Statistical methods of estimation and inference for functional MR image analysis

Investigating the hemodynamic response to iTBS of the left DLPFC: A concurrent iTBS/fNIRS study

BACKGROUND

Intermittent theta burst stimulation (iTBS) targeting the left dorsolateral prefrontal cortex (DLPFC) is an established treatment regimen for major depressive disorder, but its instantaneous effects on neural excitability during and immediately after the stimulation remain unclear. This study aimed to investigate the hemodynamic response in the bilateral DLPFC during and immediately after iTBS and explored factors that may modulate iTBS-induced excitability.

METHODS

We measured the prefrontal hemodynamic response before, during, and after iTBS using concurrent iTBS/functional near-infrared spectroscopy (fNIRS) in healthy participants across multiple sessions (3-11 visits, ≥48 hours apart). We investigated the moderating effect of several inter- and intra-individual variables. To this end, we analyzed the average change of oxygenated (HbO) and deoxygenated hemoglobin (HbR) in the stimulated and contralateral DLPFC and used generalized linear mixed models (GLMMs) to test for potential moderators.

RESULTS

Twenty participants completed 157 concurrent iTBS/fNIRS sessions in total. HbR increased significantly during iTBS (0.247 ± 0.032, p < 0.001) in the stimulated DLPFC, while the contralateral DLPFC showed significant decreases in HbR during (-0.046 ± 0.017, p = 0.024) and after the stimulation (-0.05 ± 0.018, p = 0.015). No significant change in HbO was observed. GLMM revealed that age (β = 0.033, p = 0.004), sex (β = -0.248, p = 0.004), education years (β = -0.094, p < 0.001), the personality trait agreeableness (β = -0.013, p = 0.005), and positive affect (β = -0.032, p = 0.012) significantly influenced local HbR response during iTBS, and sex (β = 0.305, p = 0.012) significantly influenced local HbO response during iTBS.

CONCLUSION

This study revealed a pronounced increase in HbR during iTBS in the stimulated DLPFC, alongside decreased HbR contralaterally both during and post-stimulation. Furthermore, our study highlights the importance of individual factors in understanding iTBS effects on cortical excitability.

Out-of-phase transcranial alternating current stimulation modulates the neurodynamics of inhibitory control

Transcranial alternating current stimulation (tACS) is an efficient neuromodulation technique that enhances cognitive function in a non-invasive manner. Using functional magnetic resonance imaging, we investigated whether tACS with different phase lags (0° and 180°) between the dorsal anterior cingulate and left dorsolateral prefrontal cortices modulated inhibitory control performance during the Stroop task. We found out-of-phase tACS mediated improvements in task performance, which was neurodynamically reflected as putamen, dorsolateral prefrontal, and primary motor cortical activation as well as prefrontal-based top-down functional connectivity. Our observations uncover the neurophysiological bases of tACS-phase-dependent neuromodulation and provide a feasible non-invasive approach to effectively modulate inhibitory control.

Functional and structural reorganization in brain tumors: a machine learning approach using desynchronized functional oscillations

Neuroimaging studies have allowed for non-invasive mapping of brain networks in brain tumors. Although tumor core and edema are easily identifiable using standard MRI acquisitions, imaging studies often neglect signals, structures, and functions within their presence. Therefore, both functional and diffusion signals, as well as their relationship with global patterns of connectivity reorganization, are poorly understood. Here, we explore the functional activity and the structure of white matter fibers considering the contribution of the whole tumor in a surgical context. First, we find intertwined alterations in the frequency domain of local and spatially distributed resting-state functional signals, potentially arising within the tumor. Second, we propose a fiber tracking pipeline capable of using anatomical information while still reconstructing bundles in tumoral and peritumoral tissue. Finally, using machine learning and healthy anatomical information, we predict structural rearrangement after surgery given the preoperative brain network. The generative model also disentangles complex patterns of connectivity reorganization for different types of tumors. Overall, we show the importance of carefully designing studies including MR signals within damaged brain tissues, as they exhibit and relate to non-trivial patterns of both structural and functional (dis-)connections or activity.

Lexical-Semantic Content, Not Syntactic Structure, Is the Main Contributor to ANN-Brain Similarity of fMRI Responses in the Language Network

Representations from artificial neural network (ANN) language models have been shown to predict human brain activity in the language network. To understand what aspects of linguistic stimuli contribute to ANN-to-brain similarity, we used an fMRI data set of responses to n = 627 naturalistic English sentences (Pereira et al., 2018) and systematically manipulated the stimuli for which ANN representations were extracted. In particular, we (i) perturbed sentences' word order, (ii) removed different subsets of words, or (iii) replaced sentences with other sentences of varying semantic similarity. We found that the lexical-semantic content of the sentence (largely carried by content words) rather than the sentence's syntactic form (conveyed via word order or function words) is primarily responsible for the ANN-to-brain similarity. In follow-up analyses, we found that perturbation manipulations that adversely affect brain predictivity also lead to more divergent representations in the ANN's embedding space and decrease the ANN's ability to predict upcoming tokens in those stimuli. Further, results are robust as to whether the mapping model is trained on intact or perturbed stimuli and whether the ANN sentence representations are conditioned on the same linguistic context that humans saw. The critical result-that lexical-semantic content is the main contributor to the similarity between ANN representations and neural ones-aligns with the idea that the goal of the human language system is to extract meaning from linguistic strings. Finally, this work highlights the strength of systematic experimental manipulations for evaluating how close we are to accurate and generalizable models of the human language network.

Superior Attentional Efficiency of Auditory Cue via the Ventral Auditory-thalamic Pathway

Auditory commands are often executed more efficiently than visual commands. However, empirical evidence on the underlying behavioral and neural mechanisms remains scarce. In two experiments, we manipulated the delivery modality of informative cues and the prediction violation effect and found consistently enhanced RT benefits for the matched auditory cues compared with the matched visual cues. At the neural level, when the bottom-up perceptual input matched the prior prediction induced by the auditory cue, the auditory-thalamic pathway was significantly activated. Moreover, the stronger the auditory-thalamic connectivity, the higher the behavioral benefits of the matched auditory cue. When the bottom-up input violated the prior prediction induced by the auditory cue, the ventral auditory pathway was specifically involved. Moreover, the stronger the ventral auditory-prefrontal connectivity, the larger the behavioral costs caused by the violation of the auditory cue. In addition, the dorsal frontoparietal network showed a supramodal function in reacting to the violation of informative cues irrespective of the delivery modality of the cue. Taken together, the results reveal novel behavioral and neural evidence that the superior efficiency of the auditory cue is twofold: The auditory-thalamic pathway is associated with improvements in task performance when the bottom-up input matches the auditory cue, whereas the ventral auditory-prefrontal pathway is involved when the auditory cue is violated.

The joint effect and hemodynamic mechanism of PA and PM2.5 exposure on cognitive function: A randomized controlled trial study

BACKGROUND

While PM2.5 has been shown to impair cognitive function, physical activity (PA) is known to enhance it. Nonetheless, considering the increased inhalation of PM2.5 during exercise, the potential of PA to counteract the detrimental effects of PM2.5, along with the underlying hemodynamic mechanisms, remains uncertain.

