For the nervous system, there is evidence of relative shortening of the spinal cord, reflected by both reduced cord length to vertebral column ratio and a change in cross-sectional morphology of the cord. The cerebellar tonsils are low-lying in AIS subjects while significant regional volume differences in the brain are also evident between AIS subjects and controls. / From the results of this series of study, AIS girls are found to have morphological difference in multiple aspects when compared with age- and sex-matched normal controls. / Idiopathic scoliosis is a common worldwide problem and has been treated for many decades; however, there still remain uncertain areas about this disorder. Its involvement and impact on different parts of the human body remain underestimated due to lack of technology in imaging for objective assessment in the past. / In the skeletal system, AIS girls have generalized osteopenia and abnormal growth of the appendiceal skeleton. For the axial skeleton, abnormal ossification patterns have been found affecting both the longitudinal growth and axial growth pattern of the vertebral column. There is overgrowth of the anterior vertebral column, reversed asymmetry of the neural arch and smaller pedicle at the concavity of the scoliotic curve in AIS, suggestive of asynchronous growth between membraneous and endochondral ossifications. In the skull, both calvarium and basicranium are found have regional difference (including foramen magnum) between AIS subjects and controls, which is again probably reflecting a systemic process of asynchronous growth between membraneous and endochondral ossification. / It was concluded that the hypothesis "In adolescent idiopathic scoliosis, advanced magnetic resonance imaging techniques can be used to identify systemic features which are suggestive of asynchronous neuro-osseous growth of the disorder" was confirmed. (Abstract shortened by UMI.) / Taking together, the abnormalities in the skeletal system and nervous system are likely to be inter-related and reflecting a systemic process of asynchronous neuro-osseous growth. The above findings help to explain a number of well documented neurological abnormalities in AIS: Anatomically, there is increased incidence of Chiari malformation and syringomyelia in AIS subjects, while functionally, abnormal somatosensory evoked potential (SSEP) results, impaired postural balance, poor performance on combined visual and proprioceptive testing and spatial orientation testing as well as reports of abnormal nystagmus response to caloric testing are known to be associated with AIS. / The advances in imaging technique and image analysis technology have provided a novel approach for the understanding of the phenotypic presentation of neuro-osseous changes in AIS subjects as compared with normal controls. Dynamic imaging also assists in functional assessment of pulmonary function and respiratory mechanism in AIS subjects. / The hypothesis to be tested in this series of studies is: "In adolescent idiopathic scoliosis, advanced magnetic resonance imaging techniques can be used to identify systemic features which are suggestive of asynchronous neuro-osseous growth of the disorder". This thesis was based on a series of eight studies which were aimed to explore the "unknown" anatomical features in the skeletal and neural systems in AIS by the application of new advanced technique of MR imaging and sophisticated image analysis programs. / We are the first group who has undertaken a comprehensive morphological assessment of the skeletal and nervous systems in AIS subjects based on imaging findings which have not been reported previously. For the first time in literature, the spinal cord and vertebral column, brain and skull were thoroughly analyzed in AIS subjects and compared with age- and sex-matched normal controls. Detailed correlations with clinical information, neurological tests have also been made. As an appendix, MR imaging findings of the pulmonary system in AIS, including the lung, chest wall and diaphragms are also presented at the end of the thesis. / Chu Chiu-wing, Winnie. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0976. / Thesis (M.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (p. 248-267). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / School code: 1307.

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Tai, Chi Kin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (p. 56-59). / Abstracts in English and Chinese. / Chapter 1 --- Introduction --- p.7 / Chapter 2 --- Theoretical Background --- p.9 / Chapter 2.1 --- Nuclear Magnetic Resonance --- p.9 / Chapter 2.1.1 --- Nuclear spin and macroscopic magnetization --- p.10 / Chapter 2.1.2 --- Precession and Larmor Frequency --- p.12 / Chapter 2.1.3 --- Radio-frequency excitation --- p.13 / Chapter 2.1.4 --- Radio-frequency relaxation --- p.15 / Chapter 2.1.5 --- Spin echoes --- p.17 / Chapter 2.1.6 --- Contrast mechanisms --- p.17 / Chapter 2.2 --- Magnetic Resonance Imaging --- p.20 / Chapter 2.2.1 --- MRI machine hardware --- p.20 / Chapter 2.2.2 --- Slice selection --- p.22 / Chapter 2.2.3 --- Frequency encoding --- p.23 / Chapter 2.2.4 --- Phase encoding --- p.26 / Chapter 2.2.5 --- Pulse sequences --- p.26 / Chapter 2.2.6 --- Field of view and resolution --- p.28 / Chapter 3 --- Parallel Magnetic Resonance Imaging --- p.30 / Chapter 3.1 --- Motivation --- p.30 / Chapter 3.1.1 --- Aliasing --- p.31 / Chapter 3.2 --- Coil array and coil sensitivities --- p.32 / Chapter 3.3 --- Sensitivity encoding --- p.32 / Chapter 3.3.1 --- Estimation of coil sensitivities --- p.33 / Chapter 3.3.2 --- SENSE reconstruction --- p.33 / Chapter 3.4 --- pMRI reconstruction by TV regularization --- p.35 / Chapter 3.4.1 --- Model for coil images --- p.35 / Chapter 3.4.2 --- Total variation-regularization approach --- p.36 / Chapter 4 --- Reconstruction Results --- p.39 / Chapter 4.1 --- Simulation --- p.39 / Chapter 4.1.1 --- Reconstruction quality --- p.41 / Chapter 4.1.2 --- Reconstruction results --- p.43 / Chapter 4.2 --- MRI phantom experiments --- p.44 / Chapter 4.2.1 --- Reconstruction quality --- p.48 / Chapter 4.2.2 --- Reconstruction results --- p.49 / Chapter 4.3 --- In-vivo MRI images --- p.51 / Chapter 5 --- Discussions and Conclusions --- p.54 / Bibliography --- p.56

