Multishot versus single-shot pulse sequences in very high field fMRI: a comparison using retinotopic mapping

High-resolution functional MRI is a leading application for very high field (7 Tesla) human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR) and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm) using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR) than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI.     

Interleaved EPI Based fMRI Improved by Multiplexed Sensitivity Encoding (MUSE) and Simultaneous Multi-Band Imaging

Functional magnetic resonance imaging (fMRI) is a non-invasive and powerful imaging tool for detecting brain activities. The majority of fMRI studies are performed with single-shot echo-planar imaging (EPI) due to its high temporal resolution. Recent studies have demonstrated that, by increasing the spatial-resolution of fMRI, previously unidentified neuronal networks can be measured. However, it is challenging to improve the spatial resolution of conventional single-shot EPI based fMRI. Although multi-shot interleaved EPI is superior to single-shot EPI in terms of the improved spatial-resolution, reduced geometric distortions, and sharper point spread function (PSF), interleaved EPI based fMRI has two main limitations: 1) the imaging throughput is lower in interleaved EPI; 2) the magnitude and phase signal variations among EPI segments (due to physiological noise, subject motion, and B₀ drift) are translated to significant in-plane aliasing artifact across the field of view (FOV). Here we report a method that integrates multiple approaches to address the technical limitations of interleaved EPI-based fMRI. Firstly, the multiplexed sensitivity-encoding (MUSE) post-processing algorithm is used to suppress in-plane aliasing artifacts resulting from time-domain signal instabilities during dynamic scans. Secondly, a simultaneous multi-band interleaved EPI pulse sequence, with a controlled aliasing scheme incorporated, is implemented to increase the imaging throughput. Thirdly, the MUSE algorithm is then generalized to accommodate fMRI data obtained with our multi-band interleaved EPI pulse sequence, suppressing both in-plane and through-plane aliasing artifacts. The blood-oxygenation-level-dependent (BOLD) signal detectability and the scan throughput can be significantly improved for interleaved EPI-based fMRI. Our human fMRI data obtained from 3 Tesla systems demonstrate the effectiveness of the developed methods. It is expected that future fMRI studies requiring high spatial-resolvability and fidelity will largely benefit from the reported techniques.     

Wavelet Domain Radiofrequency Pulse Design Applied to Magnetic Resonance Imaging

A new method for designing radiofrequency (RF) pulses with numerical optimization in the wavelet domain is presented. Numerical optimization may yield solutions that might otherwise have not been discovered with analytic techniques alone. Further, processing in the wavelet domain reduces the number of unknowns through compression properties inherent in wavelet transforms, providing a more tractable optimization problem. This algorithm is demonstrated with simultaneous multi-slice (SMS) spin echo refocusing pulses because reduced peak RF power is necessary for SMS diffusion imaging with high acceleration factors. An iterative, nonlinear, constrained numerical minimization algorithm was developed to generate an optimized RF pulse waveform. Wavelet domain coefficients were modulated while iteratively running a Bloch equation simulator to generate the intermediate slice profile of the net magnetization. The algorithm minimizes the L2-norm of the slice profile with additional terms to penalize rejection band ripple and maximize the net transverse magnetization across each slice. Simulations and human brain imaging were used to demonstrate a new RF pulse design that yields an optimized slice profile and reduced peak energy deposition when applied to a multiband single-shot echo planar diffusion acquisition. This method may be used to optimize factors such as magnitude and phase spectral profiles and peak RF pulse power for multiband simultaneous multi-slice (SMS) acquisitions. Wavelet-based RF pulse optimization provides a useful design method to achieve a pulse waveform with beneficial amplitude reduction while preserving appropriate magnetization response for magnetic resonance imaging.     

