Mon Feb 22 09:12:21 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014 /home/dgmh/Applications/freesurfer/bin/recon-all -i madanlalsethiya17072014_brain.nii.gz -s madanlalsethiya17072014 subjid madanlalsethiya17072014 setenv SUBJECTS_DIR /home/dgmh/Desktop/bet_recon FREESURFER_HOME /home/dgmh/Applications/freesurfer Actual FREESURFER_HOME /home/dgmh/Applications/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160211 Linux dgmh-HP-280-G1-MT 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 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 14571 maxlocks unlimited maxsignal 14571 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3971780 2069664 1902116 249760 126420 1024956 -/+ buffers/cache: 918288 3053492 Swap: 4117500 0 4117500 ######################################## program versions used $Id: recon-all,v 1.564 2016/02/11 20:24:09 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:22-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:22-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-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: $ TimeStamp: 2016/02/22-03:42:22-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:22-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:23-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:24-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:25-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-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 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:26-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:27-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:27-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:27-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:27-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:42:27-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/dgmh/Applications/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/dgmh/Applications/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014 mri_convert /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014_brain.nii.gz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig/001.mgz mri_convert /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014_brain.nii.gz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig/001.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014_brain.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999621, -0.0275273, 0) j_ras = (-0.0267342, 0.970428, 0.239906) k_ras = (0.00660396, -0.239815, 0.970796) writing to /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig/001.mgz... Started at Mon Feb 22 09:12:21 IST 2016 Ended at Mon Feb 22 09:12:28 IST 2016 #@#%# recon-all-run-time-hours 0.002 recon-all -s madanlalsethiya17072014 finished without error at Mon Feb 22 09:12:28 IST 2016 New invocation of recon-all Mon Feb 22 09:16:14 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014 /home/dgmh/Applications/freesurfer/bin/recon-all -autorecon1 -noskullstrip -s madanlalsethiya17072014 subjid madanlalsethiya17072014 setenv SUBJECTS_DIR /home/dgmh/Desktop/bet_recon FREESURFER_HOME /home/dgmh/Applications/freesurfer Actual FREESURFER_HOME /home/dgmh/Applications/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160211 Linux dgmh-HP-280-G1-MT 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 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 14571 maxlocks unlimited maxsignal 14571 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3971780 2243920 1727860 249932 126580 1191340 -/+ buffers/cache: 926000 3045780 Swap: 4117500 0 4117500 ######################################## program versions used $Id: recon-all,v 1.564 2016/02/11 20:24:09 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-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: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-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 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:46:14-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/dgmh/Applications/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/dgmh/Applications/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Feb 22 09:16:14 IST 2016 Found 1 runs /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/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/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig/001.mgz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/rawavg.mgz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014 mri_convert /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/rawavg.mgz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig.mgz --conform mri_convert /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/rawavg.mgz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999621, -0.0275273, 0) j_ras = (-0.0267342, 0.970428, 0.239906) k_ras = (0.00660396, -0.239815, 0.970796) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig.mgz... mri_add_xform_to_header -c /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/transforms/talairach.xfm /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig.mgz /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Feb 22 09:16:20 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri /home/dgmh/Applications/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 1.26 2016/02/11 20:24:09 nicks Exp $ Linux dgmh-HP-280-G1-MT 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Mon Feb 22 09:16:20 IST 2016 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.5210 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5210/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5210/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.14321e-09, 4.65661e-10) j_ras = (0, -1.49012e-08, -1) k_ras = (2.67755e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5210/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Feb 22 09:16:22 IST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.5210/nu0.mnc ./tmp.mri_nu_correct.mni.5210/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5210/0/ -iterations 1000 -distance 50 [dgmh@dgmh-HP-280-G1-MT:/home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/] [2016-02-22 09:16:22] running: /home/dgmh/Applications/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.5210/0/ ./tmp.mri_nu_correct.mni.5210/nu0.mnc ./tmp.mri_nu_correct.mni.5210/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000975184 mri_convert ./tmp.mri_nu_correct.mni.5210/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.5210/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.5210/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.14321e-09, 4.65661e-10) j_ras = (0, -1.49012e-08, -1) k_ras = (2.67755e-09, 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 Feb 22 09:16:55 IST 2016 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 Feb 22 09:16:56 IST 2016 Ended at Mon Feb 22 09:17:38 IST 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Feb 22 09:17:40 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5031, pval=0.1531 >= threshold=0.0050) awk -f /home/dgmh/Applications/freesurfer/bin/extract_talairach_avi_QA.awk /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/transforms/talairach_avi.log tal_QC_AZS /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/transforms/talairach_avi.log TalAviQA: 0.96117 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Mon Feb 22 09:17:40 IST 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri /home/dgmh/Applications/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 1.26 2016/02/11 20:24:09 nicks Exp $ Linux dgmh-HP-280-G1-MT 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Mon Feb 22 09:17:40 IST 2016 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.5800 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5800/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5800/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.14321e-09, 4.65661e-10) j_ras = (0, -1.49012e-08, -1) k_ras = (2.67755e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5800/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Feb 22 09:17:42 IST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.5800/nu0.mnc ./tmp.mri_nu_correct.mni.5800/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5800/0/ [dgmh@dgmh-HP-280-G1-MT:/home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/] [2016-02-22 09:17:42] running: /home/dgmh/Applications/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.5800/0/ ./tmp.mri_nu_correct.mni.5800/nu0.mnc ./tmp.mri_nu_correct.mni.5800/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 Number of iterations: 14 CV of field change: 0.000954732 -------------------------------------------------------- Iteration 2 Mon Feb 22 09:18:02 IST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.5800/nu1.mnc ./tmp.mri_nu_correct.mni.5800/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5800/1/ [dgmh@dgmh-HP-280-G1-MT:/home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/] [2016-02-22 09:18:02] running: /home/dgmh/Applications/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.5800/1/ ./tmp.mri_nu_correct.mni.5800/nu1.mnc ./tmp.mri_nu_correct.mni.5800/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 5 CV of field change: 0.00074581 mri_binarize --i ./tmp.mri_nu_correct.mni.5800/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5800/ones.mgz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.5800/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5800/ones.mgz sysname Linux hostname dgmh-HP-280-G1-MT machine x86_64 user dgmh input ./tmp.mri_nu_correct.mni.5800/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5800/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.5800/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5800/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5800/input.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5800/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5800/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5800/input.mean.dat sysname Linux hostname dgmh-HP-280-G1-MT machine x86_64 user dgmh UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5800/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.5800/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5800/ones.mgz --i ./tmp.mri_nu_correct.mni.5800/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5800/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5800/output.