External Email - Use Caution Dear Dr Bruce, Thank you very much for your guidance. I ran recon-all on a subject "test" using Freesurfer V6.0 and the following command line is reported in the "recon-all.log":
/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair FLAIR.nii.gz -s test When I search for normalization of flair, I only find how Freesurfer normalized T1. I searched for "nonmax_suppress" and it is not in the log file. I am just wondering what I am doing wrong. Thanks again for any highlights about the correct method to normalize FLAIR Sincerely, Hi JamesB there is T2/FLAIR normalization in recon-all if you process it through there. You can look for "nonmax_suppress" if you want to find the command line cheers Bruce On Fri, Sep 23, 2022 at 2:06 PM James Brown <jb1979...@gmail.com> wrote: > Dear Freesurfer experts, > We appreciate any advice or guidance from your community of professionals > and experts in the field about the issue below. > > Thank you for your kindness. > > 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 > > On Wed, Sep 21, 2022 at 10:18 AM James Brown <jb1979...@gmail.com> wrote: > >> 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.
