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Elena, 

There are three issues:
(1) zero should be zeros.
(2) I'd double check the column order. Subject is usually the very last set of columns.
(3) Most importantly, even though the contrast will run, it is not a valid contrast. Any paper reporting between-subject effects (e.g. group differences [group*condition effects are okay]) in a flexible factorial design with repeated measures should be sent back to the authors to be reanalyzed properly. For a full explanation of why its invalid to look at the group main effects or overall group differences, please see my other posts on the topic.


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 19, 2013 at 10:47 AM, Elena Ivleva <[log in to unmask]> wrote:

Dear Experts,

 

I am trying to run F contrast in flexible factorial design (SPM5) for my fMRI data with a task.

 

I have 3 factors: subject (n=103), group (5 groups), condition (7 conditions).

Thus, 3 main effects: group, condition, subject, plus group x condition interaction (appearing in this order in the design matrix).

 

To define main effect of group (F contrast) I tried:

1 0 0 0 -1 zero(1,7) zero(1,103) zero(1,35); 0 1 0 0 -1 zero(1,7) zero(1,103) zero(1,35); 0 0 1 0 -1 zero(1,7) zero(1,103) zero(1,35); 0 0 0 1 -1 zero(1,7) zero(1,103) zero(1,35)

 

It does not run (when I click ‘Submit’, the contrast does not go through).

I would very much appreciate any suggestions. Much thanks in advance,

Elena    

 

From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of John Ashburner
Sent: Thursday, September 19, 2013 6:04 AM
To: [log in to unmask]
Subject: Re: [SPM] coregistration

 

The initial joint intensity histogram in the pdf file seems to be empty, which would suggest that the images did not overlap at all before attempting to run the coregistration.  Prior to running it, I'd suggest using Checkreg to ensure that the images are reasonably well aligned beforehand (within about 3 cm and 15 degrees of each other).  Coregistration in SPM is a local optimisation procedure, which requires starting estimates that are not too far from the solution.

Best regards,

-John

 

On 18 September 2013 19:49, Elveda Yildirim <[log in to unmask]> wrote:


Dear SPM Users,


   I have ten subjects. I have done reorientation before doing any pre-processing steps. I chose the origin of structural image as AC and reoriented with itself and functional images. I got every steps properly for 7 subjects.However I got a problem for 3 subjects in coregistration step.I attached the coregistration figure which I got.I did these steps many times carefully, but I got the same result.

 Is anyone could help me? What's wrong with that? Any help will be much more appreciated.

Thanks,
Elveda

 



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