Accurate registration of Functional Magnetic Resonance Imaging (FMRI) T2-weighted volumes to same-subject high-resolution T1-weighted structural volumes is important for Blood Oxygenation Level Dependent (BOLD) FMRI and crucial for applications such as cortical surface-based analyses and pre-surgical planning. Such registration is generally implemented by minimizing a cost functional, which measures the mismatch between two image volumes over the group of proper affine transformations. Widely used cost functionals, such as mutual information (MI) and correlation ratio (CR), appear to yield decent alignments when visually judged by matching outer brain contours. However, close inspection reveals that internal brain structures are often significantly misaligned. Poor registration is most evident in the ventricles and sulcal folds, where CSF is concentrated. This observation motivated our development of an improved modality-specific cost functional which uses a weighted local Pearson coefficient (LPC) to align T2- and T1-weighted images. In the absence of an alignment gold standard, we used three human observers blinded to registration method to provide an independent assessment of the quality of the registration for each cost functional. We found that LPC performed significantly better (p<0.001) than generic cost functionals including MI and CR. Generic cost functionals were very often not minimal near the best alignment, thereby suggesting that optimization is not the cause of their failure. Lastly, we emphasize the importance of precise visual inspection of alignment quality and present an automated method for generating composite images that help capture errors of misalignment.

The field of cognitive neuroscience is weighing evidence about whether to move from standard field strength to ultra-high field (UHF). The present study contributes to the evidence by comparing a cognitive neuroscience paradigm at 3 Tesla (3T) and 7 Tesla (7T). The goal was to test and demonstrate the practical effects of field strength on a standard GO/NOGO task using accessible preprocessing and analysis tools. Two independent matched healthy samples (N = 31 each) were analyzed at 3T and 7T. Results show gains at 7T in statistical strength, the detection of smaller effects and group-level power. With an increased availability of UHF scanners, these gains may be exploited by cognitive neuroscientists and other neuroimaging researchers to develop more efficient or comprehensive experimental designs and, given the same sample size, achieve greater statistical power at 7T.

Recently, resting-state functional magnetic resonance imaging (R-fMRI) has emerged as a powerful tool for investigating functional brain organization changes in a variety of neurological and psychiatric disorders. However, the current techniques may need further development to better define the reference brain networks for quantifying the functional connectivity differences between normal and diseased subject groups. In this study, we introduced a new clustering-based method that can clearly define the reference clusters. By employing group difference information to guide the clustering, the voxels within the reference clusters will have homogeneous functional connectivity changes above predefined levels. This method identified functional clusters that were significantly different between the amnestic mild cognitively impaired (aMCI) and age-matched cognitively normal (CN) subjects. The results indicated that the distribution of the clusters and their functionally disconnected regions resembled the altered memory network regions previously identified in task fMRI studies. In conclusion, the new clustering method provides an advanced approach for studying functional brain organization changes associated with brain diseases.

Neuroimaging faces the daunting challenge of multiple testing - an instance of multiplicity - that is associated with two other issues to some extent: low inference efficiency and poor reproducibility. Typically, the same statistical model is applied to each spatial unit independently in the approach of massively univariate modeling. In dealing with multiplicity, the general strategy employed in the field is the same regardless of the specifics: trust the local "unbiased" effect estimates while adjusting the extent of statistical evidence at the global level. However, in this approach, modeling efficiency is compromised because each spatial unit (e.g., voxel, region, matrix element) is treated as an isolated and independent entity during massively univariate modeling. In addition, the required step of multiple testing "correction" by taking into consideration spatial relatedness, or neighborhood leverage, can only partly recoup statistical efficiency, resulting in potentially excessive penalization as well as arbitrariness due to thresholding procedures. Moreover, the assigned statistical evidence at the global level heavily relies on the data space (whole brain or a small volume). The present paper reviews how Stein's paradox (1956) motivates a Bayesian multilevel (BML) approach that, rather than fighting multiplicity, embraces it to our advantage through a global calibration process among spatial units. Global calibration is accomplished via a Gaussian distribution for the cross-region effects whose properties are not a priori specified, but a posteriori determined by the data at hand through the BML model. Our framework therefore incorporates multiplicity as integral to the modeling structure, not a separate correction step. By turning multiplicity into a strength, we aim to achieve five goals: 1) improve the model efficiency with a higher predictive accuracy, 2) control the errors of incorrect magnitude and incorrect sign, 3) validate each model relative to competing candidates, 4) reduce the reliance and sensitivity on the choice of data space, and 5) encourage full results reporting. Our modeling proposal reverberates with recent proposals to eliminate the dichotomization of statistical evidence ("significant" vs. "non-significant"), to improve the interpretability of study findings, as well as to promote reporting the full gamut of results (not only "significant" ones), thereby enhancing research transparency and reproducibility.

