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
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

#####################
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 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  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  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  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  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  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 


 ======= 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  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  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_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_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  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_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: 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.uk  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  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  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  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  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  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 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



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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 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