Dear Alfonso and CONN users,

I have a question concerning how the ANOVA is computed in CONN. To give a bit of context:

In a PPI analysis in which I have one group (15 subjects) and 3 conditions, I selected the "between-conditions contrast" as "any differences (F-test)" (or [-1 1 0;0 -1 1]). The connectivity between two given regions was described by the following statistics, according to CONN:

F(2,13) = 4.50, p = .03

Then, in order to double-check, I extracted each one of the 3 effects (one per condition, by selecting "any effects (F-test)" in "between-conditions contrast", then clicking on plot effects, then getting the effect values in MATLAB's command window) for the 15 subjects and wrote a model in R (aov(Contrast~Session+Error(Subj/Session),data=data)). It provided me the following statistics:

F(2,28) = 4.31, p = .02

The statistics are the similar but not the same. I see that there is a difference between the two methods in the second number of degrees of freedom (df2). The way I understand it, for within-subjects measures, it should be computed by:

df2 - df total - df subjects - df factor, in which
- df total = number of observations (across all levels of the within-subjects factor, n) – 1
- df_subjects = number of participants (N) – 1
- df_factor = number of levels (k) – 1

So, in my example: df2 = 45-1 - 15-1 - 3-1 = 44 - 14 - 2 = 28, as R indicates.

Could you please help me understand where this discrepancy comes from? Maybe from the way I'm defining the "between-conditions contrast"?

Many thanks!
Gustavo