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5800/ones.mgz --i ./tmp.mri_nu_correct.mni.5800/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5800/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5800/output.mean.dat sysname Linux hostname dgmh-HP-280-G1-MT machine x86_64 user dgmh UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5800/ones.mgz Loading ./tmp.mri_nu_correct.mni.5800/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.5800/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5800/nu2.mnc ./tmp.mri_nu_correct.mni.5800/nu2.mnc mul .91435623880657881471 Saving result to './tmp.mri_nu_correct.mni.5800/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5800/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.5800/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.5800/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.14321e-09, 4.65661e-10) j_ras = (0, -1.49012e-08, -1) k_ras = (2.67755e-09, 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 5 seconds. mapping (43, 112) to ( 3, 110) Mon Feb 22 09:18:44 IST 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Feb 22 09:18:45 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.18354 0.04058 0.02805 -0.36301; -0.03641 1.24841 0.40788 -56.55572; -0.01350 -0.54375 1.12030 -100.96094; 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 104 gm peak at 78 (78), valley at 57 (57) csf peak at 40, setting threshold to 65 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 100 gm peak at 75 (75), valley at 38 (38) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 29 seconds. Started at Mon Feb 22 09:16:14 IST 2016 Ended at Mon Feb 22 09:20:14 IST 2016 #@#%# recon-all-run-time-hours 0.067 recon-all -s madanlalsethiya17072014 finished without error at Mon Feb 22 09:20:14 IST 2016 New invocation of recon-all Mon Feb 22 09:25:20 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014 /home/dgmh/Applications/freesurfer/bin/recon-all -autorecon2 -autorecon3 -s madanlalsethiya17072014 subjid madanlalsethiya17072014 setenv SUBJECTS_DIR /home/dgmh/Desktop/bet_recon FREESURFER_HOME /home/dgmh/Applications/freesurfer Actual FREESURFER_HOME /home/dgmh/Applications/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160211 Linux dgmh-HP-280-G1-MT 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 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 14571 maxlocks unlimited maxsignal 14571 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3971780 2455804 1515976 247804 127528 1381216 -/+ buffers/cache: 947060 3024720 Swap: 4117500 0 4117500 ######################################## program versions used $Id: recon-all,v 1.564 2016/02/11 20:24:09 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-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: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-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 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-03:55:20-GMT BuildTimeStamp: Feb 11 2016 21:03:11 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: dgmh Machine: dgmh-HP-280-G1-MT Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/dgmh/Applications/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/dgmh/Applications/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Mon Feb 22 09:25:20 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_em_register -rusage /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca'... average std = 7.4 using min determinant for regularization = 5.4 0 singular and 937 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.2 or > 452.2 total sample mean = 78.8 (1019 zeros) ************************************************ spacing=8, using 2854 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2854, passno 0, spacing 8 resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (60, 69, 58) --> (196, 201, 193) using (105, 113, 126) as brain centroid... mean wm in atlas = 105, using box (88,97,109) --> (121, 129,142) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 102 +- 6.5 after smoothing, mri peak at 102, scaling input intensities by 1.029 scaling channel 0 by 1.02941 initial log_p = -4.255 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.058184 @ (-9.091, -9.091, -27.273) max log p = -4.003685 @ (4.545, -4.545, 4.545) max log p = -3.951310 @ (2.273, 2.273, -2.273) max log p = -3.949046 @ (1.136, -1.136, 1.136) max log p = -3.922047 @ (2.841, 0.568, -3.977) max log p = -3.912603 @ (-1.989, -1.420, -0.284) Found translation: (-0.3, -13.4, -28.1): log p = -3.913 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.831, old_max_log_p =-3.913 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.28409; 0.00000 1.03837 0.27823 -48.40263; 0.00000 -0.25882 0.96593 18.59704; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.810, old_max_log_p =-3.831 (thresh=-3.8) 0.92500 0.00000 0.00000 9.31646; 0.00000 1.07038 0.43207 -71.82913; 0.00000 -0.42155 0.99045 44.02038; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.792, old_max_log_p =-3.810 (thresh=-3.8) 0.99438 0.00000 0.00000 0.43594; 0.00000 1.07038 0.43207 -71.82913; 0.00000 -0.38993 0.91616 48.69507; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.792, old_max_log_p =-3.792 (thresh=-3.8) 0.99438 0.00000 0.00000 0.43594; 0.00000 1.07038 0.43207 -71.82913; 0.00000 -0.38993 0.91616 48.69507; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.714, old_max_log_p =-3.792 (thresh=-3.8) 1.01248 -0.03434 -0.01386 2.41371; 0.03193 1.01038 0.40785 -65.13599; 0.00000 -0.41214 0.96834 43.53646; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.689, old_max_log_p =-3.714 (thresh=-3.7) 1.03146 -0.03498 -0.01412 0.06416; 0.03193 1.01038 0.40785 -65.13599; 0.00000 -0.41987 0.98650 42.35872; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.689, old_max_log_p =-3.689 (thresh=-3.7) 1.03146 -0.03498 -0.01412 0.06416; 0.03193 1.01038 0.40785 -65.13599; 0.00000 -0.41987 0.98650 42.35872; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.668, old_max_log_p =-3.689 (thresh=-3.7) 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.668, old_max_log_p =-3.668 (thresh=-3.7) 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2854 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; nsamples 2854 Quasinewton: input matrix 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.668 (old=-4.255) transform before final EM align: 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 314792 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; nsamples 314792 Quasinewton: input matrix 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.2 tol 0.000000 final transform: 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 886.092000 mri_em_register stimesec 0.900000 mri_em_register ru_maxrss 607492 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158740 mri_em_register ru_majflt 18 mri_em_register ru_nswap 0 mri_em_register ru_inblock 145736 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 55 mri_em_register ru_nivcsw 5988 registration took 14 minutes and 48 seconds. #-------------------------------------- #@# CA Normalize Mon Feb 22 09:40:08 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.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 '/home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (60, 69, 58) --> (196, 201, 193) using (105, 113, 126) as brain centroid... mean wm in atlas = 105, using box (88,97,109) --> (121, 129,142) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 102 +- 6.5 after smoothing, mri peak at 102, scaling input intensities by 1.029 scaling channel 0 by 1.02941 using 245868 sample points... INFO: compute sample coordinates transform 1.03044 -0.03004 -0.00271 -1.82755; 0.02340 1.01052 0.39836 -62.90235; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (129, 70, 50) --> (193, 182, 201) Left_Cerebral_White_Matter: limiting intensities to 101.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (66, 70, 51) --> (130, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 54 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (131, 157, 85) --> (178, 195, 134) Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 1 of 8 (12.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (87, 157, 83) --> (129, 195, 134) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 23 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (113, 140, 112) --> (147, 203, 142) Brain_Stem: limiting intensities to 104.0 --> 132.0 5 of 15 (33.3%) samples deleted using 116 total control points for intensity normalization... bias field = 0.885 +- 0.096 0 of 110 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (129, 70, 50) --> (193, 182, 201) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 112 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (66, 70, 51) --> (130, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 153 (1.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (131, 157, 85) --> (178, 195, 134) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 54 (22.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (87, 157, 83) --> (129, 195, 134) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 22 of 63 (34.9%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (113, 140, 112) --> (147, 203, 142) Brain_Stem: limiting intensities to 88.0 --> 132.0 34 of 60 (56.7%) samples deleted using 442 total control points for intensity normalization... bias field = 0.995 +- 0.069 4 of 372 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (129, 70, 50) --> (193, 182, 201) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 12 of 271 (4.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (66, 70, 51) --> (130, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 282 (2.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (131, 157, 85) --> (178, 195, 134) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 33 of 93 (35.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (87, 157, 83) --> (129, 195, 134) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 48 of 80 (60.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (113, 140, 112) --> (147, 203, 142) Brain_Stem: limiting intensities to 88.0 --> 132.0 86 of 117 (73.5%) samples deleted using 843 total control points for intensity normalization... bias field = 0.999 +- 0.071 0 of 656 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 Feb 22 09:41:22 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_ca_register -rusage /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca transforms/talairach.m3z 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 for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.20 (predicted orig area = 6.