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.eduwrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer