Imagine being able to study the human brain in real-world scenarios while the subject displays natural behaviors such as locomotion, social interaction, or spatial navigation. The advent of ultrafast ultrasound imaging brings us closer to this goal with functional ultrasound imaging (fUSi), a mobile neuroimaging technique. Here, we present real-time fUSi monitoring of brain activity during walking in a subject with a clinically approved sonolucent skull implant. Our approach uses personalized 3D-printed fUSi helmets for stability, optical tracking for cross-modal validation with functional magnetic resonance imaging, advanced signal processing to estimate hemodynamic responses, and facial tracking of a lick licking paradigm. These combined efforts allowed us to show consistent fUSi signals over 20 months, even during high motion activities such as walking. These results demonstrate the feasibility of fUSi for monitoring brain activity in real-world contexts, marking an important milestone for fUSi-based insights in clinical and neuroscientific research.

Ultrasonography could allow operator-independent examination and continuous monitoring of the carotid artery (CA) but normally requires complex and expensive transducers, especially for 3-D. By employing computational ultrasound imaging (cUSi), using an aberration mask and model-based reconstruction, a monitoring device could be constructed with a more affordable simple transducer design comprising only a few elements. We aim to apply the cUSi concept to create a CA monitoring system. The system’s possible configurations for the 2-D imaging case were explored using a linear array setup emulating a cUSi device in silico, followed by in vitro testing and in vivo CA imaging. Our study shows enhanced reconstruction performance with the use of an aberrating mask, improved lateral resolution through proper choice of the mask delay variation, and more accurate reconstructions using least-squares with QR (LSQR) decomposition compared to matched filtering (MF). Together, these advancements enable B-mode reconstruction and power Doppler imaging (PDI) of the CA with sufficient quality for monitoring using a configuration of 12 transceivers coupled with a random aberration mask with a maximum delay variation of four wave periods (WPs).

Williams syndrome is a developmental disorder caused by a microdeletion entailing the loss of a single copy of 25–27 genes on chromosome 7q11.23. Patients suffer from cardiovascular and neuropsychological symptoms. Structural abnormalities of the cardiovascular system in Williams syndrome have been attributed to the hemizygous loss of the elastin (ELN) gene. In contrast, the neuropsychological consequences of Williams syndrome, including sensorimotor deficits, hypersociability, and cognitive impairments, have been mainly attributed to altered expression of transcription factors, like LIMK1, GTF2I, and GTF2IRD1, while the potential impact of altered cerebrovascular function has been largely overlooked. To study the relationship between Williams syndrome mutations and vascularization of both the heart and brain, we generated a mouse model carrying a relatively long microdeletion Del(5Ncf1-Fkbp6). Heterozygous Del(5Ncf1-Fkbp6) mice had elongated and tortuous aortas but, unlike Eln haploinsufficient mice, showed no signs of structural cardiac hypertrophy. Remarkably, we also observed structural abnormalities in coronary and brain vessels, including disorganized extracellular matrices. Importantly, the mutant mice faithfully replicated both cardiovascular and neuropsychological symptoms observed in patients. The phenotype was even more comprehensive than in former models, with structure–function correlations evident in aberrant auditory and motor behaviors resembling those in patients with Williams syndrome. Together, our findings suggest that not only cardiovascular but also neuropsychological symptoms in Williams syndrome may be driven in part by vascular abnormalities affecting both heart and brain.

