I have a data set of 20 subjects (patients) collected at location-1 with 3T Siemens scanner. Also, I have a set of age-matched 20 subjects (controls) collected at location-2 with 3T Siemens scanner.

I am interested in comparing cortical thickness between controls and patients using FreeSurfer but I am not sure if I can do that since I have both the data sets collected at two different locations.

I would really appreciate any inputs on this.

I tried to find some papers on scanner differences but all I could find was between 1.5 T vs 3T or 3T vs 7T. Is there any special covariates I need to define for this purpose (if so then at which step during analysis?) or is it not possible at all?

Thanks.