NMR spectroscopy is not only for protein structure determination, but also for drug screening and studies of dynamics and interactions. In both cases, one of the main bottleneck steps is backbone assignment. When a homologous structure is available, it can accelerate assignment. Such structure-based methods are the focus of this thesis. This thesis aims for fast and robust methods for NMR assignment problems; in particular, structure-based backbone assignment and chemical shift mapping. For speed, we identified situations where the number of 15N-labeled experiments for structure-based assignment can be reduced; in particular, when a homologous assignment or chemical shift mapping information is available. For robustness, we modeled and directly addressed the errors. Binary integer linear programming, a well-studied method in operations research, was used to model the problems and provide practically efficient solutions with optimality guarantees. Our approach improved on the most robust method for structure-based backbone assignment on 15N-labeled data by improving the accuracy by 10% on average on 9 proteins, and then by handling typing errors, which had previously been ignored. We show that such errors can have a large impact on the accuracy; decreasing the accuracy from 95% or greater to between 40% and 75%. On automatically picked peaks, which is much noisier than manually picked peaks, we achieved an accuracy of 97% on ubiquitin. In chemical shift mapping, the peak tracking is often done manually because the problem is inherently visual. We developed a computer vision approach for tracking the peak movements with average accuracy of over 95% on three proteins with less than 1.5 residues predicted per peak. One of the proteins tested is larger than any tested by existing automated methods, and it has more titration peak lists. We then combined peak tracking with backbone assignment to take into account contact information, which resulted in an average accuracy of 94% on one-to-one assignments for these three proteins. Finally, we applied peak tracking and backbone assignment to protein-ligand docking to illustrate the potential for fast 3D complex determination.

Using Graphic Processor Unit (GPU) to process the parallel operation via Compute Unified Device Architecture (CUDA) is a new technology in recent years. In the past, the GPU has been used in parallel operation but it was not easy for programming so that it couldn¡¦t be widely used in applications. CUDA is the newly-developed environment based on C language mainly for improving the complexity in programming with CUDA. The applications of GPU with CUDA has been expending to various fields gradually due to support of IEEE floating point as well as its lower cost in hardware while comparing to the super computers. Magnetic Resonance Spectroscopy (MRS) has the feature of non-invasive to probe the concentration distributed of metabolites in vivo. It can assist doctor in clinical diagnosis. The Magnetic Resonance Spectroscopy Imaging (MRSI) is imaging by many Signal Voxel Spectroscopy (SVS) to become multi-dimension MRS image. In MRSI, it can offer more information than SVS. CUDA are applied to MR image widely such as accelerating the image reconstruction and promoting the image quality, but in MRS it is seldom for the related application. In this paper, we using the CUDA to applied in MRS, the MRSI data pre-processing, to accelerate the spatial location in MRSI. In this work, we firstly use random data with different dimensions: 1D (one-dimension), 2D and 3D to evaluate the performance of Fourier transformation by using CUDA. We also finally apply some GE 2D/3D MRSI data to see how the acceleration of using CUDA works. Our results show that the acceleration rate of Fastest Fourier Transform (FFT) with CUDA in 1D, 2D and 3D random data largely increases as the data size increases. In the experiment of 2D/3D MRSI data, we find that using CUDA for accelerating the MRSI RAW-file generating procedure would avoid the data moving times, and it is not good for CUDA 1D FFT with parallel architecture while too small data amount processing in kernel. Therefore, how to solve the relationship between MRSI data format with CUDA FFT library and how to decrease the data moving time will discuss in the study.

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Magnetic Resonance Spectroscopy (MRS) can be applied to probe noninvasively the concentrations and distribution of metabolites of human tissue in vivo. As the improving of hardware and localization techniques, MRS becomes more and more important in clinical applications. Furthermore, some post-processing software, like LCModel, provide a graphical user interface for efficient and convenient analysis of MR spectroscopic imaging and thus increase the value of MRS applications. Although LCModel provides an efficient analysis and produces stable results, it can not provide metabolite map to observe the distribution of metabolite concentrations. For this reason our study processes the output data of LCModel and Digital Imaging and Communications in Medicine (DICOM) format MR images for 2D/3D metabolite map displaying. Users can use this software to observe the metabolic distribution in AP, SI and RL slice of brain tissue. In the meanwhile, as the absolute quantification of MRS has played more and more important role in clinical applications, this study also provides the LCModel end users an easy way for interpretation.

LCModel, which is performed on Linux, has been widely used for quantitative analysis of MRS. Its interface, LCMgui, converts MRS data of various formats to RAW file for LCModel analysis automatically. In this work, we had a web-based MRS analysis tool for GE MRS, GE MRS with Phase-Array and GE 2D-MRSI and improve the capability of web-based MRS analysis tool for GE 3D-MRSI, Siemens MRS/MRSI, and Philips MRS/MRSI. Meanwhile, T2 correction has been involved in the absolute quantification with LCModel. With the same echo-time, the different T2 value of each metabolite results in different degree of signal decay. In order to correct and make absolute concentrations more accurate, we exploit a factor to correct effect of different T2. Two groups of MRS data (TE = 35 and 272 ms) have been studied for comparison.

Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 126-139). Available also in a digital version from Dissertation Abstracts.

The Best PhD Thesis in the Faculties of Dentistry, Engineering, Medicine and Science (University of Hong Kong), Li Ka Shing Prize,2009-2010 / published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy