Hi Alfonso,

I have a question about this issue of study sites as covariates in CONN (see your comment below). What you described sounds to me like a full dummy coding with n-covariates for n-scanning sites and each participant scanned at these sites is coded with 1 and the others with 0. Is it possible in CONN to dummy code the scanning sites with a reference group (see figure below) with n-1 covariates?

source: https://de.mathworks.com/help/stats/dumm...

Or is it more common to code the scanning sites as full dummy variables rather than dummy variables with a reference group?

Thank you so much for your help!

Best,

Max

Originally posted by Alfonso Nieto-Castanon:

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:

Originally posted by Zahra Mor:

Dear Ali, conn users and experts, I wonder if you have found an answer to your question regarding how to correct the multi site (scanner) effect, probably through defining a categorical second level covariate? Thanks in advance!

Hey People! I have the same problem!!!! Anybody found a solution? best wishes Till