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:
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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
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