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Use the first one. It removes the noise from each session.

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 Fri, Jul 24, 2015 at 11:49 AM, Antonio Díaz Parra <[log in to unmask]> wrote:
Dear all,

I am using the VOI toolbox to extract time series over subjects with three sessions. Each session is composed of one regressor of interest plus motion parameters plus the constant term. Due to I am modelling the three sessions in the same design matrix, I am not sure as to the F contrast I have to use to retain the "Effects of interest":

1. Should I use a F-contrast matrix as [1,zeros(1,23);...
                                                              zeros(1,7),1,zeros(1,16);...
                                                              zeros(1,14),1,zeros(1,9)]?

or

2. Should I use a F-contrast vector as [1, zeros(1,6), 1, zeros(1,6), 1, zeros(1,9)] ?

I have tested both of them and the first eigenvariate changes slightly.

Many thanks in advance.

Antonio