External Email - Use Caution Dear Dr Greeve and Dr Fiscle, I am grateful to you guiding me through this. Indeed, I can see in recon-all.log how Freesurfer 7.3.2 is normalizing the Flair images. *it uses the command below:*
<mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg aseg.presurf.mgz -surface lh.white identity.nofile -surface rh.white identity.nofile FLAIR.prenorm.mgz FLAIR.norm.mgz > I tried to run the previous command without the flag -surface" and it seems to be working. using this command <mri_normalize -seed 1234 -sigma 0.5 -nonmax_supress 0 -min_dist 1 --no-skull > I would like to inquire about the following points and I highly appreciate any clarification you might provide: 1- It seems mri_normalize uses default sigma of 8 for normalizing T1 images and 0.5 for Flair. How far can we go up with this value? More specifically, when I have noticed when I increase sigma in noisy flair images in my dataset, I get better out put images in terms of less noticeable motion artifacts. Is there any cut off value for sigma? Can I use high values up to (e.g. 25)? 2- What does the flag "-min_dist" do? I tried to find information in mri_normalize man (i.e. help ) but I couldn't find information about this flag. I assume it has to do with the flag surface and they both should be used together? 3- Can I use mri_normalize on 2D flair images ? 4- Is it recommended to do whole brain normalization (white/gray and csf) or just white matter normalization within a mask. Thank you very much for all that you do. James it looks like you are using v6. In v6, the flair might not have been normalized On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote: I think you need to add something like -FLAIRpial or -T2pial so it uses it (in which case it will first normalize it), but hopefully someone else can confirm cheers Bruce On Fri, Sep 23, 2022 at 2:40 PM James Brown <jb1979...@gmail.com> wrote: > 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 >>> >>
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