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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 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