Improved sensitivity and microvascular weighting of 3T laminar fMRI with GE-BOLD using NORDIC and phase regression

The laminar pattern of proprioceptive activation in human primary motor cortex

The primary motor cortex (M1) is increasingly being recognized for its vital role in proprioceptive somatosensation. However, our current understanding of proprioceptive processing at the laminar scale is limited. Empirical findings in primates and rodents suggest a pronounced role of superficial cortical layers, but the involvement of deep layers has yet to be examined in humans. Submillimeter resolution functional magnetic resonance imaging (fMRI) has emerged in recent years, paving the way for studying layer-dependent activity in humans (laminar fMRI). In the present study, laminar fMRI was employed to investigate the influence of proprioceptive somatosensation on M1 deep layer activation using passive finger movements. Significant M1 deep layer activation was observed in response to proprioceptive stimulation across 10 healthy subjects using a vascular space occupancy (VASO)-sequence at 7 T. For further validation, two additional datasets were included which were obtained using a balanced steady-state free precession sequence with ultrahigh (0.3 mm) in-plane resolution, yielding converging results. These results were interpreted in the light of previous laminar fMRI studies and the active inference account of motor control. We propose that a considerable proportion of M1 deep layer activation is due to proprioceptive influence and that deep layers of M1 constitute a key component in proprioceptive circuits.

Effects of KCNQ potassium channel modulation on ventral tegmental area activity and connectivity in individuals with depression and anhedonia

Up to half of individuals with depression do not respond to first-line treatments, possibly due to a lack of treatment interventions informed by neurobiology. A novel therapeutic approach for depression has recently emerged from translational work targeting aberrant activity of ventral tegmental area (VTA) dopamine neurons via modulation of the KCNQ voltage-gated potassium channels. In this study, individuals with major depressive disorder (MDD) with elevated anhedonia were randomized to five weeks of the KCNQ channel opener, ezogabine (up to 900 mg/day) or placebo. Participants completed functional MRI during a monetary anticipation task and resting-state at baseline and at end-of-treatment. The clinical results were reported previously. Here, we examined VTA activity during monetary anticipation and resting-state functional connectivity between the VTA and the ventromedial prefrontal cortex (mesocortical pathway) and ventral striatum (mesolimbic pathway) at baseline and end-of-treatment. Results indicated a significant drug-by-time interaction in VTA activation during anticipation (F(1,34) = 4.36, p = 0.044), where VTA activation was reduced from pre-to-post ezogabine, compared to placebo. Mesocortical functional connectivity was also higher in depressed participants at baseline compared to a healthy control group (t(56) = 2.68, p = 0.01) and associated with VTA hyper-activity during task-based functional MRI at baseline (R = 0.352, p = 0.033). Mesocortical connectivity was also reduced from pre-to-post ezogabine, compared to placebo (significant drug-by-time interaction, F(1,33) = 4.317, p = 0.046). Together this translational work is consistent with preclinical findings highlighting VTA hyper-activity in depression, and suggesting a mechanism of action for KCNQ channel openers in normalizing this hyper-activity in individuals with both depression and anhedonia.

Functional magnetic resonance imaging in prurigo nodularis: A call to study neural sensitization phenomena

Prurigo nodularis is a chronic pruritic, inflammatory skin condition characterized by nodular skin lesions in a typical distribution pattern caused by various dermatologic and/or nondermatologic conditions. In recent years, significant advances have been made in the understanding of the cutaneous pathophysiology of prurigo nodularis, resulting in novel treatment options such as interleukin-4, -13, -17, and -31 or Janus kinase inhibitors. Many aspects of the neurophysiology are largely unknown, including the processing in the central structural and functional network involved in prurigo nodularis. Functional neuroimaging allows noninvasive assessment of brain function and structure. Due to its high spatial resolution and temporal precision, functional magnetic resonance imaging has proven to be a suitable method for exploring neural mechanisms and assessing pharmacologic effects in dermatologic research. In this systematic review, the current knowledge of functional magnetic resonance imaging in the context of prurigo nodularis and its centrally active treatment options is summarized.

