Global effects of aging on the hemodynamic response function in the human brain

In functional magnetic resonance imaging, the hemodynamic response function (HRF) is a transient, stereotypical response to local changes in cerebral hemodynamics and oxygen metabolism due to briefly (< 4 s) evoked neural activity. Accordingly, the HRF is often used as an impulse response with the assumption of linearity in data analysis. In cognitive aging studies, it has been very common to interpret differences in brain activation as age-related changes in neural activity. Contrary to this assumption, however, evidence has accrued that normal aging may also significantly affect the vasculature, thereby affecting cerebral hemodynamics and metabolism, confounding interpretation of fMRI aging studies. In this study, use was made of a multisensory stimulus to evoke the HRF in ~ 87% of cerebral cortex in cognitively intact adults with ages ranging from 22-75 years. The stimulus evokes both positive and negative HRFs, which were characterized using model-free parameters in native-space coordinates. Results showed significant age trends in HRF parameter distributions in terms of both amplitudes (e.g., peak amplitude and CNR) and temporal dynamics (e.g., full-width-at-half-maximum). This work sets the stage for using HRF methods as a biomarker for age-related pathology.

Framework for Accurate Classification of Self-Reported Stress From Multisession Functional MRI Data of Veterans With Posttraumatic Stress

Background: Posttraumatic stress disorder (PTSD) is a significant burden among combat Veterans returning from the wars in Iraq and Afghanistan. While empirically supported treatments have demonstrated reductions in PTSD symptomatology, there remains a need to improve treatment effectiveness. Functional magnetic resonance imaging (fMRI) neurofeedback has emerged as a possible treatment to ameliorate PTSD symptom severity. Virtual reality (VR) approaches have also shown promise in increasing treatment compliance and outcomes. To facilitate fMRI neurofeedback-associated therapies, it would be advantageous to accurately classify internal brain stress levels while Veterans are exposed to trauma-associated VR imagery. Methods: Across 2 sessions, we used fMRI to collect neural responses to trauma-associated VR-like stimuli among male combat Veterans with PTSD symptoms (N = 8). Veterans reported their self-perceived stress level on a scale from 1 to 8 every 15 s throughout the fMRI sessions. In our proposed framework, we precisely sample the fMRI data on cortical gray matter, blurring the data along the gray-matter manifold to reduce noise and dimensionality while preserving maximum neural information. Then, we independently applied 3 machine learning (ML) algorithms to this fMRI data collected across 2 sessions, separately for each Veteran, to build individualized ML models that predicted their internal brain states (self-reported stress responses). Results: We accurately classified the 8-class self-reported stress responses with a mean (± standard error) root mean square error of 0.6 (± 0.1) across all Veterans using the best ML approach. Conclusions: The findings demonstrate the predictive ability of ML algorithms applied to whole-brain cortical fMRI data collected during individual Veteran sessions. The framework we have developed to preprocess whole-brain cortical fMRI data and train ML models across sessions would provide a valuable tool to enable individualized real-time fMRI neurofeedback during VR-like exposure therapy for PTSD.

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.

Temporal stability of the hemodynamic response function across the majority of human cerebral cortex

The hemodynamic response function (HRF) measured with functional magnetic resonance imaging is generated by vascular and metabolic responses evoked by brief (<4 s) stimuli. It is known that the human HRF varies across cortex, between subjects, with stimulus paradigms, and even between different measurements in the same cortical location. However, our results demonstrate that strong HRFs are remarkably repeatable across sessions separated by time intervals up to 3 months. In this study, a multisensory stimulus was used to activate and measure the HRF across the majority of cortex (>70%, with lesser reliability observed in some areas of prefrontal cortex). HRFs were measured with high spatial resolution (2‐mm voxels) in central gray matter to minimize variations caused by partial‐volume effects. HRF amplitudes and temporal dynamics were highly repeatable across four sessions in 20 subjects. Positive and negative HRFs were consistently observed across sessions and subjects. Negative HRFs were generally weaker and, thus, more variable than positive HRFs. Statistical measurements showed that across‐session variability is highly correlated to the variability across events within a session; these measurements also indicated a normal distribution of variability across cortex. The overall repeatability of the HRFs over long time scales generally supports the long‐term use of event‐related functional magnetic resonance imaging protocols.

Retinotopic variations of the negative blood-oxygen-level dependent hemodynamic response function in human primary visual cortex

Functional magnetic resonance imaging (fMRI) measures blood-oxygen-level-dependent (BOLD) contrast that is generally assumed to be linearly related to excitatory neural activity. The positive hemodynamic response function (pHRF) is the positive BOLD response (PBR) evoked by a brief neural stimulation; the pHRF is often used as the impulse response for linear analysis of neural excitation. Many fMRI studies have observed a negative BOLD response (NBR) that is often associated with neural suppression. However, the temporal dynamics of the NBR evoked by a brief stimulus, the negative HRF (nHRF), remains unclear. Here, a unilateral visual stimulus was presented in a slow event-related design to elicit both pHRFs in the stimulus representation (SR), and nHRFs elsewhere. The observed nHRFs were not inverted versions of the pHRF previously reported. They were characterized by a stronger initial negative response followed by a significantly later positive peak. In contralateral primary visual cortex (V1), these differences varied with eccentricity from the SR. Similar nHRFs were observed in ipsilateral V1 with less eccentricity variation. Experiments with the blocked version of the same stimulus confirmed that brain regions presenting the unexpected nHRF dynamics correspond to those presenting a strong NBR. These data demonstrated that shift-invariant temporal linearity did not hold for the NBR while confirming that the PBR maintained rough linearity. Modeling indicated that the observed nHRFs can be created by suppression of both blood flow and oxygen metabolism. Critically, the nHRF can be misinterpreted as a pHRF due to their similarity, which could confound linear analysis for event-related fMRI experiments.NEW & NOTEWORTHY We investigate dynamics of the negative hemodynamic response function (nHRF), the negative blood-oxygen-level-dependent (BOLD) response (NBR) evoked by a brief stimulus, in human early visual cortex. Here, we show that the nHRFs are not inverted versions of the corresponding pHRFs. The nHRF has complex dynamics that varied significantly with eccentricity. The results also show shift-invariant temporal linearity does not hold for the NBR.

