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Dear Matthew,

 

thank you for this important point. I will check this. There might be just a few subjects with 8 and 32 head coil, so that it should be possible to discard them without affecting the sample size too much.

 

Do you think, you could give use some general hint to the ‘prescan normalize’ option? We cannot guess the benefit for our analysis well. Generally, if the benefit is rather low, we would tend to use the data without ‘prescan normalize’. What do you think?

 

Thank you, all best

 

Pavol

 

 

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 15:44
An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer

 

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That alone will be a huge factor in variable SNR (and receive field).  Head coils are not interchangeable like that. 


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 7:22 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

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Dear Matt,

 

unfortunately we have no highres T2w or FLAIR.

In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.

 

Thanks

 

Pavol

 

 

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 14:14
An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer

 

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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


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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:

 

  1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate
  2. 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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