External Email - Use Caution 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
