Sinead, Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths?
Nick On Fri, 2013-03-08 at 09:50 +0000, Sinead Kelly wrote: > Dear all, > > > I am currently running cortical thickness analysis using Freesurfer > v5.2 on a high performance computing cluster however, when I run the > 'recon_all' command I get the following error > > > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 > INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 > Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 > EST 2012 x86_64 x86_64 x86_64 GNU/Linux > nu_correct: Command not found. > #-------------------------------------------- > #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 > Found 1 runs > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz > Checking for (invalid) multi-frame inputs... > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > > > cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz > /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz > > > /home/users/kellys37/CT_TEST/CON3140/001 > > > mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform > > > mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading > from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.9997, 0.0244327, -0.00148148) > j_ras = (0.0239203, 0.987991, 0.152651) > k_ras = (-0.00519336, -0.15257, 0.988279) > Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, > 180) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz... > > > mri_add_xform_to_header > -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz > > > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Thu Mar 7 11:44:32 GMT 2013 > /home/users/kellys37/CT_TEST/CON3140/001/mri > > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 > --no-rescale --i orig.mgz --o orig_nu.mgz > > > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 > EST 2012 x86_64 x86_64 x86_64 GNU/Linux > > > recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013 > > > For more details, see the log > file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > I had did not encounter this error when using an older version of > Freesurfer on our clusters. Do you know if there is any way to resolve > this problem? Any advice would be appreciated. > > > Kind regards, > > > Sinead > > > -- > Sinead Kelly > Neuropsychiatric Genetics Group > Trinity Centre > St. James's Hospital > Dublin 8 > _______________________________________________ > 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.
