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.kare...@gmail.com > <mailto:swathy.kare...@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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
