Keywords: fMRI Acquisition, Simulations

Motivation: fMRI is a powerful tool for neuroimaging, but its optimization in vivo is complicated due to limited reproducibility. Simulation setup can help, but current solutions lack flexibility, control, or efficiency.

Goal(s): Develop a versatile and efficient fMRI simulator generating realistic fMRI data under various conditions: SNR levels,  acceleration factors, spatiotemporal resolutions, noise, and artifact sources.

Approach: We propose SNAKE-fMRI, a modular,  open-source fMRI simulator that operates from image to k-space and vice-versa. It can generate 3D+time k-space and images, mimicking the entire fMRI acquisition process, with potential k-t accelerations.

Results: We showcase the use of SNAKE-fMRI on a non-Cartesian k-t accelerated scenario.

Impact: With SNAKE-fMRI as an open-source, versatile, and efficient fMRI simulator, researchers can generate realistic fMRI data under a controlled and fully reproducible setup, enabling new advancements in fMRI acquisition and reconstruction methods.

Keywords: fMRI Acquisition, New Signal Preparation Schemes, Acquisition Methods, Blood Vessels, Brain, Contrast Mechanisms, fMRI (task based), fMRI Acquisition, New Signal Preparation Schemes, Novel Contrast Mechanisms, Pulse Sequence Design, RF Pulse Design & Fields, Vascular, Velocity & Flow, inflow, black-blood contrast, blood nulling, functional contrast, blood flow, blood volume, arteries, veins, flow related signal enhancement

Motivation: Magnetization-preparation schemes using inversion recovery measure aspects of hemodynamics like perfusion and blood volume, but their temporal resolution is limited by physiology, i.e., long blood arrival/transit times.

Goal(s): To study brain hemodynamics at high temporal resolutions with novel inflow saturation.

Approach: We applied saturation bands on both sides of a rapidly-sampled single imaging slice to suppress inflow-related signal and produce black-blood functional contrast sensitive to macrovascular blood volume.

Results: Phantom experiments show successful suppression of inflow signal with flow-velocity-dependence at low- and high-velocity regimes but independence at mid-regime. Human brain vessels exhibited partial signal suppression, with more functional suppression seen in larger vessels.

Impact: Fast blood nulling may be achievable using local saturation bands contiguous to an imaging slice rather than a global inversion slab, enabling functional contrasts sensitive to macrovascular blood flow-velocity and volume suitable for studying fast hemodynamics in specific vascular compartments.

Keywords: Task/Intervention Based fMRI, Contrast Agent, CBV, Data Acquisition, Data Analysis

Motivation: Conventional use of typical T2* weighted sequences such as FLASH post iron-oxide contrast injection exhibits an enhanced microvascular weighting but neglects changes in pial vessels due to strong dephasing defects.

Goal(s): Our goal is to study changes in the pial vessels which will hopefully aid in the interpretation of non-BOLD fMRI signals and help us understand the CBV fMRI signal at a deeper level.

Approach: We utilised a radial UTE sequence post-contrast injection with short TE and short readout duration 

Results: We found consistent positive signal changes in the visual cortex and pial surface.

Impact: We found positive signal changes at the pial surface and in the visual cortex upon stimulation. This might indicate the involvement of both micro- and macrovasculature and provide further insights into cerebral-blood-volume changes across vascular compartments.

Keywords: fMRI Analysis, Multimodal, Brain; Data Analysis; fMRI; Neuroscience; PET/MR

Motivation: Latest advances in functional PET (fPET)-FDG and PET-MRI have enabled us to map stimulus-driven metabolic and hemodynamic changes simultaneously within a single scan. However, existing PET-MRI studies have focused on the static, time-averaged (de)couplings of fPET-fMRI signals, neglecting the rich information embedded in their temporal dependence.

Goal(s): The goal of this study is to propose and validate an analytical framework linking dynamic, concurrent variations in fPET and fMRI signals.

Approach: The efficacy of the framework was tested on visual task and naturalistic arousal fPET-fMRI datasets.

Results: Our results demonstrated that metabolic changes modeled by concurrent fMRI signals could successfully predict instantaneous fPET-FDG dynamics.

Impact: The statistical framework proposed by our study will enable broad functional PET-MRI studies to elucidate the dynamic interplays amongst metabolic and hemodynamic processes that are otherwise obscured in the conventional, time-averaged analysis.

Keywords: fMRI Acquisition, fMRI (task based), line-scanning fMRI method

Motivation: Spin-echo-based line-scanning employing inner-volume excitation has been proposed for line-scan fMRI to avoid artifacts stemming from imperfect saturation RF pulses.

Goal(s): To measure non-contiguous and non-coplanar BOLD signals at multiple cerebral cortical areas.

Approach: We developed multi-line T2’- and T2-weighted Gradient-echo sampling of a spin-echo (GESSE) line-scanning fMRI method. 

Results: This novel approach enables the detection of fMRI activation at different visual cortical regions, showing pure T2 and TE-dependent BOLD responses. It provides a proof-of-concept to further examine interactions of high-resolution fMRI signals at multiple cortical locations along feedforward and feedback pathways.

Impact: A non-coplanar multi-line gradient-echo sampling of spin-echo (GESSE) line-scanning method was proposed as a novel approach for distinguishing macro- and micro-vascular sensitive fMRI signals by simultaneouslyacquiring T2’- and T2-weighted BOLD fMRI signals at multiple cortical locations.

Keywords: fMRI Acquisition, Contrast Mechanisms

Motivation: Efficient, distortion-free, and selective to microvessels: these attributes make bSSFP an attractive candidate for fMRI. 2D multi-slice scans in the transient state are increasingly employed as an alternative to 3D steady-state imaging to improve localization.

Goal(s): To evaluate the BOLD sensitivity of bSSFP during the transient phase as compared to the steady state.

Approach: bSSFP acquisitions in transient and steady state are utilized for task-based fMRI. Monte Carlo simulations and in vitro microsphere experiments are conducted to verify the in vivo results.

Results: An inversion of the BOLD contrast with a trend towards negative BOLD in the early transient phase can be observed.

Impact: The bSSFP BOLD contrast undergoes an inversion during the transient phase. Consequently, the BOLD response appears suppressed in transient-state imaging with a tendency to become negative, which has important implications when designing 2D multi-slice fMRI experiments with high temporal resolution.

Keywords: fMRI Acquisition, Multimodal, fMRI (resting state), functional connectivity, neuroscience

Motivation: rsfMRI network dynamics are essential for cognitive processes, however, their underlying neural bases remain unclear.

Goal(s): Here, we aim to examine the neural oscillatory events underlying the dynamic patterns of rsfMRI networks across the entire brain.

Approach: We employed simultaneous EEG-fMRI to record brain-wide rsfMRI and neural signals at default mode network. Further, EEG events were identified and temporally matched with dynamic rsfMRI network states derived from a data-driven model.

Results: Our results demonstrated robust associations between rsfMRI network dynamics and neural oscillatory events, especially slow oscillation-coupled spindle, gamma events and slow oscillation.

Impact: Our results demonstrated the different effects of spontaneous neural oscillatory events (e.g., slow oscillation, spindle, and gamma) in default mode network underlying the dynamics of rsfMRI networks.

Keywords: Task/Intervention Based fMRI, Susceptibility, functional susceptibility mapping fQSM

Motivation: fQSM has emerged as a complementary technique to fMRI but the effect of multiband acceleration factors is unknown. Some studies have used absolute QSM input but no systematic comparison has been performed.
 

Goal(s): To investigate the impact of multiband factors on task-based fQSM activations and the effect of analysing absolute versus signed QSM.

Approach: We compared fQSM with a visual stimulus for multiband factors 3 and 4, and for signed and absolute QSM inputs.

Results: Increasing multiband factors reduced cluster sizes and activation t-scores in fQSM likely due to greater g-factor noise. Absolute QSM yielded fewer, larger activation clusters than signed QSM.

Impact: fQSM activations decreased with increasing multiband acceleration, highlighting a tradeoff between multiband acceleration and fQSM sensitivity. Using absolute versus signed QSM for fQSM may result in loss of information. These factors must be carefully considered for optimal future fQSM studies.

Keywords: fMRI Acquisition, fMRI, Undersampling, Temporal Priors

Motivation: Three-dimension reduced field-of-view imaging with (k, t)-space undersampling (k-t 3D-rFOVI) can be used for high temporospatial-resolution fMRI acquisition in a focused brain volume.

Goal(s): This study aims at developing an image reconstruction method for k-t 3D-rFOVI to improve the fMRI data quality.

Approach: Timing information about stimulation tasks was integrated into image reconstruction of k-t 3D-rFOVI. Simulation and human fMRI experiments with a 6-fold acceleration factor were conducted to demonstrate the performance of the reconstruction method.

Results: The proposed reconstruction method substantially increased the sensitivity of k-t 3D-rFOVI in detecting fMRI activations and the accuracy in recovering the time course of fMRI signals.

Impact: By incorporating stimulus timing information into image reconstruction, high-quality fMRI data can be obtained using k-t 3D-rFOVI with high temporal (480 ms) and spatial (1.5 mm) resolutions over a reduced field-of-view.

Keywords: fMRI Analysis, fMRI, preclinical fMRI, awake fMRI, multimodal imaging, whisker stimulation, whisker tracking

Motivation: Anesthesia causes alterations in brain functional data and internal brain states affect sensory perception.

Goal(s): We sought to investigate how the Blood Oxygen Level Dependence (BOLD) response from spontaneous and stimulated whisker motion in awake mice is related to cerebral arousal state monitored by acetylcholine.

Approach: Mice with implanted RF coils and fiber optic cable were simultaneously imaged and acetylcholine signals were monitored to measure correlation between BOLD and acetylcholine signals.

