Dear Expert,
The recon-all -all process has stopped abruptly and error report shows that
"cannot find or read transforms/talairach.m3z". Please see the attached
file. Processing was running in 5 terminal simultaneously and it has
happened for two processing. Others exited without error. Could please tell
what should I do to continue the interrupted one.
Thanks in advance
Ramesh
Mon Jun 19 21:28:05 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147
/usr/local/freesurfer/bin/recon-all
-all -i grp147_t1.nii -s grp147 -sd subjects -use-gpu
subjid grp147
setenv SUBJECTS_DIR /mnt/research/freesurfer_analysis/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux rameshbabu 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 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 63592
maxlocks unlimited
maxsignal 63592
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16326760 1255880 6630512 30092 8440368 14665140
Swap: 16669692 0 16669692
########################################
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: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-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: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-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: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-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: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-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: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:05-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:06-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/19-15:58:06-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: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-79-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/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 /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/mnt/research/freesurfer_analysis/subjects/grp147
mri_convert /mnt/research/freesurfer_analysis/grp147_t1.nii /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig/001.mgz
mri_convert.bin /mnt/research/freesurfer_analysis/grp147_t1.nii /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /mnt/research/freesurfer_analysis/grp147_t1.nii...
TR=7.60, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0168201, -0.999244, 0.0350365)
j_ras = (-0.0190707, 0.0353557, 0.999193)
k_ras = (0.999677, -0.0161384, 0.019651)
writing to /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Mon Jun 19 21:28:08 IST 2017
Found 1 runs
/mnt/research/freesurfer_analysis/subjects/grp147/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/research/freesurfer_analysis/subjects/grp147/mri/orig/001.mgz /mnt/research/freesurfer_analysis/subjects/grp147/mri/rawavg.mgz
/mnt/research/freesurfer_analysis/subjects/grp147
mri_convert /mnt/research/freesurfer_analysis/subjects/grp147/mri/rawavg.mgz /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig.mgz --conform
mri_convert.bin /mnt/research/freesurfer_analysis/subjects/grp147/mri/rawavg.mgz /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /mnt/research/freesurfer_analysis/subjects/grp147/mri/rawavg.mgz...
TR=7.60, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0168201, -0.999244, 0.0350365)
j_ras = (-0.0190707, 0.0353557, 0.999193)
k_ras = (0.999677, -0.0161384, 0.019651)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig.mgz...
mri_add_xform_to_header -c /mnt/research/freesurfer_analysis/subjects/grp147/mri/transforms/talairach.xfm /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig.mgz /mnt/research/freesurfer_analysis/subjects/grp147/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Mon Jun 19 21:28:18 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/mnt/research/freesurfer_analysis/subjects/grp147/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 rameshbabu 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Mon Jun 19 21:28:18 IST 2017
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.12570
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12570/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.12570/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=7.60, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1.89175e-09, -1)
k_ras = (0, 1, 2.32831e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.12570/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Jun 19 21:28:21 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.12570/nu0.mnc ./tmp.mri_nu_correct.mni.12570/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12570/0/ -iterations 1000 -distance 50
[rb@rameshbabu:/mnt/research/freesurfer_analysis/subjects/grp147/mri/] [2017-06-19 21:28:21] running:
/usr/local/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.12570/0/ ./tmp.mri_nu_correct.mni.12570/nu0.mnc ./tmp.mri_nu_correct.mni.12570/nu1.imp
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 38
CV of field change: 0.000987491
mri_convert ./tmp.mri_nu_correct.mni.12570/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.12570/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.12570/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1.89175e-09, -1)
k_ras = (0, 1, 2.32831e-10)
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 Jun 19 21:29:13 IST 2017
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 Jun 19 21:29:13 IST 2017
Ended at Mon Jun 19 21:29:53 IST 2017
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Mon Jun 19 21:29:55 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7497, pval=0.6675 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/research/freesurfer_analysis/subjects/grp147/mri/transforms/talairach_avi.log
tal_QC_AZS /mnt/research/freesurfer_analysis/subjects/grp147/mri/transforms/talairach_avi.log
TalAviQA: 0.98083
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Mon Jun 19 21:29:55 IST 2017
