Keywords: Functional Connectivity, High-Field MRI, layer fMRI, ReHo

Motivation: High resolution fMRI is an emerging field, analysis pipelines are still under development. Local and short distanced time course similarities also named as Layer dependent regional homogeneity, can give us insights to map laminar dependent signal differences.

Goal(s): Using a simple metric to color code the depth dependent cortical activity.

Approach: Using mesoscale functional structure to predict and understand, time locked activity patterns in cortical ribbon without having necessity of  specific model or predefined ROI

Results: Layer dependent regional homogeneity predicts local activity patterns, also can be used as a similarity matrix to rank different runs which potentially contributes to similar layer patterns.

Impact: This work can potentially be a publicly available analysis tool to observe and quality check, can also quantify laminar separability of the acquired depth dependent high resolution fMRI data.

Keywords: fMRI Analysis, fMRI, NORDIC , VASO, laminar fMRI

Motivation: NORDIC denoising can effectively enhance the limited SNR in high-resolution fMRI. However, its application on VASO is yet to be validated. 

Goal(s): We aimed to evaluate applications of NORDIC on VASO data and to offer recommendations for its execution. 

Approach: We examined NORDIC’s capability to suppress noise while preserving the VASO signal across a wide parameter spectrum 

Results: With a proper set of parameters, NORDIC effectively suppressed noise with minimal biases on the underlying signal. 

Impact: NORDIC can substantially enhance the SNR in submillimeter VASO fMRI. We found the denoising performance to be sensitive to parameter choices and provide recommendations for safe execution.

Keywords: fMRI Acquisition, High-Field MRI, BOLD fMRI; Biophysical Simulations; High-Resolution fMRI; Vasculature

Motivation: Recent ultra-high-resolution gradient-echo BOLD-fMRI data demonstrate an unexpected reduction in sensitivity to large veins at 7T, suggesting that small voxels may experience less signal loss due to extravascular dephasing.

Goal(s): To test whether a reduction in through-plane or in-plane dephasing with small voxels may measurably contribute to reduced large-vein influences in gradient-echo BOLD.

Approach: We apply biophysical simulations of simplified vascular architecture, combined with realistic image encoding gradients.

Results: While voxels adjacent to veins are still strongly influenced, smaller voxel sizes have reduced extravascular BOLD, which impacts cerebral cortical-depth profiles of activation. The direction of the imaging encoding gradients also affects these profiles.

Impact: Rencelty available ultra-high-resolution fMRI improves spatial accuracy, and may also provide an unexpected improvement in neuronal specificity. We demonstrate that small-voxel gradient-echo BOLD achieves reduced unwanted contamination from large veins, potentially providing an fMRI method with high sensitivity AND specificity.

Keywords: fMRI Analysis, fMRI, layer fQSM

Motivation: The feasibility of high-resolution fQSM at ultra-high field and the good localization properties of fQSM as well as its quantitative nature motivated this study which aims to use fQSM for investigating layer-dependent activation. 

Goal(s): To investigate the feasibility to study layer-dependent activation with fQSM.

Approach: Data were acquired with a segmented multi-shot 3D EPI sequence at 7 Tesla, high-resolution data were denoised prior to fQSM computation. Layer-dependet fMRI and fQSM signals were extracted from 20 layers.

Results: fQSM shows distinctively different activation patterns across cortical layer compared to fMRI.

Impact: High-resolution fQSM acquired at 7 Tesla is used to study layer dependence of fQSM in comparison with BOLD fMRI. fQSM quantifies the underlaying susceptibility change more directly, therefore it might be feasible to use fQSM to study layer-dependent activation.

Keywords: fMRI Acquisition, fMRI, laminar fMRI, hippocampus

Motivation: Laminar fMRI of the human hippocampus is challenging and not easy to interpret due to differences in the direction of venous drainage.

Goal(s): Acquire robust and reproducible single-subject laminar fMRI responses using GRE-BOLD.

Approach: An autobiographical memory task was used at 7 T to elicit hippocampal activation in two subjects each scanned twice. We quantified subregion-specific cortical depth-dependent activation after accounting for physiological signal fluctuations.

Results: We show that laminar profiles differ between subjects but are to a high degree reproducible within subjects and that these profiles were consistent with previous findings at lower spatial resolution.

Impact: Our results show that for laminar fMRI of deeper brain areas, physiological fluctuations need to be corrected to obtain reproducible data. The consistent difference between subjects indicate that subject-specific vasculature needs to be considered.

Keywords: fMRI Acquisition, fMRI, layer-fMRI, UHF, EPI, VASO, sub-millimeter fMRI, 7 tesla

Motivation: Layer-fMRI can address questions of directional information flow, but it’s difficult in lower brain areas.