Dynamic susceptibility contrast (DSC) MRI is commonly part of brain tumor imaging. For quantitative analysis, measurement of the arterial input function and tissue concentration time curve is required. Usually, a linear relationship between the MR signal changes and contrast agent concentration ([Gd]) is assumed, even though this is a known simplification. The aim of this study was to develop a realistic 3D simulation model as an efficient method to assess the relationship between ΔR2(*) and [Gd] both in whole blood and brain tissue. We modified an open-source 3D simulation model to study different red blood cell configurations for assessing whole-blood ΔR2(*) versus [Gd]. The results were validated against previously obtained 2D data and in vitro data. Furthermore, hematocrit levels (30%–50%) and field strengths (1.5–3.0–7.0 T) were varied. Subsequently, realistic tumor vascular networks were derived from intraoperative high framerate Doppler ultrasound data to study the influence of vascular structure and orientation with respect to the main magnetic field (1.5–3.0–7.0 T) for the calculation of ΔR2(*) versus [Gd] in brain tissue. For whole blood, good agreement of the 3D model was found with in vitro and 2D simulation data when red blood cells were aligned with the blood flow. For brain tissue, minor differences were found between the vascular networks. The effect of vessel direction with respect to B0 was apparent in case of clear directionality of the main vessels. The dependency on field strength agreed with previous reports. In conclusion, we have shown that the relationship between ΔR2(*) and [Gd] is affected by the organization of red blood cells and orientation of blood vessels with respect to the main magnetic field, as well as the field strength. These findings are important for further optimization of the realistic 3D model that could eventually be used to improve the estimation of hemodynamic parameters from DSC-MRI.

Ultrafast imaging, which uses unfocussed transmissions to form images, provides very high frame rates at the cost of low signal-to-noise ratio (SNR). This loss of SNR becomes especially apparent when imaging deeper structures. Ultrafast imaging is mostly used in combination with Doppler processing. Even if we apply tissue-separation filters, they lead to significant energy loss and decrease the SNR. Previous work showed that this loss in SNR and, hence, penetration depth can be partially regained using coded transmissions. However, these codes are mostly either standard or randomly generated and can be improved with a design rooted in an optimization scheme. To address this limitation, we design an optimized code tailored to ultrasound imaging with unfocused transmissions represented by a generalized encoding matrix in a linear signal model. We employ the minimization of the Cramér-Rao lower bound (CRB) over the unknown coding matrix as a way to optimize the code. Due to the high computational cost of the resulting optimization problems, we also introduce a trace-constraint optimization problem based on the Fisher information matrix (FIM). Simulation results show that the optimized code provides higher SNR in deep image regions than previously tested coding schemes such as the Barker code, albeit with a trade-off for decreased resolution. On the other hand, the application of least-squares QR (LSQR) mitigates this resolution degradation. Lastly, the optimized code was tested in simulations using a numerical model of a clinical transducer setting, demonstrating its potential for higher SNR in ultrafast Doppler imaging.

Computational ultrasound imaging (cUSi) offers high-resolution 3D imaging with simpler hardware by relying on computational power. Central to cUSi is a large model matrix that stores all pulse-echo signals. For 3D imaging this matrix easily surpasses 1 terabyte, hindering in-memory storage and real-time processing. This paper presents a solution for cUSi through an aberrating layer by introducing a virtual array concept, which uses transfer functions to map data from the real to a virtual array, enabling the use of conventional reconstruction techniques like delay-and-sum (DAS). We demonstrate the mathematical similarity of this approach to using a full model matrix and validate it with promising imaging results.

Analysis of functional neuroimaging data aims to unveil spatial and temporal patterns of interest. Existing analysis methods fall into two categories: fully data-driven approaches and those reliant on prior information, e.g. the stimulus time course. While using the stimulus signal directly can help identify the activated brain areas, it is known that the relationship between stimuli and the brain's response exhibits nonlinear and time-varying characteristics. As such, relying completely on the stimulus signal to describe the brain's temporal response leads to a restricted interpretation of the brain function. In this paper, we present a new technique called Evoked Component Analysis (ECA), which leverages prior information up to a defined extent. This is achieved by including the general linear model (GLM) design matrix as a regulatory term and estimating the factor matrices in both space and time through an alternating minimization approach. We apply ECA to 2D and swept-3D functional ultrasound (fUS) experiments conducted with mice. When decomposing 2D fUS data, we employ GLM regularization at various intensities to emphasize the role of prior information. Furthermore, we show that incorporating multiple hemodynamic response functions within the design matrix can provide valuable insights into region-specific characteristics of evoked activity. Finally, we use ECA to analyze swept-3D fUS data recorded from five mice engaged in two distinct visual tasks. Swept-3D fUS images the 3D brain sequentially using a moving probe, resulting in different slice acquisition time instants. We show that ECA can estimate factor matrices with a fine resolution at each slice acquisition time instant and yield higher t-statistics compared to GLM and correlation analysis for all subjects.

Functional ultrasound (fUS) is an emerging neuroimaging modality that records changes in local blood dynamics. While it is known that the brain can respond variably to the same stimuli presented at different time instants, the extent to which fUS detects this variability based on the measured hemodynamics remains an open question. In this work, we characterize trial variability using fUS by estimating activation coefficients per trial using region-specific hemodynamic response functions. Our visual fUS experiments conducted on a mouse consistently reveal an increase of trial variability from the lateral geniculate nucleus to the visual cortex across different brain slices. These results are in parallel with prior findings in neuronal studies, suggesting a link between fluctuations of the evoked fUS response and true neural variability.

In recent decades, increasing ultrasound frame rates has been the main motivation behind many novel ultrasound imaging applications [1]-[3]. With this work, we propose an efficient ultrafast FPGA beamformer that applies coherent compounding, through a delay-reuse optimization.

Four-dimensional ultrasound imaging of complex biological systems such as the brain is technically challenging because of the spatiotemporal sampling requirements. We present computational ultrasound imaging (cUSi), an imaging method that uses complex ultrasound fields that can be generated with simple hardware and a physical wave prediction model to alleviate the sampling constraints. cUSi allows for high-resolution four-dimensional imaging of brain hemodynamics in awake and anesthetized mice.

We consider the scenario of finding the transfer function of an aberrating layer in front of a receiving ultrasound (US) array, assuming a separate non-aberrated transmit source. We propose a method for blindly estimating this transfer function without exact knowledge of the ultrasound sources or acoustic contrast image, and without directly measuring the transfer function using a separate controlled calibration experiment. Instead, the measurement data of many unknown random images is collected, such as from blood flow, and its second-order statistics are exploited. A measurement model is formulated that explicitly defines the layer's transfer function. A covariance domain problem is then defined to eliminate the image variable, and it is solved for the layer's transfer function using manifold-based optimization. The proposed approach and calibration algorithm are evaluated on a range of challenging and realistic simulations using the k-Wave toolbox. Our results show that, given a sufficiently efficient parameterization of the layer's transfer function, and by jointly estimating the transfer function at multiple frequencies, the proposed algorithm is able to obtain an accurate estimate. Subsequent simulated imaging experiments using the obtained transfer function also show increased imaging performance in various aberrating layers, including a skull layer.

Volumetric 3-D Doppler ultrasound imaging can be used to investigate large scale blood dynamics outside of the limited view that conventional 2-D power Doppler images (PDIs) provide. To create 3-D PDIs, 2-D-matrix array transducers can be used to insonify a large volume for every transmission; however, these matrices suffer from low sensitivity, high complexity, and high cost. More typically, a 1-D-Array transducer is used to scan a series of stationary 2-D PDIs, after which a 3-D volume is created by concatenating the 2-D PDIs in postprocessing, which results in long scan times due to repeated measurements. Our objective was to achieve volumetric 3-D Doppler ultrasound imaging with a high Doppler sensitivity, similar to that of a typical stationary recording using a 1-D-Array transducer, while being more affordable than using 2-D-matrix arrays. We achieved this by mounting a 1-D-Array transducer to a high-precision motorized linear stage and continuously translating over the mouse brain in a sweeping manner. For Part I of this article, we focused on creating the best vascular images by investigating how to best combine filtered beamformed ultrasound frames, which were not acquired at the same spatial locations, into PDIs. Part II focuses on the implications of sampling transient brain hemodynamics through functional ultrasound (fUS) while continuously translating over the mouse brain. In Part I, we show how the speed at which we sweep our 1-D-Array transducer affects the Doppler spectrum in a flow phantom. In vivo recordings were performed on the mouse brain while varying the sweeping speed, showing how higher sweeping speeds negatively affect the PDI quality. A weighting vector is found to combine frames while continuously moving over the mouse brain, allowing us to create swept PDIs of similar sensitivity when compared with those obtained using a stationary 1-D-Array while allowing a significantly higher 3-D Doppler volume rate and maintaining the benefits of having a low computational and monetary cost. We show that a vascular subvolume of 6 mm can be scanned in 2.5 s, with a PDI reconstructed every $200 \mu \text{m}$ , outperforming classical staged recording methods.