Depth relationships and measures of tissue thickness in dorsal midbrain

Dorsal human midbrain contains two nuclei with clear laminar organization, the superior and inferior colliculi. These nuclei extend in depth between the superficial dorsal surface of midbrain and a deep midbrain nucleus, the periaqueductal gray matter (PAG). The PAG, in turn, surrounds the cerebral aqueduct (CA). This study examined the use of two depth metrics to characterize depth and thickness relationships within dorsal midbrain using the superficial surface of midbrain and CA as references. The first utilized nearest-neighbor Euclidean distance from one reference surface, while the second used a level-set approach that combines signed distances from both reference surfaces. Both depth methods provided similar functional depth profiles generated by saccadic eye movements in a functional MRI task, confirming their efficacy for delineating depth for superficial functional activity. Next, the boundaries of the PAG were estimated using Euclidean distance together with elliptical fitting, indicating that the PAG can be readily characterized by a smooth surface surrounding PAG. Finally, we used the level-set approach to measure tissue depth between the superficial surface and the PAG, thus characterizing the variable thickness of the colliculi. Overall, this study demonstrates depth-mapping schemes for human midbrain that enables accurate segmentation of the PAG and consistent depth and thickness estimates of the superior and inferior colliculi.

Brainstem BOLD response to visual and acoustic stimuli

Understanding the fundamental roles of brainstem function resulting in proper motor control is critical to motor-rehabilitation after brain injuries. In particular, vestibular and reticular formation nuclei are thought to be associated with spasticity in chronic stroke patients. We used two kinds of stimuli in 10 healthy subjects to activate these nuclei while collecting high-resolution (1.5-mm) fMRI across the majority of brainstem. Optokinetic stimuli evoked illusory self-motion to activate the vestibular nuclei. Acoustic-startle stimuli were sets of loud tones designed to activate of the reticular formation. We summarized the response represented in a form of activation volume, mean percent signal change, and the phase delay (time lag) following the stimulus. We observed patterns of significant activations in the brainstem but did not find significant differences between the stimulus. We conclude that more sensitive measurement techniques are needed to reliably detect vestibular and reticular formation nuclei responses.

Dynamics of the cerebral blood flow response to brief neural activity in human visual cortex

The blood oxygen-level dependent (BOLD) functional magnetic resonance imaging (fMRI) signal depends on an interplay of cerebral blood flow (CBF), oxygen metabolism, and cerebral blood volume. Despite wide usage of BOLD fMRI, it is not clear how these physiological components create the BOLD signal. Here, baseline CBF and its dynamics evoked by a brief stimulus (2 s) in human visual cortex were measured at 3T. We found a stereotypical CBF response: immediate increase, rising to a peak a few second after the stimulus, followed by a significant undershoot. The BOLD hemodynamic response function (HRF) was also measured in the same session. Strong correlations between HRF and CBF peak responses indicate that the flow responses evoked by neural activation in nearby gray matter drive the early HRF. Remarkably, peak CBF and HRF were also strongly modulated by baseline perfusion. The CBF undershoot was reliable and significantly correlated with the HRF undershoot. However, late-time dynamics of the HRF and CBF suggest that oxygen metabolism can also contribute to the HRF undershoot. Combined measurement of the CBF and HRF for brief neural activation is a useful tool to understand the temporal dynamics of neurovascular and neurometabolic coupling.

Right temporal pole volume reduction in PTSD

Previous magnetic resonance imaging studies of post-traumatic stress disorder (PTSD) have reported cortical volume alterations in the parahippocampal, anterior cingulate cortex, and temporal pole. It is unclear, however, if these cortical regions are specifically associated with PTSD or associated with common comorbidities. Here, we present the result of cortical volume differences between PTSD and healthy and psychiatric controls. In this study, healthy controls (n = 67) were matched for demographic characteristics (age, sex, race) and psychiatric controls (n = 67) were matched for demographic characteristics plus all other psychiatric diagnoses (past and current) to a group of PTSD patients (N = 67). We assessed group differences of 34 bilateral cortical structure volumes using statistically defined brain regions-of-interest from FreeSurfer between PTSD patients and healthy controls. We found 10 regions to be significantly different between PTSD and healthy controls and analyzed the group differences between PTSD and psychiatric controls within these regions. The right temporal pole volume in PTSD was found to be significantly smaller than both healthy and psychiatry controls. Our finding suggests only right temporal pole volume reduction is specifically associated with PTSD, and also highlights the need for using appropriate controls in psychiatry research.