METHODS

We conducted a double-blinded, randomized controlled trial among healthy young adults in Beijing, China. Ninety-three participants were randomly allocated to groups experiencing different intensities of PA interventions, and either subjected to purified or unpurified air conditions. Cognitive function was measured by the Color-Word Matching Stroop task, and the hemodynamic response was measured using functional near-infrared spectroscopy during participants performed the Stroop task both before and after the intervention. Linear mixed-effect models were used to estimate the impact of PA and PM2.5 on cognitive function and hemodynamic response.

RESULTS

The reaction time for congruent and incongruent Stroop tasks improved by - 80.714 (95% CI: -136.733, -24.695) and - 105.843 (95% CI: -188.6, -23.085) milliseconds after high-intensity interval training (HIIT) intervention. PM2.5 and HIIT had interaction effects on cognition, such that every 1 μg/m3 increase in PM2.5 attenuated the benefits of HIIT on reaction time by 2.231 (95% CI: 0.523, 3.938) and 3.305 (95% CI: 0.791, 5.819) milliseconds for congruent and incongruent Stroop tasks. Moreover, we divided participants into high and low PM2.5 exposure groups based on average PM2.5 concentration (32.980 μg/m3), and found that HIIT intervention in high PM2.5 concentration led to 69.897 (95% CI: 9.317, 130.476) and 99.269 (95% CI: 10.054, 188.485) milliseconds increased in the reaction time of congruent and incongruent Stroop, compared with the control group among low PM2.5. Furthermore, we found a significant interaction effects of PM2.5 and moderate-intensity continuous training (MICT) on the middle frontal gyrus (MFG) and dorsolateral superior frontal gyrus (DLPFC). PM2.5 and HIIT had a significant interaction effect on the DLPFC.

CONCLUSIONS

HIIT improved cognitive function, but the cognitive benefits of HIIT were attenuated or even reversed under high PM2.5 exposure. The activation of the DLPFC and MFG could serve as hemodynamic mechanisms to explain the joint effect of PA and PM2.5.

Spatiotemporal dynamics across visual cortical laminae support a predictive coding framework for interpreting mismatch responses

Context modulates neocortical processing of sensory data. Unexpected visual stimuli elicit large responses in primary visual cortex (V1)-a phenomenon known as deviance detection (DD) at the neural level, or "mismatch negativity" (MMN) when measured with EEG. It remains unclear how visual DD/MMN signals emerge across cortical layers, in temporal relation to the onset of deviant stimuli, and with respect to brain oscillations. Here we employed a visual "oddball" sequence-a classic paradigm for studying aberrant DD/MMN in neuropsychiatric populations-and recorded local field potentials in V1 of awake mice with 16-channel multielectrode arrays. Multiunit activity and current source density profiles showed that although basic adaptation to redundant stimuli was present early (50 ms) in layer 4 responses, DD emerged later (150-230 ms) in supragranular layers (L2/3). This DD signal coincided with increased delta/theta (2-7 Hz) and high-gamma (70-80 Hz) oscillations in L2/3 and decreased beta oscillations (26-36 Hz) in L1. These results clarify the neocortical dynamics elicited during an oddball paradigm at a microcircuit level. They are consistent with a predictive coding framework, which posits that predictive suppression is present in cortical feed-back circuits, which synapse in L1, whereas "prediction errors" engage cortical feed-forward processing streams, which emanate from L2/3.

Lexical semantic content, not syntactic structure, is the main contributor to ANN-brain similarity of fMRI responses in the language network

Representations from artificial neural network (ANN) language models have been shown to predict human brain activity in the language network. To understand what aspects of linguistic stimuli contribute to ANN-to-brain similarity, we used an fMRI dataset of responses to n=627 naturalistic English sentences (Pereira et al., 2018) and systematically manipulated the stimuli for which ANN representations were extracted. In particular, we i) perturbed sentences' word order, ii) removed different subsets of words, or iii) replaced sentences with other sentences of varying semantic similarity. We found that the lexical semantic content of the sentence (largely carried by content words) rather than the sentence's syntactic form (conveyed via word order or function words) is primarily responsible for the ANN-to-brain similarity. In follow-up analyses, we found that perturbation manipulations that adversely affect brain predictivity also lead to more divergent representations in the ANN's embedding space and decrease the ANN's ability to predict upcoming tokens in those stimuli. Further, results are robust to whether the mapping model is trained on intact or perturbed stimuli, and whether the ANN sentence representations are conditioned on the same linguistic context that humans saw. The critical result-that lexical-semantic content is the main contributor to the similarity between ANN representations and neural ones-aligns with the idea that the goal of the human language system is to extract meaning from linguistic strings. Finally, this work highlights the strength of systematic experimental manipulations for evaluating how close we are to accurate and generalizable models of the human language network.

Spatiotemporal dynamics across visual cortical laminae support a predictive coding framework for interpreting mismatch responses

Context modulates neocortical processing of sensory data. Unexpected visual stimuli elicit large responses in primary visual cortex (V1) -- a phenomenon known as deviance detection (DD) at the neural level, or "mismatch negativity" (MMN) when measured with EEG. It remains unclear how visual DD/MMN signals emerge across cortical layers, in temporal relation to the onset of deviant stimuli, and with respect to brain oscillations. Here we employed a visual "oddball" sequence - a classic paradigm for studying aberrant DD/MMN in neuropsychiatric populations - and recorded local field potentials in V1 of awake mice with 16-channel multielectrode arrays. Multiunit activity and current source density profiles showed that while basic adaptation to redundant stimuli was present early (50ms) in layer 4 responses, DD emerged later (150-230ms) in supragranular layers (L2/3). This DD signal coincided with increased delta/theta (2-7Hz) and high-gamma (70-80Hz) oscillations in L2/3 and decreased beta oscillations (26-36hz) in L1. These results clarify the neocortical dynamics elicited during an oddball paradigm at a microcircuit level. They are consistent with a predictive coding framework, which posits that predictive suppression is present in cortical feed-back circuits, which synapse in L1, while "prediction errors" engage cortical feed-forward processing streams, which emanate from L2/3.

Sources of residual autocorrelation in multiband task fMRI and strategies for effective mitigation

Introduction

Analysis of task fMRI studies is typically based on using ordinary least squares within a voxel- or vertex-wise linear regression framework known as the general linear model. This use produces estimates and standard errors of the regression coefficients representing amplitudes of task-induced activations. To produce valid statistical inferences, several key statistical assumptions must be met, including that of independent residuals. Since task fMRI residuals often exhibit temporal autocorrelation, it is common practice to perform "prewhitening" to mitigate that dependence. Prewhitening involves estimating the residual correlation structure and then applying a filter to induce residual temporal independence. While theoretically straightforward, a major challenge in prewhitening for fMRI data is accurately estimating the residual autocorrelation at each voxel or vertex of the brain. Assuming a global model for autocorrelation, which is the default in several standard fMRI software tools, may under- or over-whiten in certain areas and produce differential false positive control across the brain. The increasing popularity of multiband acquisitions with faster temporal resolution increases the challenge of effective prewhitening because more complex models are required to accurately capture the strength and structure of autocorrelation. These issues are becoming more critical now because of a trend toward subject-level analysis and inference. In group-average or group-difference analyses, the within-subject residual correlation structure is accounted for implicitly, so inadequate prewhitening is of little real consequence. For individual subject inference, however, accurate prewhitening is crucial to avoid inflated or spatially variable false positive rates.

Methods

In this paper, we first thoroughly examine the patterns, sources and strength of residual autocorrelation in multiband task fMRI data. Second, we evaluate the ability of different autoregressive (AR) model-based prewhitening strategies to effectively mitigate autocorrelation and control false positives. We consider two main factors: the choice of AR model order and the level of spatial regularization of AR model coefficients, ranging from local smoothing to global averaging. We also consider determining the AR model order optimally at every vertex, but we do not observe an additional benefit of this over the use of higher-order AR models (e.g. (AR(6)). To overcome the computational challenge associated with spatially variable prewhitening, we developed a computationally efficient R implementation using parallelization and fast C++ backend code. This implementation is included in the open source R package BayesfMRI.

Results

We find that residual autocorrelation exhibits marked spatial variance across the cortex and is influenced by many factors including the task being performed, the specific acquisition protocol, mis-modeling of the hemodynamic response function, unmodeled noise due to subject head motion, and systematic individual differences. We also find that local regularization is much more effective than global averaging at mitigating autocorrelation. While increasing the AR model order is also helpful, it has a lesser effect than allowing AR coefficients to vary spatially. We find that prewhitening with an AR(6) model with local regularization is effective at reducing or even eliminating autocorrelation and controlling false positives.

Conclusion

Our analysis revealed dramatic spatial differences in autocorrelation across the cortex. This spatial topology is unique to each session, being influenced by the task being performed, the acquisition technique, various modeling choices, and individual differences. If not accounted for, these differences will result in differential false positive control and power across the cortex and across subjects.

Comparing Autoregressive and Network Features for Classification of Depression and Anxiety

Autocorrelation in functional MRI (fMRI) time series has been studied for decades, mostly considered as noise in the time series which is removed via prewhitening with an autoregressive model. Recent results suggest that the coefficients of an autoregressive model t to fMRI data may provide an indicator of underlying brain activity, suggesting that prewhitening could be removing important diagnostic information. This paper explores the explanatory value of these autoregressive features extracted from fMRI by considering the use of these features in a classification task. As a point of comparison, functional network based features are extracted from the same data and used in the same classification task. We find that in most cases, network based features provide better classification accuracy. However, using principal component analysis to combine network based features and autoregressive features for classification based on a support vector machine provides improved classification accuracy compared to single features or network features, suggesting that when properly combined there may be additional information to be gained from autoregressive features.

Disentangling emotional processing in dysphoria: An ERP and cardiac deceleration study

The present study aimed to investigate emotional processing in dysphoria. To this end, the amplitude of the Late Positive Potential (LPP) and cardiac deceleration were assessed during the passive viewing of affective (pleasant, neutral, and unpleasant) pictures in 26 individuals with dysphoria and in 25 non-depressed controls. The group with dysphoria revealed a smaller LPP amplitude than the group without dysphoria in response to pleasant and neutral, but not unpleasant, stimuli at centro-parieto-occipital sites. Interestingly, whereas both groups showed cardiac deceleration when viewing pleasant compared to neutral pictures (3-6 s time window), only individuals with dysphoria showed a prolonged cardiac deceleration in response to unpleasant stimuli as compared with neutral ones. This study suggests that dysphoria is characterized by reduced motivated attentional allocation to positive information and by sustained intake of unpleasant information. Overall, the present findings provide novel insights into the characterization of valence-specific attentional processes in dysphoria as potential vulnerability factors for clinically significant depression.

Statistical power or more precise insights into neuro-temporal dynamics? Assessing the benefits of rapid temporal sampling in fMRI

Functional magnetic resonance imaging (fMRI), a non-invasive and widely used human neuroimaging method, is most known for its spatial precision. However, there is a growing interest in its temporal sensitivity. This is despite the temporal blurring of neuronal events by the blood oxygen level dependent (BOLD) signal, the peak of which lags neuronal firing by 4-6 seconds. Given this, the goal of this review is to answer a seemingly simple question - "What are the benefits of increased temporal sampling for fMRI?". To answer this, we have combined fMRI data collected at multiple temporal scales, from 323 to 1000 milliseconds, with a review of both historical and contemporary temporal literature. After a brief discussion of technological developments that have rekindled interest in temporal research, we next consider the potential statistical and methodological benefits. Most importantly, we explore how fast fMRI can uncover previously unobserved neuro-temporal dynamics - effects that are entirely missed when sampling at conventional 1 to 2 second rates. With the intrinsic link between space and time in fMRI, this temporal renaissance also delivers improvements in spatial precision. Far from producing only statistical gains, the array of benefits suggest that the continued temporal work is worth the effort.

Data Processing in Functional Near-Infrared Spectroscopy (fNIRS) Motor Control Research

FNIRS pre-processing and processing methodologies are very important-how a researcher chooses to process their data can change the outcome of an experiment. The purpose of this review is to provide a guide on fNIRS pre-processing and processing techniques pertinent to the field of human motor control research. One hundred and twenty-three articles were selected from the motor control field and were examined on the basis of their fNIRS pre-processing and processing methodologies. Information was gathered about the most frequently used techniques in the field, which included frequency cutoff filters, wavelet filters, smoothing filters, and the general linear model (GLM). We discuss the methodologies of and considerations for these frequently used techniques, as well as those for some alternative techniques. Additionally, general considerations for processing are discussed.

Improving the sensitivity of cluster-based statistics for functional magnetic resonance imaging data

Because of the high dimensionality of neuroimaging data, identifying a statistical test that is both valid and maximally sensitive is an important challenge. Here, we present a combination of two approaches for functional magnetic resonance imaging (fMRI) data analysis that together result in substantial improvements of the sensitivity of cluster‐based statistics. The first approach is to create novel cluster definitions that optimize sensitivity to plausible effect patterns. The second is to adopt a new approach to combine test statistics with different sensitivity profiles, which we call the min(p) method. These innovations are made possible by using the randomization inference framework. In this article, we report on a set of simulations and analyses of real task fMRI data that demonstrate (a) that the proposed methods control the false‐alarm rate, (b) that the sensitivity profiles of cluster‐based test statistics vary depending on the cluster defining thresholds and cluster definitions, and (c) that the min(p) method for combining these test statistics results in a drastic increase of sensitivity (up to fivefold), compared to existing fMRI analysis methods. This increase in sensitivity is not at the expense of the spatial specificity of the inference.

To pool or not to pool: Can we ignore cross-trial variability in FMRI?

