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
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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
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
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
, September 23, 2022 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter normalization of FLAIR images
External Email - Use Caution
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
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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
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Thank you very much for the follow up. I have attached the recon-all.log
once again for your kind review
Hello James,
I apologize that your message containing the log file got rejected. Can you
please re-send it? I will manually approve it so
, 2022 at 12:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter normalization
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I received the email below. any idea how I can send the recon-all log file to
Dr Greeve? Thank you
our mail to 'Freesurfer' with the subject
Re
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I received the email below. any idea how I can send the recon-all log file
to Dr Greeve? Thank you
our mail to 'Freesurfer' with the subject
Re: White matter normalization
Is being held until the list moderator can review it for approval.
The
can you send your recon-all.log file?
On 9/15/2022 4:04 PM, James Brown wrote:
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Hi Dr Greeve,
I ran recon-all using the flag -flair. I couldn't find any command in
recon-all.log that normalizes the flair images. It seems just
normalization to the T1.
I
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Hi Dr Greeve,
I ran recon-all using the flag -flair. I couldn't find any command in
recon-all.log that normalizes the flair images. It seems just normalization
to the T1.
I would like to inquire about the flag sigma in the command "mri_normalize"
the
I'm not sure of the order. You can run recon-all passing in the flair
with -flair flair.mgz. At some point in the process it will apply a
normalization to the flair (it will not necessarily be the same
normalization that is applied to the t1)
On 9/12/2022 4:01 PM, James Brown wrote:
External Email - Use Caution
Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. I 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
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