Re: [Freesurfer] Question about recon-all

what OS are you using? what version of perl does it have? what is the output of:

env | grep MNI

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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