Hi Anna, welcome to the forum.
With these types of questions it always helps if you can provide a minimal working example. But you explained the problem well enough that I think I can come up with one.
So you have a matrix M whose columns correspond to time and some dependent variable. Let's say M looks like this:
M = [(1:100)' (1:100)'.^2+randn(100,1)];
Plot the first and second colums to see what kind of data we're looking at:
To get the average over some interval, say between t = 55 and t=65, get the indices of that range:
ind = M(:,1)>=55 & M(:,1)<65;
Then calculate the mean of column 2 over the interval: