low-pass filtering at 0.20 Hz and milder variants of WM denoising, but not with scrubbing.

The Longitudinal Effect of Meditation on Resting-State Functional Connectivity Using Dynamic Arterial Spin Labeling: A Feasibility Study

We aimed to assess whether dynamic arterial spin labeling (dASL), a novel quantitative MRI technique with minimal contamination of subject motion and physiological noises, could detect the longitudinal effect of focused attention meditation (FAM) on resting-state functional connectivity (rsFC). A total of 10 novice meditators who recorded their FAM practice time were scanned at baseline and at the 2-month follow-up. Two-month meditation practice caused significantly increased rsFC between the left medial temporal (LMT) seed and precuneus area and between the right frontal eye (RFE) seed and medial prefrontal cortex. Meditation practice time was found to be positively associated with longitudinal changes of rsFC between the default mode network (DMN) and dorsal attention network (DAN), between DMN and insula, and between DAN and the frontoparietal control network (FPN) but negatively associated with changes of rsFC between DMN and FPN, and between DAN and visual regions. These findings demonstrate the capability of dASL in identifying the FAM-induced rsFC changes and suggest that the practice of FAM can strengthen the efficient control of FPN on fast switching between DMN and DAN and enhance the utilization of attentional resources with reduced focus on visual processing.

Physiological and motion signatures in static and time-varying functional connectivity and their subject identifiability

Human brain connectivity yields significant potential as a noninvasive biomarker. Several studies have used fMRI-based connectivity fingerprinting to characterize individual patterns of brain activity. However, it is not clear whether these patterns mainly reflect neural activity or the effect of physiological and motion processes. To answer this question, we capitalize on a large data sample from the Human Connectome Project and rigorously investigate the contribution of the aforementioned processes on functional connectivity (FC) and time-varying FC, as well as their contribution to subject identifiability. We find that head motion, as well as heart rate and breathing fluctuations, induce artifactual connectivity within distinct resting-state networks and that they correlate with recurrent patterns in time-varying FC. Even though the spatiotemporal signatures of these processes yield above-chance levels in subject identifiability, removing their effects at the preprocessing stage improves identifiability, suggesting a neural component underpinning the inter-individual differences in connectivity.

Origins of 1/f-like tissue oxygenation fluctuations in the murine cortex

The concentration of oxygen in the brain spontaneously fluctuates, and the distribution of power in these fluctuations has a 1/f-like spectra, where the power present at low frequencies of the power spectrum is orders of magnitude higher than at higher frequencies. Though these oscillations have been interpreted as being driven by neural activity, the origin of these 1/f-like oscillations is not well understood. Here, to gain insight of the origin of the 1/f-like oxygen fluctuations, we investigated the dynamics of tissue oxygenation and neural activity in awake behaving mice. We found that oxygen signal recorded from the cortex of mice had 1/f-like spectra. However, band-limited power in the local field potential did not show corresponding 1/f-like fluctuations. When local neural activity was suppressed, the 1/f-like fluctuations in oxygen concentration persisted. Two-photon measurements of erythrocyte spacing fluctuations and mathematical modeling show that stochastic fluctuations in erythrocyte flow could underlie 1/f-like dynamics in oxygenation. These results suggest that the discrete nature of erythrocytes and their irregular flow, rather than fluctuations in neural activity, could drive 1/f-like fluctuations in tissue oxygenation.

Keeping the Breath in Mind: Respiration, Neural Oscillations, and the Free Energy Principle

Scientific interest in the brain and body interactions has been surging in recent years. One fundamental yet underexplored aspect of brain and body interactions is the link between the respiratory and the nervous systems. In this article, we give an overview of the emerging literature on how respiration modulates neural, cognitive and emotional processes. Moreover, we present a perspective linking respiration to the free-energy principle. We frame volitional modulation of the breath as an active inference mechanism in which sensory evidence is recontextualized to alter interoceptive models. We further propose that respiration-entrained gamma oscillations may reflect the propagation of prediction errors from the sensory level up to cortical regions in order to alter higher level predictions. Accordingly, controlled breathing emerges as an easily accessible tool for emotional, cognitive, and physiological regulation.

The effect of body posture on resting-state functional connectivity

INTRODUCTION

An important but under-investigated confound of functional MRI (fMRI) is body posture. Although it is well-established that body position changes cerebral blood flow, the amount of cerebrospinal fluid in the brain, intracranial pressure, and even the firing rate of certain cell types, there is currently no study that directly examines its effect on fMRI measurements. Moreover, fMRI is typically done in a supine position, which often does not correspond to how these processes are performed in everyday settings.

