Implementation and Application of PSF-Based EPI Distortion Correction to High Field Animal Imaging

The purpose of this work is to demonstrate the functionality and performance of a PSF-based geometric distortion correction for high-field functional animal EPI. The EPI method was extended to measure the PSF and a postprocessing chain was implemented in Matlab for offline distortion correction. The correction procedure was applied to phantom and in vivo imaging of mice and rats at 9.4T using different SE-EPI and DWI-EPI protocols. Results show the significant improvement in image quality for single- and multishot EPI. Using a reduced FOV in the PSF encoding direction clearly reduced the acquisition time for PSF data by an acceleration factor of 2 or 4, without affecting the correction quality

Development of Methodologies for Diffusion-weighted Magnetic Resonance Imaging at High Field Strength

Diffusion-weighted imaging of small animals at high field strengths is a challenging prospect due to its extreme sensitivity to motion. Periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) was introduced at 9.4T as an imaging method that is robust to motion and distortion. Proton density (PD)-weighted and T2-weighted PROPELLER data were generally superior to that acquired with single-shot, Cartesian and echo planar imaging-based methods in terms of signal-to-noise ratio (SNR), contrast-to-noise ratio and resistance to artifacts. Simulations and experiments revealed that PROPELLER image quality was dependent on the field strength and echo times specified. In particular, PD-weighted imaging at high field led to artifacts that reduced image contrast. In PROPELLER, data are acquired in progressively rotated blades in k-space and combined on a Cartesian grid. PROPELLER with echo truncation at low spatial frequencies (PETALS) was conceived as a postprocessing method that improved contrast by reducing the overlap of k-space data from different blades with different echo times. Where the addition of diffusion weighting gradients typically leads to catastrophic motion artifacts in multi-shot sequences, diffusion-weighted PROPELLER enabled the acquisition of high quality, motion-robust data. Applications in the healthy mouse brain and abdomen at 9.4T and in stroke patients at 3T are presented. PROPELLER increases the minimum scan time by approximately 50%. Consequently, methods were explored to reduce the acquisition time. Two k-space undersampling regimes were investigated by examining image fidelity as a function of degree of undersampling. Undersampling by acquiring fewer k-space blades was shown to be more robust to motion and artifacts than undersampling by expanding the distance between successive phase encoding steps. To improve the consistency of undersampled data, the non-uniform fast Fourier transform was employed. It was found that acceleration factors of up to two could be used with minimal visual impact on image fidelity. To reduce the number of scans required for isotropic diffusion weighting, the use of rotating diffusion gradients was investigated, exploiting the rotational symmetry of the PROPELLER acquisition. Fixing the diffusion weighting direction to the individual rotating blades yielded geometry and anisotropy-dependent diffusion measurements. However, alternating the orientations of diffusion weighting with successive blades led to more accurate measurements of the apparent diffusion coefficient while halving the overall acquisition time. Optimized strategies are proposed for the use of PROPELLER in rapid high resolution imaging at high field strength

Development of pulse sequences for hyperpolarized 13C magnetic resonance spectroscopic imaging of tumour metabolism

Metabolic imaging with hyperpolarized 13C-labeled cell substrates is a promising technique for imaging tissue metabolism in vivo. However, the transient nature of the hyperpolarization - and its depletion following excitation - limits the imaging time and the number of excitation pulses that can be used. A single-shot 3D imaging sequence has been developed and it is shown in this thesis to generate 13C MR images in tumour-bearing mice injected with hyperpolarized [1-13C]pyruvate. The pulse sequence acquires a stack-of-spirals at two spin echoes after a single excitation pulse and encodes the kz-dimension in an interleaved manner to enhance robustness to B0 inhomogeneity. Spectral-spatial pulses are used to acquire dynamic 3D images from selected hyperpolarized 13C-labeled metabolites. A nominal spatial/temporal resolution of 1.25 x 1.25 x 2.5 $mm^3$ x 2 s was achieved in tumour images of hyperpolarized [1-13C]pyruvate and [1-13C]lactate acquired in vivo. An advanced sequence is also described in this thesis in a later study to acquire higher resolution images with isotropic voxels (1.25 x 1.25 x 1.25 $mm^3$) at no cost of temporal resolution. EPI is a sequence widely used in hyperpolarized 13C MRI because images can be acquired rapidly with limited RF exposure. However, EPI suffers from Nyquist ghosting, which is normally corrected for by acquiring a reference scan. In this thesis a workflow for hyperpolarized 13C EPI is proposed that requires no reference scan and, therefore, that does not sacrifice a time point in the dynamic monitoring of tissue metabolism. To date, most of the hyperpolarized MRI on metabolism are based on 13C imaging, while 1H is a better imaging target for its 4 times higher gyromagnetic ratio and hence 16 times signal. In this thesis the world’s first dynamic 1H imaging in vivo of hyperpolarized [1-13C]lactate is presented, via a novel double-dual-spin-echo INEPT sequence that transfers the hyperpolarization from 13C to 1H, achieving a spatial resolution of 1.25 x 1.25 $mm^2$

