MRI-only based radiotherapy treatment planning for the rat brain on a Small Animal Radiation Research Platform (SARRP)

Computed tomography (CT) is the standard imaging modality in radiation therapy treatment planning (RTP). However, magnetic resonance (MR) imaging provides superior soft tissue contrast, increasing the precision of target volume selection. We present MR-only based RTP for a rat brain on a small animal radiation research platform (SARRP) using probabilistic voxel classification with multiple MR sequences. Six rat heads were imaged, each with one CT and five MR sequences. The MR sequences were: T1-weighted, T2-weighted, zero-echo time (ZTE), and two ultra-short echo time sequences with 20 mu s (UTE1) and 2 ms (UTE2) echo times. CT data were manually segmented into air, soft tissue, and bone to obtain the RTP reference. Bias field corrected MR images were automatically segmented into the same tissue classes using a fuzzy c-means segmentation algorithm with multiple images as input. Similarities between segmented CT and automatic segmented MR (ASMR) images were evaluated using Dice coefficient. Three ASMR images with high similarity index were used for further RTP. Three beam arrangements were investigated. Dose distributions were compared by analysing dose volume histograms. The highest Dice coefficients were obtained for the ZTE-UTE2 combination and for the T1-UTE1-T2 combination when ZTE was unavailable. Both combinations, along with UTE1-UTE2, often used to generate ASMR images, were used for further RTP. Using 1 beam, MR based RTP underestimated the dose to be delivered to the target (range: 1.4%-7.6%). When more complex beam configurations were used, the calculated dose using the ZTE-UTE2 combination was the most accurate, with 0.7% deviation from CT, compared to 0.8% for T1-UTE1-T2 and 1.7% for UTE1-UTE2. The presented MR-only based workflow for RTP on a SARRP enables both accurate organ delineation and dose calculations using multiple MR sequences. This method can be useful in longitudinal studies where CT's cumulative radiation dose might contribute to the total dose

Design of a Multi-Array Radio-Frequency Coil for Interventional MRI of the Female Breast

A new method for the simulation of radio frequency (RF) coils has been developed. This method utilizes the FEM simulation package Ansoft HFSS as a base for the modeling of RF coils with complex biological loading effects. The abilities of this software have been augmented with custom MATLAB code to enable the fast prediction of lumped element values needed to properly tune and match the coil structure as well as to perform the necessary post processing of simulation data in order to quickly generate and evaluate field data of the resonating coil and compare design variations. This method was evaluated for accuracy and implemented in the re-design of an existing four channel breast coil array for clinical imaging of the female breasts. Based on the simulation results, a commercially viable printed circuit board (PCB) implementation was developed and tested in a clinical 1.5 T MR scanner. The new design allows for wide open bilateral access to the breast regions in order to accommodate various interventional procedures. The layout has also increased axillary B1 field coverage with minor penalty to the signal-to-noise ratio of the coil array, enabling high-resolution imaging over a wide field-of-view

Design of Radio-Frequency Arrays for Ultra-High Field MRI

Magnetic Resonance Imaging (MRI) is an indispensable, non-invasive diagnostic tool for the assessment of disease and function. As an investigational device, MRI has found routine use in both basic science research and medicine for both human and non-human subjects. Due to the potential increase in spatial resolution, signal-to-noise ratio (SNR), and the ability to exploit novel tissue contrasts, the main magnetic field strength of human MRI scanners has steadily increased since inception. Beginning in the early 1980’s, 0.15 T human MRI scanners have steadily risen in main magnetic field strength with ultra-high field (UHF) 8 T MRI systems deemed to be insignificant risk by the FDA (as of 2016). However, at UHF the electromagnetic fields describing the collective behaviour of spin dynamics in human tissue assume ‘wave-like’ behaviour due to an increase in the processional frequency of nuclei at UHF. At these frequencies, the electromagnetic interactions transition from purely near-field interactions to a mixture of near- and far-field mechanisms. Due to this, the transmission field at UHF can produce areas of localized power deposition – leading to tissue heating – as well as tissue-independent contrast in the reconstructed images. Correcting for these difficulties is typically achieved via multi-channel radio-frequency (RF) arrays. This technology allows multiple transmitting elements to synthesize a more uniform field that can selectively minimize areas of local power deposition and remove transmission field weighting from the final reconstructed image. This thesis provides several advancements in the design and construction of these arrays. First, in Chapter 2 a general framework for modeling the electromagnetic interactions occurring inside an RF array is adopted from multiply-coupled waveguide filters and applied to a subset of decoupling problems encountered when constructing RF arrays. It is demonstrated that using classic filter synthesis, RF arrays of arbitrary size and geometry can be decoupled via coupling matrix synthesis. Secondly, in Chapters 3 and 4 this framework is extended for designing distributed filters for simple decoupling of RF arrays and removing the iterative tuning portion of utilizing decoupling circuits when constructing RF arrays. Lastly, in Chapter 5 the coupling matrix synthesis framework is applied to the construction of a conformal transmit/receive RF array that is shape optimized to minimize power deposition in the human head during any routine MRI examination

Body MRI artifacts in clinical practice: a physicist\u27s and radiologist\u27s perspective.

The high information content of MRI exams brings with it unintended effects, which we call artifacts. The purpose of this review is to promote understanding of these artifacts, so they can be prevented or properly interpreted to optimize diagnostic effectiveness. We begin by addressing static magnetic field uniformity, which is essential for many techniques, such as fat saturation. Eddy currents, resulting from imperfect gradient pulses, are especially problematic for new techniques that depend on high performance gradient switching. Nonuniformity of the transmit radiofrequency system constitutes another source of artifacts, which are increasingly important as magnetic field strength increases. Defects in the receive portion of the radiofrequency system have become a more complex source of problems as the number of radiofrequency coils, and the sophistication of the analysis of their received signals, has increased. Unwanted signals and noise spikes have many causes, often manifesting as zipper or banding artifacts. These image alterations become particularly severe and complex when they are combined with aliasing effects. Aliasing is one of several phenomena addressed in our final section, on artifacts that derive from encoding the MR signals to produce images, also including those related to parallel imaging, chemical shift, motion, and image subtraction

Novel MRI Technologies for Structural and Functional Imaging of Tissues with Ultra-short T₂ Values

Conventional MRI has several limitations such as long scan durations, motion artifacts, very loud acoustic noise, signal loss due to short relaxation times, and RF induced heating of electrically conducting objects. The goals of this work are to evaluate and improve the state-of-the-art methods for MRI of tissue with short T₂, to prove the feasibility of in vivo Concurrent Excitation and Acquisition, and to introduce simultaneous electroglottography measurement during functional lung MRI

Development of Advanced Acquisition and Reconstruction Techniques for Real-Time Perfusion MRI

Diese Doktorarbeit befasst sich mit der methodischen Entwicklung von Akquisition- und Rekonstruktionstechniken zur Anwendung von Echtzeit-Bildgebungstechniken auf das Gebiet der dynamischen kontrastmittelgestützten Magentresonanztomographie. Zur Unterdrückung unerwünschter Bildartefakte wird eine neue Spoiling-Technik vorgeschlagen, die auf randomisierten Phasen der Hochfrequenzanregung basiert. Diese Technik erlaubt eine schnelle, artefaktfreie Aufnahme von T1-gewichteten Rohdaten bei radialer Abtastung. Die Rekonstruktion quantitativer Parameterkarten aus solchen Rohdaten kann als nichtlineares, inverses Problem aufgefasst werden. In dieser Arbeit wird eine modellbasierte Rekonstruktionstechnik zur quantitativen T1-Kartierung entwickelt, die dieses inverse Problem mittels der iterativ regularisierten Gauß-Newton-Methode mit parameterspezifischer Regularisierung löst. In Simulationen sowie in-vitro- und in-vivo-Studien wird Genauigkeit und Präzision dieser neuen Methode geprüft, die ihre direkte Anwendung in in-vitro-Experimenten zur "first-pass"-Perfusion findet. In diesen Experimenten wird ein kommerziell verfügbares Phantom verwendet, dass in-vivo-Perfusion simuliert und gleichzeitig vollständige Kontrolle über die vorherrschenden Austauschraten erlaubt

An 8-channel receive array for improved 31 P MRSI of the whole brain at 3T.

