Hi Alfonso,

First of all, I'm sorry if the question is a duplicate. Feel free to refer me to another answer if that's the case. 

I need to run the post-hoc analysis after a 3-way (2x2x3) repeated measures ANOVA in an ROI-to-ROI analysis. I'm familiar with the procedure in CONN (second-level analysis). I'm interested in running the post-hoc analysis and the plotting with R, using the output I get from CONN. 

In CONN, in the "second-level" tab, in the field "Subject effects" I select all subjects as a covariate (all with 1 values in setup). I know how to get the subject-specific connection for a given condition (in the file ROI.mat, for example) and I can reproduce the ANOVA results in R. No problem until this point. 

However, I also have two other covariates, "age" and "hand". The analysis I'm interested uses the contrast 1 0 0, i.e., only the effect of "allSubjects", controlled by "age" and "hand". I would like to get the subject-specific connections for each condition and then run the post-hoc and plotting in R, but I can't find where they are stored (if they are stored somewhere). 

Could you please tell me if there's a way to get the corrected values for the situation I described?

Many thanks in advance!

Cheers,

Gustavo