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/mnt/research/freesurfer_analysis/subjects/grp147/mri
/usr/local/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 rameshbabu 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Mon Jun 19 21:29:55 IST 2017
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.15714
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15714/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.15714/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=7.60, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1.89175e-09, -1)
k_ras = (0, 1, 2.32831e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.15714/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Jun 19 21:29:59 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.15714/nu0.mnc ./tmp.mri_nu_correct.mni.15714/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15714/0/
[rb@rameshbabu:/mnt/research/freesurfer_analysis/subjects/grp147/mri/] [2017-06-19 21:29:59] running:
/usr/local/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.15714/0/ ./tmp.mri_nu_correct.mni.15714/nu0.mnc ./tmp.mri_nu_correct.mni.15714/nu1.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
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 20
CV of field change: 0.000992765
--------------------------------------------------------
Iteration 2 Mon Jun 19 21:30:29 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.15714/nu1.mnc ./tmp.mri_nu_correct.mni.15714/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.15714/1/
[rb@rameshbabu:/mnt/research/freesurfer_analysis/subjects/grp147/mri/] [2017-06-19 21:30:29] running:
/usr/local/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.15714/1/ ./tmp.mri_nu_correct.mni.15714/nu1.mnc ./tmp.mri_nu_correct.mni.15714/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 9
CV of field change: 0.000937496
mri_binarize --i ./tmp.mri_nu_correct.mni.15714/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15714/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /mnt/research/freesurfer_analysis/subjects/grp147/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.15714/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15714/ones.mgz
sysname Linux
hostname rameshbabu
machine x86_64
user rb
input ./tmp.mri_nu_correct.mni.15714/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.15714/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.15714/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15714/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15714/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.15714/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15714/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15714/input.mean.dat
sysname Linux
hostname rameshbabu
machine x86_64
user rb
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.15714/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.15714/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15714/ones.mgz --i ./tmp.mri_nu_correct.mni.15714/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15714/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15714/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.15714/ones.mgz --i ./tmp.mri_nu_correct.mni.15714/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15714/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15714/output.mean.dat
sysname Linux
hostname rameshbabu
machine x86_64
user rb
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.15714/ones.mgz
Loading ./tmp.mri_nu_correct.mni.15714/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.15714/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.15714/nu2.mnc ./tmp.mri_nu_correct.mni.15714/nu2.mnc mul 1.00976250205648035940
Saving result to './tmp.mri_nu_correct.mni.15714/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.15714/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.15714/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.15714/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1.89175e-09, -1)
k_ras = (0, 1, 2.32831e-10)
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 11 seconds.
mapping (10, 139) to ( 3, 110)
Mon Jun 19 21:31:41 IST 2017
mri_nu_correct.mni done
mri_add_xform_to_header -c /mnt/research/freesurfer_analysis/subjects/grp147/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Mon Jun 19 21:31:43 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/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
1.13116 -0.01427 0.01185 -0.44182;
0.04309 1.12108 0.04463 3.45891;
-0.03138 -0.01615 1.15017 -1.70882;
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 = 18
Starting OpenSpline(): npoints = 18
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 110
gm peak at 63 (63), valley at 31 (31)
csf peak at 32, setting threshold to 52
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 63 (63), valley at 31 (31)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 50 seconds.
#--------------------------------------------
#@# Skull Stripping Mon Jun 19 21:33:35 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_em_register_cuda -rusage /mnt/research/freesurfer_analysis/subjects/grp147/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221
Driver : 8.0
Runtime : 5.0
Acquiring CUDA device
Using default device
CUDA device: GeForce GT 610
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register_cuda for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/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=11.0
skull bounding box = (53, 42, 28) --> (200, 255, 206)
using (102, 113, 117) as brain centroid...
mean wm in atlas = 108, using box (84,87,95) --> (120, 139,138) to find MRI wm
before smoothing, mri peak at 109
robust fit to distribution - 109 +- 4.7
after smoothing, mri peak at 109, scaling input intensities by 0.991
scaling channel 0 by 0.990826
initial log_p = -14186.640
************************************************
First Search limited to translation only.
************************************************
max log p = -14174.203125 @ (0.000, 0.000, 0.000)
max log p = -14089.933594 @ (-4.545, -4.545, -4.545)
max log p = -13988.749023 @ (2.273, 2.273, 2.273)
max log p = -13902.438477 @ (-1.136, -1.136, 1.136)
max log p = -13902.438477 @ (0.000, 0.000, 0.000)
max log p = -13902.438477 @ (0.000, 0.000, 0.000)
Found translation: (-3.4, -3.4, -1.1): log p = -4.287
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 1.000: max_log_p=-12385.551, old_max_log_p =-4.287 (thresh=-4.3)
1.15000 0.00000 0.00000 -22.65174;
0.00000 1.22567 0.16136 -46.84568;
0.00000 -0.15011 1.14016 -2.49001;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 1 nscales = 1 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.250: max_log_p=-12087.449, old_max_log_p =-12385.551 (thresh=-12373.2)
1.10569 0.03655 0.04027 -26.77888;
-0.03552 1.16383 0.08040 -26.05353;
-0.03622 -0.06958 1.14766 -9.89652;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.250: max_log_p=-12087.449, old_max_log_p =-12087.449 (thresh=-12075.4)
1.10569 0.03655 0.04027 -26.77888;
-0.03552 1.16383 0.08040 -26.05353;
-0.03622 -0.06958 1.14766 -9.89652;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 3 nscales = 2 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.062: max_log_p=-12038.618, old_max_log_p =-12087.449 (thresh=-12075.4)
1.10916 0.01803 0.02080 -23.26810;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.062: max_log_p=-12035.316, old_max_log_p =-12038.618 (thresh=-12026.6)
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3243 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
nsamples 3243
Quasinewton: input matrix
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.711 (old=-4.375)
transform before final EM align:
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 364799 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
nsamples 364799
Quasinewton: input matrix
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 009: -log(p) = 4.1 tol 0.000000
final transform:
1.11176 0.01807 0.02085 -23.61532;
-0.01625 1.16867 0.04325 -24.82607;
-0.01919 -0.03076 1.14614 -16.41191;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec 618.024000
mri_em_register stimesec 419.040000
mri_em_register ru_maxrss 704616
mri_em_register ru_ixrss 0
mri_em_register ru_idrss 0
mri_em_register ru_isrss 0
mri_em_register ru_minflt 198122
mri_em_register ru_majflt 0
mri_em_register ru_nswap 0
mri_em_register ru_inblock 0
mri_em_register ru_oublock 16
mri_em_register ru_msgsnd 0
mri_em_register ru_msgrcv 0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw 3688426
mri_em_register ru_nivcsw 44119
registration took 28 minutes and 7 seconds.
mri_watershed -rusage /mnt/research/freesurfer_analysis/subjects/grp147/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=130 y=119 z=117 r=82
first estimation of the main basin volume: 2395721 voxels
Looking for seedpoints
2 found in the cerebellum
16 found in the rest of the brain
global maximum in x=104, y=115, z=77, Imax=255
CSF=17, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done.
Analyze...
main basin size=701210639 voxels, voxel volume =1.000
= 701210639 mmm3 = 701210.624 cm3
done.
PostAnalyze...Basin Prior
9 basins merged thanks to atlas
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=129,y=120, z=111, r=8849 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 44972
RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1035887414
LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = -1044146837
RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = -1097714118
LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1076581690
OTHER CSF_MIN=0, CSF_intensity=17, CSF_MAX=50 , nb = 1073126114
Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX TRANSITION GM_MIN GM
GLOBAL
before analyzing : 23, 24, 28, 61
after analyzing : 23, 26, 28, 34
RIGHT_CER
before analyzing : 26, 27, 29, 71
after analyzing : 26, 28, 29, 38
LEFT_CER
before analyzing : 21, 23, 28, 70
after analyzing : 21, 26, 28, 37
RIGHT_BRAIN
before analyzing : 21, 24, 30, 60
after analyzing : 21, 28, 30, 36
LEFT_BRAIN
before analyzing : 24, 26, 30, 61
after analyzing : 24, 28, 30, 36
OTHER
before analyzing : 50, 43, 42, 50
after analyzing : 36, 43, 43, 44
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...63 iterations
*********************VALIDATION*********************
curvature mean = -0.014, std = 0.012
curvature mean = 66.074, std = 6.541
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 4.02, sigma = 6.57
after rotation: sse = 4.02, sigma = 6.57
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 4.27, its var is 5.84
before Erosion-Dilatation 1.39% of inacurate vertices
after Erosion-Dilatation 0.00% of inacurate vertices
Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...46 iterations
mri_strip_skull: done peeling brain
Brain Size = 1432711 voxels, voxel volume = 1.000 mm3
= 1432711 mmm3 = 1432.711 cm3
******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec 21.120000
mri_watershed stimesec 0.248000
mri_watershed ru_maxrss 830632
mri_watershed ru_ixrss 0
mri_watershed ru_idrss 0
mri_watershed ru_isrss 0
mri_watershed ru_minflt 211068
mri_watershed ru_majflt 9
mri_watershed ru_nswap 0
mri_watershed ru_inblock 9688
mri_watershed ru_oublock 2256
mri_watershed ru_msgsnd 0
mri_watershed ru_msgrcv 0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw 43
mri_watershed ru_nivcsw 97
mri_watershed done
cp brainmask.auto.mgz brainmask.mgz
#-------------------------------------
#@# EM Registration Mon Jun 19 22:02:05 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_em_register_cuda -rusage /mnt/research/freesurfer_analysis/subjects/grp147/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221
Driver : 8.0
Runtime : 5.0
Acquiring CUDA device
Using default device
CUDA device: GeForce GT 610
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_em_register_cuda for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3 using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=27.0
skull bounding box = (67, 60, 39) --> (191, 169, 187)
using (108, 96, 113) as brain centroid...