It has been previously demonstrated that applying an aberrating mask for 2D compressive imaging using a low number of sensors (elements) can significantly improve image resolution, as evaluated via the point spread function. Here we investigate the potential to apply a similar approach for 3D flow monitoring. We conducted a 3D k-Wave simulation using a 5x5 sensor array coupled to a physical coding mask, performing B-mode and power Doppler imaging on a 3D carotid artery flow model. An approximately three times smaller lateral PSF was achieved at the cost of increased background clutter level and slightly increased axial PSF. A better definition of the vessel border and finer flow speckle were observed in power Doppler imaging. Our results suggest that 3D compressive imaging using a very low sensor count of 25 with spatial coding mask has the potential to monitor 3D carotid artery flow.

Functional ultrasound (fUS) is a novel neuroimaging technique that measures brain hemodynamics through a time series of Doppler images. The measured spatiotemporal hemodynamic changes reflect changes in neural activity through the neurovascular coupling (NVC). Often, such image time series is used to analyze dynamic functional connectivity (dFC) by directly computing a connectivity metric between the measured hemodynamic signals, ignoring the functional connectomics of underlying neural populations. This work proposes a novel fUS signal model, consisting of a hidden Markov model (HMM) cascaded with a convolutive model, that captures how fUS signals arise from a generative perspective while incorporating high-level biological functioning of neural populations. Consequently, the developed model enables inference of functional connectivity networks, being co-activation patterns (CAPs) of neural populations. Our results show that our methods can identify biologically plausible networks of functional connectivity. Furthermore, this method captures a difference in brain dynamics between wild-type and ${Shank2}^{-/-}$ mouse mutants.

Functional Ultrasound (fUS) is a relatively new modality to measure brain activity with a high spatio-temporal resolution. In order to collect full-brain information with this 2D imaging technique, fUS data is typically collected for a fixed position of the ultrasound probe for the duration of the experiment, before the probe is moved to the next position. As a result, a 3D functional volume consists of subsequent, time-disjunct 2D datasets. The gold-standard way to analyze fUS datasets is using correlation images or a general linear model. However, these analyses are performed slice by slice; thus, common information across slices is not exploited. We propose the use of two data-driven models, Independent Component Analysis (ICA) and its multiset extension Independent Vector Analysis (IVA), in order to map the mouse visual information processing pathway in 3D. We demonstrate the successful application of ICA and then of IVA, which leverages the dependence across slices in a unique fashion. Furthermore, we provide guidance as to when which approach might be desirable.

Functional ultrasound (fUS) is an emerging neuroimaging modality that indirectly measures neural activity by detecting fluctuations in local blood dynamics. fUS acquisitions typically rely on the use of a 1D array transducer, which records hemodynamic activity in a single plane. A new technique named swept-3D fUS imaging obtains a full 3D volume of the brain by continuously moving a 1D array back-and-forth over the volume of interest. The standard procedure in fUS imaging involves filtering and averaging a number of ultrasound frames obtained at a single location to compute power-Doppler images, yet, in case of swept-3D fUS, the location of the recorded slice shifts at each time instant due to probe motion. In this work, we aim at discovering task-relevant components from 3D fUS data while taking into account the spatiotemporal differences in adjacent slices. We propose an alternating optimization scheme with general liner model-based regularization, and validate our method on swept-3D fUS data by identifying active regions and time traces within the mouse brain during a visual experiment.

