Hi Donald thanks very much for your reply.Perhaps I should make my question more informative. I have 10 patients with resting state EPI scans in 2 conditions - pain free and migraine. so each patient gets 2 scans - one in painfree and one in migraine state. I want to look at areas with more BOLD signal in the migraine state vs painfree state. I was hoping to compare within subject difference between the 2 conditions and finally the average signal in the migraine state for all patients vs the average signal in the pain free state in all patients. can this be done? thanks so much for your valuable tips. farooq Date: Thu, 1 Dec 2011 14:31:27 -0500 Subject: Re: [SPM] fmri design From: [log in to unmask] To: [log in to unmask] CC: [log in to unmask] It depends on your question: (1) Are the groups different: two-sample t-test of condition1, two-sample t-test of condition2, two-sample t-test of the mean of condition1 and condition2 (2) Are the conditions different and/or is the difference between conditions different between groups: flexible factorial design with subject, group, condition factors and subject, group, condition, and group*condition effects modelled. You cannot compare the groups (between-subject effects) in this model because of the error term generated for this model, but you can compare conditions and group*condition (within-subject effects) using this model. There are a number of posts on the issues of mixed designs. 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 Thu, Dec 1, 2011 at 2:25 PM, Farooq Maniyar <[log in to unmask]> wrote: Dear SPM experts I will be very grateful for any advice on this. I am sorry this probably is a basic question. I have 2 groups of scans in same patients, one in each condition. n = 10. i would like to compare condition 2 vs condition 1. which design is best suited?... a paired t test would allow me to use only one scan for each pair (but i have 200 scans for each condition per patient). 2 sample t test will be too harsh and wrong since both conditions are in same patients. how about flexible factorial or full factorial? can somebody enlighten me on which test to use and how? thanks so much farooq Farooq Maniyar Headache Research Fellow UCSF Headache Center San Francisco CA