Hi Nick, I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters.
Thanks again for your help! Sinead On 9 March 2013 23:23, Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote: > 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 > > > > > 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. > -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8
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