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
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

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...