Ed, Create a file (named whatever you want, say, mri_nu_correct.xopts) containing one line:
mri_nu_correct.mni --distance 25 --stop 0.0001 --fwhm 0.1 and then include this at the end of your recon-all command: -expert <pathto>/mri_nu_correct.xopts and it will append those three flags to the end of the nu_correct command. Nick On Tue, 2009-04-28 at 16:05 +0200, Ed Gronenschild wrote: > Hi, > > I want to use parameters different from default for mri_nu_correct.mni. > This command uses nu_correct for which I would like to set the following > options: > > -distance 25 > -stop 0.0001 > -fwhm 0.1 > > These settings are more approriate when using 3T T1 data. > How can I invoke these in recon-all? Can I use an options file? > > Ed > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