In this work, we investigate the importance of explicitly accounting for cross-trial variability in neuroimaging data analysis. To attempt to obtain reliable estimates in a task-based experiment, each condition is usually repeated across many trials. The investigator may be interested in (a) condition-level effects, (b) trial-level effects, or (c) the association of trial-level effects with the corresponding behavior data. The typical strategy for condition-level modeling is to create one regressor per condition at the subject level with the underlying assumption that responses do not change across trials. In this methodology of complete pooling, all cross-trial variability is ignored and dismissed as random noise that is swept under the rug of model residuals. Unfortunately, this framework invalidates the generalizability from the confine of specific trials (e.g., particular faces) to the associated stimulus category ("face"), and may inflate the statistical evidence when the trial sample size is not large enough. Here we propose an adaptive and computationally tractable framework that meshes well with the current two-level pipeline and explicitly accounts for trial-by-trial variability. The trial-level effects are first estimated per subject through no pooling. To allow generalizing beyond the particular stimulus set employed, the cross-trial variability is modeled at the population level through partial pooling in a multilevel model, which permits accurate effect estimation and characterization. Alternatively, trial-level estimates can be used to investigate, for example, brain-behavior associations or correlations between brain regions. Furthermore, our approach allows appropriate accounting for serial correlation, handling outliers, adapting to data skew, and capturing nonlinear brain-behavior relationships. By applying a Bayesian multilevel model framework at the level of regions of interest to an experimental dataset, we show how multiple testing can be addressed and full results reported without arbitrary dichotomization. Our approach revealed important differences compared to the conventional method at the condition level, including how the latter can distort effect magnitude and precision. Notably, in some cases our approach led to increased statistical sensitivity. In summary, our proposed framework provides an effective strategy to capture trial-by-trial responses that should be of interest to a wide community of experimentalists.

Improved autoregressive model for correction of noise serial correlation in fast fMRI

PURPOSE

In rapidly acquired functional MRI (fast fMRI) data, the noise serial correlations (SC) can produce problematically overestimated T-statistics which lead to invalid statistical inferences. This study aims to evaluate and improve the accuracy of high-order autoregressive model (AR(p), where p is the model order) based prewhitening method in the SC correction.

METHODS

Fast fMRI images were acquired at rest (null data) using a multiband simultaneous multi-slice echo planar imaging pulse sequence with repetition time (TR) = 300 and 500 ms. The SC effect in the fast fMRI data was corrected using the prewhitening method based on two AR(p) models: (1) the conventional model (fixed AR(p)) which preselects a constant p for all the image voxels; (2) an improved model (AR_AICc ) that employs the corrected Akaike information criterion voxel-wise to automatically select the model orders for each voxel. To evaluate accuracy of SC correction, false positive characteristics were measured by assuming the presence of block and event-related tasks in the null data without image smoothing. The performance of prewhitening was also examined in smoothed images by adding pseudo task fMRI signals into the null data and comparing the detected to simulated activations (ground truth).

RESULTS

The measured false positive characteristics agreed well with the theoretical curve when using the AR_AICc , and the activation maps in the smoothed data matched the ground truth. The AR_AICc showed improved performance than the fixed AR(p) method.

CONCLUSION

The AR_AICc can effectively remove noise SC, and accurate statistical analysis results can be obtained with the AR_AICc correction in fast fMRI.

Revealing Changes in Brain Functional Networks Caused by Focused-Attention Meditation Using Tucker3 Clustering

This study examines the effects of focused-attention meditation on functional brain states in novice meditators. There are a number of feature metrics for functional brain states, such as functional connectivity, graph theoretical metrics, and amplitude of low frequency fluctuation (ALFF). It is necessary to choose appropriate metrics and also to specify the region of interests (ROIs) from a number of brain regions. Here, we use a Tucker3 clustering method, which simultaneously selects the feature vectors (graph theoretical metrics and fractional ALFF) and the ROIs that can discriminate between resting and meditative states based on the characteristics of the given data. In this study, breath-counting meditation, one of the most popular forms of focused-attention meditation, was used and brain activities during resting and meditation states were measured by functional magnetic resonance imaging. The results indicated that the clustering coefficients of the eight brain regions, Frontal Inf Oper L, Occipital Inf R, ParaHippocampal R, Cerebellum 10 R, Cingulum Mid R, Cerebellum Crus1 L, Occipital Inf L, and Paracentral Lobule R increased through the meditation. Our study also provided the framework of data-driven brain functional analysis and confirmed its effectiveness on analyzing neural basis of focused-attention meditation.

Accurate autocorrelation modeling substantially improves fMRI reliability

Given the recent controversies in some neuroimaging statistical methods, we compare the most frequently used functional Magnetic Resonance Imaging (fMRI) analysis packages: AFNI, FSL and SPM, with regard to temporal autocorrelation modeling. This process, sometimes known as pre-whitening, is conducted in virtually all task fMRI studies. Here, we employ eleven datasets containing 980 scans corresponding to different fMRI protocols and subject populations. We found that autocorrelation modeling in AFNI, although imperfect, performed much better than the autocorrelation modeling of FSL and SPM. The presence of residual autocorrelated noise in FSL and SPM leads to heavily confounded first level results, particularly for low-frequency experimental designs. SPM’s alternative pre-whitening method, FAST, performed better than SPM’s default. The reliability of task fMRI studies could be improved with more accurate autocorrelation modeling. We recommend that fMRI analysis packages provide diagnostic plots to make users aware of any pre-whitening problems.

There has been recent controversy over the validity of commonly-used software packages for functional MRI (fMRI) data analysis. Here, the authors compare the performance of three leading packages (AFNI, FSL, SPM) in terms of temporal autocorrelation modeling, a key statistical step in fMRI analysis.

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.

Investigating the impact of autocorrelation on time-varying connectivity

In recent years, a number of studies have reported on the existence of time-varying functional connectivity (TVC) in resting-state functional magnetic resonance imaging (rs-fMRI) data. The sliding-window technique is currently one of the most commonly used methods to estimate TVC. Although previous studies have shown that autocorrelation can negatively impact estimates of static functional connectivity, its impact on TVC estimates is not well known at this time. In this paper, we show both theoretically and empirically that the existence of autocorrelation within a time series can inflate the sampling variability of TVC estimated using the sliding-window technique. This can in turn increase the risk of misinterpreting noise as true TVC and negatively impact subsequent estimation of whole-brain time-varying FC profiles, or "brain states". The latter holds as more variable input measures lead to more variable output measures in the state estimation procedure. Finally, we demonstrate that prewhitening the data prior to analysis can lower the variance of the estimated TVC and improve brain state estimation. These results suggest that careful consideration is required when making inferences on TVC.

