Dear all,
I've been running the FreeSurferPipelineBatch code with some of the data that
we have and the program exits out of this when calculating the Talairach
coordinates using the recon-all script from the FreeSurfer directory. I've
attached the recon-all log file and MNI log file (orig_nu.log) I get when I run
the script.
I also get the same error when running the FreeSurferPipelineBatch script with
the example data from the HCP. Any suggestions on where I'm going wrong?
Kind regards,
Dinal Jayasekera
PhD Student in Biomedical Engineering
Washington University in St. Louis
B.S. in Biomedical Engineering | Minor in Biophysics and Electrical Engineering
The George Washington University
From: Glasser, Matthew
Sent: Friday, July 20, 2018 5:26:40 PM
To: Jayasekera, Dinal
Cc: NEUROSCIENCE tim; Hawasli, Ammar; Brown, Tim
Subject: Re: Environmental variable settings for FreeSurferPipelineBatch
This error was just recently discussed on the HCP User’s list and I don’t
remember if there was a solution. In general a lot of these errors are coming
from using Ubuntu 16.04 which we are not using and testing on (we are on
14.04). If you could roll back to 14.04 you would probably get fewer of these
kind of errors.
Matt.
________________________________
From: "Jayasekera, Dinal"
<[email protected]<mailto:[email protected]>>
Date: Friday, July 20, 2018 at 4:31 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>
Subject: Re: Environmental variable settings for FreeSurferPipelineBatch
Dear Matt,
I've been running the FreeSurferPipelineBatch code with some of the data that
we have and the program exits out of this when calculating the Talairach
coordinates using the recon-all script from the FreeSurfer directory. I've
attached the log file I get when I run the script.
I also get the same error when running the FreeSurferPipelineBatch script with
the example data from the HCP. Would this error be indicative of a missing
library from my terminal?
Kind regards,
Dinal Jayasekera
PhD Student in Biomedical Engineering
Washington University in St. Louis
B.S. in Biomedical Engineering | Minor in Biophysics and Electrical Engineering
The George Washington University
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Mon Jul 23 14:13:19 CDT 2018
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/bin/recon-all
-i /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid Control_9 -sd /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w -motioncor -talairach -nuintensitycor -normalization -openmp 8
subjid Control_9
setenv SUBJECTS_DIR /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w
FREESURFER_HOME /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer
Actual FREESURFER_HOME /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0-HCP
Linux FSL-1 4.15.0-24-generic #26~16.04.1-Ubuntu SMP Fri Jun 15 14:35:08 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 513899
maxlocks unlimited
maxsignal 513899
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 131696752 3611252 1212216 1416632 126873284 125250072
Swap: 133881852 0 133881852
########################################
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: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
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: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: Feb 1 2014 03:28:19 CVS: $Id: mris_make_surfaces.c,v 1.147 2014/01/29 20:42:02 fischl Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
$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: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
$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: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9
mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz
mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.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 /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Mon Jul 23 14:13:23 CDT 2018
Found 1 runs
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/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 /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9
mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz --conform
mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/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)
Original Data has (1, 1, 1) mm size and (181, 217, 181) 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 /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz...
mri_add_xform_to_header -c /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/transforms/talairach.xfm /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Mon Jul 23 14:13:31 CDT 2018
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux FSL-1 4.15.0-24-generic #26~16.04.1-Ubuntu SMP Fri Jun 15 14:35:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Control_9 exited with ERRORS at Mon Jul 23 14:13:35 CDT 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux FSL-1 4.15.0-24-generic #26~16.04.1-Ubuntu SMP Fri Jun 15 14:35:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Mon Jul 23 14:13:31 CDT 2018
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
tmpdir is ./tmp.mri_nu_correct.mni.14552
/mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14552/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14552/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=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.14552/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Jul 23 14:13:35 CDT 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.14552/nu0.mnc ./tmp.mri_nu_correct.mni.14552/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14552/0/ -iterations 1000 -distance 50
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
ERROR: nu_correct
