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The other thing to consider it to weight the contrast by the number of trials in each run:

A1 - 20 trials
B1 - 15 trials
A2 - 30 trials
B2 - 5 trials

[.4 -.75 0 .6 -.25 0]

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
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Fri, May 4, 2012 at 9:33 AM, Jonathan Peelle <[log in to unmask]> wrote:
Dear Julie,

> I am currently processing fMRI data that includes 2 sessions.
>
> Can anyone provide more info or a reference regarding Martin's statement to
> "Be aware when choosing the constrast because youŽll have both sessions in
> your design matrix."?
>
> For example, if I have 2 sessions and 3 conditions per session:
> 1: A B C
> 2: A B C
>
> If I wanted to define the contrast A -B, would the contrast weights be:
>
> 1 -1 0 1 -1 0
>
> or
>
> 0.5 -0.5 0 0.5 -0.5 0

These two contrasts will give you equivalent t statistics, but the
contrast estimates will be different (though the relative size is the
same), because the error scales with the contrast weights. The second
one - where the positive and negative contrast weights sum to 1 - is
technically the average of the conditions. But because the statistics
come out the same, I don't think people usually get too bothered about
it.

Hope this helps!

Best regards,

Jonathan

--
Dr. Jonathan Peelle
Center for Cognitive Neuroscience and
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104
USA
http://jonathanpeelle.net/