If you just want to normalize the flair, you can run samseg on it, ie,
samseg --i flair.mgz --o samseg.flair
in the output folder you will find a bias corrected volume
On 9/28/2022 7:42 AM, James Brown wrote:
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Dear Dr Bruce,
Thank you very much for answerin
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Dear Dr Bruce,
Thank you very much for answering my questions and for help. We highly
appreciate you.
All the best
James
1. Sigma is the smoothing kernel applied to the bias field so you can
make it pretty large depending on how high frequency y
anything without surfaces though
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of James Brown
Sent: Tuesday, September 27, 2022 7:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter normalization of FLAIR images
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Dear Dr Greeve and Dr Fiscle,
I am grateful to you guiding me through this. Indeed, I can see in
recon-all.log how Freesurfer 7.3.2 is normalizing the Flair images. *it
uses the command below:*
I tried to run the previous command without the flag -su
cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of James Brown
*Sent:* Friday, September 23, 2022 2:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] White matter normalization of
, September 23, 2022 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter normalization of FLAIR images
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Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the
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Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the following
command line is reported in the "recon-all.log":
/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
nt: Friday, September 23, 2022 2:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter normalization of FLAIR images
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Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals and
experts in
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Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals
and experts in the field about the issue below.
Thank you for your kindness.
Dear Freesurfer experts,
In order to normalize white matter intensity of T1
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Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.
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