Yan, It looks like perl is installed (normally in /usr/bin) if you are getting an output from nu_correct.
Can you send me your recon-all.log file? Also, what is the output when this is typed: which nu_correct Nick On Mon, 2007-01-22 at 11:50 -0800, yanxia wrote: > Hello Nick, > > Sorry for disturb again. > > After I type: > > nu_correct > > I can see > > > nu_correct, version 1.10 > > > > Usage: nu_correct [-help] [options] in.mnc out.mnc > > But after I tried : > > recon-all -s &subject -autorecon-all > > The program stops again because "nu_correct: No command found"! > > Do you think it is "perl" path problem? Where should "Perl" be installed? > > Thanks. > > Best Regards, > Yan > > At 11:16 AM 1/22/2007, Nick Schmansky wrote: > >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