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.003, neg=0, invalid=3294 0001: dt=306.824297, rms=0.869 (13.341%), neg=0, invalid=3294 0002: dt=180.956863, rms=0.853 (1.773%), neg=0, invalid=3294 0003: dt=517.888000, rms=0.834 (2.288%), neg=0, invalid=3294 0004: dt=110.976000, rms=0.832 (0.274%), neg=0, invalid=3294 0005: dt=1183.744000, rms=0.823 (1.001%), neg=0, invalid=3294 0006: dt=155.789474, rms=0.819 (0.543%), neg=0, invalid=3294 0007: dt=517.888000, rms=0.815 (0.457%), neg=0, invalid=3294 0008: dt=92.480000, rms=0.814 (0.121%), neg=0, invalid=3294 0009: dt=92.480000, rms=0.814 (0.042%), neg=0, invalid=3294 0010: dt=92.480000, rms=0.813 (0.061%), neg=0, invalid=3294 0011: dt=92.480000, rms=0.812 (0.092%), neg=0, invalid=3294 0012: dt=92.480000, rms=0.811 (0.147%), neg=0, invalid=3294 0013: dt=92.480000, rms=0.810 (0.169%), neg=0, invalid=3294 0014: dt=92.480000, rms=0.809 (0.171%), neg=0, invalid=3294 0015: dt=92.480000, rms=0.807 (0.142%), neg=0, invalid=3294 0016: dt=92.480000, rms=0.806 (0.139%), neg=0, invalid=3294 0017: dt=92.480000, rms=0.805 (0.143%), neg=0, invalid=3294 0018: dt=92.480000, rms=0.804 (0.179%), neg=0, invalid=3294 0019: dt=92.480000, rms=0.802 (0.157%), neg=0, invalid=3294 0020: dt=92.480000, rms=0.802 (0.104%), neg=0, invalid=3294 0021: dt=92.480000, rms=0.801 (0.074%), neg=0, invalid=3294 0022: dt=443.904000, rms=0.800 (0.097%), neg=0, invalid=3294 0023: dt=443.904000, rms=0.798 (0.311%), neg=0, invalid=3294 0024: dt=0.000000, rms=0.798 (0.009%), neg=0, invalid=3294 0025: dt=0.850000, rms=0.798 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.798, neg=0, invalid=3294 0026: dt=188.121212, rms=0.790 (1.025%), neg=0, invalid=3294 0027: dt=110.976000, rms=0.790 (0.051%), neg=0, invalid=3294 0028: dt=110.976000, rms=0.789 (0.069%), neg=0, invalid=3294 0029: dt=110.976000, rms=0.788 (0.105%), neg=0, invalid=3294 0030: dt=110.976000, rms=0.788 (0.122%), neg=0, invalid=3294 0031: dt=110.976000, rms=0.787 (0.127%), neg=0, invalid=3294 0032: dt=110.976000, rms=0.786 (0.113%), neg=0, invalid=3294 0033: dt=110.976000, rms=0.785 (0.121%), neg=0, invalid=3294 0034: dt=110.976000, rms=0.783 (0.165%), neg=0, invalid=3294 0035: dt=110.976000, rms=0.782 (0.165%), neg=0, invalid=3294 0036: dt=110.976000, rms=0.781 (0.150%), neg=0, invalid=3294 0037: dt=110.976000, rms=0.780 (0.132%), neg=0, invalid=3294 0038: dt=110.976000, rms=0.779 (0.118%), neg=0, invalid=3294 0039: dt=110.976000, rms=0.778 (0.106%), neg=0, invalid=3294 0040: dt=517.888000, rms=0.777 (0.094%), neg=0, invalid=3294 0041: dt=517.888000, rms=0.777 (0.008%), neg=0, invalid=3294 0042: dt=517.888000, rms=0.777 (0.097%), neg=0, invalid=3294 0043: dt=517.888000, rms=0.777 (-0.212%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.786, neg=0, invalid=3294 0044: dt=9.072000, rms=0.785 (0.175%), neg=0, invalid=3294 0045: dt=16.941176, rms=0.784 (0.066%), neg=0, invalid=3294 0046: dt=16.941176, rms=0.783 (0.084%), neg=0, invalid=3294 0047: dt=16.941176, rms=0.782 (0.126%), neg=0, invalid=3294 0048: dt=16.941176, rms=0.781 (0.161%), neg=0, invalid=3294 0049: dt=16.941176, rms=0.778 (0.343%), neg=0, invalid=3294 0050: dt=16.941176, rms=0.773 (0.666%), neg=0, invalid=3294 0051: dt=16.941176, rms=0.766 (0.973%), neg=0, invalid=3294 0052: dt=16.941176, rms=0.758 (1.013%), neg=0, invalid=3294 0053: dt=16.941176, rms=0.753 (0.665%), neg=0, invalid=3294 0054: dt=16.941176, rms=0.753 (-0.041%), neg=0, invalid=3294 0055: dt=2.268000, rms=0.753 (0.001%), neg=0, invalid=3294 0056: dt=2.268000, rms=0.753 (-0.010%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.754, neg=0, invalid=3294 0057: dt=89.906683, rms=0.745 (1.104%), neg=0, invalid=3294 0058: dt=67.368421, rms=0.741 (0.600%), neg=0, invalid=3294 0059: dt=54.557377, rms=0.739 (0.316%), neg=0, invalid=3294 0060: dt=36.288000, rms=0.738 (0.160%), neg=0, invalid=3294 0061: dt=36.288000, rms=0.736 (0.160%), neg=0, invalid=3294 0062: dt=36.288000, rms=0.735 (0.216%), neg=0, invalid=3294 0063: dt=36.288000, rms=0.733 (0.249%), neg=0, invalid=3294 0064: dt=36.288000, rms=0.731 (0.272%), neg=0, invalid=3294 0065: dt=36.288000, rms=0.729 (0.302%), neg=0, invalid=3294 0066: dt=36.288000, rms=0.726 (0.307%), neg=0, invalid=3294 0067: dt=36.288000, rms=0.724 (0.301%), neg=0, invalid=3294 0068: dt=36.288000, rms=0.723 (0.244%), neg=0, invalid=3294 0069: dt=36.288000, rms=0.721 (0.277%), neg=0, invalid=3294 0070: dt=36.288000, rms=0.718 (0.314%), neg=0, invalid=3294 0071: dt=36.288000, rms=0.716 (0.306%), neg=0, invalid=3294 0072: dt=36.288000, rms=0.714 (0.240%), neg=0, invalid=3294 0073: dt=36.288000, rms=0.713 (0.251%), neg=0, invalid=3294 0074: dt=36.288000, rms=0.711 (0.271%), neg=0, invalid=3294 0075: dt=36.288000, rms=0.710 (0.041%), neg=0, invalid=3294 0076: dt=36.288000, rms=0.710 (0.024%), neg=0, invalid=3294 0077: dt=7.776000, rms=0.710 (0.004%), neg=0, invalid=3294 0078: dt=0.486000, rms=0.710 (0.001%), neg=0, invalid=3294 0079: dt=0.121500, rms=0.710 (0.001%), neg=0, invalid=3294 0080: dt=0.030375, rms=0.710 (0.000%), neg=0, invalid=3294 0081: dt=0.015187, rms=0.710 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.742, neg=0, invalid=3294 0082: dt=0.031250, rms=0.741 (0.115%), neg=0, invalid=3294 0083: dt=0.002734, rms=0.741 (0.000%), neg=0, invalid=3294 0084: dt=0.001367, rms=0.741 (0.000%), neg=0, invalid=3294 0085: dt=0.000684, rms=0.741 (0.000%), neg=0, invalid=3294 0086: dt=0.000342, rms=0.741 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.742, neg=0, invalid=3294 0087: dt=0.000000, rms=0.741 (0.114%), neg=0, invalid=3294 0088: dt=0.000000, rms=0.741 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.835, neg=0, invalid=3294 0089: dt=6.912000, rms=0.804 (3.806%), neg=0, invalid=3294 0090: dt=7.483296, rms=0.797 (0.831%), neg=0, invalid=3294 0091: dt=2.357143, rms=0.797 (0.030%), neg=0, invalid=3294 0092: dt=2.357143, rms=0.797 (0.021%), neg=0, invalid=3294 0093: dt=2.357143, rms=0.797 (-0.017%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.797, neg=0, invalid=3294 0094: dt=0.000000, rms=0.797 (0.085%), neg=0, invalid=3294 0095: dt=0.000000, rms=0.797 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.871, neg=0, invalid=3294 0096: dt=0.000000, rms=0.870 (0.071%), neg=0, invalid=3294 0097: dt=0.000000, rms=0.870 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.871, neg=0, invalid=3294 0098: dt=0.000060, rms=0.870 (0.071%), neg=0, invalid=3294 0099: dt=0.000000, rms=0.870 (-0.000%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.744, neg=0, invalid=3294 0100: dt=1.009777, rms=0.719 (3.343%), neg=0, invalid=3294 0101: dt=0.096000, rms=0.718 (0.198%), neg=0, invalid=3294 0102: dt=0.096000, rms=0.718 (-0.082%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=3294 0103: dt=0.028000, rms=0.718 (0.135%), neg=0, invalid=3294 0104: dt=0.020000, rms=0.718 (0.002%), neg=0, invalid=3294 0105: dt=0.020000, rms=0.718 (-0.005%), neg=0, invalid=3294 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12974 (17) mri peak = 0.05435 (20) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (1690 voxels, overlap=0.831) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (1690 voxels, peak = 19), gca=18.6 gca peak = 0.13808 (16) mri peak = 0.06326 (21) Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1115 voxels, overlap=0.950) Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1115 voxels, peak = 20), gca=19.9 gca peak = 0.25042 (96) mri peak = 0.08505 (96) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (750 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (750 voxels, peak = 100), gca=100.3 gca peak = 0.22986 (96) mri peak = 0.09410 (97) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (712 voxels, overlap=0.992) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (712 voxels, peak = 100), gca=100.3 gca peak = 0.21624 (56) mri peak = 0.10427 (89) Right_Hippocampus (53): linear fit = 1.43 x + 0.0 (628 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.43 x + 0.0 (628 voxels, peak = 80), gca=80.4 gca peak = 0.29672 (58) mri peak = 0.07323 (88) Left_Hippocampus (17): linear fit = 1.40 x + 0.0 (520 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.40 x + 0.0 (520 voxels, peak = 81), gca=81.5 gca peak = 0.11066 (101) mri peak = 0.06782 (100) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (61310 voxels, overlap=0.961) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (61310 voxels, peak = 103), gca=102.5 gca peak = 0.10944 (101) mri peak = 0.06700 (100) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (60664 voxels, overlap=0.956) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (60664 voxels, peak = 104), gca=103.5 gca peak = 0.14864 (59) mri peak = 0.04543 (91) Left_Cerebral_Cortex (3): linear fit = 1.50 x + 0.0 (25395 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.50 x + 0.0 (25395 voxels, peak = 88), gca=88.2 gca peak = 0.16234 (58) mri peak = 0.04772 (91) Right_Cerebral_Cortex (42): linear fit = 1.50 x + 0.0 (29332 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.50 x + 0.0 (29332 voxels, peak = 87), gca=87.3 gca peak = 0.14764 (67) mri peak = 0.07453 (91) Right_Caudate (50): linear fit = 1.40 x + 0.0 (572 voxels, overlap=0.027) Right_Caudate (50): linear fit = 1.40 x + 0.0 (572 voxels, peak = 94), gca=94.1 gca peak = 0.15152 (71) mri peak = 0.08160 (91) Left_Caudate (11): linear fit = 1.21 x + 0.0 (797 voxels, overlap=0.026) Left_Caudate (11): linear fit = 1.21 x + 0.0 (797 voxels, peak = 86), gca=85.6 gca peak = 0.12476 (59) mri peak = 0.04149 (92) Left_Cerebellum_Cortex (8): linear fit = 1.58 x + 0.0 (17077 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.58 x + 0.0 (17077 voxels, peak = 93), gca=92.9 gca peak = 0.13886 (58) mri peak = 0.05089 (93) Right_Cerebellum_Cortex (47): linear fit = 1.57 x + 0.0 (20572 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.57 x + 0.0 (20572 voxels, peak = 91), gca=90.8 gca peak = 0.19332 (88) mri peak = 0.05577 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7180 voxels, overlap=0.757) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7180 voxels, peak = 95), gca=94.6 gca peak = 0.19182 (87) mri peak = 0.05201 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5661 voxels, overlap=0.898) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5661 voxels, peak = 91), gca=90.9 gca peak = 0.19349 (58) mri peak = 0.09482 (86) Left_Amygdala (18): linear fit = 1.47 x + 0.0 (253 voxels, overlap=0.066) Left_Amygdala (18): linear fit = 1.47 x + 0.0 (253 voxels, peak = 85), gca=85.0 gca peak = 0.32581 (57) mri peak = 0.11681 (82) Right_Amygdala (54): linear fit = 1.41 x + 0.0 (334 voxels, overlap=0.056) Right_Amygdala (54): linear fit = 1.41 x + 0.0 (334 voxels, peak = 81), gca=80.7 gca peak = 0.09144 (86) mri peak = 0.07386 (89) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3879 voxels, overlap=0.812) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3879 voxels, peak = 89), gca=89.0 gca peak = 0.10273 (84) mri peak = 0.07536 (90) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3323 voxels, overlap=0.534) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3323 voxels, peak = 90), gca=90.3 