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, We’ve got the tcsh installed and seems to be working. Can’t find a similar report on the list serve, so I’ve 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 I’m 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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_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/cacheavailable Mem: 32901484 2311624 1288116 121896 29301744 29874168 Swap: 16515068 1344924 15170144
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ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk https://urldefense.proofpoint.com/v2/url?u=http-3A__psyws26.psych.ox.ac.uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:23-GMT BuildTimeStamp: 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.uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: 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/talairach.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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3UXiv5lzMEopfAGkdYdn_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
##################### *Here’s 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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0yh34fYFosM&m=o9ZoiWN5Nd_2Y0sEtlItPQ7obsOIkoBMOKpxRPhTGNI&s=zOz_AYM7zsMdK1Wtpy8VaOsh9sYRG-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
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