Variable flip angle 3D-GRASE for high resolution fMRI at 7 tesla

Submillimeter fMRI Acquisition Techniques for Detection of Laminar and Columnar Level Brain Activation

Since the first demonstration in the early 1990s, functional MRI (fMRI) has emerged as one of the most powerful, noninvasive neuroimaging tools to probe brain functions. Subsequently, fMRI techniques have advanced remarkably, enabling the acquisition of functional signals with a submillimeter voxel size. This innovation has opened the possibility of investigating subcortical neural activities with respect to the cortical depths or cortical columns. For this purpose, numerous previous works have endeavored to design suitable functional contrast mechanisms and dedicated imaging techniques. Depending on the choice of the functional contrast, functional signals can be detected with high sensitivity or with improved spatial specificity to the actual activation site, and the pertaining issues have been discussed in a number of earlier works. This review paper primarily aims to provide an overview of the subcortical fMRI techniques that allow the acquisition of functional signals with a submillimeter resolution. Here, the advantages and disadvantages of the imaging techniques will be described and compared. We also summarize supplementary imaging techniques that assist in the analysis of the subcortical brain activation for more accurate mapping with reduced geometric deformation. This review suggests that there is no single universally accepted method as the gold standard for subcortical fMRI. Instead, the functional contrast and the corresponding readout imaging technique should be carefully determined depending on the purpose of the study. Due to the technical limitations of current fMRI techniques, most subcortical fMRI studies have only targeted partial brain regions. As a future prospect, the spatiotemporal resolution of fMRI will be pushed to satisfy the community's need for a deeper understanding of whole-brain functions and the underlying connectivity in order to achieve the ultimate goal of a time-resolved and layer-specific spatial scale. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 1.

3D diffusion MRI with twin navigator-based GRASE and comparison with 2D EPI for tractography in the human brain

PURPOSE

3D pulse sequences enable high-resolution acquisition with a high SNR and ideal slice profiles, which, however, is particularly difficult for diffusion MRI (dMRI) due to the additional phase errors from diffusion encoding.

METHODS

We proposed a twin navigator-based 3D diffusion-weighted gradient spin-echo (GRASE) sequence to correct the phase errors between shots and between odd and even spin echoes for human whole-brain acquisition. We then compared the SNR of 3D GRASE and 2D simultaneous multi-slice EPI within the same acquisition time. We further tested the performance of 2D versus 3D acquisition at equivalent SNR on fiber tracking and microstructural mapping, using the diffusion tensor and high-order fiber orientation density-based metrics.

RESULTS

The proposed twin navigator approach removed multi-shot phase errors to some extent in the whole brain dMRI, and the 2D navigator performed better than the 1D navigator. Comparisons of SNR between the 2D simultaneous multi-slice EPI and 3D GRASE sequences demonstrated that the SNR of the GRASE sequence was 1.4-1.5-fold higher than the EPI sequence at an equivalent scan time. More importantly, we found a significantly higher fiber cross-section in the cerebrospinal tract, as well as richer subcortical fibers (U-fibers) using the 3D GRASE sequence compared to 2D EPI.

CONCLUSION

The twin navigator-based 3D diffusion-weighted-GRASE sequence minimized the multishot phase error and effectively improved the SNR for whole-brain dMRI acquisition. We found differences in fiber tracking and microstructural mapping between 2D and 3D acquisitions, possibly due to the different slice profiles.

Customized whole brain-covering 3D GRASE in multi-delay pseudo-continuous arterial spin labeling for duplex distinct hemodynamic mapping contrasts of brain tissues and circulation pathways

Gradient and spin echo (GRASE) is widely employed in arterial spin labeling (ASL) as an efficient readout sequence. Hemodynamic parameter mappings of perfusion, such as cerebral blood flow (CBF) and arterial transit time (ATT), can be derived via multi-delay ASL acquisitions. Multi-delay ASL perfusion imaging inevitably suffers limited signal-to-noise ratio (SNR) since a motion-sensitized vessel suppressing module has to be employed to highlight perfusion signals. The present work reveals that in multi-delay ASL, manipulation of GRASE sequence on either planar imaging echo echo train for adjusted spatial resolutions or FSE echo train for modulated extent of T 2-blurring can significantly alter the mapping contrasts among tissues and among cerebral lobes under different pathways of blood circulation, and meanwhile regulates SNR. Four separate multi-delay ASL scans with different echo train designs in 3D whole brain covering GRASE were carried out for healthy subjects to evaluate the variations in regard to the parameter quantifications and SNR. Based on the quantification mappings, the GRASE acquisition with moderate spatial resolution (3.5 × 3.5 × 4 mm3) and segmented k z scheme was recognized for the first time to be recommended for more unambiguous CBF and ATT contrasts between GM and WM in conjunction with more enhanced ATT contrast between anterior and posterior cerebral circulations, with reasonably good SNR. The technical proposal is of great value for the cutting-edge research of a variety of neurological diseases of global concerns.

A plug-and-play, lightweight, single-axis gradient insert design for increasing spatiotemporal resolution in echo planar imaging-based brain imaging

The goal of this study was to introduce and evaluate the performance of a lightweight, high-performance, single-axis (z-axis) gradient insert design primarily intended for high-resolution functional magnetic resonance imaging, and aimed at providing both ease of use and a boost in spatiotemporal resolution. The optimal winding positions of the coil were obtained using a genetic algorithm with a cost function that balanced gradient performance (minimum 0.30 mT/m/A) and field linearity (≥16 cm linear region). These parameters were verified using field distribution measurements by B₀ -mapping. The correction of geometrical distortions was performed using theoretical field distribution of the coil. Simulations and measurements were performed to investigate the echo planar imaging echo-spacing reduction due to the improved gradient performance. The resulting coil featured a 16-cm linear region, a weight of 45 kg, an installation time of 15 min, and a maximum gradient strength and slew rate of 200 mT/m and 1300 T/m/s, respectively, when paired with a commercially available gradient amplifier (940 V/630 A). The field distribution measurements matched the theoretically expected field. By utilizing the theoretical field distribution, geometrical distortions were corrected to within 6% of the whole-body gradient reference image in the target region. Compared with a whole-body gradient set, a maximum reduction in echo-spacing of a factor of 2.3 was found, translating to a 344 μs echo-spacing, for a field of view of 192 mm, a receiver bandwidth of 920 kHz and a gradient amplitude of 112 mT/m. We present a lightweight, single-axis gradient insert design that can provide high gradient performance and an increase in spatiotemporal resolution with correctable geometrical distortions while also offering a short installation time of less than 15 min and minimal system modifications.

BOLD sensitivity and vessel size specificity along CPMG and GRASE echo trains

PURPOSE

To assess the vessel size specificity and sensitivity of rapid CPMG and GRASE for functional BOLD imaging for different echo train lengths, echo spacings, field strength, and refocusing flip angle schemes. In addition, the behavior of signals acquired before and after the refocusing time points is analyzed.

METHODS

Evolution of magnetization within a network of artificial cylinders is simulated with Monte Carlo methods for all relevant coherence pathways. In addition, measurements on microspheres were performed to confirm some of the theoretical results.

RESULTS

For reduced refocusing flip angles, the peak of the vessel size sensitivity curve is shifting toward larger radii with increasing echo time. Furthermore, the BOLD-related signal change along the echo train depends on the chosen refocusing flip angle scheme and in general does not follow corresponding echo amplitudes.

CONCLUSION

CPMG or GRASE can be used with low refocusing flip angles without significant loss of sensitivity to BOLD. The evolution of BOLD signal changes along the echo train can be used to design optimal k-space reordering schemes. Signals acquired before or after the spin echo time point show contributions from larger vessels similar to gradient echo sequences. Short echo spacing (time between refocusing pulses) suppresses gradient echo-related contributions from larger vessels, whereas the spin echo-related contribution from small vessels remains constant and is independent of the echo spacing.

Highly accelerated submillimeter resolution 3D GRASE with controlled T 2 blurring in T 2 -weighted functional MRI at 7 Tesla: A feasibility study

PURPOSE

To achieve highly accelerated submillimeter resolution T 2 -weighted functional MRI at 7T by developing a three-dimensional gradient and spin echo imaging (GRASE) with inner-volume selection and variable flip angles (VFA).

METHODS

GRASE imaging has disadvantages in that (a) k-space modulation causes T 2 blurring by limiting the number of slices and (b) a VFA scheme results in partial success with substantial SNR loss. In this work, accelerated GRASE with controlled T 2 blurring is developed to improve a point spread function (PSF) and temporal signal-to-noise ratio (tSNR) with a large number of slices. To this end, the VFA scheme is designed by minimizing a trade-off between SNR and blurring for functional sensitivity, and a new GRASE-optimized random encoding, which takes into account the complex signal decays of T 2 and T 2 ∗ weightings, is proposed by achieving incoherent aliasing for constrained reconstruction. Numerical and experimental studies were performed to validate the effectiveness of the proposed method over regular and VFA GRASE (R- and V-GRASE).

RESULTS

The proposed method, while achieving 0.8 mm isotropic resolution, functional MRI compared to R- and V-GRASE improves the spatial extent of the excited volume up to 36 slices with 52%-68% full width at half maximum (FWHM) reduction in PSF but approximately 2- to 3-fold mean tSNR improvement, thus resulting in higher BOLD activations.

CONCLUSIONS

We successfully demonstrated the feasibility of the proposed method in T 2 -weighted functional MRI. The proposed method is especially promising for cortical layer-specific functional MRI.

Fine-scale computations for adaptive processing in the human brain

Adapting to the environment statistics by reducing brain responses to repetitive sensory information is key for efficient information processing. Yet, the fine-scale computations that support this adaptive processing in the human brain remain largely unknown. Here, we capitalise on the sub-millimetre resolution of ultra-high field imaging to examine functional magnetic resonance imaging signals across cortical depth and discern competing hypotheses about the brain mechanisms (feedforward vs. feedback) that mediate adaptive processing. We demonstrate layer-specific suppressive processing within visual cortex, as indicated by stronger BOLD decrease in superficial and middle than deeper layers for gratings that were repeatedly presented at the same orientation. Further, we show altered functional connectivity for adaptation: enhanced feedforward connectivity from V1 to higher visual areas, short-range feedback connectivity between V1 and V2, and long-range feedback occipito-parietal connectivity. Our findings provide evidence for a circuit of local recurrent and feedback interactions that mediate rapid brain plasticity for adaptive information processing.

An equal-TE ultrafast 3D gradient-echo imaging method with high tolerance to magnetic susceptibility artifacts: Application to BOLD functional MRI

PURPOSE

To develop an ultrafast 3D gradient echo-based MRI method with constant TE and high tolerance to B₀ inhomogeneity, dubbed ERASE (equal-TE rapid acquisition with sequential excitation), and to introduce its use in BOLD functional MRI (fMRI).

THEORY AND METHODS

Essential features of ERASE, including spin behavior, were characterized, and a comparison study was conducted with conventional EPI. To demonstrate high tolerance to B₀ inhomogeneity, in vivo imaging of the mouse brain with a fiber-optic implant was performed at 9.4 T, and human brain imaging (including the orbitofrontal cortex) was performed at 3 T and 7 T. To evaluate the performance of ERASE in BOLD-fMRI, the characteristics of SNR and temporal SNR were analyzed for in vivo rat brains at 9.4 T in comparison with multislice gradient-echo EPI. Percent signal changes and t-scores are also presented.

RESULTS

For both mouse brain and human brain imaging, ERASE exhibited a high tolerance to magnetic susceptibility artifacts, showing much lower distortion and signal dropout, especially in the regions involving large magnetic susceptibility effects. For BOLD-fMRI, ERASE provided higher temporal SNR and t-scores than EPI, but exhibited similar percent signal changes in in vivo rat brains at 9.4 T.

CONCLUSION

When compared with conventional EPI, ERASE is much less sensitive, not only to EPI-related artifacts such as Nyquist ghosting, but also to B₀ inhomogeneity including magnetic susceptibility effects. It is promising for use in BOLD-fMRI, providing higher temporal SNR and t-scores with constant TE when compared with EPI, although further optimization is needed for human fMRI.

Comparison of BOLD and CBV using 3D EPI and 3D GRASE for cortical layer functional MRI at 7 T

PURPOSE

Functional MRI (fMRI) at the mesoscale of cortical layers and columns requires both sensitivity and specificity, the latter of which can be compromised if the imaging method is affected by vascular artifacts, particularly cortical draining veins at the pial surface. Recent studies have shown that cerebral blood volume (CBV) imaging is more specific to the actual laminar locus of neural activity than BOLD imaging using standard gradient-echo EPI sequences. Gradient and spin-echo (GRASE) BOLD imaging has also shown greater specificity when compared with standard gradient-echo EPI BOLD. Here we directly compare CBV and BOLD contrasts in high-resolution imaging of the primary motor cortex for laminar functional MRI in four combinations of signal labeling, CBV using slice-selective slab-inversion vascular space occupancy (VASO) and BOLD, each with 3D gradient-echo EPI and zoomed 3D-GRASE image readouts.

METHODS

Activations were measured using each sequence and contrast combination during a motor task. Activation profiles across cortical depth were measured to assess the sensitivity and specificity (pial bias) of each method.

RESULTS

Both CBV imaging using gradient-echo 3D-EPI and BOLD imaging using 3D-GRASE show similar specificity and sensitivity and are therefore useful tools for mesoscopic functional MRI in the human cortex. The combination of GRASE and VASO did not demonstrate high levels of sensitivity, nor show increased specificity.

CONCLUSION

Three-dimensional EPI with VASO contrast and 3D-GRASE with BOLD contrast both demonstrate sufficient sensitivity and specificity for laminar functional MRI to be used by neuroscientists in a wide range of investigations of depth-dependent neural circuitry in the human brain.

Compressed Sensing 3D-GRASE for faster High-Resolution MRI

Purpose

High‐resolution three‐dimensional (3D) structural MRI is useful for delineating complex or small structures of the body. However, it requires long acquisition times and high SAR, limiting its clinical use. The purpose of this work is to accelerate the acquisition of high‐resolution images by combining compressed sensing and parallel imaging (CSPI) on a 3D‐GRASE sequence and to compare it with a (CS)PI 3D‐FSE sequence. Several sampling patterns were investigated to assess their influence on image quality.

Methods

The proposed k‐space sampling patterns are based on two undersampled k‐space grids, variable density (VD) Poisson‐disc, and VD pseudo‐random Gaussian, and five different trajectories described in the literature. Bloch simulations are performed to obtain the transform point spread function and evaluate the coherence of each sampling pattern. Image resolution was assessed by the full‐width at half‐maximum (FWHM). Prospective CSPI 3D‐GRASE phantom and in vivo experiments in knee and brain are carried out to assess image quality, SNR, SAR, and acquisition time compared to PI 3D‐GRASE, PI 3D‐FSE, and CSPI 3D‐FSE acquisitions.

Results

Sampling patterns with VD Poisson‐disc obtain the lowest coherence for both PD‐weighted and T2‐weighted acquisitions. VD pseudo‐random Gaussian obtains lower FWHM, but higher sidelobes than VD Poisson‐disc. CSPI 3D‐GRASE reduces acquisition time (43% for PD‐weighted and 40% for T2‐weighted) and SAR (∼45% for PD‐weighted and T2‐weighted) compared to CSPI 3D‐FSE.

Conclusions

CSPI 3D‐GRASE reduces acquisition time compared to a CSPI 3DFSE acquisition, preserving image quality. The design of the sampling pattern is crucial for image quality in CSPI 3D‐GRASE image acquisitions.

A surface loop array for in vivo small animal MRI/fMRI on 7T human scanners

Small animals such as non-human primate (NHP) and rodent are valuable models in frontier neuroscience researches, and comparative research between the animal model and human is helpful to understand and reveal the functional brain circuits in cognition and underlying mechanism in psychological disease. Small animals can be trained or anesthetized to endure long-term and multiple imaging scans; however, the concomitant needs in subcortical structure and function investigations pose major challenges in, e.g. spatial resolution, scan time efficiency, spatial/temporal signal-to-noise-ratio, as well as apparatus mechanical fixation. In addition, comparative investigations across species are also expected to be conducted under similar physical environment (such as the main magnetic field strength, RF pulse shape, sequence protocols, gradient waveform, system stability, etc in MRI), in order to avoid possible deviation in signal detection under different platforms, as well as to reduce experiment complexity. We have proposed a novel 5-channel surface coil that is equipped on 7T human MRI scanners and designed for small animal structural and functional MRI. Through a series of in vivo experiments over an anesthetized rat and macaque, the presented coil shows its main characteristics in, i.e. flexible coil mounting, reduced FOV, high temporal SNR, and parallel imaging capability. Such design is able to compensate the relatively lower gradient slew rate of human scanners versus those with smaller bores, and thus effectively facilitates in vivo microscopic structural MR images being obtained within a shortened and safe period of anesthesia; besides, it also enables high-resolution functional MRI (i.e. spin-echo based) being achieved with reasonable temporal resolution, distortion level and functional contrast.

