Potential pitfalls when denoising resting state fMRI data using nuisance regression

Comparing Cyclicity Analysis With Pre-established Functional Connectivity Methods to Identify Individuals and Subject Groups Using Resting State fMRI

The resting state fMRI time series appears to have cyclic patterns, which indicates presence of cyclic interactions between different brain regions. Such interactions are not easily captured by pre-established resting state functional connectivity methods including zero-lag correlation, lagged correlation, and dynamic time warping distance. These methods formulate the functional interaction between different brain regions as similar temporal patterns within the time series. To use information related to temporal ordering, cyclicity analysis has been introduced to capture pairwise interactions between multiple time series. In this study, we compared the efficacy of cyclicity analysis with aforementioned similarity-based techniques in representing individual-level and group-level information. Additionally, we investigated how filtering and global signal regression interacted with these techniques. We obtained and analyzed fMRI data from patients with tinnitus and neurotypical controls at two different days, a week apart. For both patient and control groups, we found that the features generated by cyclicity and correlation (zero-lag and lagged) analyses were more reliable than the features generated by dynamic time warping distance in identifying individuals across visits. The reliability of all features, except those generated by dynamic time warping, improved as the global signal was regressed. Nevertheless, removing fluctuations >0.1 Hz deteriorated the reliability of all features. These observations underscore the importance of choosing appropriate preprocessing steps while evaluating different analytical methods in describing resting state functional interactivity. Further, using different machine learning techniques including support vector machines, discriminant analyses, and convolutional neural networks, our results revealed that the manifestation of the group-level information within all features was not sufficient enough to dissociate tinnitus patients from controls with high sensitivity and specificity. This necessitates further investigation regarding the representation of group-level information within different features to better identify tinnitus-related alternation in the functional organization of the brain. Our study adds to the growing body of research on developing diagnostic tools to identify neurological disorders, such as tinnitus, using resting state fMRI data.

The Endogenous Analgesia Signature in the Resting Brain of Healthy Adults and Migraineurs

Altered pain modulation and resting state functional connectivity (rsFC) were found to be related to migraine pathology and clinical manifestation. We examined how pain modulation psychophysical measures are related to resting-state networks and rsFC between bottom-up and top-down pain modulation areas. Thirty-two episodic migraineurs and 23 age-matched healthy individuals underwent temporal summation of pain (TSOP) and conditioned pain modulation (CPM) tests, followed by a resting-state imaging scan. No differences in temporal summation of pain and CPM were found between groups. However, in healthy individuals, more efficient CPM was correlated with 1) stronger rsFCs of the posterior cingulate cortex, with the ventromedial prefrontal cortex and with the pregenual anterior cingulate cortex; 2) weaker rsFC of the anterior insula with the angular gyrus. Conversely, in migraineurs, the association between CPM and rsFC was altered. Our results suggest that the functional connectivity within the default mode network (DMN) components and the functional coupling between the DMN and pain inhibitory brain areas is linked with pain inhibition efficiency. In migraineurs, this interplay is changed, yet enables normal pain inhibition. Our findings shed light on potential functional adaptation of the DMN and its role in pain inhibition in health and migraine. PERSPECTIVE: This article establishes evidence for the relationship between the resting-state brain and individual responses in psychophysical pain modulation tests, in both migraine and healthy individuals. The results emphasize the significant role of the default mode network in maintaining pain inhibition efficiency in health and in the presence of chronic pain.

Modulation of Distinct Intrinsic Resting State Brain Networks by Acute Exercise Bouts of Differing Intensity

Acute exercise bouts alter resting state functional connectivity (rs-FC) within cognitive, sensorimotor, and affective networks, but it remains unknown how these effects are influenced by exercise intensity.

Twenty-five male athletes underwent individual fitness assessments using an incremental treadmill test. On separate days, they performed ‘low’ (35% below lactate threshold) and ‘high’ (20% above lactate threshold) intensity exercise bouts of 30 min. Rs-fMRI and Positive and Negative Affect Scale (PANAS) were acquired before and after each exercise bout. Networks of interest were extracted from twenty-two participants (3 dropouts). Pre-to-post changes and between conditions effects were evaluated using FSL’s randomise by applying repeated measures ANOVA. Results were reported at p < 0.05, corrected for multiple comparisons using threshold free cluster enhancement.

