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I am a relatively new to SPM myself, but I hope I can give you some relevant advice on the topic. Briefly: 1) yes, you input pairs of 1st level con images 2) not sure about the factorial part of your question, but in terms of the 2nd level weights, in contrast manager you input as many zeros as the number of subjects and then specify how you want to compare your images, so you need to enter something like this: con1 > con2 (if your enter con1 as first while specifying your 2nd level model) [zeros(1, x) 1 -1] or con1<con2 [zeros(1, x) -1 1] x: number of subjects (or 1st level pairs) Any more advanced comments from SPM experts (or corrections of the above) are welcome. I have actually one question regarding the actual details of this analysis. Can I say that at the first level: images are created representing t-maps of con1 vs con2 images (if there are any I don't know where to find them) and THEN subsequently these images enter a random effects analysis? Iwo -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Kim, Jeongsik Sent: 15 June 2011 05:20 To: [log in to unmask] Subject: [SPM] Can anybody provide with explanation for paired t-test method Dear SPM users, Regarding the paired-t test using SPM8, I would like to ask overall explanation since I couldn't find any documents for reference. First of all, in order to analyze the gray matter volume difference within a group (20 subjects) before treatment and after. I did three batch processes, 1) new segmentation, 2) create templates (DARTEL), 3) normalization to MNI. After this, I couldn't proceed it anymore. What I want to know is as the followings... 1) Pairs: Should I set 20 pairs for 20 subjects? If so, for each pair(Scans[1,2]), what kind of data should I input? In some blogs, I should consider con*.img as the input. Is it right? If so, How can I generate that kind of data. 2) After the factorial design, how to define the contrast? In detail, how to composite contrast weights vector? Please let me know any information for the above... Thanks