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The contrasts are correct; however, I would make the following points: (1) I'd describe contrast 3 as (BS1-BS2)-(PS1-PS2) as that makes it clear that its an interaction. (2) There is some debate whether using the error term, which is the interaction error term is valid for the within-subject factors that have their own error. For a 2x2 design, I haven't seen any strong evidence that the interaction error term can't be applied for the within-subject comparisons. However, this only holds for 2x2 designs. Simulations for more complex designs (e.g. 3x2) have not been done. Thus, researchers should use caution about using the interaction error term for the within-subject factors of larger models. 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 Wed, Jan 15, 2014 at 7:47 AM, Yolanda Vives <[log in to unmask]> wrote: > Dear SPM users, > > Sorry if my questions are obvious, but I would like to be sure that my > analysis is correct and after looking at the different posts I am a little > bit confused. > > I have 14 subjects with two sessions each one (Factor Time: basal (B) and > post (P)), each with 2 experimental conditions (Factor Condition: S1 and > S2). I am interested in the following analysis: > > 1.- BS1 - BS2 > 2.- PS1 - PS2 > 3.- BS1 - BS2 - PS1 + PS2 > > I have used a flexible factorial design (I attach the design matrix) and I > would like to ask if the contrasts for these three tests would be the > following: > > 1.- [0 0 1 -1 1 -1 zeros(1, 16)] > 2.- [0 0 1 -1 0 0 1 -1 zeros(1,14)] > 3.- [0 0 0 0 1 -1 -1 1 zeros(1,14)] > > I would really appreciate your help. > > Thank you in advance, > Yolanda > >