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
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