Magnetic Susceptibility Artefact Correction of Spin-Echo and GradientEcho EPI Images

Distortion and other artefacts caused by an uneven magnetic field affect MR images acquired with the rapid technique echo-planar imaging (EPI). This study investigates the effectiveness of reverse gradient susceptibility correction methods on spin echo (SE) and gradient echo (GE) EPI. In addition, the effects of varying bandwidth, SENSE factor and slice thickness on the corrected images were measured. Undistorted, anatomically accurate images are necessary in relating EPI images to anatomical MRI scans. This is particularly important for diffusion weighted imaging, perfusion imaging and fMRI. Due to the ever-increasing need for better temporal resolution with existing hardware, effective artefact correction in post-processing is necessary, as is appropriate sequence optimisation. This investigation was accomplished using normalised mutual information to compare the images pre and post correction to an anatomical image as a measure of anatomical accuracy. It was found that the correction of geometric distortions is equally effective in GE-EPI and SE-EPI, and that geometric correction can reduce the impact of the aforementioned scan parameters on the anatomical accuracy of the images. Three correction methods were compared in this investigation; FSL TOPUP, EPI-EPIC and ACID HySCO. It was found that, in most situations, the EPIC susceptibility correction tool was the most effective tool at correcting geometric distortions without the generation of new artefacts. Susceptibility artefact corrections were also successfully conducted on 7T contrast enhanced single shot EPI images of a prostate tumour xenograft (nude mouse). These findings could help establish clinical and research protocol for susceptibility artefact post-processing, as well as sequence optimisation

Cortical lamina-dependent blood volume changes in human brain at 7T

Cortical layer-dependent high (sub-millimeter) resolution functional magnetic resonance imaging (fMRI) in human or animal brain can be used to address questions regarding the functioning of cortical circuits, such as the effect of different afferent and efferent connectivities on activity in specific cortical layers. The sensitivity of gradient echo (GE) blood oxygenation level-dependent (BOLD) responses to large draining veins reduces its local specificity and can render the interpretation of the underlying laminar neural activity impossible. The application of the more spatially specific cerebral blood volume (CBV)-based fMRI in humans has been hindered by the low sensitivity of the noninvasive modalities available. Here, a vascular space occupancy (VASO) variant, adapted for use at high field, is further optimized to capture layer-dependent activity changes in human motor cortex at sub-millimeter resolution. Acquired activation maps and cortical profiles show that the VASO signal peaks in gray matter at 0.8–1.6 mm depth, and deeper compared to the superficial and vein-dominated GE-BOLD responses. Validation of the VASO signal change versus well-established iron-oxide contrast agent based fMRI methods in animals showed the same cortical profiles of CBV change, after normalization for lamina-dependent baseline CBV. In order to evaluate its potential of revealing small lamina-dependent signal differences due to modulations of the input-output characteristics, layer-dependent VASO responses were investigated in the ipsilateral hemisphere during unilateral finger tapping. Positive activation in ipsilateral primary motor cortex and negative activation in ipsilateral primary sensory cortex were observed. This feature is only visible in high-resolution fMRI where opposing sides of a sulcus can be investigated independently because of a lack of partial volume effects. Based on the results presented here, we conclude that VASO offers good reproducibility, high sensitivity and lower sensitivity than GE-BOLD to changes in larger vessels, making it a valuable tool for layer-dependent fMRI studies in humans