StretchfMRI: a novel technique to quantify the contribution of the reticular formation to long-latency responses via fMRI

Increased reticulospinal (RS) function has been observed to cause both positive and negative outcomes in the recovery of motor function after corticospinal lesions such as stroke. Current knowledge of RS function is limited by the lack of accurate, noninvasive methods for measuring RS function. Recent studies suggest that the RS tract may be involved in processing and generating Long Latency Responses (LLRs). As such, LLRs, elicited by applying precisely controlled perturbations, can thus act as a reliable stimulus to measure brainstem function using fMRI with high signal-to-noise ratio.In this paper, we present StretchfMRI, a novel technique that enables simultaneous recording of neural and muscular activity during motor responses conditioned by robotic perturbations, which allows direct investigation of the neural correlates of LLRs.Via preliminary validation experiments, we demonstrate that our technique can reliably elicit and identify LLRs in two wrist muscles-Flexor Carpi Radialis and Extensor Carpi Ulnaris. Moreover, via a single-subject pilot experiment, we show that the occurrence of an LLR in a flexor and extensor muscles modulates neural activity in distinct regions of the brainstem. The observed somatotopic organization is in agreement with the double reciprocal model of RS function observed in animal models, in which the right medullary and left pontine reticular formation are responsible for control of the motor activity in flexors and extensors, respectively.

More than BOLD: Dual-spin populations create functional contrast

PURPOSE

Functional MRI contrast has generally been associated with changes in transverse relaxivity caused by blood oxygen concentration, the so-called blood oxygen level dependent contrast. However, this interpretation of fMRI contrast has been called into question by several recent experiments at high spatial resolution. Experiments were conducted to examine contrast dependencies that cannot be explained only by differences in relaxivity in a single-spin population.

METHODS

Measurements of functional signal and contrast were obtained in human early visual cortex during a high-contrast visual stimulation over a large range of TEs and for several flip angles. Small voxels (1.5 mm) were used to restrict the measurements to cortical gray matter in early visual areas identified using retinotopic mapping procedures.

RESULTS

Measurements were consistent with models that include 2 spin populations. The dominant population has a relatively short transverse lifetime that is strongly modulated by activation. However, functional contrast is also affected by volume changes between this short-lived population and the longer-lived population.

CONCLUSION

Some of the previously observed "nonclassical" behaviors of functional contrast can be explained by these interacting dual-spin populations.

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.

Quantitative Testing of fMRI-Compatibility of an Electrically Active Mechatronic Device for Robot-Assisted Sensorimotor Protocols

OBJECTIVE

To develop a quantitative set of methods for testing the functional magnetic resonance imaging (fMRI) compatibility of an electrically-active mechatronic device developed to support sensorimotor protocols during fMRI.

METHODS

The set of methods includes phantom and in vivo experiments to measure the effect of a progressively broader set of noise sources potentially introduced by the device. Phantom experiments measure the radio-frequency (RF) noise and temporal noise-to-signal ratio (tNSR) introduced by the device. The in vivo experiment assesses the effect of the device on measured brain activation for a human subject performing a representative sensorimotor task. The proposed protocol was validated via experiments using a 3T MRI scanner operated under nominal conditions and with the inclusion of an electrically-active mechatronic device - the MR-SoftWrist - as the equipment under test (EUT).

RESULTS

Quantitative analysis of RF noise data allows detection of active RF noise sources both in controlled RF noise conditions, and in conditions resembling improper filtering of the EUT's electrical signals. In conditions where no RF noise was detectable, the presence and operation of the EUT did not introduce any significant increase in tNSR. A quantitative analysis conducted on in vivo measurements of the number of active voxels in visual and motor areas further showed no significant difference between EUT and baseline conditions.

CONCLUSION AND SIGNIFICANCE

The proposed set of quantitative methods supports the development and troubleshooting of electrically-active mechatronic devices for use in sensorimotor protocols with fMRI, and may be used for future testing of such devices.

Evaluation of spiral acquisition variants for functional imaging of human superior colliculus at 3T field strength

PURPOSE

High-resolution functional magnetic resonance imaging of human subcortical brain structures is challenging because of their deep location in the cranium, and their comparatively weak blood oxygen level dependent responses to strong stimuli. Magnetic resonance imaging data for subcortical brain regions exhibit both low signal-to-noise ratio and low functional contrast-to-noise ratio. To overcome these challenges, this work evaluates the use of dual-echo spiral variants that combine outward and inward trajectories. Specifically, in-in, in-out, and out-out combinations are evaluated. For completeness, single-echo spiral-in and parallel-receive-accelerated echo-planar-imaging sequences are also evaluated.

METHODS

Sequence evaluation was based on comparison of functional contrast-to-noise ratio within retinotopically predefined regions of interest. Superior colliculus was chosen as sample subcortical brain region because it exhibits a strong visual response. All sequences were compared relative to a single-echo spiral-out trajectory to establish a within-session reference.

RESULTS

In superior colliculus, the dual-echo out-out outperformed the reference trajectory by 55% in contrast-to-noise ratio, while all other trajectories had performance similar to the reference. The sequences were also compared in early visual cortex. Here, both dual-echo spiral out-out and in-out outperformed the reference by ∼25%.

