Gates, K. M., Molenaar, P. C. M., Hillary, F., Ram, N., & Rovine, M. (2010). Automatic search in fMRI connectivity mapping: An alternative to Granger causality using formal equivalences between SEM path modeling, VAR, and unified SEM. NeuroImage, 53, 1118-1125.
This paper uses sequentially applied modification indices to test for the causal structure of fMRI data. In this application, I used Mplus as to test these models. The attached zipped folder provides both the Mplus code as well as an Excel spreadsheet containing the modification indices from the outputs, as well as a summary table of the chi square statistics reported in the article.