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.mni.

            Thanks in advance!

            Kind regards
            Cris






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