Hello Douglas,

Any chance to look into this issue?

On Tue, Sep 6, 2016 at 6:26 PM, Saeed Bakhshmand <saeedbakhshm...@gmail.com>
wrote:

> 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 <gr...@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.
>> >
>> > 1) FreeSurfer version: freesurfer-Linux-centos6_x86_6
>> 4-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
>> >
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Reply via email to