This paper extends our previous study (letter paper), which quantifies the difficulty of program comprehension based on brain activation measured by NIRS (Near Infra-Red Spectroscopy) during source code reading. We performed controlled experiments with 20 subjects. 3 of 20 subjects could not complete the measurement. We found that: (1) 16 of 17 shows strong brain activation during reading of obfuscated program (binomial test, p < 0:01) and (2) subjective evaluation of difficulty is correlated with brain activation (Spearman's correlation coefficient=0.46, p < 0:01).