Hannah,
There are several issues with your design and analysis:
(1) This is a repeated measures and as such you need to have an extra
EV for each subject (see
http://fsl.fmrib.ox.ac.uk/fsl/feat5/detail.html#ANOVA1factor4levelsRepeatedMeasures)
(2) If you treat this a one-way ANOVA - which you need to do in FSL --
you can keep the design matrix as is with modeling all conditions (or
you can follow the tutorial and leave one input out). I think for what
you are trying to do, you want model everything.
(3) Your contrasts will need to be:
1 -1 0 0 0 0 0 ....
0 1 -1 0 0 0 0 ....
0 0 0 1 -1 0 0 ....
0 0 0 0 1 -1 0 ...
1/2 -1/2 0 1/2 -1/2 0 0 ...
0 1/2 -1/2 0 1/2 -1/2 0 ...
For the main effect of emotion during period 1, use the the first two contrasts.
For the main effect of emotion during period 2, use the second two contrasts.
For the main effect of emotion, use the last two contrasts.
The better solution, would be to run two models --> one for period 1
and one for period 2.
Alternatively, you can build a 2x3 repeated measures ANOVA in SPM or
using GLM Flex (http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/GLM_Flex.html)
in MATLAB. GLM Flex uses partitioned variance to properly look at each
factor in you model (time and emotion).
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 Thu, Sep 13, 2012 at 7:00 PM, Shan(Hannah) Luo <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I have a within-subject design,with three conditions, happy, fear and
> neutral emotional state. I want to do a F-test looking at the main effect of
> emotional state on BOLD data. For my GLM, I have 7 EVs, EV1 ( Happy state
> during period 1), EV2 ( Fear state during period 1), EV3 ( Neutral state
> during period 1), EV4 ( Happy state during period 2), EV5 (Fear during
> period 2), and EV 6 ( Neutral during period 2), and EV7 ( taking into
> account a secondary task performance). Period 1 and Period 2 were two
> different time periods I was interested in.
>
> I was planning to do two F-tests(main effect of state during period 1 and 2
> separately), as below,
>
> Ev1 Ev2 Ev3 Ev4 Ev5 Ev6 Ev7 F1 F2
> 1 0 0 0 0 0 0 1
> 0 1 0 0 0 0 0 1
> 0 0 1 0 0 0 0 1
> 0 0 0 1 0 0 0 1
> 0 0 0 0 1 0 0 1
> 0 0 0 0 0 1 0 1
>
> For F1, Ev4~Ev7 are irrelevant. What should I do with them? And the same for
> F2 ( Ev1~Ev3 and Ev7 are irrelevant). Any thoughts would be greatly
> appreciated. Thanks ahead of time.
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