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The results should be identical. Did you remember to use a paired t-test when entering the 2 conditions in the second level model?

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Wed, Jul 1, 2015 at 11:10 AM, Maite Castro <[log in to unmask]> wrote:
Hi SPMers,

I created a contrast using two different analysis methods
a) getting the contrast in the 1st level and then analyze it in the 2nd level for all participants
b) creating the two conditions at the 1st level and then contrasting the two conditions at the second level [1 -1]

I found pretty different results and I’d like to understand why and what method is the best? Can anyone help me?

Thank you in advance

Best

Maite