A question: are there two subjects in each group (G1, G2, G3)? Or one subject in each group with two scans?

Demean: (http://mumford.fmripower.org/mean_centering/)

For two subjects case:

G1          G2          G3          CNI_1    CNI_2

1              0              0              -0.667    -9.333

1              0              0              0.333     12.667

0              1              0              0.333     1.667

0              1              0              -0.667    -6.337

0              0              1              0.333     10.667

0              0              1              0.333     -9.333

For one subject case:

You’d better get the average FA map from the two scans.  Then use the following design matrix:

G1          G2          G3          CNI_1    CNI_2

1              0              0              -0.167    1.5

0              1              0              -0.167    -3

0              0              1              0.333     1.5

Contrast1:  1 -1 0 0 0

Contrast2:  1 0  -1 0 0

Contrast3:  0 1 -1 0 0

Yingying

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of R Duke
Sent: Wednesday, May 16, 2012 3:13 PM
To: [log in to unmask]
Subject: [FSL] Randomise Contrast

Dear FSL Experts,

I have a question regarding my Randomise design matrix. I have three groups (G1, G2, G3) and two covariates of no interest (CNI). I am interested in between group FA differences and feel that I should control for my two covariates of no interest. Given this information I was wondering if the design matrix I have listed below is correct?

G1	G2	G3	CNI_1_G1	CNI_1_G2	CNI_1_G3	CNI_2_G1	CNI_2_G2	CNI_2_G3
1	0	0	1	0	0	22	0	0
1	0	0	2	0	0	44	0	0
0	1	0	0	2	0	0	33	0
0	1	0	0	1	0	0	25	0
0	0	1	0	0	2	0	0	42
0	0	1	0	0	2	0	0	22

Contrast1: 1 -1 0 0 0 0 0 0 (give me voxels where FA for G1 > FA for G2)

Contrast2: 1 0 -1 0 0 0 0 0 0 (give me voxels where FA for G1 > FA for G3)

Contrast3: 0 1 -1 0 0 0 0 0 0 (give me voxels where FA for G2 > FA for G3)

I was also wondering if this design controls for within or between group variance? 

In other words, what happens if I put my two covariates of no interest in only 2 columns (just listing the covariate of no interest across each group in two columns - one column for CNI_1 across all groups and one column for CNI_2 across all groups)? Would this be controlling for between group differences?    

Cheers!