According to the documentation you get interactions between the factors listed in -bsVars and -wsVars. That explains why I got the the interaction between AUQ1 and Stim. But to get the interaction between the two -bsVars" Treatment and AUQ1" the documentation sais that i should use colon : and not asterisk *. Asterisk meant A+B+A:B. So should it be:

1).   (original version)
3dMVM -prefix covariates -dataTable @table_plus_covariates.txt -jobs 10 \
-mask mask+tlrc \
-bsVars "Treatment+AUQ1" \
-qVars "AUQ1" \
-wsVars Stim \
.... + glt

2).   (using colon)
3dMVM -prefix covariates -dataTable @table_plus_covariates.txt -jobs 10 \
-mask mask+tlrc \
-bsVars "Treatment:AUQ1" \
-qVars "AUQ1" \
-wsVars Stim \
.... + glt

3).   (using *)
3dMVM -prefix covariates -dataTable @table_plus_covariates.txt -jobs 10 \
-mask mask+tlrc \
-bsVars "Treatment*AUQ1" \
-qVars "AUQ1" \
-wsVars Stim \
.... + glt

If I add more covariates (and the end goal is their main effects and their interactions with Treatment and Stim, how is that done?

Like this?

3).   (using *)
3dMVM -prefix covariates -dataTable @table_plus_covariates.txt -jobs 10 \
-mask mask+tlrc \
-bsVars "Treatment*AUQ1*AUQ2*AUQ3" \
-qVars "AUQ1" \
-wsVars Stim \
.... + glt

or

3).   (using *)
3dMVM -prefix covariates -dataTable @table_plus_covariates.txt -jobs 10 \
-mask mask+tlrc \
-bsVars "Treatment:AUQ1:AUQ2:AUQ3" \
-qVars "AUQ1" \
-wsVars Stim \
.... + glt

Sorry for these questions but I'm having some trouble understanding the documentation.