When analyzing resting state brain networks using BOLD (Blood Oxygen Level Dependant) signals, region of interest (ROI) based analysis has become increasing popular in fMRI studies. However one problem in this is the lack of consistent methodology from study to study. In this study, by analyzing a functional network based on resting state and task-induced BOLD signal I identified and established and set of consistent parameters for ROI analysis, and used these methods to quantify functional connectivity between brain structures for specific function and analyzed differences between the left and right hemisphere. I found that major anatomical regions of the cortex have strong functional connectivity during the resting state and that small networks within the motor and somatosensory cortex can be mapped using ROI correlation analysis. Studies in AD progression reveal similar result in deterioration of the Default Mode Network (DMN) with onset of dementia. Also hemispheric analysis suggests that the left hemisphere is more susceptible to AD pathology. Finally I discovered specific regions showing increase in connectivity with AD progression which can possibly be used as a biomarker for AD onset.