The input to all the time series analysis programs is a model of what to look for. In most cases, the model is specified by a file (or files) of numbers, 1 value per line -- each line represents a time point. In your case, you would want a file that was like so:
0
0
... 8 0's in a row
0
1
1
... 16 1's in a row
1
repeat
As Ziad mentioned, the sqwave program can generate such a file for you, which you can then use as input to 3dfim, 3dfim+, 3dDeconvolve, waver, or the AFNI GUI FIM.
However, it seems to me that you are trying to start analyzing without reading the manuals or the online educational material. That will only lead to frustration.
Finally, 48 time points is about the smallest you could have to get any worthwhile results in FMRI.
bob cox