Abnormalities of functional connectivity in the default mode network (DMN) recently have been reported in patients with amnestic mild cognitive impairment (aMCI), Alzheimer's disease (AD) or other psychiatric diseases. As such, these abnormalities may be epiphenomena instead of playing a causal role in AD progression. To date, few studies have investigated specific brain networks, which extend beyond the DMN involved in the early AD stages, especially in aMCI. The insula is one site affected by early pathological changes in AD and is a crucial hub of the human brain networks. Currently, we explored the contribution of the insula networks to cognitive performance in aMCI patients. Thirty aMCI and 26 cognitively normal (CN) subjects participated in this study. Intrinsic connectivity of the insula networks was measured, using the resting-state functional connectivity fMRI approach. We examined the differential connectivity of insula networks between groups, and the neural correlation between the altered insula networks connectivity and the cognitive performance in aMCI patients and CN subjects, respectively. Insula subregional volumes were also investigated. AMCI subjects, when compared to CN subjects, showed significantly reduced right posterior insula volumes, cognitive deficits and disrupted intrinsic connectivity of the insula networks. Specifically, decreased intrinsic connectivity was primarily located in the frontal-parietal network and the cingulo-opercular network, including the anterior prefrontal cortex (aPFC), anterior cingulate cortex, operculum, inferior parietal cortex and precuneus. Increased intrinsic connectivity was primarily situated in the visual-auditory pathway, which included the posterior superior temporal gyrus and middle occipital gyrus. Conjunction analysis was performed; and significantly decreased intrinsic connectivity in the overlapping regions of the anterior and posterior insula networks, including the bilateral aPFC, left dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, and anterior temporal pole was found. Furthermore, the disrupted intrinsic connectivity was associated with episodic memory (EM) deficits in the aMCI patients and not in the CN subjects. These findings demonstrated that the functional integration of the insula networks plays an important role in the EM process. They provided new insight into the neural mechanism underlying the memory deficits in aMCI patients.

All neuroimaging packages can handle group analysis with t-tests or general linear modeling (GLM). However, they are quite hamstrung when there are multiple within-subject factors or when quantitative covariates are involved in the presence of a within-subject factor. In addition, sphericity is typically assumed for the variance-covariance structure when there are more than two levels in a within-subject factor. To overcome such limitations in the traditional AN(C)OVA and GLM, we adopt a multivariate modeling (MVM) approach to analyzing neuroimaging data at the group level with the following advantages: a) there is no limit on the number of factors as long as sample sizes are deemed appropriate; b) quantitative covariates can be analyzed together with within-subject factors; c) when a within-subject factor is involved, three testing methodologies are provided: traditional univariate testing (UVT) with sphericity assumption (UVT-UC) and with correction when the assumption is violated (UVT-SC), and within-subject multivariate testing (MVT-WS); d) to correct for sphericity violation at the voxel level, we propose a hybrid testing (HT) approach that achieves equal or higher power via combining traditional sphericity correction methods (Greenhouse-Geisser and Huynh-Feldt) with MVT-WS. To validate the MVM methodology, we performed simulations to assess the controllability for false positives and power achievement. A real FMRI dataset was analyzed to demonstrate the capability of the MVM approach. The methodology has been implemented into an open source program 3dMVM in AFNI, and all the statistical tests can be performed through symbolic coding with variable names instead of the tedious process of dummy coding. Our data indicates that the severity of sphericity violation varies substantially across brain regions. The differences among various modeling methodologies were addressed through direct comparisons between the MVM approach and some of the GLM implementations in the field, and the following two issues were raised: a) the improper formulation of test statistics in some univariate GLM implementations when a within-subject factor is involved in a data structure with two or more factors, and b) the unjustified presumption of uniform sphericity violation and the practice of estimating the variance-covariance structure through pooling across brain regions.

