First of all, don't use -stim_base because that would treat the regressor you feed in as part of the baseline model, and that's why you didn't get any output. Secondly, it'd be better to directly include those motion regressors in the same model with 3dDeconvolve. In other words, a one-step approach with all possible effects incorporated in the model is more preferred than first removing some confounding effects followed by a second step. The reason is that one full model accounts more properly for the potential correlations among those effects.

P. S. For resting-state data analysis, it's recommended that you follow Examples 9/10 in the help of afni_proc.py.

Gang



Edited 1 time(s). Last edit at 09/30/2016 01:37PM by Gang.