mean wm in atlas = 107, using box (93,83,95) --> (123, 109,131) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.5
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
initial log_p = -10742.693
************************************************
First Search limited to translation only.
************************************************
max log p = -10729.835938 @ (0.000, 0.000, 0.000)
max log p = -10729.835938 @ (0.000, 0.000, 0.000)
max log p = -10686.592773 @ (-2.273, -2.273, -2.273)
max log p = -10560.941406 @ (-1.136, 1.136, 1.136)
max log p = -10560.941406 @ (0.000, 0.000, 0.000)
max log p = -10560.941406 @ (0.000, 0.000, 0.000)
Found translation: (-3.4, -1.1, -1.1): log p = -3.732
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 1.000: max_log_p=-9354.236, old_max_log_p =-3.732 (thresh=-3.7)
1.15000 0.00000 0.00000 -22.93101;
0.00000 1.15000 0.00000 -19.20032;
0.00000 0.00000 1.07500 -16.62992;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 1 nscales = 1 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.250: max_log_p=-9149.858, old_max_log_p =-9354.236 (thresh=-9344.9)
1.08554 0.00000 0.03322 -18.19363;
0.00000 1.19313 0.00000 -24.39371;
-0.03689 0.00000 1.05352 -5.57109;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.250: max_log_p=-9133.670, old_max_log_p =-9149.858 (thresh=-9140.7)
1.08554 0.00000 0.03322 -18.19363;
-0.00118 1.17013 0.03382 -25.18837;
-0.03757 -0.03977 1.07270 -2.80272;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.250: max_log_p=-9133.670, old_max_log_p =-9133.670 (thresh=-9124.5)
1.08554 0.00000 0.03322 -18.19363;
-0.00118 1.17013 0.03382 -25.18837;
-0.03757 -0.03977 1.07270 -2.80272;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.062: max_log_p=-9040.682, old_max_log_p =-9133.670 (thresh=-9124.5)
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
find_optimal_linear_xform: Starting reduction 0
find_optimal_linear_xform: Starting reduction 1
Result so far: scale 0.062: max_log_p=-9040.682, old_max_log_p =-9040.682 (thresh=-9031.6)
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
nsamples 2830
Quasinewton: input matrix
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.195 (old=-3.796)
transform before final EM align:
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 315557 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
nsamples 315557
Quasinewton: input matrix
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000
final transform:
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach.lta...
mri_em_register utimesec 536.520000
mri_em_register stimesec 431.968000
mri_em_register ru_maxrss 693944
mri_em_register ru_ixrss 0
mri_em_register ru_idrss 0
mri_em_register ru_isrss 0
mri_em_register ru_minflt 203983
mri_em_register ru_majflt 0
mri_em_register ru_nswap 0
mri_em_register ru_inblock 140152
mri_em_register ru_oublock 16
mri_em_register ru_msgsnd 0
mri_em_register ru_msgrcv 0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw 4315410
mri_em_register ru_nivcsw 44155
registration took 28 minutes and 11 seconds.
#--------------------------------------
#@# CA Normalize Mon Jun 19 22:30:16 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=28.0
skull bounding box = (67, 60, 39) --> (191, 169, 186)
using (108, 96, 113) as brain centroid...
mean wm in atlas = 107, using box (93,83,95) --> (123, 109,131) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.5
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
using 246344 sample points...
