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
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