METHODS

In this study, 20 healthy adults underwent resting-state fMRI under three body positions: supine, right lateral decubitus (RLD), and left lateral decubitus (LLD). We first investigated whether there were differences in overall organization of whole-brain connectivity between conditions using graph theory. Second, we examined whether functional connectivity of two most studied default mode network (DMN) seeds to the rest of the brain was altered as a function of body position.

RESULTS

Nonparametric statistical analyses revealed that global network measures differed among conditions, with the supine and LLD showing identical results compared to the RLD. There was decreased connectivity for DMN seeds in the RLD condition compared to the supine and LLD, but there were no significant differences between the latter two conditions.

DISCUSSION

Potential mechanisms underlying these alterations include gravity, changes in physiology, and body anatomy. Our results suggest that, compared to supine and LLD, the RLD position leads to changes in whole-brain and DMN connectivity. Finally, depending on the research question, combining imaging modalities that allow for more naturalistic settings can provide a better understanding of certain phenomena.

Asynchrony in Peritumoral Resting-State Blood Oxygen Level-Dependent fMRI Predicts Meningioma Grade and Invasion

BACKGROUND AND PURPOSE

Meningioma grade is determined by histologic analysis, with detectable brain invasion resulting in a diagnosis of grade II or III tumor. However, tissue undersampling is a common problem, and invasive parts of the tumor can be missed, resulting in the incorrect assignment of a lower grade. Radiographic biomarkers may be able to improve the diagnosis of grade and identify targets for biopsy. Prior work in patients with gliomas has shown that the resting-state blood oxygen level-dependent fMRI signal within these tumors is not synchronous with normal brain. We hypothesized that blood oxygen level-dependent asynchrony, a functional marker of vascular dysregulation, could predict meningioma grade.

MATERIALS AND METHODS

We identified 25 patients with grade I and 11 patients with grade II or III meningiomas. Blood oxygen level-dependent time-series were extracted from the tumor and the radiographically normal control hemisphere and were included as predictors in a multiple linear regression to generate a blood oxygen level-dependent asynchrony map, in which negative values signify synchronous and positive values signify asynchronous activity relative to healthy brain. Masks of blood oxygen level-dependent asynchrony were created for each patient, and the fraction of the mask that extended beyond the contrast-enhancing tumor was computed.

RESULTS

The spatial extent of blood oxygen level-dependent asynchrony was greater in high (grades II and III) than in low (I) grade tumors (P < 0.001) and could discriminate grade with high accuracy (area under the curve = 0.88).

CONCLUSIONS

Blood oxygen level-dependent asynchrony radiographically discriminates meningioma grade and may provide targets for biopsy collection to aid in histologic diagnosis.

Common and specific altered amplitude of low-frequency fluctuations in Parkinson's disease patients with and without freezing of gait in different frequency bands

Freezing of gait (FOG), a disabling symptom of Parkinson's disease (PD), severely affects PD patients' life quality. Previous studies found neuropathologies in functional connectivity related to FOG, but few studies detected abnormal regional activities related to FOG in PD patients. In the present study, we analyzed the amplitude of low-frequency fluctuations (ALFF) to detect brain regions showing abnormal activity in PD patients with FOG (PD-with-FOG) and without FOG (PD-without-FOG). As different frequencies of neural oscillations in brain may reflect distinct brain functional and physiological properties, we conducted this study in three frequency bands, slow-5 (0.01-0.027 Hz), slow-4 (0.027-0.073 Hz), and classical frequency band (0.01-0.08 Hz). We acquired rs-fMRI data from 18 PD-with-FOG patients, 18 PD-without-FOG patients, and 17 healthy controls, then calculated voxel-wise ALFF across the whole brain and compared ALFF among the three groups in each frequency band. We found: (1) in slow-5, both PD-with-FOG and PD-without-FOG patients showed lower ALFF in the bilateral putamen compared to healthy controls, (2) in slow-4, PD-with-FOG patients showed higher ALFF in left inferior temporal gyrus (ITG) and lower ALFF in right middle frontal gyrus (MFG) compared to either PD-without-FOG patients or healthy controls, (3) in classical frequency band, PD-with-FOG patients also showed higher ALFF in ITG compared to either PD-without-FOG patients or healthy controls. Furthermore, we found that ALFF in MFG and ITG in slow-4 provided the highest classification accuracy (96.7%) in distinguishing PD-with-FOG from PD-without-FOG patients by using a stepwise multivariate pattern analysis. Our findings indicated frequency-specific regional spontaneous neural activity related to FOG, which may help to elucidate the pathogenesis of FOG.

