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DEVELOPMENT AND EVALUATION OF MRI TEMPLATES OF THE MIITRA ATLAS
Title
DEVELOPMENT AND EVALUATION OF MRI TEMPLATES OF THE MIITRA ATLAS
Creator
RIDWAN, ABDUR RAQUIB
Date
2021
Description
Digital human brain atlases play a pivotal role in conducting wide range of neuroimaging studies and are commonly used as references for...
Show moreDigital human brain atlases play a pivotal role in conducting wide range of neuroimaging studies and are commonly used as references for spatial normalization in voxel-wise analysis, region-of interest analyses, automated tissue-segmentation, functional connectivity analyses, etc. A brain atlas typically consists of MRI-based multi-modal templates and semantic labels delineating brain regions according to the characteristics of the underlying tissue. In recent times there has been a plethora of magnetic resonance imaging (MRI) studies on older adults without dementia to explore the role of brain characteristics associated with cognitive functions in old age with the ultimate goal to develop strategies for prevention of cognitive decline. Increasing the accuracy in terms of sensitivity and specificity of such neuroimaging studies require an atlas with a comprehensive set of high-quality templates representative of the brain characteristics typical of older adults and detailed labels accurately mapping brain regions of interest. However, such an atlas has not been constructed for older adults without dementia. Hence this thesis aims to build high quality MRI templates which are the cornerstone resources needed for the development of a comprehensive, high quality, multi-channel, longitudinal, probabilistic digital human brain atlas for older adults termed as Multi-channel Illinois Institute of Technology and Rush University Aging (MIITRA) atlas. This dissertation focuses on a) to develop and evaluate a high performing 1mm isotropic structural T1-weighted brain template, b) to investigate the development and evaluation of a spatio-temporally consistent longitudinal structural T1-weighted template of the older adult brain, c) to develop and evaluate an unbiased 0.5 mm isotropic super-resolved high resolution and detail-preserving structural T1 weighted template of the older adult brain, d) to develop an unbiased 0.5 mm super-resolved high resolution and detail-preserving structural PD weighted and T2-weighted template of the older adult brain, e) to investigate and provide future directions in the development of a 0.5 mm super-resolved high resolution DTI template of the older adult brain, and f) to construct a novel approach in the development of MRI templates using both space and frequency information of spatially normalized older adult data. The thesis based on the aforementioned foundational points was constructed as follows: Firstly, this thesis presents the development of a 1mm isotropic T1-weighted structural template of the older adult brain utilizing state of the art registration algorithm ANTs with parameters carefully optimized for older adults, in an iterative groupwise spatial normalization framework. The preprocessing steps were also thoroughly investigated to ensure high quality data. It was demonstrated through systematic comparison of this new template to several other standardized and study-specific T1-weighted templates that a) it exhibited high image sharpness, b) allowed for high spatial normalization accuracy and detection of smaller inter-group morphometric differences compared to other standardized templates, c) had similar performance to that of study-specific templates and d) was highly representative of the older adult brain. Secondly, with the acquired technical know-how from the aforementioned research findings a new method was introduced for the construction of a spatio-temporally consistent longitudinal template based on high quality cross-sectional older adult data from a large cohort. The new template was compared to templates generated with previously published methods in terms of spatio-temporal consistency and image quality and was shown to have superior performance. In addition, a novel approach was introduced for image quality enhancement of the longitudinal templates utilizing both space and frequency information. Thirdly, the thesis presents a method that involves a) thoroughly refining registration parameters, b) patch-based tissue-guided sparse-representation approach in a super-resolved unbiased minimum deformation space to construct and evaluate an unbiased 0.5 mm isotropic super-resolved high resolution and detail-preserving structural T1 weighted template of the older adult brain. This method accounts for misregistration specially in the cortical regions, ensuring sharp delineation of structures representative of the older adult brain. The new template developed using this approach maintained high anatomical consistency with sharp and detailed cortical features in the brain and exhibited higher image sharpness compared to other high-resolution standardized templates and allowed for high spatial normalization accuracy when used as a reference for normalization of older adult data. Additionally, this approach of template building was investigated on DTI tensors of older adult participants, and the constructed DTI template was shown to perform better than templates developed using the best approach currently present in the literature. Finally, the thesis presents the development of an unbiased 0.5 mm super-resolved high resolution and detail-preserving structural PD weighted and T2-weighted template of the older adult brain, from nonlocal super-resolution based upsampled PD and T2w older adult participant data, using this new template building approach.
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