CONCLUSION

Dual-echo spiral variants offer improved contrast-to-noise ratio performance for high-resolution imaging for both superior colliculus and cortex. Magn Reson Med 79:1931-1940, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Real time functional MRI training to decrease motion in imaging studies: Lack of significant improvement

Functional magnetic resonance imaging (fMRI) is widely used to study brain circuitry in healthy controls and in psychiatry. A major problem of fMRI studies is motion, which affects the quality of images, is a major source of noise, and can confound data if, for example, the experimental groups move differently. Despite continual reminders to experimental subjects about keeping still, however, movement in the scanner remains a problem. The authors hypothesized that showing head movement during a scanning session may help subjects learn how to keep their head still. The authors scanned subjects and displayed in real time a plot of head movement that had three regions. The authors found, in a limited sample, that the improvements were marginal and inconsistent. Thus, they concluded that this strategy, even if likely to work for some people, is probably not sufficiently successful to be implemented at this time.

Kinesthetic Feedback During 2DOF Wrist Movements via a Novel MR-Compatible Robot

We demonstrate the interaction control capabilities of the MR-SoftWrist, a novel MR-compatible robot capable of applying accurate kinesthetic feedback to wrist pointing movements executed during fMRI. The MR-SoftWrist, based on a novel design that combines parallel piezoelectric actuation with compliant force feedback, is capable of delivering 1.5 N [Formula: see text] of torque to the wrist of an interacting subject about the flexion/extension and radial/ulnar deviation axes. The robot workspace, defined by admissible wrist rotation angles, fully includes a circle with a 20 deg radius. Via dynamic characterization, we demonstrate capability for transparent operation with low (10% of maximum torque output) backdrivability torques at nominal speeds. Moreover, we demonstrate a 5.5 Hz stiffness control bandwidth for a 14 dB range of virtual stiffness values, corresponding to 25%-125% of the device's physical reflected stiffness in the nominal configuration. We finally validate the possibility of operation during fMRI via a case study involving one healthy subject. Our validation experiment demonstrates the capability of the device to apply kinesthetic feedback to elicit distinguishable kinetic and neural responses without significant degradation of image quality or task-induced head movements. With this study, we demonstrate the feasibility of MR-compatible devices like the MR-SoftWrist to be used in support of motor control experiments investigating wrist pointing under robot-applied force fields. Such future studies may elucidate fundamental neural mechanisms enabling robot-assisted motor skill learning, which is crucial for robot-aided neurorehabilitation.

Arterial impulse model for the BOLD response to brief neural activation

The blood oxygen level dependent (BOLD) signal evoked by brief neural stimulation, the hemodynamic response function (HRF), is a critical feature of neurovascular coupling. The HRF is directly related to local transient changes in oxygen supplied by cerebral blood flow (CBF) and oxygen demand, the cerebral metabolic rate of oxygen (CMRO2). Previous efforts to explain the HRF have relied upon the hypothesis that CBF produces a non-linear venous dilation within the cortical parenchyma. Instead, the observed dynamics correspond to prompt arterial dilation without venous volume change. This work develops an alternative biomechanical model for the BOLD response based on the hypothesis that prompt upstream dilation creates an arterial flow impulse amenable to linear description. This flow model is coupled to a continuum description of oxygen transport. Measurements using high-resolution fMRI demonstrate the efficacy of the model. The model predicts substantial spatial variations of the oxygen saturation along the length of capillaries and veins, and fits the varied gamut of measured HRFs by the combined effects of corresponding CBF and CMRO2 responses. Three interesting relationships among the hemodynamic parameters are predicted. First, there is an offset linear correlation with approximately unity slope between CBF and CMRO2 responses. Second, the HRF undershoot is strongly correlated to the corresponding CBF undershoot. Third, late-time-CMRO2 response can contribute to a slow recovery to baseline, lengthening the HRF undershoot. The model provides a powerful mathematical framework to understand the dynamics of neurovascular and neurometabolic responses that form the BOLD HRF.

Accurately decoding visual information from fMRI data obtained in a realistic virtual environment

Three-dimensional interactive virtual environments (VEs) are a powerful tool for brain-imaging based cognitive neuroscience that are presently under-utilized. This paper presents machine-learning based methods for identifying brain states induced by realistic VEs with improved accuracy as well as the capability for mapping their spatial topography on the neocortex. VEs provide the ability to study the brain under conditions closer to the environment in which humans evolved, and thus to probe deeper into the complexities of human cognition. As a test case, we designed a stimulus to reflect a military combat situation in the Middle East, motivated by the potential of using real-time functional magnetic resonance imaging (fMRI) in the treatment of post-traumatic stress disorder. Each subject experienced moving through the virtual town where they encountered 1-6 animated combatants at different locations, while fMRI data was collected. To analyze the data from what is, compared to most studies, more complex and less controlled stimuli, we employed statistical machine learning in the form of Multi-Voxel Pattern Analysis (MVPA) with special attention given to artificial Neural Networks (NN). Extensions to NN that exploit the block structure of the stimulus were developed to improve the accuracy of the classification, achieving performances from 58 to 93% (chance was 16.7%) with six subjects. This demonstrates that MVPA can decode a complex cognitive state, viewing a number of characters, in a dynamic virtual environment. To better understand the source of this information in the brain, a novel form of sensitivity analysis was developed to use NN to quantify the degree to which each voxel contributed to classification. Compared with maps produced by general linear models and the searchlight approach, these sensitivity maps revealed a more diverse pattern of information relevant to the classification of cognitive state.