INFO: compute sample coordinates transform
1.08886 0.01905 0.04237 -21.92571;
-0.01833 1.17046 0.01572 -21.00750;
-0.04639 -0.02073 1.07029 -3.21303;
0.00000 0.00000 0.00000 1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 63, 36) --> (191, 166, 193)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
2 of 5817 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (70, 63, 35) --> (131, 165, 192)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 6160 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 137, 57) --> (176, 173, 108)
Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 125 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 137, 54) --> (131, 172, 108)
Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 219 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (114, 130, 89) --> (146, 190, 119)
Brain_Stem: limiting intensities to 89.0 --> 132.0
0 of 127 (0.0%) samples deleted
using 12448 total control points for intensity normalization...
bias field = 0.978 +- 0.043
105 of 12446 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 63, 36) --> (191, 166, 193)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
4 of 6282 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (70, 63, 35) --> (131, 165, 192)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
1 of 6595 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 137, 57) --> (176, 173, 108)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 233 (1.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 137, 54) --> (131, 172, 108)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
5 of 237 (2.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (114, 130, 89) --> (146, 190, 119)
Brain_Stem: limiting intensities to 88.0 --> 132.0
28 of 199 (14.1%) samples deleted
using 13546 total control points for intensity normalization...
bias field = 1.027 +- 0.037
61 of 13410 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 63, 36) --> (191, 166, 193)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
4 of 6323 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (70, 63, 35) --> (131, 165, 192)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
4 of 6486 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 137, 57) --> (176, 173, 108)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
43 of 252 (17.1%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 137, 54) --> (131, 172, 108)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
42 of 256 (16.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (114, 130, 89) --> (146, 190, 119)
Brain_Stem: limiting intensities to 88.0 --> 132.0
117 of 285 (41.1%) samples deleted
using 13602 total control points for intensity normalization...
bias field = 1.022 +- 0.033
40 of 13185 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 14 seconds.
#--------------------------------------
#@# CA Reg Mon Jun 19 22:31:30 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_ca_register_cuda -rusage /mnt/research/freesurfer_analysis/subjects/grp147/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221
Driver : 8.0
Runtime : 5.0
Acquiring CUDA device
Using default device
CUDA device: GeForce GT 610
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register_cuda for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.37 (predicted orig area = 5.9)
freeing gibbs priors...done.
average std[0] = 5.0
AllocateHost: Warning - not thread safe!
RecvAll: Did not reset gca in dst
GCAMcopyNodePositions: On GPU
RecvAll: Did not reset gca in dst
GCAMcopyNodePositions: On GPU
RecvAll: Did not reset gca in dst
GCAMcopyNodePositions: On GPU
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
GCAMcopyNodePositions: On GPU
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.812, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 10329.2 ms (avg) 10329.2 ms (tot)
0001: dt=129.472000, rms=0.718 (11.671%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 9496.29 ms (avg) 9496.29 ms (tot)
0002: dt=82.809158, rms=0.711 (0.967%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 12593.5 ms (avg) 12593.5 ms (tot)
0003: dt=272.084778, rms=0.696 (2.002%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 17423.7 ms (avg) 17423.7 ms (tot)
0004: dt=75.800003, rms=0.693 (0.530%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 17185.3 ms (avg) 17185.3 ms (tot)
0005: dt=517.888000, rms=0.680 (1.787%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 17153.8 ms (avg) 17153.8 ms (tot)
0006: dt=40.930233, rms=0.678 (0.362%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14904.4 ms (avg) 14904.4 ms (tot)
0007: dt=73.984001, rms=0.677 (0.094%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0008: dt=73.984001, rms=0.676 (0.198%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0009: dt=73.984001, rms=0.674 (0.277%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0010: dt=73.984001, rms=0.672 (0.297%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0011: dt=73.984001, rms=0.670 (0.328%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0012: dt=73.984001, rms=0.668 (0.339%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0013: dt=73.984001, rms=0.666 (0.283%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0014: dt=73.984001, rms=0.664 (0.211%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0015: dt=73.984001, rms=0.663 (0.207%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0016: dt=73.984001, rms=0.661 (0.227%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0017: dt=73.984001, rms=0.660 (0.209%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0018: dt=73.984001, rms=0.659 (0.187%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0019: dt=73.984001, rms=0.657 (0.206%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0020: dt=73.984001, rms=0.656 (0.164%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0021: dt=73.984001, rms=0.655 (0.148%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0022: dt=73.984001, rms=0.655 (0.128%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0023: dt=73.984001, rms=0.654 (0.108%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0024: dt=73.984001, rms=0.653 (0.102%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14950 ms (avg) 14950 ms (tot)
