Cortical depth dependence of the BOLD initial dip and poststimulus undershoot in human visual cortex at 7 Tesla

The temporal specificity of BOLD fMRI is systematically related to anatomical and vascular features of the human brain

The ability to detect fast responses with functional MRI depends on the speed of hemodynamic responses to neural activity, because hemodynamic responses act as a temporal low-pass filter which blurs rapid changes. However, the shape and timing of hemodynamic responses are highly variable across the brain and across stimuli. This heterogeneity of responses implies that the temporal specificity of fMRI signals, or the ability of fMRI to preserve fast information, could also vary substantially across the cortex. In this work we investigated how local differences in hemodynamic response timing affect the temporal specificity of fMRI. We used ultra-high field (7T) fMRI at high spatiotemporal resolution, studying the primary visual cortex (V1) as a model area for investigation. We used visual stimuli oscillating at slow and fast frequencies to probe the temporal specificity of individual voxels. As expected, we identified substantial variability in temporal specificity, with some voxels preserving their responses to fast neural activity more effectively than others. We investigated which voxels had the highest temporal specificity, and tested whether voxel timing was related to anatomical and vascular features. We found that low temporal specificity is only weakly explained by the presence of large veins or cerebral cortical depth. Notably, however, temporal specificity depended strongly on a voxel's position along the anterior-posterior anatomical axis of V1, with voxels within the calcarine sulcus being capable of preserving close to 25% of their amplitude as the frequency of stimulation increased from 0.05Hz to 0.20Hz, and voxels nearest to the occipital pole preserving less than 18%. These results indicate that detection biases in high-resolution fMRI will depend on the anatomical and vascular features of the area being imaged, and that these biases will differ depending on the timing of the underlying neuronal activity. While we attribute this variance primarily to hemodynamic effects, neuronal nonlinearities may also influence response timing. Importantly, this spatial heterogeneity of temporal specificity suggests that it could be exploited to achieve higher specificity in some locations, and that tailored data analysis strategies may help improve the detection and interpretation of fast fMRI responses.

The contribution of the vascular architecture and cerebrovascular reactivity to the BOLD signal formation across cortical depth

Assessment of neuronal activity using blood oxygenation level-dependent (BOLD) is confounded by how the cerebrovascular architecture modulates hemodynamic responses. To understand brain function at the laminar level, it is crucial to distinguish neuronal signal contributions from those determined by the cortical vascular organization. Therefore, our aim was to investigate the purely vascular contribution in the BOLD signal by using vasoactive stimuli and compare that with neuronal-induced BOLD responses from a visual task. To do so, we estimated the hemodynamic response function (HRF) across cortical depth following brief visual stimulations under different conditions using ultrahigh-field (7 Tesla) functional (f)MRI. We acquired gradient-echo (GE)-echo-planar-imaging (EPI) BOLD, containing contributions from all vessel sizes, and spin-echo (SE)-EPI BOLD for which signal changes predominately originate from microvessels, to distinguish signal weighting from different vascular compartments. Non-neuronal hemodynamic changes were induced by hypercapnia and hyperoxia to estimate cerebrovascular reactivity and venous cerebral blood volume ( C B V v O 2 ). Results show that increases in GE HRF amplitude from deeper to superficial layers coincided with increased macrovascular C B V v O 2 . C B V v O 2 -normalized GE-HRF amplitudes yielded similar cortical depth profiles as SE, thereby possibly improving specificity to neuronal activation. For GE BOLD, faster onset time and shorter time-to-peak were observed toward the deeper layers. Hypercapnia reduced the amplitude of visual stimulus-induced signal responses as denoted by lower GE-HRF amplitudes and longer time-to-peak. In contrast, the SE-HRF amplitude was unaffected by hypercapnia, suggesting that these responses reflect predominantly neurovascular processes that are less contaminated by macrovascular signal contributions.

Layer-fMRI VASO with short stimuli and event-related designs at 7 T

Layers and columns are the dominant processing units in the human (neo)cortex at the mesoscopic scale. While the blood oxygenation dependent (BOLD) signal has a high detection sensitivity, it is biased towards unwanted signals from large draining veins at the cortical surface. The additional fMRI contrast of vascular space occupancy (VASO) has the potential to augment the neuroscientific interpretability of layer-fMRI results by means of capturing complementary information of locally specific changes in cerebral blood volume (CBV). Specifically, VASO is not subject to unwanted sensitivity amplifications of large draining veins. Because of constrained sampling efficiency, it has been mainly applied in combination with efficient block task designs and long trial durations. However, to study cognitive processes in neuroscientific contexts, or probe vascular reactivity, short stimulation periods are often necessary. Here, we developed a VASO acquisition procedure with a short acquisition period and sub-millimeter resolution. During visual event-related stimulation, we show reliable responses in visual cortices within a reasonable number of trials (∼20). Furthermore, the short TR and high spatial specificity of our VASO implementation enabled us to show differences in laminar reactivity and onset times. Finally, we explore the generalizability to a different stimulus modality (somatosensation). With this, we showed that CBV-sensitive VASO provides the means to capture layer-specific haemodynamic responses with high spatio-temporal resolution and is able to be used with event-related paradigms.

