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Program comprehension is the cognitive process of understanding source code. Since program comprehension is an internal cognitive process, it is inherently difficult to observe and measure reliably. Novel neuroimaging measures, such as functional magnetic resonance imaging (fMRI), provide an additional perspective on program comprehension which promise new insights to program comprehension. This dissertation develops a framework for studying program comprehension with neuroimaging, psycho-physiological, eye tracking, and behavioral methods. Our framework offers a detailed, multi-modal view on program comprehension that allows us to examine even small effects. We shed light on the underlying cognitive process of program comprehension by applying our experiment framework. One major focus is to understand experienced programmers' efficient top-down comprehension. We also link programmers' cognition to common code complexity metrics. In our interdisciplinary research, we show how neuroimaging methods, such as fMRI, in combination with psycho-physiological, eye tracking and behavioral measures, is beneficial to software-engineering research. This dissertation provides a foundation to further investigate the neuro-cognitive perspective to programmers' brains, which is a critical contribution to the future of software engineering.