Sat Apr 15 19:40:07 CDT 2017 /work2/r1774/subjects/J106388 /home/ums/r1774/freesurfer/bin/recon-all -i /ptmp/r1774/inbox/J106388/J106388_20030822_spgr.img -subjid J106388 subjid J106388 setenv SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Actual FREESURFER_HOME /home1/ums/r1774/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux cputime 4032:00:00 filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 6291456 kbytes vmemoryuse unlimited descriptors 16384 memorylocked unlimited maxproc 126407 maxlocks unlimited maxsignal 126407 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 16201068 13211344 2989724 681156 265272 12329488 -/+ buffers/cache: 616584 15584484 Swap: 2097148 123532 1973616 pbsjob 45827.sequoia ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/ums/r1774/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/ums/r1774/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /work2/r1774/subjects/J106388 mri_convert /work2/r1774/inbox/J106388/J106388_20030822_spgr.img /work2/r1774/subjects/J106388/mri/orig/001.mgz mri_convert.bin /work2/r1774/inbox/J106388/J106388_20030822_spgr.img /work2/r1774/subjects/J106388/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /work2/r1774/inbox/J106388/J106388_20030822_spgr.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /work2/r1774/subjects/J106388/mri/orig/001.mgz... Started at Sat Apr 15 19:40:07 CDT 2017 Ended at Sat Apr 15 19:40:12 CDT 2017 #@#%# recon-all-run-time-hours 0.001 recon-all -s J106388 finished without error at Sat Apr 15 19:40:12 CDT 2017 New invocation of recon-all Sat Apr 15 19:40:13 CDT 2017 /work2/r1774/subjects/J106388 /home/ums/r1774/freesurfer/bin/recon-all -subjid J106388 -all -hippocampal-subfields-T1 -brainstem-structures subjid J106388 setenv SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Actual FREESURFER_HOME /home1/ums/r1774/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux cputime 4032:00:00 filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 6291456 kbytes vmemoryuse unlimited descriptors 16384 memorylocked unlimited maxproc 126407 maxlocks unlimited maxsignal 126407 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 16201068 13216908 2984160 681156 265272 12335192 -/+ buffers/cache: 616444 15584624 Swap: 2097148 123532 1973616 pbsjob 45827.sequoia ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/04/16-00:40:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: r1774 Machine: n026 Platform: Linux PlatformVersion: 3.12.67-60.64.24-default CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/ums/r1774/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/ums/r1774/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Sat Apr 15 19:40:13 CDT 2017 Found 1 runs /work2/r1774/subjects/J106388/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 /work2/r1774/subjects/J106388/mri/orig/001.mgz /work2/r1774/subjects/J106388/mri/rawavg.mgz /work2/r1774/subjects/J106388 mri_convert /work2/r1774/subjects/J106388/mri/rawavg.mgz /work2/r1774/subjects/J106388/mri/orig.mgz --conform mri_convert.bin /work2/r1774/subjects/J106388/mri/rawavg.mgz /work2/r1774/subjects/J106388/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /work2/r1774/subjects/J106388/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /work2/r1774/subjects/J106388/mri/orig.mgz... mri_add_xform_to_header -c /work2/r1774/subjects/J106388/mri/transforms/talairach.xfm /work2/r1774/subjects/J106388/mri/orig.mgz /work2/r1774/subjects/J106388/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Apr 15 19:40:29 CDT 2017 /work2/r1774/subjects/J106388/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /work2/r1774/subjects/J106388/mri /home/ums/r1774/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux Sat Apr 15 19:40:29 CDT 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.27594 /work2/r1774/subjects/J106388/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27594/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27594/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.27594/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Apr 15 19:40:34 CDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.27594/nu0.mnc ./tmp.mri_nu_correct.mni.27594/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27594/0/ -iterations 1000 -distance 50 [r1774@n026:/work2/r1774/subjects/J106388/mri/] [2017-04-15 19:40:34] running: /home/ums/r1774/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.27594/0/ ./tmp.mri_nu_correct.mni.27594/nu0.mnc ./tmp.mri_nu_correct.mni.27594/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 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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: 85 CV of field change: 0.000989292 mri_convert ./tmp.mri_nu_correct.mni.27594/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.27594/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.27594/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Apr 15 19:43:09 CDT 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Apr 15 19:43:09 CDT 2017 Ended at Sat Apr 15 19:44:44 CDT 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Apr 15 19:44:46 CDT 2017 /work2/r1774/subjects/J106388/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8345, pval=0.9628 >= threshold=0.0050) awk -f /home/ums/r1774/freesurfer/bin/extract_talairach_avi_QA.awk /work2/r1774/subjects/J106388/mri/transforms/talairach_avi.log tal_QC_AZS /work2/r1774/subjects/J106388/mri/transforms/talairach_avi.log TalAviQA: 0.97329 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Sat Apr 15 19:44:46 CDT 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /work2/r1774/subjects/J106388/mri /home/ums/r1774/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux Sat Apr 15 19:44:46 CDT 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.28839 /work2/r1774/subjects/J106388/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28839/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28839/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28839/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Apr 15 19:44:52 CDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.28839/nu0.mnc ./tmp.mri_nu_correct.mni.28839/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28839/0/ [r1774@n026:/work2/r1774/subjects/J106388/mri/] [2017-04-15 19:44:52] running: /home/ums/r1774/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.28839/0/ ./tmp.mri_nu_correct.mni.28839/nu0.mnc ./tmp.mri_nu_correct.mni.28839/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00150359 -------------------------------------------------------- Iteration 2 Sat Apr 15 19:46:21 CDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.28839/nu1.mnc ./tmp.mri_nu_correct.mni.28839/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.28839/1/ [r1774@n026:/work2/r1774/subjects/J106388/mri/] [2017-04-15 19:46:21] running: /home/ums/r1774/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.28839/1/ ./tmp.mri_nu_correct.mni.28839/nu1.mnc ./tmp.mri_nu_correct.mni.28839/nu2.imp Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000998657 mri_binarize --i ./tmp.mri_nu_correct.mni.28839/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28839/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /work2/r1774/subjects/J106388/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.28839/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28839/ones.mgz sysname Linux hostname n026 machine x86_64 user r1774 input ./tmp.mri_nu_correct.mni.28839/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.28839/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.28839/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28839/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28839/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28839/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28839/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28839/input.mean.dat sysname Linux hostname n026 machine x86_64 user r1774 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28839/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.28839/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28839/ones.mgz --i ./tmp.mri_nu_correct.mni.28839/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28839/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28839/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28839/ones.mgz --i ./tmp.mri_nu_correct.mni.28839/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28839/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28839/output.mean.dat sysname Linux hostname n026 machine x86_64 user r1774 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28839/ones.mgz Loading ./tmp.mri_nu_correct.mni.28839/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.28839/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.28839/nu2.mnc ./tmp.mri_nu_correct.mni.28839/nu2.mnc mul .96667712554826846998 Saving result to './tmp.mri_nu_correct.mni.28839/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.28839/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.28839/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.28839/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 13 seconds. mapping (17, 161) to ( 3, 110) Sat Apr 15 19:48:28 CDT 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /work2/r1774/subjects/J106388/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Apr 15 19:48:30 CDT 2017 /work2/r1774/subjects/J106388/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.14354 -0.00307 0.00525 3.27083; 0.02179 1.07977 0.20371 -10.97724; -0.03053 -0.23862 1.14709 -10.99640; 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 = 11 Starting OpenSpline(): npoints = 11 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 89 gm peak at 67 (67), valley at 24 (24) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 88 (88), valley at 23 (23) csf peak at 45, setting threshold to 73 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 24 seconds. #-------------------------------------------- #@# Skull Stripping Sat Apr 15 19:51:56 CDT 2017 /work2/r1774/subjects/J106388/mri mri_em_register -rusage /work2/r1774/subjects/J106388/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /home/ums/r1774/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/ums/r1774/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (48, 45, 31) --> (211, 244, 226) using (102, 111, 129) as brain centroid... mean wm in atlas = 108, using box (82,86,105) --> (122, 135,153) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 105 +- 8.9 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.484 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.486791 @ (-9.091, -9.091, -9.091) max log p = -4.467592 @ (4.545, 13.636, 4.545) max log p = -4.411659 @ (-2.273, 2.273, 2.273) max log p = -4.411659 @ (0.000, 0.000, 0.000) max log p = -4.403518 @ (-1.705, -1.705, -3.977) max log p = -4.403518 @ (0.000, 0.000, 0.000) Found translation: (-8.5, 5.1, -6.3): log p = -4.404 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.213, old_max_log_p =-4.404 (thresh=-4.4) 1.14016 0.13868 0.05744 -45.45818; -0.15011 1.05337 0.43632 -33.30295; 0.00000 -0.44009 1.06246 39.24962; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.206, old_max_log_p =-4.213 (thresh=-4.2) 1.13983 -0.15121 -0.02058 -4.54724; 0.13999 1.01764 0.27635 -45.69044; -0.01959 -0.29883 1.11032 16.95842; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.206, old_max_log_p =-4.206 (thresh=-4.2) 1.13983 -0.15121 -0.02058 -4.54724; 0.13999 1.01764 0.27635 -45.69044; -0.01959 -0.29883 1.11032 16.95842; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.158, old_max_log_p =-4.206 (thresh=-4.2) 1.12564 -0.00053 -0.05381 -14.92473; -0.00973 1.07609 0.25193 -32.36113; 0.05701 -0.25787 1.09640 5.00505; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.157, old_max_log_p =-4.158 (thresh=-4.2) 1.12391 0.05302 0.03445 -30.77943; -0.08342 1.07492 0.25022 -22.41058; -0.01673 -0.25729 1.09757 14.37519; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.139, old_max_log_p =-4.157 (thresh=-4.2) 1.12450 0.06185 0.03661 -32.77515; -0.09266 1.07105 0.25859 -21.71305; -0.01607 -0.26638 1.09677 15.61335; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.133, old_max_log_p =-4.139 (thresh=-4.1) 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.133, old_max_log_p =-4.133 (thresh=-4.1) 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.133 (old=-4.484) transform before final EM align: 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 1.12318 0.06178 0.03656 -32.58996; -0.09255 1.06980 0.25829 -21.52099; -0.01613 -0.26732 1.10063 15.27802; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1593.340000 mri_em_register stimesec 1.024000 mri_em_register ru_maxrss 610072 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162236 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 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 47 mri_em_register ru_nivcsw 6737 registration took 26 minutes and 35 seconds. mri_watershed -rusage /work2/r1774/subjects/J106388/touch/rusage.mri_watershed.dat -T1 -brain_atlas /home/ums/r1774/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=130 y=116 z=114 r=84 first estimation of the main basin volume: 2553390 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=105, y=107, z=78, Imax=255 CSF=15, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=7846788748 voxels, voxel volume =1.000 = 7846788748 mmm3 = 7846788.608 cm3 done. PostAnalyze...Basin Prior 72 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=116, z=113, r=9256 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45026 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1035237410 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1052646882 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1070256482 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1073892854 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=47 , nb = 1073681824 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 55, 89 after analyzing : 4, 38, 55, 50 RIGHT_CER before analyzing : 4, 6, 51, 94 after analyzing : 4, 36, 51, 50 LEFT_CER before analyzing : 5, 7, 50, 93 after analyzing : 5, 35, 50, 49 RIGHT_BRAIN before analyzing : 4, 6, 54, 87 after analyzing : 4, 38, 54, 50 LEFT_BRAIN before analyzing : 4, 6, 55, 89 after analyzing : 4, 38, 55, 50 OTHER before analyzing : 47, 31, 25, 39 after analyzing : 25, 31, 31, 33 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 65.041, std = 6.661 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.31, sigma = 3.70 after rotation: sse = 2.31, sigma = 3.70 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.38, its var is 3.02 before Erosion-Dilatation 0.11% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 1360003 voxels, voxel volume = 1.000 mm3 = 1360003 mmm3 = 1360.003 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 36.536000 mri_watershed stimesec 0.512000 mri_watershed ru_maxrss 828760 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 213163 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 6808 mri_watershed ru_oublock 2136 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 48 mri_watershed ru_nivcsw 111 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Apr 15 20:19:09 CDT 2017 /work2/r1774/subjects/J106388/mri mri_em_register -rusage /work2/r1774/subjects/J106388/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.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/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (66, 55, 45) --> (191, 183, 197) using (108, 98, 121) as brain centroid... mean wm in atlas = 107, using box (93,82,102) --> (123, 113,139) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.7 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.081 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.016648 @ (-9.091, 9.091, -9.091) max log p = -3.942364 @ (4.545, -4.545, 4.545) max log p = -3.942364 @ (0.000, 0.000, 0.000) max log p = -3.881059 @ (-1.136, 3.409, -3.409) max log p = -3.881059 @ (0.000, 0.000, 0.000) max log p = -3.881059 @ (0.000, 0.000, 0.000) Found translation: (-5.7, 8.0, -8.0): log p = -3.881 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.726, old_max_log_p =-3.881 (thresh=-3.9) 1.15000 0.00000 0.00000 -25.54465; 0.00000 1.11081 0.25882 -41.23286; 0.00000 -0.29764 0.96593 29.04753; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.726, old_max_log_p =-3.726 (thresh=-3.7) 1.15000 0.00000 0.00000 -25.54465; 0.00000 1.11081 0.25882 -41.23286; 0.00000 -0.29764 0.96593 29.04753; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.615, old_max_log_p =-3.726 (thresh=-3.7) 1.12763 0.00080 -0.00215 -20.24891; -0.00004 1.07997 0.28234 -36.87709; 0.00237 -0.34909 0.99202 35.64771; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.612, old_max_log_p =-3.615 (thresh=-3.6) 1.14746 -0.02356 -0.04465 -15.31387; 0.03614 1.05955 0.27579 -40.38513; 0.03926 -0.34888 0.99141 29.00084; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.583, old_max_log_p =-3.612 (thresh=-3.6) 1.14593 -0.00669 -0.01318 -20.17296; 0.00857 1.05285 0.29231 -36.46310; 0.01057 -0.36705 0.99096 35.86005; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.581, old_max_log_p =-3.583 (thresh=-3.6) 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.581 (old=-4.081) transform before final EM align: 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.0 tol 0.000000 final transform: 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 956.248000 mri_em_register stimesec 0.832000 mri_em_register ru_maxrss 599308 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158899 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 2136 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 84 mri_em_register ru_nivcsw 1859 registration took 15 minutes and 57 seconds. #-------------------------------------- #@# CA Normalize Sat Apr 15 20:35:06 CDT 2017 /work2/r1774/subjects/J106388/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (66, 55, 45) --> (191, 183, 197) using (108, 98, 121) as brain centroid... mean wm in atlas = 107, using box (93,82,102) --> (123, 113,139) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.7 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 1.14593 -0.00669 -0.01318 -20.17296; 0.00856 1.05161 0.29196 -36.28057; 0.01056 -0.36662 0.98980 35.94159; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 56, 40) --> (187, 163, 198) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 4618 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 56, 39) --> (131, 157, 198) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 5 of 3938 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 140, 72) --> (173, 178, 124) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 122 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (91, 140, 69) --> (130, 177, 124) Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 3 of 35 (8.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 126, 104) --> (146, 189, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 353 (0.0%) samples deleted using 9066 total control points for intensity normalization... bias field = 0.947 +- 0.056 52 of 9058 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 56, 40) --> (187, 163, 198) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 5320 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 56, 39) --> (131, 157, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 4796 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 140, 72) --> (173, 178, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 192 (3.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (91, 140, 69) --> (130, 177, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 69 (68.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 126, 104) --> (146, 189, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 139 of 455 (30.5%) samples deleted using 10832 total control points for intensity normalization... bias field = 1.046 +- 0.049 47 of 10568 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 56, 40) --> (187, 163, 198) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 2 of 5351 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 56, 39) --> (131, 157, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 4801 (0.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 140, 72) --> (173, 178, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 32 of 214 (15.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (91, 140, 69) --> (130, 177, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 63 of 104 (60.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 126, 104) --> (146, 189, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 182 of 451 (40.4%) samples deleted using 10921 total control points for intensity normalization... bias field = 1.038 +- 0.044 42 of 10465 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 58 seconds. #-------------------------------------- #@# CA Reg Sat Apr 15 20:37:04 CDT 2017 /work2/r1774/subjects/J106388/mri mri_ca_register -rusage /work2/r1774/subjects/J106388/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.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/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.32 (predicted orig area = 6.1) 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=0.954, neg=0, invalid=762 0001: dt=287.686880, rms=0.815 (14.616%), neg=0, invalid=762 0002: dt=152.012403, rms=0.787 (3.375%), neg=0, invalid=762 0003: dt=290.051842, rms=0.771 (2.067%), neg=0, invalid=762 0004: dt=148.714976, rms=0.762 (1.188%), neg=0, invalid=762 0005: dt=221.952000, rms=0.756 (0.717%), neg=0, invalid=762 0006: dt=183.272727, rms=0.751 (0.655%), neg=0, invalid=762 0007: dt=129.472000, rms=0.748 (0.375%), neg=0, invalid=762 0008: dt=517.888000, rms=0.742 (0.895%), neg=0, invalid=762 0009: dt=129.472000, rms=0.740 (0.279%), neg=0, invalid=762 0010: dt=443.904000, rms=0.737 (0.379%), neg=0, invalid=762 0011: dt=110.976000, rms=0.735 (0.269%), neg=0, invalid=762 0012: dt=887.808000, rms=0.731 (0.527%), neg=0, invalid=762 0013: dt=92.480000, rms=0.729 (0.262%), neg=0, invalid=762 0014: dt=2071.552000, rms=0.723 (0.781%), neg=0, invalid=762 0015: dt=92.480000, rms=0.721 (0.338%), neg=0, invalid=762 0016: dt=295.936000, rms=0.721 (0.056%), neg=0, invalid=762 0017: dt=295.936000, rms=0.719 (0.163%), neg=0, invalid=762 0018: dt=295.936000, rms=0.719 (0.123%), neg=0, invalid=762 0019: dt=295.936000, rms=0.717 (0.274%), neg=0, invalid=762 0020: dt=295.936000, rms=0.714 (0.338%), neg=0, invalid=762 0021: dt=295.936000, rms=0.712 (0.240%), neg=0, invalid=762 0022: dt=295.936000, rms=0.711 (0.226%), neg=0, invalid=762 0023: dt=295.936000, rms=0.708 (0.415%), neg=0, invalid=762 0024: dt=295.936000, rms=0.707 (0.136%), neg=0, invalid=762 0025: dt=295.936000, rms=0.706 (0.069%), neg=0, invalid=762 0026: dt=295.936000, rms=0.704 (0.329%), neg=0, invalid=762 0027: dt=295.936000, rms=0.704 (-0.024%), neg=0, invalid=762 0028: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0029: dt=129.472000, rms=0.702 (0.363%), neg=0, invalid=762 0030: dt=129.472000, rms=0.702 (0.067%), neg=0, invalid=762 0031: dt=129.472000, rms=0.701 (0.109%), neg=0, invalid=762 0032: dt=129.472000, rms=0.700 (0.121%), neg=0, invalid=762 0033: dt=129.472000, rms=0.699 (0.117%), neg=0, invalid=762 0034: dt=129.472000, rms=0.698 (0.097%), neg=0, invalid=762 0035: dt=369.920000, rms=0.698 (0.109%), neg=0, invalid=762 0036: dt=32.368000, rms=0.698 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.709, neg=0, invalid=762 0037: dt=36.288000, rms=0.706 (0.392%), neg=0, invalid=762 0038: dt=226.973978, rms=0.694 (1.745%), neg=0, invalid=762 0039: dt=40.236287, rms=0.688 (0.827%), neg=0, invalid=762 0040: dt=108.410104, rms=0.680 (1.191%), neg=0, invalid=762 0041: dt=19.007519, rms=0.678 (0.322%), neg=0, invalid=762 0042: dt=20.736000, rms=0.677 (0.042%), neg=0, invalid=762 0043: dt=20.736000, rms=0.677 (0.089%), neg=0, invalid=762 0044: dt=20.736000, rms=0.675 (0.177%), neg=0, invalid=762 0045: dt=20.736000, rms=0.673 (0.286%), neg=0, invalid=762 0046: dt=20.736000, rms=0.671 (0.366%), neg=0, invalid=762 0047: dt=20.736000, rms=0.668 (0.446%), neg=0, invalid=762 0048: dt=20.736000, rms=0.665 (0.468%), neg=0, invalid=762 0049: dt=20.736000, rms=0.662 (0.444%), neg=0, invalid=762 0050: dt=20.736000, rms=0.659 (0.431%), neg=0, invalid=762 0051: dt=20.736000, rms=0.656 (0.421%), neg=0, invalid=762 0052: dt=20.736000, rms=0.654 (0.386%), neg=0, invalid=762 0053: dt=20.736000, rms=0.652 (0.346%), neg=0, invalid=762 0054: dt=20.736000, rms=0.650 (0.299%), neg=0, invalid=762 0055: dt=20.736000, rms=0.648 (0.245%), neg=0, invalid=762 0056: dt=20.736000, rms=0.647 (0.204%), neg=0, invalid=762 0057: dt=20.736000, rms=0.645 (0.193%), neg=0, invalid=762 0058: dt=20.736000, rms=0.644 (0.172%), neg=0, invalid=762 0059: dt=20.736000, rms=0.643 (0.172%), neg=0, invalid=762 0060: dt=20.736000, rms=0.642 (0.155%), neg=0, invalid=762 0061: dt=20.736000, rms=0.641 (0.145%), neg=0, invalid=762 0062: dt=20.736000, rms=0.640 (0.145%), neg=0, invalid=762 0063: dt=20.736000, rms=0.639 (0.148%), neg=0, invalid=762 0064: dt=20.736000, rms=0.639 (0.127%), neg=0, invalid=762 0065: dt=20.736000, rms=0.638 (0.125%), neg=0, invalid=762 0066: dt=20.736000, rms=0.637 (0.096%), neg=0, invalid=762 0067: dt=20.736000, rms=0.637 (0.090%), neg=0, invalid=762 0068: dt=103.680000, rms=0.636 (0.039%), neg=0, invalid=762 0069: dt=103.680000, rms=0.636 (0.043%), neg=0, invalid=762 0070: dt=103.680000, rms=0.636 (0.050%), neg=0, invalid=762 0071: dt=103.680000, rms=0.635 (0.174%), neg=0, invalid=762 0072: dt=103.680000, rms=0.635 (-0.728%), neg=0, invalid=762 0073: dt=7.776000, rms=0.635 (0.010%), neg=0, invalid=762 0074: dt=2.268000, rms=0.635 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=762 0075: dt=67.029586, rms=0.633 (0.359%), neg=0, invalid=762 0076: dt=25.920000, rms=0.633 (0.028%), neg=0, invalid=762 0077: dt=25.920000, rms=0.633 (0.010%), neg=0, invalid=762 0078: dt=25.920000, rms=0.633 (0.008%), neg=0, invalid=762 0079: dt=25.920000, rms=0.633 (0.011%), neg=0, invalid=762 0080: dt=25.920000, rms=0.633 (0.007%), neg=0, invalid=762 0081: dt=331.776000, rms=0.632 (0.131%), neg=0, invalid=762 0082: dt=36.288000, rms=0.631 (0.036%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0083: dt=2.800000, rms=0.664 (0.113%), neg=0, invalid=762 0084: dt=2.000000, rms=0.664 (0.006%), neg=0, invalid=762 0085: dt=2.000000, rms=0.664 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0086: dt=2.400000, rms=0.664 (0.102%), neg=0, invalid=762 0087: dt=1.600000, rms=0.664 (0.001%), neg=0, invalid=762 0088: dt=1.600000, rms=0.664 (0.003%), neg=0, invalid=762 0089: dt=1.600000, rms=0.664 (-0.015%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.752, neg=0, invalid=762 0090: dt=6.102564, rms=0.732 (2.675%), neg=0, invalid=762 0091: dt=6.933333, rms=0.728 (0.570%), neg=0, invalid=762 0092: dt=0.720000, rms=0.728 (-0.002%), neg=0, invalid=762 0093: dt=0.720000, rms=0.728 (0.001%), neg=0, invalid=762 0094: dt=0.720000, rms=0.728 (0.000%), neg=0, invalid=762 0095: dt=0.720000, rms=0.728 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.729, neg=0, invalid=762 0096: dt=0.000000, rms=0.728 (0.060%), neg=0, invalid=762 0097: dt=0.000000, rms=0.728 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.808, neg=0, invalid=762 0098: dt=0.000000, rms=0.807 (0.049%), neg=0, invalid=762 0099: dt=0.000000, rms=0.807 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.808, neg=0, invalid=762 0100: dt=0.080000, rms=0.807 (0.051%), neg=0, invalid=762 0101: dt=0.028000, rms=0.807 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.672, neg=0, invalid=762 0102: dt=0.892198, rms=0.653 (2.809%), neg=0, invalid=762 0103: dt=0.096000, rms=0.652 (0.169%), neg=0, invalid=762 0104: dt=0.096000, rms=0.652 (-0.113%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0105: dt=0.028000, rms=0.652 (0.093%), neg=0, invalid=762 0106: dt=0.000023, rms=0.652 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.19186 (27) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (2006 voxels, overlap=0.336) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (2006 voxels, peak = 30), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.18128 (26) Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (1565 voxels, overlap=0.247) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1565 voxels, peak = 26), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.07595 (93) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (799 voxels, overlap=0.674) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (799 voxels, peak = 92), gca=91.7 gca peak = 0.20183 (93) mri peak = 0.06911 (94) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (732 