Sat Jun 2 09:08:26 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 /home/jianfeng/freesurfer/bin/recon-all -i He_Aiqun_ReoT1.nii -s He_Aiqun_ReoT1 -all subjid He_Aiqun_ReoT1 setenv SUBJECTS_DIR /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Actual FREESURFER_HOME /home/jianfeng/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux Precision-WorkStation-T3500 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 47878 maxlocks unlimited maxsignal 47878 maxmessage 819200 maxnice 0 maxrtprio 50 maxrttime unlimited total used free shared buff/cache available Mem: 12297844 1806228 7260536 67696 3231080 10058944 Swap: 12578812 0 12578812 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/06/02-13:08:26-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: jianfeng Machine: Precision-WorkStation-T3500 Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/jianfeng/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/jianfeng/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 mri_convert /home/jianfeng/Desktop/EP/He_Aiqun_ReoT1.nii /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig/001.mgz mri_convert.bin /home/jianfeng/Desktop/EP/He_Aiqun_ReoT1.nii /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/jianfeng/Desktop/EP/He_Aiqun_ReoT1.nii... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.00838916, -0.998707, -0.050145) j_ras = (0.0261959, -0.050349, 0.998388) k_ras = (0.999622, -0.00706201, -0.0265844) writing to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Jun 2 09:08:39 EDT 2018 Found 1 runs /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig/001.mgz /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 mri_convert /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz --conform mri_convert.bin /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.00838916, -0.998707, -0.050145) j_ras = (0.0261959, -0.050349, 0.998388) k_ras = (0.999622, -0.00706201, -0.0265844) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz... mri_add_xform_to_header -c /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/transforms/talairach.xfm /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Jun 2 09:08:55 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri /home/jianfeng/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 Precision-WorkStation-T3500 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sat Jun 2 09:08:55 EDT 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.14044 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14044/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.14044/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, 0) j_ras = (3.72529e-09, -3.4197e-09, -1) k_ras = (4.65661e-10, 1, 2.32831e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.14044/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Jun 2 09:08:58 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.14044/nu0.mnc ./tmp.mri_nu_correct.mni.14044/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14044/0/ -iterations 1000 -distance 50 [jianfeng@Precision-WorkStation-T3500:/home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/] [2018-06-02 09:08:59] running: /home/jianfeng/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.14044/0/ ./tmp.mri_nu_correct.mni.14044/nu0.mnc ./tmp.mri_nu_correct.mni.14044/nu1.imp 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Processing:.................................................................Done Number of iterations: 49 CV of field change: 0.000979084 mri_convert ./tmp.mri_nu_correct.mni.14044/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.14044/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.14044/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, 0) j_ras = (3.72529e-09, -3.4197e-09, -1) k_ras = (4.65661e-10, 1, 2.32831e-10) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Jun 2 09:10:31 EDT 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Jun 2 09:10:31 EDT 2018 Ended at Sat Jun 2 09:11:19 EDT 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Jun 2 09:11:21 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7629, pval=0.6675 >= threshold=0.0050) awk -f /home/jianfeng/freesurfer/bin/extract_talairach_avi_QA.awk /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/transforms/talairach_avi.log tal_QC_AZS /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/transforms/talairach_avi.log TalAviQA: 0.98177 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Jun 2 09:11:21 EDT 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri /home/jianfeng/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 Precision-WorkStation-T3500 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sat Jun 2 09:11:21 EDT 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.14896 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14896/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.14896/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, 0) j_ras = (3.72529e-09, -3.4197e-09, -1) k_ras = (4.65661e-10, 1, 2.32831e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.14896/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Jun 2 09:11:24 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.14896/nu0.mnc ./tmp.mri_nu_correct.mni.14896/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14896/0/ [jianfeng@Precision-WorkStation-T3500:/home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/] [2018-06-02 09:11:24] running: /home/jianfeng/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.14896/0/ ./tmp.mri_nu_correct.mni.14896/nu0.mnc ./tmp.mri_nu_correct.mni.14896/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000975601 -------------------------------------------------------- Iteration 2 Sat Jun 2 09:12:21 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.14896/nu1.mnc ./tmp.mri_nu_correct.mni.14896/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.14896/1/ [jianfeng@Precision-WorkStation-T3500:/home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/] [2018-06-02 09:12:21] running: /home/jianfeng/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.14896/1/ ./tmp.mri_nu_correct.mni.14896/nu1.mnc ./tmp.mri_nu_correct.mni.14896/nu2.imp 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 Number of iterations: 29 CV of field change: 0.000965403 mri_binarize --i ./tmp.mri_nu_correct.mni.14896/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14896/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.14896/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14896/ones.mgz sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng input ./tmp.mri_nu_correct.mni.14896/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14896/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.14896/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14896/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14896/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.14896/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14896/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14896/input.mean.dat sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng UseRobust 0 Loading ./tmp.mri_nu_correct.mni.14896/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.14896/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14896/ones.mgz --i ./tmp.mri_nu_correct.mni.14896/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14896/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14896/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.14896/ones.mgz --i ./tmp.mri_nu_correct.mni.14896/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14896/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14896/output.mean.dat sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng UseRobust 0 Loading ./tmp.mri_nu_correct.mni.14896/ones.mgz Loading ./tmp.mri_nu_correct.mni.14896/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.14896/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.14896/nu2.mnc ./tmp.mri_nu_correct.mni.14896/nu2.mnc mul 1.04781806018679375418 Saving result to './tmp.mri_nu_correct.mni.14896/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.14896/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.14896/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.14896/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, 0) j_ras = (3.72529e-09, -3.4197e-09, -1) k_ras = (4.65661e-10, 1, 2.32831e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 12 seconds. mapping (17, 96) to ( 3, 110) Sat Jun 2 09:13:59 EDT 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Jun 2 09:14:00 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 1.07709 0.00475 -0.01474 1.52495; 0.00329 1.11733 0.05146 2.39001; -0.00851 -0.01838 1.15730 -2.95190; 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 = 12 Starting OpenSpline(): npoints = 12 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 78 (78), valley at 60 (60) csf peak at 12, 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 76 (76), valley at 58 (58) csf peak at 10, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 4 minutes and 2 seconds. #-------------------------------------------- #@# Skull Stripping Sat Jun 2 09:18:03 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_em_register -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /home/jianfeng/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/jianfeng/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=10.0 skull bounding box = (45, 20, 31) --> (213, 209, 215) using (101, 83, 123) as brain centroid... mean wm in atlas = 108, using box (80,60,100) --> (121, 106,145) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 5.6 after smoothing, mri peak at 104, scaling input intensities by 1.038 scaling channel 0 by 1.03846 initial log_p = -4.729 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.628183 @ (-9.091, 27.273, -9.091) max log p = -4.582044 @ (4.545, -4.545, -4.545) max log p = -4.529973 @ (2.273, -6.818, 6.818) max log p = -4.525087 @ (3.409, 3.409, -7.955) max log p = -4.516175 @ (-2.841, -3.977, 5.114) max log p = -4.516175 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 15.3, -9.7): log p = -4.516 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.290, old_max_log_p =-4.516 (thresh=-4.5) 1.15000 0.00000 0.00000 -20.69151; 0.00000 1.07500 0.00000 13.32841; 0.00000 0.00000 1.15000 -27.74643; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.121, old_max_log_p =-4.290 (thresh=-4.3) 1.06375 0.00000 0.00000 -9.77401; 0.00000 1.32897 0.00000 -9.61142; 0.00000 0.00000 1.15000 -27.74643; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.121, old_max_log_p =-4.121 (thresh=-4.1) 1.06375 0.00000 0.00000 -9.77401; 0.00000 1.32897 0.00000 -9.61142; 0.00000 0.00000 1.15000 -27.74643; 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=-4.096, old_max_log_p =-4.121 (thresh=-4.1) 1.06375 0.00000 0.00000 -9.77401; 0.00000 1.35316 -0.03833 -9.62738; 0.00000 0.04267 1.12783 -31.82168; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.088, old_max_log_p =-4.096 (thresh=-4.1) 1.08311 -0.00290 -0.03753 -7.30417; 0.00000 1.35104 -0.07521 -6.75062; 0.03480 0.08687 1.12537 -42.91361; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.083, old_max_log_p =-4.088 (thresh=-4.1) 1.10286 0.04207 0.03693 -24.28507; -0.03378 1.37858 -0.00269 -12.79675; -0.03550 -0.00146 1.10677 -21.36355; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.083, old_max_log_p =-4.083 (thresh=-4.1) 1.10286 0.04207 0.03693 -24.28507; -0.03378 1.37858 -0.00269 -12.79675; -0.03550 -0.00146 1.10677 -21.36355; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.065, old_max_log_p =-4.083 (thresh=-4.1) 1.10384 0.05344 0.03680 -26.17904; -0.04225 1.37964 -0.02112 -9.08979; -0.03601 0.02108 1.10528 -22.31574; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.062, old_max_log_p =-4.065 (thresh=-4.1) 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 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 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.062 (old=-4.729) transform before final EM align: 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 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 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.5 tol 0.000000 final transform: 1.10384 0.05344 0.03680 -26.17904; -0.04220 1.37802 -0.02110 -9.38127; -0.03605 0.02110 1.10657 -22.47151; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1723.656000 mri_em_register stimesec 2.848000 mri_em_register ru_maxrss 613840 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 156663 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 23 mri_em_register ru_nivcsw 759 registration took 28 minutes and 46 seconds. mri_watershed -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mri_watershed.dat -T1 -brain_atlas /home/jianfeng/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=128 y=97 z=123 r=84 first estimation of the main basin volume: 2561930 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=102, y=88, z=86, Imax=255 CSF=21, 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=726477670 voxels, voxel volume =1.000 = 726477670 mmm3 = 726477.696 cm3 done. PostAnalyze...Basin Prior 2 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=128,y=102, z=118, r=9055 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45728 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1036443231 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1044261364 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1094605169 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=37 , nb = 1071202400 OTHER CSF_MIN=4, CSF_intensity=13, CSF_MAX=35 , nb = 1075392394 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 8, 42, 73 after analyzing : 5, 30, 42, 40 RIGHT_CER before analyzing : 4, 7, 49, 73 after analyzing : 4, 35, 49, 44 LEFT_CER before analyzing : 4, 5, 39, 73 after analyzing : 4, 27, 39, 38 RIGHT_BRAIN before analyzing : 5, 8, 41, 72 after analyzing : 5, 30, 41, 40 LEFT_BRAIN before analyzing : 37, 39, 42, 73 after analyzing : 37, 41, 42, 49 OTHER before analyzing : 35, 52, 69, 90 after analyzing : 35, 63, 69, 69 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.012 curvature mean = 65.791, std = 7.412 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.99, sigma = 6.24 after rotation: sse = 3.99, sigma = 6.24 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.23, its var is 5.62 before Erosion-Dilatation 