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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