Hi List,
We just upgraded our Linux Box to Fedora 23 and installed csh so recon-all would run, yet we’re still getting crashed analyses.
Here is the error from my recon-all.error file: ------------------------------ SUBJECT 2_03T_N12_12_18441 DATE Thu Jan 21 16:20:16 GMT 2016 USER dsbarron HOST psyws26.psych.ox.ac.uk PROCESSOR x86_64 OS Linux Linux psyws26.psych.ox.ac.uk 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
Here is the error when I try to call just the mrinucorrect.mni function:
bash-4.3$ mri_nu_correct.mni mri_nu_correct.mni:1: parser error : Start tag expected, '<' not found #! /bin/tcsh -f ^ Document not parsed successfully.
Any suggestions/ideas? Please help! Thanks!
Cheers, Daniel
Hi Daniel,
maybe you need to also install the tcsh package.
Best, Martin
On 01/21/2016 12:39 PM, Barron, Daniel wrote:
Hi List,
We just upgraded our Linux Box to Fedora 23 and installed csh so recon-all would run, yet we’re still getting crashed analyses.
Here is the error from my recon-all.error file:
SUBJECT 2_03T_N12_12_18441 DATE Thu Jan 21 16:20:16 GMT 2016 USER dsbarron HOST psyws26.psych.ox.ac.uk PROCESSOR x86_64 OS Linux Linux psyws26.psych.ox.ac.uk 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
Here is the error when I try to call just the mrinucorrect.mni function:
bash-4.3$ mri_nu_correct.mni mri_nu_correct.mni:1: parser error : Start tag expected, '<' not found #! /bin/tcsh -f ^ Document not parsed successfully.
Any suggestions/ideas? Please help! Thanks!
Cheers, Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.ukhttps://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.ukhttps://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.ukhttps://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/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.ukhttps://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 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 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mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
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.ukhttps://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.ukhttps://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.ukhttps://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.ukhttps://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.ukhttps://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.ukhttps://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.ukhttps://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.ukhttps://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
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
######################################## 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.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 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 BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 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 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk 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======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 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_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: dsbarron Machine: psyws26.psych.ox.ac.uk 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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi ZK, It was SLED 11.4. Thanks for looking into it. Appreciate your time. db
On 1/26/16, 11:04 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zkaufman@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/cacheavailable 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
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======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 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. uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_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/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
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After a bit of investigating, Ive determined that the error you've encountered is due to a conflict with the mni tools shipped with freesurfer v5.3, and the latest version of perl (version 5.22, shipped with Fedora 23).
This has been fixed in the dev version of freesurfer and thus will be fixed in the upcoming release of freesurfer version 6.0. So you basically have 2 options if you want to use freesurfer on your platform:
1) Update to the newest Development Version of freesurfer:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Or, 2) Use perlbrew (http://perlbrew.pl/) to role back your version of perl:
$> \curl -L http://install.perlbrew.pl | bash $> perlbrew install perl-5.20.1 $> perlbrew switch perl-5.20.1
Hope this helps.
-Zeke
On 01/26/2016 11:09 AM, Barron, Daniel wrote:
Hi ZK, It was SLED 11.4. Thanks for looking into it. Appreciate your time. db
On 1/26/16, 11:04 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zkaufman@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/cacheavailable 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. uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: 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 BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 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. uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_1AEwRrd74&e=Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/01/25-18:43:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 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. uk&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_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=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y h34fYFosM&m=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI&s=gsKhS9Mym34PR3U Xiv5lzMEopfAGkdYdn_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/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
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Barron, Daniel -
Martin Reuter -
Z K