Hi Emily,
1) AFNI programs can use sub-brick selection on input datasets,
so running 3dmaskave on EPI+tlrc'[0..17]' will take just those
first 18 time points as input.
2) Yes, 3dfim+ should work the same way (though we do not
really encourage use of that program anymore).
3) N/A
4) Given a dataset that is a time series of Fischer-z
correlations, consider using "3dTstat -stdev" to get
the standard deviation of the correlation maps.
Does this cover what you need?
- rick