On Fri, 2008-12-05 at 13:51 -0600, Devdutta W wrote:
> Nick,
> When I type nu_estimate_np_and_em, I did indeed see the message you
> mentioned. I also checked and found perl at /usr/bin/.
> I didn't find any other installations of the mni tools in my path.
> Are these the only things that usually cause recon-all to fail like
> this? Any other ideas why it is failing?
>
> Thanks,
> Dev
>
> On Fri, Dec 5, 2008 at 1:07 PM, Nick Schmansky
> <
nicks@nmr.mgh.harvard.edu> wrote:
> Dev,
>
> What happens when you type:
>
> nu_estimate_np_and_em
>
>
> you should see:
>
> nu_estimate_np_and_em, version 1.10
>
> Usage: nu_estimate_np_and_em [-help] [options]
> input_volume.mnc
> nu_field.imp
> Incorrect number of arguments
>
>
> do you have perl installed at /usr/bin/perl ?
>
> do you have another installation of the mni tools in your
> path, other
> than the one included with freesurfer?
>
> Nick
>
>
>
>
> On Fri, 2008-12-05 at 12:07 -0600, Devdutta W wrote:
> > Hello,
> > I am a new freesurfer user. I have been trying to run
> recon-all on
> > our data and have been unable to do so because recon-all
> crashes
> > everytime at the same spot.
> > Here is the error I get when I run recon-all with autorecon1
> or when I
> > run it with -nuintensitycor
> >
> > Iteration 1 Fri Dec 5 12:03:19 CST 2008
> > nu_correct -
> >
> clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc ./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/
> > nu_correct: couldn't find program "nu_estimate_np_and_em"
> > nu_correct: couldn't find program "nu_evaluate"
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_estimate_np_and_em"
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_estimate_np_and_em"
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_estimate_np_and_em"
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_estimate_np_and_em"
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_estimate_np_and_em"
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_estimate_np_and_em"
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530
> > add_default_args: warning: adding default arguments for
> unregistered
> > program "nu_evaluate"
> at /usr/local/imsw/freesurfer/mni/bin/nu_correct
> > line 530
> > spawn: error: program "nu_estimate_np_and_em" not registered
> > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60
> > ERROR: nu_correct
> > Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13
> EDT 2008
> > i686 i686 i386 GNU/Linux
> >
> > recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008
> >
> > I have made sure that the "nu_estimate_np_and_em" as well as
> > "nu_evalutate" are both in the appropriate directory. I
> have also set
> > the environment properly.
> > Can anybody help me solve this? I appreciate any help or
> suggestions.
> >
> > Thank you,
> > Dev
>
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