Considerable work has demonstrated that inferior frontal gyrus (IFG), anterior insula cortex (AIC) and the supplementary motor area (SMA) are responsive during inhibitory control tasks. However, there is disagreement as to whether this relates to response selection/ inhibition or attentional processing. The current study investigates this by using a Go/No-go task with a factorial design. We observed that both left IFG and dorsal pre-SMA were responsive to no-go cues irrespective of cue frequency. This suggests a role for both in the inhibition of motor responses. Generalized psychophysiological interaction (gPPI) analyses suggest that inferior frontal gyrus may implement this function through interaction with basal ganglia and by suppressing the visual representation of cues associated with no-go responses. Anterior insula cortex and a more ventral portion of pre-SMA showed greater responsiveness to low frequency relative to higher frequency stimuli, irrespective of response type. This may reflect the hypothesized role of anterior insula cortex in marking low frequency items for additional processing (cf. Menon and Uddin, 2010). Consistent with this, the gPPI analysis revealed significantly greater anterior insula cortex connectivity with visual cortex in response to low relative to high frequency cues.

Advanced neuroimaging studies have identified brain correlates of pathological impulsivity in a variety of neuropsychiatric disorders. However, whether and how these spatially separate and functionally integrated neural correlates collectively contribute to aberrant impulsive behaviors remains unclear. Building on recent progress in neuroeconomics toward determining a biological account of human behaviors, we employed resting-state functional MRI to characterize the nature of the links between these neural correlates and to investigate their impact on impulsivity. We demonstrated that through functional connectivity with the ventral medial prefrontal cortex, the δ-network (regions of the executive control system, such as the dorsolateral prefrontal cortex) and the β-network (regions of the reward system involved in the mesocorticolimbic pathway), jointly influence impulsivity measured by the Barratt impulsiveness scale scores. In control nondrug-using subjects, the functional link between the β- and δ-networks is balanced, and the δ-network competitively controls impulsivity. However, in abstinent heroin-dependent subjects, the link is imbalanced, with stronger β-network connectivity and weaker δ-network connectivity. The imbalanced link is associated with impulsivity, indicating that the β- and δ-networks may mutually reinforce each other in abstinent heroin-dependent subjects. These findings of an aberrant link between the β- and δ-networks in abstinent heroin-dependent subjects may shed light on the mechanism of aberrant behaviors of drug addiction and may serve as an endophenotype to mark individual subjects' self-control capacity.

Haptic object perception begins with continuous exploratory contact, and the human brain needs to accumulate sensory information continuously over time. However, it is still unclear how the primary sensorimotor cortex (PSC) interacts with these higher-level regions during haptic exploration over time. This functional magnetic resonance imaging (fMRI) study investigates time-dependent haptic object processing by examining brain activity during haptic 3D curve and roughness estimations. For this experiment, we designed sixteen haptic stimuli (4 kinds of curves × 4 varieties of roughness) for the haptic curve and roughness estimation tasks. Twenty participants were asked to move their right index and middle fingers along the surface twice and to estimate one of the two features-roughness or curvature-depending on the task instruction. We found that the brain activity in several higher-level regions (e.g., the bilateral posterior parietal cortex) linearly increased as the number of curves increased during the haptic exploration phase. Surprisingly, we found that the contralateral PSC was parametrically modulated by the number of curves only during the late exploration phase but not during the early exploration phase. In contrast, we found no similar parametric modulation activity patterns during the haptic roughness estimation task in either the contralateral PSC or in higher-level regions. Thus, our findings suggest that haptic 3D object perception is processed across the cortical hierarchy, whereas the contralateral PSC interacts with other higher-level regions across time in a manner that is dependent upon the features of the object.

