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Hi Negar, It doesn’t matter whether the patients or controls are assigned as group 1 or group 2. What matters is setting up the contrasts so you know what you are testing. F tests are non-directional, that is, is testing for a difference without telling you in which direction the difference is. T tests are directional and a contract of [1 -1] is testing for voxels with evidence of being lower in group 2 compared to group 1, and visa versa for [-1 1]. Regards, Kevin London From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Negar Chabi Sent: Sunday, January 04, 2015 21:16 To: [log in to unmask] Subject: [SPM] Model Specification problem Dear SPM experts I have been working on SPM to analyze SPECT images and find abnormalities by comparing SPECT images of the patients with the normal control group images. I am completely new in SPM. For preprocessing I perform Coregistration, Normalization and Smoothing. After that for model specification I don't know which design (sample t-test, ANOVA. ) to choose? In two sample t-test, for example, there exists two mandatory selections “Group 1 scans”and“Group 2 scans”. Now my question is this: What (patient or control group) should I select for each above-mentioned group? Then for the results section I should define contrast (t contrast or f contrast). Again, I don't know how to define it? I would greatly appreciate if kindly help me in this case. Best. -- Negar Chabi Msc of medical engineering Persian Gulf Nuclear Medicine Research Center Bushehr University of Medical sciences ********************************************************************************* This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message and any attachments are those of the individual sender, and are not necessarily the views of The Sydney Children's Hospitals Network. This note also confirms that this email message has been virus scanned and although no computer viruses were detected, The Sydney Childrens Hospital's Network accepts no liability for any consequential damage resulting from email containing computer viruses. *********************************************************************************