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (732 voxels, peak = 92), gca=91.6 gca peak = 0.21683 (55) mri peak = 0.10024 (79) Right_Hippocampus (53): linear fit = 1.38 x + 0.0 (876 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.38 x + 0.0 (876 voxels, peak = 76), gca=76.2 gca peak = 0.30730 (58) mri peak = 0.12981 (78) Left_Hippocampus (17): linear fit = 1.33 x + 0.0 (872 voxels, overlap=0.015) Left_Hippocampus (17): linear fit = 1.33 x + 0.0 (872 voxels, peak = 77), gca=76.9 gca peak = 0.11430 (101) mri peak = 0.08920 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (57657 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (57657 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.09679 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (60944 voxels, overlap=0.779) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (60944 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.04258 (90) Left_Cerebral_Cortex (3): linear fit = 1.51 x + 0.0 (19098 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.51 x + 0.0 (19098 voxels, peak = 89), gca=89.4 gca peak = 0.15082 (58) mri peak = 0.04347 (90) Right_Cerebral_Cortex (42): linear fit = 1.51 x + 0.0 (20489 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.51 x + 0.0 (20489 voxels, peak = 88), gca=87.9 gca peak = 0.14161 (67) mri peak = 0.17449 (80) Right_Caudate (50): linear fit = 1.17 x + 0.0 (355 voxels, overlap=0.002) Right_Caudate (50): linear fit = 1.17 x + 0.0 (355 voxels, peak = 79), gca=78.7 gca peak = 0.15243 (71) mri peak = 0.12130 (80) Left_Caudate (11): linear fit = 1.07 x + 0.0 (733 voxels, overlap=0.573) Left_Caudate (11): linear fit = 1.07 x + 0.0 (733 voxels, peak = 76), gca=75.6 gca peak = 0.13336 (57) mri peak = 0.04761 (82) Left_Cerebellum_Cortex (8): linear fit = 1.47 x + 0.0 (18149 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.47 x + 0.0 (18149 voxels, peak = 84), gca=83.5 gca peak = 0.13252 (56) mri peak = 0.04512 (79) Right_Cerebellum_Cortex (47): linear fit = 1.46 x + 0.0 (18994 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.46 x + 0.0 (18994 voxels, peak = 81), gca=81.5 gca peak = 0.18181 (84) mri peak = 0.05848 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (7267 voxels, overlap=0.784) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (7267 voxels, peak = 93), gca=92.8 gca peak = 0.20573 (83) mri peak = 0.04063 (77) Right_Cerebellum_White_Matter (46): linear fit = 0.95 x + 0.0 (5734 voxels, overlap=0.654) Right_Cerebellum_White_Matter (46): linear fit = 0.95 x + 0.0 (5734 voxels, peak = 79), gca=79.3 gca peak = 0.21969 (57) mri peak = 0.10444 (75) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (313 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (313 voxels, peak = 76), gca=75.5 gca peak = 0.39313 (56) mri peak = 0.11034 (77) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (234 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (234 voxels, peak = 74), gca=73.6 gca peak = 0.14181 (85) mri peak = 0.10637 (90) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4775 voxels, overlap=0.802) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4775 voxels, peak = 87), gca=87.1 gca peak = 0.11978 (83) mri peak = 0.11225 (89) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3722 voxels, overlap=0.626) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3722 voxels, peak = 88), gca=88.4 gca peak = 0.13399 (79) mri peak = 0.07661 (89) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2244 voxels, overlap=0.257) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2244 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.08002 (85) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2299 voxels, overlap=0.451) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2299 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.12769 (89) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8441 voxels, overlap=0.107) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8441 voxels, peak = 89), gca=89.2 gca peak = 0.13281 (86) mri peak = 0.08205 (91) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (917 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (917 voxels, peak = 89), gca=89.0 gca peak = 0.12801 (89) mri peak = 0.09434 (91) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1059 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1059 voxels, peak = 92), gca=92.1 gca peak = 0.20494 (23) mri peak = 0.10813 (26) gca peak = 0.15061 (21) mri peak = 0.08414 (43) Fourth_Ventricle (15): linear fit = 1.85 x + 0.0 (615 voxels, overlap=0.068) Fourth_Ventricle (15): linear fit = 1.85 x + 0.0 (615 voxels, peak = 39), gca=38.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_Cortex = 0.14995 (59) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Cerebral_Cortex = 0.15082 (58) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.34 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.677, neg=0, invalid=762 0107: dt=76.126180, rms=0.642 (5.181%), neg=0, invalid=762 0108: dt=142.084142, rms=0.635 (1.004%), neg=0, invalid=762 0109: dt=517.888000, rms=0.627 (1.259%), neg=0, invalid=762 0110: dt=73.984000, rms=0.626 (0.109%), neg=0, invalid=762 0111: dt=443.904000, rms=0.623 (0.512%), neg=0, invalid=762 0112: dt=295.936000, rms=0.619 (0.646%), neg=0, invalid=762 0113: dt=8.092000, rms=0.619 (0.003%), neg=0, invalid=762 0114: dt=8.092000, rms=0.619 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=762 0115: dt=129.472000, rms=0.618 (0.282%), neg=0, invalid=762 0116: dt=517.888000, rms=0.614 (0.525%), neg=0, invalid=762 0117: dt=32.368000, rms=0.614 (0.013%), neg=0, invalid=762 0118: dt=32.368000, rms=0.614 (0.004%), neg=0, invalid=762 0119: dt=32.368000, rms=0.614 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.615, neg=0, invalid=762 0120: dt=76.153846, rms=0.608 (0.989%), neg=0, invalid=762 0121: dt=204.267898, rms=0.592 (2.697%), neg=0, invalid=762 0122: dt=31.104000, rms=0.588 (0.704%), neg=0, invalid=762 0123: dt=91.745665, rms=0.586 (0.262%), neg=0, invalid=762 0124: dt=175.527426, rms=0.580 (1.142%), neg=0, invalid=762 0125: dt=30.675862, rms=0.578 (0.358%), neg=0, invalid=762 0126: dt=62.208000, rms=0.577 (0.102%), neg=0, invalid=762 0127: dt=414.720000, rms=0.571 (1.055%), neg=0, invalid=762 0128: dt=31.104000, rms=0.569 (0.413%), neg=0, invalid=762 0129: dt=36.288000, rms=0.568 (0.076%), neg=0, invalid=762 0130: dt=580.608000, rms=0.564 (0.665%), neg=0, invalid=762 0131: dt=36.288000, rms=0.562 (0.374%), neg=0, invalid=762 0132: dt=124.416000, rms=0.561 (0.196%), neg=0, invalid=762 0133: dt=36.288000, rms=0.561 (0.059%), neg=0, invalid=762 0134: dt=414.720000, rms=0.559 (0.232%), neg=0, invalid=762 0135: dt=36.288000, rms=0.558 (0.209%), neg=0, invalid=762 0136: dt=124.416000, rms=0.558 (0.114%), neg=0, invalid=762 0137: dt=62.208000, rms=0.557 (0.074%), neg=0, invalid=762 0138: dt=248.832000, rms=0.556 (0.148%), neg=0, invalid=762 0139: dt=36.288000, rms=0.556 (0.083%), neg=0, invalid=762 0140: dt=145.152000, rms=0.555 (0.105%), neg=0, invalid=762 0141: dt=36.288000, rms=0.555 (0.036%), neg=0, invalid=762 0142: dt=36.288000, rms=0.555 (0.031%), neg=0, invalid=762 0143: dt=36.288000, rms=0.555 (0.048%), neg=0, invalid=762 0144: dt=36.288000, rms=0.554 (0.065%), neg=0, invalid=762 0145: dt=36.288000, rms=0.554 (0.081%), neg=0, invalid=762 0146: dt=36.288000, rms=0.553 (0.096%), neg=0, invalid=762 0147: dt=36.288000, rms=0.553 (0.104%), neg=0, invalid=762 0148: dt=36.288000, rms=0.553 (0.021%), neg=0, invalid=762 0149: dt=36.288000, rms=0.552 (0.040%), neg=0, invalid=762 0150: dt=36.288000, rms=0.552 (0.020%), neg=0, invalid=762 0151: dt=2.268000, rms=0.552 (0.003%), neg=0, invalid=762 0152: dt=0.035437, rms=0.552 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0153: dt=145.152000, rms=0.549 (0.591%), neg=0, invalid=762 0154: dt=36.288000, rms=0.549 (0.106%), neg=0, invalid=762 0155: dt=145.152000, rms=0.548 (0.156%), neg=0, invalid=762 0156: dt=82.944000, rms=0.547 (0.094%), neg=0, invalid=762 0157: dt=62.208000, rms=0.547 (0.099%), neg=0, invalid=762 0158: dt=36.288000, rms=0.547 (0.025%), neg=0, invalid=762 0159: dt=36.288000, rms=0.546 (0.034%), neg=0, invalid=762 0160: dt=36.288000, rms=0.546 (0.058%), neg=0, invalid=762 0161: dt=36.288000, rms=0.546 (0.080%), neg=0, invalid=762 0162: dt=36.288000, rms=0.545 (0.096%), neg=0, invalid=762 0163: dt=36.288000, rms=0.545 (0.107%), neg=0, invalid=762 0164: dt=36.288000, rms=0.544 (0.108%), neg=0, invalid=762 0165: dt=36.288000, rms=0.543 (0.109%), neg=0, invalid=762 0166: dt=36.288000, rms=0.543 (0.108%), neg=0, invalid=762 0167: dt=36.288000, rms=0.542 (0.112%), neg=0, invalid=762 0168: dt=36.288000, rms=0.542 (0.117%), neg=0, invalid=762 0169: dt=36.288000, rms=0.541 (0.113%), neg=0, invalid=762 0170: dt=36.288000, rms=0.540 (0.111%), neg=0, invalid=762 0171: dt=36.288000, rms=0.540 (0.106%), neg=0, invalid=762 0172: dt=36.288000, rms=0.539 (0.103%), neg=0, invalid=762 0173: dt=36.288000, rms=0.539 (0.104%), neg=0, invalid=762 0174: dt=36.288000, rms=0.539 (0.017%), neg=0, invalid=762 0175: dt=36.288000, rms=0.538 (0.025%), neg=0, invalid=762 0176: dt=36.288000, rms=0.538 (0.034%), neg=0, invalid=762 0177: dt=36.288000, rms=0.538 (0.038%), neg=0, invalid=762 0178: dt=36.288000, rms=0.538 (0.047%), neg=0, invalid=762 0179: dt=36.288000, rms=0.538 (0.047%), neg=0, invalid=762 0180: dt=36.288000, rms=0.537 (0.050%), neg=0, invalid=762 0181: dt=36.288000, rms=0.537 (0.056%), neg=0, invalid=762 0182: dt=36.288000, rms=0.537 (0.058%), neg=0, invalid=762 0183: dt=36.288000, rms=0.536 (0.058%), neg=0, invalid=762 0184: dt=36.288000, rms=0.536 (0.061%), neg=0, invalid=762 0185: dt=36.288000, rms=0.536 (0.063%), neg=0, invalid=762 0186: dt=36.288000, rms=0.535 (0.065%), neg=0, invalid=762 0187: dt=36.288000, rms=0.535 (0.063%), neg=0, invalid=762 0188: dt=36.288000, rms=0.535 (0.065%), neg=0, invalid=762 0189: dt=36.288000, rms=0.534 (0.061%), neg=0, invalid=762 0190: dt=36.288000, rms=0.534 (0.067%), neg=0, invalid=762 0191: dt=36.288000, rms=0.534 (0.068%), neg=0, invalid=762 0192: dt=36.288000, rms=0.533 (0.067%), neg=0, invalid=762 0193: dt=36.288000, rms=0.533 (0.064%), neg=0, invalid=762 0194: dt=36.288000, rms=0.533 (0.060%), neg=0, invalid=762 0195: dt=36.288000, rms=0.532 (0.055%), neg=0, invalid=762 0196: dt=36.288000, rms=0.532 (0.056%), neg=0, invalid=762 0197: dt=36.288000, rms=0.532 (0.057%), neg=0, invalid=762 0198: dt=36.288000, rms=0.531 (0.055%), neg=0, invalid=762 0199: dt=36.288000, rms=0.531 (0.053%), neg=0, invalid=762 0200: dt=36.288000, rms=0.531 (0.054%), neg=0, invalid=762 0201: dt=36.288000, rms=0.531 (0.047%), neg=0, invalid=762 0202: dt=36.288000, rms=0.530 (0.048%), neg=0, invalid=762 0203: dt=36.288000, rms=0.530 (0.050%), neg=0, invalid=762 0204: dt=36.288000, rms=0.530 (0.046%), neg=0, invalid=762 0205: dt=36.288000, rms=0.530 (0.046%), neg=0, invalid=762 0206: dt=36.288000, rms=0.529 (0.042%), neg=0, invalid=762 0207: dt=36.288000, rms=0.529 (0.040%), neg=0, invalid=762 0208: dt=36.288000, rms=0.529 (0.042%), neg=0, invalid=762 0209: dt=36.288000, rms=0.529 (0.036%), neg=0, invalid=762 0210: dt=36.288000, rms=0.529 (0.037%), neg=0, invalid=762 0211: dt=36.288000, rms=0.528 (0.039%), neg=0, invalid=762 0212: dt=36.288000, rms=0.528 (0.039%), neg=0, invalid=762 0213: dt=36.288000, rms=0.528 (0.038%), neg=0, invalid=762 0214: dt=36.288000, rms=0.528 (0.031%), neg=0, invalid=762 0215: dt=36.288000, rms=0.528 (0.032%), neg=0, invalid=762 0216: dt=36.288000, rms=0.527 (0.030%), neg=0, invalid=762 0217: dt=36.288000, rms=0.527 (0.034%), neg=0, invalid=762 0218: dt=36.288000, rms=0.527 (0.030%), neg=0, invalid=762 0219: dt=36.288000, rms=0.527 (0.027%), neg=0, invalid=762 0220: dt=36.288000, rms=0.527 (0.004%), neg=0, invalid=762 0221: dt=36.288000, rms=0.527 (0.007%), neg=0, invalid=762 0222: dt=4.536000, rms=0.527 (0.001%), neg=0, invalid=762 0223: dt=1.944000, rms=0.527 (0.000%), neg=0, invalid=762 0224: dt=0.060750, rms=0.527 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0225: dt=24.351220, rms=0.532 (0.206%), neg=0, invalid=762 0226: dt=84.176707, rms=0.529 (0.590%), neg=0, invalid=762 0227: dt=38.400000, rms=0.527 (0.402%), neg=0, invalid=762 0228: dt=11.200000, rms=0.526 (0.285%), neg=0, invalid=762 0229: dt=2.800000, rms=0.525 (0.033%), neg=0, invalid=762 0230: dt=1.400000, rms=0.525 (0.015%), neg=0, invalid=762 0231: dt=0.350000, rms=0.525 (0.004%), neg=0, invalid=762 0232: dt=0.175000, rms=0.525 (0.002%), neg=0, invalid=762 0233: dt=0.125000, rms=0.525 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0234: dt=44.800000, rms=0.520 (1.001%), neg=0, invalid=762 0235: dt=25.600000, rms=0.519 (0.251%), neg=0, invalid=762 0236: dt=11.200000, rms=0.518 (0.147%), neg=0, invalid=762 0237: dt=8.000000, rms=0.518 (0.071%), neg=0, invalid=762 0238: dt=0.010937, rms=0.518 (-0.000%), neg=0, invalid=762 0239: dt=0.010937, rms=0.518 (0.000%), neg=0, invalid=762 0240: dt=0.001367, rms=0.518 (0.000%), neg=0, invalid=762 0241: dt=0.000684, rms=0.518 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0242: dt=12.448780, rms=0.530 (0.723%), neg=0, invalid=762 0243: dt=13.824000, rms=0.526 (0.811%), neg=0, invalid=762 0244: dt=16.128000, rms=0.525 (0.186%), neg=0, invalid=762 0245: dt=11.520000, rms=0.523 (0.308%), neg=0, invalid=762 0246: dt=7.333333, rms=0.523 (0.050%), neg=0, invalid=762 0247: dt=7.333333, rms=0.522 (0.079%), neg=0, invalid=762 0248: dt=7.333333, rms=0.522 (0.107%), neg=0, invalid=762 0249: dt=3.666667, rms=0.522 (0.019%), neg=0, invalid=762 0250: dt=1.833333, rms=0.522 (0.008%), neg=0, invalid=762 0251: dt=0.252000, rms=0.522 (0.002%), neg=0, invalid=762 0252: dt=0.252000, rms=0.522 (0.001%), neg=0, invalid=762 0253: dt=0.063000, rms=0.522 (0.001%), neg=0, invalid=762 0254: dt=0.015750, rms=0.522 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0255: dt=17.493333, rms=0.519 (0.538%), neg=0, invalid=762 0256: dt=14.101695, rms=0.518 (0.134%), neg=0, invalid=762 0257: dt=13.161290, rms=0.518 (0.118%), neg=0, invalid=762 0258: dt=10.838710, rms=0.517 (0.084%), neg=0, invalid=762 0259: dt=10.962963, rms=0.517 (0.068%), neg=0, invalid=762 0260: dt=10.926829, rms=0.517 (0.057%), neg=0, invalid=762 0261: dt=10.553191, rms=0.516 (0.054%), neg=0, invalid=762 0262: dt=10.000000, rms=0.516 (0.044%), neg=0, invalid=762 0263: dt=10.000000, rms=0.516 (0.051%), neg=0, invalid=762 0264: dt=10.000000, rms=0.515 (0.071%), neg=0, invalid=762 0265: dt=10.000000, rms=0.515 (0.094%), neg=0, invalid=762 0266: dt=10.000000, rms=0.514 (0.109%), neg=0, invalid=762 0267: dt=10.000000, rms=0.514 (0.120%), neg=0, invalid=762 0268: dt=10.000000, rms=0.513 (0.110%), neg=0, invalid=762 0269: dt=10.000000, rms=0.513 (0.114%), neg=0, invalid=762 0270: dt=10.000000, rms=0.512 (0.127%), neg=0, invalid=762 0271: dt=10.000000, rms=0.511 (0.119%), neg=0, invalid=762 0272: dt=10.000000, rms=0.511 (0.108%), neg=0, invalid=762 0273: dt=10.000000, rms=0.510 (0.092%), neg=0, invalid=762 0274: dt=10.000000, rms=0.510 (0.100%), neg=0, invalid=762 0275: dt=10.000000, rms=0.509 (0.084%), neg=0, invalid=762 0276: dt=10.000000, rms=0.509 (0.076%), neg=0, invalid=762 0277: dt=10.000000, rms=0.509 (0.075%), neg=0, invalid=762 0278: dt=10.000000, rms=0.509 (0.020%), neg=0, invalid=762 0279: dt=10.000000, rms=0.509 (-0.007%), neg=0, invalid=762 0280: dt=2.304000, rms=0.509 (0.000%), neg=0, invalid=762 0281: dt=4.032000, rms=0.509 (0.001%), neg=0, invalid=762 0282: dt=4.032000, rms=0.509 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0283: dt=0.000000, rms=0.522 (0.038%), neg=0, invalid=762 0284: dt=0.000000, rms=0.522 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0285: dt=0.000000, rms=0.522 (0.038%), neg=0, invalid=762 0286: dt=0.000000, rms=0.522 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.499, neg=0, invalid=762 0287: dt=0.112000, rms=0.496 (0.696%), neg=0, invalid=762 0288: dt=0.320000, rms=0.489 (1.451%), neg=0, invalid=762 0289: dt=0.384000, rms=0.485 (0.728%), neg=0, invalid=762 0290: dt=0.384000, rms=0.484 (0.324%), neg=0, invalid=762 0291: dt=0.384000, rms=0.483 (0.190%), neg=0, invalid=762 0292: dt=0.320000, rms=0.482 (0.122%), neg=0, invalid=762 0293: dt=0.320000, rms=0.482 (0.089%), neg=0, invalid=762 0294: dt=0.112000, rms=0.482 (0.033%), neg=0, invalid=762 0295: dt=0.112000, rms=0.481 (0.028%), neg=0, invalid=762 0296: dt=0.112000, rms=0.481 (0.054%), neg=0, invalid=762 0297: dt=0.112000, rms=0.481 (0.065%), neg=0, invalid=762 0298: dt=0.112000, rms=0.480 (0.073%), neg=0, invalid=762 0299: dt=0.112000, rms=0.480 (0.077%), neg=0, invalid=762 0300: dt=0.112000, rms=0.480 (0.078%), neg=0, invalid=762 0301: dt=0.112000, rms=0.479 (0.070%), neg=0, invalid=762 0302: dt=0.112000, rms=0.479 (0.065%), neg=0, invalid=762 0303: dt=0.112000, rms=0.479 (0.057%), neg=0, invalid=762 0304: dt=0.112000, rms=0.479 (0.048%), neg=0, invalid=762 0305: dt=0.112000, rms=0.478 (0.036%), neg=0, invalid=762 0306: dt=0.112000, rms=0.478 (0.028%), neg=0, invalid=762 0307: dt=0.112000, rms=0.478 (0.019%), neg=0, invalid=762 0308: dt=0.112000, rms=0.478 (0.012%), neg=0, invalid=762 0309: dt=0.000000, rms=0.478 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0310: dt=0.287500, rms=0.476 (0.595%), neg=0, invalid=762 0311: dt=0.320000, rms=0.474 (0.267%), neg=0, invalid=762 0312: dt=0.320000, rms=0.474 (0.106%), neg=0, invalid=762 0313: dt=0.112000, rms=0.474 (0.018%), neg=0, invalid=762 0314: dt=0.112000, rms=0.474 (0.014%), neg=0, invalid=762 0315: dt=0.112000, rms=0.473 (0.023%), neg=0, invalid=762 0316: dt=0.112000, rms=0.473 (0.024%), neg=0, invalid=762 0317: dt=0.112000, rms=0.473 (0.020%), neg=0, invalid=762 0318: dt=0.112000, rms=0.473 (0.011%), neg=0, invalid=762 0319: dt=0.000000, rms=0.473 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0320: dt=0.000000, rms=0.471 (0.051%), neg=0, invalid=762 0321: dt=0.000000, rms=0.471 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0322: dt=110.976000, rms=0.471 (0.070%), neg=0, invalid=762 0323: dt=295.936000, rms=0.471 (0.070%), neg=0, invalid=762 0324: dt=295.936000, rms=0.471 (-0.518%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0325: dt=7.776000, rms=0.471 (0.061%), neg=0, invalid=762 0326: dt=2.268000, rms=0.471 (0.002%), neg=0, invalid=762 0327: dt=2.268000, rms=0.471 (0.000%), neg=0, invalid=762 0328: dt=2.268000, rms=0.471 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0329: dt=124.416000, rms=0.469 (0.426%), neg=0, invalid=762 0330: dt=36.288000, rms=0.468 (0.128%), neg=0, invalid=762 0331: dt=36.288000, rms=0.468 (0.083%), neg=0, invalid=762 0332: dt=36.288000, rms=0.467 (0.098%), neg=0, invalid=762 0333: dt=36.288000, rms=0.467 (0.124%), neg=0, invalid=762 0334: dt=36.288000, rms=0.466 (0.125%), neg=0, invalid=762 0335: dt=36.288000, rms=0.466 (0.149%), neg=0, invalid=762 0336: dt=36.288000, rms=0.465 (0.127%), neg=0, invalid=762 0337: dt=36.288000, rms=0.464 (0.108%), neg=0, invalid=762 0338: dt=36.288000, rms=0.464 (0.096%), neg=0, invalid=762 0339: dt=145.152000, rms=0.464 (0.042%), neg=0, invalid=762 0340: dt=145.152000, rms=0.464 (-0.427%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0341: dt=11.200000, rms=0.464 (0.157%), neg=0, invalid=762 0342: dt=11.200000, rms=0.463 (0.066%), neg=0, invalid=762 0343: dt=11.200000, rms=0.463 (0.053%), neg=0, invalid=762 0344: dt=11.200000, rms=0.463 (0.036%), neg=0, invalid=762 0345: dt=11.200000, rms=0.463 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=762 0346: dt=44.800000, rms=0.458 (1.171%), neg=0, invalid=762 0347: dt=21.488372, rms=0.457 (0.253%), neg=0, invalid=762 0348: dt=44.800000, rms=0.456 (0.224%), neg=0, invalid=762 0349: dt=44.800000, rms=0.456 (-0.257%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=762 0350: dt=7.920398, rms=0.456 (0.423%), neg=0, invalid=762 0351: dt=9.216000, rms=0.456 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0352: dt=9.216000, rms=0.455 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 12 iterations, nbhd size=1, neg = 0 0353: dt=9.216000, rms=0.455 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0354: dt=9.216000, rms=0.455 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0355: dt=11.234043, rms=0.454 (0.070%), neg=0, invalid=762 0356: dt=4.571429, rms=0.454 (0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0357: dt=18.433460, rms=0.449 (1.174%), neg=0, invalid=762 0358: dt=7.583815, rms=0.449 (0.125%), neg=0, invalid=762 0359: dt=7.583815, rms=0.448 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0360: dt=7.583815, rms=0.448 (0.070%), neg=0, invalid=762 0361: dt=7.583815, rms=0.448 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 11 iterations, nbhd size=1, neg = 0 0362: dt=20.000000, rms=0.447 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0363: dt=4.032000, rms=0.447 (0.003%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0364: dt=0.000000, rms=0.452 (0.051%), neg=0, invalid=762 0365: dt=0.000000, rms=0.452 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0366: dt=0.000050, rms=0.452 (0.051%), neg=0, invalid=762 0367: dt=0.000000, rms=0.452 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=762 iter 0, gcam->neg = 778 after 14 iterations, nbhd size=1, neg = 0 0368: dt=1.762168, rms=0.427 (4.048%), neg=0, invalid=762 0369: dt=0.000013, rms=0.427 (0.010%), neg=0, invalid=762 0370: dt=0.000013, rms=0.427 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0371: dt=0.064000, rms=0.426 (0.101%), neg=0, invalid=762 0372: dt=0.007000, rms=0.426 (0.006%), neg=0, invalid=762 0373: dt=0.007000, rms=0.426 (0.000%), neg=0, invalid=762 0374: dt=0.007000, rms=0.426 (-0.003%), neg=0, invalid=762 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 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0375: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0376: dt=0.361250, rms=0.416 (0.000%), neg=0, invalid=762 0377: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0378: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0379: dt=36.288000, rms=0.416 (0.022%), neg=0, invalid=762 0380: dt=103.680000, rms=0.416 (0.033%), neg=0, invalid=762 0381: dt=145.152000, rms=0.416 (0.053%), neg=0, invalid=762 0382: dt=36.288000, rms=0.416 (0.025%), neg=0, invalid=762 0383: dt=36.288000, rms=0.416 (0.005%), neg=0, invalid=762 0384: dt=36.288000, rms=0.416 (0.012%), neg=0, invalid=762 0385: dt=36.288000, rms=0.415 (0.023%), neg=0, invalid=762 0386: dt=36.288000, rms=0.415 (0.027%), neg=0, invalid=762 0387: dt=36.288000, rms=0.415 (0.025%), neg=0, invalid=762 0388: dt=36.288000, rms=0.415 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0389: dt=6.400000, rms=0.416 (0.020%), neg=0, invalid=762 0390: dt=0.700000, rms=0.416 (0.000%), neg=0, invalid=762 0391: dt=0.700000, rms=0.416 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 iter 0, gcam->neg = 15 after 9 iterations, nbhd size=1, neg = 0 0392: dt=98.285714, rms=0.413 (0.525%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0393: dt=20.649886, rms=0.412 (0.334%), neg=0, invalid=762 0394: dt=25.600000, rms=0.412 (0.048%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0395: dt=25.600000, rms=0.411 (0.083%), neg=0, invalid=762 0396: dt=25.600000, rms=0.411 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0397: dt=25.600000, rms=0.411 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0398: dt=25.600000, rms=0.410 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 13 iterations, nbhd size=1, neg = 0 0399: dt=25.600000, rms=0.409 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 10 iterations, nbhd size=1, neg = 0 0400: dt=25.600000, rms=0.409 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 7 iterations, nbhd size=0, neg = 0 0401: dt=25.600000, rms=0.409 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0402: dt=32.000000, rms=0.409 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0403: dt=32.000000, rms=0.409 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0404: dt=1.008000, rms=0.412 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0405: dt=0.864000, rms=0.412 (0.003%), neg=0, invalid=762 0406: dt=0.864000, rms=0.412 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0407: dt=11.733333, rms=0.411 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 13 iterations, nbhd size=1, neg = 0 0408: dt=25.600000, rms=0.410 (0.244%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 5 iterations, nbhd size=0, neg = 0 0409: dt=5.076923, rms=0.410 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0410: dt=5.076923, rms=0.410 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0411: dt=5.076923, rms=0.410 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 12 iterations, nbhd size=1, neg = 0 0412: dt=5.076923, rms=0.409 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 7 iterations, nbhd size=0, neg = 0 0413: dt=5.076923, rms=0.409 (0.058%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0414: dt=0.000060, rms=0.414 (0.000%), neg=0, invalid=762 0415: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0416: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.406, neg=0, invalid=762 iter 0, gcam->neg = 492 after 14 iterations, nbhd size=1, neg = 0 0417: dt=0.977546, rms=0.400 (1.386%), neg=0, invalid=762 0418: dt=0.007000, rms=0.400 (0.000%), neg=0, invalid=762 0419: dt=0.007000, rms=0.400 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=762 0420: dt=0.256000, rms=0.400 (0.166%), neg=0, invalid=762 0421: dt=0.448000, rms=0.399 (0.228%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 13 iterations, nbhd size=1, neg = 0 0422: dt=0.448000, rms=0.398 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0423: dt=0.448000, rms=0.398 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 2 iterations, nbhd size=0, neg = 0 0424: dt=0.448000, rms=0.397 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 12 iterations, nbhd size=1, neg = 0 0425: dt=0.448000, rms=0.397 (-0.033%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 5 hours, 7 minutes and 26 seconds. mri_ca_register utimesec 18430.816000 mri_ca_register stimesec 11.692000 mri_ca_register ru_maxrss 1328988 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5314024 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 2248 mri_ca_register ru_oublock 63880 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 886 mri_ca_register ru_nivcsw 42016 FSRUNTIME@ mri_ca_register 5.1238 hours 1 threads #-------------------------------------- #@# SubCort Seg Sun Apr 16 01:44:30 CDT 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname n026 machine x86_64 setenv SUBJECTS_DIR /work2/r1774/subjects cd /work2/r1774/subjects/J106388/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.08 Atlas used for the 3D morph was /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.16061 (27) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (4169 voxels, overlap=0.391) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (4169 voxels, peak = 26), gca=26.1 gca peak = 0.17677 (13) mri peak = 0.18194 (27) Right_Lateral_Ventricle (43): linear fit = 1.88 x + 0.0 (3758 voxels, overlap=0.184) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3758 voxels, peak = 25), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.09826 (93) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (507 voxels, overlap=0.757) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (507 voxels, peak = 93), gca=92.6 gca peak = 0.16930 (96) mri peak = 0.11488 (95) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (560 voxels, overlap=0.837) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (560 voxels, peak = 94), gca=93.6 gca peak = 0.24553 (55) mri peak = 0.11760 (79) Right_Hippocampus (53): linear fit = 1.38 x + 0.0 (1008 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.38 x + 0.0 (1008 voxels, peak = 76), gca=75.6 gca peak = 0.30264 (59) mri peak = 0.11257 (76) Left_Hippocampus (17): linear fit = 1.32 x + 0.0 (913 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.32 x + 0.0 (913 voxels, peak = 78), gca=77.6 gca peak = 0.07580 (103) mri peak = 0.10433 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34320 voxels, overlap=0.735) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34320 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.11456 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35962 voxels, overlap=0.658) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35962 voxels, peak = 105), gca=104.5 gca peak = 0.09712 (58) mri peak = 0.04029 (84) Left_Cerebral_Cortex (3): linear fit = 1.47 x + 0.0 (17969 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.47 x + 0.0 (17969 voxels, peak = 85), gca=85.0 gca peak = 0.11620 (58) mri peak = 0.04458 (80) Right_Cerebral_Cortex (42): linear fit = 1.41 x + 0.0 (15226 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.41 x + 0.0 (15226 voxels, peak = 82), gca=82.1 gca peak = 0.30970 (66) mri peak = 0.13517 (80) Right_Caudate (50): linear fit = 1.21 x + 0.0 (725 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.21 x + 0.0 (725 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.11396 (80) Left_Caudate (11): linear fit = 1.09 x + 0.0 (700 voxels, overlap=0.506) Left_Caudate (11): linear fit = 1.09 x + 0.0 (700 voxels, peak = 75), gca=74.9 gca peak = 0.13902 (56) mri peak = 0.07453 (81) Left_Cerebellum_Cortex (8): linear fit = 1.43 x + 0.0 (18718 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.43 x + 0.0 (18718 voxels, peak = 80), gca=80.4 gca peak = 0.14777 (55) mri peak = 0.08321 (77) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (18491 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (18491 voxels, peak = 76), gca=75.6 gca peak = 0.16765 (84) mri peak = 0.12987 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (4466 voxels, overlap=0.010) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (4466 voxels, peak = 94), gca=94.5 gca peak = 0.18739 (84) mri peak = 0.13345 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5484 voxels, overlap=0.556) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5484 voxels, peak = 92), gca=92.0 gca peak = 0.29869 (57) mri peak = 0.12861 (79) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (371 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (371 voxels, peak = 77), gca=76.7 gca peak = 0.33601 (57) mri peak = 0.14797 (81) Right_Amygdala (54): linear fit = 1.40 x + 0.0 (421 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.40 x + 0.0 (421 voxels, peak = 80), gca=80.1 gca peak = 0.11131 (90) mri peak = 0.12528 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3579 voxels, overlap=0.786) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3579 voxels, peak = 90), gca=89.6 gca peak = 0.11793 (83) mri peak = 0.12266 (89) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3923 voxels, overlap=0.678) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3923 voxels, peak = 89), gca=89.2 gca peak = 0.08324 (81) mri peak = 0.07956 (83) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1634 voxels, overlap=0.707) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1634 voxels, peak = 88), gca=87.9 gca peak = 0.10360 (77) mri peak = 0.10530 (83) Right_Putamen (51): linear fit = 1.07 x + 0.0 (1392 voxels, overlap=0.546) Right_Putamen (51): linear fit = 1.07 x + 0.0 (1392 voxels, peak = 82), gca=82.0 gca peak = 0.08424 (78) mri peak = 0.11623 (88) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10748 voxels, overlap=0.414) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10748 voxels, peak = 84), gca=83.9 gca peak = 0.12631 (89) mri peak = 0.12110 (92) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1101 voxels, overlap=0.679) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1101 voxels, peak = 93), gca=93.0 gca peak = 0.14500 (87) mri peak = 0.11441 (91) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1218 voxels, overlap=0.811) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1218 voxels, peak = 90), gca=90.0 gca peak = 0.14975 (24) mri peak = 0.16000 (27) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (56 voxels, overlap=1.009) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (56 voxels, peak = 24), gca=23.6 gca peak = 0.19357 (14) mri peak = 0.18952 (27) Fourth_Ventricle (15): linear fit = 1.83 x + 0.0 (493 voxels, overlap=0.172) Fourth_Ventricle (15): linear fit = 1.83 x + 0.0 (493 voxels, peak = 26), gca=25.