PANAS revealed a significant increase in positive mood after both exercise conditions. Significant effects were observed between conditions in the right affective and reward network (ARN), the right fronto parietal network (FPN) and the sensorimotor network (SMN). Pre-to-post comparisons after ‘low’ exercise intensity revealed a significant increase in rs-FC in the left and right FPN, while after ‘high’-intensity exercise rs-FC decreased in the SMN and the dorsal attention network (DAN) and increased in the left ARN.

Supporting recent findings, this study is the first to report distinct rs-FC alterations driven by exercise intensity: (i) Increased rs-FC in FPN may indicate beneficial functional plasticity for cognitive/attentional processing, (ii) increased rs-FC in ARN may be linked to endogenous opioid-mediated internal affective states. Finally, (iii) decreased rs-FC in the SMN may signify persistent motor fatigue. The distinct effects on rs-FC fit with theories of transient persistent network alterations after acute exercise bouts that are mediated by different exercise intensities and impact differentially on cognitive/attentional or affective responses.

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.

Effective degrees of freedom of the Pearson's correlation coefficient under autocorrelation

The dependence between pairs of time series is commonly quantified by Pearson's correlation. However, if the time series are themselves dependent (i.e. exhibit temporal autocorrelation), the effective degrees of freedom (EDF) are reduced, the standard error of the sample correlation coefficient is biased, and Fisher's transformation fails to stabilise the variance. Since fMRI time series are notoriously autocorrelated, the issue of biased standard errors - before or after Fisher's transformation - becomes vital in individual-level analysis of resting-state functional connectivity (rsFC) and must be addressed anytime a standardised Z-score is computed. We find that the severity of autocorrelation is highly dependent on spatial characteristics of brain regions, such as the size of regions of interest and the spatial location of those regions. We further show that the available EDF estimators make restrictive assumptions that are not supported by the data, resulting in biased rsFC inferences that lead to distorted topological descriptions of the connectome on the individual level. We propose a practical "xDF" method that accounts not only for distinct autocorrelation in each time series, but instantaneous and lagged cross-correlation. We find the xDF correction varies substantially over node pairs, indicating the limitations of global EDF corrections used previously. In addition to extensive synthetic and real data validations, we investigate the impact of this correction on rsFC measures in data from the Young Adult Human Connectome Project, showing that accounting for autocorrelation dramatically changes fundamental graph theoretical measures relative to no correction.

Large-scale comparative neuroimaging: Where are we and what do we need?

Neuroimaging has a lot to offer comparative neuroscience. Although invasive "gold standard" techniques have a better spatial resolution, neuroimaging allows fast, whole-brain, repeatable, and multi-modal measurements of structure and function in living animals and post-mortem tissue. In the past years, comparative neuroimaging has increased in popularity. However, we argue that its most significant potential lies in its ability to collect large-scale datasets of many species to investigate principles of variability in brain organisation across whole orders of species-an ambition that is presently unfulfilled but achievable. We briefly review the current state of the field and explore what the current obstacles to such an approach are. We propose some calls to action.

Impact of sampling rate on statistical significance for single subject fMRI connectivity analysis

A typical time series in functional magnetic resonance imaging (fMRI) exhibits autocorrelation, that is, the samples of the time series are dependent. In addition, temporal filtering, one of the crucial steps in preprocessing of functional magnetic resonance images, induces its own autocorrelation. While performing connectivity analysis in fMRI, the impact of the autocorrelation is largely ignored. Recently, autocorrelation has been addressed by variance correction approaches, which are sensitive to the sampling rate. In this article, we aim to investigate the impact of the sampling rate on the variance correction approaches. Toward this end, we first derived a generalized expression for the variance of the sample Pearson correlation coefficient (SPCC) in terms of the sampling rate and the filter cutoff frequency, in addition to the autocorrelation and cross-covariance functions of the time series. Through simulations, we illustrated the importance of the variance correction for a fixed sampling rate. Using the real resting state fMRI data sets, we demonstrated that the data sets with higher sampling rates were more prone to false positives, in agreement with the existing empirical reports. We further demonstrated with single subject results that for the data sets with higher sampling rates, the variance correction strategy restored the integrity of true connectivity.

