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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