Hi Dr Greeve,

I greatly apologize if I missed in the log file (attached) how freesurfer normalizes flair.  but I couldn't figure it out. Thanks for guidance

James

can you send your recon-all.log file?

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On Thu, Sep 15, 2022 at 4:04 PM James Brown <jb1979000@gmail.com> wrote:

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 default is 8. when it is recommended to increase this value? and how much can weincrease it?

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)

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On Mon, Sep 12, 2022 at 4:01 PM James Brown <jb1979000@gmail.com> wrote:

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 T1_N3.mgzT1_norm.mgz

mri_convert T1_norm.mgz T1_norm.nii.gz

I would like to apply bias field correction on FLAIR images then normalize white matter intensity. 

I tried N4biasfieldcorrection from ANTS but it didn't work as expected. Reviewing documents about N4biasfieldcorrection I realize that the algorithm has been developed to correct bias field correction in T1.

Are the steps above valid for FLAIR images or it can only be applied on T1 images. We appreciate any feedback about the proper way to correct FLAIR images for bias field and normalize white matter intensity.

Thank you

JamesB