Resting-state fMRI signals contain spectral signatures of local hemodynamic response timing

Functional magnetic resonance imaging (fMRI) has proven to be a powerful tool for noninvasively measuring human brain activity; yet, thus far, fMRI has been relatively limited in its temporal resolution. A key challenge is understanding the relationship between neural activity and the blood-oxygenation-level-dependent (BOLD) signal obtained from fMRI, generally modeled by the hemodynamic response function (HRF). The timing of the HRF varies across the brain and individuals, confounding our ability to make inferences about the timing of the underlying neural processes. Here, we show that resting-state fMRI signals contain information about HRF temporal dynamics that can be leveraged to understand and characterize variations in HRF timing across both cortical and subcortical regions. We found that the frequency spectrum of resting-state fMRI signals significantly differs between voxels with fast versus slow HRFs in human visual cortex. These spectral differences extended to subcortex as well, revealing significantly faster hemodynamic timing in the lateral geniculate nucleus of the thalamus. Ultimately, our results demonstrate that the temporal properties of the HRF impact the spectral content of resting-state fMRI signals and enable voxel-wise characterization of relative hemodynamic response timing. Furthermore, our results show that caution should be used in studies of resting-state fMRI spectral properties, because differences in fMRI frequency content can arise from purely vascular origins. This finding provides new insight into the temporal properties of fMRI signals across voxels, which is crucial for accurate fMRI analyses, and enhances the ability of fast fMRI to identify and track fast neural dynamics.

An Isolated CNN Architecture for Classification of Finger-Tapping Tasks Using Initial Dip Images: A Functional Near-Infrared Spectroscopy Study

This work investigates the classification of finger-tapping task images constructed for the initial dip duration of hemodynamics (HR) associated with the small brain area of the left motor cortex using functional near-infrared spectroscopy (fNIRS). Different layers (i.e., 16-layers, 19-layers, 22-layers, and 25-layers) of isolated convolutional neural network (CNN) designed from scratch are tested to classify the right-hand thumb and little finger-tapping tasks. Functional t-maps of finger-tapping tasks (thumb, little) were constructed for various durations (0.5 to 4 s with a uniform interval of 0.5 s) for the initial dip duration using a three gamma functions-based designed HR function. The results show that the 22-layered isolated CNN model yielded the highest classification accuracy of 89.2% with less complexity in classifying the functional t-maps of thumb and little fingers associated with the same small brain area using the initial dip. The results further demonstrated that the active brain area of the two tapping tasks from the same small brain area are highly different and well classified using functional t-maps of the initial dip (0.5 to 4 s) compared to functional t-maps generated for delayed HR (14 s). This study shows that the images constructed for initial dip duration can be helpful in the future for fNIRS-based diagnosis or cortical analysis of abnormal cerebral oxygen exchange in patients.

The hemodynamic initial-dip consists of both volumetric and oxymetric changes reflecting localized spiking activity

The initial-dip is a transient decrease frequently observed in functional neuroimaging signals, immediately after stimulus onset, believed to originate from a rise in deoxy-hemoglobin (HbR) caused by local neural activity. It has been shown to be more spatially specific than the hemodynamic response, and is believed to represent focal neuronal activity. However, despite being observed in various neuroimaging modalities (such as fMRI, fNIRS, etc), its origins are disputed, and its precise neuronal correlates are unknown. Here we show that the initial-dip is dominated by a decrease in total-hemoglobin (HbT). We also find a biphasic response in deoxy-Hb (HbR), with an early decrease and later rebound. Both the HbT-dip and HbR-rebound were strongly correlated to highly localized spiking activity. However, HbT decreases were always large enough to counter the spiking-induced increase in HbR. We find that the HbT-dip counters spiking induced HbR increases, imposing an upper-limit to HbR concentration in the capillaries. Building on our results, we explore the possibility of active venule dilation (purging) as a possible mechanism for the HbT dip.

Functional magnetic resonance imaging of headache: Issues, best-practices, and new directions, a narrative review

OBJECTIVE

To ensure readers are informed consumers of functional magnetic resonance imaging (fMRI) research in headache, to outline ongoing challenges in this area of research, and to describe potential considerations when asked to collaborate on fMRI research in headache, as well as to suggest future directions for improvement in the field.

BACKGROUND

Functional MRI has played a key role in understanding headache pathophysiology, and mapping networks involved with headache-related brain activity have the potential to identify intervention targets. Some investigators have also begun to explore its use for diagnosis.

METHODS/RESULTS

The manuscript is a narrative review of the current best practices in fMRI in headache research, including guidelines on transparency and reproducibility. It also contains an outline of the fundamentals of MRI theory, task-related study design, resting-state functional connectivity, relevant statistics and power analysis, image preprocessing, and other considerations essential to the field.

CONCLUSION

Best practices to increase reproducibility include methods transparency, eliminating error, using a priori hypotheses and power calculations, using standardized instruments and diagnostic criteria, and developing large-scale, publicly available datasets.

Resting-state fMRI signals contain spectral signatures of local hemodynamic response timing

Functional magnetic resonance imaging (fMRI) has proven to be a powerful tool for noninvasively measuring human brain activity; yet, thus far, fMRI has been relatively limited in its temporal resolution. A key challenge is understanding the relationship between neural activity and the blood-oxygenation-level-dependent (BOLD) signal obtained from fMRI, generally modeled by the hemodynamic response function (HRF). The timing of the HRF varies across the brain and individuals, confounding our ability to make inferences about the timing of the underlying neural processes. Here we show that resting-state fMRI signals contain information about HRF temporal dynamics that can be leveraged to understand and characterize variations in HRF timing across both cortical and subcortical regions. We found that the frequency spectrum of resting-state fMRI signals significantly differs between voxels with fast versus slow HRFs in human visual cortex. These spectral differences extended to subcortex as well, revealing significantly faster hemodynamic timing in the lateral geniculate nucleus of the thalamus. Ultimately, our results demonstrate that the temporal properties of the HRF impact the spectral content of resting-state fMRI signals and enable voxel-wise characterization of relative hemodynamic response timing. Furthermore, our results show that caution should be used in studies of resting-state fMRI spectral properties, as differences can arise from purely vascular origins. This finding provides new insight into the temporal properties of fMRI signals across voxels, which is crucial for accurate fMRI analyses, and enhances the ability of fast fMRI to identify and track fast neural dynamics.

