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Right I would recommend pre-scan normalize on for all images being acquired in
a study. There are important considerations for fMRI, diffusion, and ASL (and
even auxiliary scans like SE fieldmaps) not just T1w/T2w/FLAIR. That said, I
was guessing that the FreeSurfer’s built in normalization could handle a 12CH
receive field (based on my distant recollection of them) better than a 32CH
receive field.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce"
<bfis...@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 17, 2020 at 9:39 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer
I would guess it is pretty important for a 12 channel also, although it depends
on field strength and also needs a body coil transmit to be maximally
effective. In general we use it whenever we can
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Glasser, Matthew
Sent: Thursday, September 17, 2020 10:15 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution
Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil
it isn’t so important to have on. It’s pretty much required for a 32CH coil,
as the bias field is quite fast.
Matt.
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Mikolas, Pavol"
<pavol.miko...@uniklinikum-dresden.de<mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 9:02 AM
To: 'Freesurfer support list'
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution
That alone will be a huge factor in variable SNR (and receive field). Head
coils are not interchangeable like that.
Matt.
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Mikolas, Pavol"
<pavol.miko...@uniklinikum-dresden.de<mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Freesurfer support list'
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Mikolas, Pavol"
<pavol.miko...@uniklinikum-dresden.de<mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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:
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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