Dear Matthieu,
your design matrix looks fine, I would just not include the last column
(constant term). For the main effect of group, you can use an
F-contrast: [1 -1 0 0 0; 0 1 -1 0 0] (i.e. diff(eye(3))).
Contrast images contain a linear combination of the parameter estimates
(betas) while the spm* images contain test statistics (t or F) assessing
the significance of such effects. See this video lecture:
http://www.fil.ion.ucl.ac.uk/spm/course/video/#Contrasts
Best regards,
Guillaume.
On 23/02/15 16:29, Matthieu Vanhoutte wrote:
> Dear SPM's experts,
>
> I am studying perfusion images on 3 groups (control, left disease, right
> disease) and 3 covariates (age, sexe, constant).
>
> My purpose is to see group effect, control > left and control > right
> contrasts. According to this aim I chose a full factorial design with
> one factor (group) that has three levels (control, left disease, right
> disease). I defined for each subject 3 covariates : sex (0 : male, 1 :
> female), age and constant (=1). You can find joined to this mail my SPM
> design matrix.
>
> All my perfusion images have been normalized onto a particular T1
> template different from the T1 SPM canonical template.
>
> I ran the script that computed automatically contrast for this full
> factorial design, but don't know which of them are the good ones.
>
> I) Firstly is my design matrix well defined ?
>
> II) Then based on this design matrix, how should I define the contrasts
> to see :
> 1) group effect : F-contrast [1 1 1 0 0 0] ?
> 2) control > left : T-contrast [1 -1 0 0 0 0] ?
> 3) control > right : T-contrast [1 0 -1 0 0 0] ?
>
> III) Finally, what is the difference between con*.nii an spmT*.nii
> output images ?
> Because I could see superimposed on my particular T1 template that the
> con*.nii image was so good looking and values well defined inside the
> mask of my T1 template on precised anatomical areas. Contrary to this
> coherent con*.nii image, the spmT*.nii image was not good looking, had
> values defined outside the T1 template mask and the values defined
> inside the mask weren't well located on anatomical areas.
>
> Many thanks in advance for helping !
>
> Best regards,
>
> -------------------------------------
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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