Baseline oxygen consumption decreases with cortical depth

The cerebral cortex is organized in cortical layers that differ in their cellular density, composition, and wiring. Cortical laminar architecture is also readily revealed by staining for cytochrome oxidase-the last enzyme in the respiratory electron transport chain located in the inner mitochondrial membrane. It has been hypothesized that a high-density band of cytochrome oxidase in cortical layer IV reflects higher oxygen consumption under baseline (unstimulated) conditions. Here, we tested the above hypothesis using direct measurements of the partial pressure of O2 (pO2) in cortical tissue by means of 2-photon phosphorescence lifetime microscopy (2PLM). We revisited our previously developed method for extraction of the cerebral metabolic rate of O2 (CMRO2) based on 2-photon pO2 measurements around diving arterioles and applied this method to estimate baseline CMRO2 in awake mice across cortical layers. To our surprise, our results revealed a decrease in baseline CMRO2 from layer I to layer IV. This decrease of CMRO2 with cortical depth was paralleled by an increase in tissue oxygenation. Higher baseline oxygenation and cytochrome density in layer IV may serve as an O2 reserve during surges of neuronal activity or certain metabolically active brain states rather than reflecting baseline energy needs. Our study provides to our knowledge the first quantification of microscopically resolved CMRO2 across cortical layers as a step towards better understanding of brain energy metabolism.

Characterization of the blood oxygen level dependent hemodynamic response function in human subcortical regions with high spatiotemporal resolution

Subcortical brain regions are absolutely essential for normal human function. These phylogenetically early brain regions play critical roles in human behaviors such as the orientation of attention, arousal, and the modulation of sensory signals to cerebral cortex. Despite the critical health importance of subcortical brain regions, there has been a dearth of research on their neurovascular responses. Blood oxygen level dependent (BOLD) functional MRI (fMRI) experiments can help fill this gap in our understanding. The BOLD hemodynamic response function (HRF) evoked by brief (<4 s) neural activation is crucial for the interpretation of fMRI results because linear analysis between neural activity and the BOLD response relies on the HRF. Moreover, the HRF is a consequence of underlying local blood flow and oxygen metabolism, so characterization of the HRF enables understanding of neurovascular and neurometabolic coupling. We measured the subcortical HRF at 9.4T and 3T with high spatiotemporal resolution using protocols that enabled reliable delineation of HRFs in individual subjects. These results were compared with the HRF in visual cortex. The HRF was faster in subcortical regions than cortical regions at both field strengths. There was no significant undershoot in subcortical areas while there was a significant post-stimulus undershoot that was tightly coupled with its peak amplitude in cortex. The different BOLD temporal dynamics indicate different vascular dynamics and neurometabolic responses between cortex and subcortical nuclei.

Laminar-specific functional connectivity mapping with multi-slice line-scanning fMRI

Despite extensive studies detecting laminar functional magnetic resonance imaging (fMRI) signals to illustrate the canonical microcircuit, the spatiotemporal characteristics of laminar-specific information flow across cortical regions remain to be fully investigated in both evoked and resting conditions at different brain states. Here, we developed a multislice line-scanning fMRI (MS-LS) method to detect laminar fMRI signals in adjacent cortical regions with high spatial (50 μm) and temporal resolution (100 ms) in anesthetized rats. Across different trials, we detected either laminar-specific positive or negative blood-oxygen-level-dependent (BOLD) responses in the surrounding cortical region adjacent to the most activated cortex under the evoked condition. Specifically, in contrast to typical Layer (L) 4 correlation across different regions due to the thalamocortical projections for trials with positive BOLD, a strong correlation pattern specific in L2/3 was detected for trials with negative BOLD in adjacent regions, which indicated brain state-dependent laminar-fMRI responses based on corticocortical interaction. Also, in resting-state (rs-) fMRI study, robust lag time differences in L2/3, 4, and 5 across multiple cortices represented the low-frequency rs-fMRI signal propagation from caudal to rostral slices. In summary, our study provided a unique laminar fMRI mapping scheme to better characterize trial-specific intra- and inter-laminar functional connectivity in evoked and resting-state MS-LS.

Optical measurement of microvascular oxygenation and blood flow responses in awake mouse cortex during functional activation

The cerebral cortex has a number of conserved morphological and functional characteristics across brain regions and species. Among them, the laminar differences in microvascular density and mitochondrial cytochrome c oxidase staining suggest potential laminar variability in the baseline O₂ metabolism and/or laminar variability in both O₂ demand and hemodynamic response. Here, we investigate the laminar profile of stimulus-induced intravascular partial pressure of O₂ (pO2) transients to stimulus-induced neuronal activation in fully awake mice using two-photon phosphorescence lifetime microscopy. Our results demonstrate that stimulus-induced changes in intravascular pO₂ are conserved across cortical layers I-IV, suggesting a tightly controlled neurovascular response to provide adequate O₂ supply across cortical depth. In addition, we observed a larger change in venular O₂ saturation (ΔsO₂) compared to arterioles, a gradual increase in venular ΔsO₂ response towards the cortical surface, and absence of the intravascular "initial dip" previously reported under anesthesia. This study paves the way for quantification of layer-specific cerebral O₂ metabolic responses, facilitating investigation of brain energetics in health and disease and informed interpretation of laminar blood oxygen level dependent functional magnetic resonance imaging signals.