Functional MRI of arousals in nonrapid eye movement sleep

Arousals commonly occur during human sleep and have been associated with several sleep disorders. Arousals are characterized as an abrupt electroencephalography (EEG) frequency change to higher frequencies during sleep. However, the human brain regions involved in arousal are not yet clear. Simultaneous EEG and functional magnetic resonance imaging (fMRI) data were recorded during the early portion of the sleep period in healthy young adults. Arousals were identified based on the EEG data, and fMRI signal changes associated with 83 arousals from 19 subjects were analyzed. Subcortical regions, including the midbrain, thalamus, basal ganglia, and cerebellum, were activated with arousal. Cortices, including the temporal gyrus, occipital gyrus, and frontal gyrus, were deactivated with arousal. The activations associated with arousal in the subcortical regions were consistent with previous findings of subcortical involvement in behavioral arousal and consciousness. Cortical deactivations may serve as a mechanism to direct incoming sensory stimuli to specific brain regions, thereby monitoring environmental perturbations during sleep.

Testosterone and Resting State Connectivity of the Parahippocampal Gyrus in Men With History of Deployment-Related Mild Traumatic Brain Injury

INTRODUCTION

The purpose of this study was to explore the effect of low testosterone level on whole-brain resting state (RS) connectivity in male veterans with symptoms such as sleep disturbance, fatiguability, pain, anxiety, irritability, or aggressiveness persisting after mild traumatic brain injury (mTBI). Follow-up analyses were performed to determine if sleep scores affected the results.

MATERIALS AND METHODS

In our cross-sectional design study, RS magnetic resonance imaging scans on 28 veterans were performed, and testosterone, sleep quality, mood, and post-traumatic stress symptoms were measured. For each participant, we computed the average correlation of each voxel's time-series with the rest of the voxels in the brain, then used AFNI's 3dttest++ on the group data to determine whether the effects of testosterone level on whole-brain connectivity were significant. We then performed follow-up region of interest-based RS analyses of testosterone, with and without sleep quality as a covariate. The study protocol was approved by the National Institute of Health's Combined Neuroscience Institutional Review Board.

RESULTS

Sixteen participants reported repeated blast exposure in theater, leading to symptoms; the rest reported exposure to a single blast or a nonblast TBI. Thirty-three percent had testosterone levels <300 ng/dL. Testosterone level was lower in participants who screened positive for post-traumatic stress disorder compared to those who screened negative, but it did not reach statistical significance. Whole-brain connectivity and testosterone level were positively correlated in the left parahippocampal gyrus (LPhG), especially in its connectivity with frontal areas, the lingual gyrus, cingulate, insula, caudate, and right parahippocampal gyrus. Further analysis revealed that the effect of testosterone on LPhG connectivity is only partially mediated by sleep quality. Sleep quality by itself had an effect on connectivity of the thalamus, cerebellum, precuneus, and posterior cingulate.

CONCLUSION

Lower testosterone levels were correlated with lower connectivity of the LPhG. Weaknesses of this study include a retrospective design based on self-report of mTBI and the lack of a control group without TBI. Without a control group or pre-injury testosterone measures, we were not able to attribute the rate of low testosterone in our participants to TBI per se. Also testosterone levels were checked only once. The high rate of low testosterone level that we found suggests there may be an association between low testosterone level and greater post-traumatic stress disorder symptoms following deployment, but the causality of the relationships between TBI and deployment stress, testosterone level, behavioral symptomatology, and LPhG connectivity remains to be determined. Our study on men with persistent symptoms postdeployment and post-mTBI may help us understand the role of low testosterone and sleep quality in persistent symptoms and may be important in developing therapeutic interventions. Our results highlight the role of the LPhG, as we found that whole-brain connectivity in that region was positively associated with testosterone level, with only a limited portion of that effect attributable to sleep quality.

Investigating the effects of healthy cognitive aging on brain functional connectivity using 4.7 T resting-state functional magnetic resonance imaging

Functional changes in the aging human brain have been previously reported using functional magnetic resonance imaging (fMRI). Earlier resting-state fMRI studies revealed an age-associated weakening of intra-system functional connectivity (FC) and age-associated strengthening of inter-system FC. However, the majority of such FC studies did not investigate the relationship between age and network amplitude, without which correlation-based measures of FC can be challenging to interpret. Consequently, the main aim of this study was to investigate how three primary measures of resting-state fMRI signal-network amplitude, network topography, and inter-network FC-are affected by healthy cognitive aging. We acquired resting-state fMRI data on a 4.7 T scanner for 105 healthy participants representing the entire adult lifespan (18-85 years of age). To study age differences in network structure, we combined ICA-based network decomposition with sparse graphical models. Older adults displayed lower blood-oxygen-level-dependent (BOLD) signal amplitude in all functional systems, with sensorimotor networks showing the largest age differences. Our age comparisons of network topography and inter-network FC demonstrated a substantial amount of age invariance in the brain's functional architecture. Despite architecture similarities, old adults displayed a loss of communication efficiency in our inter-network FC comparisons, driven primarily by the FC reduction in frontal and parietal association cortices. Together, our results provide a comprehensive overview of age effects on fMRI-based FC.

Changed functional connectivity at rest in functional illiterates after extensive literacy training

Background

About 6.2 million adults in Germany cannot read and write properly despite attending school for several years. They are considered to be functional illiterates (FI). Since the ability to read and write is crucial for being employed and socially accepted, we developed a special literacy training to overcome these deficits.

Methods

In this study, we investigate training-related changes in intrinsic functional connectivity (iFC) at rest in a group of 20 FI and 20 adult normal readers using resting state functional magnetic resonance imaging (rsfMRI). We used independent component analysis (ICA) to define different networks.

Results

Before training, the between group analysis showed increased iFC in FI in a left-fronto-parietal network (LFPN; anterior insula, medial frontal cortex, lateral and frontal parietal regions) and in the Basal Ganglia network (BGN: thalamus, caudate, putamen, pallidum, amygdala, supplementary motor cortex and cingulate gyrus). Furthermore, the Visual Network-1 (VN1; temporal occipital fusiform gyrus, lateral occipital cortex, occipital pole, lingual gyrus, thalamus) showed decreased iFC in FI. After training the FI group showed reversal of the “hyperconnectivity” in middle frontal gyrus and in the frontal orbital cortex and between supramarginal gyrus and the BGN. Furthermore, functional connectivity increased in FI VN1 (lateral occipital cortex, insular cortex). These changes in connectivity correlated with gains in reading speed and spelling accuracy.

Conclusions

These findings show that poor reading and writing abilities are associated with abnormalities in iFC in several brain areas subserving cognitive processes important for reading. Intensive literacy training induces changes in the functional connectivity between and within neural networks important for literacy skills.

Reconstruction of respiratory variation signals from fMRI data

Functional MRI signals can be heavily influenced by systemic physiological processes in addition to local neural activity. For example, widespread hemodynamic fluctuations across the brain have been found to correlate with natural, low-frequency variations in the depth and rate of breathing over time. Acquiring peripheral measures of respiration during fMRI scanning not only allows for modeling such effects in fMRI analysis, but also provides valuable information for interrogating brain-body physiology. However, physiological recordings are frequently unavailable or have insufficient quality. Here, we propose a computational technique for reconstructing continuous low-frequency respiration volume (RV) fluctuations from fMRI data alone. We evaluate the performance of this approach across different fMRI preprocessing strategies. Further, we demonstrate that the predicted RV signals can account for similar patterns of temporal variation in resting-state fMRI data compared to measured RV fluctuations. These findings indicate that fluctuations in respiration volume can be extracted from fMRI alone, in the common scenario of missing or corrupted respiration recordings. The results have implications for enriching a large volume of existing fMRI datasets through retrospective addition of respiratory variations information.

Distinctive Interaction Between Cognitive Networks and the Visual Cortex in Early Blind Individuals

In early blind individuals, brain activation by a variety of nonperceptual cognitive tasks extends to the visual cortex, while in the sighted it is restricted to supramodal association areas. We hypothesized that such activation results from the integration of different sectors of the visual cortex into typical task-dependent networks. We tested this hypothesis with fMRI in blind and sighted subjects using tasks assessing speech comprehension, incidental long-term memory and both verbal and nonverbal executive control, in addition to collecting resting-state data. All tasks activated the visual cortex in blind relative to sighted subjects, which enabled its segmentation according to task sensitivity. We then assessed the unique brain-scale functional connectivity of the segmented areas during resting state. Language-related seeds were preferentially connected to frontal and temporal language areas; the seed derived from the executive task was connected to the right dorsal frontoparietal executive network; and the memory-related seed was uniquely connected to mesial frontoparietal areas involved in episodic memory retrieval. Thus, using a broad set of language, executive, and memory tasks in the same subjects, combined with resting state connectivity, we demonstrate the selective integration of different patches of the visual cortex into brain-scale networks with distinct localization, lateralization, and functional roles.

Respiratory-related brain pulsations are increased in epilepsy-a two-centre functional MRI study

Resting-state functional MRI has shown potential for detecting changes in cerebral blood oxygen level-dependent signal in patients with epilepsy, even in the absence of epileptiform activity. Furthermore, it has been suggested that coefficient of variation mapping of fast functional MRI signal may provide a powerful tool for the identification of intrinsic brain pulsations in neurological diseases such as dementia, stroke and epilepsy. In this study, we used fast functional MRI sequence (magnetic resonance encephalography) to acquire ten whole-brain images per second. We used the functional MRI data to compare physiological brain pulsations between healthy controls (n = 102) and patients with epilepsy (n = 33) and furthermore to drug-naive seizure patients (n = 9). Analyses were performed by calculating coefficient of variation and spectral power in full band and filtered sub-bands. Brain pulsations in the respiratory-related frequency sub-band (0.11-0.51 Hz) were significantly (P < 0.05) increased in patients with epilepsy, with an increase in both signal variance and power. At the individual level, over 80% of medicated and drug-naive seizure patients exhibited areas of abnormal brain signal power that correlated well with the known clinical diagnosis, while none of the controls showed signs of abnormality with the same threshold. The differences were most apparent in the basal brain structures, respiratory centres of brain stem, midbrain and temporal lobes. Notably, full-band, very low frequency (0.01-0.1 Hz) and cardiovascular (0.8-1.76 Hz) brain pulses showed no differences between groups. This study extends and confirms our previous results of abnormal fast functional MRI signal variance in epilepsy patients. Only respiratory-related brain pulsations were clearly increased with no changes in either physiological cardiorespiratory rates or head motion between the subjects. The regional alterations in brain pulsations suggest that mechanisms driving the cerebrospinal fluid homeostasis may be altered in epilepsy. Magnetic resonance encephalography has both increased sensitivity and high specificity for detecting the increased brain pulsations, particularly in times when other tools for locating epileptogenic areas remain inconclusive.

Removal of high frequency contamination from motion estimates in single-band fMRI saves data without biasing functional connectivity

Denoising fMRI data requires assessment of frame-to-frame head motion and removal of the biases motion introduces. This is usually done through analysis of the parameters calculated during retrospective head motion correction (i.e., 'motion' parameters). However, it is increasingly recognized that respiration introduces factitious head motion via perturbations of the main (B0) field. This effect appears as higher-frequency fluctuations in the motion parameters (>0.1 ​Hz, here referred to as 'HF-motion'), primarily in the phase-encoding direction. This periodicity can sometimes be obscured in standard single-band fMRI (TR 2.0-2.5 ​s) due to aliasing. Here we examined (1) how prevalent HF-motion effects are in seven single-band datasets with TR from 2.0 to 2.5 ​s and (2) how HF-motion affects functional connectivity. We demonstrate that HF-motion is more common in older adults, those with higher body mass index, and those with lower cardiorespiratory fitness. We propose a low-pass filtering approach to remove the contamination of high frequency effects from motion summary measures, such as framewise displacement (FD). We demonstrate that in most datasets this filtering approach saves a substantial amount of data from FD-based frame censoring, while at the same time reducing motion biases in functional connectivity measures. These findings suggest that filtering motion parameters is an effective way to improve the fidelity of head motion estimates, even in single band datasets. Particularly large data savings may accrue in datasets acquired in older and less fit participants.

Breathing is coupled with voluntary action and the cortical readiness potential

Voluntary action is a fundamental element of self-consciousness. The readiness potential (RP), a slow drift of neural activity preceding self-initiated movement, has been suggested to reflect neural processes underlying the preparation of voluntary action; yet more than fifty years after its introduction, interpretation of the RP remains controversial. Based on previous research showing that internal bodily signals affect sensory processing and ongoing neural activity, we here investigated the potential role of interoceptive signals in voluntary action and the RP. We report that (1) participants initiate voluntary actions more frequently during expiration, (2) this respiration-action coupling is absent during externally triggered actions, and (3) the RP amplitude is modulated depending on the respiratory phase. Our findings demonstrate that voluntary action is coupled with the respiratory system and further suggest that the RP is associated with fluctuations of ongoing neural activity that are driven by the involuntary and cyclic motor act of breathing.

Voluntary action and free will have been associated with cortical activity, referred to as “the readiness potential” that precedes self-initiated actions by about 1 s. Here, the authors show that the involuntary and cyclic motor act of breathing is coupled with voluntary action and the readiness potential.

Physiological changes in sleep that affect fMRI inference

fMRI relies on a localized cerebral blood flow (CBF) response to changes in cortical neuronal activity. An underappreciated aspect however is its sensitivity to contributions from autonomic physiology that may affect CBF through changes in vascular resistance and blood pressure. As is reviewed here, this is crucial to consider in fMRI studies of sleep, given the close linkage between the regulation of arousal state and autonomic physiology. Typical methods for separating these effects are based on the use of reference signals that may include physiological parameters such as heart rate and respiration; however, the use of time-invariant models may not be adequate due to the possibly changing relationship between reference and fMRI signals with arousal state. In addition, recent research indicates that additional physiological reference signals may be needed to accurately describe changes in systemic physiology, including sympathetic indicators such as finger skin vascular tone and blood pressure.

Functional Alterations of White Matter in Chronic Never-Treated and Treated Schizophrenia Patients

BACKGROUND

Schizophrenia is one of the most severe psychiatric disorders and dysfunction of gray matter (GM) has been usually investigated by resting-state functional (f)MRI. However, functional organization of white matter (WM) in chronic schizophrenia remains unclear.