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.39 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.26 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15817 (24) mri peak = 0.16061 (27) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (4169 voxels, overlap=0.802) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (4169 voxels, peak = 24), gca=24.4 gca peak = 0.14042 (19) mri peak = 0.18194 (27) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (3758 voxels, overlap=0.350) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (3758 voxels, peak = 25), gca=24.6 gca peak = 0.25137 (91) mri peak = 0.09826 (93) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (507 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (507 voxels, peak = 91), gca=90.5 gca peak = 0.20155 (94) mri peak = 0.11488 (95) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (560 voxels, overlap=1.008) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (560 voxels, peak = 94), gca=93.5 gca peak = 0.21456 (76) mri peak = 0.11760 (79) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1008 voxels, overlap=0.891) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1008 voxels, peak = 76), gca=76.0 gca peak = 0.28770 (74) mri peak = 0.11257 (76) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (913 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (913 voxels, peak = 75), gca=75.1 gca peak = 0.07875 (103) mri peak = 0.10433 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34320 voxels, overlap=0.757) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34320 voxels, peak = 103), gca=103.0 gca peak = 0.07908 (105) mri peak = 0.11456 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35962 voxels, overlap=0.674) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35962 voxels, peak = 105), gca=105.0 gca peak = 0.06751 (85) mri peak = 0.04029 (84) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (17969 voxels, overlap=0.941) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (17969 voxels, peak = 83), gca=82.9 gca peak = 0.08366 (82) mri peak = 0.04458 (80) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (15226 voxels, overlap=0.946) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (15226 voxels, peak = 82), gca=82.0 gca peak = 0.21552 (80) mri peak = 0.13517 (80) Right_Caudate (50): linear fit = 1.00 x + 0.0 (725 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (725 voxels, peak = 80), gca=80.0 gca peak = 0.16154 (84) mri peak = 0.11396 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (700 voxels, overlap=0.992) Left_Caudate (11): linear fit = 1.00 x + 0.0 (700 voxels, peak = 84), gca=84.0 gca peak = 0.10275 (79) mri peak = 0.07453 (81) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18718 voxels, overlap=0.898) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18718 voxels, peak = 79), gca=79.0 gca peak = 0.11452 (75) mri peak = 0.08321 (77) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (18491 voxels, overlap=0.925) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (18491 voxels, peak = 76), gca=76.1 gca peak = 0.15219 (95) mri peak = 0.12987 (94) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4466 voxels, overlap=0.921) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4466 voxels, peak = 94), gca=93.6 gca peak = 0.17316 (92) mri peak = 0.13345 (92) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5484 voxels, overlap=0.970) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5484 voxels, peak = 91), gca=90.6 gca peak = 0.28440 (78) mri peak = 0.12861 (79) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (371 voxels, overlap=0.991) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (371 voxels, peak = 78), gca=78.0 gca peak = 0.30168 (80) mri peak = 0.14797 (81) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (421 voxels, overlap=0.994) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (421 voxels, peak = 80), gca=80.0 gca peak = 0.10584 (89) mri peak = 0.12528 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3579 voxels, overlap=0.764) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3579 voxels, peak = 90), gca=90.3 gca peak = 0.10245 (87) mri peak = 0.12266 (89) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3923 voxels, overlap=0.830) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3923 voxels, peak = 86), gca=85.7 gca peak = 0.08290 (88) mri peak = 0.07956 (83) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1634 voxels, overlap=0.931) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1634 voxels, peak = 87), gca=86.7 gca peak = 0.09497 (82) mri peak = 0.10530 (83) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1392 voxels, overlap=0.820) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1392 voxels, peak = 82), gca=82.0 gca peak = 0.08812 (84) mri peak = 0.11623 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10748 voxels, overlap=0.706) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10748 voxels, peak = 84), gca=84.0 gca peak = 0.13237 (93) mri peak = 0.12110 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1101 voxels, overlap=0.802) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1101 voxels, peak = 93), gca=92.5 gca peak = 0.14574 (90) mri peak = 0.11441 (91) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1218 voxels, overlap=0.903) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1218 voxels, peak = 90), gca=90.0 gca peak = 0.17274 (25) mri peak = 0.16000 (27) Third_Ventricle (14): linear fit = 1.02 x + 0.0 (56 voxels, overlap=1.000) Third_Ventricle (14): linear fit = 1.02 x + 0.0 (56 voxels, peak = 26), gca=25.6 gca peak = 0.16542 (20) mri peak = 0.18952 (27) Fourth_Ventricle (15): linear fit = 1.42 x + 0.0 (493 voxels, overlap=0.264) Fourth_Ventricle (15): linear fit = 1.42 x + 0.0 (493 voxels, peak = 28), gca=28.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16743 (42) gca peak Left_Thalamus = 0.72551 (104) gca peak CSF = 0.23865 (46) gca peak Left_Accumbens_area = 0.49853 (68) gca peak Left_undetermined = 0.96707 (30) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11916 (35) gca peak Right_Inf_Lat_Vent = 0.18665 (32) gca peak Right_Accumbens_area = 0.32708 (79) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14507 (37) gca peak Fifth_Ventricle = 0.62949 (40) gca peak WM_hypointensities = 0.07625 (76) gca peak non_WM_hypointensities = 0.07897 (44) gca peak Optic_Chiasm = 0.68920 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.19 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 47519 voxels changed in iteration 0 of unlikely voxel relabeling 256 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 74769 gm and wm labels changed (%42 to gray, %58 to white out of all changed labels) 355 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 64263 changed. image ll: -2.078, PF=0.500 pass 2: 17236 changed. image ll: -2.077, PF=0.500 pass 3: 5061 changed. pass 4: 1775 changed. 57511 voxels changed in iteration 0 of unlikely voxel relabeling 756 voxels changed in iteration 1 of unlikely voxel relabeling 25 voxels changed in iteration 2 of unlikely voxel relabeling 10 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5456 voxels changed in iteration 0 of unlikely voxel relabeling 66 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5078 voxels changed in iteration 0 of unlikely voxel relabeling 53 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4445 voxels changed in iteration 0 of unlikely voxel relabeling 37 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 5395.608000 mri_ca_label stimesec 1.992000 mri_ca_label ru_maxrss 2097368 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 796362 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63872 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 73 mri_ca_label ru_nivcsw 13409 auto-labeling took 89 minutes and 58 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /work2/r1774/subjects/J106388/mri/transforms/cc_up.lta J106388 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /work2/r1774/subjects/J106388/mri/transforms/cc_up.lta reading aseg from /work2/r1774/subjects/J106388/mri/aseg.auto_noCCseg.mgz reading norm from /work2/r1774/subjects/J106388/mri/norm.mgz 26322 voxels in left wm, 24324 in right wm, xrange [127, 134] searching rotation angles z=[-8 6], y=[-7 7] searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 global minimum found at slice 130.0, rotations (0.68, -1.39) final transformation (x=130.0, yr=0.677, zr=-1.387): 0.99964 0.02420 0.01181 -5.59915; -0.02420 0.99971 -0.00029 35.20566; -0.01182 0.00000 0.99993 17.54421; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 96 112 eigenvectors: 0.00003 0.00527 0.99999; -0.05791 -0.99831 0.00526; 0.99832 -0.05791 0.00028; error in mid anterior detected - correcting... writing aseg with callosum to /work2/r1774/subjects/J106388/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Sun Apr 16 03:15:19 CDT 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Apr 16 03:15:19 CDT 2017 /work2/r1774/subjects/J106388/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE 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... 562 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 109 gm peak at 76 (76), valley at 18 (18) csf peak at 20, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 88 (88), valley at 50 (50) csf peak at 47, setting threshold to 74 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 5 minutes and 3 seconds. #-------------------------------------------- #@# Mask BFS Sun Apr 16 03:20:27 CDT 2017 /work2/r1774/subjects/J106388/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1269088 voxels in mask (pct= 7.56) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Apr 16 03:20:30 CDT 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 104.3 +- 4.9 [80.0 --> 125.0] GM (71.0) : 69.4 +- 13.1 [30.0 --> 95.0] setting bottom of white matter range to 82.5 setting top of gray matter range to 95.6 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... 2281 sparsely connected voxels removed... thickening thin strands.... 20 segments, 927 filled 611 bright non-wm voxels segmented. 2906 diagonally connected voxels added... white matter segmentation took 2.3 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE 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 0.77 minutes reading wm segmentation from wm.seg.mgz... 28 voxels added to wm to prevent paths from MTL structures to cortex 2804 additional wm voxels added 0 additional wm voxels added SEG EDIT: 51485 voxels turned on, 68332 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 27 found - 27 modified | TOTAL: 27 pass 2 (xy+): 0 found - 27 modified | TOTAL: 27 pass 1 (xy-): 23 found - 23 modified | TOTAL: 50 pass 2 (xy-): 0 found - 23 modified | TOTAL: 50 pass 1 (yz+): 17 found - 17 modified | TOTAL: 67 pass 2 (yz+): 0 found - 17 modified | TOTAL: 67 pass 1 (yz-): 32 found - 32 modified | TOTAL: 99 pass 2 (yz-): 0 found - 32 modified | TOTAL: 99 pass 1 (xz+): 24 found - 24 modified | TOTAL: 123 pass 2 (xz+): 0 found - 24 modified | TOTAL: 123 pass 1 (xz-): 13 found - 13 modified | TOTAL: 136 pass 2 (xz-): 0 found - 13 modified | TOTAL: 136 Iteration Number : 1 pass 1 (+++): 16 found - 16 modified | TOTAL: 16 pass 2 (+++): 0 found - 16 modified | TOTAL: 16 pass 1 (+++): 14 found - 14 modified | TOTAL: 30 pass 2 (+++): 0 found - 14 modified | TOTAL: 30 pass 1 (+++): 26 found - 26 modified | TOTAL: 56 pass 2 (+++): 0 found - 26 modified | TOTAL: 56 pass 1 (+++): 21 found - 21 modified | TOTAL: 77 pass 2 (+++): 0 found - 21 modified | TOTAL: 77 Iteration Number : 1 pass 1 (++): 31 found - 31 modified | TOTAL: 31 pass 2 (++): 0 found - 31 modified | TOTAL: 31 pass 1 (+-): 23 found - 23 modified | TOTAL: 54 pass 2 (+-): 0 found - 23 modified | TOTAL: 54 pass 1 (--): 31 found - 31 modified | TOTAL: 85 pass 2 (--): 0 found - 31 modified | TOTAL: 85 pass 1 (-+): 24 found - 24 modified | TOTAL: 109 pass 2 (-+): 0 found - 24 modified | TOTAL: 109 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 2 found - 2 modified | TOTAL: 11 pass 2 (xz+): 0 found - 2 modified | TOTAL: 11 pass 1 (xz-): 6 found - 6 modified | TOTAL: 17 pass 2 (xz-): 0 found - 6 modified | TOTAL: 17 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 2 found - 2 modified | TOTAL: 6 pass 2 (+-): 0 found - 2 modified | TOTAL: 6 pass 1 (--): 0 found - 0 modified | TOTAL: 6 pass 1 (-+): 3 found - 3 modified | TOTAL: 9 pass 2 (-+): 0 found - 3 modified | TOTAL: 9 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 = 350 (out of 573212: 0.061059) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Apr 16 03:23:38 CDT 2017 /work2/r1774/subjects/J106388/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 1.14593 -0.00669 -0.01318 -20.17297; 0.00856 1.05161 0.29196 -36.28059; 0.01056 -0.36662 0.98980 35.94160; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.14593 -0.00669 -0.01318 -20.17297; 0.00856 1.05161 0.29196 -36.28059; 0.01056 -0.36662 0.98980 35.94160; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1272 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 123, 154), TAL = (2.0, 26.0, 5.0) talairach voxel to voxel transform 0.87250 0.00870 0.00905 17.59138; -0.00409 0.86221 -0.25438 40.34187; -0.01082 0.31927 0.91598 -21.55710; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 123, 154) --> (2.0, 26.0, 5.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, 26.00, 5.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 26.00, 5.00) SRC: (114.29, 106.78, 157.61) search lh wm seed point around talairach space (-16.00, 26.00, 5.00), SRC: (145.70, 106.63, 157.22) 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 Sun Apr 16 03:24:41 CDT 2017 /work2/r1774/subjects/J106388/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 4 found - 4 modified | TOTAL: 6 pass 2 (xy-): 0 found - 4 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 2 found - 2 modified | TOTAL: 11 pass 2 (yz-): 0 found - 2 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 2 found - 2 modified | TOTAL: 14 pass 2 (xz-): 0 found - 2 modified | TOTAL: 14 Iteration Number : 1 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 : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 2 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-): 0 found - 0 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 (++): 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 (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 = 20 (out of 279904: 0.007145) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1328 vertices, 1442 faces slice 60: 7325 vertices, 7599 faces slice 70: 16011 vertices, 16356 faces slice 80: 26304 vertices, 26660 faces slice 90: 37510 vertices, 37889 faces slice 100: 48277 vertices, 48715 faces slice 110: 59551 vertices, 59982 faces slice 120: 70877 vertices, 71298 faces slice 130: 82078 vertices, 82545 faces slice 140: 93456 vertices, 93912 faces slice 150: 102978 vertices, 103400 faces slice 160: 111160 vertices, 111532 faces slice 170: 118085 vertices, 118406 faces slice 180: 124188 vertices, 124466 faces slice 190: 128384 vertices, 128571 faces slice 200: 129172 vertices, 129276 faces slice 210: 129172 vertices, 129276 faces slice 220: 129172 vertices, 129276 faces slice 230: 129172 vertices, 129276 faces slice 240: 129172 vertices, 129276 faces slice 250: 129172 vertices, 129276 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... 129172 voxel in cpt #1: X=-104 [v=129172,e=387828,f=258552] located at (-27.656946, -13.527816, 18.178793) For the whole surface: X=-104 [v=129172,e=387828,f=258552] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Apr 16 03:24:51 CDT 2017 /work2/r1774/subjects/J106388/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-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 2 found - 2 modified | TOTAL: 5 pass 2 (xz+): 0 found - 2 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 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 : 1 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 (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 = 5 (out of 276755: 0.001807) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 756 vertices, 833 faces slice 60: 6340 vertices, 6674 faces slice 70: 15374 vertices, 15732 faces slice 80: 26095 vertices, 26496 faces slice 90: 36802 vertices, 37193 faces slice 100: 47829 vertices, 48235 faces slice 110: 58830 vertices, 59249 faces slice 120: 69839 vertices, 70267 faces slice 130: 81406 vertices, 81841 faces slice 140: 92678 vertices, 93126 faces slice 150: 102066 vertices, 102471 faces slice 160: 109825 vertices, 110170 faces slice 170: 116495 vertices, 116800 faces slice 180: 122057 vertices, 122330 faces slice 190: 125515 vertices, 125701 faces slice 200: 126304 vertices, 126404 faces slice 210: 126304 vertices, 126404 faces slice 220: 126304 vertices, 126404 faces slice 230: 126304 vertices, 126404 faces slice 240: 126304 vertices, 126404 faces slice 250: 126304 vertices, 126404 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... 126304 voxel in cpt #1: X=-100 [v=126304,e=379212,f=252808] located at (24.391548, -14.116750, 19.856474) For the whole surface: X=-100 [v=126304,e=379212,f=252808] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Apr 16 03:25:01 CDT 2017 /work2/r1774/subjects/J106388/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 Sun Apr 16 03:25:09 CDT 2017 /work2/r1774/subjects/J106388/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 Sun Apr 16 03:25:16 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.2 mm, total surface area = 68142 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.074 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.058 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.054 (target=0.015) step 050: RMS=0.052 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.051 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 58.756000 mris_inflate stimesec 0.068000 mris_inflate ru_maxrss 167036 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22007 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9096 mris_inflate ru_oublock 9096 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 241 mris_inflate ru_nivcsw 111 #-------------------------------------------- #@# Inflation1 rh Sun Apr 16 03:26:15 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.8 mm, total surface area = 66974 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.0 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.054 (target=0.015) step 040: RMS=0.050 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.047 (target=0.015) step 055: RMS=0.046 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 57.644000 mris_inflate stimesec 0.088000 mris_inflate ru_maxrss 163376 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 21606 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8888 mris_inflate ru_oublock 8896 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 239 mris_inflate ru_nivcsw 117 #-------------------------------------------- #@# QSphere lh Sun Apr 16 03:27:13 CDT 2017 /work2/r1774/subjects/J106388/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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.58 (0.00-->8.29) (max @ vno 46662 --> 47856) face area 0.03 +- 0.04 (-0.12-->0.96) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.336... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.892, avgs=0 005/300: dt: 0.9000, rms radial error=175.632, avgs=0 010/300: dt: 0.9000, rms radial error=175.072, avgs=0 015/300: dt: 0.9000, rms radial error=174.337, avgs=0 020/300: dt: 0.9000, rms radial error=173.501, avgs=0 025/300: dt: 0.9000, rms radial error=172.608, avgs=0 030/300: dt: 0.9000, rms radial error=171.686, avgs=0 035/300: dt: 0.9000, rms radial error=170.747, avgs=0 040/300: dt: 0.9000, rms radial error=169.800, avgs=0 045/300: dt: 0.9000, rms radial error=168.852, avgs=0 050/300: dt: 0.9000, rms radial error=167.904, avgs=0 055/300: dt: 0.9000, rms radial error=166.958, avgs=0 060/300: dt: 0.9000, rms radial error=166.017, avgs=0 065/300: dt: 0.9000, rms radial error=165.080, avgs=0 070/300: dt: 0.9000, rms radial error=164.149, avgs=0 075/300: dt: 0.9000, rms radial error=163.223, avgs=0 080/300: dt: 0.9000, rms radial error=162.302, avgs=0 085/300: dt: 0.9000, rms radial error=161.385, avgs=0 090/300: dt: 0.9000, rms radial error=160.476, avgs=0 095/300: dt: 0.9000, rms radial error=159.575, avgs=0 100/300: dt: 0.9000, rms radial error=158.679, avgs=0 105/300: dt: 0.9000, rms radial error=157.787, avgs=0 110/300: dt: 0.9000, rms radial error=156.901, avgs=0 115/300: dt: 0.9000, rms radial error=156.019, avgs=0 120/300: dt: 0.9000, rms radial error=155.142, avgs=0 125/300: dt: 0.9000, rms radial error=154.270, avgs=0 130/300: dt: 0.9000, rms radial error=153.402, avgs=0 135/300: dt: 0.9000, rms radial error=152.540, avgs=0 140/300: dt: 0.9000, rms radial error=151.682, avgs=0 145/300: dt: 0.9000, rms radial error=150.829, avgs=0 150/300: dt: 0.9000, rms radial error=149.982, avgs=0 155/300: dt: 0.9000, rms radial error=149.139, avgs=0 160/300: dt: 0.9000, rms radial error=148.300, avgs=0 165/300: dt: 0.9000, rms radial error=147.467, avgs=0 170/300: dt: 0.9000, rms radial error=146.638, avgs=0 175/300: dt: 0.9000, rms radial error=145.814, avgs=0 180/300: dt: 0.9000, rms radial error=144.994, avgs=0 185/300: dt: 0.9000, rms radial error=144.179, avgs=0 190/300: dt: 0.9000, rms radial error=143.368, avgs=0 195/300: dt: 0.9000, rms radial error=142.562, avgs=0 200/300: dt: 0.9000, rms radial error=141.760, avgs=0 205/300: dt: 0.9000, rms radial error=140.963, avgs=0 210/300: dt: 0.9000, rms radial error=140.170, avgs=0 215/300: dt: 0.9000, rms radial error=139.381, avgs=0 220/300: dt: 0.9000, rms radial error=138.597, avgs=0 225/300: dt: 0.9000, rms radial error=137.817, avgs=0 230/300: dt: 0.9000, rms radial error=137.042, avgs=0 235/300: dt: 0.9000, rms radial error=136.270, avgs=0 240/300: dt: 0.9000, rms radial error=135.504, avgs=0 245/300: dt: 0.9000, rms radial error=134.741, avgs=0 250/300: dt: 0.9000, rms radial error=133.983, avgs=0 255/300: dt: 0.9000, rms radial error=133.228, avgs=0 260/300: dt: 0.9000, rms radial error=132.478, avgs=0 265/300: dt: 0.9000, rms radial error=131.733, avgs=0 270/300: dt: 0.9000, rms radial error=130.991, avgs=0 275/300: dt: 0.9000, rms radial error=130.254, avgs=0 280/300: dt: 0.9000, rms radial error=129.520, avgs=0 285/300: dt: 0.9000, rms radial error=128.791, avgs=0 290/300: dt: 0.9000, rms radial error=128.066, avgs=0 295/300: dt: 0.9000, rms radial error=127.344, avgs=0 300/300: dt: 0.9000, rms radial error=126.627, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14737.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2352.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00026 epoch 3 (K=160.0), pass 1, starting sse = 218.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00607 epoch 4 (K=640.0), pass 1, starting sse = 17.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/14 = 0.00822 final distance error %24.71 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours mris_sphere utimesec 372.432000 mris_sphere stimesec 0.072000 mris_sphere ru_maxrss 167208 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22054 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 9096 mris_sphere ru_oublock 9096 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 133 mris_sphere ru_nivcsw 693 FSRUNTIME@ mris_sphere 0.1035 hours 1 threads #-------------------------------------------- #@# QSphere rh Sun Apr 16 03:33:25 CDT 2017 /work2/r1774/subjects/J106388/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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.04 +- 0.58 (0.00-->7.80) (max @ vno 48832 --> 49999) face area 0.03 +- 0.04 (-0.15-->0.71) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.344... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.643, avgs=0 005/300: dt: 0.9000, rms radial error=175.385, avgs=0 010/300: dt: 0.9000, rms radial error=174.830, avgs=0 015/300: dt: 0.9000, rms radial error=174.103, avgs=0 020/300: dt: 0.9000, rms radial error=173.275, avgs=0 025/300: dt: 0.9000, rms radial error=172.389, avgs=0 030/300: dt: 0.9000, rms radial error=171.472, avgs=0 035/300: dt: 0.9000, rms radial error=170.538, avgs=0 040/300: dt: 0.9000, rms radial error=169.597, avgs=0 045/300: dt: 0.9000, rms radial error=168.653, avgs=0 050/300: dt: 0.9000, rms radial error=167.710, avgs=0 055/300: dt: 0.9000, rms radial error=166.769, avgs=0 060/300: dt: 0.9000, rms radial error=165.833, avgs=0 065/300: dt: 0.9000, rms radial error=164.902, avgs=0 070/300: dt: 0.9000, rms radial error=163.975, avgs=0 075/300: dt: 0.9000, rms radial error=163.052, avgs=0 080/300: dt: 0.9000, rms radial error=162.135, avgs=0 085/300: dt: 0.9000, rms radial error=161.222, avgs=0 090/300: dt: 0.9000, rms radial error=160.316, avgs=0 095/300: dt: 0.9000, rms radial error=159.414, avgs=0 100/300: dt: 0.9000, rms radial error=158.517, avgs=0 105/300: dt: 0.9000, rms radial error=157.624, avgs=0 110/300: dt: 0.9000, rms radial error=156.737, avgs=0 115/300: dt: 0.9000, rms radial error=155.857, avgs=0 120/300: dt: 0.9000, rms radial error=154.983, avgs=0 125/300: dt: 0.9000, rms radial error=154.113, avgs=0 130/300: dt: 0.9000, rms radial error=153.247, avgs=0 135/300: dt: 0.9000, rms radial error=152.387, avgs=0 140/300: dt: 0.9000, rms radial error=151.531, avgs=0 145/300: dt: 0.9000, rms radial error=150.680, avgs=0 150/300: dt: 0.9000, rms radial error=149.833, avgs=0 155/300: dt: 0.9000, rms radial error=148.992, avgs=0 160/300: dt: 0.9000, rms radial error=148.156, avgs=0 165/300: dt: 0.9000, rms radial error=147.325, avgs=0 170/300: dt: 0.9000, rms radial error=146.498, avgs=0 175/300: dt: 0.9000, rms radial error=145.676, avgs=0 180/300: dt: 0.9000, rms radial error=144.858, avgs=0 185/300: dt: 0.9000, rms radial error=144.045, avgs=0 190/300: dt: 0.9000, rms radial error=143.237, avgs=0 195/300: dt: 0.9000, rms radial error=142.433, avgs=0 200/300: dt: 0.9000, rms radial error=141.633, avgs=0 205/300: dt: 0.9000, rms radial error=140.837, avgs=0 210/300: dt: 0.9000, rms radial error=140.047, avgs=0 215/300: dt: 0.9000, rms radial error=139.260, avgs=0 220/300: dt: 0.9000, rms radial error=138.478, avgs=0 225/300: dt: 0.9000, rms radial error=137.700, avgs=0 230/300: dt: 0.9000, rms radial error=136.926, avgs=0 235/300: dt: 0.9000, rms radial error=136.156, avgs=0 240/300: dt: 0.9000, rms radial error=135.391, avgs=0 245/300: dt: 0.9000, rms radial error=134.630, avgs=0 250/300: dt: 0.9000, rms radial error=133.874, avgs=0 255/300: dt: 0.9000, rms radial error=133.121, avgs=0 260/300: dt: 0.9000, rms radial error=132.373, avgs=0 265/300: dt: 0.9000, rms radial error=131.629, avgs=0 270/300: dt: 0.9000, rms radial error=130.889, avgs=0 275/300: dt: 0.9000, rms radial error=130.153, avgs=0 280/300: dt: 0.9000, rms radial error=129.421, avgs=0 285/300: dt: 0.9000, rms radial error=128.694, avgs=0 290/300: dt: 0.9000, rms radial error=127.970, avgs=0 295/300: dt: 0.9000, rms radial error=127.250, avgs=0 300/300: dt: 0.9000, rms radial error=126.535, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14261.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2227.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 3 (K=160.0), pass 1, starting sse = 200.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00344 epoch 4 (K=640.0), pass 1, starting sse = 16.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00794 final distance error %24.09 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours mris_sphere utimesec 368.372000 mris_sphere stimesec 0.068000 mris_sphere ru_maxrss 163544 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 21654 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 8896 mris_sphere ru_oublock 8896 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 71 mris_sphere ru_nivcsw 851 FSRUNTIME@ mris_sphere 0.1024 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sun Apr 16 03:39:34 CDT 2017 /work2/r1774/subjects/J106388/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Apr 16 03:39:34 CDT 2017 /work2/r1774/subjects/J106388/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Apr 16 03:39:34 CDT 2017 mris_fix_topology -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 J106388 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-104 (nv=129172, nf=258552, ne=387828, g=53) 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 12 iterations marking ambiguous vertices... 8786 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 3 -merging segment 11 into 13 -merging segment 35 into 37 52 defects to be corrected 0 vertices coincident reading input surface /work2/r1774/subjects/J106388/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0537 (-4.5268) -vertex loglikelihood: -5.9357 (-2.9678) -normal dot loglikelihood: -3.5206 (-3.5206) -quad curv loglikelihood: -6.4152 (-3.2076) Total Loglikelihood : -24.9252 CORRECTING DEFECT 0 (vertices=270, convex hull=178, v0=235) After retessellation of defect 0 (v0=235), euler #=-49 (124018,370350,246283) : difference with theory (-49) = 0 CORRECTING DEFECT 1 (vertices=95, convex hull=88, v0=575) After retessellation of defect 1 (v0=575), euler #=-48 (124038,370443,246357) : difference with theory (-48) = 0 CORRECTING DEFECT 2 (vertices=213, convex hull=193, v0=1872) After retessellation of defect 2 (v0=1872), euler #=-46 (124050,370570,246474) : difference with theory (-47) = -1 CORRECTING DEFECT 3 (vertices=58, convex hull=37, v0=4257) After retessellation of defect 3 (v0=4257), euler #=-45 (124056,370604,246503) : difference with theory (-46) = -1 CORRECTING DEFECT 4 (vertices=51, convex hull=97, v0=7031) After retessellation of defect 4 (v0=7031), euler #=-44 (124074,370701,246583) : difference with theory (-45) = -1 CORRECTING DEFECT 5 (vertices=54, convex hull=33, v0=9687) After retessellation of defect 5 (v0=9687), euler #=-43 (124076,370719,246600) : difference with theory (-44) = -1 CORRECTING DEFECT 6 (vertices=73, convex hull=35, v0=16163) After retessellation of defect 6 (v0=16163), euler #=-42 (124079,370741,246620) : difference with theory (-43) = -1 CORRECTING DEFECT 7 (vertices=106, convex hull=172, v0=30356) After retessellation of defect 7 (v0=30356), euler #=-41 (124149,371027,246837) : difference with theory (-42) = -1 CORRECTING DEFECT 8 (vertices=122, convex hull=176, v0=31553) After retessellation of defect 8 (v0=31553), euler #=-40 (124221,371331,247070) : difference with theory (-41) = -1 CORRECTING DEFECT 9 (vertices=41, convex hull=39, v0=34742) After retessellation of defect 9 (v0=34742), euler #=-39 (124227,371364,247098) : difference with theory (-40) = -1 CORRECTING DEFECT 10 (vertices=45, convex hull=62, v0=37078) After retessellation of defect 10 (v0=37078), euler #=-38 (124247,371445,247160) : difference with theory (-39) = -1 CORRECTING DEFECT 11 (vertices=40, convex hull=35, v0=39060) After retessellation of defect 11 (v0=39060), euler #=-36 (124251,371469,247182) : difference with theory (-38) = -2 CORRECTING DEFECT 12 (vertices=124, convex hull=38, v0=39573) After retessellation of defect 12 (v0=39573), euler #=-35 (124258,371503,247210) : difference with theory (-37) = -2 CORRECTING DEFECT 13 (vertices=139, convex hull=137, v0=40764) After retessellation of defect 13 (v0=40764), euler #=-34 (124311,371720,247375) : difference with theory (-36) = -2 CORRECTING DEFECT 14 (vertices=145, convex hull=38, v0=44310) After retessellation of defect 14 (v0=44310), euler #=-33 (124332,371795,247430) : difference with theory (-35) = -2 CORRECTING DEFECT 15 (vertices=29, convex hull=77, v0=44816) After retessellation of defect 15 (v0=44816), euler #=-32 (124346,371868,247490) : difference with theory (-34) = -2 CORRECTING DEFECT 16 (vertices=68, convex hull=86, v0=46380) After retessellation of defect 16 (v0=46380), euler #=-31 (124369,371974,247574) : difference with theory (-33) = -2 CORRECTING DEFECT 17 (vertices=55, convex hull=71, v0=49082) After retessellation of defect 17 (v0=49082), euler #=-30 (124383,372040,247627) : difference with theory (-32) = -2 CORRECTING DEFECT 18 (vertices=19, convex hull=43, v0=53049) After retessellation of defect 18 (v0=53049), euler #=-29 (124394,372087,247664) : difference with theory (-31) = -2 CORRECTING DEFECT 19 (vertices=9, convex hull=20, v0=57062) After retessellation of defect 19 (v0=57062), euler #=-28 (124394,372093,247671) : difference with theory (-30) = -2 CORRECTING DEFECT 20 (vertices=69, convex hull=90, v0=59946) After retessellation of defect 20 (v0=59946), euler #=-27 (124412,372188,247749) : difference with theory (-29) = -2 CORRECTING DEFECT 21 (vertices=1616, convex hull=536, v0=60404) XL defect detected... After retessellation of defect 21 (v0=60404), euler #=-29 (124567,372972,248376) : difference with theory (-28) = 1 CORRECTING DEFECT 22 (vertices=68, convex hull=119, v0=61763) After retessellation of defect 22 (v0=61763), euler #=-28 (124615,373170,248527) : difference with theory (-27) = 1 CORRECTING DEFECT 23 (vertices=19, convex hull=57, v0=67514) After retessellation of defect 23 (v0=67514), euler #=-27 (124629,373234,248578) : difference with theory (-26) = 1 CORRECTING DEFECT 24 (vertices=6, convex hull=25, v0=71154) After retessellation of defect 24 (v0=71154), euler #=-26 (124630,373246,248590) : difference with theory (-25) = 1 CORRECTING DEFECT 25 (vertices=25, convex hull=30, v0=71628) After retessellation of defect 25 (v0=71628), euler #=-25 (124633,373264,248606) : difference with theory (-24) = 1 CORRECTING DEFECT 26 (vertices=51, convex hull=81, v0=77421) After retessellation of defect 26 (v0=77421), euler #=-24 (124658,373372,248690) : difference with theory (-23) = 1 CORRECTING DEFECT 27 (vertices=38, convex hull=55, v0=83115) After retessellation of defect 27 (v0=83115), euler #=-23 (124680,373461,248758) : difference with theory (-22) = 1 CORRECTING DEFECT 28 (vertices=101, convex hull=50, v0=84355) After retessellation of defect 28 (v0=84355), euler #=-22 (124689,373506,248795) : difference with theory (-21) = 1 CORRECTING DEFECT 29 (vertices=90, convex hull=86, v0=86107) After retessellation of defect 29 (v0=86107), euler #=-21 (124716,373622,248885) : difference with theory (-20) = 1 CORRECTING DEFECT 30 (vertices=25, convex hull=48, v0=87300) After retessellation of defect 30 (v0=87300), euler #=-20 (124724,373664,248920) : difference with theory (-19) = 1 CORRECTING DEFECT 31 (vertices=33, convex hull=64, v0=87305) After retessellation of defect 31 (v0=87305), euler #=-19 (124734,373720,248967) : difference with theory (-18) = 1 CORRECTING DEFECT 32 (vertices=7, convex hull=26, v0=88450) After retessellation of defect 32 (v0=88450), euler #=-18 (124735,373731,248978) : difference with theory (-17) = 1 CORRECTING DEFECT 33 (vertices=107, convex hull=100, v0=89477) After retessellation of defect 33 (v0=89477), euler #=-17 (124779,373905,249109) : difference with theory (-16) = 1 CORRECTING DEFECT 34 (vertices=209, convex hull=109, v0=89650) After retessellation of defect 34 (v0=89650), euler #=-15 (124815,374060,249230) : difference with theory (-15) = 0 CORRECTING DEFECT 35 (vertices=35, convex hull=30, v0=89765) After retessellation of defect 35 (v0=89765), euler #=-14 (124823,374094,249257) : difference with theory (-14) = 0 CORRECTING DEFECT 36 (vertices=12, convex hull=21, v0=89807) After retessellation of defect 36 (v0=89807), euler #=-13 (124826,374109,249270) : difference with theory (-13) = 0 CORRECTING DEFECT 37 (vertices=8, convex hull=12, v0=90760) After retessellation of defect 37 (v0=90760), euler #=-12 (124827,374116,249277) : difference with theory (-12) = 0 CORRECTING DEFECT 38 (vertices=77, convex hull=91, v0=91787) After retessellation of defect 38 (v0=91787), euler #=-11 (124866,374275,249398) : difference with theory (-11) = 0 CORRECTING DEFECT 39 (vertices=108, convex hull=35, v0=94123) After retessellation of defect 39 (v0=94123), euler #=-10 (124878,374324,249436) : difference with theory (-10) = 0 CORRECTING DEFECT 40 (vertices=22, convex hull=29, v0=94395) After retessellation of defect 40 (v0=94395), euler #=-9 (124880,374338,249449) : difference with theory (-9) = 0 CORRECTING DEFECT 41 (vertices=48, convex hull=85, v0=95141) After retessellation of defect 41 (v0=95141), euler #=-8 (124898,374429,249523) : difference with theory (-8) = 0 CORRECTING DEFECT 42 (vertices=27, convex hull=58, v0=95281) After retessellation of defect 42 (v0=95281), euler #=-7 (124907,374482,249568) : difference with theory (-7) = 0 CORRECTING DEFECT 43 (vertices=169, convex hull=136, v0=97297) After retessellation of defect 43 (v0=97297), euler #=-6 (124962,374715,249747) : difference with theory (-6) = 0 CORRECTING DEFECT 44 (vertices=23, convex hull=53, v0=97745) After retessellation of defect 44 (v0=97745), euler #=-5 (124971,374763,249787) : difference with theory (-5) = 0 CORRECTING DEFECT 45 (vertices=151, convex hull=82, v0=97863) After retessellation of defect 45 (v0=97863), euler #=-4 (124980,374827,249843) : difference with theory (-4) = 0 CORRECTING DEFECT 46 (vertices=34, convex hull=22, v0=105450) After retessellation of defect 46 (v0=105450), euler #=-3 (124983,374841,249855) : difference with theory (-3) = 0 CORRECTING DEFECT 47 (vertices=65, convex hull=59, v0=105489) After retessellation of defect 47 (v0=105489), euler #=-2 (125004,374925,249919) : difference with theory (-2) = 0 CORRECTING DEFECT 48 (vertices=15, convex hull=24, v0=107508) After retessellation of defect 48 (v0=107508), euler #=-1 (125009,374947,249937) : difference with theory (-1) = 0 CORRECTING DEFECT 49 (vertices=26, convex hull=20, v0=107782) After retessellation of defect 49 (v0=107782), euler #=0 (125010,374956,249946) : difference with theory (0) = 0 CORRECTING DEFECT 50 (vertices=116, convex hull=119, v0=114683) After retessellation of defect 50 (v0=114683), euler #=1 (125051,375131,250081) : difference with theory (1) = 0 CORRECTING DEFECT 51 (vertices=56, convex hull=43, v0=117656) After retessellation of defect 51 (v0=117656), euler #=2 (125059,375171,250114) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.03-->10.75) (max @ vno 78857 --> 79707) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.03-->10.75) (max @ vno 78857 --> 79707) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 187 mutations (34.9%), 349 crossovers (65.1%), 579 vertices were eliminated building final representation... 4113 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125059, nf=250114, ne=375171, g=0) writing corrected surface to /work2/r1774/subjects/J106388/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 46.6 minutes 0 defective edges removing intersecting faces 000: 445 intersecting 001: 21 intersecting 002: 8 intersecting 003: 6 intersecting 004: 4 intersecting 005: 3 intersecting mris_fix_topology utimesec 2793.824000 mris_fix_topology stimesec 0.284000 mris_fix_topology ru_maxrss 414380 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 57241 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 25480 mris_fix_topology ru_oublock 11848 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 148 mris_fix_topology ru_nivcsw 7730 FSRUNTIME@ mris_fix_topology lh 0.7763 hours 1 threads #@# Fix Topology rh Sun Apr 16 04:26:09 CDT 2017 mris_fix_topology -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 J106388 rh 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-100 (nv=126304, nf=252808, ne=379212, g=51) 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 7 iterations marking ambiguous vertices... 8036 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 39 defects to be corrected 0 vertices coincident reading input surface /work2/r1774/subjects/J106388/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7722 (-4.3861) -vertex loglikelihood: -5.9023 (-2.9512) -normal dot loglikelihood: -3.5967 (-3.5967) -quad curv loglikelihood: -6.3928 (-3.1964) Total Loglikelihood : -24.6640 CORRECTING DEFECT 0 (vertices=396, convex hull=346, v0=578) After retessellation of defect 0 (v0=578), euler #=-34 (121704,363700,241962) : difference with theory (-36) = -2 CORRECTING DEFECT 1 (vertices=88, convex hull=94, v0=639) After retessellation of defect 1 (v0=639), euler #=-33 (121735,363835,242067) : difference with theory (-35) = -2 CORRECTING DEFECT 2 (vertices=171, convex hull=172, v0=2350) After retessellation of defect 2 (v0=2350), euler #=-32 (121794,364091,242265) : difference with theory (-34) = -2 CORRECTING DEFECT 3 (vertices=66, convex hull=32, v0=6222) After retessellation of defect 3 (v0=6222), euler #=-31 (121801,364121,242289) : difference with theory (-33) = -2 CORRECTING DEFECT 4 (vertices=13, convex hull=25, v0=6263) After retessellation of defect 4 (v0=6263), euler #=-30 (121802,364133,242301) : difference with theory (-32) = -2 CORRECTING DEFECT 5 (vertices=96, convex hull=129, v0=12586) After retessellation of defect 5 (v0=12586), euler #=-29 (121833,364287,242425) : difference with theory (-31) = -2 CORRECTING DEFECT 6 (vertices=64, convex hull=95, v0=23605) After retessellation of defect 6 (v0=23605), euler #=-28 (121867,364431,242536) : difference with theory (-30) = -2 CORRECTING DEFECT 7 (vertices=55, convex hull=80, v0=24965) After retessellation of defect 7 (v0=24965), euler #=-27 (121899,364557,242631) : difference with theory (-29) = -2 CORRECTING DEFECT 8 (vertices=23, convex hull=52, v0=37879) After retessellation of defect 8 (v0=37879), euler #=-26 (121913,364620,242681) : difference with theory (-28) = -2 CORRECTING DEFECT 9 (vertices=29, convex hull=54, v0=41064) After retessellation of defect 9 (v0=41064), euler #=-25 (121931,364697,242741) : difference with theory (-27) = -2 CORRECTING DEFECT 10 (vertices=58, convex hull=33, v0=41676) After retessellation of defect 10 (v0=41676), euler #=-24 (121940,364736,242772) : difference with theory (-26) = -2 CORRECTING DEFECT 11 (vertices=218, convex hull=172, v0=42981) After retessellation of defect 11 (v0=42981), euler #=-23 (121949,364844,242872) : difference with theory (-25) = -2 CORRECTING DEFECT 12 (vertices=29, convex hull=49, v0=44094) After retessellation of defect 12 (v0=44094), euler #=-22 (121956,364883,242905) : difference with theory (-24) = -2 CORRECTING DEFECT 13 (vertices=7, convex hull=17, v0=45219) After retessellation of defect 13 (v0=45219), euler #=-21 (121956,364888,242911) : difference with theory (-23) = -2 CORRECTING DEFECT 14 (vertices=2480, convex hull=824, v0=51099) XL defect detected... After retessellation of defect 14 (v0=51099), euler #=-22 (122597,367274,244655) : difference with theory (-22) = 0 CORRECTING DEFECT 15 (vertices=178, convex hull=212, v0=62215) After retessellation of defect 15 (v0=62215), euler #=-21 (122662,367575,244892) : difference with theory (-21) = 0 CORRECTING DEFECT 16 (vertices=9, convex hull=23, v0=66457) After retessellation of defect 16 (v0=66457), euler #=-20 (122663,367586,244903) : difference with theory (-20) = 0 CORRECTING DEFECT 17 (vertices=53, convex hull=38, v0=69384) After retessellation of defect 17 (v0=69384), euler #=-19 (122677,367641,244945) : difference with theory (-19) = 0 CORRECTING DEFECT 18 (vertices=68, convex hull=77, v0=73164) After retessellation of defect 18 (v0=73164), euler #=-18 (122707,367762,245037) : difference with theory (-18) = 0 CORRECTING DEFECT 19 (vertices=19, convex hull=20, v0=75391) After retessellation of defect 19 (v0=75391), euler #=-17 (122708,367772,245047) : difference with theory (-17) = 0 CORRECTING DEFECT 20 (vertices=10, convex hull=29, v0=78502) After retessellation of defect 20 (v0=78502), euler #=-16 (122710,367789,245063) : difference with theory (-16) = 0 CORRECTING DEFECT 21 (vertices=8, convex hull=27, v0=81970) After retessellation of defect 21 (v0=81970), euler #=-15 (122711,367801,245075) : difference with theory (-15) = 0 CORRECTING DEFECT 22 (vertices=33, convex hull=54, v0=82407) After retessellation of defect 22 (v0=82407), euler #=-14 (122721,367850,245115) : difference with theory (-14) = 0 CORRECTING DEFECT 23 (vertices=63, convex hull=64, v0=84874) After retessellation of defect 23 (v0=84874), euler #=-13 (122738,367926,245175) : difference with theory (-13) = 0 CORRECTING DEFECT 24 (vertices=44, convex hull=47, v0=86518) After retessellation of defect 24 (v0=86518), euler #=-12 (122752,367985,245221) : difference with theory (-12) = 0 CORRECTING DEFECT 25 (vertices=16, convex hull=47, v0=89328) After retessellation of defect 25 (v0=89328), euler #=-11 (122754,368011,245246) : difference with theory (-11) = 0 CORRECTING DEFECT 26 (vertices=44, convex hull=82, v0=92272) After retessellation of defect 26 (v0=92272), euler #=-10 (122772,368102,245320) : difference with theory (-10) = 0 CORRECTING DEFECT 27 (vertices=11, convex hull=35, v0=92433) After retessellation of defect 27 (v0=92433), euler #=-9 (122775,368122,245338) : difference with theory (-9) = 0 CORRECTING DEFECT 28 (vertices=5, convex hull=17, v0=94626) After retessellation of defect 28 (v0=94626), euler #=-8 (122776,368129,245345) : difference with theory (-8) = 0 CORRECTING DEFECT 29 (vertices=7, convex hull=21, v0=95454) After retessellation of defect 29 (v0=95454), euler #=-7 (122777,368138,245354) : difference with theory (-7) = 0 CORRECTING DEFECT 30 (vertices=17, convex hull=31, v0=97142) After retessellation of defect 30 (v0=97142), euler #=-6 (122780,368156,245370) : difference with theory (-6) = 0 CORRECTING DEFECT 31 (vertices=55, convex hull=53, v0=97316) After retessellation of defect 31 (v0=97316), euler #=-5 (122804,368247,245438) : difference with theory (-5) = 0 CORRECTING DEFECT 32 (vertices=49, convex hull=69, v0=98834) After retessellation of defect 32 (v0=98834), euler #=-4 (122822,368325,245499) : difference with theory (-4) = 0 CORRECTING DEFECT 33 (vertices=24, convex hull=24, v0=99564) After retessellation of defect 33 (v0=99564), euler #=-3 (122827,368349,245519) : difference with theory (-3) = 0 CORRECTING DEFECT 34 (vertices=31, convex hull=26, v0=104350) After retessellation of defect 34 (v0=104350), euler #=-2 (122831,368370,245537) : difference with theory (-2) = 0 CORRECTING DEFECT 35 (vertices=20, convex hull=45, v0=114014) After retessellation of defect 35 (v0=114014), euler #=-1 (122840,368414,245573) : difference with theory (-1) = 0 CORRECTING DEFECT 36 (vertices=92, convex hull=97, v0=117730) After retessellation of defect 36 (v0=117730), euler #=0 (122868,368541,245673) : difference with theory (0) = 0 CORRECTING DEFECT 37 (vertices=35, convex hull=63, v0=122050) After retessellation of defect 37 (v0=122050), euler #=1 (122885,368615,245731) : difference with theory (1) = 0 CORRECTING DEFECT 38 (vertices=36, convex hull=88, v0=123728) After retessellation of defect 38 (v0=123728), euler #=2 (122899,368691,245794) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.01-->9.59) (max @ vno 77769 --> 124627) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.01-->9.59) (max @ vno 77769 --> 124627) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 142 mutations (36.8%), 244 crossovers (63.2%), 368 vertices were eliminated building final representation... 3405 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=122899, nf=245794, ne=368691, g=0) writing corrected surface to /work2/r1774/subjects/J106388/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 51.9 minutes 0 defective edges removing intersecting faces 000: 443 intersecting 001: 24 intersecting mris_fix_topology utimesec 3114.632000 mris_fix_topology stimesec 0.240000 mris_fix_topology ru_maxrss 420456 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56129 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 25280 mris_fix_topology ru_oublock 11624 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 250 mris_fix_topology ru_nivcsw 5981 FSRUNTIME@ mris_fix_topology rh 0.8653 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 125059 - 375171 + 250114 = 2 --> 0 holes F =2V-4: 250114 = 250118-4 (0) 2E=3F: 750342 = 750342 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 122899 - 368691 + 245794 = 2 --> 0 holes F =2V-4: 245794 = 245798-4 (0) 2E=3F: 737382 = 737382 (0) total defect index = 0 /work2/r1774/subjects/J106388/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 91 intersecting 001: 15 intersecting 002: 8 intersecting 003: 6 intersecting 004: 4 intersecting 005: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /work2/r1774/subjects/J106388/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 93 intersecting 001: 9 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Apr 16 05:18:21 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs J106388 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /work2/r1774/subjects/J106388/mri/filled.mgz... reading volume /work2/r1774/subjects/J106388/mri/brain.finalsurfs.mgz... reading volume /work2/r1774/subjects/J106388/mri/../mri/aseg.presurf.mgz... reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... 15243 bright wm thresholded. 760 bright non-wm voxels segmented. reading original surface position from /work2/r1774/subjects/J106388/surf/lh.orig... computing class statistics... border white: 253970 voxels (1.51%) border gray 256307 voxels (1.53%) WM (96.0): 97.2 +- 6.3 [70.0 --> 110.0] GM (77.0) : 74.4 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.5 (was 40) setting MAX_GRAY to 91.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.84) (max @ vno 79732 --> 124549) face area 0.28 +- 0.13 (0.00-->6.98) mean absolute distance = 0.60 +- 0.83 3196 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-5.2, GM=78+-15.7 mean inside = 93.7, mean outside = 79.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=88.9, 71 (71) missing vertices, mean dist -0.1 [0.7 (%51.2)->0.5 (%48.8))] %46 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.24 (0.05-->6.94) (max @ vno 124549 --> 76824) face area 0.28 +- 0.13 (0.00-->5.99) mean absolute distance = 0.52 +- 0.84 7493 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1497435.9, rms=6.409 001: dt: 0.5000, sse=915547.2, rms=4.169 (34.954%) 002: dt: 0.5000, sse=694997.5, rms=2.873 (31.070%) 003: dt: 0.5000, sse=632652.7, rms=2.381 (17.143%) 004: dt: 0.5000, sse=616517.9, rms=2.240 (5.932%) rms = 2.21, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=614134.1, rms=2.214 (1.145%) 006: dt: 0.2500, sse=558059.7, rms=1.469 (33.658%) 007: dt: 0.2500, sse=548597.1, rms=1.322 (10.008%) rms = 1.29, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=547008.4, rms=1.291 (2.336%) rms = 1.26, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=545327.0, rms=1.261 (2.293%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.0, 77 (16) missing vertices, mean dist -0.3 [0.8 (%53.5)->0.2 (%46.5))] %51 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n026, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.24 (0.07-->7.46) (max @ vno 124549 --> 76824) face area 0.33 +- 0.16 (0.00-->7.78) mean absolute distance = 0.56 +- 0.67 5140 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=853675.7, rms=3.302 010: dt: 0.5000, sse=713618.8, rms=2.231 (32.437%) 011: dt: 0.5000, sse=679465.2, rms=1.880 (15.734%) rms = 1.84, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=677146.2, rms=1.835 (2.382%) 013: dt: 0.2500, sse=641711.9, rms=1.409 (23.228%) 014: dt: 0.2500, sse=632681.4, rms=1.280 (9.149%) 015: dt: 0.2500, sse=630229.6, rms=1.221 (4.575%) 016: dt: 0.2500, sse=626611.4, rms=1.162 (4.864%) rms = 1.13, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=627472.4, rms=1.132 (2.563%) rms = 1.10, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=623129.4, rms=1.099 (2.904%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.0, 96 (7) missing vertices, mean dist -0.4 [0.7 (%61.3)->0.3 (%38.7))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n026, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.87 +- 0.26 (0.05-->7.74) (max @ vno 77801 --> 124460) face area 0.32 +- 0.17 (0.00-->8.79) mean absolute distance = 0.45 +- 0.51 4311 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=855253.9, rms=3.379 019: dt: 0.5000, sse=698869.3, rms=2.128 (37.017%) 020: dt: 0.5000, sse=665039.2, rms=1.651 (22.425%) 021: dt: 0.5000, sse=653564.3, rms=1.572 (4.812%) rms = 1.63, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=627512.9, rms=1.242 (20.944%) 023: dt: 0.2500, sse=619576.1, rms=1.078 (13.249%) rms = 1.03, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=617594.6, rms=1.033 (4.119%) rms = 1.00, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=615959.8, rms=1.000 (3.224%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.8, 89 (3) missing vertices, mean dist -0.2 [0.5 (%58.0)->0.3 (%42.0))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n026, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /work2/r1774/subjects/J106388/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=661179.1, rms=1.874 026: dt: 0.5000, sse=610568.8, rms=1.097 (41.493%) rms = 1.27, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=597959.0, rms=0.916 (16.456%) rms = 0.87, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=597476.4, rms=0.872 (4.772%) rms = 0.83, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=593771.4, rms=0.827 (5.175%) positioning took 0.5 minutes generating cortex label... 10 non-cortical segments detected only using segment with 6713 vertices erasing segment 1 (vno[0] = 42784) erasing segment 2 (vno[0] = 44976) erasing segment 3 (vno[0] = 79806) erasing segment 4 (vno[0] = 83754) erasing segment 5 (vno[0] = 83777) erasing segment 6 (vno[0] = 84664) erasing segment 7 (vno[0] = 85721) erasing segment 8 (vno[0] = 87891) erasing segment 9 (vno[0] = 124691) writing cortex label to /work2/r1774/subjects/J106388/label/lh.cortex.label... writing curvature file /work2/r1774/subjects/J106388/surf/lh.curv writing smoothed area to lh.area writing curvature file /work2/r1774/subjects/J106388/surf/lh.area vertex spacing 0.87 +- 0.27 (0.03-->7.97) (max @ vno 77801 --> 124460) face area 0.32 +- 0.17 (0.00-->9.37) refinement took 5.4 minutes #-------------------------------------------- #@# Make White Surf rh Sun Apr 16 05:23:47 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs J106388 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /work2/r1774/subjects/J106388/mri/filled.mgz... reading volume /work2/r1774/subjects/J106388/mri/brain.finalsurfs.mgz... reading volume /work2/r1774/subjects/J106388/mri/../mri/aseg.presurf.mgz... reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... 