A line through the brain: implementation of human line-scanning at 7T for ultra-high spatiotemporal resolution fMRI

Functional magnetic resonance imaging (fMRI) is a widely used tool in neuroscience to detect neurally evoked responses, e.g. the blood oxygenation level-dependent (BOLD) signal. Typically, BOLD fMRI has millimeter spatial resolution and temporal resolution of one to few seconds. To study the sub-millimeter structures and activity of the cortical gray matter, the field needs an fMRI method with high spatial and temporal resolution. Line-scanning fMRI achieves very high spatial resolution and high sampling rate, at the cost of a sacrifice in volume coverage. Here, we present a human line-scanning implementation on a 7T MRI system. First, we investigate the quality of the saturation pulses that suppress MR signal outside the line. Second, we established the best coil combination for reconstruction. Finally, we applied the line-scanning method in the occipital lobe during a visual stimulation task, showing BOLD responses along cortical depth, every 250 µm with a 200 ms repetition time (TR). We found a good correspondence of t-statistics values with 2D gradient-echo echo planar imaging (GE-EPI) BOLD fMRI data with the same temporal resolution and voxel volume (R = 0.6 ± 0.2). In summary, we demonstrate the feasibility of line-scanning in humans and this opens line-scanning fMRI for applications in cognitive and clinical neuroscience.

Contribution of animal models toward understanding resting state functional connectivity

Functional connectivity, which reflects the spatial and temporal organization of intrinsic activity throughout the brain, is one of the most studied measures in human neuroimaging research. The noninvasive acquisition of resting state functional magnetic resonance imaging (rs-fMRI) allows the characterization of features designated as functional networks, functional connectivity gradients, and time-varying activity patterns that provide insight into the intrinsic functional organization of the brain and potential alterations related to brain dysfunction. Functional connectivity, hence, captures dimensions of the brain's activity that have enormous potential for both clinical and preclinical research. However, the mechanisms underlying functional connectivity have yet to be fully characterized, hindering interpretation of rs-fMRI studies. As in other branches of neuroscience, the identification of the neurophysiological processes that contribute to functional connectivity largely depends on research conducted on laboratory animals, which provide a platform where specific, multi-dimensional investigations that involve invasive measurements can be carried out. These highly controlled experiments facilitate the interpretation of the temporal correlations observed across the brain. Indeed, information obtained from animal experimentation to date is the basis for our current understanding of the underlying basis for functional brain connectivity. This review presents a compendium of some of the most critical advances in the field based on the efforts made by the animal neuroimaging community.

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.

Sub-millimetre resolution laminar fMRI using Arterial Spin Labelling in humans at 7 T

Laminar fMRI at ultra-high magnetic field strength is typically carried out using the Blood Oxygenation Level-Dependent (BOLD) contrast. Despite its unrivalled sensitivity to detecting activation, the BOLD contrast is limited in its spatial specificity due to signals stemming from intra-cortical ascending and pial veins. Alternatively, regional changes in perfusion (i.e., cerebral blood flow through tissue) are colocalised to neuronal activation, which can be non-invasively measured using Arterial Spin Labelling (ASL) MRI. In addition, ASL provides a quantitative marker of neuronal activation in terms of perfusion signal, which is simultaneously acquired along with the BOLD signal. However, ASL for laminar imaging is challenging due to the lower SNR of the perfusion signal and higher RF power deposition i.e., specific absorption rate (SAR) of ASL sequences. In the present study, we present for the first time in humans, isotropic sub-millimetre spatial resolution functional perfusion images using Flow-sensitive Alternating Inversion Recovery (FAIR) ASL with a 3D-EPI readout at 7 T. We show that robust statistical activation maps can be obtained with perfusion-weighting in a single session. We observed the characteristic BOLD amplitude increase towards the superficial laminae, and, in apparent discrepancy, the relative perfusion profile shows a decrease of the amplitude and the absolute perfusion profile a much smaller increase towards the cortical surface. Considering the draining vein effect on the BOLD signal using model-based spatial “convolution”, we show that the empirically measured perfusion and BOLD profiles are, in fact, consistent with each other. This study demonstrates that laminar perfusion fMRI in humans is feasible at 7 T and that caution must be exercised when interpreting BOLD signal laminar profiles as direct representation of the cortical distribution of neuronal activity.

An in-vivo study of BOLD laminar responses as a function of echo time and static magnetic field strength

Layer specific functional MRI requires high spatial resolution data. To compensate the associated poor signal to noise ratio it is common to integrate the signal from voxels at a given cortical depth. If the region is sufficiently large then physiological noise will be the dominant noise source. In this work, activation profiles in response to the same visual stimulus are compared at 1.5 T, 3 T and 7 T using a multi-echo, gradient echo (GE) FLASH sequence, with a 0.75 mm isotropic voxel size and the cortical integration approach. The results show that after integrating over a cortical volume of 40, 60 and 100 mm³ (at 7 T, 3 T, and 1.5 T, respectively), the signal is in the physiological noise dominated regime. The activation profiles obtained are similar for equivalent echo times. BOLD-like noise is found to be the dominant source of physiological noise. Consequently, the functional contrast to noise ratio is not strongly echo-time or field-strength dependent. We conclude that laminar GE-BOLD fMRI at lower field strengths is feasible but that larger patches of cortex will need to be examined, and that the acquisition efficiency is reduced.

Hemodynamic response varies across tactile stimuli with different temporal structures

Tactile stimuli can be distinguished based on their temporal features (e.g., duration, local frequency, and number of pulses), which are fundamental for vibrotactile frequency perception. Characterizing how the hemodynamic response changes in shape across experimental conditions is important for designing and interpreting fMRI studies on tactile information processing. In this study, we focused on periodic tactile stimuli with different temporal structures and explored the hemodynamic response function (HRF) induced by these stimuli. We found that HRFs were stimulus‐dependent in tactile‐related brain areas. Continuous stimuli induced a greater area of activation and a stronger and narrower hemodynamic response than intermittent stimuli with the same duration. The magnitude of the HRF increased with increasing stimulus duration. By normalizing the characteristics into topographic matrix, nonlinearity was obvious. These results suggested that stimulation patterns and duration within a cycle may be key characters for distinguishing different stimuli. We conclude that different temporal structures of tactile stimuli induced different HRFs, which are essential for vibrotactile perception and should be considered in fMRI experimental designs and analyses.

