afni.nimh.nih.gov

It seems the macro I used to create the output matrices prints to stderr instead of stdout. To capture stderr, you can use an '&' in the pipes like this

1dSEM -theta txtIMGstu_thetas_model1.1D -C SEM_corr.1D -DF 101.195 -psi SEM_resvarcorr.1D -forest_growth -stop_cost .01 -leafpicker -limits -1 1 |& tee outlog.txt

The '|&" redirects both stdout and stderr. Sorry about this additional complication.