Hi D J, 

thank you for your answer.

1. Ok, I see. But the fact is that I used an example from Beatriz and Martin in their paper in Insight Journal about shape analysis MANCOVA where they showed a similar matrix with, age, IQ and clinical score at the end of the matrix. I quote : " Hypothesis : Is there a significant clinical score influence AFTER CORRECTION for group, gender, age and IQ ? Example command :
infile --numGroupTypes 2 --numIndependent 3 --interactionTest --testColumn 2"

I assume that is something similar to my arguments. But I will try with the arguments "columnIndependent". I have another question about that, how can you know the number of the column for the covariates. In my case, I thought that my independent variables were 0,1,2 columns. 

2. Oh, I thought MANOVA permutation test were designed for group comparison.. Then do you know how to combine correlation and covariates correction ? I a little bit lost. 



Thank you.

Clément B