You need an F-test (I label this as the omnibus F-test) that has N rows, where N is the number of conditions.

In your 2 sample t-test:
[1 0; 0 1]

Then plot the F-test.

For more complicated designs, this might not always be eye(N). But you can build the contrast for each condition and put it into a single F-contrast.

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
Office: (773) 406-2464
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On Mon, Aug 29, 2011 at 1:47 PM, Claire (Jung Eun) Han <[log in to unmask]> wrote:
Dear experts,

I would like to plot the contrast estimate and 90% C.I. for the areas that activated for a contrast of interest.
For anova, our lab created and used a f-contrast to plot the contrast estimate (which shows the effect size for each condition for coordinates at activation).
I do not know which contrast that I need to create which can be used to plot the contrast estimate. In other words, what contrast should I put when the SPM interface asks me after choosing to 'plot' and then 'Contrast estimates and 90% C.I.'...My aim is to look at the effect size for each condition for each group (compared to the 'baseline').

It was a two samples t test done. I have attached the graphics that may help.
Hope my explanations are clear...

Thanks,
Claire