PURPOSE: To demonstrate a 1 H/31 P whole human brain volume coil configuration for 3 Tesla with separate 31 P transmit and receive components that maintains 1 H MRS performance and delivers optimal 31 P MRSI with 1 H decoupling. METHODS: We developed an 8-channel 31 P receive array coil covering the head to be used as an insert for a commercial double-tuned 1 H/31 P birdcage transmit-receive coil. This retains the possibility of using low-power rectangular pulses for 1 H-decoupled 3D 31 P MRSI (nominal resolution 17.6 cm3 ; acquisition duration 13 min) but increases the SNR with the receive sensitivity of 31 P surface coils. The performance of the combined coil setup was evaluated by measuring 1 H and 31 P SNR with and without the 31 P receive array and by assessing the effect of the receive array on the transmit efficiencies of the birdcage coil. RESULTS: Compared to the birdcage coil alone, the 31 P insert in combination with the birdcage achieved an average 31 P SNR gain of 1.4 ± 0.4 in a center partition of the brain. The insert did not cause losses in 1 H MRS performance and transmit efficiency, whereas for 31 P approximately 20% more power was needed to achieve the same γB1. CONCLUSION: The new coil configuration allows 1 H MRSI and optimal 1 H-decoupled 3D 31 P MRSI, with increased SNR of the human brain without patient repositioning, for clinical and research purposes at 3 Tesla.C. Rodgers is funded by the Wellcome Trust and the Royal Society (Grant Number 098436/Z/12/Z)

The VHP-F Computational Phantom and its Applications for Electromagnetic Simulations

Modeling of the electromagnetic, structural, thermal, or acoustic response of the human body to various external and internal stimuli is limited by the availability of anatomically accurate and numerically efficient computational models. The models currently approved for use are generally of proprietary or fixed format, preventing new model construction or customization. 1. This dissertation develops a new Visible Human Project - Female (VHP-F) computational phantom, constructed via segmentation of anatomical cryosection images taken in the axial plane of the human body. Its unique property is superior resolution on human head. In its current form, the VHP-F model contains 33 separate objects describing a variety of human tissues within the head and torso. Each obejct is a non-intersecting 2-manifold model composed of contiguous surface triangular elements making the VHP-F model compatible with major commercial and academic numerical simulators employing the Finite Element Method (FEM), Boundary Element Method (BEM), Finite Volume Method (FVM), and Finite-Difference Time-Domain (FDTD) Method. 2. This dissertation develops a new workflow used to construct the VHP-F model that may be utilized to build accessible custom models from any medical image data source. The workflow is customizable and flexible, enabling the creation of standard and parametrically varying models facilitating research on impacts associated with fluctuation of body characteristics (for example, skin thickness) and dynamic processes such as fluid pulsation. 3. This dissertation identifies, enables, and quantifies three new specific computational bioelectromagnetic problems, each of which is solved with the help of the developed VHP-F model: I. Transcranial Direct Current Stimulation (tDCS) of human brain motor cortex with extracephalic versus cephalic electrodes; II. RF channel characterization within cerebral cortex with novel small on-body directional antennas; III. Body Area Network (BAN) characterization and RF localization within the human body using the FDTD method and small antenna models with coincident phase centers. Each of those problems has been (or will be) the subject of a separate dedicated MS thesis

Multiple resonant multiconductor transmission line resonator design using circulant block matrix algebra

