Dear all,<div><br></div><div>I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the &#39;recon_all&#39; command I get the following error</div>
<div><br></div><div><div>Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0</div><div>Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0</div><div>INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140</div>
<div>Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0</div><div>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</div><div>nu_correct: Command not found.</div>
<div>#--------------------------------------------</div><div>#@# MotionCor Thu Mar  7 11:44:10 GMT 2013</div><div>Found 1 runs</div><div>/home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz</div><div>Checking for (invalid) multi-frame inputs...</div>
<div>WARNING: only one run found. This is OK, but motion</div><div>correction cannot be performed on one run, so I&#39;ll</div><div>copy the run to rawavg and continue.</div><div><br></div><div> cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz </div>
<div><br></div><div>/home/users/kellys37/CT_TEST/CON3140/001</div><div><br></div><div> mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform </div>
<div><br></div><div>mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform </div><div>$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $</div>
<div>reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz...</div><div>TR=0.00, TE=0.00, TI=0.00, flip angle=0.00</div><div>i_ras = (-0.9997, 0.0244327, -0.00148148)</div><div>j_ras = (0.0239203, 0.987991, 0.152651)</div>
<div>k_ras = (-0.00519336, -0.15257, 0.988279)</div><div>Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels.</div><div>Data is conformed to 1 mm size and 256 voxels for all directions</div><div>
changing data type from float to uchar (noscale = 0)...</div><div>MRIchangeType: Building histogram </div><div>Reslicing using trilinear interpolation </div><div>writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...</div>
<div><br></div><div> 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 </div>
<div><br></div><div>INFO: extension is mgz</div><div>#--------------------------------------------</div><div>#@# Talairach Thu Mar  7 11:44:32 GMT 2013</div><div>/home/users/kellys37/CT_TEST/CON3140/001/mri</div><div><br>
</div><div> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz </div><div><br></div><div>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</div>
<div><br></div><div>recon-all -s 001 exited with ERRORS at Thu Mar  7 11:44:38 GMT 2013</div><div><br></div><div>For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log</div><div>
To report a problem, see <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting">http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a></div><div><br></div><div><br></div><div>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.</div>
<div><br></div><div>Kind regards,</div><div><br></div><div>Sinead</div><div><br></div>-- <br><div>Sinead Kelly</div>
<div>Neuropsychiatric Genetics Group</div>
<div>Trinity Centre</div>
<div>St. James&#39;s Hospital</div>
<div>Dublin 8</div>
</div>