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 <nicks@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
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




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--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8