Hi Hong,

Yes, the CON_Subject* files in a second-level results folder contain contrast files for each subject (these are created whenever you specify a within-subjects contrast that includes more than one element). For example, if you are comparing two conditions A and B with a between-conditions contrast [1 -1], the CON_Subject* files will contain the difference in Fisher-transformed correlation values between the two conditions for each subject. These are equivalent to the con_*.img files generated by the SPM first-level analyses. You may take these files and enter them into SPM for additional repeated-measure second-level analyses (or if you prefer you may enter the original Fisher-transformed correlation values for each condition and for each source ROI, which are stored in conn_*/results/firstlevel/ANALYSIS##/BETA_Subject*)

The contrast files named CON_Subject* files are generated when you click on 'compute results for all sources' (seed-to-voxel analyses separately for each seed ROI; these analyses require the generation of, at most, one within-subject contrast file per subject), while the contrast files named CON_Subject*_compA### are generated when you click on 'seed-to-voxel results explorer' (since these analyses may require the computation of multiple within-subject contrast for each file, indicated by the additional numbers in ###; for example if you are performing a multivariate test across multiple seed ROIs or across multiple components in a MVPA analysis you will see several CON_Subject*_compA### files for each subject)

Let me know if this clarifies.

Best
Alfonso





Originally posted by Hong Yin: