An incresing number of contributions in Quantitative an Computational Neuroscience have stressed that cognitive processes should be understood as a complex network of segregated brain areas. Among these contributions, functional connectivity studies the covariance over time among segregated brain regions that compound a functional network. The sample consisted of two groups of 12 participants, matched by age, with high and low spelling skills (HSS and LSS, respectively). During an fMRI session, two different block-design experiments involving homophone spelling Spanish language were applied to each group. In the first task, individuals were asked assess the presence or absence of an homophone orthographic error. While in the second task, they were asked to detect the presence or absence of an "i" in the word presented, regardless of the spelling.This work has permitted to identify certain issues in the application of SEM to functional connectivity research.