Mapping curvature domains in human V4 using CBV-sensitive layer-fMRI at 3T

Introduction

A full understanding of how we see our world remains a fundamental research question in vision neuroscience. While topographic profiling has allowed us to identify different visual areas, the exact functional characteristics and organization of areas up in the visual hierarchy (beyond V1 & V2) is still debated. It is hypothesized that visual area V4 represents a vital intermediate stage of processing spatial and curvature information preceding object recognition. Advancements in magnetic resonance imaging hardware and acquisition techniques (e.g., non-BOLD functional MRI) now permits the capture of cortical layer-specific functional properties and organization of the human brain (including the visual system) at high precision.

Methods

Here, we use functional cerebral blood volume measures to study the modularity in how responses to contours (curvature) are organized within area V4 of the human brain. To achieve this at 3 Tesla (a clinically relevant field strength) we utilize optimized high-resolution 3D-Echo Planar Imaging (EPI) Vascular Space Occupancy (VASO) measurements.

Results

Data here provide the first evidence of curvature domains in human V4 that are consistent with previous findings from non-human primates. We show that VASO and BOLD tSNR maps for functional imaging align with high field equivalents, with robust time series of changes to visual stimuli measured across the visual cortex. V4 curvature preference maps for VASO show strong modular organization compared to BOLD imaging contrast. It is noted that BOLD has a much lower sensitivity (due to known venous vasculature weightings) and specificity to stimulus contrast. We show evidence that curvature domains persist across the cortical depth. The work advances our understanding of the role of mid-level area V4 in human processing of curvature and shape features.

Impact

Knowledge of how the functional architecture and hierarchical integration of local contours (curvature) contribute to formation of shapes can inform computational models of object recognition. Techniques described here allow for quantification of individual differences in functional architecture of mid-level visual areas to help drive a better understanding of how changes in functional brain organization relate to difference in visual perception.

Affective Visual Circuit Dysfunction in Trauma and Stress-Related Disorders

Posttraumatic stress disorder (PTSD) is widely recognized as involving disruption of core neurocircuitry that underlies processing, regulation, and response to threat. In particular, the prefrontal cortex-hippocampal-amygdala circuit is a major contributor to posttraumatic dysfunction. However, the functioning of core threat neurocircuitry is partially dependent on sensorial inputs, and previous research has demonstrated that dense, reciprocal connections exist between threat circuits and the ventral visual stream. Furthermore, emergent evidence suggests that trauma exposure and resultant PTSD symptoms are associated with altered structure and function of the ventral visual stream. In the current review, we discuss evidence that both threat and visual circuitry together are an integral part of PTSD pathogenesis. An overview of the relevance of visual processing to PTSD is discussed in the context of both basic and translational research, highlighting the impact of stress on affective visual circuitry. This review further synthesizes emergent literature to suggest potential timing-dependent effects of traumatic stress on threat and visual circuits that may contribute to PTSD development. We conclude with recommendations for future research to move the field toward a more complete understanding of PTSD neurobiology.

NORDIC denoising on VASO data

The use of submillimeter resolution functional magnetic resonance imaging (fMRI) is increasing in popularity due to the prospect of studying human brain activation non-invasively at the scale of cortical layers and columns. This method, known as laminar fMRI, is inherently signal-to-noise ratio (SNR)-limited, especially at lower field strengths, with the dominant noise source being of thermal origin. Furthermore, laminar fMRI is challenged with signal displacements due to draining vein effects in conventional gradient-echo blood oxygen level-dependent (BOLD) imaging contrasts. fMRI contrasts such as cerebral blood volume (CBV)-sensitive vascular space occupancy (VASO) sequences have the potential to mitigate draining vein effects. However, VASO comes along with another reduction in detection sensitivity. NOise Reduction with DIstribution Corrected (NORDIC) PCA (principal component analysis) is a denoising technique specifically aimed at suppressing thermal noise, which has proven useful for increasing the SNR of high-resolution functional data. While NORDIC has been examined for BOLD acquisitions, its application to VASO data has been limited, which was the focus of the present study. We present a preliminary analysis to evaluate NORDIC's capability to suppress thermal noise while preserving the VASO signal across a wide parameter space at 3T. For the data presented here, with a proper set of parameters, NORDIC reduced thermal noise with minimal bias on the underlying signal and preserved spatial resolution. Denoising performance was found to vary with different implementation strategies and parameter choices, for which we provide recommendations. We conclude that when applied properly, NORDIC has the potential to overcome the sensitivity limitations of laminar-specific VASO fMRI. Since very few groups currently have 3T VASO data, by sharing our analysis and code, we can compile and compare the effects of NORDIC across a broader range of acquisition parameters and study designs. Such a communal effort will help develop robust recommendations that will increase the utility of laminar fMRI at lower field strengths.

