You could try 3dDespike. The purpose of 3dToutcount is really just to alert you to potential problems, so that you can visually inspect the data and decide what the cause of the anomalies might be (head movement, scanner glitches, etc.). For example, in the case of head movement, you should try 3dvolreg before trying to repair the data in any other way. But in the case of intermittent scanner hiccups, 3dDespike is a way to go. There is no "best" or "optimal" thing to do. Judgment is necessary.