The purpose of this dissertation is to provide a theoretical model to design RF coils using multiconductor transmission line (MTL) structures for MRI applications. In this research, an MTL structure is represented as a multiport network using its port admittance matrix. Resonant conditions and closed-form solutions for different port resonant modes are calculated by solving the eigenvalue problem of port admittance matrix using block matrix algebra. A mathematical proof to show that the solution of the characteristic equation of the port admittance matrix is equivalent to solving the source side input impedance is presented. The proof is derived by writing the transmission chain parameter matrix of an MTL structure, and mathematically manipulating the chain parameter matrix to produce a solution to the characteristic equation of the port admittance matrix. A port admittance matrix can be formulated to take one of the forms depending on the type of MTL structure: a circulant matrix, or a circulant block matrix (CB), or a block circulant circulant block matrix (BCCB). A circulant matrix can be diagonalized by a simple Fourier matrix, and a BCCB matrix can be diagonalized by using matrices formed from Kronecker products of Fourier matrices. For a CB matrix, instead of diagonalizing to compute the eigenvalues, a powerful technique called “reduced dimension method� can be used. In the reduced dimension method, the eigenvalues of a circulant block matrix are computed as a set of the eigenvalues of matrices of reduced dimension. The required reduced dimension matrices are created using a combination of the polynomial representor of a circulant matrix and a permutation matrix. A detailed mathematical formulation of the reduced dimension method is presented in this thesis. With the application of the reduced dimension method for a 2n+1 MTL structure, the computation of eigenvalues for a 4n X 4n port admittance matrix is simplified to the computation of eigenvalues of 2n matrices of size 2 X 2. In addition to reduced computations, the model also facilitates analytical formulations for coil resonant conditions. To demonstrate the effectiveness of the proposed methods (2n port model and reduced dimension method), a two-step approach was adopted. First, a standard published RF coil was analyzed using the proposed models. The obtained resonant conditions are then compared with the published values and are verified by full-wave numerical simulations. Second, two new dual tuned coils, a surface coil design using the 2n port model, and a volume coil design using the reduced dimensions method are proposed, constructed, and bench tested. Their validation was carried out by employing 3D EM simulations as well as undertaking MR imaging on clinical scanners. Imaging experiments were conducted on phantoms, and the investigations indicate that the RF coils achieve good performance characteristics and a high signal-to-noise ratio in the regions of interest

A 64-channel personal computer based image reconstruction system and applications in single echo acquisition magnetic resonance elastography and ultra-fast magnetic resonance imaging.

Emerging technologies in parallel magnetic resonance imaging (MRI) with massive receiver arrays have paved the way for ultra-fast imaging at increasingly high frame rates. With the increase in the number of receiver channels used to implement parallel imaging techniques, there is a corresponding increase in the amount of data that needs to be processed, slowing down the process of image reconstruction. To develop a complete reconstruction system which is easy to assemble in a single computer for a real-time rendition of images is a relevant challenge demanding dedicated resources for high speed digital data transfer and computation. We have enhanced a 64 channel parallel receiver system designed for single echo acquisition (SEA) MRI into a real-time imaging system by interfacing it with two commercially available digital signal processor (DSP) boards which are capable of transferring large amounts of digital data via a dedicated bus from two high performance digitizer boards. The resulting system has been used to demodulate raw image data in real-time data and store them at rates of 200 frames per second (fps) and subsequently display the processed data at rates of 26 fps. A further interest in realtime reconstruction techniques is to reduce the data handling issues. Novel ways to minimize the digitized data are presented using reduced sampling rate techniques. The proposed techniques reduce the amount of data generated by a factor of 5 without compromising the SNR and with no additional hardware. Finally, the usability of this tool is demonstrated by investigating fast imaging applications. Of particular interest among them are MR elastography applications. An exploratory study of SEA MRE was done to study the temperature dependency of shear stiffness in an agarose gel and the results correlate well with existing literature. With the ability to make MRE images in a single echo, the SEA MRE technique has an advantage over the conventional MRE techniques