Intersession Instability in fNIRS-Based Emotion Recognition

Emotion recognition based on neural signals is a promising technique for the detection of patients' emotions for enhancing healthcare. However, emotion-related neural signals, such as from functional near infrared spectroscopy (fNIRS), can be affected by various psychophysiological and environmental factors. There is a paucity of literature regarding data instability and classification instability in fNIRS-based emotion recognition systems, phenomenon which may lead to user dissatisfaction and abandonment. We collected data in an fNIRS-based 2-class emotion recognition test-retest experiment (3 week interval) with visual stimuli emotion induction to examine data instability and its impact on classification accuracy. We found a 22.2% average deterioration of emotion classification accuracy between the two sessions, suggesting that classification instability is a serious problem. We found that the changes in the distributions of the selected neural signal features, as evaluated by Kullback-Leibler (KL) divergence, were a likely cause of the accuracy decline. We analyzed the data instability and our results showed that instability of spatial activation patterns and instability of the hemodynamic response in the most activated region are correlated with accuracy decline. Finally, we propose a method for mitigating classification instability in fNIRS-based emotion recognition based on feature selection for stable features, the first such method to our knowledge. This new feature selection criterion considers not only the separability of features (evaluated by Fisher Score) but also their stability over time (evaluated by KL divergence between feature distributions at different time points). Testing showed that this method led to an approximately 5% improvement in cross-session generalization accuracy.

Experimental design modulates variance in BOLD activation: The variance design general linear model

Typical fMRI studies have focused on either the mean trend in the blood-oxygen-level-dependent (BOLD) time course or functional connectivity (FC). However, other statistics of the neuroimaging data may contain important information. Despite studies showing links between the variance in the BOLD time series (BV) and age and cognitive performance, a formal framework for testing these effects has not yet been developed. We introduce the variance design general linear model (VDGLM), a novel framework that facilitates the detection of variance effects. We designed the framework for general use in any fMRI study by modeling both mean and variance in BOLD activation as a function of experimental design. The flexibility of this approach allows the VDGLM to (a) simultaneously make inferences about a mean or variance effect while controlling for the other and (b) test for variance effects that could be associated with multiple conditions and/or noise regressors. We demonstrate the use of the VDGLM in a working memory application and show that engagement in a working memory task is associated with whole-brain decreases in BOLD variance.

A comparison of denoising pipelines in high temporal resolution task-based functional magnetic resonance imaging data

It has been known for decades that head motion/other artifacts affect the blood oxygen level-dependent signal. Recent recommendations predominantly focus on denoising resting state data, which may not apply to task data due to the different statistical relationships that exist between signal and noise sources. Several blind-source denoising strategies (FIX and AROMA) and more standard motion parameter (MP) regression (0, 12, or 24 parameters) analyses were therefore compared across four sets of event-related functional magnetic resonance imaging (erfMRI) and block-design (bdfMRI) datasets collected with multiband 32- (repetition time [TR] = 460 ms) or older 12-channel (TR = 2,000 ms) head coils. The amount of motion varied across coil designs and task types. Quality control plots indicated small to moderate relationships between head motion estimates and percent signal change in both signal and noise regions. Blind-source denoising strategies eliminated signal as well as noise relative to MP24 regression; however, the undesired effects on signal depended both on algorithm (FIX > AROMA) and design (bdfMRI > erfMRI). Moreover, in contrast to previous results, there were minimal differences between MP12/24 and MP0 pipelines in both erfMRI and bdfMRI designs. MP12/24 pipelines were detrimental for a task with both longer block length (30 ± 5 s) and higher correlations between head MPs and design matrix. In summary, current results suggest that there does not appear to be a single denoising approach that is appropriate for all fMRI designs. However, even nonaggressive blind-source denoising approaches appear to remove signal as well as noise from task-related data at individual subject and group levels.

Anticipatory alpha oscillation predicts attentional selection and hemodynamic response

In covert visual attention, one fundamental question is how advance knowledge facilitates subsequent neural processing and behavioral performance. In this study, with a rapid event-related simultaneous electroencephalography (EEG) and functional near infrared spectroscopy recording in humans, we explored the potential contribution of anticipatory electrophysiological activation and hemodynamic activation by examining how anticipatory low-frequency oscillations and changes in oxygenated hemoglobin (HbO) concentration influence the subsequent event-related potential (ERP) marker of attentional selection. We found that expecting a target led to both a posterior lateralization of alpha-band (8-12 Hz) oscillation power and a lateralization of HbO response over the visual cortex. Importantly, the magnitude of cue-induced alpha lateralization was positively correlated with the nearby HbO lateralization in the visual cortex, and such a cue-induced alpha lateralization predicted the subsequent target-evoked N2pc amplitudes assumed to reflect attentional selection. Our results suggest that each individual's attentional selection biomarker as reflected by N2pc is predictable in advance via the anticipation-induced alpha lateralization, and such cue-induced alpha lateralization seems to play an important role in the functional coupling effects between the low-frequency EEG and the nearby hemodynamic activation.

Autoconnectivity: A new perspective on human brain function

BACKGROUND

Autocorrelation (AC) in fMRI time-series is a well-known phenomenon, typically attributed to colored noise and therefore removed from the data. We hypothesize that AC reflects systematic and meaningful signal fluctuations that may be tied to neural activity and provide evidence to support this hypothesis.

NEW METHOD

Each fMRI time-series is modeled as an autoregressive process from which the autocorrelation is quantified. Then, autocorrelation during resting-state fMRI and auditory oddball (AOD) task in schizophrenia and healthy volunteers is examined.

RESULTS

During resting-state, AC was higher in the visual cortex while during AOD task, frontal part of the brain exhibited higher AC in both groups. AC values were significantly lower in specific brain regions in schizophrenia patients (such as thalamus during resting-state) compared to healthy controls in two independent datasets. Moreover, AC values had significant negative correlation with patients' symptoms. AC differences discriminated patients from healthy controls with high accuracy (resting-state).

COMPARISON WITH EXISTING METHODS

Contrary to most prior works, the results suggest AC shows meaningful patterns that are discriminative between patients and controls. Our results are in line with recent works attributing autocorrelation to feedback loop of brain's regulatory circuit.

CONCLUSIONS

Autoconnectivity is cognitive state dependent (resting-state vs. task) and mental state dependent (healthy vs. schizophrenia). The concept of autoconnectivity resembles a recurrent neural network and provides a new perspective of functional integration in the brain. These findings may have important implications for understanding of brain function in health and disease as well as for analysis of fMRI time-series.

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.

Reduced prefrontal-temporal cortical activation during verbal fluency task in obsessive-compulsive disorder: A multi-channel near-infrared spectroscopy study

Functional neuroimaging studies by near-infrared spectroscopy (NIRS) have focused on the role of the prefrontal cortex (PFC) in the pathophysiology of obsessive-compulsive disorder (OCD). However, the reported areas in the PFC were inconsistent in OCD, and correlations between hemodynamic response and clinical symptoms have not been investigated. This study aimed to evaluate the hemodynamic response related to the verbal fluency task (VFT) and assess the relationship between activation and clinical status in OCD patients using a 52-channel NIRS with a wide coverage over the prefrontal and temporal cortices. Seventy patients with OCD and 70 age-, gender- and education level-matched healthy control subjects were examined by NIRS. The relative concentration changes of oxygenated hemoglobin ([oxy-Hb]) were measured. The Yale-Brown obsessive-compulsive scale (Y-BOCS) was used to evaluate the severity of OCD symptoms. Compared to healthy controls group, OCD patients showed smaller [oxy-Hb] changes in most areas of the prefrontal and temporal cortex, including the bilateral orbitofrontal cortex (OFC), right dorsolateral prefrontal cortex (DLPFC), bilateral inferior prefrontal cortex (IPFC), bilateral frontopolar cortex (FPC), left superior temporal gyrus (STG), and bilateral middle temporal gyrus (MTG). Furthermore, the [oxy-Hb] changes in the right FPC were negatively correlated with the Y-BOCS obsessions score and Y-BOCS total score, and the [oxy-Hb] changes in the left OFC were negatively correlated with the Y-BOCS compulsions score. These results suggest that patients with OCD have reduced prefrontal-temporal cortex hemodynamic responses, and that the abnormalities of brain activation were associated with the severity of OCD symptoms.

Gain-loss situation modulates neural responses to self-other decision making under risk

Although self-other behavioral differences in decision making under risk have been observed in some contexts, little is known about the neural mechanisms underlying such differences. Using functional magnetic resonance imaging (fMRI) and the cups task, in which participants choose between risky and sure options for themselves and others in gain and loss situations, we found that people were more risk-taking when making decisions for themselves than for others in loss situations but were equally risk-averse in gain situations. Significantly stronger activations were observed in the dorsomedial prefrontal cortex (dmPFC) and anterior insula (AI) when making decisions for the self than for others in loss situations but not in gain situations. Furthermore, the activation in the dmPFC was stronger when people made sure choices for others than for themselves in gain situations but not when they made risky choices, and was both stronger when people made sure and risky choices for themselves than for others in loss situations. These findings suggest that gain-loss situation modulates self-other differences in decision making under risk, and people are highly likely to differentiate the self from others when making decisions in loss situations.

Cluster-based permutation tests of MEG/EEG data do not establish significance of effect latency or location

Cluster-based permutation tests are gaining an almost universal acceptance as inferential procedures in cognitive neuroscience. They elegantly handle the multiple comparisons problem in high-dimensional magnetoencephalographic and EEG data. Unfortunately, the power of this procedure comes hand in hand with the allure for unwarranted interpretations of the inferential output, the most prominent of which is the overestimation of the temporal, spatial, and frequency precision of statistical claims. This leads researchers to statements about the onset or offset of a certain effect that is not supported by the permutation test. In this article, we outline problems and common pitfalls of using and interpreting cluster-based permutation tests. We illustrate these with simulated data in order to promote a more intuitive understanding of the method. We hope that raising awareness about these issues will be beneficial to common scientific practices, while at the same time increasing the popularity of cluster-based permutation procedures.

Accounting for Non-Gaussian Sources of Spatial Correlation in Parametric Functional Magnetic Resonance Imaging Paradigms II: A Method to Obtain First-Level Analysis Residuals with Uniform and Gaussian Spatial Autocorrelation Function and Independent and Identically Distributed Time-Series

In a recent study Eklund et al. have shown that cluster-wise family-wise error (FWE) rate-corrected inferences made in parametric statistical method-based functional magnetic resonance imaging (fMRI) studies over the past couple of decades may have been invalid, particularly for cluster defining thresholds less stringent than p < 0.001; principally because the spatial autocorrelation functions (sACFs) of fMRI data had been modeled incorrectly to follow a Gaussian form, whereas empirical data suggest otherwise. Hence, the residuals from general linear model (GLM)-based fMRI activation estimates in these studies may not have possessed a homogenously Gaussian sACF. Here we propose a method based on the assumption that heterogeneity and non-Gaussianity of the sACF of the first-level GLM analysis residuals, as well as temporal autocorrelations in the first-level voxel residual time-series, are caused by unmodeled MRI signal from neuronal and physiological processes as well as motion and other artifacts, which can be approximated by appropriate decompositions of the first-level residuals with principal component analysis (PCA), and removed. We show that application of this method yields GLM residuals with significantly reduced spatial correlation, nearly Gaussian sACF and uniform spatial smoothness across the brain, thereby allowing valid cluster-based FWE-corrected inferences based on assumption of Gaussian spatial noise. We further show that application of this method renders the voxel time-series of first-level GLM residuals independent, and identically distributed across time (which is a necessary condition for appropriate voxel-level GLM inference), without having to fit ad hoc stochastic colored noise models. Furthermore, the detection power of individual subject brain activation analysis is enhanced. This method will be especially useful for case studies, which rely on first-level GLM analysis inferences.

COMPLEX-VALUED TIME SERIES MODELING FOR IMPROVED ACTIVATION DETECTION IN FMRI STUDIES

A complex-valued data-based model with pth order autoregressive errors and general real/imaginary error covariance structure is proposed as an alternative to the commonly-used magnitude-only data-based autoregressive model for fMRI time series. Likelihood-ratio-test-based activation statistics are derived for both models and compared for experimental and simulated data. For a dataset from a right-hand finger-tapping experiment, the activation map obtained using complex-valued modeling more clearly identifies the primary activation region (left functional central sulcus) than the magnitude-only model. Such improved accuracy in mapping the left functional central sulcus has important implications in neurosurgical planning for tumor and epilepsy patients. Additionally, we develop magnitude and phase detrending procedures for complex-valued time series and examine the effect of spatial smoothing. These methods improve the power of complex-valued data-based activation statistics. Our results advocate for the use of the complex-valued data and the modeling of its dependence structures as a more efficient and reliable tool in fMRI experiments over the current practice of using only magnitude-valued datasets.

Sustained versus instantaneous connectivity differentiates cognitive functions of processing speed and episodic memory

Synchrony of brain activity over time describes the functional connectivity between brain regions but does not address the temporal component of this relationship. We propose a complementary method of analysis by introducing the width of cross-correlation curves between functional MRI (fMRI) time series as a metric of the relative duration of synchronous activity between brain regions, or "sustained connectivity". Using resting-state fMRI, cognitive, and demographics data from 1,003 subjects included in the Human Connectome Project, we find that sustained connectivity is a reproducible trait in individuals, heritable, more transient in females, and shows changes with age in early adulthood. Sustained connectivity in sensory brain regions is specifically associated with differences in processing speed across subjects, particularly in men. In contrast, traditional functional connectivity was correlated with a measure of episodic memory, but not with processing speed. Individual differences in hemodynamic response function (HRF) are closely approximated by sustained connectivity and width of the HRF is also correlated with processing speed across individuals, suggesting that variability in hemodynamic response may be influenced by transient versus sustained neural activity rather than simply differences in vascularity and signal transduction. Sustained connectivity may provide new opportunities to study brain dynamics in clinical populations.

An asymptotic theory for cross-correlation between auto-correlated sequences and its application on neuroimaging data

BACKGROUND

Functional connectivity is among the most important tools to study brain. The correlation coefficient, between time series of different brain areas, is the most popular method to quantify functional connectivity. Correlation coefficient in practical use assumes the data to be temporally independent. However, the time series data of brain can manifest significant temporal auto-correlation.

NEW METHOD

A widely applicable method is proposed for correcting temporal auto-correlation. We considered two types of time series models: (1) auto-regressive-moving-average model, (2) nonlinear dynamical system model with noisy fluctuations, and derived their respective asymptotic distributions of correlation coefficient. These two types of models are most commonly used in neuroscience studies. We show the respective asymptotic distributions share a unified expression.

RESULT

We have verified the validity of our method, and shown our method exhibited sufficient statistical power for detecting true correlation on numerical experiments. Employing our method on real dataset yields more robust functional network and higher classification accuracy than conventional methods.

COMPARISON WITH EXISTING METHODS

Our method robustly controls the type I error while maintaining sufficient statistical power for detecting true correlation in numerical experiments, where existing methods measuring association (linear and nonlinear) fail.

CONCLUSIONS

In this work, we proposed a widely applicable approach for correcting the effect of temporal auto-correlation on functional connectivity. Empirical results favor the use of our method in functional network analysis.

Explicit Performance in Girls and Implicit Processing in Boys: A Simultaneous fNIRS-ERP Study on Second Language Syntactic Learning in Young Adolescents

Learning a second language (L2) proceeds with individual approaches to proficiency in the language. Individual differences including sex, as well as working memory (WM) function appear to have strong effects on behavioral performance and cortical responses in L2 processing. Thus, by considering sex and WM capacity, we examined neural responses during L2 sentence processing as a function of L2 proficiency in young adolescents. In behavioral tests, girls significantly outperformed boys in L2 tests assessing proficiency and grammatical knowledge, and in a reading span test (RST) assessing WM capacity. Girls, but not boys, showed significant correlations between L2 tests and RST scores. Using functional near-infrared spectroscopy (fNIRS) and event-related potential (ERP) simultaneously, we measured cortical responses while participants listened to syntactically correct and incorrect sentences. ERP data revealed a grammaticality effect only in boys in the early time window (100–300 ms), implicated in phrase structure processing. In fNIRS data, while boys had significantly increased activation in the left prefrontal region implicated in syntactic processing, girls had increased activation in the posterior language-related region involved in phonology, semantics, and sentence processing with proficiency. Presumably, boys implicitly focused on rule-based syntactic processing, whereas girls made full use of linguistic knowledge and WM function. The present results provide important fundamental data for learning and teaching in L2 education.

Brain activity during phonation in healthy female singers with supraglottic compression: an fMRI pilot study

This pilot study evaluated the usability of functional magnetic resonance imaging (fMRI) to detect brain activation during phonation in healthy female singers with supraglottic compression. Four healthy female classical singers (mean age: 26 years) participated in the study. All subjects had normal vocal folds and vocal characteristics and showed supraglottic compression. The fMRI experiment was carried out using a block design paradigm. Brain activation during phonation and exhalation was analyzed using Brain Voyager software (Brain Innovation B.V., Maastricht, The Netherlands). An fMRI data analysis showed a significant effect of phonation control in the bilateral pre/postcentral gyrus, and in the frontal, cingulate, superior and middle temporal gyrus, as well as in the parietal lobe, insula, lingual gyrus, cerebellum, thalamus and brainstem. These activation areas are consistent with previous reports using other fMRI protocols. In addition, a significant effect of phonation compared to exhalation control was found in the bilateral superior temporal gyrus, and the pre/postcentral gyrus. This fMRI pilot study allowed to detect a normal pattern of brain activity during phonation in healthy female singers with supraglottic compression using the proposed protocol. However, the pilot study detected problems with the experimental material/procedures that would necessitate refining the fMRI protocol. The phonation tasks were not capable to show brain activation difference between high-pitched and comfortable phonation. Further fMRI studies manipulating vocal parameters during phonation of the vowels /a/ and /i/ may elicit more distinctive hemodynamic response (HDR) activity patterns relative to voice modulation.

Effects of the Blob on settlement of spotted sand bass, Paralabrax maculatofasciatus, to Mission Bay, San Diego, CA

The West Coast of the United States experienced variable and sometimes highly unusual oceanographic conditions between 2012 and 2015. In particular, a warm mass of surface water known as the Pacific Warm Anomaly (popularly as “The Blob”) impinged on southern California in 2014, and warm-water conditions remained during the 2015 El Niño. We examine how this oceanographic variability affected delivery and individual characteristics of larval spotted sand bass (Paralabrax maculatofasciatus) to an estuarine nursery habitat in southern California. To quantify P. maculatofasciatus settlement patterns, three larval collectors were installed near the mouth of Mission Bay, San Diego CA, and retrieved weekly from June–October of 2012–2015. During ‘Blob‘ conditions in 2014 and 2015, lower settlement rates of spotted sand bass were associated with higher sea surface temperature and lower wind speed, chlorophyll a (chl a) and upwelling. Overall, the number of settlers per day peaked at intermediate chl a values across weeks. Individual characteristics of larvae that settled in 2014–2015 were consistent with a poor feeding environment. Although settlers were longer in length in 2014–15, fish in these years had slower larval otolith growth, a longer larval duration, and a trend towards lower condition, traits that are often associated with lower survival and recruitment. This study suggests that future settlement and recruitment of P. maculatofasciatus and other fishes with similar life histories may be adversely affected in southern California if ocean temperatures continue to rise in the face of climate change.

Segmenting hippocampal subfields from 3T MRI with multi-modality images

Hippocampal subfields play important roles in many brain activities. However, due to the small structural size, low signal contrast, and insufficient image resolution of 3T MR, automatic hippocampal subfields segmentation is less explored. In this paper, we propose an automatic learning-based hippocampal subfields segmentation method using 3T multi-modality MR images, including structural MRI (T1, T2) and resting state fMRI (rs-fMRI). The appearance features and relationship features are both extracted to capture the appearance patterns in structural MR images and also the connectivity patterns in rs-fMRI, respectively. In the training stage, these extracted features are adopted to train a structured random forest classifier, which is further iteratively refined in an auto-context model by adopting the context features and the updated relationship features. In the testing stage, the extracted features are fed into the trained classifiers to predict the segmentation for each hippocampal subfield, and the predicted segmentation is iteratively refined by the trained auto-context model. To our best knowledge, this is the first work that addresses the challenging automatic hippocampal subfields segmentation using relationship features from rs-fMRI, which is designed to capture the connectivity patterns of different hippocampal subfields. The proposed method is validated on two datasets and the segmentation results are quantitatively compared with manual labels using the leave-one-out strategy, which shows the effectiveness of our method. From experiments, we find a) multi-modality features can significantly increase subfields segmentation performance compared to those only using one modality; b) automatic segmentation results using 3T multi-modality MR images could be partially comparable to those using 7T T1 MRI.

Multivariate Brain Prediction of Heart Rate and Skin Conductance Responses to Social Threat

Psychosocial stressors induce autonomic nervous system (ANS) responses in multiple body systems that are linked to health risks. Much work has focused on the common effects of stress, but ANS responses in different body systems are dissociable and may result from distinct patterns of cortical-subcortical interactions. Here, we used machine learning to develop multivariate patterns of fMRI activity predictive of heart rate (HR) and skin conductance level (SCL) responses during social threat in humans (N = 18). Overall, brain patterns predicted both HR and SCL in cross-validated analyses successfully (r_HR = 0.54, r_SCL = 0.58, both p < 0.0001). These patterns partly reflected central stress mechanisms common to both responses because each pattern predicted the other signal to some degree (r_HR→SCL = 0.21 and r_SCL→HR = 0.22, both p < 0.01), but they were largely physiological response specific. Both patterns included positive predictive weights in dorsal anterior cingulate and cerebellum and negative weights in ventromedial PFC and local pattern similarity analyses within these regions suggested that they encode common central stress mechanisms. However, the predictive maps and searchlight analysis suggested that the patterns predictive of HR and SCL were substantially different across most of the brain, including significant differences in ventromedial PFC, insula, lateral PFC, pre-SMA, and dmPFC. Overall, the results indicate that specific patterns of cerebral activity track threat-induced autonomic responses in specific body systems. Physiological measures of threat are not interchangeable, but rather reflect specific interactions among brain systems.