15243 bright wm thresholded. 760 bright non-wm voxels segmented. reading original surface position from /work2/r1774/subjects/J106388/surf/rh.orig... computing class statistics... border white: 253970 voxels (1.51%) border gray 256307 voxels (1.53%) WM (96.0): 97.2 +- 6.3 [70.0 --> 110.0] GM (77.0) : 74.4 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.5 (was 40) setting MAX_GRAY to 91.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.32) (max @ vno 77769 --> 122353) face area 0.28 +- 0.13 (0.00-->5.12) mean absolute distance = 0.64 +- 0.86 3012 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-5.2, GM=78+-13.9 mean inside = 93.6, mean outside = 80.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=88.6, 48 (48) missing vertices, mean dist -0.1 [0.7 (%49.3)->0.6 (%50.7))] %47 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.24 (0.03-->6.84) (max @ vno 122353 --> 122237) face area 0.28 +- 0.13 (0.00-->6.14) mean absolute distance = 0.53 +- 0.85 7306 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1483329.0, rms=6.395 001: dt: 0.5000, sse=897498.3, rms=4.146 (35.176%) 002: dt: 0.5000, sse=681250.6, rms=2.844 (31.404%) 003: dt: 0.5000, sse=619352.1, rms=2.348 (17.448%) 004: dt: 0.5000, sse=603461.2, rms=2.195 (6.483%) rms = 2.15, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=598928.0, rms=2.153 (1.917%) 006: dt: 0.2500, sse=548394.9, rms=1.437 (33.262%) 007: dt: 0.2500, sse=539894.0, rms=1.295 (9.909%) rms = 1.26, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=537173.8, rms=1.258 (2.796%) rms = 1.23, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=535955.4, rms=1.226 (2.608%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.8, 54 (16) missing vertices, mean dist -0.3 [0.8 (%54.5)->0.2 (%45.5))] %53 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n026, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.25 (0.04-->7.70) (max @ vno 122353 --> 122237) face area 0.33 +- 0.16 (0.00-->8.51) mean absolute distance = 0.55 +- 0.66 4531 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=852206.2, rms=3.335 010: dt: 0.5000, sse=711322.9, rms=2.281 (31.593%) 011: dt: 0.5000, sse=673601.4, rms=1.937 (15.097%) 012: dt: 0.5000, sse=666684.1, rms=1.869 (3.473%) rms = 1.86, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=665534.8, rms=1.858 (0.634%) 014: dt: 0.2500, sse=632254.0, rms=1.363 (26.626%) 015: dt: 0.2500, sse=626818.2, rms=1.238 (9.183%) 016: dt: 0.2500, sse=624917.8, rms=1.180 (4.669%) rms = 1.15, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=621834.2, rms=1.148 (2.732%) rms = 1.11, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=619067.4, rms=1.114 (2.943%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=91.8, 69 (10) missing vertices, mean dist -0.3 [0.7 (%61.6)->0.3 (%38.4))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n026, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.26 (0.05-->7.99) (max @ vno 122353 --> 122237) face area 0.33 +- 0.17 (0.00-->9.01) mean absolute distance = 0.44 +- 0.51 4033 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=841656.1, rms=3.344 019: dt: 0.5000, sse=689359.3, rms=2.093 (37.401%) 020: dt: 0.5000, sse=648714.8, rms=1.627 (22.290%) 021: dt: 0.5000, sse=640444.8, rms=1.549 (4.740%) rms = 1.60, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=620505.9, rms=1.220 (21.250%) 023: dt: 0.2500, sse=614977.0, rms=1.070 (12.330%) rms = 1.03, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=613677.1, rms=1.033 (3.461%) rms = 1.00, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=620178.6, rms=0.999 (3.218%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.6, 90 (9) missing vertices, mean dist -0.2 [0.5 (%58.1)->0.3 (%41.9))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n026, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /work2/r1774/subjects/J106388/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=661936.5, rms=1.829 026: dt: 0.5000, sse=606158.6, rms=1.087 (40.571%) rms = 1.26, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=593826.2, rms=0.907 (16.557%) rms = 0.87, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=602018.6, rms=0.868 (4.267%) rms = 0.82, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=589664.1, rms=0.820 (5.583%) positioning took 0.6 minutes generating cortex label... 12 non-cortical segments detected only using segment with 6385 vertices erasing segment 1 (vno[0] = 64179) erasing segment 2 (vno[0] = 65157) erasing segment 3 (vno[0] = 67122) erasing segment 4 (vno[0] = 70211) erasing segment 5 (vno[0] = 75162) erasing segment 6 (vno[0] = 77266) erasing segment 7 (vno[0] = 80594) erasing segment 8 (vno[0] = 83630) erasing segment 9 (vno[0] = 84717) erasing segment 10 (vno[0] = 99781) erasing segment 11 (vno[0] = 122573) writing cortex label to /work2/r1774/subjects/J106388/label/rh.cortex.label... writing curvature file /work2/r1774/subjects/J106388/surf/rh.curv writing smoothed area to rh.area writing curvature file /work2/r1774/subjects/J106388/surf/rh.area vertex spacing 0.88 +- 0.27 (0.05-->7.86) (max @ vno 122237 --> 122353) face area 0.32 +- 0.17 (0.00-->8.69) refinement took 5.5 minutes #-------------------------------------------- #@# Smooth2 lh Sun Apr 16 05:29:16 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Sun Apr 16 05:29:23 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Sun Apr 16 05:29:30 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_inflate -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.1 mm, total surface area = 71273 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.172 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 57.252000 mris_inflate stimesec 0.116000 mris_inflate ru_maxrss 161852 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 21867 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8800 mris_inflate ru_oublock 9784 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 131 mris_inflate ru_nivcsw 118 #-------------------------------------------- #@# Inflation2 rh Sun Apr 16 05:30:27 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_inflate -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.8 mm, total surface area = 70966 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.175 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 1.2 minutes mris_inflate utimesec 73.228000 mris_inflate stimesec 0.072000 mris_inflate ru_maxrss 159128 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 21185 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8648 mris_inflate ru_oublock 9616 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 96 mris_inflate ru_nivcsw 200 #-------------------------------------------- #@# Curv .H and .K lh Sun Apr 16 05:31:41 CDT 2017 /work2/r1774/subjects/J106388/surf mris_curvature -w lh.white.preaparc total integrated curvature = 17.167*4pi (215.727) --> -16 handles ICI = 178.3, FI = 1405.5, variation=23518.966 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 165 vertices thresholded to be in k1 ~ [-1.95 0.37], k2 ~ [-0.12 0.36] total integrated curvature = 0.518*4pi (6.512) --> 0 handles ICI = 1.3, FI = 8.1, variation=139.651 116 vertices thresholded to be in [-0.15 0.04] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 134 vertices thresholded to be in [-0.76 0.18] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.030 done. #-------------------------------------------- #@# Curv .H and .K rh Sun Apr 16 05:33:19 CDT 2017 /work2/r1774/subjects/J106388/surf mris_curvature -w rh.white.preaparc total integrated curvature = 18.777*4pi (235.955) --> -18 handles ICI = 181.3, FI = 1426.3, variation=23859.106 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 142 vertices thresholded to be in k1 ~ [-0.27 0.54], k2 ~ [-0.13 0.08] total integrated curvature = 0.546*4pi (6.856) --> 0 handles ICI = 1.3, FI = 7.4, variation=128.483 113 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 121 vertices thresholded to be in [-0.15 0.27] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Sun Apr 16 05:34:55 CDT 2017 /work2/r1774/subjects/J106388/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm J106388 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ J106388/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 244 ] Gb_filter = 0 WARN: S lookup min: -0.027426 WARN: S explicit min: 0.000000 vertex = 37 #----------------------------------------- #@# Curvature Stats rh Sun Apr 16 05:35:00 CDT 2017 /work2/r1774/subjects/J106388/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm J106388 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ J106388/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 243 ] Gb_filter = 0 WARN: S lookup min: -0.576477 WARN: S explicit min: 0.000000 vertex = 772 #-------------------------------------------- #@# Sphere lh Sun Apr 16 05:35:05 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_sphere -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.323... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n026, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.10 pass 1: epoch 2 of 3 starting distance error %19.07 unfolding complete - removing small folds... starting distance error %18.99 removing remaining folds... final distance error %19.01 MRISunfold() return, current seed 1234 -01: dt=0.0000, 90 negative triangles 167: dt=0.9900, 90 negative triangles 168: dt=0.9900, 43 negative triangles 169: dt=0.9900, 33 negative triangles 170: dt=0.9900, 23 negative triangles 171: dt=0.9900, 27 negative triangles 172: dt=0.9900, 23 negative triangles 173: dt=0.9900, 21 negative triangles 174: dt=0.9900, 20 negative triangles 175: dt=0.9900, 11 negative triangles 176: dt=0.9900, 15 negative triangles 177: dt=0.9900, 14 negative triangles 178: dt=0.9900, 9 negative triangles 179: dt=0.9900, 9 negative triangles 180: dt=0.9900, 7 negative triangles 181: dt=0.9900, 4 negative triangles 182: dt=0.9900, 7 negative triangles 183: dt=0.9900, 4 negative triangles 184: dt=0.9900, 5 negative triangles 185: dt=0.9900, 3 negative triangles 186: dt=0.9900, 1 negative triangles 187: dt=0.9900, 3 negative triangles 188: dt=0.9900, 2 negative triangles 189: dt=0.9900, 1 negative triangles 190: dt=0.9900, 1 negative triangles 191: dt=0.9900, 2 negative triangles 192: dt=0.9900, 5 negative triangles 193: dt=0.9900, 2 negative triangles 194: dt=0.9900, 1 negative triangles 195: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.07 hours mris_sphere utimesec 3865.960000 mris_sphere stimesec 0.468000 mris_sphere ru_maxrss 222300 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 37357 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8800 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 156 mris_sphere ru_nivcsw 9395 FSRUNTIME@ mris_sphere 1.0742 hours 1 threads #-------------------------------------------- #@# Sphere rh Sun Apr 16 06:39:32 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_sphere -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.329... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n026, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.75 pass 1: epoch 2 of 3 starting distance error %18.67 unfolding complete - removing small folds... starting distance error %18.63 removing remaining folds... final distance error %18.65 MRISunfold() return, current seed 1234 -01: dt=0.0000, 199 negative triangles 170: dt=0.9900, 199 negative triangles 171: dt=0.9900, 105 negative triangles 172: dt=0.9900, 71 negative triangles 173: dt=0.9900, 62 negative triangles 174: dt=0.9900, 58 negative triangles 175: dt=0.9900, 52 negative triangles 176: dt=0.9900, 49 negative triangles 177: dt=0.9900, 48 negative triangles 178: dt=0.9900, 50 negative triangles 179: dt=0.9900, 44 negative triangles 180: dt=0.9900, 42 negative triangles 181: dt=0.9900, 40 negative triangles 182: dt=0.9900, 39 negative triangles 183: dt=0.9900, 38 negative triangles 184: dt=0.9900, 38 negative triangles 185: dt=0.9900, 37 negative triangles 186: dt=0.9900, 35 negative triangles 187: dt=0.9900, 35 negative triangles 188: dt=0.9900, 37 negative triangles 189: dt=0.9900, 33 negative triangles 190: dt=0.9900, 31 negative triangles 191: dt=0.9900, 32 negative triangles 192: dt=0.9900, 32 negative triangles 193: dt=0.9900, 30 negative triangles 194: dt=0.9900, 31 negative triangles 195: dt=0.9900, 30 negative triangles 196: dt=0.9900, 30 negative triangles 197: dt=0.9900, 31 negative triangles 198: dt=0.9900, 29 negative triangles 199: dt=0.9900, 27 negative triangles 200: dt=0.9900, 28 negative triangles 201: dt=0.9900, 28 negative triangles 202: dt=0.9900, 27 negative triangles 203: dt=0.9900, 29 negative triangles 204: dt=0.9900, 25 negative triangles 205: dt=0.9900, 25 negative triangles 206: dt=0.9900, 27 negative triangles 207: dt=0.9900, 27 negative triangles 208: dt=0.9900, 24 negative triangles 209: dt=0.9900, 23 negative triangles 210: dt=0.9900, 23 negative triangles 211: dt=0.9900, 22 negative triangles 212: dt=0.9900, 21 negative triangles 213: dt=0.9900, 17 negative triangles 214: dt=0.9900, 17 negative triangles 215: dt=0.9900, 16 negative triangles 216: dt=0.9900, 16 negative triangles 217: dt=0.9900, 20 negative triangles 218: dt=0.9900, 16 negative triangles 219: dt=0.9900, 15 negative triangles 220: dt=0.9900, 11 negative triangles 221: dt=0.9900, 11 negative triangles 222: dt=0.9900, 11 negative triangles 223: dt=0.9900, 8 negative triangles 224: dt=0.9900, 6 negative triangles 225: dt=0.9900, 8 negative triangles 226: dt=0.9900, 9 negative triangles 227: dt=0.9900, 7 negative triangles 228: dt=0.9900, 6 negative triangles 229: dt=0.9900, 9 negative triangles 230: dt=0.9900, 6 negative triangles 231: dt=0.9900, 2 negative triangles 232: dt=0.9900, 1 negative triangles 233: dt=0.9900, 5 negative triangles 234: dt=0.9900, 1 negative triangles 235: dt=0.9900, 5 negative triangles 236: dt=0.9900, 1 negative triangles 237: dt=0.9900, 2 negative triangles 238: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.02 hours mris_sphere utimesec 3657.212000 mris_sphere stimesec 0.520000 mris_sphere ru_maxrss 219712 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 36424 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8648 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 39 mris_sphere ru_nivcsw 6841 FSRUNTIME@ mris_sphere 1.0162 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Sun Apr 16 07:40:31 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_register -curv -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /home/ums/r1774/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /work2/r1774/subjects/J106388/scripts cmdline mris_register -curv -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /home/ums/r1774/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /home/ums/r1774/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n026, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n026, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 5.342 curvature mean = 0.027, std = 0.821 curvature mean = 0.024, std = 0.871 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 311263.6, tmin=1.5675 d=32.00 min @ (0.00, 8.00, 8.00) sse = 213936.9, tmin=3.1529 d=16.00 min @ (4.00, 0.00, -4.00) sse = 182736.7, tmin=4.8198 d=4.00 min @ (0.00, 1.00, 1.00) sse = 177885.5, tmin=7.9810 d=1.00 min @ (0.25, 0.00, 0.00) sse = 177873.9, tmin=11.1351 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 177849.8, tmin=12.7030 tol=1.0e+00, sigma=0.5, host= n026, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 12.70 min curvature mean = -0.007, std = 0.834 curvature mean = 0.009, std = 0.952 curvature mean = -0.010, std = 0.845 curvature mean = 0.003, std = 0.981 curvature mean = -0.012, std = 0.847 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.026, std = 0.260 curvature mean = 0.034, std = 0.246 curvature mean = 0.049, std = 0.426 curvature mean = 0.036, std = 0.304 curvature mean = 0.014, std = 0.634 curvature mean = 0.036, std = 0.328 curvature mean = 0.007, std = 0.774 curvature mean = 0.037, std = 0.339 curvature mean = 0.002, std = 0.866 MRISregister() return, current seed 0 -01: dt=0.0000, 47 negative triangles 109: dt=0.9900, 47 negative triangles 110: dt=0.9405, 62 negative triangles expanding nbhd size to 1 111: dt=0.9900, 58 negative triangles 112: dt=0.9900, 48 negative triangles 113: dt=0.9900, 49 negative triangles 114: dt=0.9900, 55 negative triangles 115: dt=0.9900, 53 negative triangles 116: dt=0.9900, 54 negative triangles 117: dt=0.9900, 50 negative triangles 118: dt=0.9900, 48 negative triangles 119: dt=0.9900, 46 negative triangles 120: dt=0.9900, 44 negative triangles 121: dt=0.9900, 41 negative triangles 122: dt=0.9900, 39 negative triangles 123: dt=0.9900, 36 negative triangles 124: dt=0.9900, 36 negative triangles 125: dt=0.9900, 35 negative triangles 126: dt=0.9900, 33 negative triangles 127: dt=0.9900, 34 negative triangles 128: dt=0.9900, 29 negative triangles 129: dt=0.9900, 28 negative triangles 130: dt=0.9900, 28 negative triangles 131: dt=0.9900, 27 negative triangles 132: dt=0.9900, 25 negative triangles 133: dt=0.9900, 24 negative triangles 134: dt=0.9900, 24 negative triangles 135: dt=0.9900, 22 negative triangles 136: dt=0.9900, 23 negative triangles 137: dt=0.9900, 21 negative triangles 138: dt=0.9900, 21 negative triangles 139: dt=0.9900, 20 negative triangles 140: dt=0.9900, 18 negative triangles 141: dt=0.9900, 18 negative triangles 142: dt=0.9900, 22 negative triangles 143: dt=0.9900, 20 negative triangles 144: dt=0.9900, 19 negative triangles 145: dt=0.9900, 18 negative triangles 146: dt=0.9900, 17 negative triangles 147: dt=0.9900, 18 negative triangles 148: dt=0.9900, 20 negative triangles 149: dt=0.9900, 20 negative triangles 150: dt=0.9900, 17 negative triangles 151: dt=0.9900, 16 negative triangles 152: dt=0.9900, 18 negative triangles 153: dt=0.9900, 15 negative triangles 154: dt=0.9900, 16 negative triangles 155: dt=0.9900, 15 negative triangles 156: dt=0.9900, 14 negative triangles 157: dt=0.9900, 16 negative triangles 158: dt=0.9900, 16 negative triangles 159: dt=0.9900, 15 negative triangles 160: dt=0.9900, 15 negative triangles 161: dt=0.9900, 14 negative triangles 162: dt=0.9900, 14 negative triangles 163: dt=0.9900, 14 negative triangles 164: dt=0.9900, 13 negative triangles 165: dt=0.9900, 13 negative triangles 166: dt=0.9900, 14 negative triangles 167: dt=0.9900, 12 negative triangles 168: dt=0.9900, 13 negative triangles 169: dt=0.9900, 14 negative triangles 170: dt=0.9900, 12 negative triangles 171: dt=0.9900, 13 negative triangles 172: dt=0.9900, 13 negative triangles 173: dt=0.9900, 12 negative triangles 174: dt=0.9900, 13 negative triangles 175: dt=0.9900, 13 negative triangles 176: dt=0.9900, 11 negative triangles 177: dt=0.9900, 10 negative triangles 178: dt=0.9900, 10 negative triangles 179: dt=0.9900, 8 negative triangles 180: dt=0.9900, 7 negative triangles 181: dt=0.9900, 8 negative triangles 182: dt=0.9900, 6 negative triangles 183: dt=0.9900, 4 negative triangles 184: dt=0.9900, 2 negative triangles 185: dt=0.9900, 3 negative triangles 186: dt=0.9900, 1 negative triangles 187: dt=0.9900, 1 negative triangles 188: dt=0.9900, 1 negative triangles 189: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.29 hours mris_register utimesec 4649.312000 mris_register stimesec 0.496000 mris_register ru_maxrss 218820 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 29303 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 8800 mris_register ru_oublock 8800 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 153 mris_register ru_nivcsw 9200 FSRUNTIME@ mris_register 1.2917 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Sun Apr 16 08:58:01 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_register -curv -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /home/ums/r1774/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /work2/r1774/subjects/J106388/scripts cmdline mris_register -curv -rusage /work2/r1774/subjects/J106388/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /home/ums/r1774/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /home/ums/r1774/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n026, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n026, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.351 curvature mean = 0.026, std = 0.814 curvature mean = 0.021, std = 0.872 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 340510.2, tmin=1.5079 d=32.00 min @ (-8.00, -8.00, 8.00) sse = 233810.8, tmin=3.0468 d=16.00 min @ (0.00, 4.00, 0.00) sse = 204785.1, tmin=4.6292 d=8.00 min @ (-2.00, -2.00, 2.00) sse = 203039.5, tmin=6.2030 d=4.00 min @ (1.00, 1.00, -1.00) sse = 200311.1, tmin=7.7963 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 199954.5, tmin=9.4616 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 199918.7, tmin=11.0069 tol=1.0e+00, sigma=0.5, host= n026, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 12.56 min curvature mean = -0.002, std = 0.821 curvature mean = 0.007, std = 0.952 curvature mean = -0.006, std = 0.832 curvature mean = 0.002, std = 0.981 curvature mean = -0.006, std = 0.834 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.025, std = 0.312 curvature mean = 0.032, std = 0.241 curvature mean = 0.042, std = 0.357 curvature mean = 0.033, std = 0.297 curvature mean = 0.015, std = 0.537 curvature mean = 0.033, std = 0.324 curvature mean = 0.008, std = 0.655 curvature mean = 0.033, std = 0.334 curvature mean = 0.003, std = 0.742 MRISregister() return, current seed 0 -01: dt=0.0000, 93 negative triangles 116: dt=0.9900, 93 negative triangles expanding nbhd size to 1 117: dt=0.9900, 133 negative triangles 118: dt=0.9900, 103 negative triangles 119: dt=0.9900, 96 negative triangles 120: dt=0.9405, 96 negative triangles 121: dt=0.9405, 100 negative triangles 122: dt=0.9405, 100 negative triangles 123: dt=0.9405, 93 negative triangles 124: dt=0.9405, 91 negative triangles 125: dt=0.9405, 85 negative triangles 126: dt=0.9405, 79 negative triangles 127: dt=0.9405, 66 negative triangles 128: dt=0.9405, 65 negative triangles 129: dt=0.9405, 65 negative triangles 130: dt=0.9405, 57 negative triangles 131: dt=0.9405, 51 negative triangles 132: dt=0.9405, 54 negative triangles 133: dt=0.9405, 52 negative triangles 134: dt=0.9405, 50 negative triangles 135: dt=0.9405, 46 negative triangles 136: dt=0.9405, 42 negative triangles 137: dt=0.9405, 36 negative triangles 138: dt=0.9405, 31 negative triangles 139: dt=0.9405, 32 negative triangles 140: dt=0.9405, 26 negative triangles 141: dt=0.9405, 23 negative triangles 142: dt=0.9405, 22 negative triangles 143: dt=0.9405, 22 negative triangles 144: dt=0.9405, 17 negative triangles 145: dt=0.9405, 17 negative triangles 146: dt=0.9405, 14 negative triangles 147: dt=0.9405, 12 negative triangles 148: dt=0.9405, 14 negative triangles 149: dt=0.9405, 13 negative triangles 150: dt=0.9405, 13 negative triangles 151: dt=0.9405, 10 negative triangles 152: dt=0.9405, 9 negative triangles 153: dt=0.9405, 7 negative triangles 154: dt=0.9405, 9 negative triangles 155: dt=0.9405, 7 negative triangles 156: dt=0.9405, 7 negative triangles 157: dt=0.9405, 5 negative triangles 158: dt=0.9405, 5 negative triangles 159: dt=0.9405, 4 negative triangles 160: dt=0.9405, 5 negative triangles 161: dt=0.9405, 5 negative triangles 162: dt=0.9405, 3 negative triangles 163: dt=0.9405, 3 negative triangles 164: dt=0.9405, 4 negative triangles 165: dt=0.9405, 3 negative triangles 166: dt=0.9405, 3 negative triangles 167: dt=0.9405, 3 negative triangles 168: dt=0.9405, 3 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.13 hours mris_register utimesec 4060.152000 mris_register stimesec 0.436000 mris_register ru_maxrss 211356 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 28744 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 8648 mris_register ru_oublock 8648 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 163 mris_register ru_nivcsw 8421 FSRUNTIME@ mris_register 1.1281 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Sun Apr 16 10:05:43 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Apr 16 10:05:45 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Sun Apr 16 10:05:48 CDT 2017 /work2/r1774/subjects/J106388/scripts mrisp_paint -a 5 /home/ums/r1774/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /home/ums/r1774/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Sun Apr 16 10:05:50 CDT 2017 /work2/r1774/subjects/J106388/scripts mrisp_paint -a 5 /home/ums/r1774/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /home/ums/r1774/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sun Apr 16 10:05:52 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 J106388 lh ../surf/lh.sphere.reg /home/ums/r1774/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /home/ums/r1774/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 788 labels changed using aseg relabeling using gibbs priors... 000: 2884 changed, 125059 examined... 001: 703 changed, 12184 examined... 002: 143 changed, 3933 examined... 003: 39 changed, 883 examined... 004: 16 changed, 239 examined... 005: 7 changed, 99 examined... 006: 6 changed, 43 examined... 007: 6 changed, 27 examined... 008: 2 changed, 21 examined... 009: 1 changed, 11 examined... 010: 1 changed, 9 examined... 011: 1 changed, 5 examined... 012: 1 changed, 6 examined... 013: 1 changed, 6 examined... 014: 0 changed, 8 examined... 234 labels changed using aseg 000: 102 total segments, 63 labels (238 vertices) changed 001: 41 total segments, 2 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2040 vertices marked for relabeling... 2040 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Cortical Parc rh Sun Apr 16 10:06:10 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 J106388 rh ../surf/rh.sphere.reg /home/ums/r1774/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /home/ums/r1774/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 954 labels changed using aseg relabeling using gibbs priors... 000: 2575 changed, 122899 examined... 001: 546 changed, 11228 examined... 002: 135 changed, 3208 examined... 003: 39 changed, 815 examined... 004: 14 changed, 241 examined... 005: 8 changed, 80 examined... 006: 1 changed, 39 examined... 007: 3 changed, 8 examined... 008: 0 changed, 13 examined... 167 labels changed using aseg 000: 91 total segments, 52 labels (232 vertices) changed 001: 42 total segments, 3 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1903 vertices marked for relabeling... 1903 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 17 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sun Apr 16 10:06:28 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs J106388 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /work2/r1774/subjects/J106388/mri/filled.mgz... reading volume /work2/r1774/subjects/J106388/mri/brain.finalsurfs.mgz... reading volume /work2/r1774/subjects/J106388/mri/../mri/aseg.presurf.mgz... reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... 15243 bright wm thresholded. 760 bright non-wm voxels segmented. reading original surface position from /work2/r1774/subjects/J106388/surf/lh.orig... computing class statistics... border white: 253970 voxels (1.51%) border gray 256307 voxels (1.53%) WM (96.0): 97.2 +- 6.3 [70.0 --> 110.0] GM (77.0) : 74.4 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.5 (was 40) setting MAX_GRAY to 91.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-5.2, GM=78+-15.7 mean inside = 93.7, mean outside = 79.