transfer function measurement with maximum length sequence?

Hey,

    I'm desperately and unsuccessfully trying to do a transfer function measurement with maximum length sequence. I'm using cross spectra techniques to compute the transfer function calculations but am having trouble in using the maximum length sequence correctly. I think I should get 2 periods of the mls signal, one to excite the filter and the other to do the calculations. it was suggested to get the signal over two peridos by doing c=cat(1,x,x) but after how do i do the calculations over the second period?

 N=1023;      %length of signals being tested

 [x fs bits] = wavread('mls1023');     %read in mls signal, input signal in x

 [b,a] = cheby1(9,0.5,0.3);        %generate a LTI system (a simple filter)

 y=filter(b,a,x);

    thanks in advance

   Catarina