Philippe and Wiveka,

That seems to be a very clever way to obtain the between group comparisons at run1 and run2 with the 2nd script. Did the script work? I am very interested to know because I wonder whether the program would sputter since you have only half of all index combinations (12 out of 24) available. For example, "-dset 1 1 2" intrinsically does not exist. Both 3dANOVA2 and 3dANOVA3 assume balanced design.

Is there a way to add another factor that would examine the BOLD response for multiple contrasts, namely, Neg vs Neutral, Pos vs. Neutral, and Neg vs. Pos contrasts. Or do we have to run 3dANOVA3 three separate times – once for each contrast?

Currently you can only run up to three factors with the available ANFI ANOVA programs. If you are brave enough, you can either try 3dRegAna by converting the ANOVA analysis into a regression model, or run 3dDeconvolve by coding with complicated dummy variables, but that is just too much extra work. Until a more flexible program is born, you probably have to stick to 3dANOVA3 for each contrast.

Gang