Dear Alfonso and CONN community,

I'm analyzing the resting-state data from my study, in which each participant underwent 2 scans X 2 conditions.
This means that I my conditions are: Pre_Real, Pre_Sham, Post_Real, and Post_Sham.

Accordingly, I defined my repeated-measures ANOVA: AllSubjects [1], and Pre_Real, Pre_Sham, Post_Real, Post_Sham [-1 1 1 -1] (as specified in the CONN manual, p.26).

However, I have a reason to suspect that there might be a carryover effect. Therefore, I decided to perform a paired t-test, comparing only the Pre_Real and Pre_Sham, so I selected only the 2 of them and defined the contrast as [-1 1]. Here, I got some significant results (which is a cause for concern)

Additionally, I have a reason to believe that controlling for the order in which the participants received their treatments - would neutralize the order effect.
To this end, I defined the order effect using 2 second-level dichotomous covariates - Real_first and Sham_first, which are the opposite of each other. I'm not sure that this is the way to do it, though.

Given the experimental design's within-subject nature, I'd like to ask the following questions:
1. Did I define the carryover effect test correctly? or should I instead use the contrast Pre_Real, Pre_Sham, Post_Real, Post_Sham [-1 1 0 0]?
2. How should I define the order effect in order to check for its influence and possible association with the carryover effect?

Sorry for the long post and thanks in advance,

Subtly,

Yuval.