gca peak = 0.13860 (78) mri peak = 0.06630 (99) Left_Putamen (12): linear fit = 1.27 x + 0.0 (2187 voxels, overlap=0.015) Left_Putamen (12): linear fit = 1.27 x + 0.0 (2187 voxels, peak = 99), gca=99.4 gca peak = 0.12691 (78) mri peak = 0.07713 (101) Right_Putamen (51): linear fit = 1.30 x + 0.0 (1963 voxels, overlap=0.017) Right_Putamen (51): linear fit = 1.30 x + 0.0 (1963 voxels, peak = 102), gca=101.8 gca peak = 0.11764 (82) mri peak = 0.08712 (81) Brain_Stem (16): linear fit = 1.05 x + 0.0 (8142 voxels, overlap=0.629) Brain_Stem (16): linear fit = 1.05 x + 0.0 (8142 voxels, peak = 87), gca=86.5 gca peak = 0.10015 (86) mri peak = 0.06818 (100) Right_VentralDC (60): linear fit = 1.20 x + 0.0 (797 voxels, overlap=0.075) Right_VentralDC (60): linear fit = 1.20 x + 0.0 (797 voxels, peak = 103), gca=102.8 gca peak = 0.11151 (90) mri peak = 0.05855 (102) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1151 voxels, overlap=0.226) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1151 voxels, peak = 103), gca=103.0 gca peak = 0.19608 (23) mri peak = 0.03228 (15) gca peak = 0.13512 (19) mri peak = 0.07495 (19) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (484 voxels, overlap=0.905) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (484 voxels, peak = 18), gca=17.6 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.12743 (29) gca peak Left_Cerebellum_Cortex = 0.12476 (59) gca peak Left_Thalamus = 0.71074 (95) gca peak Third_Ventricle = 0.19608 (23) gca peak CSF = 0.17789 (37) gca peak Left_Accumbens_area = 0.50032 (62) gca peak Left_undetermined = 0.97690 (28) gca peak Left_vessel = 0.36001 (53) gca peak Left_choroid_plexus = 0.12300 (45) gca peak Right_Cerebral_Cortex = 0.16234 (58) gca peak Right_Inf_Lat_Vent = 0.21149 (25) gca peak Right_Cerebellum_Cortex = 0.13886 (58) gca peak Right_Accumbens_area = 0.31737 (65) gca peak Right_vessel = 0.50186 (52) gca peak Right_choroid_plexus = 0.10991 (44) gca peak Fifth_Ventricle = 0.55462 (35) gca peak WM_hypointensities = 0.10555 (76) gca peak non_WM_hypointensities = 0.08508 (48) gca peak Optic_Chiasm = 0.30852 (73) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 1.50 x + 0: 88 estimating mean gm scale to be 1.45 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.09 x + 0.0 setting left cbm cortex = 1.45 x + 0.00 setting right cbm cortex = 1.45 x + 0.00 Left_Putamen too bright - rescaling by 0.932 (from 1.275) to 92.7 (was 99.4) Left_Pallidum too bright - rescaling by 0.996 (from 1.045) to 99.9 (was 100.3) Right_Putamen too bright - rescaling by 0.911 (from 1.305) to 92.7 (was 101.8) Right_Pallidum too bright - rescaling by 0.996 (from 1.045) to 99.9 (was 100.3) saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.747, neg=0, invalid=3294 0106: dt=90.259359, rms=0.681 (8.839%), neg=0, invalid=3294 0107: dt=184.754717, rms=0.667 (2.107%), neg=0, invalid=3294 0108: dt=129.472000, rms=0.664 (0.461%), neg=0, invalid=3294 0109: dt=369.920000, rms=0.659 (0.647%), neg=0, invalid=3294 0110: dt=73.984000, rms=0.658 (0.151%), neg=0, invalid=3294 0111: dt=73.984000, rms=0.658 (0.064%), neg=0, invalid=3294 0112: dt=73.984000, rms=0.657 (0.106%), neg=0, invalid=3294 0113: dt=73.984000, rms=0.656 (0.156%), neg=0, invalid=3294 0114: dt=73.984000, rms=0.655 (0.185%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0115: dt=73.984000, rms=0.654 (0.188%), neg=0, invalid=3294 0116: dt=73.984000, rms=0.653 (0.168%), neg=0, invalid=3294 0117: dt=73.984000, rms=0.652 (0.162%), neg=0, invalid=3294 0118: dt=73.984000, rms=0.651 (0.138%), neg=0, invalid=3294 0119: dt=73.984000, rms=0.650 (0.170%), neg=0, invalid=3294 0120: dt=73.984000, rms=0.648 (0.177%), neg=0, invalid=3294 0121: dt=73.984000, rms=0.647 (0.189%), neg=0, invalid=3294 0122: dt=73.984000, rms=0.646 (0.186%), neg=0, invalid=3294 0123: dt=73.984000, rms=0.645 (0.165%), neg=0, invalid=3294 0124: dt=73.984000, rms=0.644 (0.143%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0125: dt=73.984000, rms=0.643 (0.146%), neg=0, invalid=3294 0126: dt=73.984000, rms=0.642 (0.147%), neg=0, invalid=3294 0127: dt=73.984000, rms=0.641 (0.142%), neg=0, invalid=3294 0128: dt=73.984000, rms=0.640 (0.135%), neg=0, invalid=3294 0129: dt=73.984000, rms=0.640 (0.123%), neg=0, invalid=3294 0130: dt=73.984000, rms=0.639 (0.105%), neg=0, invalid=3294 0131: dt=443.904000, rms=0.639 (0.026%), neg=0, invalid=3294 0132: dt=443.904000, rms=0.637 (0.202%), neg=0, invalid=3294 0133: dt=443.904000, rms=0.637 (-0.751%), neg=0, invalid=3294 0134: dt=23.120000, rms=0.637 (0.004%), neg=0, invalid=3294 0135: dt=5.780000, rms=0.637 (0.001%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=3294 0136: dt=92.480000, rms=0.637 (0.132%), neg=0, invalid=3294 0137: dt=443.904000, rms=0.636 (0.167%), neg=0, invalid=3294 0138: dt=369.920000, rms=0.634 (0.220%), neg=0, invalid=3294 0139: dt=32.368000, rms=0.634 (0.010%), neg=0, invalid=3294 0140: dt=32.368000, rms=0.634 (0.014%), neg=0, invalid=3294 0141: dt=32.368000, rms=0.634 (-0.008%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=3294 0142: dt=161.581749, rms=0.630 (1.087%), neg=0, invalid=3294 0143: dt=134.813688, rms=0.621 (1.372%), neg=0, invalid=3294 0144: dt=41.813333, rms=0.619 (0.325%), neg=0, invalid=3294 0145: dt=145.152000, rms=0.616 (0.431%), neg=0, invalid=3294 0146: dt=101.600000, rms=0.615 (0.299%), neg=0, invalid=3294 0147: dt=66.577933, rms=0.613 (0.323%), neg=0, invalid=3294 0148: dt=36.288000, rms=0.612 (0.095%), neg=0, invalid=3294 0149: dt=36.288000, rms=0.611 (0.087%), neg=0, invalid=3294 0150: dt=36.288000, rms=0.611 (0.153%), neg=0, invalid=3294 0151: dt=36.288000, rms=0.609 (0.194%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0152: dt=36.288000, rms=0.608 (0.214%), neg=0, invalid=3294 0153: dt=36.288000, rms=0.606 (0.273%), neg=0, invalid=3294 0154: dt=36.288000, rms=0.605 (0.263%), neg=0, invalid=3294 0155: dt=36.288000, rms=0.603 (0.237%), neg=0, invalid=3294 0156: dt=36.288000, rms=0.602 (0.221%), neg=0, invalid=3294 0157: dt=36.288000, rms=0.601 (0.193%), neg=0, invalid=3294 0158: dt=36.288000, rms=0.600 (0.161%), neg=0, invalid=3294 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0159: dt=36.288000, rms=0.599 (0.134%), neg=0, invalid=3294 0160: dt=36.288000, rms=0.598 (0.126%), neg=0, invalid=3294 0161: dt=36.288000, rms=0.598 (0.114%), neg=0, invalid=3294 0162: dt=36.288000, rms=0.597 (0.090%), neg=0, invalid=3294 0163: dt=103.680000, rms=0.597 (0.018%), neg=0, invalid=3294 0164: dt=103.680000, rms=0.597 (0.041%), neg=0, invalid=3294 0165: dt=103.680000, rms=0.597 (-0.009%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=3294 0166: dt=92.878049, rms=0.595 (0.332%), neg=0, invalid=3294 0167: dt=82.944000, rms=0.594 (0.154%), neg=0, invalid=3294 0168: dt=82.944000, rms=0.594 (-0.029%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.607, neg=0, invalid=3294 0169: dt=11.200000, rms=0.605 (0.343%), neg=0, invalid=3294 0170: dt=19.200000, rms=0.604 (0.176%), neg=0, invalid=3294 0171: dt=19.200000, rms=0.603 (0.193%), neg=0, invalid=3294 0172: dt=19.200000, rms=0.602 (0.194%), neg=0, invalid=3294 0173: dt=19.200000, rms=0.601 (0.174%), neg=0, invalid=3294 0174: dt=19.200000, rms=0.599 (0.271%), neg=0, invalid=3294 0175: dt=19.200000, rms=0.596 (0.489%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0176: dt=19.200000, rms=0.592 (0.654%), neg=0, invalid=3294 0177: dt=19.200000, rms=0.589 (0.611%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0178: dt=19.200000, rms=0.586 (0.403%), neg=0, invalid=3294 0179: dt=19.200000, rms=0.586 (0.152%), neg=0, invalid=3294 0180: dt=19.200000, rms=0.586 (-0.058%), neg=0, invalid=3294 0181: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.586, neg=0, invalid=3294 0182: dt=11.200000, rms=0.585 (0.120%), neg=0, invalid=3294 0183: dt=0.002734, rms=0.585 (0.000%), neg=0, invalid=3294 0184: dt=0.002734, rms=0.585 (-0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.609, neg=0, invalid=3294 0185: dt=0.000000, rms=0.609 (0.056%), neg=0, invalid=3294 0186: dt=0.000000, rms=0.609 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=3294 0187: dt=0.000000, rms=0.609 (0.056%), neg=0, invalid=3294 0188: dt=0.000000, rms=0.609 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.656, neg=0, invalid=3294 0189: dt=1.024000, rms=0.646 (1.580%), neg=0, invalid=3294 0190: dt=0.384000, rms=0.646 (0.069%), neg=0, invalid=3294 0191: dt=0.384000, rms=0.646 (-0.036%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=3294 0192: dt=0.384000, rms=0.645 (0.118%), neg=0, invalid=3294 0193: dt=0.080000, rms=0.645 (0.004%), neg=0, invalid=3294 0194: dt=0.080000, rms=0.645 (0.000%), neg=0, invalid=3294 0195: dt=0.080000, rms=0.645 (-0.013%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.607, neg=0, invalid=3294 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0196: dt=0.988554, rms=0.582 (4.185%), neg=0, invalid=3294 0197: dt=0.080000, rms=0.581 (0.215%), neg=0, invalid=3294 0198: dt=0.080000, rms=0.581 (-0.090%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.581, neg=0, invalid=3294 0199: dt=0.028000, rms=0.581 (0.086%), neg=0, invalid=3294 0200: dt=0.001750, rms=0.581 (-0.001%), neg=0, invalid=3294 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.566, neg=0, invalid=3294 0201: dt=8.092000, rms=0.566 (0.004%), neg=0, invalid=3294 0202: dt=4.624000, rms=0.566 (0.001%), neg=0, invalid=3294 0203: dt=4.624000, rms=0.566 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=3294 0204: dt=32.368000, rms=0.566 (0.029%), neg=0, invalid=3294 0205: dt=32.368000, rms=0.566 (0.010%), neg=0, invalid=3294 0206: dt=32.368000, rms=0.566 (0.006%), neg=0, invalid=3294 0207: dt=32.368000, rms=0.566 (-0.007%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.566, neg=0, invalid=3294 0208: dt=64.000000, rms=0.565 (0.290%), neg=0, invalid=3294 0209: dt=211.836257, rms=0.558 (1.225%), neg=0, invalid=3294 0210: dt=17.207547, rms=0.557 (0.121%), neg=0, invalid=3294 0211: dt=17.207547, rms=0.557 (0.001%), neg=0, invalid=3294 0212: dt=17.207547, rms=0.557 (-0.070%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=3294 0213: dt=98.415094, rms=0.555 (0.376%), neg=0, invalid=3294 0214: dt=145.152000, rms=0.552 (0.536%), neg=0, invalid=3294 0215: dt=20.736000, rms=0.551 (0.069%), neg=0, invalid=3294 0216: dt=20.736000, rms=0.551 (0.006%), neg=0, invalid=3294 0217: dt=20.736000, rms=0.551 (-0.023%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0218: dt=38.400000, rms=0.549 (0.773%), neg=0, invalid=3294 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0219: dt=56.463768, rms=0.543 (1.092%), neg=0, invalid=3294 0220: dt=9.600000, rms=0.542 (0.243%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0221: dt=9.600000, rms=0.542 (-0.014%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=3294 0222: dt=25.600000, rms=0.541 (0.201%), neg=0, invalid=3294 0223: dt=32.000000, rms=0.540 (0.168%), neg=0, invalid=3294 0224: dt=32.000000, rms=0.540 (-0.037%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.547, neg=0, invalid=3294 0225: dt=0.000000, rms=0.547 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.547, neg=0, invalid=3294 0226: dt=0.000000, rms=0.547 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.561, neg=0, invalid=3294 0227: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=3294 0228: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.537, neg=0, invalid=3294 iter 0, gcam->neg = 36 after 2 iterations, nbhd size=0, neg = 0 0229: dt=0.820400, rms=0.520 (3.045%), neg=0, invalid=3294 0230: dt=0.064000, rms=0.520 (0.110%), neg=0, invalid=3294 0231: dt=0.064000, rms=0.520 (-0.118%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=3294 0232: dt=0.012000, rms=0.520 (0.003%), neg=0, invalid=3294 0233: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=3294 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 18 minutes and 26 seconds. mri_ca_register utimesec 7228.908000 mri_ca_register stimesec 28.688000 mri_ca_register ru_maxrss 1261580 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 7521324 mri_ca_register ru_majflt 157317 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 3379544 mri_ca_register ru_oublock 63072 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 157473 mri_ca_register ru_nivcsw 236954 FSRUNTIME@ mri_ca_register 2.3071 hours 1 threads #-------------------------------------- #@# Remove Neck Mon Feb 22 11:59:52 IST 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 6.65 removing structures at least 25 mm from brain... 11640381 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 11 seconds. #-------------------------------------- #@# SubCort Seg Mon Feb 22 12:01:08 IST 2016 mri_ca_label -rusage /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz sysname Linux hostname dgmh-HP-280-G1-MT machine x86_64 setenv SUBJECTS_DIR /home/dgmh/Desktop/bet_recon cd /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_ca_label -rusage /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.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 /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca... reading input volume from norm.mgz... average std[0] = 7.4 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 6.65 Atlas used for the 3D morph was /home/dgmh/Applications/freesurfer/average/RB_all_2015-08-04.gca average std = 7.4 using min determinant for regularization = 5.4 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16337 (20) mri peak = 0.04840 (20) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2955 voxels, overlap=0.927) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2955 voxels, peak = 20), gca=20.5 gca peak = 0.19190 (13) mri peak = 0.05591 (21) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (2076 voxels, overlap=0.892) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (2076 voxels, peak = 19), gca=18.9 gca peak = 0.24200 (96) mri peak = 0.11101 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (566 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (566 voxels, peak = 101), gca=101.3 gca peak = 0.14904 (91) mri peak = 0.09534 (96) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (458 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (458 voxels, peak = 95), gca=95.1 gca peak = 0.25211 (57) mri peak = 0.09607 (89) Right_Hippocampus (53): linear fit = 1.47 x + 0.0 (730 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.47 x + 0.0 (730 voxels, peak = 84), gca=83.5 gca peak = 0.31987 (57) mri peak = 0.06879 (88) Left_Hippocampus (17): linear fit = 1.45 x + 0.0 (520 voxels, overlap=0.025) Left_Hippocampus (17): linear fit = 1.45 x + 0.0 (520 voxels, peak = 82), gca=82.4 gca peak = 0.08094 (102) mri peak = 0.06783 (103) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45051 voxels, overlap=0.864) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45051 voxels, peak = 104), gca=103.5 gca peak = 0.08600 (104) mri peak = 0.06851 (101) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (42753 voxels, overlap=0.853) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (42753 voxels, peak = 106), gca=105.6 gca peak = 0.09612 (57) mri peak = 0.04614 (85) Left_Cerebral_Cortex (3): linear fit = 1.45 x + 0.0 (24794 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.45 x + 0.0 (24794 voxels, peak = 82), gca=82.4 gca peak = 0.11462 (58) mri peak = 0.04605 (87) Right_Cerebral_Cortex (42): linear fit = 1.46 x + 0.0 (24129 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.46 x + 0.0 (24129 voxels, peak = 84), gca=84.4 gca peak = 0.25255 (66) mri peak = 0.07709 (93) Right_Caudate (50): linear fit = 1.36 x + 0.0 (526 voxels, overlap=0.025) Right_Caudate (50): linear fit = 1.36 x + 0.0 (526 voxels, peak = 89), gca=89.4 gca peak = 0.18480 (77) mri peak = 0.08086 (88) Left_Caudate (11): linear fit = 1.18 x + 0.0 (620 voxels, overlap=0.094) Left_Caudate (11): linear fit = 1.18 x + 0.0 (620 voxels, peak = 91), gca=91.2 gca peak = 0.12729 (58) mri peak = 0.04378 (88) Left_Cerebellum_Cortex (8): linear fit = 1.50 x + 0.0 (17468 voxels, overlap=0.002) Left_Cerebellum_Cortex (8): linear fit = 1.50 x + 0.0 (17468 voxels, peak = 87), gca=87.3 gca peak = 0.12622 (58) mri peak = 0.05010 (89) Right_Cerebellum_Cortex (47): linear fit = 1.51 x + 0.0 (19075 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.51 x + 0.0 (19075 voxels, peak = 88), gca=87.9 gca peak = 0.15410 (88) mri peak = 0.06619 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8259 voxels, overlap=0.826) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8259 voxels, peak = 95), gca=95.5 gca peak = 0.15661 (88) mri peak = 0.07425 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7918 voxels, overlap=0.885) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7918 voxels, peak = 92), gca=92.0 gca peak = 0.30376 (59) mri peak = 0.13439 (88) Left_Amygdala (18): linear fit = 1.47 x + 0.0 (226 voxels, overlap=0.058) Left_Amygdala (18): linear fit = 1.47 x + 0.0 (226 voxels, peak = 86), gca=86.4 gca peak = 0.35132 (58) mri peak = 0.10089 (90) Right_Amygdala (54): linear fit = 1.52 x + 0.0 (437 voxels, overlap=0.038) Right_Amygdala (54): linear fit = 1.52 x + 0.0 (437 voxels, peak = 88), gca=88.4 gca peak = 0.10548 (89) mri peak = 0.07440 (90) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3332 voxels, overlap=0.812) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3332 voxels, peak = 91), gca=91.2 gca peak = 0.10706 (82) mri peak = 0.07278 (90) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3714 voxels, overlap=0.490) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3714 voxels, peak = 90), gca=89.8 gca peak = 0.08512 (74) mri peak = 0.07471 (100) Left_Putamen (12): linear fit = 1.25 x + 0.0 (1325 voxels, overlap=0.015) Left_Putamen (12): linear fit = 1.25 x + 0.0 (1325 voxels, peak = 92), gca=92.1 gca peak = 0.08440 (78) mri peak = 0.08860 (101) Right_Putamen (51): linear fit = 1.26 x + 0.0 (1344 voxels, overlap=0.016) Right_Putamen (51): linear fit = 1.26 x + 0.0 (1344 voxels, peak = 99), gca=98.7 gca peak = 0.07263 (80) mri peak = 0.08475 (81) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9929 voxels, overlap=0.615) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9929 voxels, peak = 85), gca=85.2 gca peak = 0.13309 (90) mri peak = 0.06122 (97) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1008 voxels, overlap=0.768) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1008 voxels, peak = 99), gca=99.5 gca peak = 0.15558 (86) mri peak = 0.05010 (90) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1154 voxels, overlap=0.786) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1154 voxels, peak = 93), gca=93.3 gca peak = 0.17913 (26) mri peak = 0.06987 (15) Third_Ventricle (14): linear fit = 0.55 x + 0.0 (95 voxels, overlap=0.382) Third_Ventricle (14): linear fit = 0.55 x + 0.0 (95 voxels, peak = 14), gca=14.2 gca peak = 0.17310 (16) mri peak = 0.07910 (24) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (172 voxels, overlap=0.777) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (172 voxels, peak = 18), gca=17.5 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.21424 (27) gca peak Left_Cerebellum_Cortex = 0.12729 (58) gca peak Left_Thalamus = 1.00000 (95) gca peak Third_Ventricle = 0.17913 (26) gca peak CSF = 0.22008 (37) gca peak Left_Accumbens_area = 0.78455 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09096 (57) gca peak Right_Inf_Lat_Vent = 0.24233 (28) gca peak Right_Cerebellum_Cortex = 0.12622 (58) gca peak Right_Amygdala = 0.35132 (58) gca peak Right_Accumbens_area = 0.41783 (64) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11536 (37) gca peak Fifth_Ventricle = 0.55384 (33) gca peak WM_hypointensities = 0.10945 (75) gca peak non_WM_hypointensities = 0.07381 (29) gca peak Optic_Chiasm = 0.66945 (76) not using caudate to estimate GM means setting label Right_Amygdala based on Left_Amygdala = 1.47 x + 0: 86 estimating mean gm scale to be 1.46 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.19 x + 0.0 setting left cbm cortex = 1.46 x + 0.00 setting right cbm cortex = 1.46 x + 0.00 Right_Putamen too bright - rescaling by 0.954 (from 1.265) to 94.1 (was 98.7) Right_Pallidum too bright - rescaling by 1.001 (from 1.055) to 101.4 (was 101.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16670 (20) mri peak = 0.04840 (20) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2955 voxels, overlap=0.910) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2955 voxels, peak = 20), gca=20.5 gca peak = 0.12160 (19) mri peak = 0.05591 (21) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (2076 voxels, overlap=0.759) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (2076 voxels, peak = 21), gca=20.6 gca peak = 0.20347 (98) mri peak = 0.11101 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (566 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (566 voxels, peak = 98), gca=98.0 gca peak = 0.13112 (98) mri peak = 0.09534 (96) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (458 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (458 voxels, peak = 99), gca=99.5 gca peak = 0.21452 (83) mri peak = 0.09607 (89) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (730 voxels, overlap=0.930) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (730 voxels, peak = 82), gca=81.8 gca peak = 0.21950 (87) mri peak = 0.06879 (88) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (520 voxels, overlap=1.005) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (520 voxels, peak = 88), gca=88.3 gca peak = 0.08164 (105) mri peak = 0.06783 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45051 voxels, overlap=0.904) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45051 voxels, peak = 104), gca=104.5 gca peak = 0.08536 (105) mri peak = 0.06851 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42753 voxels, overlap=0.901) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42753 voxels, peak = 104), gca=104.5 gca peak = 0.07014 (83) mri peak = 0.04614 (85) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (24794 voxels, overlap=0.966) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (24794 voxels, peak = 83), gca=83.0 gca peak = 0.08044 (84) mri peak = 0.04605 (87) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (24129 voxels, overlap=0.940) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (24129 voxels, peak = 83), gca=82.7 gca peak = 0.19253 (90) mri peak = 0.07709 (93) Right_Caudate (50): linear fit = 1.00 x + 0.0 (526 voxels, overlap=0.998) Right_Caudate (50): linear fit = 1.00 x + 0.0 (526 voxels, peak = 90), gca=90.0 gca peak = 0.13236 (92) mri peak = 0.08086 (88) Left_Caudate (11): linear fit = 1.00 x + 0.0 (620 voxels, overlap=0.997) Left_Caudate (11): linear fit = 1.00 x + 0.0 (620 voxels, peak = 92), gca=92.0 gca peak = 0.08901 (83) mri peak = 0.04378 (88) Left_Cerebellum_Cortex (8): linear fit = 1.05 x + 0.0 (17468 voxels, overlap=0.851) Left_Cerebellum_Cortex (8): linear fit = 1.05 x + 0.0 (17468 voxels, peak = 88), gca=87.6 gca peak = 0.09363 (82) mri peak = 0.05010 (89) Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (19075 voxels, overlap=0.911) Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (19075 voxels, peak = 87), gca=86.5 gca peak = 0.14249 (95) mri peak = 0.06619 (93) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (8259 voxels, overlap=0.989) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (8259 voxels, peak = 93), gca=92.6 gca peak = 0.17324 (92) mri peak = 0.07425 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7918 voxels, overlap=0.990) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7918 voxels, peak = 92), gca=91.5 gca peak = 0.32052 (84) mri peak = 0.13439 (88) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (226 voxels, overlap=1.010) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (226 voxels, peak = 85), gca=85.3 gca peak = 0.34793 (84) mri peak = 0.10089 (90) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (437 voxels, overlap=0.996) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (437 voxels, peak = 87), gca=86.9 gca peak = 0.12191 (91) mri peak = 0.07440 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3332 voxels, overlap=0.902) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3332 voxels, peak = 91), gca=90.5 gca peak = 0.11492 (90) mri peak = 0.07278 (90) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3714 voxels, overlap=0.924) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3714 voxels, peak = 90), gca=90.0 gca peak = 0.08076 (100) mri peak = 0.07471 (100) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1325 voxels, overlap=0.849) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1325 voxels, peak = 102), gca=101.5 gca peak = 0.07592 (90) mri peak = 0.08860 (101) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1344 voxels, overlap=0.680) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1344 voxels, peak = 94), gca=94.0 gca peak = 0.07881 (86) mri peak = 0.08475 (81) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9929 voxels, overlap=0.870) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9929 voxels, peak = 86), gca=85.6 gca peak = 0.10752 (99) mri peak = 0.06122 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1008 voxels, overlap=0.844) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1008 voxels, peak = 99), gca=99.5 gca peak = 0.15598 (94) mri peak = 0.05010 (90) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1154 voxels, overlap=0.937) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1154 voxels, peak = 94), gca=94.5 gca peak = 0.13994 (31) mri peak = 0.06987 (15) Third_Ventricle (14): linear fit = 0.50 x + 0.0 (95 voxels, overlap=0.213) Third_Ventricle (14): linear fit = 0.50 x + 0.0 (95 voxels, peak = 16), gca=15.7 gca peak = 0.16301 (18) mri peak = 0.07910 (24) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (172 voxels, overlap=0.739) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (172 voxels, peak = 20), gca=20.2 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.15257 (48) gca peak Left_Thalamus = 0.64824 (138) gca peak Third_Ventricle = 0.13994 (31) gca peak CSF = 0.21330 (44) gca peak Left_Accumbens_area = 0.45743 (74) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09068 (35) gca peak Right_Inf_Lat_Vent = 0.19547 (34) gca peak Right_Accumbens_area = 0.28304 (87) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11504 (37) gca peak Fifth_Ventricle = 0.55240 (38) gca peak WM_hypointensities = 0.09868 (76) gca peak non_WM_hypointensities = 0.08334 (44) gca peak Optic_Chiasm = 0.64956 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.08 x + 0.0 Left_Putamen too bright - rescaling by 0.926 (from 1.015) to 94.0 (was 101.5) Right_Putamen too bright - rescaling by 1.000 (from 1.045) to 94.0 (was 94.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 84563 voxels changed in iteration 0 of unlikely voxel relabeling 136 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 131575 gm and wm labels changed (%30 to gray, %70 to white out of all changed labels) 774 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 100247 changed. image ll: -2.138, PF=0.500 pass 2: 26641 changed. image ll: -2.134, PF=0.500 pass 3: 8564 changed. pass 4: 3371 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... mri_ca_label utimesec 1651.576000 mri_ca_label stimesec 8.632000 mri_ca_label ru_maxrss 1415708 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 852888 mri_ca_label ru_majflt 52242 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1496128 mri_ca_label ru_oublock 416 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 52996 mri_ca_label ru_nivcsw 47921 auto-labeling took 35 minutes and 2 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/transforms/cc_up.lta madanlalsethiya17072014 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/transforms/cc_up.lta reading aseg from /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/aseg.auto_noCCseg.mgz reading norm from /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/norm.mgz 10334 voxels in left wm, 25256 in right wm, xrange [126, 131] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 global minimum found at slice 129.0, rotations (-0.85, -0.68) final transformation (x=129.0, yr=-0.845, zr=-0.681): 0.99982 0.01189 -0.01475 -0.48532; -0.01189 0.99993 0.00018 19.51966; 0.01475 0.00000 0.99989 4.11078; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 110 122 eigenvectors: -0.00776 0.01265 0.99989; -0.29134 -0.95657 0.00984; 0.95659 -0.29124 0.01111; writing aseg with callosum to /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Mon Feb 22 12:36:43 IST 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Feb 22 12:36:43 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 4899 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction 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 100 gm peak at 75 (75), valley at 57 (57) csf peak at 37, setting threshold to 62 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 98 gm peak at 74 (74), valley at 29 (29) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 49 seconds. #-------------------------------------------- #@# Mask BFS Mon Feb 22 12:39:36 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1303981 voxels in mask (pct= 7.77) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Feb 22 12:39:39 IST 2016 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 106.0 +- 5.3 [80.0 --> 125.0] GM (69.0) : 65.8 +- 13.3 [30.0 --> 96.0] setting bottom of white matter range to 79.1 setting top of gray matter range to 92.5 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 6937 sparsely connected voxels removed... thickening thin strands.... 20 segments, 519 filled 3478 bright non-wm voxels segmented. 15132 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.99 minutes reading wm segmentation from wm.seg.mgz... 2197 voxels added to wm to prevent paths from MTL structures to cortex 6163 additional wm voxels added 0 additional wm voxels added SEG EDIT: 55584 voxels turned on, 54040 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 54 found - 54 modified | TOTAL: 54 pass 2 (xy+): 0 found - 54 modified | TOTAL: 54 pass 1 (xy-): 50 found - 50 modified | TOTAL: 104 pass 2 (xy-): 0 found - 50 modified | TOTAL: 104 pass 1 (yz+): 77 found - 77 modified | TOTAL: 181 pass 2 (yz+): 0 found - 77 modified | TOTAL: 181 pass 1 (yz-): 78 found - 78 modified | TOTAL: 259 pass 2 (yz-): 0 found - 78 modified | TOTAL: 259 pass 1 (xz+): 103 found - 103 modified | TOTAL: 362 pass 2 (xz+): 0 found - 103 modified | TOTAL: 362 pass 1 (xz-): 90 found - 90 modified | TOTAL: 452 pass 2 (xz-): 0 found - 90 modified | TOTAL: 452 Iteration Number : 1 pass 1 (+++): 61 found - 61 modified | TOTAL: 61 pass 2 (+++): 0 found - 61 modified | TOTAL: 61 pass 1 (+++): 190 found - 190 modified | TOTAL: 251 pass 2 (+++): 0 found - 190 modified | TOTAL: 251 pass 1 (+++): 50 found - 50 modified | TOTAL: 301 pass 2 (+++): 0 found - 50 modified | TOTAL: 301 pass 1 (+++): 242 found - 242 modified | TOTAL: 543 pass 2 (+++): 0 found - 242 modified | TOTAL: 543 Iteration Number : 1 pass 1 (++): 166 found - 166 modified | TOTAL: 166 pass 2 (++): 0 found - 166 modified | TOTAL: 166 pass 1 (+-): 350 found - 350 modified | TOTAL: 516 pass 2 (+-): 1 found - 351 modified | TOTAL: 517 pass 3 (+-): 0 found - 351 modified | TOTAL: 517 pass 1 (--): 191 found - 191 modified | TOTAL: 708 pass 2 (--): 0 found - 191 modified | TOTAL: 708 pass 1 (-+): 378 found - 378 modified | TOTAL: 1086 pass 2 (-+): 0 found - 378 modified | TOTAL: 1086 Iteration Number : 2 pass 1 (xy+): 45 found - 45 modified | TOTAL: 45 pass 2 (xy+): 0 found - 45 modified | TOTAL: 45 pass 1 (xy-): 49 found - 49 modified | TOTAL: 94 pass 2 (xy-): 0 found - 49 modified | TOTAL: 94 pass 1 (yz+): 25 found - 25 modified | TOTAL: 119 pass 2 (yz+): 0 found - 25 modified | TOTAL: 119 pass 1 (yz-): 86 found - 86 modified | TOTAL: 205 pass 2 (yz-): 0 found - 86 modified | TOTAL: 205 pass 1 (xz+): 55 found - 55 modified | TOTAL: 260 pass 2 (xz+): 0 found - 55 modified | TOTAL: 260 pass 1 (xz-): 51 found - 51 modified | TOTAL: 311 pass 2 (xz-): 0 found - 51 modified | TOTAL: 311 Iteration Number : 2 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 