Localization of human brain areas activated for chaotic and ordered pattern perception

The aim of our work was to localize cortical areas involved in the processing of incomplete figures using functional MRI (fMRI) for 8 healthy volunteers (18-30 year old) with the did of anatomical and fMRI fast imaging technique: echo planar imaging (EPI), whole brain scan (36 slices) matrix 64 x 64, 3.7 second. We used 1.5 T MR-scanner and BOLD-method (Blood Oxygenation Level Dependent), based on distinctions of magnetic properties of hemoglobin. Fast imaging technique on modern MR-scanners with > or = 1.5 T provides precise statistical maps of oxygenation increase with high spatial resolution. For test stimuli we used matrix of Gabor grating. We used two types of 10 x 10 matrices with chaotic and ordered orientation of Gabor gratings. The size, brightness and contrast of the stimuli were identical. The chaotic and ordered patterns activated different brain areas. We establish that ordered patterns activated only primary visual cortex - V1 and V2, (BA17-18), wheareas chaotic patterns activated in addition primary visual cortex, the V3,V4,V5 (BA19) of the occipital cortex and the area 7 of parietal area (BA7) classification. Decision making for that task is localized in prefrontal and frontal cortex, including (BA 6, 9, 10).     

Dependence of magnetic resonance image (MRI) intensity values on relaxation times, pulse intervals and other signal attenuation factors

Magnetic resonance image (MRI) pixel intensities were investigated using a phantom containing several uniform size chambers filled with solutions of known relaxation times, as well as head scans of patients and volunteers. Intensities were measured with a variety of pulse intervals typically used for imaging with spin echo, (SE) and inversion recovery (IR) sequences at 0.15 Tesla using the back projection (R-THETA) method, and at 0.27 Tesla using the 2-dimensional Fourier transform (2DFT) technique. The results were compared with the calculated dependence of MRI signal intensity on relaxation times and pulse interval parameters using the well known functions containing exponential forms. The experimental and the calculated pixel intensity time dependence did not always agree. We infer that factors other than the conventional functions for T1 and T2 signal decay are important. These factors may include the attenuation of the radiofrequency (RF) signals through inhomogenious lossy dielectric materials (e.g., tissues and organs), the location (coordinate) of the portion of the sample to be imaged relative to the RF coils, and the timing and amplitude of gradient pulses relative to the RF input and the detected signals. The flow velocity and diffusions are also important determinants of the signal from blood vessels and body fluids. We point out the necessity for further investigation toward more comprehensive understanding of MRI intensities.     

Functional magnetic resonance imaging of the primary motor cortex in humans: response to increased functional demands

Functional magnetic resonance imaging (fMRI) studies have been performed on 20 right handed volunteers at 1.5 Tesla using echo planar imaging (EPI) protocol. Index finger tapping invoked localized activation in the primary motor area. Consistent and highly reproducible activation in the primary motor area was observed in six different sessions of a volunteer over a period of one month. Increased tapping rate resulted in increase in the blood oxygenation level dependent (BOLD) signal intensity as well as the volume/area of activation (pixels) in the contra-lateral primary motor area up to tapping rate of 120 taps/min (2 Hz), beyond which it saturates. Activation in supplementary motor area was also observed. The obtained results are correlated to increased functional demands.     

Cortical activation during finger tapping in thyroid dysfunction: A functional magnetic resonance imaging study

Thyroid dysfunction is associated with attention deficit and impairment of the motor system (muscle weakness and fatigue). This paper investigates possible motor function deficit in thyroid patients, compared to the controls. Functional MRI studies (fMRI) were carried out in five hypo and five hyperthyroid patients and six healthy volunteers. Whole brain imaging was performed using echo planar imaging (EPI) technique, on a 1.5T whole body MR system (Siemens Magnetom Vision). The task paradigm consisted of 8 cycles of active and reference phases of 6 measurements each, with right index finger tapping at a rate of 120 taps/min. Post-processing was performed using statistical parametric mapping on a voxel-by-voxel basis using SPM99. Clusters of activation were found in the contralateral hemisphere in primary somatomotor area (M1), supplementary motor area (SMA), somatosensory, auditory receptive and integration areas, inferior temporal lobe, thalamus and cerebellum. Increased clusters of activation were observed in M1 in thyroid subjects as compared to controls and with bilateral activation of the primary motor cortex in two hyperthyroid patients. The results are explained in terms of increased functional demands in thyroid patients compared to volunteers for the execution of the same task.     

