It's possible that the differences between time points are different for each of the acquisition protocols. In that case, by adding a different acquisition protocol, you may be increasing the variability of your effect across subjects, in which case you'd need a bigger effect size to be able to detect it. You can include the protocol as a linear regressor, but it's unlikely that this is a perfect solution. If you have a choice, it's best to stick to the same protocol.

Thank you for your reply. I see that it is not a good idea to mix within subjects DWI acquisition protocols. Regarding between subjects DWI acquisiton protocols, I only have one sample and my aim is to evaluate within subjects changes after a treatment (I'm not going to evaluate between subjects). In this case, could I use different acquisition protocols between subjects? And if I finally used different acquisition protocols should I correct for that in a second level?

Thanks,

M. Cano

De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nombre de Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu]
Enviado: lunes, 19 de marzo de 2018 12:39
Para: Freesurfer support list
Asunto: Re: [Freesurfer] Different DWI protocols

Probably not a good idea, depending on how the data are balanced across acquisition protocols. If you find differences between time points of subjects or between subjects, you want to be ensure that those differences are not because of acquisition differences. If, for example time point is always collected with one protocol and time point 2 is always collected with another, you won’t be able to tell.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Cano Catala, Marta" <MCANOCATALA@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, March 19, 2018 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Different DWI protocols

Dear TRACULA experts,

I'm running a longitudinal trac-all analysis and I'm wondering whether or not I could include different DWI acquisition protocols both between subjects and within subjects in the same analysis.

Thank you,

M. Cano