SIGNIFICANCE STATEMENT

We show that threat-induced increases in heart rate and skin conductance share some common representations in the brain, located mainly in the vmPFC, temporal and parahippocampal cortices, thalamus, and brainstem. However, despite these similarities, the brain patterns that predict these two autonomic responses are largely distinct. This evidence for largely output-measure-specific regulation of autonomic responses argues against a common system hypothesis and provides evidence that different autonomic measures reflect distinct, measurable patterns of cortical-subcortical interactions.

Improving temporal resolution in fMRI using a 3D spiral acquisition and low rank plus sparse (L+S) reconstruction

Rapid whole-brain dynamic Magnetic Resonance Imaging (MRI) is of particular interest in Blood Oxygen Level Dependent (BOLD) functional MRI (fMRI). Faster acquisitions with higher temporal sampling of the BOLD time-course provide several advantages including increased sensitivity in detecting functional activation, the possibility of filtering out physiological noise for improving temporal SNR, and freezing out head motion. Generally, faster acquisitions require undersampling of the data which results in aliasing artifacts in the object domain. A recently developed low-rank (L) plus sparse (S) matrix decomposition model (L+S) is one of the methods that has been introduced to reconstruct images from undersampled dynamic MRI data. The L+S approach assumes that the dynamic MRI data, represented as a space-time matrix M, is a linear superposition of L and S components, where L represents highly spatially and temporally correlated elements, such as the image background, while S captures dynamic information that is sparse in an appropriate transform domain. This suggests that L+S might be suited for undersampled task or slow event-related fMRI acquisitions because the periodic nature of the BOLD signal is sparse in the temporal Fourier transform domain and slowly varying low-rank brain background signals, such as physiological noise and drift, will be predominantly low-rank. In this work, as a proof of concept, we exploit the L+S method for accelerating block-design fMRI using a 3D stack of spirals (SoS) acquisition where undersampling is performed in the k_z-t domain. We examined the feasibility of the L+S method to accurately separate temporally correlated brain background information in the L component while capturing periodic BOLD signals in the S component. We present results acquired in control human volunteers at 3T for both retrospective and prospectively acquired fMRI data for a visual activation block-design task. We show that a SoS fMRI acquisition with an acceleration of four and L+S reconstruction can achieve a brain coverage of 40 slices at 2mm isotropic resolution and 64 x 64 matrix size every 500ms.

Effect of confounding variables on hemodynamic response function estimation using averaging and deconvolution analysis: An event-related NIRS study

Slow and rapid event-related designs are used in fMRI and functional near-infrared spectroscopy (fNIRS) experiments to temporally characterize the brain hemodynamic response to discrete events. Conventional averaging (CA) and the deconvolution method (DM) are the two techniques commonly used to estimate the Hemodynamic Response Function (HRF) profile in event-related designs. In this study, we conducted a series of simulations using synthetic and real NIRS data to examine the effect of the main confounding factors, including event sequence timing parameters, different types of noise, signal-to-noise ratio (SNR), temporal autocorrelation and temporal filtering on the performance of these techniques in slow and rapid event-related designs. We also compared systematic errors in the estimates of the fitted HRF amplitude, latency and duration for both techniques. We further compared the performance of deconvolution methods based on Finite Impulse Response (FIR) basis functions and gamma basis sets. Our results demonstrate that DM was much less sensitive to confounding factors than CA. Event timing was the main parameter largely affecting the accuracy of CA. In slow event-related designs, deconvolution methods provided similar results to those obtained by CA. In rapid event-related designs, our results showed that DM outperformed CA for all SNR, especially above -5 dB regardless of the event sequence timing and the dynamics of background NIRS activity. Our results also show that periodic low-frequency systemic hemodynamic fluctuations as well as phase-locked noise can markedly obscure hemodynamic evoked responses. Temporal autocorrelation also affected the performance of both techniques by inducing distortions in the time profile of the estimated hemodynamic response with inflated t-statistics, especially at low SNRs. We also found that high-pass temporal filtering could substantially affect the performance of both techniques by removing the low-frequency components of HRF profiles. Our results emphasize the importance of characterization of event timing, background noise and SNR when estimating HRF profiles using CA and DM in event-related designs.

Multi-echo fMRI: A review of applications in fMRI denoising and analysis of BOLD signals

In recent years the field of fMRI research has enjoyed expanded technical abilities related to resolution, as well as use across many fields of brain research. At the same time, the field has also dealt with uncertainty related to many known and unknown effects of artifact in fMRI data. In this review we discuss an emerging fMRI technology, called multi-echo (ME)-fMRI, which focuses on improving the fidelity and interpretability of fMRI. Where the essential problem of standard single-echo fMRI is the indeterminacy of sources of signals, whether BOLD or artifact, this is not the case for ME-fMRI. By acquiring multiple echo images per slice, the ME approach allows T₂* decay to be modeled at every voxel at every time point. Since BOLD signals arise by changes in T₂* over time, an fMRI experiment sampling the T₂* signal decay can be analyzed to distinguish BOLD from artifact signal constituents. While the ME approach has a long history of use in theoretical and validation studies, modern MRI systems enable whole-brain multi-echo fMRI at high resolution. This review covers recent multi-echo fMRI acquisition methods, and the analysis steps for this data to make fMRI at once more principled, straightforward, and powerful. After a brief overview of history and theory, T₂* modeling and applications will be discussed. These applications include T₂* mapping and combining echoes from ME data to increase BOLD contrast and mitigate dropout artifacts. Next, the modeling of fMRI signal changes to detect signal origins in BOLD-related T₂* versus artifact-related S₀ changes will be reviewed. A focus is on the use of ME-fMRI data to extract and classify components from spatial ICA, called multi-echo ICA (ME-ICA). After describing how ME-fMRI and ME-ICA lead to a general model for analysis of fMRI signals, applications in animal and human imaging will be discussed. Applications include removing motion artifacts in resting state data at subject and group level. New imaging methods such as multi-band multi-echo fMRI and imaging at 7T are demonstrated throughout the review, and a practical analysis pipeline is described. The review culminates with evidence from recent studies of major boosts in statistical power from using multi-echo fMRI for detecting activation and connectivity in healthy individuals and patients with neuropsychiatric disease. In conclusion, the review shows evidence that the multi-echo approach expands the range of experiments that is practicable using fMRI. These findings suggest a compelling future role of the multi-echo approach in subject-level and clinical fMRI.