Correction of spherical single lens aberration using digital image processing for cellular phone camera

制度:新 ; 報告番号:甲3276号 ; 学位の種類:博士(工学) ; 授与年月日:2011/2/21 ; 早大学位記番号:新558

Phase imaging for reducing macrovascular signal contributions in high-resolution fMRI

High resolution functional MRI allows for the investigation of neural activity within the cortical sheet. One consideration in high resolution fMRI is the choice of which sequence to use during imaging, as all methods come with sensitivity and specificity tradeoffs. The most used fMRI sequence is gradient-echo echo planar imaging (GE-EPI) which has the highest sensitivity but is not specific to microvasculature. GE-EPI results in a signal with pial vessel bias which increases complexity of performing studies targeted at structures within the cortex. This work seeks to explore the use of MRI phase signal as a macrovascular filter to correct this bias. First, an in-house phase combination method was designed and tested on the 7T MRI system. This method, the fitted SVD method, uses a low-resolution singular value decomposition and fitting to a polynomial basis to provide computationally efficient, phase sensitive, coil combination that is insensitive to motion. Second, a direct comparison of GE-EPI, GE-EPI with phase regression (GE-EPI-PR), and spin echo EPI (SE-EPI) was performed in humans completing a visual task. The GE-EPI-PR activation showed higher spatial similarity with SE-EPI than GE-EPI across the cortical surface. GE-EPI-PR produced a similar laminar profile to SE-EPI while maintaining a higher contrast-to-noise ratio across layers, making it a useful method in low SNR studies such as high-resolution fMRI. The final study extended this work to a resting state macaque experiment. Macaques are a common model for laminar fMRI as they allow for simultaneous imaging and electrophysiology. We hypothesized that phase regression could improve spatial specificity of the resting state data. Further analysis showed the phase data contained both system and respiratory artifacts which prevented the technique performing as expected under two physiological cleaning strategies. Future work will have to examine on-scanner physiology correction to obtain a phase timeseries without artifacts to allow for the phase regression technique to be used in macaques. This work demonstrates that phase regression reduces signal contributions from pial vessels and will improve specificity in human layer fMRI studies. This method can be completed easily with complex fMRI data which can be created using our fitted SVD method

Development of novel magnetic resonance methods for advanced parametric mapping of the right ventricle

The detection of diffuse fibrosis is of particular interest in congenital heart disease patients, including repaired Tetralogy of Fallot (rTOF), as clinical outcome is linked to the accurate identification of diffuse fibrosis. In the Left Ventricular (LV) myocardium native T1 mapping and Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) are promising approaches for detection of diffuse fibrosis. In the Right Ventricle (RV) current techniques are limited due to the thinner, mobile and complex shaped compact myocardium. This thesis describes technical development of RV tissue characterisation methods. An interleaved variable density spiral DT-CMR method was implemented on a clinical 3T scanner allowing both ex and in vivo imaging. A range of artefact corrections were implemented and tested (gradient timing delays, off-resonance and T2* corrections). The off- resonance and T2* corrections were evaluated using computational simulation demonstrating that for in vivo acquisitions, off-resonance correction is essential. For the first-time high-resolution Stimulated Echo Acquisition Mode (STEAM) DT-CMR data was acquired in both healthy and rTOF ex-vivo hearts using an interleaved spiral trajectory and was shown to outperform single-shot EPI methods. In vivo the first DT-CMR data was shown from the RV using both an EPI and an interleaved spiral sequence. Both sequences provided were reproducible in healthy volunteers. Results suggest that the RV conformation of cardiomyocytes differs from the known structure in the LV. A novel STEAM-SAturation-recovery Single-sHot Acquisition (SASHA) sequence allowed the acquisition of native T1 data in the RV. The excellent blood and fat suppression provided by STEAM is leveraged to eliminate partial fat and blood signal more effectively than Modified Look-Locker Imaging (MOLLI) sequences. STEAM-SASHA T1 was validated in a phantom showing more accurate results in the native myocardial T1 range than MOLLI. STEAM-SASHA demonstrated good reproducibility in healthy volunteers and initial promising results in a single rTOF patient.Open Acces