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Hello FreeSurfer Developers,
I'm attempting to run recon-all on schizophrenia patients and
controls. For some reason freesurfer is crashing.
I wanted to know the reason for frequent crashing.
I'm using Ubuntu 16.04 LTS and
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.
Below I have attached the recon-all.log file for your reference.
Kindly help me to sort this out.
Thank you
Regards
*Vittal*
Tue Jan 8 01:59:38 EST 2019
/usr/local/freesurfer/subjects/insp019
/usr/local/freesurfer/bin/recon-all
-i /home/milkyway2/Desktop/INSP-019-NR-1-Structural.nii -s insp019 -all
subjid insp019
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux milkyway2 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 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 128124
maxlocks unlimited
maxsignal 128124
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32859472 947404 30511832 100636 1400236 31292176
Swap: 33473532 0 33473532
########################################
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: 2019/01/08-06:59:38-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic 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: 2019/01/08-06:59:38-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic 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: 2019/01/08-06:59:38-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:39-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic 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: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic 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: 2019/01/08-06:59:40-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:41-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:41-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:41-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2019/01/08-06:59:41-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: root Machine: milkyway2 Platform: Linux PlatformVersion: 4.15.0-43-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/usr/local/freesurfer/subjects/insp019
mri_convert /home/milkyway2/Desktop/INSP-019-NR-1-Structural.nii /usr/local/freesurfer/subjects/insp019/mri/orig/001.mgz
mri_convert /home/milkyway2/Desktop/INSP-019-NR-1-Structural.nii /usr/local/freesurfer/subjects/insp019/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/milkyway2/Desktop/INSP-019-NR-1-Structural.nii...
TR=2200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999248, -0.00998125, -0.0374719)
j_ras = (0.0125137, 0.997609, 0.0679675)
k_ras = (0.0367039, -0.0683853, 0.996984)
writing to /usr/local/freesurfer/subjects/insp019/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Jan 8 01:59:45 EST 2019
Found 1 runs
/usr/local/freesurfer/subjects/insp019/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 /usr/local/freesurfer/subjects/insp019/mri/orig/001.mgz /usr/local/freesurfer/subjects/insp019/mri/rawavg.mgz
/usr/local/freesurfer/subjects/insp019
mri_convert /usr/local/freesurfer/subjects/insp019/mri/rawavg.mgz /usr/local/freesurfer/subjects/insp019/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/insp019/mri/rawavg.mgz /usr/local/freesurfer/subjects/insp019/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/insp019/mri/rawavg.mgz...
TR=2200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999248, -0.00998125, -0.0374719)
j_ras = (0.0125137, 0.997609, 0.0679675)
k_ras = (0.0367039, -0.0683853, 0.996984)
Original Data has (1, 1, 1) mm size and (176, 232, 200) 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 /usr/local/freesurfer/subjects/insp019/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/insp019/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/insp019/mri/orig.mgz /usr/local/freesurfer/subjects/insp019/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Jan 8 01:59:51 EST 2019
/usr/local/freesurfer/subjects/insp019/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux milkyway2 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s insp019 exited with ERRORS at Tue Jan 8 01:59:53 EST 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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