> I computed independentlly a t-statistic for BOLD signal between Baseline line condition and condition A
> across all voxels. majority of the tvalues are positive and STS voxels show postive t scores.
...
> one thing not clear to me is when I just compute a t-score between baseline condition and motion present
> condition i get alot of voxels with positive t-scores especially in areas expected to respond to stimulus.

Specifically how did you independently obtain the t-statistic for the difference between condition A and the baseline?

How did you set up the 3dDeconvolve command? Did you write the script yourself or did you use afni_proce.py? Was the baseline estimated separately for each run? It may be more helpful if you paste your 3dDeconvolve script here.

Gang