Enabling brain-wide mapping of layer-specific functional connectivity at 3T via layer-dependent fMRI with draining-vein suppression

Layer-dependent functional magnetic resonance imaging (fMRI) is a promising yet challenging approach for investigating layer-specific functional connectivity (FC). Achieving a brain-wide mapping of layer-specific FC requires several technical advancements, including sub-millimeter spatial resolution, sufficient temporal resolution, functional sensitivity, global brain coverage, and high spatial specificity. Although gradient echo (GE)-based echo planar imaging (EPI) is commonly used for rapid fMRI acquisition, it faces significant challenges due to the draining-vein contamination. In this study, we addressed these limitations by integrating velocity-nulling (VN) gradients into a GE-BOLD fMRI sequence to suppress vascular signals from the vessels with fast-flowing velocity. The extravascular contamination from pial veins was mitigated using a GE-EPI sequence at 3T rather than 7T, combined with phase regression methods. Additionally, we incorporated advanced techniques, including simultaneous multislice (SMS) acceleration and NOise Reduction with DIstribution Corrected principal component analysis (NORDIC PCA) denoising, to improve temporal resolution, spatial coverage, and signal sensitivity. This resulted in a VN fMRI sequence with 0.9-mm isotropic spatial resolution, a repetition time (TR) of 4 seconds, and brain-wide coverage. The VN gradient strength was determined based on results from a button-pressing task. Using resting-state data, we validated layer-specific FC through seed-based analyses, identifying distinct connectivity patterns in the superficial and deep layers of the primary motor cortex (M1), with significant inter-layer differences. Further analyses with a seed in the primary sensory cortex (S1) demonstrated the reliability of the method. Brain-wide layer-dependent FC analyses yielded results consistent with prior literature, reinforcing the efficacy of VN fMRI in resolving layer-specific functional connectivity. Given the widespread availability of 3T scanners, this technical advancement has the potential for significant impact across multiple domains of neuroscience research.

Hemispheric divergence of interoceptive processing across psychiatric disorders

Interactions between top-down attention and bottom-up visceral inputs are assumed to produce conscious perceptions of interoceptive states, and while each process has been independently associated with aberrant interoceptive symptomatology in psychiatric disorders, the neural substrates of this interface are unknown. We conducted a preregistered functional neuroimaging study of 46 individuals with anxiety, depression, and/or eating disorders (ADE) and 46 propensity-matched healthy comparisons (HC), comparing their neural activity across two interoceptive tasks differentially recruiting top-down or bottom-up processing within the same scan session. During an interoceptive attention task, top-down attention was voluntarily directed towards cardiorespiratory or visual signals. In contrast, during an interoceptive perturbation task, intravenous infusions of isoproterenol (a peripherally-acting beta-adrenergic receptor agonist) were administered in a double-blinded and placebo-controlled fashion to drive bottom-up cardiorespiratory sensations. Across both tasks, neural activation converged upon the insular cortex, localizing within the granular and ventral dysgranular subregions bilaterally. However, contrasting hemispheric differences emerged, with the ADE group exhibiting (relative to HCs) an asymmetric pattern of overlap in the left insula, with increased or decreased proportions of co-activated voxels within the left or right dysgranular insula, respectively. The ADE group also showed less agranular anterior insula activation during periods of bodily uncertainty (i.e. when anticipating possible isoproterenol-induced changes that never arrived). Finally, post-task changes in insula functional connectivity were associated with anxiety and depression severity. These findings confirm the dysgranular mid-insula as a key cortical interface where attention and prediction meet real-time bodily inputs, especially during heightened awareness of interoceptive states. Furthermore, the dysgranular mid-insula may indeed be a 'locus of disruption' for psychiatric disorders.