1.08% of inacurate vertices after Erosion-Dilatation 1.71% 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...52 iterations mri_strip_skull: done peeling brain Brain Size = 1369592 voxels, voxel volume = 1.000 mm3 = 1369592 mmm3 = 1369.592 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 35.840000 mri_watershed stimesec 0.448000 mri_watershed ru_maxrss 835092 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212266 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2152 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 0 mri_watershed ru_nivcsw 44 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Jun 2 09:47:27 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_em_register -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /home/jianfeng/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/jianfeng/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=21.0 skull bounding box = (62, 41, 47) --> (194, 152, 199) using (106, 78, 123) as brain centroid... mean wm in atlas = 107, using box (90,64,104) --> (122, 91,141) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 5.2 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.456 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.097991 @ (-9.091, 27.273, -9.091) max log p = -3.964585 @ (4.545, -13.636, -4.545) max log p = -3.925476 @ (2.273, 2.273, 2.273) max log p = -3.900909 @ (-1.136, 1.136, 1.136) max log p = -3.900909 @ (0.000, 0.000, 0.000) max log p = -3.895033 @ (-0.852, -0.284, 0.852) Found translation: (-4.3, 16.8, -9.4): log p = -3.895 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.682, old_max_log_p =-3.895 (thresh=-3.9) 1.07500 0.00000 0.00000 -14.08626; 0.00000 1.23625 0.00000 -7.46103; 0.00000 0.00000 1.07500 -25.48646; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.682, old_max_log_p =-3.682 (thresh=-3.7) 1.07500 0.00000 0.00000 -14.08626; 0.00000 1.23625 0.00000 -7.46103; 0.00000 0.00000 1.07500 -25.48646; 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=-3.560, old_max_log_p =-3.682 (thresh=-3.7) 1.09381 0.00010 -0.03451 -10.61096; 0.00000 1.16777 -0.00258 1.43022; 0.03718 -0.00308 1.09439 -30.21796; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.555, old_max_log_p =-3.560 (thresh=-3.6) 1.07339 -0.00010 0.03645 -16.45349; 0.00000 1.16777 -0.00258 1.43022; -0.03444 -0.00308 1.09431 -19.06951; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.553, old_max_log_p =-3.555 (thresh=-3.6) 1.05381 -0.00000 0.00061 -9.69585; 0.00000 1.16777 -0.00258 1.43022; 0.00071 -0.00314 1.11544 -27.98413; 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=-3.528, old_max_log_p =-3.553 (thresh=-3.5) 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.528, old_max_log_p =-3.528 (thresh=-3.5) 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 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 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.528 (old=-4.456) transform before final EM align: 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 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 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1160.936000 mri_em_register stimesec 2.348000 mri_em_register ru_maxrss 603024 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157889 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 0 mri_em_register ru_nivcsw 526 registration took 19 minutes and 23 seconds. #-------------------------------------- #@# CA Normalize Sat Jun 2 10:06:50 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/jianfeng/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/jianfeng/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=21.0 skull bounding box = (62, 41, 47) --> (194, 152, 200) using (106, 78, 124) as brain centroid... mean wm in atlas = 107, using box (90,64,105) --> (122, 91,142) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 5.1 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246344 sample points... INFO: compute sample coordinates transform 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30094; -0.00808 0.00626 1.11665 -27.94268; 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, 44, 49) --> (191, 147, 199) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 5592 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 44, 49) --> (130, 147, 199) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 3 of 5869 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 117, 68) --> (176, 154, 117) Left_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 6 of 330 (1.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 117, 66) --> (128, 153, 118) Right_Cerebellum_White_Matter: limiting intensities to 107.0 --> 132.0 5 of 405 (1.