Nuisance effects in inter-scan functional connectivity estimates before and after nuisance regression

In resting-state functional MRI, the correlation between blood-oxygenation-level-dependent (BOLD) signals across brain regions is used to estimate the functional connectivity (FC) of the brain. FC estimates are prone to the influence of nuisance factors including scanner-related artifacts and physiological modulations of the BOLD signal. Nuisance regression is widely performed to reduce the effect of nuisance factors on FC estimates on a per-scan basis. However, a dedicated analysis of nuisance effects on the variability of FC metrics across a collection of scans has been lacking. This work investigates the effects of nuisance factors on the variability of FC estimates across a collection of scans both before and after nuisance regression. Inter-scan variations in FC estimates are shown to be significantly correlated with the geometric norms of various nuisance terms, including head motion measurements, signals derived from white-matter and cerebrospinal regions, and the whole-brain global signal (GS) both before and after nuisance regression. In addition, it is shown that GS regression (GSR) can introduce GS norm-related fluctuations that are negatively correlated with inter-scan FC estimates. The empirical results are shown to be largely consistent with the predictions of a theoretical framework previously developed for the characterization of dynamic FC measures. This work shows that caution must be exercised when interpreting inter-scan FC measures across scans both before and after nuisance regression.

Cerebral Autoregulation Evidenced by Synchronized Low Frequency Oscillations in Blood Pressure and Resting-State fMRI

Resting-state functional magnetic resonance imaging (rs-fMRI) is a widely used technique for mapping the brain’s functional architecture, so delineating the main sources of variance comprising the signal is crucial. Low frequency oscillations (LFO) that are not of neural origin, but which are driven by mechanisms related to cerebral autoregulation (CA), are present in the blood-oxygenation-level-dependent (BOLD) signal within the rs-fMRI frequency band. In this study we use a MR compatible device (Caretaker, Biopac) to obtain a non-invasive estimate of beat-to-beat mean arterial pressure (MAP) fluctuations concurrently with rs-fMRI at 3T. Healthy adult subjects (n = 9; 5 male) completed two 20-min rs-fMRI scans. MAP fluctuations were decomposed into different frequency scales using a discrete wavelet transform, and oscillations at approximately 0.1 Hz show a high degree of spatially structured correlations with matched frequency fMRI fluctuations. On average across subjects, MAP fluctuations at this scale of the wavelet decomposition explain ∼2.2% of matched frequency fMRI signal variance. Additionally, a simultaneous multi-slice multi-echo acquisition was used to collect 10-min rs-fMRI at three echo times at 7T in a separate group of healthy adults (n = 5; 5 male). Multiple echo times were used to estimate the R₂^∗ decay at every time point, and MAP was shown to strongly correlate with this signal, which suggests a purely BOLD (i.e., blood flow related) origin. This study demonstrates that there is a significant component of the BOLD signal that has a systemic physiological origin, and highlights the fact that not all localized BOLD signal changes necessarily reflect blood flow supporting local neural activity. Instead, these data show that a proportion of BOLD signal fluctuations in rs-fMRI are due to localized control of blood flow that is independent of local neural activity, most likely reflecting more general systemic autoregulatory processes. Thus, fMRI is a promising tool for studying flow changes associated with cerebral autoregulation with high spatial resolution.