NOise Reduction with DIstribution Corrected (NORDIC) principal component analysis improves brain activity detection across rodent and human functional MRI contexts

NOise Reduction with DIstribution Corrected (NORDIC) principal component analysis (PCA) has been shown to selectively suppress thermal noise and improve the temporal signal-to-noise ratio (tSNR) in human functional magnetic resonance imaging (fMRI). However, the feasibility to improve data quality for rodent fMRI using NORDIC PCA remains uncertain. NORDIC PCA may also be particularly beneficial for improving topological brain mapping, as conventional mapping requires precise spatiotemporal signals from large datasets (ideally ~1 hour acquisition) for individual representations. In this study, we evaluated the effects of NORDIC PCA compared with "Standard" processing in various rodent fMRI contexts that range from task-evoked optogenetic fMRI to resting-state fMRI. We also evaluated the effects of NORDIC PCA on human resting-state and retinotopic mapping fMRI via population receptive field (pRF) modeling. In rodent optogenetic fMRI, apart from doubling the tSNR, NORDIC PCA resulted in a larger number of activated voxels and a significant decrease in the variance of evoked brain responses without altering brain morphology. In rodent resting-state fMRI, we found that NORDIC PCA induced a nearly threefold increase in tSNR and preserved task-free relative cerebrovascular reactivity (rCVR) across cortical depth. NORDIC PCA further improved the detection of TGN020-induced aquaporin-4 inhibition on rCVR compared with Standard processing without NORDIC PCA. NORDIC PCA also increased the tSNR for both human resting-state and pRF fMRI, and for the latter also increased activation cluster sizes while retaining retinotopic organization. This suggests that NORDIC PCA preserves the spatiotemporal precision of fMRI signals needed for pRF analysis, and effectively captures small activity changes with high sensitivity. Taken together, these results broadly demonstrate the value of NORDIC PCA for the enhanced detection of neural dynamics across various rodent and human fMRI contexts. This can in turn play an important role in improving fMRI image quality and sensitivity for translational and preclinical neuroimaging research.

Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC

Functional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise-the dominant contributing noise component in high-resolution fMRI. NOise Reduction with DIstribution Corrected Principal Component Analysis (NORDIC PCA) is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. While investigating auditory functional responses poses unique challenges, we anticipated NORDIC to have a positive impact on the data on the basis of previous applications. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we did observe a reduction in the average response amplitude (percent signal change) within regions of interest, which may suggest that a portion of the signal of interest, which could not be distinguished from general i.i.d. noise, was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high-resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.

Optimization and validation of multi-echo, multi-contrast SAGE acquisition in fMRI

The purpose of this study was to optimize and validate a multi-contrast, multi-echo fMRI method using a combined spin- and gradient-echo (SAGE) acquisition. It was hypothesized that SAGE-based blood oxygen level-dependent (BOLD) functional MRI (fMRI) will improve sensitivity and spatial specificity while reducing signal dropout. SAGE-fMRI data were acquired with five echoes (2 gradient-echoes, 2 asymmetric spin-echoes, and 1 spin-echo) across 12 protocols with varying acceleration factors, and temporal SNR (tSNR) was assessed. The optimized protocol was then implemented in working memory and vision tasks in 15 healthy subjects. Task-based analysis was performed using individual echoes, quantitative dynamic relaxation times T2 * and T2, and echo time-dependent weighted combinations of dynamic signals. These methods were compared to determine the optimal analysis method for SAGE-fMRI. Implementation of a multiband factor of 2 and sensitivity encoding (SENSE) factor of 2.5 yielded adequate spatiotemporal resolution while minimizing artifacts and loss in tSNR. Higher BOLD contrast-to-noise ratio (CNR) and tSNR were observed for SAGE-fMRI relative to single-echo fMRI, especially in regions with large susceptibility effects and for T2-dominant analyses. Using a working memory task, the extent of activation was highest with T2 *-weighting, while smaller clusters were observed with quantitative T2 * and T2. SAGE-fMRI couples the high BOLD sensitivity from multi-gradient-echo acquisitions with improved spatial localization from spin-echo acquisitions, providing two contrasts for analysis. SAGE-fMRI provides substantial advantages, including improving CNR and tSNR for more accurate analysis.

