Note that you should not use the development version for final analysis. 
It should be treated as an alpha version. Any data you analyze will need 
to be reanalyzed with a fully released version


On 09/21/2016 12:36 PM, Z K wrote:
> Hello Saeed,
>
> The MNI tools shipped with freesurfer 5.3 are not compatible with the 
> newer versions of perl being shipped on all the newer linux distros. 
> This has been fixed in our development version and in the upcoming 
> freesurfer 6 release.
>
> So to get around this issue you will need to download and install the 
> development version of freesurfer from this page (see "Development 
> Version"):
>
>   ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>
> -Zeke
>
>
> On 09/21/2016 12:08 PM, Saeed Bakhshmand wrote:
>> Hello Douglas,
>>
>> Any chance to look into this issue?
>>
>> On Tue, Sep 6, 2016 at 6:26 PM, Saeed Bakhshmand
>> <saeedbakhshm...@gmail.com <mailto: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 <mailto: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
>> <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
>>         >
>>         >
>>         >
>>         > _______________________________________________
>>         > Freesurfer mailing list
>>         > Freesurfer@nmr.mgh.harvard.edu
>>         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>         > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>         --
>>         Douglas N. Greve, Ph.D.
>>         MGH-NMR Center
>>         gr...@nmr.mgh.harvard.edu <mailto:gr...@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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>>         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <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
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>>         contains patient information, please contact the Partners
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>>
>>
>>
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>
>

-- 
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/

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