Goal(s): We want to make layer-fMRI work in low brain structures, despite commonly low tSNR, EPI distortions, and EPI phase errors.

Approach: We tested the efficacy of four advanced acquisition approaches to mitigate these challenges: pTx, dual-polarity readouts, multi-shot segmentation, and aggressive GRAPPA.

Results: We found that pTx and high GRAPPA had limited impact for improved image quality. Though, multi-shot segmentation and dual-polarity readouts allowed layer-fMRI applications in low brain areas.

Impact: This work helps to fulfill the promise of layer-fMRI beyond the top 50% of the cortex.  

Keywords: fMRI Analysis, fMRI

Motivation: Vascular biases in BOLD fMRI hinder the interpretation of neural activity from hemodynamics. Correction methods based on myogenic challenges hold promise in improving specificity, but their limitations for high-resolution imaging have not been fully explored.

Goal(s): To compare neurogenic and myogenic responses and quantify the extent to which biases can be removed in high-resolution imaging.

Approach: We imaged visual and breathhold responses and compared the amplitude and delay of responses across V1 and across cortical depths.

Results: Amplitude calibration virtually eliminated intercortical and interregional biases even in small ROIs within V1. Delay calibration was not effective, due to different delay patterns across conditions.

Impact: BOLD amplitude calibration with breathhold tasks can suppress biases in BOLD estimates across cortical depths and ROIs. However, our work highlights fundamental differences in the dynamics of myogenic and neurogenic responses that precluded satisfactory calibration of hemodynamic delays.

Keywords: Functional Connectivity, Neuroscience

Motivation: The dexterity of individuated finger movements is fundamental to daily hand use; yet specific brain networks serving each finger remains poorly understood. 

Goal(s): Our objective is to unravel mesoscale connections associated with finger-specific neural circuits.  

Approach: In 2 macaque monkeys, single digit locations were functionally mapped in cortical areas 3b via fMRI. Pulsed INS (infrared neural stimulation) targeted to these sites elicited mesoscale BOLD activation at functionally connected sites resulting in brainwide single digit networks. 

Results: INS-induced BOLD activations revealed the distinct networks associated with each finger. Index finger connected with sensorimotor, multisensory and emotion circuits, supporting flexibility and stability in fine movement.

Impact: This research identifies specific brain networks underlying single digit maps in SI, and will be relevant for understanding hand dexterity, neurorehabilitation, and prosthesis development.

Keywords: Task/Intervention Based fMRI, fMRI (task based)

Motivation: This research aims to investigate visual perception in awake macaques using 7T MRI, enhancing our comprehension of BOLD responses during a contrast discrimination task and developing a quantifiable method for neuromodulation.

Goal(s): The specific objectives include directly observing BOLD responses at mesoscale during a contrast discrimination task.

Approach: The study utilized 7T MRI while macaques performed a 2AFC task, allowing simultaneous stimulus presentation and BOLD response measurement.

Results: The study successfully mapped BOLD responses during behavioral tasks, revealing contrast sensitivities in the visual cortex. Notably, it identified BOLD signal decreases in ambiguous contrast conditions, shedding light on perceptual uncertainty in stimulus discrimination.

Impact: These findings may advance quantification of behavioral an neural processes, helping to bridged the gap between human non-invasive and monkey invasive studies.

Keywords: Functional Connectivity, Brain Connectivity

Motivation: To understand the circuitry underlying the pulvinar and limbic cortical areas in the brain.

Goal(s): To map at mesoscale functional connections between medial pulvinar (PM) and insular and cingulate cortices in Macaque monkey.

Approach: Infrared neural stimulation was delivered via optic fibers to sequential sites in PM in Macaques and BOLD responses at connected sites mapped in 7T MRI.

Results: We find connectivity of PM with cingulate cortex was patchy and columnar, with sequential sites in PM producing mediolateral topographic activation. A functional topology of these patches was observed in cingulate.

Impact: The specificity and mesoscale nature of functional connections from medial pulvinar to limbic systems, providing new treatment ideas for mental disorders.

Keywords: Task/Intervention Based fMRI, Neuroscience, foveolar vision；ultra-high field fMRI; awake monkey

Motivation: Foveolar vision (central 1º of vision) is important for many visual behaviors; however, its cortical representation is poorly understood. 

Goal(s): To understand the functional organization of foveolar visual cortex in macaque monkey. 

Approach: Use human 7T to conduct fMRI of foveal visual cortex at submillimeter resolution (0.6mm in-plane) in awake fixating macaque monkeys. 

Results: We found at least 8 distinct loci of foveolar representation per hemisphere, one each for dorsal and ventral V1/V2, V2/V3, V3/V4, V4/TEO. These loci surround a substantial cortical territory (the foveolar core) which lies outside topographic cortex. 

