Letting YS be Your Structure,
fn = fieldnames(YS);
for K = 1 : length(fn)
fin = fn{K};
means.(fin) = reshape(mean(vertcat(YS.(fin)),2),size(YS));
end
This will produce a structure means with field names the same as the field names in YS, each of which is an array that is the mean of the field at the corresponding structure entry.
