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Dear Tom,

Thanks for the prompt response. I am afraid averaging in my case is not the solution; since each of the sessions are acquired  under different experimental factors (i.e. drugs).  

So, for each session, I am interested in differences among the 7 conditions. But, i am also interested in differences between sessions. In fact the main effects are less important than contrasts. The reason for preferring ANOVA over t-test is because I want to control for (as much as possible) within-subject correlations between sessions, as well as between conditions.  

Would you still think t-test is the best way to go?

(If I may brave a "meta" GLM design; how many permutations must I do in randomise?) 

Thanks a lot,
Naj   


On Tue, Apr 14, 2009 at 9:31 PM, Thomas Nichols <[log in to unmask]> wrote:
Dear Naj,

Randomise, in as much as it implements a GLM, should be able to address most of your questions.

While you say you have a 'two-way within-subject ANOVA', if one of your factors are session, I won't actually consider that a factor... just average over it with a contrast in Feat (if using fmri) or just average the session results w/ fslmaths.  Hence you basically just have a one-way ANOVA with 7 conditions.

BUT, are you really interested in a 6- or 7-degrees-of-freedom F-test?  Testing for any differences among all those conditions (6 DF)? Or testing for any non-zero effect in any of those conditions (7DF)?

Rather, I bet you probably have some specific question to ask between those 6 conditions, and each question can be answered with a (1DF) t-test.  If this is the case you don't need anything more fancy than a 1-sample t-test on the appropriate contrast (or computed average difference).

Does this help?

-Tom



On Tue, Apr 14, 2009 at 4:48 PM, Najmeh Khalili M. <[log in to unmask]> wrote:
Hi,

I am wondering if randomise is suitable for performing a two-way within-subject ANOVA (3 sessions x 7 condition) to determine main effects, interaction and post-hoc contrasts?

I apologize if this question is already answered, but I cannot trace it back in archives or the tutorial. Any hint is appreciated.

Best
Naj



____________________________________________
Thomas Nichols, PhD
Director, Modelling & Genetics
GlaxoSmithKline Clinical Imaging Centre

Senior Research Fellow
Oxford University FMRIB Centre