Hi Kody,

scanner effects across vendor could be larger than disease effects. You can attempt an analysis but you will have a tough time to publish it given these differences and no real way to control for scanner effects. Maybe scan 5-10 people on all these scanners and show that scanner effects remain small for the regions of interest (of course this would not help i there is an interaction, e.g. with diesease or age) but at least it could help convince reviewers. Also if you only analyse the first 2 time points and find large differences, you could argue that they are real, because the same scanner should not course large effects. But who knows (different head coils? Different callibrations, software versions?…). Better to test with a few subjects.

Best, Martin

On 7. Jun 2018, at 20:15, zalewk zalewk@uw.edu wrote:

Good afternoon Freesurfer team,

I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same type of scanner, there was an effort made to match them) at time point 1 and 2 with a Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal analysis on this cohort?

Best, Kody Zalewski

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