Global signal regression strengthens association between resting-state functional connectivity and behavior

Global signal regression (GSR) is one of the most debated preprocessing strategies for resting-state functional MRI. GSR effectively removes global artifacts driven by motion and respiration, but also discards globally distributed neural information and introduces negative correlations between certain brain regions. The vast majority of previous studies have focused on the effectiveness of GSR in removing imaging artifacts, as well as its potential biases. Given the growing interest in functional connectivity fingerprinting, here we considered the utilitarian question of whether GSR strengthens or weakens associations between resting-state functional connectivity (RSFC) and multiple behavioral measures across cognition, personality and emotion. By applying the variance component model to the Brain Genomics Superstruct Project (GSP), we found that behavioral variance explained by whole-brain RSFC increased by an average of 47% across 23 behavioral measures after GSR. In the Human Connectome Project (HCP), we found that behavioral variance explained by whole-brain RSFC increased by an average of 40% across 58 behavioral measures, when GSR was applied after ICA-FIX de-noising. To ensure generalizability, we repeated our analyses using kernel regression. GSR improved behavioral prediction accuracies by an average of 64% and 12% in the GSP and HCP datasets respectively. Importantly, the results were consistent across methods. A behavioral measure with greater RSFC-explained variance (using the variance component model) also exhibited greater prediction accuracy (using kernel regression). A behavioral measure with greater improvement in behavioral variance explained after GSR (using the variance component model) also enjoyed greater improvement in prediction accuracy after GSR (using kernel regression). Furthermore, GSR appeared to benefit task performance measures more than self-reported measures. Since GSR was more effective at removing motion-related and respiratory-related artifacts, GSR-related increases in variance explained and prediction accuracies were unlikely the result of motion-related or respiratory-related artifacts. However, it is worth emphasizing that the current study focused on whole-brain RSFC, so it remains unclear whether GSR improves RSFC-behavioral associations for specific connections or networks. Overall, our results suggest that at least in the case for young healthy adults, GSR strengthens the associations between RSFC and most (although not all) behavioral measures. Code for the variance component model and ridge regression can be found here: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/preprocessing/Li2019_GSR.

General functional connectivity: Shared features of resting-state and task fMRI drive reliable and heritable individual differences in functional brain networks

Intrinsic connectivity, measured using resting-state fMRI, has emerged as a fundamental tool in the study of the human brain. However, due to practical limitations, many studies do not collect enough resting-state data to generate reliable measures of intrinsic connectivity necessary for studying individual differences. Here we present general functional connectivity (GFC) as a method for leveraging shared features across resting-state and task fMRI and demonstrate in the Human Connectome Project and the Dunedin Study that GFC offers better test-retest reliability than intrinsic connectivity estimated from the same amount of resting-state data alone. Furthermore, at equivalent scan lengths, GFC displayed higher estimates of heritability than resting-state functional connectivity. We also found that predictions of cognitive ability from GFC generalized across datasets, performing as well or better than resting-state or task data alone. Collectively, our work suggests that GFC can improve the reliability of intrinsic connectivity estimates in existing datasets and, subsequently, the opportunity to identify meaningful correlates of individual differences in behavior. Given that task and resting-state data are often collected together, many researchers can immediately derive more reliable measures of intrinsic connectivity through the adoption of GFC rather than solely using resting-state data. Moreover, by better capturing heritable variation in intrinsic connectivity, GFC represents a novel endophenotype with broad applications in clinical neuroscience and biomarker discovery.

On time delay estimation and sampling error in resting-state fMRI

Accumulating evidence indicates that resting-state functional magnetic resonance imaging (rsfMRI) signals correspond to propagating electrophysiological infra-slow activity (<0.1 Hz). Thus, pairwise correlations (zero-lag functional connectivity (FC)) and temporal delays among regional rsfMRI signals provide useful, complementary descriptions of spatiotemporal structure in infra-slow activity. However, the slow nature of fMRI signals implies that practical scan durations cannot provide sufficient independent temporal samples to stabilize either of these measures. Here, we examine factors affecting sampling variability in both time delay estimation (TDE) and FC. Although both TDE and FC accuracy are highly sensitive to data quantity, we use surrogate fMRI time series to study how the former is additionally related to the magnitude of a given pairwise correlation and, to a lesser extent, the temporal sampling rate. These contingencies are further explored in real data comprising 30-min rsfMRI scans, where sampling error (i.e., limited accuracy owing to insufficient data quantity) emerges as a significant but underappreciated challenge to FC and, even more so, to TDE. Exclusion of high-motion epochs exacerbates sampling error; thus, both sides of the bias-variance (or data quality-quantity) tradeoff associated with data exclusion should be considered when analyzing rsfMRI data. Finally, we present strategies for TDE in motion-corrupted data, for characterizing sampling error in TDE and FC, and for mitigating the influence of sampling error on lag-based analyses.