Hemispheric divergence of interoceptive processing across psychiatric disorders

Interactions between top-down attention and bottom-up visceral inputs are assumed to produce conscious perceptions of interoceptive states, and while each process has been independently associated with aberrant interoceptive symptomatology in psychiatric disorders, the neural substrates of this interface are unknown. We conducted a preregistered functional neuroimaging study of 46 individuals with anxiety, depression, and/or eating disorders (ADE) and 46 propensity-matched healthy comparisons (HC), comparing their neural activity across two interoceptive tasks differentially recruiting top-down or bottom-up processing within the same scan session. During an interoceptive attention task, top-down attention was voluntarily directed towards cardiorespiratory or visual signals, whereas during an interoceptive perturbation task, intravenous infusions of isoproterenol (a peripherally-acting beta-adrenergic receptor agonist) were administered in a double-blinded and placebo-controlled fashion to drive bottom-up cardiorespiratory sensations. Across both tasks, neural activation converged upon the insular cortex, localizing within the granular and ventral dysgranular subregions bilaterally. However, contrasting hemispheric differences emerged, with the ADE group exhibiting (relative to HCs) an asymmetric pattern of overlap in the left insula, with increased or decreased proportions of co-activated voxels within the left or right dysgranular insula, respectively. The ADE group also showed less agranular anterior insula activation during periods of bodily uncertainty (i.e., when anticipating possible isoproterenol-induced changes that never arrived). Finally, post-task changes in insula functional connectivity were associated with anxiety and depression severity. These findings confirm the dysgranular mid-insula as a key cortical interface where attention and prediction meet real-time bodily inputs, especially during heightened awareness of interoceptive states. Further, the dysgranular mid-insula may indeed be a "locus of disruption" for psychiatric disorders.

Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC

Functional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise - the dominant contributing noise component in high resolution fMRI. NORDIC PCA is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. As investigating auditory functional responses poses unique challenges, we anticipated that the benefit of this technique would be especially pronounced. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we also observed a reduction in the average response amplitude (percent signal), which may suggest that a small amount of signal was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.

XCP-D: A Robust Pipeline for the post-processing of fMRI data

Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.

Microvascular Specificity of Spin Echo BOLD fMRI: Impact of EPI Echo Train Length

A spatially specific fMRI acquisition requires specificity to the microvasculature that serves active neuronal sites. Macrovascular contributions will reduce the microvascular specificity but can be reduced by using spin echo (SE) sequences that use a π pulse to refocus static field inhomogeneities near large veins. The microvascular specificity of a SE-echo planar imaging (SE-EPI) scan depends on the echo train length (ETL)-duration, but the dependence is not well-characterized in humans at 7T. To determine how microvascular-specific SE-EPI BOLD is in humans at 7T, we developed a Monte Carlo voxel model that computes the signal of a proton ensemble residing in a vasculature subjected to a SE-EPI pulse sequence. We characterized the ETL-duration dependence of the microvascular specificity by simulating the BOLD signal as a function of ETL, the range adhering to experimentally realistic readouts. We performed a validation experiment for our simulation observations, in which we acquired a set of SE-EPI BOLD time series with varying ETL during a hyperoxic gas challenge. Both our simulations and measurements show an increase in macrovascular contamination as a function of ETL, with an increase of 30% according to our simulation and 60% according to our validation experiment between the shortest and longest ETL durations (23.1 - 49.7 ms). We conclude that the microvascular specificity decreases heavily with increasing ETL-durations. We recommend reducing the ETL-duration as much as possible to minimize macrovascular contamination in SE-EPI BOLD experiments. We additionally recommend scanning at high resolutions to minimize partial volume effects with CSF. CSF voxels show a large BOLD response, which can be attributed to both the presence of large veins (high blood volume) and molecular oxygen-induced T1-shortening (significant in a hyperoxia experiment). The magnified BOLD signal in a GM-CSF partial volume voxel reduces the desired microvascular specificity and, therefore, will hinder the interpretation of functional MRI activation patterns.