Functional ultrasound (fUS) using a 1-D-array transducer normally is insufficient to capture volumetric functional activity due to being restricted to imaging a single brain slice at a time. Typically, for volumetric fUS, functional recordings are repeated many times as the transducer is moved to a new location after each recording, resulting in a nonunique average mapping of the brain response and long scan times. Our objective was to perform volumetric 3-D fUS in an efficient and cost-effective manner. This was achieved by mounting a 1-D-array transducer to a high-precision motorized linear stage and continuously translating over the mouse brain in a sweeping manner. We show how the speed at which the 1-D-array is translated over the brain affects the sampling of the hemodynamic response (HR) during visual stimulation as well as the quality of the resulting power Doppler image (PDI). Functional activation maps were compared between stationary recordings, where only one functional slice is obtained for every recording, and our swept-3-D method, where volumetric fUS was achieved in a single functional recording. The results show that the activation maps obtained with our method closely resemble those obtained during a stationary recording for that same location, while our method is not restricted to functional imaging of a single slice. Lastly, a mouse brain subvolume of 6 mm is scanned at a volume rate of 1.5 s per volume, with a functional PDI reconstructed every 200\mu \text{m} , highlighting swept-3-D's potential for volumetric fUS. Our method provides an affordable alternative to volumetric fUS using 2-D-matrix transducers, with a high SNR due to using a fully sampled 1-D-array transducer, and without the need to repeat functional measurements for every 2-D slice, as is most often the case when using a 1-D-array. This places our swept-3-D method as a potentially valuable addition to conventional 2-D fUS, especially when investigating whole-brain functional connectivity, or when shorter recording durations are desired.

We intend to develop an ultrasound compressive imaging device to perform carotid artery (CA) function and flow monitoring/imaging by using just a few single element transducers equipped with spatial coding masks. The spatially unique impulse responses can be exploited in compressive reconstructions. To explore the potential of different configurations, in this study we emulated such a device using a linear array system. We combined its elements with individual digital delays into a small number of groups. The results suggest our spatial coding mask approach based on reconstructions regularized with a least squares method has potential for CA monitoring with only 10 to 12 sensors.

The original version of this article was revised to update the Figure 8 (panel B) image. The correct image should have a yellow shape as presented below. (Figure presented.). The original article has been corrected.

Functional ultrasound (fUS) indirectly measures brain activity by detecting changes in cerebral blood volume following neural activation. Conventional approaches model such functional neuroimaging data as the convolution between an impulse response, known as the hemodynamic response function (HRF), and a binarized representation of the input signal based on the stimulus onsets, the so-called experimental paradigm (EP). However, the EP may not characterize the whole complexity of the activity-inducing signals that evoke the hemodynamic changes. Furthermore, the HRF is known to vary across brain areas and stimuli. To achieve an adaptable framework that can capture such dynamics of the brain function, we model the multivariate fUS time-series as convolutive mixtures and apply block-term decomposition on a set of lagged fUS autocorrelation matrices, revealing both the region-specific HRFs and the source signals that induce the hemodynamic responses. We test our approach on two mouse-based fUS experiments. In the first experiment, we present a single type of visual stimulus to the mouse, and deconvolve the fUS signal measured within the mouse brain’s lateral geniculate nucleus, superior colliculus and visual cortex. We show that the proposed method is able to recover back the time instants at which the stimulus was displayed, and we validate the estimated region-specific HRFs based on prior studies. In the second experiment, we alter the location of the visual stimulus displayed to the mouse, and aim at differentiating the various stimulus locations over time by identifying them as separate sources.