0025: dt=517.888000, rms=0.652 (0.122%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 15383.2 ms (avg) 15383.2 ms (tot)
0026: dt=55.488003, rms=0.652 (0.031%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0027: dt=55.488003, rms=0.652 (0.038%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0028: dt=55.488003, rms=0.652 (0.026%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0029: dt=55.488003, rms=0.652 (0.019%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
blurring input image with Gaussian with sigma=0.500...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.652, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14005.7 ms (avg) 14005.7 ms (tot)
0030: dt=129.472000, rms=0.651 (0.071%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14973.4 ms (avg) 14973.4 ms (tot)
0031: dt=295.936005, rms=0.650 (0.231%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14009.6 ms (avg) 14009.6 ms (tot)
0032: dt=32.368000, rms=0.649 (0.025%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0033: dt=32.368000, rms=0.649 (0.001%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0034: dt=32.368000, rms=0.649 (-0.024%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.653, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 15941.5 ms (avg) 15941.5 ms (tot)
0035: dt=192.000000, rms=0.642 (1.664%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 15800.7 ms (avg) 15800.7 ms (tot)
0036: dt=96.189346, rms=0.632 (1.560%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 11677.5 ms (avg) 11677.5 ms (tot)
0037: dt=18.133333, rms=0.630 (0.295%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 15770.5 ms (avg) 15770.5 ms (tot)
0038: dt=145.152008, rms=0.626 (0.568%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 16027.4 ms (avg) 16027.4 ms (tot)
0039: dt=74.039215, rms=0.621 (0.782%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 13804.7 ms (avg) 13804.7 ms (tot)
0040: dt=15.552000, rms=0.621 (0.108%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0041: dt=15.552000, rms=0.620 (0.080%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0042: dt=15.552000, rms=0.620 (0.106%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0043: dt=15.552000, rms=0.619 (0.154%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0044: dt=15.552000, rms=0.617 (0.227%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0045: dt=15.552000, rms=0.615 (0.292%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0046: dt=15.552000, rms=0.613 (0.323%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0047: dt=15.552000, rms=0.612 (0.313%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0048: dt=15.552000, rms=0.610 (0.303%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0049: dt=15.552000, rms=0.608 (0.270%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0050: dt=15.552000, rms=0.606 (0.277%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0051: dt=15.552000, rms=0.605 (0.294%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0052: dt=15.552000, rms=0.603 (0.308%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0053: dt=15.552000, rms=0.601 (0.288%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0054: dt=15.552000, rms=0.599 (0.259%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0055: dt=15.552000, rms=0.598 (0.245%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0056: dt=15.552000, rms=0.597 (0.216%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0057: dt=15.552000, rms=0.596 (0.187%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0058: dt=15.552000, rms=0.595 (0.173%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0059: dt=15.552000, rms=0.593 (0.178%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0060: dt=15.552000, rms=0.592 (0.169%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0061: dt=15.552000, rms=0.592 (0.158%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0062: dt=15.552000, rms=0.591 (0.135%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0063: dt=15.552000, rms=0.590 (0.115%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0064: dt=15.552000, rms=0.589 (0.099%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 16774.4 ms (avg) 16774.4 ms (tot)
0065: dt=82.944000, rms=0.589 (0.088%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0066: dt=82.944000, rms=0.589 (-0.412%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
blurring input image with Gaussian with sigma=0.500...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.589, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 15656.6 ms (avg) 15656.6 ms (tot)
0067: dt=20.736000, rms=0.589 (0.052%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 13105.4 ms (avg) 13105.4 ms (tot)
0068: dt=124.416000, rms=0.587 (0.199%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 15291.1 ms (avg) 15291.1 ms (tot)
0069: dt=36.288002, rms=0.587 (0.041%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0070: dt=36.288002, rms=0.587 (0.070%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0071: dt=36.288002, rms=0.586 (0.063%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0072: dt=36.288002, rms=0.586 (0.076%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0073: dt=36.288002, rms=0.586 (0.066%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.602, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 12954 ms (avg) 12954 ms (tot)