Results: We found stimulating the whiskers produced the expected contralateral BOLD response in awake animals but also an acetylcholine spike in the ipsilateral side indicating whole-brain dynamic activation occurs in awake mice.

Impact: This work shows feasibility of simultaneous high-resolution EPI-based functional imaging and fiber photometry of acetylcholine response to whisker stimulation in awake mice as a multimodal method for investigating brain state from external sensory stimulation using implantable RF coils.

Keywords: fMRI Acquisition, High-Field MRI, Infants, multi-echo EPI, 7T, functional connectivity, developmental neuroimaging

Motivation: Imaging infants with traditional voxel sizes is suboptimal due to their smaller brains. 7T imaging allows for higher spatial resolutions, while multi-echo fMRI provides optimal contrast across the brain.

Goal(s): Establish the feasibility of high-resolution multi-echo fMRI in infants at 7T.

Approach: Acquire data in the same infant at 3T/7T within the same week, allowing for direct comparisons, while also considering unique safety guidelines for 7T infant imaging.

Results: Initial data demonstrate 3T/7T multi-echo fMRI in the same infant, establishing the feasibility of high-resolution ME-fMRI at 7T in infants with high contrast, sensitivity, and stronger functional connections.

Impact: This first demonstration of multi-echo fMRI at 7T, including the use of voxel volumes (1.6 mm³) that are half the volume of what is normally used in 3T infant fMRI (2.0 mm³), promises opportunities to advance developmental neuroimaging.

Keywords: fMRI Acquisition, fMRI

Motivation: There are reports that line-scan MRI methods can directly measure neural activity (the DIANA response).

Goal(s): In light of replication failures, we sought to understand the noise profile of the line-scan acquisition.

Approach: Using the line-scan protocol (3T GE UHP scanner, N=5) we measured human visual cortex while subjects viewed a blank screen.

Results: The noise has a 1/f temporal spectrum that can be confused with certain stimulus-driven responses. This noise spreads into the surrounding volume in the phase-encoding direction. We explain the pattern of results with a model of the sequence that incorporates time-varying contrast fluctuations.

Impact: Line-scan MRI is particularly susceptible to physiological noise because of its long acquisition time to create a single image. For this reason, the sequence will have difficulty measuring small contrast fluctuations due to neural electrical activity.

Keywords: fMRI Acquisition, fMRI, sliding-window, high temporal resolution, BOLD

Motivation: Higher temporal resolution in fMRI has been increasingly sought after, primarily because of a greater interest in the high-frequency components of BOLD, but also because high temporal resolution is essential to get rid of physiological artifacts.

Goal(s): In light of this mounting interest, we explore the sliding-window approach to improve the temporal resolution, specifically using SPARKLING fMRI.

Approach:  A simulation study is conducted for 2D BOLD fMRI at realistic SNR. 

Results: It demonstrates the possibility through the sliding window approach to detect oscillations beyond 0.2Hz in the BOLD response and separate the physiological noise from the neural activity.

Impact: Such a strategy can be extended to 3D imaging in a straightforward manner, thereby making whole-brain high spatiotemporal resolution fMRI feasible.   

Keywords: fMRI Acquisition, Brain, functional MRI

Motivation: Cerebral blood volume (CBV) fMRI has inherent limitations regarding its imaging efficiency, restricting the spatial volume coverage and spatiotemporal resolution

Goal(s): To improve imaging efficiency for whole-brain VASO fMRI with high temporal resolution

Approach: we introduce a view sharing approach combined with flexible temporal encoding

Results: Proposed method achieves whole-brain VASO and BOLD imaging in 8.3 seconds, while resulting in higher VASO and BOLD activations with high sensitivity

Impact: We confirmed that 1) a view-sharing approach allows VASO and BOLD signal detection without contrast confounding and 2) the random encoding coupled with view sharing significantly improves the imaging efficiency by achieving an 8.3 second whole-brain VASO imaging.  

Keywords: Task/Intervention Based fMRI, Data Analysis, Cerebrovascular reactivity

Motivation: Breath-hold BOLD fMRI may be regarded as a proxy of deoxygenated cerebral blood volume (CBV_dHb), instead of cerebrovascular reactivity (CVR) when blood flow changes are uniform in response to breath-hold.

Goal(s): We aimed to test this assumption in healthy volunteers.

Approach: We measured the spatial uniformity of CVR derived from arterial spin labelling and BOLD fMRI data acquired simultaneously during a breath-holding task.

Results: Breath-hold induced a more uniform fractional increase in CBF than in BOLD signal. Thus, the spatial variability in apparent BOLD-CVR is likely due to variation in CBV_dHb with little variability arising from spatial differences in vascular reactivity.

Impact: Under isometabolic conditions in healthy volunteers, owing to the uniform change in blood flow induced by breath-hold, it is possible to infer maps of deoxygenated cerebral blood volume based on BOLD fMRI breath-hold data.