Linear systems analysis for laminar fMRI: Evaluating BOLD amplitude scaling for luminance contrast manipulations

A fundamental assumption of nearly all functional magnetic resonance imaging (fMRI) analyses is that the relationship between local neuronal activity and the blood oxygenation level dependent (BOLD) signal can be described as following linear systems theory. With the advent of ultra-high field (7T and higher) MRI scanners, it has become possible to perform sub-millimeter resolution fMRI in humans. A novel and promising application of sub-millimeter fMRI is measuring responses across cortical depth, i.e. laminar imaging. However, the cortical vasculature and associated directional blood pooling towards the pial surface strongly influence the cortical depth-dependent BOLD signal, particularly for gradient-echo BOLD. This directional pooling may potentially affect BOLD linearity across cortical depth. Here we assess whether the amplitude scaling assumption for linear systems theory holds across cortical depth. For this, we use stimuli with different luminance contrasts to elicit different BOLD response amplitudes. We find that BOLD amplitude across cortical depth scales with luminance contrast, and that this scaling is identical across cortical depth. Although nonlinearities may be present for different stimulus configurations and acquisition protocols, our results suggest that the amplitude scaling assumption for linear systems theory across cortical depth holds for luminance contrast manipulations in sub-millimeter laminar BOLD fMRI.

Neuroimaging of vascular reserve in patients with cerebrovascular diseases

Cerebrovascular reactivity, defined broadly as the ability of brain parenchyma to adjust cerebral blood flow in response to altered metabolic demand or a vasoactive stimulus, is being measured with increasing frequency and may have a use for portending new or recurrent stroke risk in patients with cerebrovascular disease. The purpose of this review is to outline (i) the physiological basis of variations in cerebrovascular reactivity, (ii) available approaches for measuring cerebrovascular reactivity in research and clinical settings, and (iii) clinically-relevant cerebrovascular reactivity findings in the context of patients with cerebrovascular disease, including atherosclerotic arterial steno-occlusion, non-atherosclerotic arterial steno-occlusion, anemia, and aging. Literature references summarizing safety considerations for these procedures and future directions for standardizing protocols and post-processing procedures across centers are presented in the specific context of major unmet needs in the setting of cerebrovascular disease.

Resolving laminar activation in human V1 using ultra-high spatial resolution fMRI at 7T

The mesoscopic organization of the human neocortex is of great interest for cognitive neuroscience. However, fMRI in humans typically maps the functional units of cognitive processing on a macroscopic level. With the advent of ultra-high field MRI (≥7T), it has become possible to acquire fMRI data with sub-millimetre resolution, enabling probing the laminar and columnar circuitry in humans. Currently, laminar BOLD responses are not directly observed but inferred via data analysis, due to coarse spatial resolution of fMRI (e.g. 0.7-0.8 mm isotropic) relative to the extent of histological laminae. In this study, we introduce a novel approach for mapping the cortical BOLD response at the spatial scale of cortical layers and columns at 7T (an unprecedented 0.1 mm, either in the laminar or columnar direction). We demonstrate experimentally and using simulations, the superiority of the novel approach compared to standard approaches for human laminar fMRI in terms of effective spatial resolution in either laminar or columnar direction. In addition, we provide evidence that the laminar BOLD signal profile is not homogeneous even over short patches of cortex. In summary, the proposed novel approach affords the ability to directly study the mesoscopic organization of the human cortex, thus, bridging the gap between human cognitive neuroscience and invasive animal studies.

Clinical 7 T MRI: Are we there yet? A review about magnetic resonance imaging at ultra-high field

In recent years, ultra-high field MRI (7 T and above) has received more interest for clinical imaging. Indeed, a number of studies have shown the benefits from the application of this powerful tool not only for research purposes, but also in realms of improved diagnostics and patient management. The increased signal-to-noise ratio and higher spatial resolution compared with conventional and high-field clinical scanners allow imaging of small anatomical detail and subtle pathological findings. Furthermore, greater spectral resolution achieved at ultra-high field allows the resolution of metabolites for MR spectroscopic imaging. All these advantages have a significant impact on many neurological diseases, including multiple sclerosis, cerebrovascular disease, brain tumors, epilepsy and neurodegenerative diseases, in part because the pathology can be subtle and lesions small in these diseases, therefore having higher signal and resolution will help lesion detection. In this review, we discuss the main clinical neurological applications and some technical challenges which remain with ultra-high field MRI.

Stimulus-dependent hemodynamic response timing across the human subcortical-cortical visual pathway identified through high spatiotemporal resolution 7T fMRI