On the analysis of rapidly sampled fMRI data

Recent advances in parallel imaging and simultaneous multi-slice techniques have permitted whole-brain fMRI acquisitions at sub-second sampling intervals, without significantly sacrificing the spatial coverage and resolution. Apart from probing brain function at finer temporal scales, faster sampling rates may potentially lead to enhanced functional sensitivity, owing possibly to both cleaner neural representations (due to less aliased physiological noise) and additional statistical benefits (due to more degrees of freedom for a fixed scan duration). Accompanying these intriguing aspects of fast acquisitions, however, confusion has also arisen regarding (1) how to preprocess/analyze these fast fMRI data, and (2) what exactly is the extent of benefits with fast acquisitions, i.e., how fast is fast enough for a specific research aim? The first question is motivated by the altered spectral distribution and noise characteristics at short sampling intervals, while the second question seeks to reconcile the complicated trade-offs between the functional contrast-to-noise ratio and the effective degrees of freedom. Although there have been recent efforts to empirically approach different aspects of these two questions, in this work we discuss, from a theoretical perspective accompanied by some illustrative, proof-of-concept experimental in vivo human fMRI data, a few considerations that are rarely mentioned, yet are important for both preprocessing and optimizing statistical inferences for studies that employ acquisitions with sub-second sampling intervals. Several summary recommendations include concerns regarding advisability of relying on low-pass filtering to de-noise physiological contributions, employment of statistical models with sufficient complexity to account for the substantially increased serial correlation, and cautions regarding using rapid sampling to enhance functional sensitivity given that different analysis models may associate with distinct trade-offs between contrast-to-noise ratios and the effective degrees of freedom. As an example, we demonstrate that as TR shortens, the intrinsic differences in how noise is accommodated in general linear models and Pearson correlation analyses (assuming Gaussian distributed stochastic signals and noise) can result in quite different outcomes, either gaining or losing statistical power.

Making Sense of Connectivity

In addition to the assessment of local alterations of specific brain regions, the investigation of entire networks with in vivo neuroimaging techniques has gained increasing attention. In general, connectivity analysis refers to the investigation of links between brain regions, with the aim to characterize their interactions and information transfer. These may represent or relate to different physiological characteristics (structural, functional, or metabolic information) and can be calculated across different levels of granularity (2 regions vs whole brain). In this article, we provide an overview of different connectivity analysis approaches with interpretations and limitations as well as examples in pharmacological imaging and clinical applications. Structural connectivity obtained from diffusion MRI enables the reconstruction of neuronal fiber tracts. These physical links represent major constraints of functional connections, which are in turn defined as correlations between signal time courses. In addition, molecular connectivity approaches based on PET imaging enable the assessment of interregional associations of metabolic demands and neurotransmitter systems. Application of these approaches in clinical investigations has demonstrated novel alterations in various neurological and psychiatric disorders on a network level. Future work should aim for the combined assessment of multiple imaging modalities and to establish robust biomarkers for clinical use. These advancements will further improve the biological interpretation of connectivity metrics and networks of the human brain.