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.87 +- 0.27 (0.03-->7.97) (max @ vno 77801 --> 124460) face area 0.31 +- 0.17 (0.00-->9.31) mean absolute distance = 0.75 +- 0.93 3431 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 45 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 51 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 55 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 54 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown mean border=88.9, 161 (161) missing vertices, mean dist 0.4 [0.6 (%26.5)->0.8 (%73.5))] %47 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.05-->8.25) (max @ vno 77801 --> 124460) face area 0.31 +- 0.16 (0.00-->8.85) mean absolute distance = 0.52 +- 0.85 7926 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1484712.4, rms=6.170 001: dt: 0.5000, sse=1050990.5, rms=4.494 (27.163%) 002: dt: 0.5000, sse=849560.3, rms=3.468 (22.839%) 003: dt: 0.5000, sse=757105.4, rms=2.880 (16.939%) 004: dt: 0.5000, sse=711497.4, rms=2.535 (12.002%) 005: dt: 0.5000, sse=687954.6, rms=2.339 (7.732%) 006: dt: 0.5000, sse=674624.7, rms=2.215 (5.309%) rms = 2.17, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=668311.6, rms=2.174 (1.856%) 008: dt: 0.2500, sse=612555.9, rms=1.390 (36.052%) 009: dt: 0.2500, sse=603623.8, rms=1.223 (12.027%) rms = 1.18, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=601115.6, rms=1.180 (3.479%) rms = 1.15, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=599517.0, rms=1.148 (2.695%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 39 points - only 0.00% unknown deleting segment 1 with 9 points - only 0.00% unknown deleting segment 2 with 42 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 51 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 52 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=90.1, 96 (26) missing vertices, mean dist -0.3 [0.8 (%53.9)->0.2 (%46.1))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n026, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.25 (0.04-->8.60) (max @ vno 77801 --> 124460) face area 0.33 +- 0.17 (0.00-->10.41) mean absolute distance = 0.56 +- 0.67 4977 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=867583.5, rms=3.323 012: dt: 0.5000, sse=723019.6, rms=2.218 (33.269%) 013: dt: 0.5000, sse=682415.8, rms=1.857 (16.256%) rms = 1.83, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=679074.2, rms=1.827 (1.604%) 015: dt: 0.2500, sse=653537.2, rms=1.414 (22.645%) 016: dt: 0.2500, sse=643434.8, rms=1.286 (8.998%) 017: dt: 0.2500, sse=640131.4, rms=1.226 (4.688%) 018: dt: 0.2500, sse=636601.9, rms=1.165 (4.953%) rms = 1.13, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=635087.8, rms=1.132 (2.819%) rms = 1.10, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=638315.0, rms=1.098 (3.034%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 39 points - only 0.00% unknown deleting segment 1 with 10 points - only 0.00% unknown deleting segment 2 with 45 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 51 points - only 0.00% unknown deleting segment 5 with 14 points - only 0.00% unknown deleting segment 6 with 99 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown deleting segment 8 with 39 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=92.1, 97 (15) missing vertices, mean dist -0.4 [0.7 (%61.2)->0.3 (%38.8))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n026, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.87 +- 0.26 (0.05-->8.73) (max @ vno 77801 --> 124460) face area 0.33 +- 0.18 (0.00-->10.88) mean absolute distance = 0.45 +- 0.51 4218 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=862733.1, rms=3.363 021: dt: 0.5000, sse=701921.4, rms=2.139 (36.404%) 022: dt: 0.5000, sse=658770.5, rms=1.660 (22.370%) 023: dt: 0.5000, sse=656339.4, rms=1.588 (4.357%) rms = 1.64, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=632262.8, rms=1.260 (20.660%) 025: dt: 0.2500, sse=624081.2, rms=1.091 (13.435%) rms = 1.04, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=621329.6, rms=1.044 (4.272%) rms = 1.01, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=620480.2, rms=1.011 (3.132%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 39 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 2 with 43 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 52 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 15 points - only 0.00% unknown deleting segment 7 with 139 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown deleting segment 9 with 34 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown deleting segment 16 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 17 with 2 points - only 0.00% unknown mean border=92.9, 106 (11) missing vertices, mean dist -0.2 [0.5 (%58.2)->0.3 (%41.8))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n026, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /work2/r1774/subjects/J106388/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=665140.8, rms=1.883 028: dt: 0.5000, sse=614365.8, rms=1.104 (41.378%) rms = 1.27, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=601142.9, rms=0.926 (16.072%) rms = 0.88, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=602601.2, rms=0.884 (4.619%) rms = 0.84, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=597076.2, rms=0.838 (5.213%) positioning took 0.6 minutes generating cortex label... 14 non-cortical segments detected only using segment with 6675 vertices erasing segment 0 (vno[0] = 36973) erasing segment 2 (vno[0] = 41753) erasing segment 3 (vno[0] = 42784) erasing segment 4 (vno[0] = 44976) erasing segment 5 (vno[0] = 46025) erasing segment 6 (vno[0] = 52898) erasing segment 7 (vno[0] = 77353) erasing segment 8 (vno[0] = 82714) erasing segment 9 (vno[0] = 84664) erasing segment 10 (vno[0] = 84675) erasing segment 11 (vno[0] = 87891) erasing segment 12 (vno[0] = 100236) erasing segment 13 (vno[0] = 124691) writing cortex label to /work2/r1774/subjects/J106388/label/lh.cortex.label... writing curvature file /work2/r1774/subjects/J106388/surf/lh.curv writing smoothed area to lh.area writing curvature file /work2/r1774/subjects/J106388/surf/lh.area vertex spacing 0.87 +- 0.28 (0.03-->8.80) (max @ vno 77801 --> 124460) face area 0.32 +- 0.17 (0.00-->10.54) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=63.9, 203 (203) missing vertices, mean dist 1.7 [1.3 (%0.0)->2.7 (%100.0))] %18 local maxima, %39 large gradients and %38 min vals, 114 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=22278482.0, rms=30.198 001: dt: 0.0500, sse=20576162.0, rms=28.991 (3.997%) 002: dt: 0.0500, sse=19352936.0, rms=28.091 (3.103%) 003: dt: 0.0500, sse=18390464.0, rms=27.362 (2.594%) 004: dt: 0.0500, sse=17586858.0, rms=26.739 (2.279%) 005: dt: 0.0500, sse=16885190.0, rms=26.182 (2.082%) 006: dt: 0.0500, sse=16254662.0, rms=25.671 (1.951%) 007: dt: 0.0500, sse=15675584.0, rms=25.193 (1.863%) 008: dt: 0.0500, sse=15136157.0, rms=24.739 (1.801%) 009: dt: 0.0500, sse=14628111.0, rms=24.304 (1.759%) 010: dt: 0.0500, sse=14145067.0, rms=23.883 (1.733%) positioning took 1.1 minutes mean border=63.7, 138 (111) missing vertices, mean dist 1.3 [0.2 (%0.1)->2.1 (%99.9))] %18 local maxima, %40 large gradients and %37 min vals, 89 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=15252919.0, rms=24.827 011: dt: 0.0500, sse=14785677.0, rms=24.429 (1.604%) 012: dt: 0.0500, sse=14337701.0, rms=24.041 (1.589%) 013: dt: 0.0500, sse=13906454.0, rms=23.661 (1.579%) 014: dt: 0.0500, sse=13490848.0, rms=23.289 (1.571%) 015: dt: 0.0500, sse=13089623.0, rms=22.925 (1.566%) 016: dt: 0.0500, sse=12702320.0, rms=22.567 (1.560%) 017: dt: 0.0500, sse=12328274.0, rms=22.216 (1.555%) 018: dt: 0.0500, sse=11967475.0, rms=21.872 (1.548%) 019: dt: 0.0500, sse=11619052.0, rms=21.535 (1.542%) 020: dt: 0.0500, sse=11282150.0, rms=21.203 (1.539%) positioning took 1.1 minutes mean border=63.4, 149 (87) missing vertices, mean dist 1.1 [0.1 (%1.3)->1.8 (%98.7))] %18 local maxima, %40 large gradients and %37 min vals, 76 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11419428.0, rms=21.338 021: dt: 0.0500, sse=11080244.0, rms=21.001 (1.578%) 022: dt: 0.0500, sse=10752364.0, rms=20.670 (1.575%) 023: dt: 0.0500, sse=10432498.0, rms=20.343 (1.586%) 024: dt: 0.0500, sse=10124885.0, rms=20.022 (1.575%) 025: dt: 0.0500, sse=9828774.0, rms=19.709 (1.565%) 026: dt: 0.0500, sse=9542645.0, rms=19.401 (1.561%) 027: dt: 0.0500, sse=9264955.0, rms=19.098 (1.563%) 028: dt: 0.0500, sse=8992606.0, rms=18.796 (1.583%) 029: dt: 0.0500, sse=8724423.0, rms=18.493 (1.610%) 030: dt: 0.0500, sse=8460666.0, rms=18.191 (1.636%) positioning took 1.2 minutes mean border=63.4, 185 (68) missing vertices, mean dist 0.9 [0.1 (%13.4)->1.6 (%86.6))] %18 local maxima, %41 large gradients and %36 min vals, 80 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8546003.0, rms=18.285 031: dt: 0.5000, sse=6583191.0, rms=15.872 (13.195%) 032: dt: 0.5000, sse=5002566.0, rms=13.615 (14.219%) 033: dt: 0.5000, sse=3757543.5, rms=11.539 (15.248%) 034: dt: 0.5000, sse=2847408.0, rms=9.737 (15.620%) 035: dt: 0.5000, sse=2247685.0, rms=8.346 (14.284%) 036: dt: 0.5000, sse=1885611.2, rms=7.370 (11.688%) 037: dt: 0.5000, sse=1665467.1, rms=6.715 (8.886%) 038: dt: 0.5000, sse=1530571.8, rms=6.269 (6.650%) 039: dt: 0.5000, sse=1446706.1, rms=5.982 (4.573%) 040: dt: 0.5000, sse=1393966.9, rms=5.784 (3.318%) 041: dt: 0.5000, sse=1361164.8, rms=5.666 (2.035%) 042: dt: 0.5000, sse=1341379.8, rms=5.581 (1.498%) rms = 5.53, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1328051.5, rms=5.534 (0.844%) 044: dt: 0.2500, sse=1179393.4, rms=4.881 (11.810%) 045: dt: 0.2500, sse=1143137.9, rms=4.720 (3.299%) rms = 4.73, time step reduction 2 of 3 to 0.125... 046: dt: 0.1250, sse=1127940.9, rms=4.647 (1.544%) 047: dt: 0.1250, sse=1108657.1, rms=4.550 (2.072%) rms = 4.54, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1106397.2, rms=4.537 (0.284%) positioning took 2.7 minutes mean border=62.8, 2204 (29) missing vertices, mean dist 0.2 [0.2 (%52.6)->0.7 (%47.4))] %21 local maxima, %39 large gradients and %33 min vals, 88 gradients ignored tol=1.0e-04, sigma=1.0, host= n026, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1165045.4, rms=4.572 rms = 4.59, time step reduction 1 of 3 to 0.250... 049: dt: 0.2500, sse=1077159.0, rms=4.131 (9.649%) 050: dt: 0.2500, sse=995513.3, rms=3.679 (10.927%) 051: dt: 0.2500, sse=965238.4, rms=3.505 (4.749%) 052: dt: 0.2500, sse=952549.1, rms=3.431 (2.095%) rms = 3.39, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=945064.2, rms=3.387 (1.284%) 054: dt: 0.1250, sse=904242.8, rms=3.107 (8.256%) rms = 3.06, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=897301.4, rms=3.060 (1.524%) positioning took 1.3 minutes mean border=62.7, 2561 (11) missing vertices, mean dist 0.1 [0.1 (%59.2)->0.5 (%40.8))] %27 local maxima, %34 large gradients and %32 min vals, 111 gradients ignored tol=1.0e-04, sigma=0.5, host= n026, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=896817.3, rms=3.162 rms = 3.52, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=873894.6, rms=3.004 (4.997%) 057: dt: 0.2500, sse=865040.1, rms=2.950 (1.798%) rms = 2.94, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=862900.8, rms=2.941 (0.291%) 059: dt: 0.1250, sse=853441.1, rms=2.864 (2.605%) rms = 2.84, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=850587.6, rms=2.844 (0.698%) positioning took 1.1 minutes mean border=62.3, 4368 (11) missing vertices, mean dist 0.1 [0.1 (%54.0)->0.4 (%46.0))] %32 local maxima, %28 large gradients and %31 min vals, 116 gradients ignored tol=1.0e-04, sigma=0.2, host= n026, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /work2/r1774/subjects/J106388/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=865903.1, rms=2.953 rms = 3.29, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=846175.2, rms=2.808 (4.920%) 062: dt: 0.2500, sse=834554.6, rms=2.731 (2.734%) rms = 2.71, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=831070.1, rms=2.711 (0.730%) 064: dt: 0.1250, sse=821630.2, rms=2.629 (3.011%) rms = 2.60, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=818109.8, rms=2.603 (1.004%) positioning took 1.1 minutes writing curvature file /work2/r1774/subjects/J106388/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /work2/r1774/subjects/J106388/surf/lh.area.pial vertex spacing 0.91 +- 0.34 (0.06-->8.29) (max @ vno 124522 --> 83825) face area 0.33 +- 0.24 (0.00-->13.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 125059 vertices processed 25000 of 125059 vertices processed 50000 of 125059 vertices processed 75000 of 125059 vertices processed 100000 of 125059 vertices processed 125000 of 125059 vertices processed 0 of 125059 vertices processed 25000 of 125059 vertices processed 50000 of 125059 vertices processed 75000 of 125059 vertices processed 100000 of 125059 vertices processed 125000 of 125059 vertices processed thickness calculation complete, 79:287 truncations. 44748 vertices at 0 distance 101122 vertices at 1 distance 57031 vertices at 2 distance 21971 vertices at 3 distance 8436 vertices at 4 distance 3129 vertices at 5 distance 1165 vertices at 6 distance 417 vertices at 7 distance 155 vertices at 8 distance 61 vertices at 9 distance 33 vertices at 10 distance 38 vertices at 11 distance 21 vertices at 12 distance 13 vertices at 13 distance 15 vertices at 14 distance 15 vertices at 15 distance 19 vertices at 16 distance 19 vertices at 17 distance 6 vertices at 18 distance 6 vertices at 19 distance 4 vertices at 20 distance writing curvature file /work2/r1774/subjects/J106388/surf/lh.thickness positioning took 17.7 minutes #-------------------------------------------- #@# Make Pial Surf rh Sun Apr 16 10:24:10 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs J106388 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /work2/r1774/subjects/J106388/mri/filled.mgz... reading volume /work2/r1774/subjects/J106388/mri/brain.finalsurfs.mgz... reading volume /work2/r1774/subjects/J106388/mri/../mri/aseg.presurf.mgz... reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... 15243 bright wm thresholded. 760 bright non-wm voxels segmented. reading original surface position from /work2/r1774/subjects/J106388/surf/rh.orig... computing class statistics... border white: 253970 voxels (1.51%) border gray 256307 voxels (1.53%) WM (96.0): 97.2 +- 6.3 [70.0 --> 110.0] GM (77.0) : 74.4 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.5 (was 40) setting MAX_GRAY to 91.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-5.2, GM=78+-13.9 mean inside = 93.6, mean outside = 80.0 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.27 (0.05-->7.86) (max @ vno 122237 --> 122353) face area 0.32 +- 0.17 (0.00-->8.64) mean absolute distance = 0.76 +- 0.93 3350 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 45 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 151 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown deleting segment 9 with 33 points - only 0.00% unknown mean border=88.7, 133 (131) missing vertices, mean dist 0.4 [0.6 (%26.2)->0.8 (%73.8))] %48 local maxima, %47 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.08-->7.91) (max @ vno 122353 --> 122237) face area 0.32 +- 0.16 (0.00-->8.39) mean absolute distance = 0.52 +- 0.86 7594 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1466568.1, rms=6.172 001: dt: 0.5000, sse=1025904.8, rms=4.424 (28.329%) 002: dt: 0.5000, sse=830155.6, rms=3.367 (23.889%) 003: dt: 0.5000, sse=738853.4, rms=2.779 (17.461%) 004: dt: 0.5000, sse=697790.5, rms=2.453 (11.711%) 005: dt: 0.5000, sse=680664.9, rms=2.272 (7.394%) 006: dt: 0.5000, sse=663310.1, rms=2.161 (4.897%) rms = 2.12, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=661112.3, rms=2.119 (1.944%) 008: dt: 0.2500, sse=609251.7, rms=1.380 (34.861%) 009: dt: 0.2500, sse=604574.4, rms=1.223 (11.385%) rms = 1.18, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=598235.9, rms=1.182 (3.392%) rms = 1.15, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=596606.7, rms=1.148 (2.858%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 56 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 68 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 41 points - only 0.00% unknown mean border=90.0, 86 (26) missing vertices, mean dist -0.3 [0.8 (%54.8)->0.2 (%45.2))] %53 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n026, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.26 (0.07-->8.16) (max @ vno 122353 --> 122237) face area 0.34 +- 0.18 (0.00-->9.46) mean absolute distance = 0.55 +- 0.66 4524 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=858330.1, rms=3.313 012: dt: 0.5000, sse=726141.7, rms=2.243 (32.285%) 013: dt: 0.5000, sse=683139.9, rms=1.893 (15.595%) 014: dt: 0.5000, sse=675578.8, rms=1.836 (3.029%) rms = 1.82, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=675858.1, rms=1.817 (1.046%) 016: dt: 0.2500, sse=643588.4, rms=1.333 (26.644%) 017: dt: 0.2500, sse=636007.8, rms=1.209 (9.302%) 018: dt: 0.2500, sse=632971.4, rms=1.145 (5.289%) rms = 1.11, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=630375.1, rms=1.114 (2.737%) rms = 1.08, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=627614.2, rms=1.079 (3.133%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 65 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 85 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown deleting segment 8 with 44 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=91.9, 96 (18) missing vertices, mean dist -0.3 [0.7 (%61.5)->0.3 (%38.5))] %66 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n026, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.87 +- 0.27 (0.05-->8.12) (max @ vno 122353 --> 122237) face area 0.33 +- 0.18 (0.00-->9.44) mean absolute distance = 0.44 +- 0.51 3908 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=841414.0, rms=3.315 021: dt: 0.5000, sse=691959.8, rms=2.080 (37.234%) 022: dt: 0.5000, sse=655379.2, rms=1.623 (21.969%) 023: dt: 0.5000, sse=646636.8, rms=1.532 (5.658%) rms = 1.58, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=624148.2, rms=1.212 (20.873%) 025: dt: 0.2500, sse=619902.6, rms=1.062 (12.384%) rms = 1.03, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=618078.9, rms=1.025 (3.429%) rms = 0.99, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=613455.6, rms=0.992 (3.206%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 65 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 165 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 18 points - only 0.00% unknown deleting segment 7 with 37 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=92.7, 113 (15) missing vertices, mean dist -0.2 [0.5 (%58.2)->0.3 (%41.8))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n026, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /work2/r1774/subjects/J106388/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=652498.1, rms=1.804 028: dt: 0.5000, sse=618488.6, rms=1.070 (40.704%) rms = 1.25, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=597912.8, rms=0.900 (15.835%) rms = 0.86, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=597514.5, rms=0.861 (4.372%) rms = 0.82, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=594562.6, rms=0.820 (4.743%) positioning took 0.5 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6358 vertices erasing segment 1 (vno[0] = 65157) erasing segment 2 (vno[0] = 67122) erasing segment 3 (vno[0] = 70211) erasing segment 4 (vno[0] = 75162) erasing segment 5 (vno[0] = 78191) erasing segment 6 (vno[0] = 80594) erasing segment 7 (vno[0] = 83630) erasing segment 8 (vno[0] = 84717) erasing segment 9 (vno[0] = 99782) erasing segment 10 (vno[0] = 122573) writing cortex label to /work2/r1774/subjects/J106388/label/rh.cortex.label... writing curvature file /work2/r1774/subjects/J106388/surf/rh.curv writing smoothed area to rh.area writing curvature file /work2/r1774/subjects/J106388/surf/rh.area vertex spacing 0.87 +- 0.28 (0.02-->8.09) (max @ vno 122237 --> 122353) face area 0.32 +- 0.18 (0.00-->9.20) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 30 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=64.0, 178 (178) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.8 (%100.0))] %18 local maxima, %40 large gradients and %38 min vals, 104 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21566318.0, rms=29.946 001: dt: 0.0500, sse=19919120.0, rms=28.749 (3.999%) 002: dt: 0.0500, sse=18731206.0, rms=27.853 (3.115%) 003: dt: 0.0500, sse=17795638.0, rms=27.127 (2.608%) 004: dt: 0.0500, sse=17013120.0, rms=26.504 (2.296%) 005: dt: 0.0500, sse=16331192.0, rms=25.949 (2.094%) 006: dt: 0.0500, sse=15720066.0, rms=25.441 (1.957%) 007: dt: 0.0500, sse=15160460.0, rms=24.967 (1.863%) 008: dt: 0.0500, sse=14639317.0, rms=24.517 (1.801%) 009: dt: 0.0500, sse=14149101.0, rms=24.086 (1.757%) 010: dt: 0.0500, sse=13684028.0, rms=23.670 (1.727%) positioning took 1.1 minutes mean border=63.8, 106 (76) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.2 (%99.9))] %18 local maxima, %40 large gradients and %37 min vals, 88 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14852493.0, rms=24.690 011: dt: 0.0500, sse=14402743.0, rms=24.298 (1.587%) 012: dt: 0.0500, sse=13970954.0, rms=23.916 (1.573%) 013: dt: 0.0500, sse=13555583.0, rms=23.542 (1.562%) 014: dt: 0.0500, sse=13155618.0, rms=23.177 (1.553%) 015: dt: 0.0500, sse=12769404.0, rms=22.818 (1.547%) 016: dt: 0.0500, sse=12396463.0, rms=22.467 (1.541%) 017: dt: 0.0500, sse=12036449.0, rms=22.122 (1.535%) 018: dt: 0.0500, sse=11689215.0, rms=21.784 (1.527%) 019: dt: 0.0500, sse=11353580.0, rms=21.452 (1.523%) 020: dt: 0.0500, sse=11028902.0, rms=21.126 (1.519%) positioning took 1.1 minutes mean border=63.5, 112 (51) missing vertices, mean dist 1.1 [0.1 (%1.1)->1.8 (%98.9))] %18 local maxima, %40 large gradients and %36 min vals, 79 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11157131.0, rms=21.255 021: dt: 0.0500, sse=10830376.0, rms=20.924 (1.557%) 022: dt: 0.0500, sse=10514500.0, rms=20.599 (1.554%) 023: dt: 0.0500, sse=10205927.0, rms=20.276 (1.566%) 024: dt: 0.0500, sse=9909325.0, rms=19.961 (1.554%) 025: dt: 0.0500, sse=9623508.0, rms=19.653 (1.545%) 026: dt: 0.0500, sse=9347429.0, rms=19.350 (1.540%) 027: dt: 0.0500, sse=9079979.0, rms=19.052 (1.539%) 028: dt: 0.0500, sse=8818415.0, rms=18.756 (1.553%) 029: dt: 0.0500, sse=8561193.0, rms=18.461 (1.576%) 030: dt: 0.0500, sse=8308556.0, rms=18.166 (1.598%) positioning took 1.1 minutes mean border=63.4, 148 (39) missing vertices, mean dist 0.9 [0.1 (%12.0)->1.6 (%88.0))] %18 local maxima, %41 large gradients and %36 min vals, 56 gradients ignored tol=1.0e-04, sigma=2.0, host= n026, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8421286.0, rms=18.295 031: dt: 0.5000, sse=6541238.0, rms=15.951 (12.812%) 032: dt: 0.5000, sse=5034198.5, rms=13.781 (13.602%) 033: dt: 0.5000, sse=3827094.2, rms=11.766 (14.624%) 034: dt: 0.5000, sse=2912121.2, rms=9.962 (15.333%) 035: dt: 0.5000, sse=2280852.2, rms=8.503 (14.638%) 036: dt: 0.5000, sse=1875098.6, rms=7.407 (12.890%) 037: dt: 0.5000, sse=1634852.9, rms=6.680 (9.825%) 038: dt: 0.5000, sse=1491912.4, rms=6.197 (7.229%) 039: dt: 0.5000, sse=1409028.9, rms=5.905 (4.715%) 040: dt: 0.5000, sse=1358997.4, rms=5.711 (3.276%) 041: dt: 0.5000, sse=1329058.8, rms=5.599 (1.959%) 042: dt: 0.5000, sse=1310064.2, rms=5.517 (1.465%) rms = 5.48, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1299822.5, rms=5.479 (0.696%) 044: dt: 0.2500, sse=1150954.4, rms=4.805 (12.297%) 045: dt: 0.2500, sse=1115242.8, rms=4.641 (3.409%) rms = 4.65, time step reduction 2 of 3 to 0.125... 046: dt: 0.1250, sse=1100739.1, rms=4.569 (1.556%) 047: dt: 0.1250, sse=1082264.4, rms=4.473 (2.100%) rms = 4.46, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1079885.0, rms=4.459 (0.320%) positioning took 2.6 minutes mean border=62.7, 2094 (18) missing vertices, mean dist 0.2 [0.2 (%51.3)->0.7 (%48.7))] %22 local maxima, %40 large gradients and %32 min vals, 72 gradients ignored tol=1.0e-04, sigma=1.0, host= n026, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1154805.2, rms=4.573 rms = 4.58, time step reduction 1 of 3 to 0.250... 049: dt: 0.2500, sse=1066860.4, rms=4.124 (9.821%) 050: dt: 0.2500, sse=986965.4, rms=3.671 (10.980%) 051: dt: 0.2500, sse=957094.6, rms=3.495 (4.796%) 052: dt: 0.2500, sse=943207.6, rms=3.412 (2.374%) rms = 3.38, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=937853.8, rms=3.380 (0.932%) 054: dt: 0.1250, sse=902022.8, rms=3.130 (7.417%) rms = 3.09, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=896141.2, rms=3.089 (1.309%) positioning took 1.3 minutes mean border=62.6, 2560 (13) missing vertices, mean dist 0.1 [0.1 (%57.3)->0.6 (%42.7))] %29 local maxima, %33 large gradients and %32 min vals, 97 gradients ignored tol=1.0e-04, sigma=0.5, host= n026, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=895780.1, rms=3.197 rms = 3.53, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=875138.4, rms=3.054 (4.469%) 057: dt: 0.2500, sse=866208.3, rms=3.001 (1.739%) rms = 2.99, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=864633.4, rms=2.995 (0.211%) 059: dt: 0.1250, sse=854917.2, rms=2.917 (2.590%) rms = 2.90, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=852219.9, rms=2.898 (0.645%) positioning took 1.1 minutes mean border=62.2, 4334 (11) missing vertices, mean dist 0.1 [0.1 (%52.9)->0.4 (%47.1))] %33 local maxima, %28 large gradients and %31 min vals, 108 gradients ignored tol=1.0e-04, sigma=0.2, host= n026, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /work2/r1774/subjects/J106388/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=866479.4, rms=3.002 rms = 3.29, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=846923.6, rms=2.857 (4.817%) 062: dt: 0.2500, sse=834554.2, rms=2.775 (2.880%) rms = 2.75, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=830283.8, rms=2.749 (0.941%) 064: dt: 0.1250, sse=821630.8, rms=2.673 (2.747%) rms = 2.65, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=818664.4, rms=2.651 (0.841%) positioning took 1.0 minutes writing curvature file /work2/r1774/subjects/J106388/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /work2/r1774/subjects/J106388/surf/rh.area.pial vertex spacing 0.91 +- 0.35 (0.09-->7.94) (max @ vno 122453 --> 122452) face area 0.34 +- 0.24 (0.00-->9.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 122899 vertices processed 25000 of 122899 vertices processed 50000 of 122899 vertices processed 75000 of 122899 vertices processed 100000 of 122899 vertices processed 0 of 122899 vertices processed 25000 of 122899 vertices processed 50000 of 122899 vertices processed 75000 of 122899 vertices processed 100000 of 122899 vertices processed thickness calculation complete, 141:207 truncations. 43375 vertices at 0 distance 98564 vertices at 1 distance 57012 vertices at 2 distance 22204 vertices at 3 distance 8339 vertices at 4 distance 3188 vertices at 5 distance 1076 vertices at 6 distance 385 vertices at 7 distance 136 vertices at 8 distance 68 vertices at 9 distance 45 vertices at 10 distance 27 vertices at 11 distance 16 vertices at 12 distance 26 vertices at 13 distance 13 vertices at 14 distance 6 vertices at 15 distance 6 vertices at 16 distance 3 vertices at 17 distance 3 vertices at 18 distance 1 vertices at 19 distance 1 vertices at 20 distance writing curvature file /work2/r1774/subjects/J106388/surf/rh.thickness positioning took 17.2 minutes #-------------------------------------------- #@# Surf Volume lh Sun Apr 16 10:41:25 CDT 2017 /work2/r1774/subjects/J106388/surf /work2/r1774/subjects/J106388/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume J106388 lh /work2/r1774/subjects/J106388/surf/lh.volume masking with /work2/r1774/subjects/J106388/label/lh.cortex.label Total face volume 160017 Total vertex volume 157727 (mask=0) #@# J106388 lh 157727 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Apr 16 10:41:29 CDT 2017 /work2/r1774/subjects/J106388/surf /work2/r1774/subjects/J106388/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume J106388 rh /work2/r1774/subjects/J106388/surf/rh.volume masking with /work2/r1774/subjects/J106388/label/rh.cortex.label Total face volume 158801 Total vertex volume 156907 (mask=0) #@# J106388 rh 156907 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Apr 16 10:41:33 CDT 2017 /work2/r1774/subjects/J106388/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon J106388 SUBJECTS_DIR is /work2/r1774/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 110 writing volume /work2/r1774/subjects/J106388/mri/ribbon.mgz mris_volmask took 10.05 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Apr 16 10:51:36 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab J106388 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/lh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 160017 Total vertex volume 157727 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1798 1181 2223 2.141 0.537 0.115 0.024 14 1.6 bankssts 800 505 1386 2.560 0.607 0.112 0.013 10 0.3 caudalanteriorcingulate 3016 1966 3787 1.981 0.508 0.130 0.033 29 4.4 caudalmiddlefrontal 1667 1162 1716 1.529 0.406 0.159 0.037 26 2.7 cuneus 699 434 1488 2.895 0.912 0.118 0.035 7 1.1 entorhinal 3995 2667 6436 2.353 0.768 0.147 0.045 52 7.4 fusiform 6781 4122 8764 2.131 0.544 0.125 0.032 72 9.6 inferiorparietal 4285 2765 7076 2.439 0.723 0.150 0.054 70 10.6 inferiortemporal 1313 809 1751 2.221 0.718 0.143 0.053 21 2.7 isthmuscingulate 6259 4116 6731 1.675 0.515 0.148 0.038 84 10.7 lateraloccipital 3849 2395 5447 2.413 0.701 0.128 0.033 44 5.3 lateralorbitofrontal 3187 2163 3549 1.599 0.549 0.132 0.029 39 3.9 lingual 2897 1909 3937 2.037 0.592 0.134 0.035 43 3.9 medialorbitofrontal 5065 2934 7883 2.491 0.718 0.129 0.040 62 9.0 middletemporal 947 566 1486 2.485 0.702 0.125 0.039 12 1.4 parahippocampal 1919 1277 2238 1.751 0.552 0.122 0.032 19 2.5 paracentral 2268 1319 3364 2.432 0.531 0.107 0.028 18 2.5 parsopercularis 1099 580 1859 2.591 0.582 0.099 0.024 9 1.0 parsorbitalis 2240 1347 3109 2.221 0.516 0.124 0.033 21 3.2 parstriangularis 1228 876 984 1.343 0.284 0.153 0.038 16 1.9 pericalcarine 5246 3463 5600 1.588 0.503 0.109 0.022 37 4.8 postcentral 1460 929 1876 2.099 0.677 0.141 0.043 22 2.7 posteriorcingulate 6495 4192 7146 1.738 0.602 0.119 0.029 57 8.1 precentral 5267 3279 6700 2.064 0.547 0.127 0.034 58 7.1 precuneus 1332 831 1908 2.044 0.977 0.131 0.040 21 2.1 rostralanteriorcingulate 8869 5399 11038 2.068 0.566 0.134 0.038 107 14.1 rostralmiddlefrontal 8811 5192 13498 2.511 0.651 0.113 0.031 83 11.7 superiorfrontal 7630 4889 8841 1.828 0.519 0.131 0.032 80 10.3 superiorparietal 5450 3274 8434 2.432 0.716 0.110 0.030 47 7.2 superiortemporal 6397 3909 8004 2.135 0.604 0.135 0.035 73 9.9 supramarginal 308 166 618 2.684 0.463 0.116 0.039 4 0.3 frontalpole 773 442 2172 3.369 0.708 0.124 0.054 13 1.7 temporalpole 562 340 702 2.022 0.573 0.110 0.021 5 0.4 transversetemporal 3971 2407 5938 2.614 0.960 0.117 0.051 60 6.