Measurement of population receptive fields in human early visual cortex using back-projection tomography

Properties of human visual population receptive fields (pRFs) are currently estimated by performing measurements of visual stimulation using functional magnetic resonance imaging (fMRI), and then fitting the results using a predefined model shape for the pRF. Various models exist and different models may be appropriate under different circumstances, but the validity of the models has never been verified, suggesting the need for a model-free approach. Here, we demonstrate that pRFs can be directly reconstructed using a back-projection-tomography approach that requires no a priori model. The back-projection method involves sweeping thin contrast-defined bars across the visual field whose orientation and direction is rotated through 0°-180° in discrete increments. The measured fMRI time series within a cortical location can be approximated as a projection of the pRF along the long axis of the bar. The signals produced by a set of bar sweeps encircling the visual field form a sinogram. pRFs were reconstructed from these sinograms with a novel scheme that corrects for the blur introduced by the hemodynamic response and the stimulus-bar width. pRF positions agree well with the conventional model-based approach. Notably, a subset of the reconstructed pRFs shows significant asymmetry for both their excitatory and suppressive regions. Reconstructing pRFs using the tomographic approach is a fast, reliable, and accurate way to noninvasively estimate human pRF parameters and visual-field maps without the need for any a priori shape assumption.

Tonotopic organization in the depth of human inferior colliculus

Experiments in animal models indicate that inferior colliculus (IC), the primary auditory midbrain structure, represents sound frequency in a particular spatial organization, a tonotopy, that proceeds from dorsal and superficial to ventral and deeper tissue. Experiments are presented that use high-resolution, sparse-sampling functional magnetic resonance imaging (fMRI) at 3 T to determine if tonotopic gradients can be reliably measured in human IC using high-resolution fMRI. Stimuli were sequences of bandpass-filtered noise with different center frequencies, presented sequentially while fMRI data were collected. Four subjects performed an adaptive frequency-discrimination task throughout the experiment. Results show statistically significant tonotopic gradients within both ICs of all subjects. Frequency gradients as a function of depth were measured using surface-based analysis methods that make virtual penetrations into the IC tissue. This organization was evident over substantial portions of the IC, at locations that are consistent with the expected location of the central nucleus of IC. The results confirm a laminar tonotopy in the human IC at 3 T, but with a heterogeneous, patchy character. The success of these surface-based analysis methods will enable more detailed non-invasive explorations of the functional architecture of other subcortical human auditory structures that have complex, laminar organization.

Model of the transient neurovascular response based on prompt arterial dilation

Brief neural stimulation results in a stereotypical pattern of vascular and metabolic response that is the basis for popular brain-imaging methods such as functional magnetic resonance imagine. However, the mechanisms of transient oxygen transport and its coupling to cerebral blood flow (CBF) and oxygen metabolism (CMRO2) are poorly understood. Recent experiments show that brief stimulation produces prompt arterial vasodilation rather than venous vasodilation. This work provides a neurovascular response model for brief stimulation based on transient arterial effects using one-dimensional convection-diffusion transport. Hemoglobin oxygen dissociation is included to enable predictions of absolute oxygen concentrations. Arterial CBF response is modeled using a lumped linear flow model, and CMRO2 response is modeled using a gamma function. Using six parameters, the model successfully fit 161/166 measured extravascular oxygen time courses obtained for brief visual stimulation in cat cerebral cortex. Results show how CBF and CMRO2 responses compete to produce the observed features of the hemodynamic response: initial dip, hyperoxic peak, undershoot, and ringing. Predicted CBF and CMRO2 response amplitudes are consistent with experimental measurements. This model provides a powerful framework to quantitatively interpret oxygen transport in the brain; in particular, its intravascular oxygen concentration predictions provide a new model for fMRI responses.

Computational modeling of the transient hemodynamic response in cerebral cortex

Neural activity triggers a vascular response in the brain that leads to transient changes in oxygen transport, and this mechanism is the basis for popular and powerful functional imaging methods. However, there is limited understanding of oxygen delivery to cerebral cortex both in steady state and during transient perturbations. In this study, a computational model for oxygen transport in the brain was developed and used to fit polarographic oxygen measurements during transient stimulation in cerebral cortex. The hemodynamic response function (HRF) was modeled with convection-diffusion transport in a four-compartment system (erythrocyte, intravascular, extravascular, and intracellular) that includes oxygen dissociation from hemoglobin. This model explained the dynamics of oxygen transport in cortex after brief visual stimulation, successfully fitting ~90% of experimental measurements within a realistic range of parameters for steady-state flow speed and oxygen consumption, as well as flow and oxygen uptake perturbations.

Shape-based regularization of electron tomographic reconstruction

We introduce a tomographic reconstruction method implemented using a shape-based regularization technique. Spatial models of known features in the structure being reconstructed are integrated into the reconstruction process as regularizers. Our regularization scheme is driven locally through shape information obtained from segmentation and compared with a known spatial model. We demonstrated our method on tomography data from digital phantoms, simulated data, and experimental electron tomography (ET) data of virus complexes. Our reconstruction showed reduced blurring and an improvement in the resolution of the reconstructed volume was also measured. This method also produced improved demarcation of spike boundaries in viral membranes when compared with popular techniques like weighted back projection and the algebraic reconstruction technique. Improved ET reconstructions will provide better structure elucidation and improved feature visualization, which can aid in solving key biological issues. Our method can also be generalized to other tomographic modalities.