Modular preprocessing pipelines can reintroduce artifacts into fMRI data

The preprocessing pipelines typically used in both task and resting-state functional magnetic resonance imaging (rs-fMRI) analysis are modular in nature: They are composed of a number of separate filtering/regression steps, including removal of head motion covariates and band-pass filtering, performed sequentially and in a flexible order. In this article, we illustrate the shortcomings of this approach, as we show how later preprocessing steps can reintroduce artifacts previously removed from the data in prior preprocessing steps. We show that each regression step is a geometric projection of data onto a subspace, and that performing a sequence of projections can move the data into subspaces no longer orthogonal to those previously removed, reintroducing signal related to nuisance covariates. Thus, linear filtering operations are not commutative, and the order in which the preprocessing steps are performed is critical. These issues can arise in practice when any combination of standard preprocessing steps including motion regression, scrubbing, component-based correction, physiological correction, global signal regression, and temporal filtering are performed sequentially. In this work, we focus primarily on rs-fMRI. We illustrate the problem both theoretically and empirically through application to a test-retest rs-fMRI data set, and suggest remedies. These include (a) combining all steps into a single linear filter, or (b) sequential orthogonalization of covariates/linear filters performed in series.

The Functional Connectivity Between the Nucleus Accumbens and the Ventromedial Prefrontal Cortex as an Endophenotype for Bipolar Disorder

BACKGROUND

Alterations in functional connectivity between the nucleus accumbens (NAcc) and frontal cortices have been previously associated with the presence of psychiatric syndromes, including bipolar disorder (BD). Whether these alterations are a consequence or a risk factor for mental disorders remains unresolved.

METHODS

This study included 35 patients with BD, 30 nonaffected siblings of patients with BD, and 23 healthy control subjects to probe functional connectivity at rest between NAcc and the rest of the brain in a cross-sectional design. Blood oxygen level-dependent time series at rest from NAcc were used as seed region in a voxelwise correlational analysis. The strength of the correlations found was compared across groups after Fisher's Z transformation.

RESULTS

We found increased functional connectivity between the NAcc and the ventromedial prefrontal cortex-comprising mainly the subgenual anterior cingulate-in patients compared with healthy control subjects. Participants at increased genetic risk but yet resilient-nonaffected siblings-showed functional connectivity values midway between the former two groups.

CONCLUSIONS

Our results are indicative of the potential for the connectivity between NAcc and the ventromedial prefrontal cortex to represent an endophenotype for BD.

Effect of prewhitening in resting-state functional near-infrared spectroscopy data

Near-infrared spectroscopy (NIRS) offers the potential to characterize resting-state functional connectivity (RSFC) in populations that are not easily assessed otherwise, such as young infants. In addition to the advantages of NIRS, one should also consider that the RS-NIRS signal requires specific data preprocessing and analysis. In particular, the RS-NIRS signal shows a colored frequency spectrum, which can be observed as temporal autocorrelation, thereby introducing spurious correlations. To address this issue, prewhitening of the RS-NIRS signal has been recently proposed as a necessary step to remove the signal temporal autocorrelation and therefore reduce false-discovery rates. However, the impact of this step on the analysis of experimental RS-NIRS data has not been thoroughly assessed prior to the present study. Here, the results of a standard preprocessing pipeline in a RS-NIRS dataset acquired in infants are compared with the results after incorporating two different prewhitening algorithms. Our results with a standard preprocessing replicated previous studies. Prewhitening altered RSFC patterns and disrupted the antiphase relationship between oxyhemoglobin and deoxyhemoglobin. We conclude that a better understanding of the effect of prewhitening on RS-NIRS data is still needed before directly considering its incorporation to the standard preprocessing pipeline.

Disrupted modular organization of primary sensory brain areas in schizophrenia

Abnormal brain resting-state functional connectivity has been consistently observed in patients affected by schizophrenia (SCZ) using functional MRI and other neuroimaging techniques. Graph theoretical methods provide a framework to investigate these defective functional interactions and their effects on the organization of brain connectivity networks. A few studies have shown altered distribution of connectivity within and between functional modules in SCZ patients, an indication of imbalanced functional segregation ad integration. However, no major alterations of modular organization have been reported in patients, and unambiguous identification of the neural substrates affected remains elusive. Recently, it has been demonstrated that current modularity analysis methods suffer from a fundamental and severe resolution limit, as they fail to detect features that are smaller than a scale determined by the size of the entire connectivity network. This resolution limit is likely to have hampered the ability to resolve differences between patients and controls in previous studies. Here, we apply Surprise, a novel resolution limit-free approach, to study the modular organization of resting state functional connectivity networks in a large cohort of SCZ patients and in matched healthy controls. Leveraging these important methodological advances we find new evidence of substantial fragmentation and reorganization involving primary sensory, auditory and visual areas in SCZ patients. Conversely, frontal and prefrontal areas, typically associated with higher cognitive functions, appear to be largely unaffected, with changes selectively involving language and speech processing areas. Our findings support the hypothesis that cognitive dysfunction in SCZ may involve deficits occurring already at early stages of sensory processing.

