Hi,

Even if the two sites are the same Siemens model, you are going to have difficultly convincing people that any differences you find might not just be a site effect. In my opinion, this falls into the “not possible at all” category.

cheers,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mharms@wustl.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Martin Juneja <mj70481@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 29, 2016 at 1:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Cortical thickness using qdec (between scanners)

Hello FS experts,

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.