High-resolution functional magnetic resonance imaging methods for human midbrain

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon measuring activity on the surface of cerebral cortex rather than in subcortical regions such as midbrain and brainstem. Subcortical fMRI must overcome two challenges: spatial resolution and physiological noise. Here we describe an optimized set of techniques developed to perform high-resolution fMRI in human SC, a structure on the dorsal surface of the midbrain; the methods can also be used to image other brainstem and subcortical structures. High-resolution (1.2 mm voxels) fMRI of the SC requires a non-conventional approach. The desired spatial sampling is obtained using a multi-shot (interleaved) spiral acquisition (1). Since, T(2)* of SC tissue is longer than in cortex, a correspondingly longer echo time (T(E) ~ 40 msec) is used to maximize functional contrast. To cover the full extent of the SC, 8-10 slices are obtained. For each session a structural anatomy with the same slice prescription as the fMRI is also obtained, which is used to align the functional data to a high-resolution reference volume. In a separate session, for each subject, we create a high-resolution (0.7 mm sampling) reference volume using a T(1)-weighted sequence that gives good tissue contrast. In the reference volume, the midbrain region is segmented using the ITK-SNAP software application (2). This segmentation is used to create a 3D surface representation of the midbrain that is both smooth and accurate (3). The surface vertices and normals are used to create a map of depth from the midbrain surface within the tissue (4). Functional data is transformed into the coordinate system of the segmented reference volume. Depth associations of the voxels enable the averaging of fMRI time series data within specified depth ranges to improve signal quality. Data is rendered on the 3D surface for visualization. In our lab we use this technique for measuring topographic maps of visual stimulation and covert and overt visual attention within the SC (1). As an example, we demonstrate the topographic representation of polar angle to visual stimulation in SC.

Measurements and modeling of transient blood flow perturbations induced by brief somatosensory stimulation

Proper interpretation of BOLD fMRI and other common functional imaging methods requires an understanding of neurovascular coupling. We used laser speckle-contrast optical imaging to measure blood-flow responses in rat somatosensory cortex elicited by brief (2 s) forepaw stimulation. Results show a large increase in local blood flow speed followed by an undershoot and possible late-time oscillations. The blood flow measurements were modeled using the impulse response of a simple linear network, a four-element windkessel. This model yielded excellent fits to the detailed time courses of activated regions. The four-element windkessel model thus provides a simple explanation and interpretation of the transient blood-flow response, both its initial peak and its late-time behavior.

Surface-based analysis methods for high-resolution functional magnetic resonance imaging

Functional magnetic resonance imaging (fMRI) has become a popular technique for studies of human brain activity. Typically, fMRI is performed with >3-mm sampling, so that the imaging data can be regarded as two-dimensional samples that average through the 1.5-4-mm thickness of cerebral cortex. The increasing use of higher spatial resolutions, <1.5-mm sampling, complicates the analysis of fMRI, as one must now consider activity variations within the depth of the brain tissue. We present a set of surface-based methods to exploit the use of high-resolution fMRI for depth analysis. These methods utilize white-matter segmentations coupled with deformable-surface algorithms to create a smooth surface representation at the gray-white interface and pial membrane. These surfaces provide vertex positions and normals for depth calculations, enabling averaging schemes that can increase contrast-to-noise ratio, as well as permitting the direct analysis of depth profiles of functional activity in the human brain.

Topography of covert visual attention in human superior colliculus

Experiments were performed to examine the topography of covert visual attention signals in human superior colliculus (SC), both across its surface and in its depth. We measured the retinotopic organization of SC to direct visual stimulation using a 90° wedge of moving dots that slowly rotated around fixation. Subjects (n = 5) were cued to perform a difficult speed-discrimination task in the rotating region. To measure the retinotopy of covert attention, we used a full-field array of similarly moving dots. Subjects were cued to perform the same speed-discrimination task within a 90° wedge-shaped region, and only the cue rotated around fixation. High-resolution functional magnetic resonance imaging (fMRI, 1.2 mm voxels) data were acquired throughout SC. These data were then aligned to a high-resolution T1-weighted reference volume. The SC was segmented in this volume so that the surface of the SC could be computationally modeled and to permit calculation of a depth map for laminar analysis. Retinotopic maps were obtained for both direct visual stimulation and covert attention. These maps showed a similar spatial distribution to visual stimulation maps observed in rhesus macaque and were in registration with each other. Within the depth of SC, both visual attention and stimulation produced activity primarily in the superficial and intermediate layers, but stimulation activity extended significantly more deeply than attention.