Focused hyperthermia with a magnetic resonance imaging (MRI) unit and an interstitial grounded probe

The feasibility of using a commercial magnetic resonance imaging (MRI) scanner to do either imaging or hyperthermic treatment was demonstrated. Radiofrequency (RF) induced focal heating of phantoms and animal tissues was performed using a MRI scanner as the RF power source and a grounded interstitial probe as a device to produce hyperthermia via eddy current convergence. In the therapeutic mode, a pulse width of 900 microseconds and interval of 50 ms were used to give 2% duty cycle (closest simulation to continuous wave (CW) mode without bypassing imaging filters). Temperature in the vicinity of the grounded probe was measured with a field nonperturbing fluoroptic probe. Temperatures increased 4.5 degrees C in 5 minutes in a dielectrically uniform phantom, 3.1 degrees C in 6.7 minutes in rats' leg muscles, and 5.0 degrees C in 6.0 minutes in rats' peritoneum. The MRI of the phantom with the grounded probe and the fluoroptic probe was obtained using spin echo sequences. The potential advantage of this approach is visualization of deep-seated tumors and hyperthermic treatment with minimal modification of the MRI scanner.     

A Rotational Cylindrical fMRI Phantom for Image Quality Control

Purpose

A novel phantom for image quality testing for functional magnetic resonance imaging (fMRI) scans is described.

Methods

The cylindrical, rotatable, ~4.5L phantom, with eight wedge-shaped compartments, is used to simulate rest and activated states. The compartments contain NiCl₂ doped agar gel with alternating concentrations of agar (1.4%, 1.6%) to produce T₁ and T₂ values approximating brain grey matter. The Jacard index was used to compare the image distortions for echo planar imaging (EPI) and gradient recalled echo (GRE) scans. Contrast to noise ratio (_CNR) was compared across the imaging volume for GRE and EPI.

Results

The mean T₂ for the two agar concentrations were found to be 106.5±4.8, 94.5±4.7 ms, and T₁ of 1500±40 and 1485±30 ms, respectively. The Jacard index for GRE was generally found to be higher than for EPI (0.95 versus 0.8). The CNR varied from 20 to 50 across the slices and echo times used for EPI scans, and from 20 to 40 across the slices for the GRE scans. The phantom provided a reproducible CNR over 25 days.

Conclusions

The phantom provides a quantifiable signal change over a head-size imaging volume with EPI and GRE sequences, which was used for image quality assessment.     

Functional magnetic resonance imaging: imaging techniques and contrast mechanisms.

Functional magnetic resonance imaging (fMRI) is a widely used technique for generating images or maps of human brain activity. The applications of the technique are widespread in cognitive neuroscience and it is hoped they will eventually extend into clinical practice. The activation signal measured with fMRI is predicated on indirectly measuring changes in the concentration of deoxyhaemoglobin which arise from an increase in blood oxygenation in the vicinity of neuronal firing. The exact mechanisms of this blood oxygenation level dependent (BOLD) contrast are highly complex. The signal measured is dependent on both the underlying physiological events and the imaging physics. BOLD contrast, although sensitive, is not a quantifiable measure of neuronal activity. A number of different imaging techniques and parameters can be used for fMRI, the choice of which depends on the particular requirements of each functional imaging experiment. The high-speed MRI technique, echo-planar imaging provides the basis for most fMRI experiments. The problems inherent to this method and the ways in which these may be overcome are particularly important in the move towards performing functional studies on higher field MRI systems. Future developments in techniques and hardware are also likely to enhance the measurement of brain activity using MRI.     