Impact: The foveolar core may represent a higher-order specialization for foveal behaviors.

Keywords: fMRI Acquisition, fMRI

Motivation: To identify the best sequence for future multimodal studies, the simultaneous fMRI and cortical optical imaging in mice were used for evaluation of consistency of neuronal activation with EPI or ZTE scans.

Goal(s): The goal of this work is to establish a general framework for simultaneous fMRI and wide-field optical imaging.

Approach: ZTE and EPI were evaluated during sensory stimulation and at rest with simultaneously wide field optical imaging. 

Results: High quality images were obtained from 7 mice, 4 with calcium indicators and three with voltage indicators. The localized neuronal activations at cortex have great consistency with both EPI and ZTE scans.

Impact: The validation opens a pathway for further imaging cell-specific fluorescence activities. The integration of these two complementary neuroimaging modalities opens a broad range of future applications for systems level neuroscience and preclinical studies of pathological brain function.

Keywords: Task/Intervention Based fMRI, fMRI (task based), ocular dominance column

Motivation: Most fMRI column studies don’t consider the potentially different laminar responses along the cortical depth.

Goal(s): In this work, we demonstrate the feasibility of mapping ocular dominance columns (ODCs) at multiple cortical depths in the cat visual cortex using CBV-weighted fMRI. 

Approach: To enable monocular input to either eye of a cat, we customized a cat goggle that can avoid light leakage and switch eyes easily.

Results: By employing mesoscopic fMRI at ultrahigh magnetic field (9.4 Tesla), we observed relatively irregular ODC stripes in the cat visual cortex with a large width and length variation, extending across the cortex with varying response strength.

Impact: The successful ODC mapping across multiple cortical depths using high-resolution fMRI in the cat brain enables investigation of layer-specific neural circuits and column mapping on the effect of combined stimulus dimensions at both the thalamocortical and intracortical level.

Keywords: fMRI Acquisition, fMRI, Highe resolution fMRI

Motivation: Recently, line-scanning fMRI has been used to map laminar BOLD response, because it can enhance spatial resolution to sub-millimetre with sub-second TR. Some animal studies at high field scanner have been reported. 

Goal(s): Line-scan scheme that can keep thin line profiles and provide multi T2* relaxed conditions for BOLD signal measuring is requested for layer fMRI.

Approach: We developed a multi-shot spin echo EPI based line-scan scheme with a readout train after spin echo time.

Results: Our 1D line-scanning finger tapping/grabbing fMRI results show the capability of this sequence to study differences in cortical layers in the human cortex.

Impact: The proposed line-scanning sequence can detect different BOLD response at different layers at M1/S1 in high resolution fMRI studies at 3T and 7T

Keywords: fMRI Acquisition, fMRI, Laminar fMRI

Motivation: To explore the potential of layer-specific imaging of the brain at standard clinical field (3T) and ultra-high field strengths (7T)

Goal(s): To assess the feasibility of sub-millimetre BOLD fMRI at 3T compared to 7T and characterise activation maps and laminar profiles

Approach: 12 healthy participants scanned using product 2D-EPI at four resolutions on both 3T and 7T scanners. Data were meticulously processed using ANTs and AFNI following NORDIC-PCA denoising.

Results: We demonstrate that sub-millimetre GE-BOLD fMRI at 3T is feasible using a standard fMRI sequence, has sufficient tSNR and reliable BOLD activation maps.

Impact: Our work broadens accessibility to high-resolution fMRI at 3T. Thus, encouraging new directions in neuroimaging and enabling a deeper understanding of human brain function in health and disease, impacting not only neuroscientists but also the broader scientific and medical communities.

Keywords: Task/Intervention Based fMRI, High-Field MRI

Motivation: This study seeks to address the challenge of human layer-specific fMRI at 5.0T whole-body MRI scanner.

Goal(s): Develop Layer-specific VASO fMRI based on the slice-selective slab-inversion vascular space occupancy (SS-SI VASO) pulse sequence at 5.0T scanner.

Approach: The SS-SI VASO pulse sequence with GOIA RF pulse at 5.0T scanner has been developed with the five processing steps, including noise reduction with distribution corrected (NORDIC), motion correction, BOLD correction and contrast combination, quality measures, and functional activity.

Results: The preliminary results have shown that the in vivo experiment of finger tapping for VASO fMRI at 5.0T scanner is feasible as similar as BOLD fMRI.

Impact: The preliminary experiments provided by layer-specific VASO fMRI at 5.0T scanner can help scientists and doctors in accurately identifying and diagnosing primary motor cortex or other brain applications.