I've become good friends with the 3dMVM program and help file, but recently I discovered something that could potentially undermine said friendship...

What is the difference between using -wsE2 and -wsMVT? I have a within-subject variable with 6 levels and it would seem both are appropriate and/or do the same thing but potentially produce different outputs (testing empirically now...)?

Here are the help excerpts for each option:

-wsE2: If at least one within-subject factor is involved in the model, any
omnibus F-test associated with a within-subject factor is assessed
with both univariate and within-subject multivariate tests. Use
the option only if at least one within-subject factor has more
than two levels.

-wsMVT: If at least one within-subject factor is involved in the model, this
option provides within-subject multivariate testing for any effect
associated with a within-subject variable. The testing strategy is
different from the conventional univariate GLM, see more details in
Chen et al. (2014), Applications of Multivariate Modeling to
Neuroimaging Group Analysis: A Comprehensive Alternative to
Univariate General Linear Model. NeuroImage 99, 571-588. If
all the within-subject factors have two levels, the multivariate
testing would render the same results as the univariate version.
So use the option only if at least one within-subject factor has
more than two levels. The F-statistics from the multivariate
testing are labeled with -wsMVT- in the sub-brick names. Note that
the conventional univariate F-statistics are automatically included
in the beginning of the output regardless the presence of this option.

Thanks!