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Dear SPM list, I am trying to enter contrasts for my paired t analysis but cannot seem to enter the correct contrasts. For my experiment, I have 9 subjects who were scanned on both a GE and Siemens scanner. So, the conditions are GE (1) and Siemens (2). We are also trying to determine if using scanner as a covariate will properly alleviate any differences we may see. I entered my paired scans as Pair 1: 1-GE,2- Siemens; Pair 2: 1-GE, 2-Siemens, etc. The contrast I want to run is condition 1 - condition 2 (GE-SN). So far I have tried the following without success: t-test repmat(0,1,9) 0 1 -1 repmat (0,1,10) 1 -1 0 0 0 0 0 0 0 0 0 1 -1 F test reduce columns 1:10 Please advise me on how to enter the contrast for an analysis of GE scans - Siemens scans (Condition 1 - Condition 2). I have a attached a jpeg of the design matrix for clarification. Thank you very much, in advance, for your help, Christa