Radek

If you want to do a repeated measures mixed effects design you should
enter the subject effects. Since you didn't specify the contrasts you
used I wonder if you may have setup an average effect of group rather
than the main effect of group. Assuming you have two groups, for
example, the main effect should be a difference, which should also
model differences at the subject level between groups and with respect
to any interactions.

-----
Darren Gitelman



2009/4/1 Radek Mareček <[log in to unmask]>:
> Dear SPMers,
>
> we have an experiment with 2 groups of subjects (controls/patients) and
> 3 conditions for each subject. We set the 2nd level analysis using
> flexible factorial design option in SPM5.
>
> The main effect of subject, group and condition and interaction of
> group/condition were included in design matrix.
>
> The contrast weights for main effect of group was set according to
> technical note of Jan Glascher and Darren Gitelman.
>
> The problem is when the main effect of subject is included in design
> matrix. This results in widespread activation on 0.05 FWE level with
> very high t-values. When the main effect of subject factor is not
> included in the design matrix the activation is less extensive (and
> probably more credible).
> This is in accord with the Darren Gitelman's note of improved
> sensitivity of a model where the main effect of subject is included in
> the design matrix.
>
> The question:
> When the subject effect is included the inter-subject variability
> doesn't end up in residuals (or at least not all) which induce higher
> t-values. But isn't the inter-subject variability crucial for assesing
> of significance of tested effect?
> Am I completely wrong? Which design is more resonable then?
>
> Thank you for any comments or notes on this issue.
>
>
> Radek Marecek
> Dep. of Neurology
> St. Anne's University Hospital
> Masaryk University
> Brno, Czech Republic
>