Recent developments in fMRI acquisition techniques now enable fast sampling with whole-brain coverage, suggesting fMRI can be used to track changes in neural activity at increasingly rapid timescales. When images are acquired at fast rates, the limiting factor for fMRI temporal resolution is the speed of the hemodynamic response. Given that HRFs may vary substantially in subcortical structures, characterizing the speed of subcortical hemodynamic responses, and how the hemodynamic response shape changes with stimulus duration (i.e. the hemodynamic nonlinearity), is needed for designing and interpreting fast fMRI studies of these regions. We studied the temporal properties and nonlinearities of the hemodynamic response function (HRF) across the human subcortical visual system, imaging superior colliculus (SC), lateral geniculate nucleus of the thalamus (LGN) and primary visual cortex (V1) with high spatiotemporal resolution 7 Tesla fMRI. By presenting stimuli of varying durations, we mapped the timing and nonlinearity of hemodynamic responses in these structures at high spatiotemporal resolution. We found that the hemodynamic response is consistently faster and narrower in subcortical structures than in cortex. However, the nonlinearity in LGN is similar to that in cortex, with shorter duration stimuli eliciting larger and faster responses than would have been predicted by a linear model. Using oscillatory visual stimuli, we tested the frequency response in LGN and found that its BOLD response tracked high-frequency (0.5 Hz) oscillations. The LGN response magnitudes were comparable to V1, allowing oscillatory BOLD signals to be detected in LGN despite the small size of this structure. These results suggest that the increase in the speed and amplitude of the hemodynamic response when neural activity is brief may be the key physiological driver of fast fMRI signals, enabling detection of high-frequency oscillations with fMRI. We conclude that subcortical visual structures exhibit fast and nonlinear hemodynamic responses, and that these dynamics enable detection of fast BOLD signals even within small deep brain structures when imaging is performed at ultra-high field.

Existence of Initial Dip for BCI: An Illusion or Reality

A tight coupling between the neuronal activity and the cerebral blood flow (CBF) is the motivation of many hemodynamic response (HR)-based neuroimaging modalities. The increase in neuronal activity causes the increase in CBF that is indirectly measured by HR modalities. Upon functional stimulation, the HR is mainly categorized in three durations: (i) initial dip, (ii) conventional HR (i.e., positive increase in HR caused by an increase in the CBF), and (iii) undershoot. The initial dip is a change in oxygenation prior to any subsequent increase in CBF and spatially more specific to the site of neuronal activity. Despite additional evidence from various HR modalities on the presence of initial dip in human and animal species (i.e., cat, rat, and monkey); the existence/occurrence of an initial dip in HR is still under debate. This article reviews the existence and elusive nature of the initial dip duration of HR in intrinsic signal optical imaging (ISOI), functional magnetic resonance imaging (fMRI), and functional near-infrared spectroscopy (fNIRS). The advent of initial dip and its elusiveness factors in ISOI and fMRI studies are briefly discussed. Furthermore, the detection of initial dip and its role in brain-computer interface using fNIRS is examined in detail. The best possible application for the initial dip utilization and its future implications using fNIRS are provided.

Feasibility of identifying the ideal locations for motor intention decoding using unimodal and multimodal classification at 7T-fMRI

Invasive Brain-Computer Interfaces (BCIs) require surgeries with high health-risks. The risk-to-benefit ratio of the procedure could potentially be improved by pre-surgically identifying the ideal locations for mental strategy classification. We recorded high-spatiotemporal resolution blood-oxygenation-level-dependent (BOLD) signals using functional MRI at 7 Tesla in eleven healthy participants during two motor imagery tasks. BCI diagnostic task isolated the intent to imagine movements, while BCI simulation task simulated the neural states that may be yielded in a real-life BCI-operation scenario. Imagination of movements were classified from the BOLD signals in sub-regions of activation within a single or multiple dorsal motor network regions. Then, the participant's decoding performance during the BCI simulation task was predicted from the BCI diagnostic task. The results revealed that drawing information from multiple regions compared to a single region increased the classification accuracy of imagined movements. Importantly, systematic unimodal and multimodal classification revealed the ideal combination of regions that yielded the best classification accuracy at the individual-level. Lastly, a given participant's decoding performance achieved during the BCI simulation task could be predicted from the BCI diagnostic task. These results show the feasibility of 7T-fMRI with unimodal and multimodal classification being utilized for identifying ideal sites for mental strategy classification.

Optimized partial-coverage functional analysis pipeline (OPFAP): a semi-automated pipeline for skull stripping and co-registration of partial-coverage, ultra-high-field functional images

OBJECTIVE

Ultra-high-field functional MRI (UHF-fMRI) allows for higher spatiotemporal resolution imaging. However, higher-resolution imaging entails coverage limitations. Processing partial-coverage images using standard pipelines leads to sub-optimal results. We aimed to develop a simple, semi-automated pipeline for processing partial-coverage UHF-fMRI data using widely used image processing algorithms.

MATERIALS AND METHODS

We developed automated pipelines for optimized skull stripping and co-registration of partial-coverage UHF functional images, using built-in functions of the Centre for Functional Magnetic Resonance Imaging of the Brain's (FMRIB's) Software library (FSL) and advanced normalization tools. We incorporated the pipelines into the FSL's functional analysis pipeline and provide a semi-automated optimized partial-coverage functional analysis pipeline (OPFAP).

RESULTS

Compared to the standard pipeline, the OPFAP yielded images with 15 and 30% greater volume of non-zero voxels after skull stripping the functional and anatomical images, respectively (all p = 0.0004), which reflected the conservation of cortical voxels lost when the standard pipeline was used. The OPFAP yielded the greatest Dice and Jaccard coefficients (87 and 80%, respectively; all p < 0.0001) between the co-registered participant gyri maps and the template gyri maps, demonstrating the goodness of the co-registration results. Furthermore, the greatest volume of group-level activation in the most number of functionally relevant regions was observed when the OPFAP was used. Importantly, group-level activations were not observed when using the standard pipeline.

CONCLUSION

These results suggest that the OPFAP should be used for processing partial-coverage UHF-fMRI data for detecting high-resolution macroscopic blood oxygenation level-dependent activations.

