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Adjustment means to remove the effect of all the other columns not in the contrast. In gPPI, the omnibus contrast does not include any of the covariates (e.g. movement and other noise). The adjustment then removes them from the BOLD signal. The reason for the adjustment is that you are trying to isolate the neural of the BOLD signal. In the second-level, you are wanting to extract the data to make your own plot outside of SPM. Thus, you want the data as input into SPM, you don't want the adjusted signal. Hope this helps. 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 Fri, Jan 17, 2014 at 11:32 AM, Mark <[log in to unmask]> wrote: > Hi Donald, > > Thanks for you reply. Sorry there was an error: In (3), if I did not > adjust data for the F contrast, there would still be correlation. > > I'm confused when should I adjust and when I don't have to adjust. In > PPI/gPPI, we have to adjust to account for null space. Why no adjustment > here? Also, I noticed that extracted eigenvalues with adjustment and > without adjustment are highly correlated with each other. So what's the > relationship between them? > > Thanks again > > Mark > >