Hi Isabelle,

The run order for afni_proc.py is exactly as you give it
to the program. So it is up to you to provide the EPI
datasets in the order that they should be applied.

If you use separate 3dDeconvolve commands, then the
timing files would each have only the 2 rows (for 2 runs).
But if you give it all to afni_proc.py, then the files should
have lines for all 4 runs (since they would be processed
together).

I think you are okay as you are, just present the files to
afni_proc.py in the order that you would like them used.
Runs 1 and 2 would be the first two EPI time series, and
3 and 4 would be the next.

Of course, processing this all at once seems to make
sense here, using a single afni_proc.py command and
timing files that include all 4 (?) runs.

- rick