In vivo High Angular Resolution Diffusion-Weighted Imaging of Mouse Brain at 16.4 Tesla

Magnetic Resonance Imaging (MRI) of the rodent brain at ultra-high magnetic fields (> 9.4 Tesla) offers a higher signal-to-noise ratio that can be exploited to reduce image acquisition time or provide higher spatial resolution. However, significant challenges are presented due to a combination of longer T ₁ and shorter T ₂/T₂* relaxation times and increased sensitivity to magnetic susceptibility resulting in severe local-field inhomogeneity artefacts from air pockets and bone/brain interfaces. The Stejskal-Tanner spin echo diffusion-weighted imaging (DWI) sequence is often used in high-field rodent brain MRI due to its immunity to these artefacts. To accurately determine diffusion-tensor or fibre-orientation distribution, high angular resolution diffusion imaging (HARDI) with strong diffusion weighting (b >3000 s/mm²) and at least 30 diffusion-encoding directions are required. However, this results in long image acquisition times unsuitable for live animal imaging. In this study, we describe the optimization of HARDI acquisition parameters at 16.4T using a Stejskal-Tanner sequence with echo-planar imaging (EPI) readout. EPI segmentation and partial Fourier encoding acceleration were applied to reduce the echo time (TE), thereby minimizing signal decay and distortion artefacts while maintaining a reasonably short acquisition time. The final HARDI acquisition protocol was achieved with the following parameters: 4 shot EPI, b = 3000 s/mm², 64 diffusion-encoding directions, 125×150 μm² in-plane resolution, 0.6 mm slice thickness, and 2h acquisition time. This protocol was used to image a cohort of adult C57BL/6 male mice, whereby the quality of the acquired data was assessed and diffusion tensor imaging (DTI) derived parameters were measured. High-quality images with high spatial and angular resolution, low distortion and low variability in DTI-derived parameters were obtained, indicating that EPI-DWI is feasible at 16.4T to study animal models of white matter (WM) diseases.     

Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity

Functional magnetic resonance imaging (fMRI) can provide maps of brain activation with millimeter spatial resolution but is limited in its temporal resolution to the order of seconds. Here, we describe a technique that combines structural and functional MRI with magnetoencephalography (MEG) to obtain spatiotemporal maps of human brain activity with millisecond temporal resolution. This new technique was used to obtain dynamic statistical parametric maps of cortical activity during semantic processing of visually presented words. An initial wave of activity was found to spread rapidly from occipital visual cortex to temporal, parietal, and frontal areas within 185 ms, with a high degree of temporal overlap between different areas. Repetition effects were observed in many of the same areas following this initial wave of activation, providing evidence for the involvement of feedback mechanisms in repetition priming.     

Technical artifacts in magnetic resonance imaging

Various artifacts of Magnetic Resonance Imaging (MRI) typically associated with currently available imaging techniques such as projection reconstruction and two-dimensional fourier transform (2D-FT) are described and illustrated. Examples of MRI artifacts were obtained with an imaging unit with a super conducting magnet operated at .15 Tesla and .27 Tesla with corresponding proton resonance frequency of 6.4 MHz and 11.25 MHz. The .15 Tesla images were obtained using projection reconstruction and the .27 Tesla using the 2D-FT method. Instrument related artifacts include those due to direct current (DC), projection, gradient offset, active shimming, phase encoding, and pulse sequencing. Other often encountered artifacts are related to the patient. These include those due to motion, ferromagnetic effect, and tissue contents. The cause of these artifacts and how (if possible) they may be eliminated or minimized is discussed.     

