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Dear Sarah, > 1) The creation of the templates. The templates are an average of the > structural scans I input, correct? For example: When looking for template 6 > to run normlisation, there is only one template 6, in the folder of the > first of the 21 subjects I entered in the new segment volumes. It looks to > be an average of the scans. Yes, that's right. > 2) If the templates created are an average, should I preprocess ALL of my > data in one batch? I have one group of healthy adults, and another > clinical/patient group. I will be looking at group differences. I'm not > 100% clear on what the template does, so I'm not clear on whether I need to > process everyone together, or if I need to process each group separately? The segmentation is independent for each subject, but you're right that the template creation should be done with all of your data so that everyone contributes to the template (with one small caveat, see below). The idea is that DARTEL creates an average brain from all of your subjects. The warp from each subject's native space to this template space is computed as the template is created; at the end of template creation, then, you have the template itself, but perhaps more importantly you have the warps that take each subject into this common space. (These warps can be used to help bring subjects into MNI space as well - which is just a different common space.) In general, you want all of your subjects in your template. The exception might be if you have more than 1 group of subjects, as in your case, and the groups are not equal in size. In this case I would randomly select equal numbers from each group to create a template, and then normalize everyone to this template. The reason for doing this is that you don't want your template to be biased towards one group more than the other (which may in turn exert some bias on the normalization). Hope this helps! Best regards, Jonathan -- Dr. Jonathan Peelle Center for Cognitive Neuroscience and Department of Neurology University of Pennsylvania 3 West Gates 3400 Spruce Street Philadelphia, PA 19104 USA http://jonathanpeelle.net/