Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness).
1) How should the contrast vector for a group comparison while factoring out age and gender be built? I didn't quite understand the example in the tutorial <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Contrasts>based on intercept/offset. In my case, shouldn't I have 4 elements in the vector (group1, group2, age, gender), with the first two elements receiving perhaps 1 and -1, since they are directly compared, and the last two elements 0 and 0 since I am not directly interested in their effect on the dependent variable? 2) Are the structures described in the .label files produced by mri_annotation2label in common (MNI) or in that subject's individual space? 3) For my thickness analysis, I have in mind an ROI for which I have a set of centre coordinates from a meta-analysis of relevant functional studies. What is the best way of defining the mask for this ROI as a function of those coordinates, rather than taking the eponymous region from the Destrieux or the Desikan atlas? 4) Exactly which of recon-all's outputs has to be inspected, for each subject, in order to tell whether the surface reconstruction has gone well? 5) Is it statistically correct to run the same design both with a DODS FSGD and with a DOSS FSGD? It's not entirely clear to me what assumptions each one (DODS, DOSS) makes of the data, and which one I should select in my case. Thank you very much indeed. Tudor
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