External Email - Use Caution
Dear all,
I have been running version 4 of the HCP Pipelines which now used FreeSurfer
6.0. I get the following error when running recon-all using their
FreeSurferPipelineBatch script:
nu_evaluate: crashed while running minc_modify_header (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)
ERROR: nu_correct
I didn't get this error previously when running FreeSurfer 5.3.0 on the same
set of data. Are the MNI tools distributed through FreeSurfer 6.0 sensitive to
the operating system and its version? Does anyone have a record of it working
on an Ubuntu 14.04 OS?
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
2) Platform: Ubuntu 14.04
3) recon-all.log: see attached
Kind regards,
Dinal Jayasekera<https://dinaljay.weebly.com/>
PhD Candidate | InSITE Fellow<https://www.insitefellows.org/>
Ammar Hawasli Lab<https://hawaslilab.weebly.com/>
Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx>
| Washington University in St. Louis<https://wustl.edu/>
Fri Apr 5 18:06:14 CDT 2019
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/FreeSurfer/custom/recon-all.v6.hires
-subjid NSI_27 -sd /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w -all -i /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -T2 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz -emregmask /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2pial -openmp 8 -conf2hires
subjid NSI_27
setenv SUBJECTS_DIR /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w
FREESURFER_HOME /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6
Actual FREESURFER_HOME /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 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 514029
maxlocks unlimited
maxsignal 514029
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 131691112 128643524 3047588 52028 37652832 85154680
-/+ buffers/cache: 5836012 125855100
Swap: 1998952 664 1998288
########################################
program versions used
$Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic 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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic 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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic 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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:15-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:15-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:15-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/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 /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27
mri_convert /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz
mri_convert.bin /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz...
TR=2500.00, 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 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Fri Apr 5 18:06:30 CDT 2019
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27
mri_convert --no_scale 1 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/T2raw.mgz
mri_convert.bin --no_scale 1 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/T2raw.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz...
TR=3200.00, 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 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Fri Apr 5 18:06:45 CDT 2019
Found 1 runs
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/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 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27
mri_convert /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz --conform
mri_convert.bin /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz...
TR=2500.00, 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 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz...
mri_add_xform_to_header -c /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/transforms/talairach.xfm /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz
INFO: extension is mgz
mri_vol2vol --mov /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz --targ /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz --regheader --interp nearest --o /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/extern.emreg.mask.mgz
movvol /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz
targvol /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz
outvol /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/extern.emreg.mask.mgz
invert 0
tal 0
talres 2
regheader 1
noresample 0
interp nearest (0)
precision float (3)
Gdiag_no -1
Synth 0
SynthSeed 1554748358
Computing registration based on scanner-to-scanner
Final tkRAS-to-tkRAS Matrix is:
1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 -1.00000 0.00000 -0.00001;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox Matrix is:
1.42857 0.00000 0.00000 -52.85715;
0.00000 0.00000 1.42857 -27.35713;
0.00000 -1.42857 0.00000 312.85715;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output registration matrix is identity
mri_vol2vol done
#--------------------------------------------
#@# Talairach Fri Apr 5 18:07:00 CDT 2019
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri
/home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/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 fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Fri Apr 5 18:07:00 CDT 2019
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.30912
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30912/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30912/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2500.00, 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.30912/nu0.mnc...
Outputting Volume: ............................................................
--------------------------------------------------------
Iteration 1 Fri Apr 5 18:07:13 CDT 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.30912/nu0.mnc ./tmp.mri_nu_correct.mni.30912/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30912/0/ -iterations 1000 -distance 50
[functionalspinelab@fsl:/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/] [2019-04-05 18:07:13] running:
/home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/mni/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.30912/0/ ./tmp.mri_nu_correct.mni.30912/nu0.mnc ./tmp.mri_nu_correct.mni.30912/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
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Processing:.................................................................Done
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Processing:.................................................................Done
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Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 35
CV of field change: 0.000990652
Outputting Volume: ............................................................
Outputting Volume: ............................................................
minc_modify_header: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.
nu_evaluate: crashed while running minc_modify_header (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)
ERROR: nu_correct
Linux fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s NSI_27 exited with ERRORS at Fri Apr 5 18:08:55 CDT 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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