Hi Jodi,
The result of the catenation is one dataset that contains
2 12-min runs, not one run of ~1435 seconds. You simply
need to communicate this to 3dDeconvolve, so it processes
the data correctly.
Apply an option like '-concat my_runs.1D', where my_runs.1D
might look like this (assuming each 12-min run is 240 TRs
of duration 3 seconds):
0
240
While the polort is important, it is also important for
3dDeconvolve to know how many runs to model, since the
baseline model is constructed per run (i.e. if it uses
polort 5 for these 2 runs, that will be 6*2=12 baseline
regressors).
- rick