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 <saeedbakhshmand@gmail.com mailto:saeedbakhshmand@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 -odtfloat 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 thispage(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 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/BugReportinghttp://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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