it looks like you are using v6. In v6, the flair might not have been normalized

On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote:
I think you need to add something like -FLAIRpial or -T2pial so it uses it (in which case it will first normalize it), but hopefully someone else can confirm

cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of James Brown <jb1979000@gmail.com>
Sent: Friday, September 23, 2022 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu <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 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 FLAIR.nii.gz -s test

When I search for normalization of flair, I only find how Freesurfer normalized T1.
I searched for "nonmax_suppress" and it is not in the log file. I am just wondering what I am doing wrong. Thanks again for any highlights about the correct method to normalize FLAIR

Sincerely,



Hi JamesB
there is T2/FLAIR normalization in recon-all if you process it through there. You can look for "nonmax_suppress" if you want to find the command line
cheers Bruce

On Fri, Sep 23, 2022 at 2:06 PM James Brown <jb1979000@gmail.com> wrote:
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 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.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then normalize white matter intensity. 
We tried N4biasfieldcorrection from ANTS but it didn't work as expected. Reviewing documents about N4biasfieldcorrection we realize that the algorithm has been developed to correct bias field correction in T1 not clear if it works on FLAIR images.
Are the steps above valid for normalizing FLAIR images or can it only be applied on T1 images? I would like to send a "recon-all.log" file that includes the processing steps of FLAIR. Is there any link I can use to upload the file. It gets rejected every time I send it due to size limitations. 

We appreciate any feedback about the proper way to correct FLAIR images for bias fields and normalize white matter intensity in FLAIR images.
Thank you
JamesB

On Wed, Sep 21, 2022 at 10:18 AM James Brown <jb1979000@gmail.com> wrote:
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.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz
We would like to apply bias field correction on FLAIR images then normalize white matter intensity. 
We tried N4biasfieldcorrection from ANTS but it didn't work as expected. Reviewing documents about N4biasfieldcorrection we realize that the algorithm has been developed to correct bias field correction in T1 not clear if it works on FLAIR images.
Are the steps above valid for normalizing FLAIR images or can it only be applied on T1 images? I would like to send a "recon-all.log" file that includes the processing steps of FLAIR. Is there any link I can use to upload the file. It gets rejected every time I send it due to size limitations. 

We appreciate any feedback about the proper way to correct FLAIR images for bias fields and normalize white matter intensity in FLAIR images.
Thank you
JamesB

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