Hello,

Oddly it seems that 'nu_correct' is not in your PATH, which is supposed to be set after you source the SetUpFreeSurfer.csh file. Can you please provide me with the following information:

-Do you have the file $FREESURFER_HOME/mni/bin/nu_correct? -Can you respond with the output of the terminal after you source the SetUpFreeSurfer.csh file? -And lastly, can you also respond with the output of the command 'echo $PATH' after your source the SetUpFreeSurfer.csh file?

This will help diagnose why recon-all is not finding that command. Thanks.

-Zeke

On 09/12/2013 01:37 AM, swathy p.s wrote:

---------- Forwarded message ---------- From: *swathy p.s* <swathy.karekad@gmail.com mailto:swathy.karekad@gmail.com> Date: Wed, Sep 11, 2013 at 1:47 AM Subject: talairach transforms To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach -subjid Stress_v12

Terminal window display was as shown bellow

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 root root 346264 Sep 10 23:10 /usr/local/freesurfer/subjects/Stress_v12/scripts/recon-all.log Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# Talairach Tue Sep 10 23:11:50 EDT 2013 /usr/local/freesurfer/subjects/Stress_v12/mri

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux

recon-all -s Stress_v12 exited with ERRORS at Tue Sep 10 23:11:55 EDT 2013

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