Pros and cons of ultra-high-field MRI/MRS for human application

Magnetic resonance imaging and spectroscopic techniques are widely used in humans both for clinical diagnostic applications and in basic research areas such as cognitive neuroimaging. In recent years, new human MR systems have become available operating at static magnetic fields of 7 T or higher (≥300 MHz proton frequency). Imaging human-sized objects at such high frequencies presents several challenges including non-uniform radiofrequency fields, enhanced susceptibility artifacts, and higher radiofrequency energy deposition in the tissue. On the other side of the scale are gains in signal-to-noise or contrast-to-noise ratio that allow finer structures to be visualized and smaller physiological effects to be detected. This review presents an overview of some of the latest methodological developments in human ultra-high field MRI/MRS as well as associated clinical and scientific applications. Emphasis is given to techniques that particularly benefit from the changing physical characteristics at high magnetic fields, including susceptibility-weighted imaging and phase-contrast techniques, imaging with X-nuclei, MR spectroscopy, CEST imaging, as well as functional MRI. In addition, more general methodological developments such as parallel transmission and motion correction will be discussed that are required to leverage the full potential of higher magnetic fields, and an overview of relevant physiological considerations of human high magnetic field exposure is provided.

Cortical depth profiles of luminance contrast responses in human V1 and V2 using 7 T fMRI

Neural activity in early visual cortex is modulated by luminance contrast. Cortical depth (i.e., laminar) contrast responses have been studied in monkey early visual cortex, but not in humans. In addition to the high spatial resolution needed and the ensuing low signal-to-noise ratio, laminar studies in humans using fMRI are hampered by the strong venous vascular weighting of the fMRI signal. In this study, we measured luminance contrast responses in human V1 and V2 with high-resolution fMRI at 7 T. To account for the effect of intracortical ascending veins, we applied a novel spatial deconvolution model to the fMRI depth profiles. Before spatial deconvolution, the contrast response in V1 showed a slight local maximum at mid cortical depth, whereas V2 exhibited a monotonic signal increase toward the cortical surface. After applying the deconvolution, both V1 and V2 showed a pronounced local maximum at mid cortical depth, with an additional peak in deep grey matter, especially in V1. Moreover, we found a difference in contrast sensitivity between V1 and V2, but no evidence for variations in contrast sensitivity as a function of cortical depth. These findings are in agreement with results obtained in nonhuman primates, but further research will be needed to validate the spatial deconvolution approach.

Controlling T2 blurring in 3D RARE arterial spin labeling acquisition through optimal combination of variable flip angles and k-space filtering

PURPOSE

To improve the SNR efficiency and reduce the T₂ blurring of 3D rapid acquisition with relaxation enhancement stack-of-spiral arterial spin labeling imaging by using variable refocusing flip angles and k-space filtering.

METHODS

An algorithm for determining the optimal combination of variable flip angles and filtering correction is proposed. The flip angles are designed using extended phase graph physical simulations in an analytical and global optimization framework, with an optional constraint on deposited power. Optimal designs for correcting to Hann and Fermi window functions were compared with conventional constant amplitude or variable flip angle only designs on 6 volunteers.

RESULTS

With the Fermi window correction, the proposed optimal designs provided 39.8 and 27.3% higher SNR (P < .05) than conventional constant amplitude and variable flip angle designs. Even when power deposition was limited to 50% of the constant amplitude design, the proposed method outperformed the SNR (P < .05) of these 2 conventional approaches by 32.5 and 20.7%. The sharpness and the contrast between gray and white matter were improved with the k-space filtering correction for all of the flip angle designs. The improvements were moderate for the Hann window correction.

CONCLUSION

This work demonstrates that variable flip angles can be derived as the output of an optimization problem. The combined design of variable flip angle and k-space filtering provided superior SNR to designs primarily emphasizing either approach singly.

Visually-Driven Maps in Area 3b

Sensory perception relies on the precise neuronal encoding of modality-specific environmental features in primary sensory cortices. Some studies have reported the penetration of signals from other modalities even into early sensory areas. So far, no comprehensive account of maps induced by "foreign sources" exists. We addressed this question using surface-based topographic mapping techniques applied to ultra-high resolution fMRI neuroimaging data, measured in female participants. We show that fine-grained finger maps in human primary somatosensory cortex, area 3b, are somatotopically activated not only during tactile mechanical stimulation, but also when viewing the same fingers being touched. Visually-induced maps were weak in amplitude, but overlapped with the stronger tactile maps tangential to the cortical sheet when finger touches were observed in both first- and third-person perspectives. However, visually-induced maps did not overlap tactile maps when the observed fingers were only approached by an object but not actually touched. Our data provide evidence that "foreign source maps" in early sensory cortices are present in the healthy human brain, that their arrangement is precise, and that their induction is feature-selective. The computations required to generate such specific responses suggest that counterflow (feedback) processing may be much more spatially specific than has been often assumed.SIGNIFICANCE STATEMENT Using ultra-high field fMRI, we provide empirical evidence that viewing touches activates topographically aligned single finger maps in human primary somatosensory cortical area 3b. This shows that "foreign source maps" in early sensory cortices are topographic, precise, and feature-selective in healthy human participants with intact sensory pathways.

Pushing the limits of ultra-high resolution human brain imaging with SMS-EPI demonstrated for columnar level fMRI

Encoding higher spatial resolution in simultaneous multi-slice (SMS) EPI is highly dependent on gradient performance, high density receiver coil arrays and pulse sequence optimization. We simulate gradient amplitude and slew rate determination of EPI imaging performance in terms of minimum TE, echo spacing (ES) and spatial resolution. We discuss the effects of image zooming in pulse sequences that have been used for sub-millimeter resolutions and the trade-offs in using partial Fourier and parallel imaging to reduce TE, PSF and ES. Using optimizations for SMS EPI pulse sequences with available gradient and receiver hardware, experimental results in ultra-high resolution (UHR) (0.45-0.5mm isotropic) SMS-EPI fMRI and mapping ocular dominance columns (ODC) in human brain at 0.5 mm isotropic resolution are demonstrated. We discuss promising future directions of UHR fMRI.

Techniques for blood volume fMRI with VASO: From low-resolution mapping towards sub-millimeter layer-dependent applications

Quantitative cerebral blood volume (CBV) fMRI has the potential to overcome several specific limitations of BOLD fMRI. It provides direct physiological interpretability and promises superior localization specificity in applications of sub-millimeter resolution fMRI applications at ultra-high magnetic fields (7T and higher). Non-invasive CBV fMRI using VASO (vascular space occupancy), however, is inherently limited with respect to its data acquisition efficiency, restricting its imaging coverage and achievable spatial and temporal resolution. This limitation may be reduced with recent advanced acceleration and reconstruction strategies that allow two-dimensional acceleration, such as in simultaneous multi-slice (SMS) 2D-EPI or 3D-EPI in combination with CAIPIRINHA field-of-view shifting. In this study, we sought to determine the functional sensitivity and specificity of these readout strategies with VASO over a broad range of spatial resolutions; spanning from low spatial resolution (3mm) whole-cortex to sub-millimeter (0.75mm) slab-of-cortex (for cortical layer-dependent applications). In the thermal-noise-dominated regime of sub-millimeter resolutions, 3D-EPI-VASO provides higher temporal stability and sensitivity to detect changes in CBV compared to 2D-EPI-VASO. In this regime, 3D-EPI-VASO unveils task activation located in the cortical laminae with little contamination from surface veins, in contrast to the cortical surface weighting of GE-BOLD fMRI. In the physiological-noise-dominated regime of lower resolutions, however, 2D-SMS-VASO shows superior performance compared to 3D-EPI-VASO. Due to its superior sensitivity at a layer-dependent level, 3D-EPI VASO promises to play an important role in future neuroscientific applications of layer-dependent fMRI.

High resolution data analysis strategies for mesoscale human functional MRI at 7 and 9.4T

The advent of ultra-high field functional magnetic resonance imaging (fMRI) has greatly facilitated submillimeter resolution acquisitions (voxel volume below (1 mm³)), allowing the investigation of cortical columns and cortical depth dependent (i.e. laminar) structures in the human brain. Advanced data analysis techniques are essential to exploit the information in high resolution functional measures. In this article, we use recent, exemplary 9.4 T human functional and anatomical data to review the advantages and disadvantages of (1) pooling high resolution data across regions of interest for cortical depth profile analysis, (2) pooling across cortical depths for mapping patches of cortex while discarding depth-dependent (i.e. columnar) effects, and (3) isotropic sampling without pooling to assess individual voxel’s responses. A set of cortical depth meshes may be a solution to sampling information tangentially while keeping correspondence across depths. For quantitative analysis of the spatial organization in fine-grained structures, a cortical grid approach is advantageous. We further extend this general framework by combining it with a previously introduced cortical layer volume-preserving (equi-volume) approach. This framework can readily accommodate the research questions which allow for spatial smoothing within or across layers. We demonstrate and discuss that equi-volume sampling yields a slight advantage over equidistant sampling given the current limitations of fMRI voxel size, participant motion, coregistration and segmentation. Our 9.4 T human anatomical and functional data indicate the advantage over lower fields including 7 T and demonstrate the practical applicability of T₂^* and T₂-weighted fMRI acquisitions.

