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 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) 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.
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Platform: x86_64
- 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
- recon-all.log: see attached
Saeed
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