Dane,

Sorry for the slow response!

To model varying durations across trials, I suggest that you use dmUBLOCK(-X) in 3dDeconvolve, where X is the duration which you want to explicitly associate the effect estimate (beta) with. Consider adopting the same X value across all subjects so that the effects are consistent, comparable and interpretable at the group level.

As far as I know, there is no ideal way to remove some effects/conditions of no interest from the original signal. The reason is that the estimated/modeled effects are very crude, and there is a huge amount of variation across trials. In addition, the assumed regressors are just a poor man's best approximation at the moment. Thus, you can only remove the major components of an effect. If you're determined to try, 3dSynthesize combined with 3dcalc is probably the way to go.

Gang