Nowadays, brain research is one of the hot topics in the field of science. With the rapid development of electrophysiology and neuroimaging techniques, people could obtain many kinds of data recorded from the brain. To deal with these data effectively will help us to understand the brain. According to the complexity of the brain, we applied the synthetical analysis to the brain research. We therefore adopted the the strategy of segregation and integration, and investigated the brain structure and function from the different levels and viewpoints while using the multimodal data. The main works and constributions of this dissertation are as follows: (1) Based on the point of segregation and integration, we investigated the neural encoding in motor cortex while the monkey was trained to perform the reach-to-grasp task. We designed the reach-to-grasp task with two movement directions and three movement orientations, and proposed the partial directed coherence, which was based on multivariate vector autoregressive model, to investigate the neural interaction. The results showed that there were not only the movement direction-related neurons but also the movement orientation-related neurons, and meanwhile, there might be some information pathways controlling different functional parameters among neurons. (2) Based on the point of segregation and integration, we applied the MRI-based cortical thickness to investigate the gender effect on brain structure. We proposed the framework to construct the weighted morphogical-based network, and used the graph theory to measure the properties of network. We performed the statistical analysis on the large sample (n=184), and found not only the gender difference on some local regions but also the gender consistency on the network level. (3) Based on the multimodal imaging data, for the first time, we combined the structural and functional analysis to investigate the humans with amblyopia. According to the principle of retinotopic mapping, we proposed a new volume-based computational framework to delineate the visual areas and detect their functional activation. The results illustrated that the cortical deficits existed in several visual areas, and the whole functional deficit was most relevant to the cortical volume in the occipital lobe.
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