Yan, 'nu_correct' is a binary from the MNI toolkit which is included with Freesurfer in the $FREESURFER_HOME/mni/bin directory. It requires 'perl' to run, and sometimes the path in nu_correct does not match the systems perl path. To fix that situation, type:
$FREESURFER_HOME/bin/fixup_mni_paths Then setup Freesurfer again and type: nu_correct and you should see: nu_correct, version 1.10 Usage: nu_correct [-help] [options] in.mnc out.mnc To use Freesurfer to reconstruct the surface with a skull-stripped data set, consult this table and make sure all the outputs from the - autorecon1 stage are available, before running -autorecon2 and - autorecon3: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Nick On Mon, 2007-01-22 at 11:02 -0800, yanxia wrote: > Dear All, > > I have a MRI dataset without skull (did skull-stripping with FSL), > and try to reconstruct the surface. I run: > > recon-all -s $subject_name -autorecon-all > > But the program stops because "nu_correct: Command not found"! > > Question: > 1> whether installation was not correct so not to find "nu_correct"? > 2> what is best way or command to reconstruct the surface with a > skull-stripped data set? > > Thanks. > > Best Regards, > Yan > > _______________________________________________ > 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
