Hello everyone!I write to you because I can't get the process done in
freesurfer. I attach the log file. Thank you!
Mon Jan 22 01:16:35 CET 2018
/home/andraderenew/Downloads/SUBJECTS_DIR/bert
/home/andraderenew/Downloads/freesurfer/bin/recon-all
-i /home/andraderenew/Downloads/SUBJECTS_DIR/sample-001.nii.gz -s bert -all
subjid bert
setenv SUBJECTS_DIR /home/andraderenew/Downloads/SUBJECTS_DIR
FREESURFER_HOME /home/andraderenew/Downloads/freesurfer
Actual FREESURFER_HOME /home/andraderenew/Downloads/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux ubuntu 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 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 3712
maxlocks unlimited
maxsignal 3712
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 994868 653428 107284 7324 234156 146784
Swap: 1046524 589148 457376
########################################
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: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-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: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-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: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:35-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:36-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-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: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-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: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/22-00:16:37-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: andraderenew Machine: ubuntu Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /home/andraderenew/Downloads/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/andraderenew/Downloads/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/home/andraderenew/Downloads/SUBJECTS_DIR/bert
mri_convert /home/andraderenew/Downloads/SUBJECTS_DIR/sample-001.nii.gz /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig/001.mgz
mri_convert.bin /home/andraderenew/Downloads/SUBJECTS_DIR/sample-001.nii.gz /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/andraderenew/Downloads/SUBJECTS_DIR/sample-001.nii.gz...
TR=7.25, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Mon Jan 22 01:16:40 CET 2018
Found 1 runs
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/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/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig/001.mgz /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/rawavg.mgz
/home/andraderenew/Downloads/SUBJECTS_DIR/bert
mri_convert /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/rawavg.mgz /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig.mgz --conform
mri_convert.bin /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/rawavg.mgz /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/rawavg.mgz...
TR=7.25, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig.mgz...
mri_add_xform_to_header -c /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/transforms/talairach.xfm /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig.mgz /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Mon Jan 22 01:16:48 CET 2018
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
/home/andraderenew/Downloads/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 ubuntu 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Mon Jan 22 01:16:48 CET 2018
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.17242
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17242/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.17242/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=7.25, 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.17242/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Jan 22 01:16:51 CET 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.17242/nu0.mnc ./tmp.mri_nu_correct.mni.17242/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17242/0/ -iterations 1000 -distance 50
[andraderenew@ubuntu:/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/] [2018-01-22 01:16:52] running:
/home/andraderenew/Downloads/freesurfer/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.17242/0/ ./tmp.mri_nu_correct.mni.17242/nu0.mnc ./tmp.mri_nu_correct.mni.17242/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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: 29
CV of field change: 0.000957436
mri_convert ./tmp.mri_nu_correct.mni.17242/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.17242/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.17242/nu1.mnc...
TR=0.00, 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)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
writing to orig_nu.mgz...
Mon Jan 22 01:17:50 CET 2018
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
Started at Mon Jan 22 01:17:50 CET 2018
Ended at Mon Jan 22 01:18:46 CET 2018
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Mon Jan 22 01:18:48 CET 2018
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7190, pval=0.4932 >= threshold=0.0050)
awk -f /home/andraderenew/Downloads/freesurfer/bin/extract_talairach_avi_QA.awk /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/transforms/talairach_avi.log
tal_QC_AZS /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/transforms/talairach_avi.log
TalAviQA: 0.98348
z-score: 1
#--------------------------------------------
#@# Nu Intensity Correction Mon Jan 22 01:18:48 CET 2018
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
/home/andraderenew/Downloads/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux ubuntu 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Mon Jan 22 01:18:48 CET 2018
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.18177
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18177/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.18177/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=7.25, 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.18177/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Jan 22 01:18:51 CET 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.18177/nu0.mnc ./tmp.mri_nu_correct.mni.18177/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18177/0/
[andraderenew@ubuntu:/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/] [2018-01-22 01:18:51] running:
/home/andraderenew/Downloads/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18177/0/ ./tmp.mri_nu_correct.mni.18177/nu0.mnc ./tmp.mri_nu_correct.mni.18177/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 23
CV of field change: 0.000997107
--------------------------------------------------------
Iteration 2 Mon Jan 22 01:19:32 CET 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.18177/nu1.mnc ./tmp.mri_nu_correct.mni.18177/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.18177/1/
[andraderenew@ubuntu:/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/] [2018-01-22 01:19:32] running:
/home/andraderenew/Downloads/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18177/1/ ./tmp.mri_nu_correct.mni.18177/nu1.mnc ./tmp.mri_nu_correct.mni.18177/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 18
CV of field change: 0.00095863
mri_binarize --i ./tmp.mri_nu_correct.mni.18177/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18177/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.18177/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18177/ones.mgz
sysname Linux
hostname ubuntu
machine x86_64
user andraderenew
input ./tmp.mri_nu_correct.mni.18177/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.18177/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18177/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18177/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18177/input.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18177/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18177/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18177/input.mean.dat
sysname Linux
hostname ubuntu
machine x86_64
user andraderenew
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.18177/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.18177/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18177/ones.mgz --i ./tmp.mri_nu_correct.mni.18177/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18177/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18177/output.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18177/ones.mgz --i ./tmp.mri_nu_correct.mni.18177/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18177/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18177/output.mean.dat
sysname Linux
hostname ubuntu
machine x86_64
user andraderenew
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.18177/ones.mgz
Loading ./tmp.mri_nu_correct.mni.18177/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.18177/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.18177/nu2.mnc ./tmp.mri_nu_correct.mni.18177/nu2.mnc mul 1.05123077215796365196
Saving result to './tmp.mri_nu_correct.mni.18177/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.18177/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.18177/nu2.mnc nu.mgz --like orig.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.18177/nu2.mnc...