pass 1 (+++): 21 found - 21 modified | TOTAL: 24 pass 2 (+++): 0 found - 21 modified | TOTAL: 24 pass 1 (+++): 0 found - 0 modified | TOTAL: 24 pass 1 (+++): 21 found - 21 modified | TOTAL: 45 pass 2 (+++): 0 found - 21 modified | TOTAL: 45 Iteration Number : 2 pass 1 (++): 22 found - 22 modified | TOTAL: 22 pass 2 (++): 0 found - 22 modified | TOTAL: 22 pass 1 (+-): 18 found - 18 modified | TOTAL: 40 pass 2 (+-): 0 found - 18 modified | TOTAL: 40 pass 1 (--): 22 found - 22 modified | TOTAL: 62 pass 2 (--): 0 found - 22 modified | TOTAL: 62 pass 1 (-+): 18 found - 18 modified | TOTAL: 80 pass 2 (-+): 0 found - 18 modified | TOTAL: 80 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 4 found - 4 modified | TOTAL: 8 pass 2 (xy-): 0 found - 4 modified | TOTAL: 8 pass 1 (yz+): 6 found - 6 modified | TOTAL: 14 pass 2 (yz+): 0 found - 6 modified | TOTAL: 14 pass 1 (yz-): 6 found - 6 modified | TOTAL: 20 pass 2 (yz-): 0 found - 6 modified | TOTAL: 20 pass 1 (xz+): 5 found - 5 modified | TOTAL: 25 pass 2 (xz+): 0 found - 5 modified | TOTAL: 25 pass 1 (xz-): 3 found - 3 modified | TOTAL: 28 pass 2 (xz-): 0 found - 3 modified | TOTAL: 28 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 5 found - 5 modified | TOTAL: 5 pass 2 (+-): 0 found - 5 modified | TOTAL: 5 pass 1 (--): 1 found - 1 modified | TOTAL: 6 pass 2 (--): 0 found - 1 modified | TOTAL: 6 pass 1 (-+): 2 found - 2 modified | TOTAL: 8 pass 2 (-+): 0 found - 2 modified | TOTAL: 8 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2562 (out of 664108: 0.385781) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Feb 22 12:42:21 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03044 -0.03004 -0.00271 -1.82756; 0.02340 1.01052 0.39836 -62.90234; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03044 -0.03004 -0.00271 -1.82756; 0.02340 1.01052 0.39836 -62.90234; -0.00816 -0.41229 0.99219 42.20874; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2093 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) need search nearby using seed (125, 113, 95), TAL = (3.0, -33.0, 15.0) talairach voxel to voxel transform 0.96981 0.02570 -0.00767 3.71246; -0.02200 0.84972 -0.34122 67.81155; -0.00117 0.35330 0.86602 -14.33215; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 113, 95) --> (3.0, -33.0, 15.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (3.00, -33.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -33.00, 15.00) SRC: (109.66, 129.06, 107.74) search lh wm seed point around talairach space (-15.00, -33.00, 15.00), SRC: (144.57, 128.27, 107.70) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Mon Feb 22 12:43:00 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 4 found - 4 modified | TOTAL: 8 pass 2 (xy-): 0 found - 4 modified | TOTAL: 8 pass 1 (yz+): 1 found - 1 modified | TOTAL: 9 pass 2 (yz+): 0 found - 1 modified | TOTAL: 9 pass 1 (yz-): 2 found - 2 modified | TOTAL: 11 pass 2 (yz-): 0 found - 2 modified | TOTAL: 11 pass 1 (xz+): 4 found - 4 modified | TOTAL: 15 pass 2 (xz+): 0 found - 4 modified | TOTAL: 15 pass 1 (xz-): 1 found - 1 modified | TOTAL: 16 pass 2 (xz-): 0 found - 1 modified | TOTAL: 16 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 22 (out of 333027: 0.006606) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ slice 60: 1187 vertices, 1324 faces slice 70: 9446 vertices, 9852 faces slice 80: 22771 vertices, 23311 faces slice 90: 37826 vertices, 38613 faces slice 100: 53012 vertices, 53827 faces slice 110: 66023 vertices, 66896 faces slice 120: 79540 vertices, 80439 faces slice 130: 93044 vertices, 94081 faces slice 140: 107129 vertices, 108292 faces slice 150: 122147 vertices, 123401 faces slice 160: 135685 vertices, 136969 faces slice 170: 147772 vertices, 149044 faces slice 180: 155695 vertices, 156941 faces slice 190: 162580 vertices, 163822 faces slice 200: 165801 vertices, 166959 faces slice 210: 165986 vertices, 167098 faces slice 220: 165986 vertices, 167098 faces slice 230: 165986 vertices, 167098 faces slice 240: 165986 vertices, 167098 faces slice 250: 165986 vertices, 167098 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 165986 voxel in cpt #1: X=-1112 [v=165986,e=501294,f=334196] located at (-29.321762, -5.930482, 3.724760) For the whole surface: X=-1112 [v=165986,e=501294,f=334196] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Feb 22 12:43:07 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 10 found - 10 modified | TOTAL: 11 pass 2 (xy-): 0 found - 10 modified | TOTAL: 11 pass 1 (yz+): 1 found - 1 modified | TOTAL: 12 pass 2 (yz+): 0 found - 1 modified | TOTAL: 12 pass 1 (yz-): 6 found - 6 modified | TOTAL: 18 pass 2 (yz-): 0 found - 6 modified | TOTAL: 18 pass 1 (xz+): 2 found - 2 modified | TOTAL: 20 pass 2 (xz+): 0 found - 2 modified | TOTAL: 20 pass 1 (xz-): 9 found - 9 modified | TOTAL: 29 pass 2 (xz-): 0 found - 9 modified | TOTAL: 29 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 3 found - 3 modified | TOTAL: 6 pass 2 (+-): 0 found - 3 modified | TOTAL: 6 pass 1 (--): 0 found - 0 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 41 (out of 327252: 0.012529) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ slice 60: 2026 vertices, 2170 faces slice 70: 9627 vertices, 9984 faces slice 80: 21909 vertices, 22439 faces slice 90: 36964 vertices, 37690 faces slice 100: 52714 vertices, 53481 faces slice 110: 66577 vertices, 67381 faces slice 120: 81178 vertices, 82100 faces slice 130: 94075 vertices, 95017 faces slice 140: 107392 vertices, 108477 faces slice 150: 120432 vertices, 121535 faces slice 160: 134362 vertices, 135613 faces slice 170: 145755 vertices, 146916 faces slice 180: 153185 vertices, 154301 faces slice 190: 159529 vertices, 160665 faces slice 200: 163196 vertices, 164195 faces slice 210: 163266 vertices, 164232 faces slice 220: 163266 vertices, 164232 faces slice 230: 163266 vertices, 164232 faces slice 240: 163266 vertices, 164232 faces slice 250: 163266 vertices, 164232 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 163266 voxel in cpt #1: X=-966 [v=163266,e=492696,f=328464] located at (28.569849, -6.588481, 4.543922) For the whole surface: X=-966 [v=163266,e=492696,f=328464] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Feb 22 12:43:14 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Mon Feb 22 12:43:20 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Feb 22 12:43:25 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.7 mm, total surface area = 77598 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.228 (target=0.015) step 005: RMS=0.186 (target=0.015) step 010: RMS=0.167 (target=0.015) step 015: RMS=0.162 (target=0.015) step 020: RMS=0.158 (target=0.015) step 025: RMS=0.155 (target=0.015) step 030: RMS=0.150 (target=0.015) step 035: RMS=0.146 (target=0.015) step 040: RMS=0.145 (target=0.015) step 045: RMS=0.143 (target=0.015) step 050: RMS=0.141 (target=0.015) step 055: RMS=0.140 (target=0.015) step 060: RMS=0.140 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 43.148000 mris_inflate stimesec 0.048000 mris_inflate ru_maxrss 222112 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 27293 mris_inflate ru_majflt 44 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10384 mris_inflate ru_oublock 11728 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 45 mris_inflate ru_nivcsw 5471 #-------------------------------------------- #@# Inflation1 rh Mon Feb 22 12:44:09 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.6 mm, total surface area = 76803 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.222 (target=0.015) step 005: RMS=0.182 (target=0.015) step 010: RMS=0.163 (target=0.015) step 015: RMS=0.156 (target=0.015) step 020: RMS=0.151 (target=0.015) step 025: RMS=0.148 (target=0.015) step 030: RMS=0.142 (target=0.015) step 035: RMS=0.140 (target=0.015) step 040: RMS=0.137 (target=0.015) step 045: RMS=0.136 (target=0.015) step 050: RMS=0.134 (target=0.015) step 055: RMS=0.134 (target=0.015) step 060: RMS=0.133 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.180000 mris_inflate stimesec 0.048000 mris_inflate ru_maxrss 218052 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26836 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11528 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 5066 #-------------------------------------------- #@# QSphere lh Mon Feb 22 12:44:52 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.92 +- 0.70 (0.00-->13.58) (max @ vno 94138 --> 94166) face area 0.03 +- 0.05 (-0.49-->0.90) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.355... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.706, avgs=0 005/300: dt: 0.9000, rms radial error=174.442, avgs=0 010/300: dt: 0.9000, rms radial error=173.872, avgs=0 015/300: dt: 0.9000, rms radial error=173.121, avgs=0 020/300: dt: 0.9000, rms radial error=172.265, avgs=0 025/300: dt: 0.9000, rms radial error=171.350, avgs=0 030/300: dt: 0.9000, rms radial error=170.403, avgs=0 035/300: dt: 0.9000, rms radial error=169.455, avgs=0 040/300: dt: 0.9000, rms radial error=168.505, avgs=0 045/300: dt: 0.9000, rms radial error=167.552, avgs=0 050/300: dt: 0.9000, rms radial error=166.600, avgs=0 055/300: dt: 0.9000, rms radial error=165.650, avgs=0 060/300: dt: 0.9000, rms radial error=164.704, avgs=0 065/300: dt: 0.9000, rms radial error=163.764, avgs=0 070/300: dt: 0.9000, rms radial error=162.828, avgs=0 075/300: dt: 0.9000, rms radial error=161.897, avgs=0 080/300: dt: 0.9000, rms radial error=160.972, avgs=0 085/300: dt: 0.9000, rms radial error=160.055, avgs=0 090/300: dt: 0.9000, rms radial error=159.144, avgs=0 095/300: dt: 0.9000, rms radial error=158.238, avgs=0 100/300: dt: 0.9000, rms radial error=157.337, avgs=0 105/300: dt: 0.9000, rms radial error=156.442, avgs=0 110/300: dt: 0.9000, rms radial error=155.551, avgs=0 115/300: dt: 0.9000, rms radial error=154.666, avgs=0 120/300: dt: 0.9000, rms radial error=153.785, avgs=0 125/300: dt: 0.9000, rms radial error=152.910, avgs=0 130/300: dt: 0.9000, rms radial error=152.039, avgs=0 135/300: dt: 0.9000, rms radial error=151.173, avgs=0 140/300: dt: 0.9000, rms radial error=150.314, avgs=0 145/300: dt: 0.9000, rms radial error=149.460, avgs=0 150/300: dt: 0.9000, rms radial error=148.611, avgs=0 155/300: dt: 0.9000, rms radial error=147.767, avgs=0 160/300: dt: 0.9000, rms radial error=146.929, avgs=0 165/300: dt: 0.9000, rms radial error=146.096, avgs=0 170/300: dt: 0.9000, rms radial error=145.267, avgs=0 175/300: dt: 0.9000, rms radial error=144.443, avgs=0 180/300: dt: 0.9000, rms radial error=143.623, avgs=0 185/300: dt: 0.9000, rms radial error=142.807, avgs=0 190/300: dt: 0.9000, rms radial error=141.996, avgs=0 195/300: dt: 0.9000, rms radial error=141.189, avgs=0 200/300: dt: 0.9000, rms radial error=140.388, avgs=0 205/300: dt: 0.9000, rms radial error=139.591, avgs=0 210/300: dt: 0.9000, rms radial error=138.799, avgs=0 215/300: dt: 0.9000, rms radial error=138.012, avgs=0 220/300: dt: 0.9000, rms radial error=137.229, avgs=0 225/300: dt: 0.9000, rms radial error=136.451, avgs=0 230/300: dt: 0.9000, rms radial error=135.676, avgs=0 235/300: dt: 0.9000, rms radial error=134.907, avgs=0 240/300: dt: 0.9000, rms radial error=134.141, avgs=0 245/300: dt: 0.9000, rms radial error=133.380, avgs=0 250/300: dt: 0.9000, rms radial error=132.622, avgs=0 255/300: dt: 0.9000, rms radial error=131.868, avgs=0 260/300: dt: 0.9000, rms radial error=131.118, avgs=0 265/300: dt: 0.9000, rms radial error=130.373, avgs=0 270/300: dt: 0.9000, rms radial error=129.632, avgs=0 275/300: dt: 0.9000, rms radial error=128.894, avgs=0 280/300: dt: 0.9000, rms radial error=128.161, avgs=0 285/300: dt: 0.9000, rms radial error=127.432, avgs=0 290/300: dt: 0.9000, rms radial error=126.707, avgs=0 295/300: dt: 0.9000, rms radial error=125.987, avgs=0 300/300: dt: 0.9000, rms radial error=125.270, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19516.