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You need 3 factors:
(1) subject -- independent, equal variance
(2) group -- independent, unequal variance
(3) condition -- dependent, equal variance

Factors to include in the model
Main effect --> 1
Main effect --> 2
Main effect --> 3
Interaction --> [2 3]

Use the flexible factorial or GLM Flex (google GLM Flex and schultz)

Do not interpret the group effects as they are invalid unless you use GLM Flex. The condition and group*condition effects are valid.


Best Regards, Donald McLaren
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Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
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On Sat, Feb 4, 2012 at 10:56 AM, Jose Soares <[log in to unmask]> wrote:
Dear SPMrs,

I am trying to perform a 2nd level analysis to compare 2 different groups in 2 different conditions. The main idea is to compare (A and B groups, 1 and 2 conditions) A (1-2) versus B (1-2). I have the *.cons files for A1,A2,B1 and B2.

How can I specify my 2nd level? How many factors and levels do I need?

Thanks for all the help,

Miguel.