External Email - Use Caution
Dear freesurfer team,
I have been having a problem running freesurfer on one computer. The same commands and data work fine on other machines.
The error message is:
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
Looking through the message board, others have had a similar problem.
I have tried many of the suggestions offered without success.
Note that I have the problem using freesurfer-6.0.0 as well as freesurfer-5.3.3-HCP
Information on the error messages, OS and some of the things I have tried are described below.
I have seen a few inquiries of this type never resolved as far as I can tell:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056844.htm...
https://neurostars.org/t/fmriprep-crashing-during-freesurfer-nu-correct/2108
Anything you can suggest would be appreciated.
Thanks,
Sally
------------------------------------------------------------------------------------------------------------------------
I did make sure it is not a space problem:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050008....
------------------------------------------------------------------------------------------------------------------------
I successfully tried the minc commands which used /opt/minc/1.9.16/bin - the files were created: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050030....
mri_convert.bin orig.mgz orig.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2300.00, 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)
writing to orig.nii...
<nifti_image.../>
Using s-form transform:
-1.0000, 0.0000, 0.0000, 127.0000,
0.0000, 0.0000, 1.0000, -145.1500,
0.0000, -1.0000, 0.0000, 147.0000,
0.0000, 0.0000, 0.0000, 1.0000,
name | start | step | cosines
yspace | -145.1500 | 1.0000 | 0.0000 1.0000 0.0000
zspace | 147.0000 | -1.0000 | -0.0000 -0.0000 1.0000
xspace | 127.0000 | -1.0000 | 1.0000 -0.0000 -0.0000
mri_convert.bin junk.mnc junk.mgh
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from junk.mnc...
TR=0.00, 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)
writing to junk.mgh...
------------------------------------------------------------------------------------------------------------------------
Here's the OS info:
CentOS Linux release 7.4.1708 (Core)
------------------------------------------------------------------------------------------------------------------------
Here's the contents of recon-all.error:
------------------------------
SUBJECT FS_TEST
DATE Tue Jan 22 17:07:30 GMT 2019
USER me
HOST mycomputer
PROCESSOR x86_64
OS Linux
Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/usr/local/freesurfer-6.0.0/bin/recon-all
PWD <path to data>/FS_TEST/mri
CMD mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
------------------------------------------------------------------------------------------------------------------------
Here's the contents of FS_TEST/mri/mri_nu_correct.mni.log
------------------------------
<path to data>/FS_TEST/mri
/usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Tue Jan 22 17:07:26 GMT 2019
Program nu_correct, built from:
N3 1.12.00
tmpdir is ./tmp.mri_nu_correct.mni.81524
<path to data>/FS_TEST/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2300.00, 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.81524/nu0.mnc...
--------------------------------------------------------
Iteration 1 Tue Jan 22 17:07:29 GMT 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50
Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc
[me@mycomputer:<path to data>/FS_TEST/mri/] [2019-01-22 17:07:29] running:
/opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.imp
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
ERROR: nu_correct
------------------------------------------------------------------------------------------------------------------------
## The file that nu_correct is looking for is there:
ls FS_TEST/mri/tmp.mri_nu_correct.mni.81524/nu0.mnc
FS_TEST/mri/tmp.mri_nu_correct.mni.81524/nu0.mnc
------------------------------------------------------------------------------------------------------------------------
Here's the contents of FS_TEST/scripts/recon-all.log
--------------------------------------------------------
Tue Jan 22 17:07:02 GMT 2019
<path to data>/FS_TEST
/usr/local/freesurfer-6.0.0/bin/recon-all
-i T1w_acpc_dc_restore.nii.gz -subjid FS_TEST -all
subjid FS_TEST
setenv SUBJECTS_DIR <path to data>
FREESURFER_HOME /usr/local/freesurfer-6.0.0
Actual FREESURFER_HOME /usr/local/freesurfer-6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 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 4096
maxlocks unlimited
maxsignal 514889
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 131844476 1382916 504384 2483852 129957176 127079832
Swap: 4194300 226832 3967468
########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
N3 1.12.00
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/freesurfer-6.0.0/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer-6.0.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
<path to data>/FS_TEST
mri_convert <path to data>/T1w_acpc_dc_restore.nii.gz <path to data>/FS_TEST/mri/orig/001.mgz
mri_convert.bin <path to data>/T1w_acpc_dc_restore.nii.gz <path to data>/FS_TEST/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from <path to data>/T1w_acpc_dc_restore.nii.gz...
TR=2300.00, 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)
writing to <path to data>/FS_TEST/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Jan 22 17:07:12 GMT 2019
Found 1 runs
<path to data>/FS_TEST/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 <path to data>/FS_TEST/mri/orig/001.mgz <path to data>/FS_TEST/mri/rawavg.mgz
<path to data>/FS_TEST
mri_convert <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST/mri/orig.mgz --conform
mri_convert.bin <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from <path to data>/FS_TEST/mri/rawavg.mgz...
TR=2300.00, 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)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to <path to data>/FS_TEST/mri/orig.mgz...
mri_add_xform_to_header -c <path to data>/FS_TEST/mri/transforms/talairach.xfm <path to data>/FS_TEST/mri/orig.mgz <path to data>/FS_TEST/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Jan 22 17:07:26 GMT 2019
<path to data>/FS_TEST/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
<path to data>/FS_TEST/mri
/usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Tue Jan 22 17:07:26 GMT 2019
Program nu_correct, built from:
N3 1.12.00
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.81524
<path to data>/FS_TEST/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2300.00, 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.81524/nu0.mnc...
--------------------------------------------------------
Iteration 1 Tue Jan 22 17:07:29 GMT 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50
Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc
[me@mycomputer:<path to data>/FS_TEST/mri/] [2019-01-22 17:07:29] running:
/opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.imp
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
ERROR: nu_correct
Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s FS_TEST exited with ERRORS at Tue Jan 22 17:07:30 GMT 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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