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I'm assuming you mean a two-sample t-test where you say Independence is NO (e.g. measurements are dependent). They are fundamentally different. The Paired T-test is equivalent to the one-sample T-test of the difference images. This is the relationship defined in all statistical texts for paired comparisons. Setting Independence to NO tries to estimate the dependence, but has a different error term and different degrees of freedom. As such, this approach is not statistically valid. Use the paired t--test. If you are looking for an easier way to input the data, look at the flexible factorial designs. I'll also point out the following issues that we are working on resolving: Group effects (even if its one group*) in repeated measures designs and N-way within-subject ANOVAs. If you want either of these cases, then SPM won't produce the correct statistics in the flexible factorial model. * This would be if you have pre and post scans and ask where the average is different than 0. SPM will produce an inflated statistic from the flex. factorial model. The only way to currently do this is to average the pre- and post and then do a one-sample t-test. Hope this helps. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School 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 Tue, Aug 9, 2011 at 4:37 PM, Sweegers, Carly <[log in to unmask]>wrote: > Hello, I was wondering if there are any statistical differences between > the 2nd level paired t-test and the dependent version of the two sample > t-test? For my design everything is repeated measures so I wonder if a > dependent two sample is acceptable instead of the paired t-test. > > > > thanks in advance, > > > > Carly >