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 <pazcristia...@gmail.com> Date: 2013/6/12 Subject: Re: [Freesurfer] mri_nu_correct.mni options To: Bruce Fischl <fis...@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 <fis...@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 <fis...@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<http://ftp.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni> >> . >> >> Thanks in advance! >> >> Kind regards >> Cris >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >>
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