The effects of capillary transit time heterogeneity on the BOLD signal

Neurovascular coupling mechanisms give rise to vasodilation and functional hyperemia upon neural activation, thereby altering blood oxygenation. This blood oxygenation level dependent (BOLD) contrast allows studies of activation patterns in the working human brain by functional MRI (fMRI). The BOLD-weighted fMRI signal shows characteristic transients in relation to functional activation, such as the so-called initial dip, overshoot, and post-stimulus undershoot. These transients are modulated by other physiological stimuli and in disease, but the underlying physiological mechanisms remain incompletely understood. Capillary transit time heterogeneity (CTH) has been shown to affect oxygen extraction, and hence blood oxygenation. Here, we examine how recently reported redistributions of capillary blood flow during functional activation would be expected to affect BOLD signal transients. We developed a three-compartment (hemoglobin, plasma, and tissue) model to predict the BOLD signal, incorporating the effects of dynamic changes in CTH. Our model predicts that the BOLD signal represents the superposition of a positive component resulting from increases in cerebral blood flow (CBF), and a negative component, resulting from elevated tissue metabolism and homogenization of capillary flows (reduced CTH). The model reproduces salient features of BOLD signal dynamics under conditions such as hypercapnia, hyperoxia, and caffeine intake, where both brain physiology and BOLD characteristics are altered. Neuroglial signaling and metabolism could affect CBF and capillary flow patterns differently. Further studies of neurovascular and neuro-capillary coupling mechanisms may help us relate BOLD signals to the firing of certain neuronal populations based on their respective BOLD "fingerprints."

Characterization of the hemodynamic response function across the majority of human cerebral cortex

A brief (<4 s) period of neural activation evokes a stereotypical sequence of vascular and metabolic events to create the hemodynamic response function (HRF) measured using functional magnetic resonance imaging (fMRI). Linear analysis of fMRI data requires that the HRF be treated as an impulse response, so the character and temporal stability of the HRF are critical issues. Here, a simple audiovisual stimulus combined with a fast-paced task was used to evoke a strong HRF across a majority, ∼77%, of cortex during a single scanning session. High spatiotemporal resolution (2-mm voxels, 1.25-s acquisition time) was used to focus HRF measurements specifically on the gray matter for whole brain. The majority of activated cortex responds with positive HRFs, while ∼27% responds with negative (inverted) HRFs. Spatial patterns of the HRF response amplitudes were found to be similar across subjects. Timing of the initial positive lobe of the HRF was relatively stable across the cortical surface with a mean of 6.1 ± 0.6 s across subjects, yet small but significant timing variations were also evident in specific regions of cortex. The results provide guidance for linear analysis of fMRI data. More importantly, this method provides a means to quantify neurovascular function across most of the brain, with potential clinical utility for the diagnosis of brain pathologies such as traumatic brain injury.

Analysis strategies for high-resolution UHF-fMRI data

Functional MRI (fMRI) benefits from both increased sensitivity and specificity with increasing magnetic field strength, making it a key application for Ultra-High Field (UHF) MRI scanners. Most UHF-fMRI studies utilize the dramatic increases in sensitivity and specificity to acquire high-resolution data reaching sub-millimeter scales, which enable new classes of experiments to probe the functional organization of the human brain. This review article surveys advanced data analysis strategies developed for high-resolution fMRI at UHF. These include strategies designed to mitigate distortion and artifacts associated with higher fields in ways that attempt to preserve spatial resolution of the fMRI data, as well as recently introduced analysis techniques that are enabled by these extremely high-resolution data. Particular focus is placed on anatomically-informed analyses, including cortical surface-based analysis, which are powerful techniques that can guide each step of the analysis from preprocessing to statistical analysis to interpretation and visualization. New intracortical analysis techniques for laminar and columnar fMRI are also reviewed and discussed. Prospects for single-subject individualized analyses are also presented and discussed. Altogether, there are both specific challenges and opportunities presented by UHF-fMRI, and the use of proper analysis strategies can help these valuable data reach their full potential.

Laminar fMRI: What can the time domain tell us?

The rapid developments in functional MRI (fMRI) acquisition methods and hardware technologies in recent years, particularly at high field (≥7 T), have enabled unparalleled visualization of functional detail at a laminar or columnar level, bringing fMRI close to the intrinsic resolution of brain function. These advances highlight the potential of high resolution fMRI to be a valuable tool to study the fundamental processing performed in cortical micro-circuits, and their interactions such as feedforward and feedback processes. Notably, because fMRI measures neuronal activity via hemodynamics, the ultimate resolution it affords depends on the spatial specificity of hemodynamics to neuronal activity at a detailed spatial scale, and by the evolution of this specificity over time. Several laminar (≤1 mm spatial resolution) fMRI studies have examined spatial characteristics of the measured hemodynamic signals across cortical depth, in light of understanding or improving the spatial specificity of laminar fMRI. Few studies have examined temporal features of the hemodynamic response across cortical depth. Temporal features of the hemodynamic response offer an additional means to improve the specificity of fMRI, and could help target neuronal processes and neurovascular coupling relationships across laminae, for example by differences in the onset times of the response across cortical depth. In this review, we discuss factors that affect the timing of neuronal and hemodynamic responses across laminae, touching on the neuronal laminar organization, and focusing on the laminar vascular organization. We provide an overview of hemodynamics across the cortical vascular tree based on optical imaging studies, and review temporal aspects of hemodynamics that have been examined across cortical depth in high spatiotemporal resolution fMRI studies. Last, we discuss the limits and potential of high spatiotemporal resolution fMRI to study laminar neurovascular coupling and neuronal processes.