Absence of radiofrequency heating from auditory implants during magnetic resonance imaging

The possibility of tissue heating due to an auditory brainstem implant (ABI) or a modified cochlear implant (CI) during magnetic resonance imaging (MRI) of the head was tested on a full-sized human phantom using a realistic phantom head consisting of simulated skull, brain, and muscle. Dielectric properties of the brain, muscle, and bone materials were similar to those of human tissues at 64 MHz. The body consisted of homogeneous phantom muscle enclosed in a human-shaped fiberglass shell. Thermographic and fiber-optic temperature measurements were conducted to reveal any heating. Thermograms of sagittal, frontal, and horizontal planes of the head with the ABI and CI electrodes were taken immediately before and after a 26 min MRI scan. The MRI sequence was set at 94 excitations and 25 ms echo time to induce maximum radiofrequency heating, as suggested by the General Electric Company. The difference of these two thermograms gives the heating results. In two uncut phantom heads, Teflon tubes were placed along the implanted ABI and CI, and temperature data were recorded via fiber-optic probes before, during, and after the MRI. Results showed no observable heating associated with the ABI and the modified CI during worst-case MRI of the head. © 1995 Wiley-Liss, Inc.     

Comparing structural and functional graph theory features in the human brain using multimodal MRI

Recent advances in magnetic resonance imaging (MRI) are allowing neuroscientists to gain critical insights into the neural networks mediating a variety of cognitive processes. This work investigates structural and functional connectivity in the human brain under different experimental conditions through multimodal MRI acquisitions. To define the nodes of a full-brain network, a set of regions was identified from resting-state functional MRI (fMRI) data using spatial independent component analysis (sICA) and a hierarchical clustering technique. Diffusion-weighted imaging (DWI) data were acquired from the same subjects and a probabilistic fiber tracking method was used to estimate the structure of this network. Using features originating from graph theory, such as small-world properties and network efficiency, we characterized the structural and functional connectivities of the full-brain network and we compared them quantitatively. We showed that structural and functional networks shared some properties in terms of topology as measured by the distribution of the node degrees, hence supporting the existence of an underlying anatomical substrate for functional networks.     

Optimizing the Magnetization-Prepared Rapid Gradient-Echo (MP-RAGE) Sequence

The three-dimension (3D) magnetization-prepared rapid gradient-echo (MP-RAGE) sequence is one of the most popular sequences for structural brain imaging in clinical and research settings. The sequence captures high tissue contrast and provides high spatial resolution with whole brain coverage in a short scan time. In this paper, we first computed the optimal k-space sampling by optimizing the contrast of simulated images acquired with the MP-RAGE sequence at 3.0 Tesla using computer simulations. Because the software of our scanner has only limited settings for k-space sampling, we then determined the optimal k-space sampling for settings that can be realized on our scanner. Subsequently we optimized several major imaging parameters to maximize normal brain tissue contrasts under the optimal k-space sampling. The optimal parameters are flip angle of 12°, effective inversion time within 900 to 1100 ms, and delay time of 0 ms. In vivo experiments showed that the quality of images acquired with our optimal protocol was significantly higher than that of images obtained using recommended protocols in prior publications. The optimization of k-spacing sampling and imaging parameters significantly improved the quality and detection sensitivity of brain images acquired with MP-RAGE.     

Simultaneous PET-MRI: a new approach for functional and morphological imaging

Noninvasive imaging at the molecular level is an emerging field in biomedical research. This paper introduces a new technology synergizing two leading imaging methodologies: positron emission tomography (PET) and magnetic resonance imaging (MRI). Although the value of PET lies in its high-sensitivity tracking of biomarkers in vivo, it lacks resolving morphology. MRI has lower sensitivity, but produces high soft-tissue contrast and provides spectroscopic information and functional MRI (fMRI). We have developed a three-dimensional animal PET scanner that is built into a 7-T MRI. Our evaluations show that both modalities preserve their functionality, even when operated isochronously. With this combined imaging system, we simultaneously acquired functional and morphological PET-MRI data from living mice. PET-MRI provides a powerful tool for studying biology and pathology in preclinical research and has great potential for clinical applications. Combining fMRI and spectroscopy with PET paves the way for a new perspective in molecular imaging.     

High-resolution functional magnetic resonance imaging of the animal brain

To fully understand brain function, one must look beyond the level of a single neuron. By elucidating the spatial properties of the columnar and laminar functional architectures, information regarding the neural processing in the brain can be gained. To map these fine functional structures noninvasively and repeatedly, functional magnetic resonance imaging (fMRI) can be employed. In this article the basic principles of fMRI are introduced, including specific hardware requirements and the equipment necessary for animal magnetic resonance research. Since fMRI measures a change in secondary hemodynamic responses induced by neural activity, it is critical to understand the principles and potential pitfalls of fMRI techniques. Thus, the underlying physics of conventional blood oxygenation, cerebral blood flow, and cerebral blood volume-based fMRI techniques are extensively discussed. Tissue-specific signal change is close to the site of neural activity, while signals from large vessels can be distant from the actual active site. Thus, methods to minimize large vessel contributions and to maximize tissue signals are described. The fundamental limitation of fMRI spatial resolution is the intrinsic hemodynamic response. Based on our high-resolution fMRI studies, the hemodynamic response is regulated at submillimeter functional domains and thus spatial resolution can be achieved to an order of 100 microm. Since hemodynamic responses are sluggish, it is difficult to obtain very high temporal resolution. By using an approach with multiple experiments with different stimulus conditions, temporal resolution can be improved on the order of 100 ms. With current fMRI technologies, submillimeter columnar- and laminar-specific specific functional images can be obtained from animal brains.     

Pathogenesis and brain functional imaging in nocturnal enuresis: A review

Nocturnal enuresis is a common and distressing developmental disease, which may cause various degrees of psychosocial stress and impairment to self-esteem in affected children as well as agitation to their parents or caregivers. Nevertheless, the etiology and pathogenesis of nocturnal enuresis are not understood. Currently, nocturnal enuresis is generally considered a multifactorial disease associated with a complex interaction of somatic, psychosocial, and environmental factors. A variety of postulations have been proposed to explain the occurrence and progression of nocturnal enuresis, including hereditary aberration, abnormal circadian rhythm of antidiuretic hormone secretion during sleep, bladder dysfunction, abnormal sleep, difficulties in arousal, neuropsychological disorders, and maturational delays of the brain. In recent decades, the introduction of functional neuroimaging technologies has provided new approaches for uncovering the mechanisms underlying nocturnal enuresis. The main neuroimaging modalities have included brain morphometry based on structural magnetic resonance imaging (MRI), task-based and event-related functional MRI (fMRI), and resting-state fMRI. The relevant studies have indicated that nocturnal enuresis is associated with functional and structural alterations of the brain. In this review, we briefly summarized the popular hypotheses regarding the pathogenesis of nocturnal enuresis and the current progress of functional neuroimaging studies in examining the underlying mechanisms thereof.     

Mono-Exponential Fitting in T2-Relaxometry: Relevance of Offset and First Echo

Introduction

T2 relaxometry has become an important tool in quantitative MRI. Little focus has been put on the effect of the refocusing flip angle upon the offset parameter, which was introduced to account for a signal floor due to noise or to long T2 components. The aim of this study was to show that B1 imperfections contribute significantly to the offset. We further introduce a simple method to reduce the systematic error in T2 by discarding the first echo and using the offset fitting approach.

Materials and Methods

Signal curves of T2 relaxometry were simulated based on extended phase graph theory and evaluated for 4 different methods (inclusion and exclusion of the first echo, while fitting with and without the offset). We further performed T2 relaxometry in a phantom at 9.4T magnetic resonance imaging scanner and used the same methods for post-processing as in the extended phase graph simulated data. Single spin echo sequences were used to determine the correct T2 time.

Results

The simulation data showed that the systematic error in T2 and the offset depends on the refocusing pulse, the echo spacing and the echo train length. The systematic error could be reduced by discarding the first echo. Further reduction of the systematic T2 error was reached by using the offset as fitting parameter. The phantom experiments confirmed these findings.

Conclusion

The fitted offset parameter in T2 relaxometry is influenced by imperfect refocusing pulses. Using the offset as a fitting parameter and discarding the first echo is a fast and easy method to minimize the error in T2, particularly for low to intermediate echo train length.