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 2 (K=40.0), pass 1, starting sse = 3703.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00063 epoch 3 (K=160.0), pass 1, starting sse = 698.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00407 epoch 4 (K=640.0), pass 1, starting sse = 201.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/14 = 0.01024 final distance error %28.14 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 274.464000 mris_sphere stimesec 0.456000 mris_sphere ru_maxrss 222420 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 27312 mris_sphere ru_majflt 81 mris_sphere ru_nswap 0 mris_sphere ru_inblock 18264 mris_sphere ru_oublock 11728 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 91 mris_sphere ru_nivcsw 14416 FSRUNTIME@ mris_sphere 0.0770 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Feb 22 12:49:34 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.72 (0.00-->11.70) (max @ vno 97344 --> 97345) face area 0.03 +- 0.05 (-0.59-->1.17) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.355... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.966, avgs=0 005/300: dt: 0.9000, rms radial error=174.704, avgs=0 010/300: dt: 0.9000, rms radial error=174.143, avgs=0 015/300: dt: 0.9000, rms radial error=173.405, avgs=0 020/300: dt: 0.9000, rms radial error=172.562, avgs=0 025/300: dt: 0.9000, rms radial error=171.665, avgs=0 030/300: dt: 0.9000, rms radial error=170.737, avgs=0 035/300: dt: 0.9000, rms radial error=169.791, avgs=0 040/300: dt: 0.9000, rms radial error=168.836, avgs=0 045/300: dt: 0.9000, rms radial error=167.879, avgs=0 050/300: dt: 0.9000, rms radial error=166.921, avgs=0 055/300: dt: 0.9000, rms radial error=165.967, avgs=0 060/300: dt: 0.9000, rms radial error=165.021, avgs=0 065/300: dt: 0.9000, rms radial error=164.078, avgs=0 070/300: dt: 0.9000, rms radial error=163.146, avgs=0 075/300: dt: 0.9000, rms radial error=162.220, avgs=0 080/300: dt: 0.9000, rms radial error=161.300, avgs=0 085/300: dt: 0.9000, rms radial error=160.384, avgs=0 090/300: dt: 0.9000, rms radial error=159.473, avgs=0 095/300: dt: 0.9000, rms radial error=158.567, avgs=0 100/300: dt: 0.9000, rms radial error=157.668, avgs=0 105/300: dt: 0.9000, rms radial error=156.775, avgs=0 110/300: dt: 0.9000, rms radial error=155.887, avgs=0 115/300: dt: 0.9000, rms radial error=155.004, avgs=0 120/300: dt: 0.9000, rms radial error=154.127, avgs=0 125/300: dt: 0.9000, rms radial error=153.257, avgs=0 130/300: dt: 0.9000, rms radial error=152.391, avgs=0 135/300: dt: 0.9000, rms radial error=151.530, avgs=0 140/300: dt: 0.9000, rms radial error=150.674, avgs=0 145/300: dt: 0.9000, rms radial error=149.823, avgs=0 150/300: dt: 0.9000, rms radial error=148.976, avgs=0 155/300: dt: 0.9000, rms radial error=148.135, avgs=0 160/300: dt: 0.9000, rms radial error=147.299, avgs=0 165/300: dt: 0.9000, rms radial error=146.469, avgs=0 170/300: dt: 0.9000, rms radial error=145.642, avgs=0 175/300: dt: 0.9000, rms radial error=144.821, avgs=0 180/300: dt: 0.9000, rms radial error=144.005, avgs=0 185/300: dt: 0.9000, rms radial error=143.194, avgs=0 190/300: dt: 0.9000, rms radial error=142.387, avgs=0 195/300: dt: 0.9000, rms radial error=141.585, avgs=0 200/300: dt: 0.9000, rms radial error=140.788, avgs=0 205/300: dt: 0.9000, rms radial error=139.995, avgs=0 210/300: dt: 0.9000, rms radial error=139.204, avgs=0 215/300: dt: 0.9000, rms radial error=138.417, avgs=0 220/300: dt: 0.9000, rms radial error=137.635, avgs=0 225/300: dt: 0.9000, rms radial error=136.857, avgs=0 230/300: dt: 0.9000, rms radial error=136.083, avgs=0 235/300: dt: 0.9000, rms radial error=135.314, avgs=0 240/300: dt: 0.9000, rms radial error=134.549, avgs=0 245/300: dt: 0.9000, rms radial error=133.788, avgs=0 250/300: dt: 0.9000, rms radial error=133.031, avgs=0 255/300: dt: 0.9000, rms radial error=132.278, avgs=0 260/300: dt: 0.9000, rms radial error=131.530, avgs=0 265/300: dt: 0.9000, rms radial error=130.787, avgs=0 270/300: dt: 0.9000, rms radial error=130.047, avgs=0 275/300: dt: 0.9000, rms radial error=129.313, avgs=0 280/300: dt: 0.9000, rms radial error=128.582, avgs=0 285/300: dt: 0.9000, rms radial error=127.856, avgs=0 290/300: dt: 0.9000, rms radial error=127.133, avgs=0 295/300: dt: 0.9000, rms radial error=126.415, avgs=0 300/300: dt: 0.9000, rms radial error=125.700, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19207.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00026 epoch 2 (K=40.0), pass 1, starting sse = 3658.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00134 epoch 3 (K=160.0), pass 1, starting sse = 723.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00797 epoch 4 (K=640.0), pass 1, starting sse = 232.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/17 = 0.01376 final distance error %29.17 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 286.780000 mris_sphere stimesec 0.152000 mris_sphere ru_maxrss 217948 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 26332 mris_sphere ru_majflt 78 mris_sphere ru_nswap 0 mris_sphere ru_inblock 29112 mris_sphere ru_oublock 11536 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 103 mris_sphere ru_nivcsw 7299 FSRUNTIME@ mris_sphere 0.0801 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Feb 22 12:54:24 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Feb 22 12:54:24 IST 2016 /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Feb 22 12:54:24 IST 2016 mris_fix_topology -rusage /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 madanlalsethiya17072014 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ before topology correction, eno=-1112 (nv=165986, nf=334196, ne=501294, g=557) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 110324 ambiguous faces found in tessellation segmenting defects... 227 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 1 -merging segment 28 into 5 -merging segment 13 into 11 -merging segment 67 into 14 -merging segment 96 into 14 -merging segment 101 into 14 -merging segment 123 into 14 -merging segment 135 into 14 -merging segment 145 into 14 -merging segment 140 into 14 -merging segment 34 into 15 -merging segment 73 into 66 -merging segment 82 into 75 -merging segment 80 into 77 -merging segment 88 into 85 -merging segment 97 into 92 -merging segment 98 into 93 -merging segment 100 into 94 -merging segment 102 into 94 -merging segment 108 into 94 -merging segment 126 into 115 -merging segment 142 into 115 -merging segment 118 into 117 -merging segment 137 into 117 -merging segment 143 into 117 -merging segment 133 into 150 -merging segment 180 into 161 -merging segment 188 into 169 -merging segment 196 into 189 -merging segment 207 into 197 -merging segment 201 into 198 -merging segment 200 into 199 -merging segment 212 into 202 -merging segment 213 into 202 -merging segment 217 into 202 192 defects to be corrected 0 vertices coincident reading input surface /home/dgmh/Desktop/bet_recon/madanlalsethiya17072014/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2488 (-4.6244) -vertex loglikelihood: -7.0930 (-3.5465) -normal dot loglikelihood: -3.5360 (-3.5360) -quad curv loglikelihood: -6.4099 (-3.2050) Total Loglikelihood : -26.2877 CORRECTING DEFECT 0 (vertices=9, convex hull=27) After retessellation of defect 0, euler #=-126 (103175,293931,190630) : difference with theory (-189) = -63 CORRECTING DEFECT 1 (vertices=9340, convex hull=2906) XL defect detected... After retessellation of defect 1, euler #=-133 (104284,298959,194542) : difference with theory (-188) = -55 CORRECTING DEFECT 2 (vertices=82, convex hull=53) After retessellation of defect 2, euler #=-132 (104296,299013,194585) : difference with theory (-187) = -55 CORRECTING DEFECT 3 (vertices=36, convex hull=23) After retessellation of defect 3, euler #=-131 (104299,299029,194599) : difference with theory (-186) = -55 CORRECTING DEFECT 4 (vertices=8, convex hull=14) After retessellation of defect 4, euler #=-130 (104300,299037,194607) : difference with theory (-185) = -55 CORRECTING DEFECT 5 (vertices=1188, convex hull=546) XL defect detected... After retessellation of defect 5, euler #=-131 (104755,300701,195815) : difference with theory (-184) = -53 CORRECTING DEFECT 6 (vertices=43, convex hull=66) After retessellation of defect 6, euler #=-130 (104782,300806,195894) : difference with theory (-183) = -53 CORRECTING DEFECT 7 (vertices=460, convex hull=303) After retessellation of defect 7, euler #=-129 (104992,301599,196478) : difference with theory (-182) = -53 CORRECTING DEFECT 8 (vertices=144, convex hull=90) After retessellation of defect 8, euler #=-128 (105043,301800,196629) : difference with theory (-181) = -53 CORRECTING DEFECT 9 (vertices=466, convex hull=302) After retessellation of defect 9, euler #=-128 (105242,302579,197209) : difference with theory (-180) = -52 CORRECTING DEFECT 10 (vertices=691, convex hull=314) After retessellation of defect 10, euler #=-126 (105419,303290,197745) : difference with theory (-179) = -53 CORRECTING DEFECT 11 (vertices=84, convex hull=78) After retessellation of defect 11, euler #=-126 (105456,303440,197858) : difference with theory (-178) = -52 CORRECTING DEFECT 12 (vertices=27389, convex hull=7671) Excessive topologic defect encountered: could not allocate 83327595 edges for retessellation Cannot allocate memory Linux dgmh-HP-280-G1-MT 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s madanlalsethiya17072014 exited with ERRORS at Tue Feb 23 04:47:56 IST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting