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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