Automated hippocampal location and extraction
Bonnici, Heidi M.
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The hippocampus is a complex brain structure that has been studied extensively and is subject to abnormal structural change in various neuropsychiatric disorders. The highest definition in vivo method of visualizing the anatomy of this structure is structural Magnetic Resonance Imaging (MRI). Gross structure can be assessed by the naked eye inspection of MRI scans but measurement is required to compare scans from individuals within normal ranges, and to assess change over time in individuals. The gold standard of such measurement is manual tracing of the boundaries of the hippocampus on scans. This is known as a Region Of Interest (ROI) approach. ROI is laborious and there are difficulties with test-retest and inter-rater reliability. These difficulties are primarily due to uncertainty in designation of the hippocampus boundary. An improved, less labour intensive and more reliable method is clearly desirable. This thesis describes a fully automated hybrid methodology that is able to first locate and then extract hippocampal volumes from 3D 1.5T MRI T1 brain scans automatically. The hybrid algorithm uses brain atlas mappings and fuzzy inference to locate hippocampal areas and create initial hippocampal boundaries. This initial location is used to seed a deformable manifold algorithm. Rule based deformations are then applied to refine the estimate of the hippocampus locations. Finally, the hippocampus boundaries are corrected through an inference process that assures adherence to an expected hippocampus volume. The ICC values of this methodology when compared to the manual segmentation of the same hippocampi result in a 0.73 for the left and 0.81 for the right hippocampi. These values both fall within the range of reliability testing according to the manual ‘gold standard’ technique. Thus, this thesis describes the development and validation of a genuinely automated approach to hippocampal volume extraction of potential utility in studies of a range of neuropsychiatric disorders and could eventually find clinical applications.