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SPM  November 2009

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Subject:

Re: F-contrasts

From:

Rik Henson <[log in to unmask]>

Reply-To:

Rik Henson <[log in to unmask]>

Date:

Thu, 12 Nov 2009 11:41:57 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (106 lines)

Bram -
> Dear Dr. Henson,
>
> I would like to use your Matlab function for mixed design ANOVAs 
> (batch_spm_anova.m). I was wondering whether the F contrasts for main 
> effects and interaction effects outlined in the section 
> "Generalization to M-way ANOVAs"  of your chapter "Analysis of 
> Variance" in the SPM book are valid for mixed-designs or whether they 
> only hold for within-subject designs? If they are not valid, could you 
> point me to a reference were I can find how to construct the right 
> F-contrasts for mixed-design ANOVAs?
Yes, the contrast weights are equally valid for within vs 
between-subject factors.

> I already tried the SPM full factorial design, which generates F 
> contrasts automatically. Unfortunately, the results (ie. F-scores of 
> main effects and interaction effects for a single voxel) I obtained do 
> not agree with the results I obtained from a repeated measures GLM 
> with a between-subject factor (fed with the same data) in SPSS. In 
> contrast, when I average my contrast images accross conditions 
> within-subjects (so that I have only image per subject) and then run a 
> one-way between-subject ANOVA, the results from SPM and SPSS 
> (univariate GLM with between-subject factor) do agree.
Yes, that is because SPSS (by default) partitions the error for each 
within-subject ANOVA effect. You can emulate this in SPM by the 
averaging process for each contrast that you describe (and that is the 
point of the "Analysis of Variance" chapter you cite). The alternative 
is to include all conditions in the same GLM and use a pooled error. 
This will give different answers to partitioning the error (eg as in 
SPSS), as you found. I am not sure that either approach is right or 
wrong (they just make different assumptions), but there has been some 
debate about this on the SPM helpline recently (cc'ed here). But 
basically you can do either in SPM, so it's up to you and reviewers to 
decide (as long as you explain clearly in any report which you did).

Rik

>
> Yours sincerely,
>
> Bram Zandbelt
> PhD-student
> -------------------------------------------------------
> Bram Zandbelt
> Rudolf Magnus Institute of Neuroscience
> University Medical Center Utrecht
> Room A.01.126
> P.O. Box 85500
> 3508 GA Utrecht
> The Netherlands
>
> E: [log in to unmask]
> T: +31-88-7557121
> F: +31-88-7555443
>
>
>
>
>
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-- 

-------------------------------------------------------
                 Dr Richard Henson
         MRC Cognition & Brain Sciences Unit
                 15 Chaucer Road
                   Cambridge
                  CB2 7EF, UK

           Office: +44 (0)1223 355 294 x522
              Mob: +44 (0)794 1377 345
              Fax: +44 (0)1223 359 062

http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal
-------------------------------------------------------

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