Resting-state functional connectivity (rsFC) between brain regions has been used for studying training-related changes in brain function during the offline period of skill learning. However, it is difficult to infer whether the observed training-related changes in rsFC measured between two scans occur as a consequence of task performance, whether they are specific to a given task, or whether they reflect confounding factors such as diurnal fluctuations in brain physiology that impact the MRI signal. Here, we sought to elucidate whether task-specific changes in rsFC are dissociable from time-of-day related changes by evaluating rsFC changes after participants were provided training in either a visuospatial task or a motor sequence task compared to a non-training condition. Given the nature of the tasks, we focused on changes in rsFC of the hippocampal and sensorimotor cortices after short-term training, while controlling for the effect of time-of-day. We also related the change in rsFC of task-relevant brain regions to performance improvement in each task. Our results demonstrate that, even in the absence of any experimental manipulation, significant changes in rsFC can be detected between two resting state functional MRI scans performed just a few hours apart, suggesting time-of-day has a significant impact on rsFC. However, by estimating the magnitude of the time-of-day effect, our findings also suggest that task-specific changes in rsFC can be dissociated from the changes attributed to time-of-day. Taken together, our results show that rsFC can provide insights about training-related changes in brain function during the offline period of skill learning. However, demonstrating the specificity of the changes in rsFC to a given task requires a rigorous experimental design that includes multiple active and passive control conditions, and robust behavioral measures.

Performing a BOLD functional MRI (fMRI) acquisition during breath-hold (BH) tasks is a non-invasive, robust method to estimate cerebrovascular reactivity (CVR). However, movement and breathing-related artefacts caused by the BH can substantially hinder CVR estimates due to their high temporal collinearity with the effect of interest, and attention has to be paid when choosing which analysis model should be applied to the data. In this study, we evaluate the performance of multiple analysis strategies based on lagged general linear models applied on multi-echo BOLD fMRI data, acquired in ten subjects performing a BH task during ten sessions, to obtain subject-specific CVR and haemodynamic lag estimates. The evaluated approaches range from conventional regression models, i.e. including drifts and motion timecourses as nuisance regressors, applied on single-echo or optimally-combined data, to more complex models including regressors obtained from multi-echo independent component analysis with different grades of orthogonalization in order to preserve the effect of interest, i.e. the CVR. We compare these models in terms of their ability to make signal intensity changes independent from motion, as well as the reliability as measured by voxelwise intraclass correlation coefficients of both CVR and lag maps over time. Our results reveal that a conservative independent component analysis model applied on the optimally-combined multi-echo fMRI signal offers the largest reduction of motion-related effects in the signal, while yielding reliable CVR amplitude and lag estimates, although a conventional regression model applied on the optimally-combined data results in similar estimates. This work demonstrates the usefulness of multi-echo based fMRI acquisitions and independent component analysis denoising for precision mapping of CVR in single subjects based on BH paradigms, fostering its potential as a clinically-viable neuroimaging tool for individual patients. It also proves that the way in which data-driven regressors should be incorporated in the analysis model is not straight-forward due to their complex interaction with the BH-induced BOLD response.

The concept of test-retest reliability indexes the consistency of a measurement across time. High reliability is critical for any scientific study, but specifically for the study of individual differences. Evidence of poor reliability of commonly used behavioral and functional neuroimaging tasks is mounting. Reports on low reliability of task-based fMRI have called into question the adequacy of using even the most common, well-characterized cognitive tasks with robust population-level effects, to measure individual differences. Here, we lay out a hierarchical framework that estimates reliability as a correlation divorced from trial-level variability, and show that reliability tends to be underestimated under the conventional intraclass correlation framework through summary statistics based on condition-level modeling. In addition, we examine how reliability estimation between the two statistical frameworks diverges and assess how different factors (e.g., trial and subject sample sizes, relative magnitude of cross-trial variability) impact reliability estimates. As empirical data indicate that cross-trial variability is large in most tasks, this work highlights that a large number of trials (e.g., greater than 100) may be required to achieve precise reliability estimates. We reference the tools TRR and 3dLMEr for the community to apply trial-level models to behavior and neuroimaging data and discuss how to make these new measurements most useful for future studies.