Hi Elsa,
3dDeconvolve should know about the 4 runs in order to model the
baseline _separately_ per run (i.e. you should not see those
bad residuals).
Either input 4 datasets to 3dDeconvolve:
-input run1+orig run2+orig run3+orig run4+orig ...
or use the -concat option to tell 3dDeconvolve where the run
breaks occur in your all_runs dataset.
- rick