0074: dt=9.600000, rms=0.602 (0.103%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14679.6 ms (avg) 14679.6 ms (tot)
0075: dt=4.800000, rms=0.602 (0.021%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0076: dt=4.800000, rms=0.602 (0.001%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0077: dt=4.800000, rms=0.602 (-0.038%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
blurring input image with Gaussian with sigma=0.500...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.602, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 8877.44 ms (avg) 8877.44 ms (tot)
0078: dt=0.000000, rms=0.602 (0.000%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.644, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 13128.5 ms (avg) 13128.5 ms (tot)
0079: dt=4.911242, rms=0.636 (1.215%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 14981.2 ms (avg) 14981.2 ms (tot)
0080: dt=0.180000, rms=0.636 (0.001%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0081: dt=0.180000, rms=0.636 (-0.003%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
blurring input image with Gaussian with sigma=0.500...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.636, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 12880 ms (avg) 12880 ms (tot)
0082: dt=0.000000, rms=0.636 (0.000%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.693, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 9566.96 ms (avg) 9566.96 ms (tot)
0083: dt=0.865000, rms=0.690 (0.375%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 9152.18 ms (avg) 9152.18 ms (tot)
0084: dt=1.280000, rms=0.688 (0.303%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 8593.88 ms (avg) 8593.88 ms (tot)
0085: dt=1.024000, rms=0.687 (0.120%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0086: dt=1.024000, rms=0.687 (0.044%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0087: dt=1.024000, rms=0.687 (-0.106%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
blurring input image with Gaussian with sigma=0.500...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.687, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 7409.67 ms (avg) 7409.67 ms (tot)
0088: dt=1.024000, rms=0.686 (0.130%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 9843.75 ms (avg) 9843.75 ms (tot)
0089: dt=0.003000, rms=0.686 (-0.001%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
resetting metric properties...
GCAMcopyNodePositions: On GPU
RecvAll: Did not reset gca in dst
GCAMcopyNodePositions: On GPU
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
RecvAll: Did not reset gca in dst
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.638, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 9587.01 ms (avg) 9587.01 ms (tot)
0090: dt=0.448000, rms=0.622 (2.491%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 8481.07 ms (avg) 8481.07 ms (tot)
0091: dt=0.000000, rms=0.622 (0.009%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
0092: dt=0.050000, rms=0.622 (-0.353%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
blurring input image with Gaussian with sigma=0.500...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.622, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 12125 ms (avg) 12125 ms (tot)
0093: dt=-0.000018, rms=0.622 (0.000%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 8252.23 ms (avg) 8252.23 ms (tot)
0094: dt=0.000000, rms=0.622 (0.000%), neg=0, invalid=762
RecvAll: Did not reset gca in dst
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.10636 ( 5)
Left_Lateral_Ventricle (4): linear fit = 0.23 x + 0.0 (434 voxels, overlap=0.232)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (434 voxels, peak = 5), gca=8.0
gca peak = 0.15565 (16)
mri peak = 0.11903 ( 7)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (590 voxels, overlap=0.093)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (590 voxels, peak = 6), gca=6.4
gca peak = 0.26829 (96)
mri peak = 0.11380 (101)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (826 voxels, overlap=0.351)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (826 voxels, peak = 103), gca=103.2
gca peak = 0.20183 (93)
mri peak = 0.13793 (101)
Left_Pallidum (13): linear fit = 1.08 x + 0.0 (714 voxels, overlap=0.489)
Left_Pallidum (13): linear fit = 1.08 x + 0.0 (714 voxels, peak = 100), gca=100.0
gca peak = 0.21683 (55)
mri peak = 0.09324 (60)
Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (650 voxels, overlap=0.716)
Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (650 voxels, peak = 59), gca=59.1
gca peak = 0.30730 (58)
mri peak = 0.09602 (60)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (670 voxels, overlap=0.997)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (670 voxels, peak = 61), gca=60.6
gca peak = 0.11430 (101)
mri peak = 0.13375 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (57298 voxels, overlap=0.549)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (57298 voxels, peak = 106), gca=105.5
gca peak = 0.12076 (102)
mri peak = 0.14745 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (56410 voxels, overlap=0.587)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (56410 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.03159 (61)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19570 voxels, overlap=0.965)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19570 voxels, peak = 60), gca=60.5
gca peak = 0.15082 (58)
mri peak = 0.03285 (62)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21590 voxels, overlap=0.990)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21590 voxels, peak = 59), gca=59.4
gca peak = 0.14161 (67)
mri peak = 0.09323 (75)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (828 voxels, overlap=0.335)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (828 voxels, peak = 76), gca=76.0
gca peak = 0.15243 (71)
mri peak = 0.06897 (80)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (952 voxels, overlap=0.576)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (952 voxels, peak = 80), gca=79.9
gca peak = 0.13336 (57)
mri peak = 0.04049 (61)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (22541 voxels, overlap=0.745)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (22541 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.04800 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (23251 voxels, overlap=0.670)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (23251 voxels, peak = 62), gca=62.4
gca peak = 0.18181 (84)
mri peak = 0.09531 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8125 voxels, overlap=0.409)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8125 voxels, peak = 89), gca=89.5
gca peak = 0.20573 (83)
mri peak = 0.12991 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7128 voxels, overlap=0.322)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7128 voxels, peak = 89), gca=89.2
gca peak = 0.21969 (57)
mri peak = 0.09933 (56)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (370 voxels, overlap=0.989)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (370 voxels, peak = 58), gca=58.4
gca peak = 0.39313 (56)
mri peak = 0.11546 (63)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (515 voxels, overlap=0.792)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (515 voxels, peak = 59), gca=58.5
gca peak = 0.14181 (85)
mri peak = 0.05985 (92)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4784 voxels, overlap=0.764)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4784 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.05794 (92)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4026 voxels, overlap=0.723)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4026 voxels, peak = 90), gca=90.1
gca peak = 0.13399 (79)
mri peak = 0.05716 (87)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2187 voxels, overlap=0.785)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2187 voxels, peak = 87), gca=86.5
gca peak = 0.14159 (79)
mri peak = 0.05689 (87)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2286 voxels, overlap=0.664)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2286 voxels, peak = 87), gca=86.5
gca peak = 0.10025 (80)
mri peak = 0.08193 (88)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11001 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11001 voxels, peak = 88), gca=88.4
gca peak = 0.13281 (86)
mri peak = 0.11610 (99)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1115 voxels, overlap=0.112)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1115 voxels, peak = 96), gca=95.9
gca peak = 0.12801 (89)
mri peak = 0.09091 (95)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1331 voxels, overlap=0.389)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1331 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
mri peak = 1.00000 (39)
gca peak = 0.15061 (21)
mri peak = 0.08353 ( 5)
Fourth_Ventricle (15): linear fit = 0.52 x + 0.0 (222 voxels, overlap=0.255)
Fourth_Ventricle (15): linear fit = 0.52 x + 0.0 (222 voxels, peak = 11), gca=11.0
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.04 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
Right_Pallidum too bright - rescaling by 0.987 (from 1.075) to 101.9 (was 103.2)
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
GCAMregisterPipelineAndComputeRMS: On GPU
0000: dt=0.000, rms=0.638, neg=0, invalid=0
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 17597.1 ms (avg) 17597.1 ms (tot)
0095: dt=103.479790, rms=0.632 (0.949%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 20848.5 ms (avg) 20848.5 ms (tot)
0096: dt=92.480003, rms=0.631 (0.159%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 22945.1 ms (avg) 22945.1 ms (tot)
0097: dt=129.472000, rms=0.628 (0.332%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
FindOptimalTimestep: Complete in 21665.6 ms (avg) 21665.6 ms (tot)
0098: dt=32.368000, rms=0.628 (0.070%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution
PutOnGPU: Did not reset gca in dst
CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory.
Abort (core dumped)
ERROR: mri_ca_register with non-zero status 134
but continuing despite the error
#--------------------------------------
#@# SubCort Seg Mon Jun 19 22:55:37 IST 2017
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
sysname Linux
hostname rameshbabu
machine x86_64
setenv SUBJECTS_DIR /mnt/research/freesurfer_analysis/subjects
cd /mnt/research/freesurfer_analysis/subjects/grp147/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
== Number of threads available to mri_ca_label for OpenMP = 1 ==
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
reading 1 input volumes
reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
transforms/talairach.m3z: could not open transform
average std[0] = 7.3
reading transform from transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
No such file or directory
Linux rameshbabu 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s grp147 exited with ERRORS at Mon Jun 19 22:56:02 IST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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