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This thesis presents a method for the segmentation of dual-channel structural magnetic resonance imaging (MRI) volumes of the human brain into four tissue classes. The state-of-the-art FSL FAST segmentation software (Zhang et al., 2001) is in widespread clinical use, and so it is considered a benchmark. A significant proportion of FAST’s errors has been shown to be localised to cortical sulci and blood vessels; this issue has driven the developments in this thesis, rather than any particular clinical demand. The original theme lies in preserving and even restoring these thin structures, poorly resolved in typical clinical MRI. Bright plate-shaped sulci and dark tubular vessels are best contrasted from the other tissues using the T2- and PD-weighted data, respectively. A contrasting tube detector algorithm (based on Frangi et al., 1998) was adapted to detect both structures, with smoothing (based on Westin and Knutsson, 2006) of an intermediate tensor representation to ensure smoothness and fuller coverage of the maps. The segmentation strategy required the MRI volumes to be upscaled to an artificial high resolution where a small partial volume label set would be valid and the segmentation process would be simplified. A resolution enhancement process (based on Salvado et al., 2006) was significantly modified to smooth homogeneous regions and sharpen their boundaries in dual-channel data. In addition, it was able to preserve the mapped thin structures’ intensities or restore them to pure tissue values. Finally, the segmentation phase employed a relaxation-based labelling optimisation process (based on Li et al., 1997) to improve accuracy, rather than more efficient greedy methods which are typically used. The thin structure location prior maps and the resolution-enhanced data also helped improve the labelling accuracy, particularly around sulci and vessels. Testing was performed on the aged LBC1936 clinical dataset and on younger brain volumes acquired at the SHEFC Brain Imaging Centre (Western General Hospital, Edinburgh, UK), as well as the BrainWeb phantom. Overall, the proposed methods rivalled and often improved segmentation accuracy compared to FAST, where the ground truth was produced by a radiologist using software designed for this project. The performance in pathological and atrophied brain volumes, and the differences with the original segmentation algorithm on which it was based (van Leemput et al., 2003), were also examined. Among the suggestions for future development include a soft labelling consensus formation framework to mitigate rater bias in the ground truth, and contour-based models of the brain parenchyma to provide additional structural constraints.

A sequential imaging system using a flat bed scanner interfaced to a personal computer was developed to study seed germination and vigor. The utility of the system was demonstrated in studies relating aspects of seed vigor in impatiens seed lots and for dormancy release in two woody perennials. Impatiens seed lots were kept in storage for 6 months to obtain a range in vigor levels. The ability to see differences at the individual seed level was possible because of the development of the sequential imaging system. It was observed that seeds deteriorated both under optimum 4OC as well as 25OC storage conditions. It was determined that both germination rate and seedling growth rate were appropriate measures of seed vigor. As untreated and primed seed lots were aged, germination percentage was negatively correlated with germination rate and positively correlated with seedling growth. However, there was a lack of correlation between germination rate and seedling growth on an individual seed basis. The data suggests that germination rate and seedling growth rate appear to be measuring different aspects of vigor. Sequential imagery also showed subtle changes in seed and seedling growth as seeds came out of dormancy that would not be detectable otherwise. This technique revealed changes in seed morphology that were previously not documented for seeds with physical dormancy. The current study furthered the utility of the imaging system by the development of sequential imaging that allows for samples to be collected hourly without technician input. This permitted very accurate determinations of germination rate and seedling growth on a single seed basis.

The push toward higher magnetic fields in MRI has consistently thrown up new challenges in hardware development. The recent development of a new generation of ultra-high field scanners for human imaging is no exception. The earch presented in this thesis aims to provide solutions to new technical challenges in radio-frequency probe design. All probe designs were developed for use at 7T on a Philips Acheiva full body scanner.

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Field Cycled Magnetic Resonance Imaging offers potential for significant Signal to Noise Ratio and T₁ contrast improvements of Magnetic Resonance images. In this work the hardware and software components of a home made, low field NMR imager were modified, in order to investigate Field Cycling. Theoretical models were developed to simulate NMR signal response to different magnetic field pulse shapes and it was seen that trapezoidal magnetic field pulse waveforms, with rise/fall times considerably smaller than the T₁ relaxation times of the examined samples, give comparable results to those of an ideal, rectangular pulse. The steady state signal expressions of Field Cycled Gradient Echo and Spin Echo sequences were derived and tested experimentally. Differences between theoretical and experimental results can be attributed to the increased levels of noise and the effect of time dependent magnetic fields due to limited efficiency of the induced current cancelling scheme. The ability of the imager to measure T₁ relaxation times at different magnetic field strengths, employing Field Cycled imaging sequences, was also assessed. Results were again burdened by the above mentioned problems, as well as, by the considerable temperature changes the samples suffered during the long imaging times required for complete study.