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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