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But I want to see how BDI scores across subjects will affect their reaction to the drug, so that's actually looking for a between subject effect of the covariate. Is that possible to do in paired t test? Ting Sent from my iPhone On Jun 11, 2016, at 3:07 AM, Anderson M. Winkler <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Tin Li, In this case, with the same value for both visits, and considering that the paired t-test is to test within-subject effects, there is no need to include that covariate, as it's already taken care of by the subject-specific EVs. So, just drop this variable, say, BDI, and yet BDI (and all other things that didn't change between visits) will be taken into account regardless. All the best, Anderson On 10 June 2016 at 21:41, Ting Li <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi All, In my study, subjects come twice, one time they receive drug and another they receive placebo. We are interested in the difference between drug and placebo, so we did a paired t test. Now, we have some behavioral measures we want to put in the model to see how they modulate the brain reaction. If, for example, someone with higher BDI will have stronger reaction in some parts of the brain for drug-placebo contrast. I have set up the model as shown in the attachment, with paired t test + one more EV. Because the same subject comes twice but each person only has one behavioral result, so the second half of the covariate is just the original covariate number * -1. (Is this done correctly? or should I put zeros?) Now, what should I do for the contrast to see the covariates' effect? Is c[100001] correct? 1 1 0 0 0 2 1 0 1 0 0 4 1 0 0 1 0 -5 1 0 0 0 1 -1 -1 1 0 0 0 -2 -1 0 1 0 0 -4 -1 0 0 1 0 5 -1 0 0 0 1 1 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).