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High resolution regular cortical grids are advantageous for local applications.

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Equi-volume sampling is slightly advantageous over equidistant sampling in-vivo.

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Isotropic submillimeter cortical sampling without spatial pooling requires high SNR.

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9.4 T human T2 and T2* BOLD fMRI are practically feasible and provide high SNR.

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9.4 T T2*-weighted 0.35 mm iso. res. anatomical images for laminar contrast in vivo.

The impact of ultra-high field MRI on cognitive and computational neuroimaging

The ability to measure functional brain responses non-invasively with ultra high field MRI (7 T and above) represents a unique opportunity in advancing our understanding of the human brain. Compared to lower fields (3 T and below), ultra high field MRI has an increased sensitivity, which can be used to acquire functional images with greater spatial resolution, and greater specificity of the blood oxygen level dependent (BOLD) signal to the underlying neuronal responses. Together, increased resolution and specificity enable investigating brain functions at a submillimeter scale, which so far could only be done with invasive techniques. At this mesoscopic spatial scale, perception, cognition and behavior can be probed at the level of fundamental units of neural computations, such as cortical columns, cortical layers, and subcortical nuclei. This represents a unique and distinctive advantage that differentiates ultra high from lower field imaging and that can foster a tighter link between fMRI and computational modeling of neural networks. So far, functional brain mapping at submillimeter scale has focused on the processing of sensory information and on well-known systems for which extensive information is available from invasive recordings in animals. It remains an open challenge to extend this methodology to uniquely human functions and, more generally, to systems for which animal models may be problematic. To succeed, the possibility to acquire high-resolution functional data with large spatial coverage, the availability of computational models of neural processing as well as accurate biophysical modeling of neurovascular coupling at mesoscopic scale all appear necessary.

Sensitivity and specificity considerations for fMRI encoding, decoding, and mapping of auditory cortex at ultra-high field

Following rapid technological advances, ultra-high field functional MRI (fMRI) enables exploring correlates of neuronal population activity at an increasing spatial resolution. However, as the fMRI blood-oxygenation-level-dependent (BOLD) contrast is a vascular signal, the spatial specificity of fMRI data is ultimately determined by the characteristics of the underlying vasculature. At 7T, fMRI measurement parameters determine the relative contribution of the macro- and microvasculature to the acquired signal. Here we investigate how these parameters affect relevant high-end fMRI analyses such as encoding, decoding, and submillimeter mapping of voxel preferences in the human auditory cortex. Specifically, we compare a T₂* weighted fMRI dataset, obtained with 2D gradient echo (GE) EPI, to a predominantly T₂ weighted dataset obtained with 3D GRASE. We first investigated the decoding accuracy based on two encoding models that represented different hypotheses about auditory cortical processing. This encoding/decoding analysis profited from the large spatial coverage and sensitivity of the T₂* weighted acquisitions, as evidenced by a significantly higher prediction accuracy in the GE-EPI dataset compared to the 3D GRASE dataset for both encoding models. The main disadvantage of the T₂* weighted GE-EPI dataset for encoding/decoding analyses was that the prediction accuracy exhibited cortical depth dependent vascular biases. However, we propose that the comparison of prediction accuracy across the different encoding models may be used as a post processing technique to salvage the spatial interpretability of the GE-EPI cortical depth-dependent prediction accuracy. Second, we explored the mapping of voxel preferences. Large-scale maps of frequency preference (i.e., tonotopy) were similar across datasets, yet the GE-EPI dataset was preferable due to its larger spatial coverage and sensitivity. However, submillimeter tonotopy maps revealed biases in assigned frequency preference and selectivity for the GE-EPI dataset, but not for the 3D GRASE dataset. Thus, a T₂ weighted acquisition is recommended if high specificity in tonotopic maps is required. In conclusion, different fMRI acquisitions were better suited for different analyses. It is therefore critical that any sequence parameter optimization considers the eventual intended fMRI analyses and the nature of the neuroscience questions being asked.