Hi Till,

Exactly, simply define a set of site-specific covariates (e.g. SITE_1, SITE_2, etc.) and include these as covariates-of-no-interest in your second-level analysis (e.g. image attached). 

For example, if you have three sites and have already imported a 2nd-level SITE covariate with values 1 to 3 indicating the site of each subject, you could: 

1) discretize that variable: in the Setup.Covariates.2nd-level tab select your covariate SITE, and then click on 'Covariate tools. Discretize selected covariate'. That will create three new covariates named SITE_1, SITE_2 and SITE_3

2) (optionally / rarely-necessary) center those new site-specific covariates to your desired control-level (e.g. average across all subjects):  in the same tab select jointly SITE_1, SITE_2 and SITE_3, then click on 'Covariate tools. Orthogonalize selected covariates', and select the variable 'AllSubjects' as your only orthogonal factor

3) add those site-covariates as controls in your second-level analysis. For example, in the Results (2nd-level) tab, after defining your desired analysis (e.g. a two-sample t-test comparing PLACEBO and TREATMENT subjects), simply select the option that reads 'add/remove SITE_1 as control covariate' (and repeat for SITE_2 and SITE_3). You should be seeing something like in the example attached, which will estimate the differences between groups while controlling for site effects. 

Hope this helps
Alfonso
 
Originally posted by Till Langhammer: