I am trying to examine group differences using PALM.  I have in total 15 subjects and 3 groups, with 5 subjects per group. Each subject has 2 different seed connectivity maps. I set a design.mat map and design.con to examine group differences for the difference between the 2 seed maps as such:

EV1: set to 1 for G1 seed 1 and -1 for G1 seed 2

EV2: set to 1 for G2 seed 1 and -1 for G2 seed 2

EV3: set to 1 for G3 seed 1 and -1 for G3 seed 2

EV(4-19) to model each subject's mean.

I set the contrasts C1: 1 -1 0 and  C2: 1 0 -1 and  C3:  0  1 -1 and use an F-test 1 1 0 (1 for C1 and  1 for C2 and 0 for C3)

This design works well and gives me results.

However, I want to add 3 nuisance variables to the design. If I just add  3 more EVs with the demeaned nuisance variables for all 15 subjects I get a Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND…and  "rank deficient design ...." .

I also get a similar error message if separate the nuisance variables by group (so use 9 EVs instead of 3 only). 

Please let me know how I can fix this design.

thanks!

Paul