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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 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. 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 > > > > ------------------------------ > > UT Southwestern Medical Center > The future of medicine, today. >