External Email - Use Caution 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 <[email protected]> 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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