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab J106388 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input pial surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 160017 Total vertex volume 157727 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1798 969 2223 2.141 0.537 0.087 0.019 29 1.5 bankssts 800 602 1386 2.560 0.607 0.118 0.018 16 0.6 caudalanteriorcingulate 3016 2068 3787 1.981 0.508 0.112 0.025 28 3.4 caudalmiddlefrontal 1667 1247 1716 1.529 0.406 0.123 0.027 17 2.0 cuneus 699 602 1488 2.895 0.912 0.114 0.023 4 0.7 entorhinal 3995 2815 6436 2.353 0.768 0.125 0.034 64 5.8 fusiform 6781 4318 8764 2.131 0.544 0.100 0.021 72 6.5 inferiorparietal 4285 2973 7076 2.439 0.723 0.119 0.033 63 6.2 inferiortemporal 1313 863 1751 2.221 0.718 0.114 0.029 19 1.4 isthmuscingulate 6259 4324 6731 1.675 0.515 0.114 0.027 85 7.5 lateraloccipital 3849 2291 5447 2.413 0.701 0.111 0.029 63 5.1 lateralorbitofrontal 3187 2437 3549 1.599 0.549 0.121 0.028 36 4.3 lingual 2897 2081 3937 2.037 0.592 0.115 0.025 32 3.2 medialorbitofrontal 5065 3460 7883 2.491 0.718 0.101 0.024 76 5.6 middletemporal 947 659 1486 2.485 0.702 0.103 0.028 8 1.0 parahippocampal 1919 1377 2238 1.751 0.552 0.108 0.030 24 2.1 paracentral 2268 1494 3364 2.432 0.531 0.107 0.022 24 2.2 parsopercularis 1099 842 1859 2.591 0.582 0.114 0.023 9 1.1 parsorbitalis 2240 1477 3109 2.221 0.516 0.111 0.026 21 2.3 parstriangularis 1228 692 984 1.343 0.284 0.114 0.032 21 1.8 pericalcarine 5246 3868 5600 1.588 0.503 0.104 0.022 42 5.3 postcentral 1460 944 1876 2.099 0.677 0.115 0.029 15 1.7 posteriorcingulate 6495 4302 7146 1.738 0.602 0.101 0.044 98 16.7 precentral 5267 3352 6700 2.064 0.547 0.112 0.026 58 6.1 precuneus 1332 1029 1908 2.044 0.977 0.153 0.040 21 2.3 rostralanteriorcingulate 8869 5494 11038 2.068 0.566 0.109 0.027 123 9.9 rostralmiddlefrontal 8811 5765 13498 2.511 0.651 0.101 0.023 80 8.6 superiorfrontal 7630 5085 8841 1.828 0.519 0.110 0.040 165 15.2 superiorparietal 5450 3663 8434 2.432 0.716 0.097 0.021 52 4.8 superiortemporal 6397 3880 8004 2.135 0.604 0.096 0.022 73 5.7 supramarginal 308 288 618 2.684 0.463 0.151 0.029 2 0.4 frontalpole 773 831 2172 3.369 0.708 0.144 0.029 6 1.0 temporalpole 562 396 702 2.022 0.573 0.093 0.018 3 0.4 transversetemporal 3971 2148 5938 2.614 0.960 0.105 0.031 58 5.2 insula #----------------------------------------- #@# Parcellation Stats rh Sun Apr 16 10:53:03 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab J106388 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/rh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 158801 Total vertex volume 156907 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1239 833 1873 2.580 0.510 0.109 0.039 13 1.3 bankssts 1260 763 2028 2.397 0.711 0.121 0.025 17 1.3 caudalanteriorcingulate 3370 2285 4205 1.917 0.549 0.126 0.030 29 4.7 caudalmiddlefrontal 1801 1209 1836 1.555 0.435 0.147 0.034 25 2.9 cuneus 1052 592 2454 3.098 0.961 0.120 0.073 16 3.1 entorhinal 4433 2886 7014 2.347 0.582 0.131 0.035 61 6.3 fusiform 8245 5060 10894 2.167 0.594 0.129 0.036 97 12.7 inferiorparietal 4319 2679 7382 2.605 0.704 0.133 0.044 56 8.1 inferiortemporal 1317 807 1816 2.264 0.657 0.135 0.050 20 2.5 isthmuscingulate 5361 3531 6337 1.829 0.546 0.150 0.040 75 9.2 lateraloccipital 3644 2304 4935 2.345 0.725 0.136 0.034 49 5.2 lateralorbitofrontal 3465 2239 3752 1.712 0.505 0.141 0.033 49 4.9 lingual 2258 1518 3463 2.153 0.562 0.138 0.035 37 3.5 medialorbitofrontal 4645 2687 7073 2.529 0.648 0.134 0.046 65 9.2 middletemporal 977 591 1863 2.733 0.827 0.104 0.031 14 1.2 parahippocampal 1996 1431 2390 1.759 0.557 0.137 0.031 20 2.6 paracentral 1547 931 2171 2.210 0.560 0.110 0.029 13 1.9 parsopercularis 1234 694 1965 2.487 0.588 0.121 0.038 14 1.8 parsorbitalis 1958 1205 2879 2.274 0.597 0.120 0.032 18 2.6 parstriangularis 1247 985 1080 1.290 0.284 0.160 0.041 19 2.1 pericalcarine 5950 4000 6485 1.593 0.476 0.112 0.022 46 5.2 postcentral 1705 1135 2462 2.180 0.603 0.150 0.041 29 2.7 posteriorcingulate 7196 4748 7658 1.678 0.577 0.112 0.024 61 7.2 precentral 5477 3628 6946 2.025 0.593 0.143 0.039 71 9.0 precuneus 808 490 1343 2.568 0.572 0.150 0.047 17 1.5 rostralanteriorcingulate 8234 5051 11080 2.167 0.515 0.134 0.041 101 14.2 rostralmiddlefrontal 8740 5345 12432 2.320 0.643 0.117 0.030 77 11.3 superiorfrontal 6929 4419 8489 1.882 0.534 0.131 0.031 73 9.2 superiorparietal 4673 2822 6821 2.346 0.615 0.117 0.043 54 9.4 superiortemporal 5217 3196 6790 2.169 0.608 0.129 0.035 54 7.7 supramarginal 455 264 677 2.086 0.569 0.153 0.045 8 0.9 frontalpole 658 363 1749 3.559 0.904 0.121 0.047 13 1.3 temporalpole 517 286 613 2.010 0.533 0.104 0.023 5 0.5 transversetemporal 4135 2582 5887 2.496 1.018 0.119 0.039 48 6.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab J106388 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input pial surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 158801 Total vertex volume 156907 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1239 645 1873 2.580 0.510 0.099 0.026 20 1.4 bankssts 1260 927 2028 2.397 0.711 0.146 0.035 62 1.6 caudalanteriorcingulate 3370 2316 4205 1.917 0.549 0.105 0.026 36 3.6 caudalmiddlefrontal 1801 1327 1836 1.555 0.435 0.117 0.028 22 2.1 cuneus 1052 945 2454 3.098 0.961 0.139 0.034 16 1.7 entorhinal 4433 3072 7014 2.347 0.582 0.115 0.026 54 5.4 fusiform 8245 5229 10894 2.167 0.594 0.104 0.023 98 8.3 inferiorparietal 4319 3006 7382 2.605 0.704 0.111 0.031 75 5.8 inferiortemporal 1317 874 1816 2.264 0.657 0.133 0.045 36 2.6 isthmuscingulate 5361 3725 6337 1.829 0.546 0.113 0.027 78 6.5 lateraloccipital 3644 2090 4935 2.345 0.725 0.096 0.024 52 3.5 lateralorbitofrontal 3465 2396 3752 1.712 0.505 0.113 0.027 62 3.8 lingual 2258 1766 3463 2.153 0.562 0.128 0.028 23 2.8 medialorbitofrontal 4645 3013 7073 2.529 0.648 0.106 0.031 65 7.2 middletemporal 977 741 1863 2.733 0.827 0.103 0.026 11 1.0 parahippocampal 1996 1397 2390 1.759 0.557 0.111 0.026 26 2.2 paracentral 1547 1068 2171 2.210 0.560 0.112 0.023 14 1.6 parsopercularis 1234 909 1965 2.487 0.588 0.120 0.029 31 1.2 parsorbitalis 1958 1389 2879 2.274 0.597 0.115 0.024 18 2.2 parstriangularis 1247 861 1080 1.290 0.284 0.114 0.031 19 1.5 pericalcarine 5950 4497 6485 1.593 0.476 0.106 0.020 43 5.4 postcentral 1705 1172 2462 2.180 0.603 0.128 0.033 53 2.4 posteriorcingulate 7196 4821 7658 1.678 0.577 0.091 0.032 96 12.3 precentral 5477 3435 6946 2.025 0.593 0.116 0.031 98 7.7 precuneus 808 610 1343 2.568 0.572 0.139 0.047 12 1.1 rostralanteriorcingulate 8234 5287 11080 2.167 0.515 0.112 0.026 92 9.4 rostralmiddlefrontal 8740 5532 12432 2.320 0.643 0.100 0.023 88 8.2 superiorfrontal 6929 4888 8489 1.882 0.534 0.113 0.027 103 9.0 superiorparietal 4673 3136 6821 2.346 0.615 0.100 0.024 56 4.4 superiortemporal 5217 3192 6790 2.169 0.608 0.098 0.022 100 4.8 supramarginal 455 375 677 2.086 0.569 0.150 0.032 6 0.7 frontalpole 658 629 1749 3.559 0.904 0.142 0.041 7 1.3 temporalpole 517 314 613 2.010 0.533 0.074 0.013 2 0.2 transversetemporal 4135 2182 5887 2.496 1.018 0.111 0.030 70 5.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Sun Apr 16 10:54:31 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 J106388 lh ../surf/lh.sphere.reg /home/ums/r1774/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /home/ums/r1774/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 60 labels changed using aseg relabeling using gibbs priors... 000: 8012 changed, 125059 examined... 001: 1896 changed, 31625 examined... 002: 536 changed, 9976 examined... 003: 223 changed, 3098 examined... 004: 96 changed, 1301 examined... 005: 60 changed, 556 examined... 006: 29 changed, 347 examined... 007: 20 changed, 169 examined... 008: 18 changed, 111 examined... 009: 5 changed, 94 examined... 010: 5 changed, 34 examined... 011: 1 changed, 28 examined... 012: 0 changed, 5 examined... 28 labels changed using aseg 000: 228 total segments, 146 labels (2231 vertices) changed 001: 88 total segments, 7 labels (22 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 24 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1180 vertices marked for relabeling... 1180 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Sun Apr 16 10:54:53 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 J106388 rh ../surf/rh.sphere.reg /home/ums/r1774/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /home/ums/r1774/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 88 labels changed using aseg relabeling using gibbs priors... 000: 8157 changed, 122899 examined... 001: 1869 changed, 31925 examined... 002: 486 changed, 9789 examined... 003: 196 changed, 2823 examined... 004: 74 changed, 1102 examined... 005: 34 changed, 440 examined... 006: 19 changed, 210 examined... 007: 9 changed, 93 examined... 008: 6 changed, 49 examined... 009: 0 changed, 33 examined... 28 labels changed using aseg 000: 264 total segments, 179 labels (1543 vertices) changed 001: 95 total segments, 10 labels (33 vertices) changed 002: 86 total segments, 1 labels (1 vertices) changed 003: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1310 vertices marked for relabeling... 1310 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Apr 16 10:55:16 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab J106388 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/lh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 160017 Total vertex volume 157727 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1082 737 1469 2.173 0.571 0.153 0.040 15 1.9 G&S_frontomargin 1796 1065 2244 2.014 0.620 0.152 0.050 25 4.1 G&S_occipital_inf 1453 944 1695 1.658 0.605 0.125 0.037 16 2.1 G&S_paracentral 1250 731 1700 2.164 0.478 0.119 0.033 11 1.7 G&S_subcentral 613 344 1062 2.432 0.551 0.131 0.055 8 1.2 G&S_transv_frontopol 1995 1325 3246 2.402 0.674 0.117 0.029 22 2.3 G&S_cingul-Ant 1043 707 1818 2.611 0.492 0.110 0.014 10 0.6 G&S_cingul-Mid-Ant 1260 853 1484 1.953 0.624 0.153 0.049 20 2.3 G&S_cingul-Mid-Post 638 373 1005 2.361 0.640 0.134 0.043 9 1.2 G_cingul-Post-dorsal 274 154 418 2.464 0.770 0.117 0.030 3 0.3 G_cingul-Post-ventral 1456 1001 1567 1.535 0.436 0.157 0.035 23 2.4 G_cuneus 1367 693 2118 2.446 0.501 0.110 0.034 13 1.9 G_front_inf-Opercular 557 274 962 2.578 0.571 0.107 0.032 5 0.8 G_front_inf-Orbital 1440 783 2102 2.205 0.495 0.124 0.036 16 2.3 G_front_inf-Triangul 4406 2486 5964 2.112 0.591 0.129 0.039 50 7.6 G_front_middle 6686 3649 10325 2.484 0.717 0.114 0.034 71 10.0 G_front_sup 717 396 1069 2.746 0.649 0.132 0.114 28 1.3 G_Ins_lg&S_cent_ins 960 490 1809 2.970 0.802 0.112 0.051 12 1.8 G_insular_short 1860 1034 2252 1.915 0.543 0.122 0.034 21 2.7 G_occipital_middle 1159 755 1381 1.638 0.503 0.137 0.031 14 1.4 G_occipital_sup 1535 1000 2495 2.228 0.740 0.145 0.044 21 2.6 G_oc-temp_lat-fusifor 2121 1392 2585 1.646 0.607 0.134 0.031 27 2.7 G_oc-temp_med-Lingual 1574 923 3192 2.763 0.845 0.128 0.047 22 3.0 G_oc-temp_med-Parahip 2480 1347 3692 2.219 0.640 0.120 0.036 34 3.8 G_orbital 3119 1647 4407 2.287 0.578 0.132 0.042 44 5.9 G_pariet_inf-Angular 2960 1723 3802 2.095 0.621 0.129 0.034 32 4.5 G_pariet_inf-Supramar 3226 1955 4122 1.890 0.542 0.123 0.032 32 4.5 G_parietal_sup 1870 1230 2127 1.502 0.437 0.109 0.021 13 1.7 G_postcentral 2430 1514 2949 1.720 0.617 0.105 0.023 16 2.4 G_precentral 2631 1502 3658 2.067 0.530 0.126 0.037 31 4.3 G_precuneus 1086 730 1703 1.941 0.497 0.150 0.037 19 1.8 G_rectus 888 575 838 1.501 0.939 0.118 0.059 17 1.5 G_subcallosal 386 200 467 2.056 0.587 0.112 0.022 5 0.3 G_temp_sup-G_T_transv 1897 1018 3385 2.453 0.767 0.123 0.046 24 4.0 G_temp_sup-Lateral 799 535 1599 2.931 0.975 0.097 0.026 4 0.8 G_temp_sup-Plan_polar 881 506 1211 2.302 0.612 0.094 0.027 6 1.0 G_temp_sup-Plan_tempo 2266 1358 3898 2.377 0.748 0.156 0.064 47 6.7 G_temporal_inf 3177 1655 4863 2.386 0.737 0.132 0.047 47 6.6 G_temporal_middle 249 181 339 2.411 0.441 0.142 0.031 2 0.3 Lat_Fis-ant-Horizont 359 256 460 2.140 0.519 0.118 0.024 3 0.3 Lat_Fis-ant-Vertical 982 664 1154 2.192 0.573 0.134 0.034 9 1.3 Lat_Fis-post 1572 1170 1513 1.341 0.282 0.155 0.032 24 2.4 Pole_occipital 1696 982 4235 3.125 0.823 0.142 0.058 28 4.2 Pole_temporal 1761 1230 1570 1.551 0.532 0.140 0.034 22 2.3 S_calcarine 2857 2001 2266 1.350 0.255 0.129 0.032 28 4.2 S_central 1097 728 1194 1.927 0.517 0.114 0.021 8 1.0 S_cingul-Marginalis 588 391 832 2.849 0.572 0.120 0.031 4 0.8 S_circular_insula_ant 1299 876 1753 2.447 0.876 0.104 0.018 8 1.0 S_circular_insula_inf 1597 1088 2097 2.457 0.599 0.116 0.025 9 1.8 S_circular_insula_sup 831 609 1282 2.585 0.577 0.125 0.021 7 0.7 S_collat_transv_ant 443 308 341 1.534 0.452 0.166 0.049 6 0.9 S_collat_transv_post 2393 1566 2878 2.095 0.533 0.118 0.028 19 2.7 S_front_inf 1602 1013 1674 1.838 0.520 0.119 0.028 15 1.8 S_front_middle 2397 1666 3070 2.132 0.532 0.131 0.030 22 3.0 S_front_sup 692 474 780 2.117 0.482 0.130 0.031 7 0.9 S_interm_prim-Jensen 2682 1787 2843 1.879 0.483 0.132 0.028 28 3.1 S_intrapariet&P_trans 557 368 474 1.547 0.433 0.142 0.035 7 0.8 S_oc_middle&Lunatus 1141 786 1163 1.779 0.367 0.140 0.028 13 1.3 S_oc_sup&transversal 608 411 698 1.990 0.389 0.146 0.036 7 0.9 S_occipital_ant 744 526 866 2.036 0.448 0.134 0.029 7 0.9 S_oc-temp_lat 1610 1166 1970 2.042 0.653 0.141 0.030 18 2.0 S_oc-temp_med&Lingual 444 297 458 1.810 0.331 0.150 0.032 5 0.6 S_orbital_lateral 658 454 742 2.130 0.634 0.133 0.021 7 0.6 S_orbital_med-olfact 1411 912 2258 2.849 0.631 0.122 0.033 15 1.8 S_orbital-H_Shaped 2093 1375 2270 1.882 0.594 0.133 0.034 23 3.0 S_parieto_occipital 875 557 745 1.801 0.980 0.163 0.055 19 1.8 S_pericallosal 2781 1869 2830 1.813 0.604 0.131 0.028 28 3.3 S_postcentral 1570 1036 2011 2.210 0.598 0.122 0.026 14 1.7 S_precentral-inf-part 956 691 967 1.707 0.387 0.131 0.027 8 1.2 S_precentral-sup-part 700 437 907 2.419 0.662 0.128 0.021 8 0.5 S_suborbital 1046 751 1322 2.155 0.500 0.135 0.031 10 1.2 S_subparietal 1329 951 1877 2.367 0.729 0.148 0.050 15 3.2 S_temporal_inf 6573 4411 8652 2.236 0.570 0.116 0.024 50 6.6 S_temporal_sup 372 242 554 2.583 0.477 0.110 0.023 2 0.4 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Sun Apr 16 10:56:06 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab J106388 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/rh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 158801 Total vertex volume 156907 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 874 563 1181 2.111 0.540 0.156 0.045 15 1.5 G&S_frontomargin 880 553 1249 1.995 0.548 0.143 0.042 12 1.6 G&S_occipital_inf 1177 843 1642 1.736 0.635 0.128 0.034 11 1.5 G&S_paracentral 1298 740 1869 2.245 0.538 0.104 0.026 10 1.3 G&S_subcentral 1073 610 1606 2.261 0.571 0.134 0.045 17 1.9 G&S_transv_frontopol 2420 1557 3706 2.375 0.521 0.129 0.032 30 2.9 G&S_cingul-Ant 1403 870 2227 2.417 0.639 0.127 0.037 18 2.1 G&S_cingul-Mid-Ant 1418 966 1965 2.065 0.541 0.138 0.037 17 2.0 G&S_cingul-Mid-Post 711 424 1092 2.387 0.618 0.137 0.040 10 1.3 G_cingul-Post-dorsal 297 165 459 2.221 0.675 0.115 0.040 3 0.4 G_cingul-Post-ventral 1628 1108 1659 1.455 0.414 0.146 0.033 23 2.5 G_cuneus 1217 631 1811 2.381 0.637 0.103 0.031 11 1.7 G_front_inf-Opercular 510 277 803 2.300 0.585 0.130 0.044 6 1.2 G_front_inf-Orbital 810 430 1283 2.452 0.680 0.114 0.032 9 1.0 G_front_inf-Triangul 4988 3009 6895 2.080 0.540 0.137 0.042 61 9.3 G_front_middle 5613 3267 8704 2.352 0.689 0.120 0.031 55 7.7 G_front_sup 640 340 1080 3.015 0.695 0.106 0.048 10 1.0 G_Ins_lg&S_cent_ins 1111 667 1589 2.188 1.094 0.131 0.062 16 2.9 G_insular_short 2088 1166 2999 2.255 0.578 0.123 0.036 23 3.0 G_occipital_middle 1333 898 1752 1.857 0.611 0.144 0.037 18 2.2 G_occipital_sup 1941 1164 3126 2.315 0.572 0.142 0.043 33 3.6 G_oc-temp_lat-fusifor 2178 1354 2400 1.670 0.480 0.142 0.035 33 3.4 G_oc-temp_med-Lingual 2035 1170 4393 2.983 0.927 0.113 0.052 31 4.2 G_oc-temp_med-Parahip 2806 1569 4182 2.313 0.806 0.132 0.042 41 5.0 G_orbital 3563 1945 5325 2.341 0.671 0.134 0.046 51 7.0 G_pariet_inf-Angular 2384 1402 3248 2.163 0.596 0.125 0.037 24 3.9 G_pariet_inf-Supramar 2162 1359 2902 1.888 0.509 0.142 0.037 24 3.6 G_parietal_sup 2228 1468 2424 1.480 0.392 0.119 0.021 19 2.0 G_postcentral 2921 1913 3114 1.533 0.424 0.109 0.021 20 2.5 G_precentral 2462 1551 3295 1.962 0.653 0.147 0.046 39 5.1 G_precuneus 694 466 1206 2.007 0.567 0.137 0.031 11 0.9 G_rectus 563 327 509 1.496 0.888 0.108 0.059 14 1.7 G_subcallosal 359 180 498 2.220 0.584 0.101 0.026 3 0.4 G_temp_sup-G_T_transv 1644 956 2327 2.166 0.597 0.128 0.049 24 3.6 G_temp_sup-Lateral 743 430 1472 3.062 0.972 0.117 0.051 9 1.9 G_temp_sup-Plan_polar 750 478 1008 2.034 0.506 0.127 0.034 7 1.1 G_temp_sup-Plan_tempo 2344 1383 4255 2.513 0.723 0.141 0.053 39 5.1 G_temporal_inf 2964 1561 4638 2.505 0.654 0.137 0.054 48 6.7 G_temporal_middle 271 196 341 1.991 0.363 0.116 0.022 2 0.3 Lat_Fis-ant-Horizont 142 102 225 2.385 0.415 0.121 0.023 1 0.1 Lat_Fis-ant-Vertical 1265 876 1475 2.035 0.496 0.126 0.026 10 1.4 Lat_Fis-post 2387 1716 2685 1.574 0.473 0.160 0.039 35 4.1 Pole_occipital 1706 909 3666 3.061 0.790 0.130 0.070 35 5.7 Pole_temporal 1533 1065 1533 1.700 0.690 0.135 0.035 18 2.1 S_calcarine 3214 2289 2630 1.379 0.347 0.121 0.025 33 3.5 S_central 1088 743 1333 2.125 0.487 0.133 0.034 12 1.3 S_cingul-Marginalis 713 498 998 2.713 0.555 0.122 0.023 5 0.7 S_circular_insula_ant 1305 847 1794 2.654 0.813 0.103 0.018 8 1.0 S_circular_insula_inf 1171 827 1646 2.492 0.456 0.122 0.024 8 1.1 S_circular_insula_sup 1199 884 1954 2.597 0.557 0.114 0.020 8 0.9 S_collat_transv_ant 336 234 304 1.908 0.409 0.177 0.049 6 0.7 S_collat_transv_post 1552 1030 1962 2.181 0.473 0.116 0.024 13 1.5 S_front_inf 1855 1256 2232 2.047 0.447 0.123 0.029 14 2.2 S_front_middle 2450 1666 3123 2.180 0.600 0.120 0.025 19 2.7 S_front_sup 422 270 620 2.650 0.724 0.128 0.030 3 0.5 S_interm_prim-Jensen 2934 1920 3150 1.827 0.436 0.129 0.029 30 3.5 S_intrapariet&P_trans 451 309 480 1.841 0.454 0.154 0.039 7 0.7 S_oc_middle&Lunatus 1371 938 1233 1.611 0.361 0.141 0.031 17 1.8 S_oc_sup&transversal 655 418 839 2.113 0.549 0.128 0.036 6 1.0 S_occipital_ant 1123 800 1616 2.538 0.519 0.119 0.023 8 1.0 S_oc-temp_lat 1497 1053 1957 2.034 0.594 0.133 0.027 18 1.6 S_oc-temp_med&Lingual 392 272 396 1.904 0.434 0.136 0.034 5 0.5 S_orbital_lateral 577 434 603 1.840 0.518 0.152 0.021 8 0.4 S_orbital_med-olfact 1276 826 1806 2.501 0.578 0.131 0.038 14 2.0 S_orbital-H_Shaped 2299 1526 2588 1.968 0.545 0.141 0.031 27 2.8 S_parieto_occipital 1290 805 1250 2.198 0.770 0.149 0.046 28 2.4 S_pericallosal 2665 1825 2612 1.726 0.431 0.124 0.027 24 3.0 S_postcentral 1570 1085 1941 1.946 0.492 0.109 0.024 9 1.9 S_precentral-inf-part 997 696 975 1.638 0.396 0.120 0.026 10 0.9 S_precentral-sup-part 235 173 341 2.322 0.393 0.106 0.014 2 0.1 S_suborbital 1044 735 1419 2.210 0.471 0.140 0.041 10 1.6 S_subparietal 1104 759 1388 2.354 0.516 0.143 0.028 11 1.6 S_temporal_inf 5558 3704 7648 2.380 0.550 0.114 0.030 50 6.0 S_temporal_sup 234 148 248 2.099 0.379 0.153 0.026 3 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Sun Apr 16 10:56:56 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 J106388 lh ../surf/lh.sphere.reg /home/ums/r1774/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /home/ums/r1774/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1181 labels changed using aseg relabeling using gibbs priors... 000: 1880 changed, 125059 examined... 001: 419 changed, 8645 examined... 002: 130 changed, 2418 examined... 003: 49 changed, 736 examined... 004: 29 changed, 296 examined... 005: 22 changed, 176 examined... 006: 16 changed, 130 examined... 007: 18 changed, 90 examined... 008: 15 changed, 96 examined... 009: 10 changed, 70 examined... 010: 5 changed, 46 examined... 011: 3 changed, 26 examined... 012: 1 changed, 23 examined... 013: 0 changed, 6 examined... 287 labels changed using aseg 000: 60 total segments, 27 labels (243 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 872 vertices marked for relabeling... 872 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Sun Apr 16 10:57:16 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 J106388 rh ../surf/rh.sphere.reg /home/ums/r1774/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /home/ums/r1774/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1098 labels changed using aseg relabeling using gibbs priors... 000: 1792 changed, 122899 examined... 001: 388 changed, 8394 examined... 002: 126 changed, 2267 examined... 003: 48 changed, 736 examined... 004: 28 changed, 273 examined... 005: 22 changed, 167 examined... 006: 17 changed, 114 examined... 007: 15 changed, 89 examined... 008: 11 changed, 90 examined... 009: 9 changed, 56 examined... 010: 5 changed, 49 examined... 011: 4 changed, 27 examined... 012: 3 changed, 22 examined... 013: 3 changed, 20 examined... 014: 4 changed, 21 examined... 015: 8 changed, 24 examined... 016: 4 changed, 27 examined... 017: 3 changed, 23 examined... 018: 2 changed, 17 examined... 019: 3 changed, 15 examined... 020: 2 changed, 18 examined... 021: 2 changed, 10 examined... 022: 0 changed, 10 examined... 317 labels changed using aseg 000: 54 total segments, 21 labels (449 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1013 vertices marked for relabeling... 1013 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 19 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Apr 16 10:57:34 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab J106388 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/lh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 160017 Total vertex volume 157727 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1462 946 2424 2.538 0.551 0.112 0.019 17 1.1 caudalanteriorcingulate 3269 2134 4205 2.014 0.528 0.128 0.032 31 4.5 caudalmiddlefrontal 2512 1710 2705 1.653 0.492 0.152 0.036 37 4.1 cuneus 702 438 1538 2.860 0.925 0.125 0.043 8 1.3 entorhinal 3416 2313 5201 2.278 0.721 0.143 0.038 42 5.2 fusiform 6827 4147 8920 2.158 0.548 0.126 0.034 76 10.1 inferiorparietal 4389 2796 7662 2.492 0.772 0.149 0.054 72 10.6 inferiortemporal 1349 841 1798 2.222 0.714 0.147 0.053 22 2.8 isthmuscingulate 6274 4117 6740 1.668 0.501 0.148 0.038 85 10.9 lateraloccipital 4142 2636 5822 2.308 0.717 0.133 0.038 55 6.2 lateralorbitofrontal 3247 2196 3576 1.590 0.546 0.133 0.029 40 4.1 lingual 2551 1653 3293 1.900 0.757 0.131 0.034 40 3.5 medialorbitofrontal 6878 4152 10266 2.420 0.697 0.130 0.039 81 12.3 middletemporal 990 592 1545 2.460 0.711 0.124 0.038 13 1.4 parahippocampal 2204 1468 2694 1.776 0.567 0.120 0.031 21 2.7 paracentral 2100 1213 3100 2.480 0.526 0.107 0.029 16 2.4 parsopercularis 1117 618 1800 2.603 0.515 0.110 0.027 9 1.3 parsorbitalis 2875 1735 3854 2.140 0.497 0.125 0.033 29 4.0 parstriangularis 1226 876 984 1.341 0.284 0.151 0.037 16 1.9 pericalcarine 6029 3983 6419 1.619 0.518 0.116 0.024 48 6.1 postcentral 1607 1032 2026 2.102 0.678 0.145 0.045 25 3.0 posteriorcingulate 6419 4145 7083 1.754 0.615 0.119 0.029 56 8.2 precentral 5110 3178 6594 2.045 0.552 0.125 0.033 54 6.8 precuneus 1686 1091 2376 2.136 0.957 0.137 0.040 26 2.5 rostralanteriorcingulate 6646 3956 8359 2.100 0.579 0.132 0.038 77 10.7 rostralmiddlefrontal 9760 5693 14569 2.438 0.664 0.115 0.032 95 13.2 superiorfrontal 6180 3924 7111 1.851 0.522 0.128 0.032 62 8.2 superiorparietal 7543 4533 12323 2.497 0.772 0.113 0.039 89 10.4 superiortemporal 5691 3489 6966 2.095 0.605 0.134 0.033 63 8.4 supramarginal 552 334 689 2.011 0.581 0.108 0.021 5 0.4 transversetemporal 3150 1890 5084 2.843 0.735 0.111 0.035 29 4.2 insula #----------------------------------------- #@# Parcellation Stats 3 rh Sun Apr 16 10:58:27 CDT 2017 /work2/r1774/subjects/J106388/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab J106388 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/rh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 158801 Total vertex volume 156907 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 1361 817 2166 2.395 0.711 0.122 0.025 19 1.4 caudalanteriorcingulate 3537 2406 4415 1.924 0.546 0.129 0.030 32 5.0 caudalmiddlefrontal 2332 1573 2489 1.585 0.473 0.142 0.032 30 3.3 cuneus 1074 618 2527 3.140 0.964 0.112 0.060 14 2.5 entorhinal 4076 2645 6428 2.320 0.585 0.131 0.036 57 6.2 fusiform 8217 5019 10871 2.168 0.590 0.129 0.036 97 12.6 inferiorparietal 4728 2929 8101 2.602 0.683 0.132 0.043 61 8.5 inferiortemporal 1255 792 1743 2.234 0.663 0.139 0.050 19 2.4 isthmuscingulate 5363 3553 6210 1.809 0.542 0.150 0.039 76 9.0 lateraloccipital 4073 2552 5351 2.201 0.746 0.138 0.038 56 6.5 lateralorbitofrontal 3387 2184 3662 1.710 0.499 0.143 0.033 49 4.8 lingual 2016 1351 2716 1.846 0.815 0.127 0.030 29 2.3 medialorbitofrontal 5593 3325 8372 2.529 0.638 0.136 0.048 80 10.8 middletemporal 903 555 1652 2.695 0.822 0.102 0.027 12 0.9 parahippocampal 2074 1472 2503 1.786 0.566 0.137 0.033 21 2.8 paracentral 1725 1058 2453 2.233 0.544 0.115 0.029 15 2.2 parsopercularis 1051 599 1686 2.565 0.558 0.113 0.029 12 1.3 parsorbitalis 1975 1256 2816 2.230 0.583 0.121 0.030 19 2.5 parstriangularis 1205 962 1048 1.285 0.287 0.158 0.039 18 2.0 pericalcarine 6456 4378 7042 1.615 0.484 0.118 0.024 54 6.6 postcentral 1861 1222 2620 2.202 0.590 0.150 0.046 32 3.4 posteriorcingulate 6987 4580 7474 1.696 0.595 0.111 0.024 57 6.9 precentral 5687 3707 7383 2.060 0.597 0.142 0.040 75 9.7 precuneus 1074 639 1635 2.458 0.618 0.144 0.055 26 2.6 rostralanteriorcingulate 5917 3613 7954 2.198 0.504 0.134 0.040 68 10.2 rostralmiddlefrontal 11383 6944 16363 2.287 0.625 0.121 0.032 113 15.3 superiorfrontal 5730 3669 6930 1.855 0.506 0.129 0.030 57 7.3 superiorparietal 6441 3884 10430 2.537 0.774 0.118 0.042 79 12.5 superiortemporal 4865 2979 6300 2.153 0.610 0.126 0.033 47 6.7 supramarginal 479 261 560 1.984 0.522 0.101 0.023 4 0.4 transversetemporal 3286 2052 5006 2.710 0.780 0.122 0.039 38 5.3 insula #----------------------------------------- #@# WM/GM Contrast lh Sun Apr 16 10:59:14 CDT 2017 /work2/r1774/subjects/J106388/scripts pctsurfcon --s J106388 --lh-only Log file is /work2/r1774/subjects/J106388/scripts/pctsurfcon.log Sun Apr 16 10:59:15 CDT 2017 setenv SUBJECTS_DIR /work2/r1774/subjects cd /work2/r1774/subjects/J106388/scripts /home/ums/r1774/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/ums/r1774/freesurfer mri_vol2surf --mov /work2/r1774/subjects/J106388/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1508/lh.wm.mgh --regheader J106388 --cortex srcvol = /work2/r1774/subjects/J106388/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /work2/r1774/subjects/J106388/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /work2/r1774/subjects/J106388/label/lh.cortex.label Reading surface /work2/r1774/subjects/J106388/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 58130 Masking with /work2/r1774/subjects/J106388/label/lh.cortex.label Writing to /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1508/lh.wm.mgh Dim: 125059 1 1 mri_vol2surf --mov /work2/r1774/subjects/J106388/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1508/lh.gm.mgh --projfrac 0.3 --regheader J106388 --cortex srcvol = /work2/r1774/subjects/J106388/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /work2/r1774/subjects/J106388/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /work2/r1774/subjects/J106388/label/lh.cortex.label Reading surface /work2/r1774/subjects/J106388/surf/lh.white Done reading source surface Reading thickness /work2/r1774/subjects/J106388/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 66391 Masking with /work2/r1774/subjects/J106388/label/lh.cortex.label Writing to /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1508/lh.gm.mgh Dim: 125059 1 1 mri_concat /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1508/lh.wm.mgh /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1508/lh.gm.mgh --paired-diff-norm --mul 100 --o /work2/r1774/subjects/J106388/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /work2/r1774/subjects/J106388/surf/lh.w-g.pct.mgh mri_segstats --in /work2/r1774/subjects/J106388/surf/lh.w-g.pct.mgh --annot J106388 lh aparc --sum /work2/r1774/subjects/J106388/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /work2/r1774/subjects/J106388/surf/lh.w-g.pct.mgh --annot J106388 lh aparc --sum /work2/r1774/subjects/J106388/stats/lh.w-g.pct.stats --snr sysname Linux hostname n026 machine x86_64 user r1774 UseRobust 0 Constructing seg from annotation Reading annotation /work2/r1774/subjects/J106388/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /work2/r1774/subjects/J106388/surf/lh.w-g.pct.mgh Vertex Area is 0.62933 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Sun Apr 16 10:59:22 CDT 2017 /work2/r1774/subjects/J106388/scripts pctsurfcon --s J106388 --rh-only Log file is /work2/r1774/subjects/J106388/scripts/pctsurfcon.log Sun Apr 16 10:59:22 CDT 2017 setenv SUBJECTS_DIR /work2/r1774/subjects cd /work2/r1774/subjects/J106388/scripts /home/ums/r1774/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/ums/r1774/freesurfer mri_vol2surf --mov /work2/r1774/subjects/J106388/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1559/rh.wm.mgh --regheader J106388 --cortex srcvol = /work2/r1774/subjects/J106388/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /work2/r1774/subjects/J106388/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /work2/r1774/subjects/J106388/label/rh.cortex.label Reading surface /work2/r1774/subjects/J106388/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 57922 Masking with /work2/r1774/subjects/J106388/label/rh.cortex.label Writing to /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1559/rh.wm.mgh Dim: 122899 1 1 mri_vol2surf --mov /work2/r1774/subjects/J106388/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1559/rh.gm.mgh --projfrac 0.3 --regheader J106388 --cortex srcvol = /work2/r1774/subjects/J106388/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /work2/r1774/subjects/J106388/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /work2/r1774/subjects/J106388/label/rh.cortex.label Reading surface /work2/r1774/subjects/J106388/surf/rh.white Done reading source surface Reading thickness /work2/r1774/subjects/J106388/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 65892 Masking with /work2/r1774/subjects/J106388/label/rh.cortex.label Writing to /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1559/rh.gm.mgh Dim: 122899 1 1 mri_concat /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1559/rh.wm.mgh /work2/r1774/subjects/J106388/surf/tmp.pctsurfcon.1559/rh.gm.mgh --paired-diff-norm --mul 100 --o /work2/r1774/subjects/J106388/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /work2/r1774/subjects/J106388/surf/rh.w-g.pct.mgh mri_segstats --in /work2/r1774/subjects/J106388/surf/rh.w-g.pct.mgh --annot J106388 rh aparc --sum /work2/r1774/subjects/J106388/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /work2/r1774/subjects/J106388/surf/rh.w-g.pct.mgh --annot J106388 rh aparc --sum /work2/r1774/subjects/J106388/stats/rh.w-g.pct.stats --snr sysname Linux hostname n026 machine x86_64 user r1774 UseRobust 0 Constructing seg from annotation Reading annotation /work2/r1774/subjects/J106388/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /work2/r1774/subjects/J106388/surf/rh.w-g.pct.mgh Vertex Area is 0.637837 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Sun Apr 16 10:59:30 CDT 2017 /work2/r1774/subjects/J106388/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 8626 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 7406 voxels changed to hypointensity... 