A model for transient oxygen delivery in cerebral cortex

Popular hemodynamic brain imaging methods, such as blood oxygen-level dependent functional magnetic resonance imaging (BOLD fMRI), would benefit from a detailed understanding of the mechanisms by which oxygen is delivered to the cortex in response to brief periods of neural activity. Tissue oxygen responses in visual cortex following brief visual stimulation exhibit rich dynamics, including an early decrease in oxygen concentration, a subsequent large increase in concentration, and substantial late-time oscillations (“ringing”). We introduce a model that explains the full time-course of these observations made by Thompson et al. (2003). The model treats oxygen transport with a set of differential equations that include a combination of flow and diffusion in a three-compartment (intravascular, extravascular, and intracellular) system. Blood flow in this system is modeled using the impulse response of a lumped linear system that includes an inertive element; this provides a simple biophysical mechanism for the ringing. The model system is solved numerically to produce excellent fits to measurements of tissue oxygen. The results give insight into the dynamics of cerebral oxygen transfer, and can serve as the starting point to understand BOLD fMRI measurements.

Macromolecular connections of active zone material to docked synaptic vesicles and presynaptic membrane at neuromuscular junctions of mouse

Electron tomography was used to view macromolecules composing active zone material (AZM) in axon terminals at mouse neuromuscular junctions. Connections of the macromolecules to each other, to calcium channels in the presynaptic membrane, and to synaptic vesicles docked on the membrane prior to fusing with it during synaptic transmission were similar to those of AZM macromolecules at frog neuromuscular junctions previously examined by electron tomography and support the hypothesis that AZM regulates vesicle docking and fusion. A species difference in the arrangement of AZM relative to docked vesicles may help account for a greater vesicle-presynaptic membrane contact area during docking and a greater probability of fusion during synaptic transmission in mouse. Certain AZM macromolecules in mouse were connected to synaptic vesicles contacting the presynaptic membrane at sites where fusion does not occur. These secondary docked vesicles had a different relationship to the membrane and AZM macromolecules than primary docked vesicles, consistent with their having a different AZM-regulated behavior.

Multifunctional Particles: Magnetic Nanocrystals and Gold Nanorods Coated with Fluorescent Dye-Doped Silica Shells

Multifunctional colloidal core-shell nanoparticles of magnetic nanocrystals (of iron oxide or FePt) or gold nanorods encapsulated in silica shells doped with the fluorescent dye, Tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate (Rubpy) were synthesized. The as-prepared magnetic nanocrystals are initially hydrophobic and were coated with silica using a microemulsion approach, while the as-prepared gold nanorods are hydrophilic and were coated with silica using a Stöber-type of process. Each approach yielded monodisperse nanoparticles with uniform fluorescent dye-doped silica shells. These colloidal heterostructures have the potential to be used as dual-purpose tags-exhibiting a fluorescent signal that could be combined with either dark-field optical contrast (in the case of the gold nanorods), or enhanced contrast in magnetic resonance images (in the case of magnetic nanocrystal cores). The optical and magnetic properties of the fluorescent silica-coated gold nanorods and magnetic nanocrystals are reported.

Functional brain imaging with BOSS FMRI

The standard method for FMRI, using the blood oxygenation level dependent (BOLD) effect, has significant limitations that result from the coupling of functional contrast to sources of image artifact. We have developed an alternative method for FMRI based on balanced-SSFP imaging. This method uses the balanced-SSFP phase profile to invert the signal in deoxygenated blood relative to oxygenated blood. The resulting blood oxygenation sensitive steady-state (BOSS) signal decouples functional contrast from imaging, enabling significantly better image quality than BOLD FMRI. BOSS FMRI is very SNR-efficient, achieves strong functional contrast and is relatively immune to susceptibility gradients. In this paper, we present results validating the ability to detect functional activity using BOSS FMRI. One of the potential advantages of BOSS FMRI is the ability to acquire high-resolution data due to the SNR efficiency of balanced-SSFP. Preliminary high resolution results (1 x 1 x 2 mm/sup 3/) at 1.5 T are presented.

Laminar profiles of functional activity in the human brain

Functional magnetic resonance imaging (fMRI) data were obtained in human visual cortex using sub-millimeter voxels at a field strength of 3 T. Reliable functional signals were largely confined to the gray matter and these responses measure the retinotopic organization of visual cortex. Functional signals were further characterized with respect to their laminar position within the cortical gray matter. The laminar response profiles during our visuospatial attention task, normalized for cortical thickness, had a stereotypical shape, with a peak in the superficial gray matter and declining in the deeper layers. The thickness of the sheet producing functional signals was in excellent agreement with the estimated structural thickness of the gray matter throughout early visual cortex (error < 0.5 mm). Thickness measurements were highly repeatable from session-to-session (error < 0.4 mm). Hence, it is feasible and useful to use high-resolution fMRI to measure laminar activity profiles. The ability to distinguish signals arising in different lamina has significant potential scientific and clinical applications.

Neural correlates of sustained spatial attention in human early visual cortex

Attention is thought to enhance perceptual performance at attended locations through top-down attention signals that modulate activity in visual cortex. Here, we show that activity in early visual cortex is sustained during maintenance of attention in the absence of visual stimulation. We used functional magnetic resonance imaging (fMRI) to measure activity in visual cortex while human subjects performed a visual detection task in which a variable-duration delay period preceded target presentation. Portions of cortical areas V1, V2, and V3 representing the attended part of the visual field exhibited sustained increases in activity throughout the delay period. Portions of these cortical areas representing peripheral, unattended parts of the visual field displayed sustained decreases in activity. The data were well fit by a model that assumed the sustained neural activity was constant in amplitude over a time period equal to that of the actual delay period for each trial. These results demonstrate that sustained attention responses are present in early visual cortex (including primary visual cortex), in the absence of a visual stimulus, and that these responses correlate with the allocation of visuospatial attention in both the spatial and temporal domains.