Electrophysiological and hemodynamic mismatch responses in rats listening to human speech syllables

Speech is a complex auditory stimulus which is processed according to several time-scales. Whereas consonant discrimination is required to resolve rapid acoustic events, voice perception relies on slower cues. Humans, right from preterm ages, are particularly efficient to encode temporal cues. To compare the capacities of preterms to those observed in other mammals, we tested anesthetized adult rats by using exactly the same paradigm as that used in preterm neonates. We simultaneously recorded neural (using ECoG) and hemodynamic responses (using fNIRS) to series of human speech syllables and investigated the brain response to a change of consonant (ba vs. ga) and to a change of voice (male vs. female). Both methods revealed concordant results, although ECoG measures were more sensitive than fNIRS. Responses to syllables were bilateral, but with marked right-hemispheric lateralization. Responses to voice changes were observed with both methods, while only ECoG was sensitive to consonant changes. These results suggest that rats more effectively processed the speech envelope than fine temporal cues in contrast with human preterm neonates, in whom the opposite effects were observed. Cross-species comparisons constitute a very valuable tool to define the singularities of the human brain and species-specific bias that may help human infants to learn their native language.

7-T MRI in Cerebrovascular Diseases: Challenges to Overcome and Initial Results

Magnetic resonance imaging (MRI) plays a key role in the investigation of cerebrovascular diseases. Compared with computed tomography (CT) and digital subtraction angiography (DSA), its advantages in diagnosing cerebrovascular pathology include its superior tissue contrast, its ability to visualize blood vessels without the use of a contrast agent, and its use of magnetic fields and radiofrequency pulses instead of ionizing radiation. In recent years, ultrahigh field MRI at 7 tesla (7 T) has shown promise in the diagnosis of many cerebrovascular diseases. The increased signal-to-noise ratio (SNR; 2.3x and 4.7x increase compared with 3 and 1.5 T, respectively) and contrast-to-noise ratio (CNR) at this higher field strength can be exploited to obtain a higher spatial resolution and higher lesion conspicuousness, enabling assessment of smaller brain structures and lesions. Cerebrovascular diseases can be assessed at different tissue levels; for instance, changes of the arteries feeding the brain can be visualized to determine the cause of ischemic stroke, regional changes in brain perfusion can be mapped to predict outcome after revascularization, and tissue damage, including old and recent ischemic infarcts, can be evaluated as a marker of ischemic burden. For the purpose of this review, we will discriminate 3 levels of assessment of cerebrovascular diseases using MRI: Pipes, Perfusion, and Parenchyma (3 Ps). The term Pipes refers to the brain-feeding arteries from the heart and aortic arch, upwards to the carotid arteries, vertebral arteries, circle of Willis, and smaller intracranial arterial branches. Perfusion is the amount of blood arriving at the brain tissue level, and includes the vascular reserve and perfusion territories. Parenchyma refers to the acute and chronic burden of brain tissue damage, which includes larger infarcts, smaller microinfarcts, and small vessel disease manifestations such as white matter lesions, lacunar infarcts, and microbleeds. In this review, we will describe the key developments in the last decade of 7-T MRI of cerebrovascular diseases, subdivided for these 3 levels of assessment.

Noise and non-neuronal contributions to the BOLD signal: applications to and insights from animal studies

The BOLD signal reflects hemodynamic events within the brain, which in turn are driven by metabolic changes and neural activity. However, the link between BOLD changes and neural activity is indirect and can be influenced by a number of non-neuronal processes. Motion and physiological cycles have long been known to affect the BOLD signal and are present in both humans and animal models. Differences in physiological baseline can also contribute to intra- and inter-subject variability. The use of anesthesia, common in animal studies, alters neural activity, vascular tone, and neurovascular coupling. Most intriguing, perhaps, are the contributions from other processes that do not appear to be neural in origin but which may provide information about other aspects of neurophysiology. This review discusses different types of noise and non-neuronal contributors to the BOLD signal, sources of variability for animal studies, and insights to be gained from animal models.

Noise concerns and post-processing procedures in cerebral blood flow (CBF) and cerebral blood volume (CBV) functional magnetic resonance imaging

Functional neuroimaging with blood oxygenation level-dependent (BOLD) contrast has emerged as the most popular method for evaluating qualitative changes in brain function in humans. At typical human field strengths (1.5-3.0T), BOLD contrast provides a measure of changes in transverse water relaxation rates in and around capillary and venous blood, and as such provides only a surrogate marker of brain function that depends on dynamic changes in hemodynamics (e.g., cerebral blood flow and volume) and metabolism (e.g., oxygen extraction fraction and the cerebral metabolic rate of oxygen consumption). Alternative functional neuroimaging methods that are specifically sensitive to these constituents of the BOLD signal are being developed and applied in a growing number of clinical and neuroscience applications of quantitative cerebral physiology. These methods require additional considerations for interpreting and quantifying their contrast responsibly. Here, an overview of two popular methods, arterial spin labeling and vascular space occupancy, is presented specifically in the context of functional neuroimaging. Appropriate post-processing and experimental acquisition strategies are summarized with the motivation of reducing sensitivity to noise and unintended signal sources and improving quantitative accuracy of cerebral hemodynamics.

Recent applications of UHF-MRI in the study of human brain function and structure: a review

The increased availability of ultra-high-field (UHF) MRI has led to its application in a wide range of neuroimaging studies, which are showing promise in transforming fundamental approaches to human neuroscience. This review presents recent work on structural and functional brain imaging, at 7 T and higher field strengths. After a short outline of the effects of high field strength on MR images, the rapidly expanding literature on UHF applications of blood-oxygenation-level-dependent-based functional MRI is reviewed. Structural imaging is then discussed, divided into sections on imaging weighted by relaxation time, including quantitative relaxation time mapping, phase imaging and quantitative susceptibility mapping, angiography, diffusion-weighted imaging, and finally magnetization-transfer imaging. The final section discusses studies using the high spatial resolution available at UHF to identify explicit links between structure and function. Copyright © 2015 John Wiley & Sons, Ltd.