15298 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Apr 16 11:00:00 CDT 2017 /work2/r1774/subjects/J106388 mri_aparc2aseg --s J106388 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /work2/r1774/subjects subject J106388 outvol /work2/r1774/subjects/J106388/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /work2/r1774/subjects/J106388/surf/lh.white Reading lh pial surface /work2/r1774/subjects/J106388/surf/lh.pial Loading lh annotations from /work2/r1774/subjects/J106388/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /work2/r1774/subjects/J106388/surf/rh.white Reading rh pial surface /work2/r1774/subjects/J106388/surf/rh.pial Loading rh annotations from /work2/r1774/subjects/J106388/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /work2/r1774/subjects/J106388/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /work2/r1774/subjects/J106388/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.08 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 83 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 43 rescaling Left_Cerebellum_White_Matter from 86 --> 94 rescaling Left_Cerebellum_Cortex from 60 --> 79 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 84 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 94 rescaling Third_Ventricle from 25 --> 26 rescaling Fourth_Ventricle from 22 --> 28 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 75 rescaling Left_Amygdala from 56 --> 78 rescaling CSF from 32 --> 55 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 82 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 32 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 76 rescaling Right_Amygdala from 55 --> 80 rescaling Right_Accumbens_area from 65 --> 79 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 48 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 310666 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 155 changed. pass 2: 9 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /work2/r1774/subjects/J106388/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Sun Apr 16 11:05:39 CDT 2017 /work2/r1774/subjects/J106388 mri_aparc2aseg --s J106388 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /work2/r1774/subjects subject J106388 outvol /work2/r1774/subjects/J106388/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /work2/r1774/subjects/J106388/surf/lh.white Reading lh pial surface /work2/r1774/subjects/J106388/surf/lh.pial Loading lh annotations from /work2/r1774/subjects/J106388/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /work2/r1774/subjects/J106388/surf/rh.white Reading rh pial surface /work2/r1774/subjects/J106388/surf/rh.pial Loading rh annotations from /work2/r1774/subjects/J106388/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /work2/r1774/subjects/J106388/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /work2/r1774/subjects/J106388/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.08 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 83 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 43 rescaling Left_Cerebellum_White_Matter from 86 --> 94 rescaling Left_Cerebellum_Cortex from 60 --> 79 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 84 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 94 rescaling Third_Ventricle from 25 --> 26 rescaling Fourth_Ventricle from 22 --> 28 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 75 rescaling Left_Amygdala from 56 --> 78 rescaling CSF from 32 --> 55 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 82 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 32 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 76 rescaling Right_Amygdala from 55 --> 80 rescaling Right_Accumbens_area from 65 --> 79 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 48 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 310738 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 155 changed. pass 2: 9 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /work2/r1774/subjects/J106388/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sun Apr 16 11:11:18 CDT 2017 /work2/r1774/subjects/J106388 mri_aparc2aseg --s J106388 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/ums/r1774/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /work2/r1774/subjects subject J106388 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /work2/r1774/subjects/J106388/surf/lh.white Reading lh pial surface /work2/r1774/subjects/J106388/surf/lh.pial Loading lh annotations from /work2/r1774/subjects/J106388/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /work2/r1774/subjects/J106388/surf/rh.white Reading rh pial surface /work2/r1774/subjects/J106388/surf/rh.pial Loading rh annotations from /work2/r1774/subjects/J106388/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /work2/r1774/subjects/J106388/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /work2/r1774/subjects/J106388/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.08 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 83 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 43 rescaling Left_Cerebellum_White_Matter from 86 --> 94 rescaling Left_Cerebellum_Cortex from 60 --> 79 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 84 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 94 rescaling Third_Ventricle from 25 --> 26 rescaling Fourth_Ventricle from 22 --> 28 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 75 rescaling Left_Amygdala from 56 --> 78 rescaling CSF from 32 --> 55 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 82 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 32 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 76 rescaling Right_Amygdala from 55 --> 80 rescaling Right_Accumbens_area from 65 --> 79 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 48 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 310738 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 155 changed. pass 2: 9 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Sun Apr 16 11:16:47 CDT 2017 /work2/r1774/subjects/J106388/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Apr 16 11:16:47 CDT 2017 setenv SUBJECTS_DIR /work2/r1774/subjects cd /work2/r1774/subjects/J106388/mri /home/ums/r1774/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux n026 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /work2/r1774/subjects/J106388/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname n026 machine x86_64 user r1774 input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Sun Apr 16 11:16:47 CDT 2017 Ended at Sun Apr 16 11:16:59 CDT 2017 Apas2aseg-Run-Time-Sec 12 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Apr 16 11:16:59 CDT 2017 /work2/r1774/subjects/J106388 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/ums/r1774/freesurfer/ASegStatsLUT.txt --subject J106388 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/ums/r1774/freesurfer/ASegStatsLUT.txt --subject J106388 sysname Linux hostname n026 machine x86_64 user r1774 UseRobust 0 atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) Computing euler number orig.nofix lheno = -104, rheno = -100 orig.nofix lhholes = 53, rhholes = 51 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Sun Apr 16 11:22:48 CDT 2017 /work2/r1774/subjects/J106388 mri_aparc2aseg --s J106388 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /work2/r1774/subjects subject J106388 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /work2/r1774/subjects/J106388/mri/aparc+aseg.mgz Reading lh white surface /work2/r1774/subjects/J106388/surf/lh.white Reading lh pial surface /work2/r1774/subjects/J106388/surf/lh.pial Loading lh annotations from /work2/r1774/subjects/J106388/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /work2/r1774/subjects/J106388/surf/rh.white Reading rh pial surface /work2/r1774/subjects/J106388/surf/rh.pial Loading rh annotations from /work2/r1774/subjects/J106388/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /work2/r1774/subjects/J106388/mri/ribbon.mgz Loading filled from /work2/r1774/subjects/J106388/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7176 vertices from left hemi Ripped 6837 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /work2/r1774/subjects/J106388/mri/aseg.mgz Loading Ctx Seg File /work2/r1774/subjects/J106388/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 727372 Used brute-force search on 53 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 2.000000 4 k 1290.000000 Fixing Parahip RH WM Found 16 clusters 0 k 4.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 4.000000 5 k 8.000000 6 k 3.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 1226.000000 11 k 2.000000 12 k 1.000000 13 k 1.000000 14 k 4.000000 15 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject J106388 --surf-wm-vol --ctab /home/ums/r1774/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject J106388 --surf-wm-vol --ctab /home/ums/r1774/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname n026 machine x86_64 user r1774 UseRobust 0 atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /work2/r1774/subjects/J106388/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Apr 16 11:35:42 CDT 2017 mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject J106388 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject J106388 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8182 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject J106388 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4230 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject J106388 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 217 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6200 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject J106388 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5950 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject J106388 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4236 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject J106388 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 556 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14145 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject J106388 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4385 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject J106388 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 1117 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4539 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject J106388 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 383 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5024 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject J106388 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 1144 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject J106388 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 456 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2474 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject J106388 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1431 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject J106388 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1379 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1045 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2160 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1605 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2031 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2412 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1594 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7210 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2002 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 378 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1529 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 201 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3606 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3888 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 646 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 512 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject J106388 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/lh.white Reading target registration /work2/r1774/subjects/J106388/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 125059 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 542 mri_label2label: Done mris_label2annot --s J106388 --hemi lh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /work2/r1774/subjects/J106388/label cmdline mris_label2annot --s J106388 --hemi lh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname n026 machine x86_64 user r1774 subject J106388 hemi lh SUBJECTS_DIR /work2/r1774/subjects ColorTable /home/ums/r1774/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /work2/r1774/subjects/J106388/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89786 unhit vertices Writing annot to /work2/r1774/subjects/J106388/label/lh.BA_exvivo.annot mris_label2annot --s J106388 --hemi lh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /work2/r1774/subjects/J106388/label cmdline mris_label2annot --s J106388 --hemi lh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname n026 machine x86_64 user r1774 subject J106388 hemi lh SUBJECTS_DIR /work2/r1774/subjects ColorTable /home/ums/r1774/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /work2/r1774/subjects/J106388/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 105145 unhit vertices Writing annot to /work2/r1774/subjects/J106388/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab J106388 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/lh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 160017 Total vertex volume 157727 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/ums/r1774/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 922 612 1170 1.648 0.485 0.132 0.031 8 1.2 BA1_exvivo 3554 2374 3553 1.641 0.507 0.116 0.023 29 3.4 BA2_exvivo 1040 728 824 1.489 0.362 0.184 0.060 17 2.9 BA3a_exvivo 2003 1321 2265 1.597 0.556 0.109 0.021 15 1.8 BA3b_exvivo 1549 1025 1494 1.461 0.374 0.111 0.022 11 1.5 BA4a_exvivo 1195 826 983 1.302 0.272 0.100 0.019 8 0.9 BA4p_exvivo 7797 4813 10775 2.145 0.707 0.118 0.029 67 10.0 BA6_exvivo 2045 1168 2989 2.452 0.534 0.113 0.032 18 2.7 BA44_exvivo 3558 2135 4751 2.179 0.504 0.125 0.034 37 5.1 BA45_exvivo 2248 1589 2027 1.339 0.335 0.145 0.030 28 2.9 V1_exvivo 6015 4157 6451 1.571 0.509 0.149 0.036 89 9.3 V2_exvivo 2106 1333 2322 1.903 0.493 0.152 0.045 28 4.3 MT_exvivo 503 343 1014 2.827 0.644 0.107 0.031 4 0.7 perirhinal_exvivo 738 436 1773 3.141 0.912 0.143 0.060 13 1.7 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab J106388 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/lh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/lh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 160017 Total vertex volume 157727 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/ums/r1774/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 595 376 738 1.624 0.429 0.138 0.031 6 0.8 BA1_exvivo 1392 921 1235 1.396 0.310 0.094 0.014 9 0.7 BA2_exvivo 866 601 640 1.460 0.297 0.189 0.066 15 2.6 BA3a_exvivo 1137 802 1115 1.341 0.359 0.094 0.016 6 0.7 BA3b_exvivo 1471 962 1294 1.400 0.305 0.111 0.022 11 1.5 BA4a_exvivo 999 714 839 1.277 0.237 0.100 0.017 5 0.7 BA4p_exvivo 4163 2660 5666 2.024 0.694 0.117 0.027 32 5.0 BA6_exvivo 1309 757 1911 2.452 0.547 0.121 0.033 13 1.9 BA44_exvivo 1359 779 1970 2.210 0.513 0.114 0.032 12 1.7 BA45_exvivo 2374 1690 2236 1.361 0.369 0.135 0.028 26 2.8 V1_exvivo 3006 2175 3431 1.576 0.568 0.162 0.037 52 5.1 V2_exvivo 577 378 596 1.758 0.342 0.174 0.044 10 1.1 MT_exvivo 246 181 519 2.911 0.486 0.106 0.024 2 0.3 perirhinal_exvivo 420 234 973 3.109 0.902 0.163 0.081 9 1.5 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Apr 16 11:41:44 CDT 2017 mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject J106388 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4160 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject J106388 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 305 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6992 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject J106388 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject J106388 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject J106388 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6014 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject J106388 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 277 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4750 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject J106388 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 767 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13023 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject J106388 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 345 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject J106388 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 639 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5994 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject J106388 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 463 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject J106388 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 1075 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9091 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject J106388 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 227 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2159 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject J106388 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 439 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1477 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject J106388 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 376 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 1128 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 942 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2814 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1793 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1441 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1620 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 400 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7359 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1056 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 253 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3485 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 496 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 3933 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 291 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 320 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 1014 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /work2/r1774/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject J106388 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /work2/r1774/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = J106388 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /work2/r1774/subjects FREESURFER_HOME /home/ums/r1774/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /work2/r1774/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /work2/r1774/subjects/J106388/surf/rh.white Reading target registration /work2/r1774/subjects/J106388/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 122899 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 439 mri_label2label: Done mris_label2annot --s J106388 --hemi rh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /work2/r1774/subjects/J106388/label cmdline mris_label2annot --s J106388 --hemi rh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname n026 machine x86_64 user r1774 subject J106388 hemi rh SUBJECTS_DIR /work2/r1774/subjects ColorTable /home/ums/r1774/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /work2/r1774/subjects/J106388/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 87964 unhit vertices Writing annot to /work2/r1774/subjects/J106388/label/rh.BA_exvivo.annot mris_label2annot --s J106388 --hemi rh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /work2/r1774/subjects/J106388/label cmdline mris_label2annot --s J106388 --hemi rh --ctab /home/ums/r1774/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname n026 machine x86_64 user r1774 subject J106388 hemi rh SUBJECTS_DIR /work2/r1774/subjects ColorTable /home/ums/r1774/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /work2/r1774/subjects/J106388/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 103337 unhit vertices Writing annot to /work2/r1774/subjects/J106388/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab J106388 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/rh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 158801 Total vertex volume 156907 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/ums/r1774/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 871 562 1178 1.761 0.548 0.124 0.023 7 0.8 BA1_exvivo 3200 2185 3133 1.568 0.371 0.119 0.024 26 3.3 BA2_exvivo 1131 782 872 1.487 0.430 0.145 0.037 18 1.5 BA3a_exvivo 1843 1294 1893 1.447 0.457 0.115 0.023 15 1.7 BA3b_exvivo 1408 989 1420 1.422 0.340 0.104 0.018 9 1.1 BA4a_exvivo 1411 998 1308 1.403 0.447 0.113 0.024 12 1.7 BA4p_exvivo 7208 4579 9375 2.001 0.703 0.117 0.028 59 8.5 BA6_exvivo 2849 1718 3965 2.266 0.591 0.109 0.026 22 3.3 BA44_exvivo 3779 2271 5502 2.309 0.578 0.117 0.030 39 4.7 BA45_exvivo 2425 1801 2521 1.396 0.477 0.146 0.031 32 3.3 V1_exvivo 5834 3981 5990 1.606 0.423 0.156 0.041 90 10.5 V2_exvivo 1633 986 2172 2.123 0.495 0.131 0.038 18 2.4 MT_exvivo 849 480 2057 3.164 0.967 0.118 0.063 12 2.4 perirhinal_exvivo 494 263 1052 2.929 0.682 0.118 0.053 11 1.1 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab J106388 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /work2/r1774/subjects/J106388/mri/wm.mgz... reading input surface /work2/r1774/subjects/J106388/surf/rh.white... reading input pial surface /work2/r1774/subjects/J106388/surf/rh.pial... reading input white surface /work2/r1774/subjects/J106388/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 158801 Total vertex volume 156907 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/ums/r1774/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1323255 mm^3 (det: 1.472207 ) lhCtxGM: 157170.026 156168.000 diff= 1002.0 pctdiff= 0.638 rhCtxGM: 156665.062 155532.000 diff= 1133.1 pctdiff= 0.723 lhCtxWM: 208840.281 209653.500 diff= -813.2 pctdiff=-0.389 rhCtxWM: 208275.571 209476.500 diff=-1200.9 pctdiff=-0.577 SubCortGMVol 47781.000 SupraTentVol 806432.939 (804741.000) diff=1691.939 pctdiff=0.210 SupraTentVolNotVent 780311.939 (778620.000) diff=1691.939 pctdiff=0.217 BrainSegVol 920098.000 (916870.000) diff=3228.000 pctdiff=0.351 BrainSegVolNotVent 889757.000 (889736.939) diff=20.061 pctdiff=0.002 BrainSegVolNotVent 889757.000 CerebellumVol 110996.000 VentChorVol 26121.000 3rd4th5thCSF 4220.000 CSFVol 992.000, OptChiasmVol 141.000 MaskVol 1308188.000 634 408 728 1.510 0.358 0.129 0.022 6 0.6 BA1_exvivo 1849 1267 1913 1.515 0.359 0.101 0.018 11 1.3 BA2_exvivo 1059 724 773 1.473 0.385 0.156 0.040 18 1.5 BA3a_exvivo 1494 1051 1329 1.320 0.291 0.112 0.022 12 1.3 BA3b_exvivo 852 595 984 1.533 0.480 0.113 0.021 6 0.7 BA4a_exvivo 1145 837 1015 1.335 0.423 0.105 0.021 9 1.1 BA4p_exvivo 4498 2935 5695 1.883 0.676 0.118 0.027 38 4.9 BA6_exvivo 686 417 970 2.160 0.634 0.112 0.029 5 0.9 BA44_exvivo 904 499 1433 2.416 0.624 0.112 0.029 9 1.1 BA45_exvivo 2274 1702 2265 1.376 0.452 0.146 0.031 30 3.1 V1_exvivo 3049 2110 3240 1.562 0.441 0.161 0.043 51 5.8 V2_exvivo 230 159 266 1.888 0.366 0.149 0.033 3 0.3 MT_exvivo 499 292 1292 3.336 1.017 0.105 0.037 4 0.7 perirhinal_exvivo 389 215 878 2.776 0.917 0.141 0.086 8 1.3 entorhinal_exvivo #-------------------------------------------- #@# Segmentation of brainstem substructures Sun Apr 16 11:47:49 CDT 2017 /home/ums/r1774/freesurfer/bin/segmentBS.sh /home/ums/r1774/freesurfer/MCRv80 /home/ums/r1774/freesurfer J106388 /work2/r1774/subjects See log file: /work2/r1774/subjects/J106388/scripts/brainstem-structures.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Sun Apr 16 12:16:05 CDT 2017 /home/ums/r1774/freesurfer/bin/segmentSF_T1.sh /home/ums/r1774/freesurfer/MCRv80 /home/ums/r1774/freesurfer J106388 /work2/r1774/subjects left See log file: /work2/r1774/subjects/J106388/scripts/hippocampal-subfields-T1.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Sun Apr 16 12:47:01 CDT 2017 /home/ums/r1774/freesurfer/bin/segmentSF_T1.sh /home/ums/r1774/freesurfer/MCRv80 /home/ums/r1774/freesurfer J106388 /work2/r1774/subjects right See log file: /work2/r1774/subjects/J106388/scripts/hippocampal-subfields-T1.log Started at Sat Apr 15 19:40:13 CDT 2017 Ended at Sun Apr 16 13:18:53 CDT 2017 #@#%# recon-all-run-time-hours 17.644 recon-all -s J106388 finished without error at Sun Apr 16 13:18:53 CDT 2017