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There is a rise in the study of functional connectivity among various cortical regions and investigations to uncover causal links between a stimulus and the corresponding neural dynamics through electrophysiological imaging of the human brain. Animal model that exhibit simplistic representations of such networks open a doorway for such investigations and are gaining rapid popularity. In this study, we investigate and compare resting state network and auditory stimulus related activity with minimal invasive technology along computational spectral analysis on a C57/BL6 based mouse model. Somatosensory, motor and visual cortex are observed to be highly active and significantly correlated (p-value<0.05). Moreover, given the spatial limitation due to small size of the mouse head, we also describe a low-cost and effective fabrication process for the mouse EEG Polyimide Based Microelectrodes (PBM) array. The easy-to-implement fabrication process involves transfer of the pattern on a copper layer of the Kapton film followed by gold electroplating and application of insulation paint. Acoustic stimulation is done by using tube extensions for avoiding electrical coupling to EEG signals. Unlike multi-electrode array type of invasive methods that are local to a cortical region, the methods established in this study can be used for examining functional connectivity analysis, neural dynamics and cortical response at a global level.