Given your two questions; I'd recommend using 2 models:
Model 1: subject, group, C1
Model 2: subject, group, C2

I am a big advocate of using smaller models that require fewer assumptions. The main assumption that has the potential to be violated is the sphericity assumption. With the smaller models here, sphericity cannot be violated because you only have 2 measures per subject. Using two models is the same as using partitioned variance in GLM_Flex.

With a 2x2 (repeated-measures ANOVA), it it likely that sphericity won't be violated if the variance and independence are set correctly, but there is still a risk - especially with effects in a small number of voxels.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Mon, Mar 5, 2012 at 4:30 AM, sarika cherodath <[log in to unmask]> wrote:

Hello,

       This is regarding my previous question.I have now modeled the design matrix using flexible factorial, with four factors - subject, group, C1 and C2.Since I have two groups G1 (n=18)and G2(n=15) (33 subjects in total), and two conditions C1 and C2 (with two levels a and b), I modeled the interactions as

Interaction 1 - Group x C1 = (G1C1a-G1C1b)- (G2C1a-G2C1b)

Interaction 2 - Group x C2 = (G1C2a-G1C2b)- (G2C2a-G2C2b)

The contrasts entered were 

zeros(1,33 ) 0 0 0 0 0 0 1 -1 -1 1 0 0 0 0  for interaction1

zeros(1,33 ) 0 0 0 0 0 0  0  0  0  0 1 -1 -1 1  for interaction 2

What will be the correct contrasts for main effects of C1 and C2? 

Thanks in advance,

Sarika.

On Mon, Mar 5, 2012 at 11:18 AM, sarika cherodath <[log in to unmask]> wrote:

Hello again,

         I just would like to mention that i have two levels for each condition as well.So C1 has two levels (C1a,C1b), and C2 (C2a,C2b) has two levels, in addition to the two groups.

thanks.

On Mon, Mar 5, 2012 at 10:57 AM, sarika cherodath <[log in to unmask]> wrote:

Hello SPMers,

             I have two groups of subjects (G1, G2) and want to look at the effect of two conditions(C1,C2) and respective group x condition (G1C1,G1C2,G2C1,G2C2) interactions.What is the best method to model this? Will it be valid if I model both groups together using flexible factorial? Any help would be appreciated.

Thanks in advance!

--

Sarika Cherodath
Junior Research Fellow
National Brain Research Centre
Manesar, Gurgaon -122050
India

--

Sarika Cherodath
Junior Research Fellow
National Brain Research Centre
Manesar, Gurgaon -122050
India

--

Sarika Cherodath
Junior Research Fellow
National Brain Research Centre
Manesar, Gurgaon -122050
India