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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
>