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/>
>
>         _______________________________________________
>         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>
>
>
>         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
>         <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
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Reply via email to