Neuroplasticity of cognitive control networks following cognitive training for chronic traumatic brain injury

Cognitive control is the ability to coordinate thoughts and actions to achieve goals. Cognitive control impairments are one of the most persistent and devastating sequalae of traumatic brain injuries (TBI). There have been efforts to improve cognitive control in individuals with post-acute TBI. Several studies have reported changes in neuropsychological measures suggesting the efficacy of cognitive training in improving cognitive control. Yet, the neural substrates of improved cognitive control after training remains poorly understood. In the current study, we identified neural plasticity induced by cognitive control training for TBI using resting-state functional connectivity (rsFC). Fifty-six individuals with chronic mild TBI (9 years post-injury on average) were randomized into either a strategy-based cognitive training group (N = 26) or a knowledge-based training group (active control condition; N = 30) for 8 weeks. We acquired a total of 109 resting-state functional magnetic resonance imaging from 45 individuals before training, immediately post-training, and 3 months post-training. Relative to the controls, the strategy-based cognitive training group showed monotonic increases in connectivity in two cognitive control networks (i.e., cingulo-opercular and fronto-parietal networks) across time points in multiple brain regions (pvoxel < 0.001, pcluster < 0.05). Analyses of brain-behavior relationships revealed that fronto-parietal network connectivity over three time points within the strategy-based cognitive training group was positively associated with the trail making scores (pvoxel < 0.001, pcluster < 0.05). These findings suggest that training-induced neuroplasticity continues through chronic phases of TBI and that rsFC can serve as a neuroimaging biomarker of evaluating the efficacy of cognitive training for TBI.

Simultaneous Multislice Resting-State Functional Magnetic Resonance Imaging at 3 Tesla: Slice-Acceleration-Related Biases in Physiological Effects

Simultaneous multislice echo-planar imaging (SMS-EPI) can enhance the spatiotemporal resolution of resting-state functional MRI (rs-fMRI) by encoding and simultaneously imaging "groups" of slices. However, phenomena, including respiration, cardiac pulsatility, respiration volume per time (RVT), and cardiac rate variation (CRV), referred to as "physiological processes," impact SMS-EPI rs-fMRI in a manner that is yet to be well characterized. In particular, physiological noise may incur aliasing and introduce spurious signals from one slice into another within the "slice group" in rs-fMRI data, resulting in a deleterious effect on resting-state functional connectivity MRI (rs-fcMRI) maps. In the present work, we aimed to quantitatively compare the effects of physiological noise on regular EPI and SMS-EPI in terms of rs-fMRI data and resulting functional connectivity measurements. We compare SMS-EPI and regular EPI data acquired from 11 healthy young adults with matching parameters. The physiological noise characteristics were compared between the two data sets through different combinations of physiological regression steps. We observed that the physiological noise characteristics differed between SMS-EPI and regular EPI, with cardiac pulsatility contributing more to noise in regular EPI data but low-frequency heart rate variability contributing more to SMS-EPI. In addition, a significant slice-group bias was observed in the functional connectivity density maps derived from SMS-EPI data. We conclude that making appropriate corrections for physiological noise is likely more important for SMS-EPI than for regular EPI acquisitions.

