And more details about the study would also help. What field strength? Was the transmit coil a body coil? In the end though I’m not sure we are going to be able to give you an answer as it is an empirical question as to whether including them increases your variance more than it increases your power

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Glasser, Matthew
Sent: Thursday, September 17, 2020 8:14 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution

What head coil did you use? Do you have a highres T2w or FLAIR?

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.de>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution

Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:

Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate
Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.

Thank you, best regards

Pavol

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