Sinead,

In your freesurfer directory, is there an 'mni' directory?  under that
directory is a 'bin' directory where nu_correct should be.

Nick

> 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
>> > _______________________________________________
>> > 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
>

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