[Freesurfer] Fwd: mri_nu_correct.mni options

Dear Freesurfer List!

Does anyone know what the purpose of the flag: mri_nu_correct.mni --i T1.nii --o nuT1.nii *--no-float* as opposed to: mri_nu_correct.mni --i T1.mgz --o nuT1.mgz *--n 2 *?

Thank you! Cris

---------- Forwarded message ---------- From: Cristian Paz pazcristian99@gmail.com Date: 2013/6/12 Subject: Re: [Freesurfer] mri_nu_correct.mni options To: Bruce Fischl fischl@nmr.mgh.harvard.edu

OK, I understand.

I am planning to replicate the methods of a study that used mri_nu_correct.mni (probably only on T1)

About mri_nu_correct.mni - what is the purpose with the flag: mri_nu_correct.mni --i T1.nii --o nuT1.nii --no-float as opposed to: mri_nu_correct.mni --i T1.mgz --o nuT1.mgz --n 2 ?

Thank you! Cris

2013/6/12 Bruce Fischl fischl@nmr.mgh.harvard.edu

they are different. nu_correct is much gentler and doesn't allow for user intervention in the way that specifying control points does. You'll need to mess around to see what is best

Bruce On Wed, 12 Jun 2013, Cristian Paz wrote:

Hi Bruce!

...

Thank you!

So I should rather use mri_normalize instead of mri_nu_correct.mni to correct for intensity non-uniformity?

Cheers, Cristian

2013/6/12 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Cristian

  you can use mri_normalize directly on the T1, but it won't work for

the T2 unless you specify control points and tell it to only use them. There are other (more esoteric) options in mri_normalize that you could use. Look at the recon-all code for the T2-based dura correction

  cheers
  Bruce
  On Wed, 12 Jun 2013, Cristian Paz wrote:

        Dear FS'ers.

        If I want to do bias correction of T1 and T2 images, without

necessarily doing a recon-all - what are the different options/parameters I can add in the command line?

        Right now I have been testing   :

        mri_nu_correct.mni --i <input> --o <output>

        and unfortunately the output looks worse than the input.

        this wiki page was not too informative with regards to

options: http://ftp.nmr.mgh.harvard.**edu/fswiki/mri_nu_correct.mnihttp://ftp.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni .

        Thanks in advance!

        Kind regards
        Cris

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