Hi ZK,
It was SLED 11.4. Thanks for looking into it. Appreciate your time.
db
On 1/26/16, 11:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Z K" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
zkauf...@nmr.mgh.harvard.edu> wrote:
>This appears to be something specific with Fedora 23... I will attempt
>to duplicate on a Fedora 23 virtual machine as I dont have one handy.
>Can you recall what version you were running before you upgraded to
>Fedora 23 when recon-all when running successfully?
>
>On 01/25/2016 02:05 PM, Barron, Daniel wrote:
>> Hi Martin,
>> We¹ve got the tcsh installed and seems to be working. Can¹t find a
>> similar report on the list serve, so I¹ve attached the bug report info
>> below plus the orig_nu.log output, which is where the script is
>> crashing. Please help!
>> Cheers,
>> Daniel
>>
>> *Output from buggr:*
>> FREESURFER_HOME: /home/freesurfer
>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> RedHat release: Fedora release 23 (Twenty Three)
>> Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64
>> Subject Name: 2_03T_N12_12_18441
>>
>> *Command I¹m entering:*
>> for subject in 2_03T_N12_12_18441; do
>> recon-all -subjid ${subject} -all -hippo-subfields
>> done
>>
>> *Error Message (from recon-all.error):*
>> ------------------------------
>> SUBJECT 2_03T_N12_12_18441
>> DATE Mon Jan 25 18:40:30 GMT 2016
>> USER dsbarron
>> HOST psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
>>uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=>
>> PROCESSOR x86_64
>> OS Linux
>> Linux psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
>>uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=> 4.3.3-300.fc23.x86_64
>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
>> /home/freesurfer/bin/recon-all
>> PWD /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
>> CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>> --no-rescale --i orig.mgz --o orig_nu.mgz
>>
>> #####################
>> *recon-all.log:*
>>
>> Mon Jan 25 18:43:18 GMT 2016
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441
>> /home/freesurfer/bin/recon-all
>> -subjid 2_03T_N12_12_18441 -all -hippo-subfields
>> subjid 2_03T_N12_12_18441
>> setenv SUBJECTS_DIR /home/dsbarron/Schmidt/Freesurfer
>> FREESURFER_HOME /home/freesurfer
>> Actual FREESURFER_HOME /home/freesurfer
>> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> Linux psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
>>uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=> 4.3.3-300.fc23.x86_64
>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> cputime unlimited
>> filesize unlimited
>> datasize unlimited
>> stacksize 8192 kbytes
>> coredumpsize 0 kbytes
>> memoryuse unlimited
>> vmemoryuse unlimited
>> descriptors 1024
>> memorylocked 64 kbytes
>> maxproc 128183
>> maxlocks unlimited
>> maxsignal 128183
>> maxmessage 819200
>> maxnice 0
>> maxrtprio 0
>> maxrttime unlimited
>>
>> total used free shared buff/cache
>> available
>> Mem: 32901484 2311624 1288116 121896 29301744
>> 29874168
>> Swap: 16515068 1344924 15170144
>>
>> ########################################
>> program versions used
>> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
>> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
>> mri_convert -all-info
>> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
>> $Name: stable5 $ TimeStamp: 2016/01/25-18:43:18-GMT BuildTimeStamp:
>> May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05
>> 21:55:16 mreuter Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>>h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U
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>> Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC
>> CompilerVersion: 40400
>> FLIRT version 5.5
>> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
>> mri_convert --version
>> stable5
>> ProgramName: tkregister2_cmdl ProgramArguments: --all-info
>> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:19-GMT
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>> Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC
>> CompilerVersion: 40400
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>> 00:04:27 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>> 00:04:33 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>> 00:04:34 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>> nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>> May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16
>> 00:09:33 greve Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
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>> Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC
>> CompilerVersion: 40400
>> #######################################
>> GCADIR /home/freesurfer/average
>> GCA RB_all_2008-03-26.gca
>> GCASkull RB_all_withskull_2008-03-26.gca
>> AvgCurvTif average.curvature.filled.buckner40.tif
>> GCSDIR /home/freesurfer/average
>> GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>> #######################################
>> #--------------------------------------------
>> #@# MotionCor Mon Jan 25 18:43:23 GMT 2016
>> Found 1 runs
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig/001.mgz
>> Checking for (invalid) multi-frame inputs...
>> WARNING: only one run found. This is OK, but motion
>> correction cannot be performed on one run, so I'll
>> copy the run to rawavg and continue.
>>
>> cp
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig/001.mgz
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/rawavg.mgz
>>
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441
>>
>> mri_convert
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/rawavg.mgz
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig.mgz
>>--conform
>>
>> mri_convert
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/rawavg.mgz
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig.mgz
>>--conform
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/rawavg.mgz...
>> TR=2040.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 1, 0)
>> k_ras = (0, 0, 1)
>> Original Data has (0.90625, 0.90625, 0.8) mm size and (208, 256, 208)
>> voxels.
>> Data is conformed to 1 mm size and 256 voxels for all directions
>> changing data type from float to uchar (noscale = 0)...
>> MRIchangeType: Building histogram
>> Reslicing using trilinear interpolation
>> writing to
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig.mgz...
>>
>> mri_add_xform_to_header -c
>>
>>/home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/transforms/talai
>>rach.xfm
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig.mgz
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri/orig.mgz
>>
>> INFO: extension is mgz
>> #--------------------------------------------
>> #@# Talairach Mon Jan 25 18:43:37 GMT 2016
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
>>
>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o orig_nu.mgz
>>
>> Linux psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
>>uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=> 4.3.3-300.fc23.x86_64
>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s 2_03T_N12_12_18441 exited with ERRORS at Mon Jan 25
>> 18:43:39 GMT 2016
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>>
>> #####################
>> *Here¹s also the orig_nu.log in case that helps:*
>> *
>> *
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
>> /home/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 psyws26.psych.ox.ac.uk
>>
>><https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.
>>uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM&m=o9ZoiWN5Nd_2Y0sEtlItPQ7obsOIkoBMOKpxRPhTGNI&s=zOz_AYM7zsMdK1W
>>tpy8VaOsh9sYRG-F7vDaX5fwzyOI&e=> 4.3.3-300.fc23.x86_64
>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> Mon Jan 25 19:01:28 GMT 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.28137
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
>> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28137/nu0.mnc -odt float
>> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28137/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=2040.00, 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.28137/nu0.mnc...
>>
>> --------------------------------------------------------
>> Iteration 1 Mon Jan 25 19:01:31 GMT 2016
>> nu_correct -clobber ./tmp.mri_nu_correct.mni.28137/nu0.mnc
>> ./tmp.mri_nu_correct.mni.28137/nu1.mnc -tmpdir
>> ./tmp.mri_nu_correct.mni.28137/0/ -iterations 1000 -distance 50
>> Can't use 'defined(@array)' (Maybe you should just omit the defined()?)
>> at /home/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
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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