TR=0.00, 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)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 33 seconds.
mapping (10, 162) to ( 3, 110)
Mon Jan 22 01:21:16 CET 2018
mri_nu_correct.mni done
mri_add_xform_to_header -c /home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Mon Jan 22 01:21:18 CET 2018
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
mri_normalize -g 1 -mprage nu.mgz T1.mgz
using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
1.10414 -0.00919 -0.01423 -5.36488;
-0.00769 0.94721 0.29028 -46.86255;
0.01426 -0.25822 1.06262 24.15019;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 20
Starting OpenSpline(): npoints = 20
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 105
gm peak at 57 (57), valley at 23 (23)
csf peak at 29, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 55 (55), valley at 21 (21)
csf peak at 28, setting threshold to 46
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 28 seconds.
#--------------------------------------------
#@# Skull Stripping Mon Jan 22 01:23:47 CET 2018
/home/andraderenew/Downloads/SUBJECTS_DIR/bert/mri
mri_em_register -rusage /home/andraderenew/Downloads/SUBJECTS_DIR/bert/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /home/andraderenew/Downloads/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/home/andraderenew/Downloads/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9 using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=7.0
skull bounding box = (45, 45, 16) --> (211, 255, 239)
using (100, 115, 128) as brain centroid...
mean wm in atlas = 108, using box (80,89,100) --> (120, 140,155) to find MRI wm
before smoothing, mri peak at 104
robust fit to distribution - 104 +- 7.8
after smoothing, mri peak at 104, scaling input intensities by 1.038
scaling channel 0 by 1.03846
initial log_p = -4.419
************************************************
First Search limited to translation only.
************************************************
max log p = -4.296256 @ (-9.091, -9.091, -9.091)
max log p = -4.127731 @ (4.545, -4.545, -4.545)
max log p = -4.079831 @ (2.273, -2.273, -2.273)
max log p = -4.064560 @ (-1.136, 1.136, 3.409)
max log p = -4.062497 @ (0.568, -0.568, -1.705)
max log p = -4.062497 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, -15.3, -14.2): log p = -4.062
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.783, old_max_log_p =-4.062 (thresh=-4.1)
1.06375 0.00000 0.00000 -10.98281;
0.00000 1.19413 0.31997 -69.83015;
0.00000 -0.25882 0.96593 30.82699;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.783, old_max_log_p =-3.783 (thresh=-3.8)
1.06375 0.00000 0.00000 -10.98281;
0.00000 1.19413 0.31997 -69.83015;
0.00000 -0.25882 0.96593 30.82699;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.707, old_max_log_p =-3.783 (thresh=-3.8)
1.10364 0.00000 0.00000 -16.07749;
0.00000 1.17911 0.28395 -65.07129;
0.00000 -0.21384 0.95729 25.23553;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.704, old_max_log_p =-3.707 (thresh=-3.7)
1.08295 0.00000 0.00000 -13.43462;
0.00000 1.15700 0.27862 -63.06043;
0.00000 -0.21384 0.95729 25.23553;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.673, old_max_log_p =-3.704 (thresh=-3.7)
1.08603 0.03361 0.02572 -21.01215;
-0.03553 1.14546 0.31649 -60.98079;
-0.01743 -0.26094 0.94498 36.40415;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Killed
Linux ubuntu 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Mon Jan 22 01:48:29 CET 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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