Hi Dr. Chen,
We spoke about the experimental design and 3dSynthesize a bit in a previous posting:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,162913,163126#msg-163126 Let me know if you have questions after reviewing.
You did raise the option of beta series to measure trial by trial correlations there. Definitely see the advantage however the end goal is to do some effective connectivity analyses using GIMME (
https://www.sciencedirect.com/science/article/abs/pii/S1053811912006404) which requires extracting time series for different conditions as well. Therefore while not ideal we thought we'd see how effective the deconvolution was for unwinding the task conditions and it seemed 3dsynthesize was our best hope of that.
~Dane