PURPOSE

To investigate the WM functional alterations in chronic never-treated schizophrenia and the effects of long-term antipsychotic treatment.

STUDY TYPE

Prospective.

SUBJECTS

Twenty-five never-treated, 41 matched antipsychotic-treated schizophrenia, and 25 healthy comparison subjects.

FIELD STRENGTH/SEQUENCE

Resting state (rs)-fMRI, T₁ -weighted images (T₁ WI), and diffusion tensor imaging (DTI) covering the whole brain were acquired with a 3.0T scanner.

ASSESSMENT

Amplitude of low-frequency fluctuations (ALFF) in WM and the correlation coefficients between WM and GM were examined and compared among the three participant groups by two reviewers independently. Independent component analysis (ICA) was added to evaluate WM-fMRI signals. Statistical Tests: Analysis of covariance (ANCOVA); Pearson correlation analysis.

RESULTS

Never-treated patients demonstrated lower ALFF in splenium of corpus callosum (SCC) relative to treated patients and controls (P < 0.001, false discovery rate [FDR]-corrected). While the extracted independent component also located in SCC and showed significantly decreased connectivity in never-treated patients when compared to controls (P < 0.05, FDR-corrected). The correlation coefficients of WM-GM displayed greater reductions in the genu of corpus callosum (GCC), pontine crossing tract (PC), bilateral cingulum (hippocampus) (CGH), and bilateral corticospinal tract (CST) in treated patients relative to controls (P < 0.05, FDR-corrected).

DATA CONCLUSION

These findings provide new insight into WM functional alterations over the long-term course of schizophrenia with and without the potential effects of antipsychotic medication. Functional change and abnormal connectivity in SCC were both found greater in untreated patients than treated patients relative to healthy controls, suggesting that long-term antipsychotic treatment may show some protective effects on WM functional organization.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;52:752-763.

BOLD and EEG signal variability at rest differently relate to aging in the human brain

Variability of neural activity is regarded as a crucial feature of healthy brain function, and several neuroimaging approaches have been employed to assess it noninvasively. Studies on the variability of both evoked brain response and spontaneous brain signals have shown remarkable changes with aging but it is unclear if the different measures of brain signal variability - identified with either hemodynamic or electrophysiological methods - reflect the same underlying physiology. In this study, we aimed to explore age differences of spontaneous brain signal variability with two different imaging modalities (EEG, fMRI) in healthy younger (25 ​± ​3 years, N ​= ​135) and older (67 ​± ​4 years, N ​= ​54) adults. Consistent with the previous studies, we found lower blood oxygenation level dependent (BOLD) variability in the older subjects as well as less signal variability in the amplitude of low-frequency oscillations (1-12 ​Hz), measured in source space. These age-related reductions were mostly observed in the areas that overlap with the default mode network. Moreover, age-related increases of variability in the amplitude of beta-band frequency EEG oscillations (15-25 ​Hz) were seen predominantly in temporal brain regions. There were significant sex differences in EEG signal variability in various brain regions while no significant sex differences were observed in BOLD signal variability. Bivariate and multivariate correlation analyses revealed no significant associations between EEG- and fMRI-based variability measures. In summary, we show that both BOLD and EEG signal variability reflect aging-related processes but are likely to be dominated by different physiological origins, which relate differentially to age and sex.

Model-based physiological noise removal in fast fMRI

Recent improvements in the speed and sensitivity of fMRI acquisition techniques suggest that fast fMRI can be used to detect and precisely localize sub-second neural dynamics. This enhanced temporal resolution has enormous potential for neuroscientists. However, physiological noise poses a major challenge for the analysis of fast fMRI data. Physiological noise scales with sensitivity, and its autocorrelation structure is altered in rapidly sampled data, suggesting that new approaches are needed for physiological noise removal in fast fMRI. Existing strategies either rely on external physiological recordings, which can be noisy or difficult to collect, or employ data-driven approaches which make assumptions that may not hold true in fast fMRI. We created a statistical model of harmonic regression with autoregressive noise (HRAN) to estimate and remove cardiac and respiratory noise from the fMRI signal directly. This technique exploits the fact that cardiac and respiratory noise signals are fully sampled (rather than aliasing) when imaging at fast rates, allowing us to track and model physiology over time without requiring external physiological measurements. We then created a joint model of neural hemodynamics, and physiological and autocorrelated noise to more accurately remove noise. We first verified that HRAN accurately estimates cardiac and respiratory dynamics and that our model demonstrates goodness-of-fit in fast fMRI data. In task-driven data, we then demonstrated that HRAN is able to remove physiological noise while leaving the neural signal intact, thereby increasing detection of task-driven voxels. Finally, we established that in both simulations and fast fMRI data HRAN is able to improve statistical inferences as compared with gold-standard physiological noise removal techniques. In conclusion, we created a tool that harnesses the novel information in fast fMRI to remove physiological noise, enabling broader use of the technology to study human brain function.

Omission of temporal nuisance regressors from dual regression can improve accuracy of fMRI functional connectivity maps

Functional connectivity (FC) maps from brain fMRI data can be derived with dual regression, a proposed alternative to traditional seed-based FC (SFC) methods that detect temporal correlation between a predefined region (seed) and other regions in the brain. As with SFC, incorporating nuisance regressors (NR) into the dual regression must be done carefully, to prevent potential bias and insensitivity of FC estimates. Here, we explore the potentially untoward effects on dual regression that may occur when NR correlate highly with the signal of interest, using both synthetic and real fMRI data to elucidate mechanisms responsible for loss of accuracy in FC maps. Our tests suggest significantly improved accuracy in FC maps derived with dual regression when highly correlated temporal NR were omitted. Single-map dual regression, a simplified form of dual regression that uses neither spatial nor temporal NR, offers a viable alternative whose FC maps may be more easily interpreted, and in some cases be more accurate than those derived with standard dual regression.

Axial variation of deoxyhemoglobin density as a source of the low-frequency time lag structure in blood oxygenation level-dependent signals

Perfusion-related information is reportedly embedded in the low-frequency component of a blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signal. The blood-propagation pattern through the cerebral vascular tree is detected as an interregional lag variation of spontaneous low-frequency oscillations (sLFOs). Mapping of this lag, or phase, has been implicitly treated as a projection of the vascular tree structure onto real space. While accumulating evidence supports the biological significance of this signal component, the physiological basis of the “perfusion lag structure,” a requirement for an integrative resting-state fMRI-signal model, is lacking. In this study, we conducted analyses furthering the hypothesis that the sLFO is not only largely of systemic origin, but also essentially intrinsic to blood, and hence behaves as a virtual tracer. By summing the small fluctuations of instantaneous phase differences between adjacent vascular regions, a velocity response to respiratory challenges was detected. Regarding the relationship to neurovascular coupling, the removal of the whole lag structure, which can be considered as an optimized global-signal regression, resulted in a reduction of inter-individual variance while preserving the fMRI response. Examination of the T2* and S₀, or non-BOLD, components of the fMRI signal revealed that the lag structure is deoxyhemoglobin dependent, while paradoxically presenting a signal-magnitude reduction in the venous side of the cerebral vasculature. These findings provide insight into the origin of BOLD sLFOs, suggesting that they are highly intrinsic to the circulating blood.

Hypothesis: Pulmonary Afferent Activity Patterns During Slow, Deep Breathing Contribute to the Neural Induction of Physiological Relaxation

Control of respiration provides a powerful voluntary portal to entrain and modulate central autonomic networks. Slowing and deepening breathing as a relaxation technique has shown promise in a variety of cardiorespiratory and stress-related disorders, but few studies have investigated the physiological mechanisms conferring its benefits. Recent evidence suggests that breathing at a frequency near 0.1 Hz (6 breaths per minute) promotes behavioral relaxation and baroreflex resonance effects that maximize heart rate variability. Breathing around this frequency appears to elicit resonant and coherent features in neuro-mechanical interactions that optimize physiological function. Here we explore the neurophysiology of slow, deep breathing and propose that coincident features of respiratory and baroreceptor afferent activity cycling at 0.1 Hz entrain central autonomic networks. An important role is assigned to the preferential recruitment of slowly-adapting pulmonary afferents (SARs) during prolonged inhalations. These afferents project to discrete areas in the brainstem within the nucleus of the solitary tract (NTS) and initiate inhibitory actions on downstream targets. Conversely, deep exhalations terminate SAR activity and activate arterial baroreceptors via increases in blood pressure to stimulate, through NTS projections, parasympathetic outflow to the heart. Reciprocal SAR and baroreceptor afferent-evoked actions combine to enhance sympathetic activity during inhalation and parasympathetic activity during exhalation, respectively. This leads to pronounced heart rate variability in phase with the respiratory cycle (respiratory sinus arrhythmia) and improved ventilation-perfusion matching. NTS relay neurons project extensively to areas of the central autonomic network to encode important features of the breathing pattern that may modulate anxiety, arousal, and attention. In our model, pronounced respiratory rhythms during slow, deep breathing also support expression of slow cortical rhythms to induce a functional state of alert relaxation, and, via nasal respiration-based actions on olfactory signaling, recruit hippocampal pathways to boost memory consolidation. Collectively, we assert that the neurophysiological processes recruited during slow, deep breathing enhance the cognitive and behavioral therapeutic outcomes obtained through various mind-body practices. Future studies are required to better understand the physio-behavioral processes involved, including in animal models that control for confounding factors such as expectancy biases.

