External Email - Use Caution Thank you very much for the follow up. I have attached the recon-all.log once again for your kind review
Hello James, I apologize that your message containing the log file got rejected. Can you please re-send it? I will manually approve it so your conversation with Doug can continue. Liam Sennott On Fri, Sep 16, 2022 at 10:25 AM James Brown <jb1979...@gmail.com> wrote: > Hi Dr Greeve, > I greatly apologize if I missed in the log file (attached) how freesurfer > normalizes flair. but I couldn't figure it out. Thanks for guidance > > James > > > > can you send your recon-all.log file? > > > > > On Thu, Sep 15, 2022 at 4:04 PM James Brown <jb1979...@gmail.com> wrote: > >> Hi Dr Greeve, >> I ran recon-all using the flag -flair. I couldn't find any command in >> recon-all.log that normalizes the flair images. It seems just normalization >> to the T1. >> I would like to inquire about the flag sigma in the command >> "mri_normalize" the default is 8. when it is recommended to increase this >> value? and how much can weincrease it? >> >> 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 Mon, Sep 12, 2022 at 4:01 PM James Brown <jb1979...@gmail.com> wrote: >> >>> 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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