A Complex Interplay of Vitamin B1 and B6 Metabolism with Cognition, Brain Structure, and Functional Connectivity in Older Adults

Aging is associated with brain atrophy, functional brain network reorganization and decline of cognitive performance, albeit characterized by high interindividual variability. Among environmental influencing factors accounting for this variability, nutrition and particularly vitamin supply is thought to play an important role. While evidence exists that supplementation of vitamins B6 and B1 might be beneficial for cognition and brain structure, at least in deficient states and neurodegenerative diseases, little is known about this relation during healthy aging and in relation to reorganization of functional brain networks. We thus assessed the relation between blood levels of vitamins B1 and B6 and cognitive performance, cortical folding, and functional resting-state connectivity in a large sample of older adults (N > 600; age: 55-85 years), drawn from the population-based 1000BRAINS study. In addition to blood sampling, subjects underwent structural and functional resting-state neuroimaging as well as extensive neuropsychological testing in the domains of executive functions, (working) memory, attention, and language. Brain regions showing changes in the local gyrification index as calculated using FreeSurfer in relation to vitamin levels were used for subsequent seed-based resting-state functional connectivity analysis. For B6, a positive correlation with local cortical folding was found throughout the brain, while only slight changes in functional connectivity were observed. Contrarily, for B1, a negative correlation with cortical folding as well as problem solving and visuo-spatial working memory performance was found, which was accompanied by pronounced increases of interhemispheric and decreases of intrahemispheric functional connectivity. While the effects for B6 expand previous knowledge on beneficial effects of B6 supplementation on brain structure, they also showed that additional effects on cognition might not be recognizable in healthy older subjects with normal B6 blood levels. The cortical atrophy and pronounced functional reorganization associated with B1, contrarily, was more in line with the theory of a disturbed B1 metabolism in older adults, leading to B1 utilization deficits, and thus, an effective B1 deficiency in the brain, despite normal to high-normal blood levels.

Functional Networks in Disorders of Consciousness

Severe brain injury may cause disruption of neural networks that sustain arousal and awareness, the two essential components of consciousness. Despite the potentially devastating immediate and long-term consequences, disorders of consciousness (DoC) are poorly understood in terms of their underlying neurobiology, the relationship between pathophysiology and recovery, and the predictors of treatment efficacy. Recent advances in neuroimaging techniques have enabled the study of network connectivity, providing great potential to improve the clinical care of patients with DoC. Initial discoveries in this field were made using positron emission tomography (PET). More recently, functional magnetic resonance (fMRI) techniques have added to our understanding of functional network dynamics in this population. Both methods have shown that whether at rest or performing a goal-oriented task, functional networks essential for processing intrinsic thoughts and extrinsic stimuli are disrupted in patients with DoC compared with healthy subjects. Atypical connectivity has been well established in the default mode network as well as in other cortical and subcortical networks that may be required for consciousness. Moreover, the degree of altered connectivity may be related to the severity of impaired consciousness, and recovery of consciousness has been shown to be associated with restoration of connectivity. In this review, we discuss PET and fMRI studies of functional and effective connectivity in patients with DoC and suggest how this field can move toward clinical application of functional network mapping in the future.

Resting State fMRI Functional Connectivity Analysis Using Dynamic Time Warping

Traditional resting-state network concept is based on calculating linear dependence of spontaneous low frequency fluctuations of the BOLD signals of different brain areas, which assumes temporally stable zero-lag synchrony across regions. However, growing amount of experimental findings suggest that functional connectivity exhibits dynamic changes and a complex time-lag structure, which cannot be captured by the static zero-lag correlation analysis. Here we propose a new approach applying Dynamic Time Warping (DTW) distance to evaluate functional connectivity strength that accounts for non-stationarity and phase-lags between the observed signals. Using simulated fMRI data we found that DTW captures dynamic interactions and it is less sensitive to linearly combined global noise in the data as compared to traditional correlation analysis. We tested our method using resting-state fMRI data from repeated measurements of an individual subject and showed that DTW analysis results in more stable connectivity patterns by reducing the within-subject variability and increasing robustness for preprocessing strategies. Classification results on a public dataset revealed a superior sensitivity of the DTW analysis to group differences by showing that DTW based classifiers outperform the zero-lag correlation and maximal lag cross-correlation based classifiers significantly. Our findings suggest that analysing resting-state functional connectivity using DTW provides an efficient new way for characterizing functional networks.