Twitches, Blinks, and Fidgets: Important Generators of Ongoing Neural Activity

Animals and humans continuously engage in small, spontaneous motor actions, such as blinking, whisking, and postural adjustments ("fidgeting"). These movements are accompanied by changes in neural activity in sensory and motor regions of the brain. The frequency of these motions varies in time, is affected by sensory stimuli, arousal levels, and pathology. These fidgeting behaviors can be entrained by sensory stimuli. Fidgeting behaviors will cause distributed, bilateral functional activation in the 0.01 to 0.1 Hz frequency range that will show up in functional magnetic resonance imaging and wide-field calcium neuroimaging studies, and will contribute to the observed functional connectivity among brain regions. However, despite the large potential of these behaviors to drive brain-wide activity, these fidget-like behaviors are rarely monitored. We argue that studies of spontaneous and evoked brain dynamics in awake animals and humans should closely monitor these fidgeting behaviors. Differences in these fidgeting behaviors due to arousal or pathology will "contaminate" ongoing neural activity, and lead to apparent differences in functional connectivity. Monitoring and accounting for the brain-wide activations by these behaviors is essential during experiments to differentiate fidget-driven activity from internally driven neural dynamics.

Vascular and neural basis of the BOLD signal

Neural activity in the brain is usually coupled to increases in local cerebral blood flow, leading to the increase in oxygenation that generates the BOLD fMRI signal. Recent work has begun to elucidate the vascular and neural mechanisms underlying the BOLD signal. The dilatory response is distributed throughout the vascular network. Arteries actively dilate within a second following neural activity increases, while venous distensions are passive and have a time course that last tens of seconds. Vasodilation, and thus local blood flow, is controlled by the activity of both neurons and astrocytes via multiple different pathways. The relationship between sensory-driven neural activity and the vascular dynamics in sensory areas are well-captured with a linear convolution model. However, depending on the behavioral state or brain region, the coupling between neural activity and hemodynamic signals can be weak or even inverted.

The relationship between heart rate and functional connectivity of brain regions involved in autonomic control

The peripheral autonomic nervous system (ANS) adjusts the heart rate (HR) to intrinsic and extrinsic demands. It is controlled by a group of functionally connected brain regions assembling the so-called central autonomic network (CAN). More specifically, forebrain cortical regions, limbic and brainstem structures within the CAN have been identified as important components of circuits involved in HR regulation. The present study aimed to investigate whether functional connectivity (FC) between these regions varies in subjects with different heart rates. Thus, 84 healthy subjects were separated according to their HR in slow, medium and fast. We observed a direct association between HR and FC in CAN regions, where stronger FC was related to slower HR. This relationship, however, is non-linear, follows an exponential course and is not restricted to CAN areas only. The network-based analysis (NBS) using time series from 262 independent anatomical ROIs revealed significantly increased functional connectivity in subjects with slow HR compared to subjects with fast HR mainly in regions being part of the salience network, but also of the default-mode network. We additionally simulated the effect of aliasing on the functional connectivity using several TRs and heart rates to exclude the possibility that FC differences might be due to different aliasing effects in the data. The result of the simulation indicated that aliasing cannot explain our findings. Thus, present results imply a functionally meaningful coupling between FC and HR that need to be accounted for in future studies. Moreover, given the established link between HR and emotional, cognitive and social processes, present findings may also be considered to explain individual differences in brain activation or connectivity when using corresponding paradigms in the MR scanner to investigate such processes.

Global fluctuations of cerebral blood flow indicate a global brain network independent of systemic factors

Global synchronization across specialized brain networks is a common feature of network models and in-vivo electrical measurements. Although the imaging of specialized brain networks with blood oxygenation sensitive resting state functional magnetic resonance imaging (rsfMRI) has enabled detailed study of regional networks, the study of globally correlated fluctuations with rsfMRI is confounded by spurious contributions to the global signal from systemic physiologic factors and other noise sources. Here we use an alternative rsfMRI method, arterial spin labeled perfusion MRI, to characterize global correlations and their relationship to correlations and anti-correlations between regional networks. Global fluctuations that cannot be explained by systemic factors dominate the fluctuations in cerebral blood flow. Power spectra of these fluctuations are band limited to below 0.05 Hz, similar to prior measurements of regional network fluctuations in the brain. Removal of these global fluctuations prior to measurement of regional networks reduces all regional network fluctuation amplitudes to below the global fluctuation amplitude and changes the strength and sign of inter network correlations. Our findings support large amplitude, globally synchronized activity across networks that require a reassessment of regional network amplitude and correlation measures.

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.