Failure in testing newly installed FreeSurfer - Freesurfer

4 Sep 2016

Sure:

/usr/local/freesurfer/subjects/bert/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o
orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux saeed-CDS-Custom-Configuration 4.4.0-36-generic #55-Ubuntu SMP
Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Tue Sep  6 18:25:41 EDT 2016
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
tmpdir is ./tmp.mri_nu_correct.mni.9207
/usr/local/freesurfer/subjects/bert/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9207/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9207/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.9207/nu0.mnc...

--------------------------------------------------------
Iteration 1 Tue Sep  6 18:25:43 EDT 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.9207/nu0.mnc
./tmp.mri_nu_correct.mni.9207/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.9207/0/ -iterations 1000 -distance 50
Can't use 'defined(@array)' (Maybe you should just omit the
defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em
line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)
ERROR: nu_correct

On Tue, Sep 6, 2016 at 1:07 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    I think it is probably an MNI problem. Can you run the following
    command
    and send the terminal output?

    mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
    --no-rescale --i orig.mgz --o orig_nu.mgz

    On 09/04/2016 06:13 PM, Saeed mahdizadeh bakhshmand wrote:
    > Hello FreeSurfer Developers,
    >
    > I'm trying to test a very basic command (recon-all) according
    to this
    page(https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
    <https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer>)
    after installing FreeSurfer and I receive following error after
    a few seconds:
    >    ERROR:recon-all -s bert exited with ERRORS at Sun Sep  4
    17:18:51 EDT 2016
    >
    > I've searched the list and no similar errors have been
    reported. Does anyone have any thoughts on how to trouble-shoot
    this one? Also, Ive attached the recon-all.log in case it's of
    any use.
    >
    > 1) FreeSurfer version:
    freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
    > 2) Platform: x86_64
    > 3) uname -a: Linux saeed-CDS-Custom-Configuration
    4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016
    x86_64 x86_64 x86_64 GNU/Linux
    > 4) recon-all.log: see attached
    >
    > Saeed
    >
    >
    >
    > _______________________________________________
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    <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    <https://gate.nmr.mgh.harvard.edu/filedrop2>
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
    <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

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