how to use GLM and/or MANOVA

Pretty sure I'm doing this wrong and could use help.
Have two populations of subjects. Take 6 individuals from each. Administer 50 different stimuli to each individual (stimuli are qualitatively different, not quantitatively). Need to see if there is an overall difference in 50 responses due to population, and if any responses to specific stimuli are different between populations. In Matlab I have done this: [b,d,stats] = glmfit([pop stim],[resp]); where pop = 1 or -1, stim = 1,2,...50. Thanks!