Hi,
We have newly installed Freesurfer. We are a novice. We were trying to segment
our data set. We used the following command. We attached the log.
Command: recon-all -s testsample -all
Output:
[iplneurosurgery@localhost /]$ recon-all -s testsample -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/iplneurosurgery/Documents/freesurfer/subjects
Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
-rw-rw-r--. 1 iplneurosurgery iplneurosurgery 18906 Mar 11 12:15
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.log
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18
13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission
denied.
'/usr/local/freesurfer/bin/recon-all' ->
'/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Sat Mar 11 14:48:00 IST 2017
Found 1 runs
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/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
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
mri_convert
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
--conform
mri_convert.bin
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
--conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-0.989525, -0.140773, -0.0319737)
j_ras = (0.144349, -0.962296, -0.230541)
k_ras = (0.00168578, -0.232741, 0.972537)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz...
mri_add_xform_to_header -c
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
--proto-iters 1000 --distance 50
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
/usr/local/freesurfer/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 localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18
13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission
denied.
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.10571
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-1, 9.77889e-09, 1.16415e-09)
j_ras = (5.82077e-09, 0, -1)
k_ras = (1.21945e-08, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.10571/nu0.mnc...
--------------------------------------------------------
Iteration 1 Sat Mar 11 14:48:07 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10571/nu0.mnc
./tmp.mri_nu_correct.mni.10571/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.10571/0/ -iterations 1000 -distance 50
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission
denied.
ERROR: nu_correct
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18
13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s testsample exited with ERRORS at Sat Mar 11 14:48:07 IST 2017
freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: Cent OS 7
uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64
x86_64 x86_64 GNU/Linux
Sent from Outlook<http://aka.ms/weboutlook>
Sat Mar 11 12:15:53 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
/usr/local/freesurfer/bin/recon-all
-s testsample -i //home/iplneurosurgery/Documents/freesurfer/T1WeightedImage/000000.dcm
subjid testsample
setenv SUBJECTS_DIR /home/iplneurosurgery/Documents/freesurfer/subjects
FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 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 127616
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32702736 1462896 29668012 14072 1571828 30732136
Swap: 16777212 0 16777212
########################################
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: 2017/03/11-06:45:53-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.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: 2017/03/11-06:45:53-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:53-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:53-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:53-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:53-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:54-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:55-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.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: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.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: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:56-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-06:45:57-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /home/iplneurosurgery/Documents/freesurfer/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/iplneurosurgery/Documents/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
mri_convert /home/iplneurosurgery/Documents/freesurfer/T1WeightedImage/000000.dcm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz
mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/T1WeightedImage/000000.dcm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/iplneurosurgery/Documents/freesurfer/T1WeightedImage/000000.dcm...
Starting DICOMRead2()
dcmfile = /home/iplneurosurgery/Documents/freesurfer/T1WeightedImage/000000.dcm
dcmdir = /home/iplneurosurgery/Documents/freesurfer/T1WeightedImage
Ref Series No = 602
Found 25 files, checking for dicoms
Found 23 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.0101147 1.39645 5.83522
Vs: -0.00168578 0.232741 0.972537
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 23
ndcmfiles = 23
PE Dir = ROW (dicom read)
Loading pixel data
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-0.989525, -0.140773, -0.0319737)
j_ras = (0.144349, -0.962296, -0.230541)
k_ras = (0.00168578, -0.232741, 0.972537)
writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz...
Started at Sat Mar 11 12:15:53 IST 2017
Ended at Sat Mar 11 12:15:57 IST 2017
#@#%# recon-all-run-time-hours 0.001
recon-all -s testsample finished without error at Sat Mar 11 12:15:57 IST 2017
New invocation of recon-all
Sat Mar 11 14:48:00 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
/usr/local/freesurfer/bin/recon-all
-s testsample -all
subjid testsample
setenv SUBJECTS_DIR /home/iplneurosurgery/Documents/freesurfer/subjects
FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 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 127616
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32702736 2362092 21895516 43228 8445128 29747436
Swap: 16777212 0 16777212
########################################
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: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.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: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.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: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.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: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/11-09:18:00-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: iplneurosurgery Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.6.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /home/iplneurosurgery/Documents/freesurfer/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/iplneurosurgery/Documents/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
#--------------------------------------------
#@# MotionCor Sat Mar 11 14:48:00 IST 2017
Found 1 runs
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/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 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
mri_convert /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-0.989525, -0.140773, -0.0319737)
j_ras = (0.144349, -0.962296, -0.230541)
k_ras = (0.00168578, -0.232741, 0.972537)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz...
mri_add_xform_to_header -c /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
/usr/local/freesurfer/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 localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.10571
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-1, 9.77889e-09, 1.16415e-09)
j_ras = (5.82077e-09, 0, -1)
k_ras = (1.21945e-08, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.10571/nu0.mnc...
--------------------------------------------------------
Iteration 1 Sat Mar 11 14:48:07 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10571/nu0.mnc ./tmp.mri_nu_correct.mni.10571/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10571/0/ -iterations 1000 -distance 50
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
ERROR: nu_correct
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s testsample exited with ERRORS at Sat Mar 11 14:48:07 IST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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