High-resolution imaging reveals highly selective nonface clusters in the fusiform face area

A region in ventral human cortex (fusiform face area, FFA) thought to be important for face perception responds strongly to faces and less strongly to nonface objects. This pattern of response may reflect a uniform face-selective neural population or activity averaged across populations with heterogeneous selectivity. Using high-resolution functional magnetic resonance imaging (MRI), we found that the FFA has a reliable heterogeneous structure: localized subregions within the FFA highly selective to faces are spatially interdigitated with localized subregions highly selective to different object categories. We found a preponderance of face-selective responses in the FFA, but no difference in selectivity to faces compared to nonfaces. Thus, standard fMRI of the FFA reflects averaging of heterogeneous highly selective neural populations of differing sizes, rather than higher selectivity to faces. These results suggest that visual processing in this region is not exclusive to faces. Overall, our approach provides a framework for understanding the fine-scale structure of neural representations in the human brain.

Topographic maps of visual spatial attention in human parietal cortex

Functional magnetic resonance imaging (fMRI) was used to measure activity in human parietal cortex during performance of a visual detection task in which the focus of attention systematically traversed the visual field. Critically, the stimuli were identical on all trials (except for slight contrast changes in a fully randomized selection of the target locations) whereas only the cued location varied. Traveling waves of activity were observed in posterior parietal cortex consistent with shifts in covert attention in the absence of eye movements. The temporal phase of the fMRI signal in each voxel indicated the corresponding visual field location. Visualization of the distribution of temporal phases on a flattened representation of parietal cortex revealed at least two distinct topographically organized cortical areas within the intraparietal sulcus (IPS), each representing the contralateral visual field. Two cortical areas were proposed based on this topographic organization, which we refer to as IPS1 and IPS2 to indicate their locations within the IPS. This nomenclature is neutral with respect to possible homologies with well-established cortical areas in the monkey brain. The two proposed cortical areas exhibited relatively little response to passive visual stimulation in comparison with early visual areas. These results provide evidence for multiple topographic maps in human parietal cortex.

Functional brain imaging using a blood oxygenation sensitive steady state

Blood oxygenation level dependent (BOLD) functional MRI (fMRI) is an important method for functional neuroimaging that is sensitive to changes in blood oxygenation related to brain activation. While BOLD imaging has good spatial coverage and resolution relative to other neuroimaging methods (such as positron emission tomography (PET)), it has significant limitations relative to other MRI techniques, including poor spatial resolution, low signal levels, limited contrast, and image artifacts. These limitations derive from the coupling of BOLD functional contrast to sources of image degradation. This work presents an alternative method for fMRI that may over-come these limitations by establishing a blood oxygenation sensitive steady-state (BOSS) that inverts the signal from deoxygenated blood relative to the water signal. BOSS fMRI allows the imaging parameters to be optimized independently of the functional contrast, resulting in fewer image artifacts and higher signal-to-noise ratio (SNR). In addition, BOSS fMRI has greater functional contrast than BOLD. BOSS fMRI requires careful shimming and multiple acquisitions to obtain a precise alignment of the magnetization to the SSFP frequency response.

Neuronal correlates of perception in early visual cortex

We used functional magnetic resonance imaging (fMRI) to measure activity in human early visual cortex (areas V1, V2 and V3) during a challenging contrast-detection task. Subjects attempted to detect the presence of slight contrast increments added to two kinds of background patterns. Behavioral responses were recorded so that the corresponding cortical activity could be grouped into the usual signal detection categories: hits, false alarms, misses and correct rejects. For both kinds of background patterns, the measured cortical activity was retinotopically specific. Hits and false alarms were associated with significantly more cortical activity than were correct rejects and misses. That false alarms evoked more activity than misses indicates that activity in early visual cortex corresponded to the subjects' percepts, rather than to the physically presented stimulus.

What does fMRI tell us about neuronal activity?

In recent years, cognitive neuroscientists have taken great advantage of functional magnetic resonance imaging (fMRI) as a non-invasive method of measuring neuronal activity in the human brain. But what exactly does fMRI tell us? We know that its signals arise from changes in local haemodynamics that, in turn, result from alterations in neuronal activity, but exactly how neuronal activity, haemodynamics and fMRI signals are related is unclear. It has been assumed that the fMRI signal is proportional to the local average neuronal activity, but many factors can influence the relationship between the two. A clearer understanding of how neuronal activity influences the fMRI signal is needed if we are correctly to interpret functional imaging data.

Neuronal basis of the motion aftereffect reconsidered

Several fMRI studies have reported MT+ response increases correlated with perception of the motion aftereffect (MAE). However, attention can strongly affect MT+ responses, and subjects may naturally attend more to the MAE than control trials without MAE. We found that requiring subjects to attend to motion on both MAE and control trials produced equal levels of MT+ response, suggesting that attention may have confounded the interpretation of previous experiments; in our data, attention accounts for the entire effect. After eliminating this confound, we observed that direction-selective motion adaptation produced a direction-selective imbalance in MT+ responses (and earlier visual areas), and yielded a corresponding asymmetry in speed discrimination thresholds. These findings provide physiological evidence that population level response imbalances underlie the MAE, and quantify the relative proportions of direction-selective neurons across human visual areas.