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 111, 99) --> (145, 171, 127) Brain_Stem: limiting intensities to 104.0 --> 132.0 62 of 320 (19.4%) samples deleted using 12516 total control points for intensity normalization... bias field = 0.950 +- 0.083 4 of 12440 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 44, 49) --> (191, 147, 199) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 6198 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 44, 49) --> (130, 147, 199) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 42 of 6565 (0.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 117, 68) --> (176, 154, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 513 (2.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 117, 66) --> (128, 153, 118) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 480 (0.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 111, 99) --> (145, 171, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 273 of 605 (45.1%) samples deleted using 14361 total control points for intensity normalization... bias field = 1.055 +- 0.075 6 of 13926 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 44, 49) --> (191, 147, 199) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 6188 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 44, 49) --> (130, 147, 199) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 6549 (0.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 117, 68) --> (176, 154, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 78 of 574 (13.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 117, 66) --> (128, 153, 118) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 88 of 515 (17.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 111, 99) --> (145, 171, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 462 of 650 (71.1%) samples deleted using 14476 total control points for intensity normalization... bias field = 1.049 +- 0.065 6 of 13547 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 11 seconds. #-------------------------------------- #@# CA Reg Sat Jun 2 10:09:02 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_ca_register -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/jianfeng/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/jianfeng/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.37 (predicted orig area = 5.8) 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=0.836, neg=0, invalid=762 0001: dt=203.317375, rms=0.745 (10.921%), neg=0, invalid=762 0002: dt=162.373402, rms=0.725 (2.621%), neg=0, invalid=762 0003: dt=192.688172, rms=0.717 (1.076%), neg=0, invalid=762 0004: dt=173.971831, rms=0.713 (0.643%), neg=0, invalid=762 0005: dt=295.936000, rms=0.708 (0.618%), neg=0, invalid=762 0006: dt=129.472000, rms=0.706 (0.368%), neg=0, invalid=762 0007: dt=517.888000, rms=0.702 (0.563%), neg=0, invalid=762 0008: dt=110.976000, rms=0.700 (0.298%), neg=0, invalid=762 0009: dt=1183.744000, rms=0.695 (0.612%), neg=0, invalid=762 0010: dt=92.480000, rms=0.693 (0.377%), neg=0, invalid=762 0011: dt=295.936000, rms=0.692 (0.102%), neg=0, invalid=762 0012: dt=295.936000, rms=0.691 (0.127%), neg=0, invalid=762 0013: dt=295.936000, rms=0.690 (0.223%), neg=0, invalid=762 0014: dt=295.936000, rms=0.687 (0.369%), neg=0, invalid=762 0015: dt=295.936000, rms=0.685 (0.317%), neg=0, invalid=762 0016: dt=295.936000, rms=0.683 (0.245%), neg=0, invalid=762 0017: dt=295.936000, rms=0.680 (0.440%), neg=0, invalid=762 0018: dt=295.936000, rms=0.678 (0.304%), neg=0, invalid=762 0019: dt=295.936000, rms=0.677 (0.215%), neg=0, invalid=762 0020: dt=295.936000, rms=0.675 (0.302%), neg=0, invalid=762 0021: dt=295.936000, rms=0.673 (0.200%), neg=0, invalid=762 0022: dt=295.936000, rms=0.672 (0.192%), neg=0, invalid=762 0023: dt=295.936000, rms=0.671 (0.219%), neg=0, invalid=762 0024: dt=295.936000, rms=0.669 (0.177%), neg=0, invalid=762 0025: dt=295.936000, rms=0.668 (0.162%), neg=0, invalid=762 0026: dt=295.936000, rms=0.667 (0.196%), neg=0, invalid=762 0027: dt=295.936000, rms=0.666 (0.101%), neg=0, invalid=762 0028: dt=295.936000, rms=0.665 (0.176%), neg=0, invalid=762 0029: dt=295.936000, rms=0.664 (0.133%), neg=0, invalid=762 0030: dt=295.936000, rms=0.664 (0.093%), neg=0, invalid=762 0031: dt=295.936000, rms=0.663 (0.120%), neg=0, invalid=762 0032: dt=295.936000, rms=0.662 (0.113%), neg=0, invalid=762 0033: dt=221.952000, rms=0.662 (0.012%), neg=0, invalid=762 0034: dt=221.952000, rms=0.662 (0.004%), neg=0, invalid=762 0035: dt=221.952000, rms=0.662 (0.025%), neg=0, invalid=762 0036: dt=221.952000, rms=0.662 (0.029%), neg=0, invalid=762 0037: dt=221.952000, rms=0.661 (0.030%), neg=0, invalid=762 0038: dt=221.952000, rms=0.661 (0.024%), neg=0, invalid=762 0039: dt=221.952000, rms=0.661 (0.026%), neg=0, invalid=762 0040: dt=221.952000, rms=0.661 (0.028%), neg=0, invalid=762 0041: dt=221.952000, rms=0.661 (0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=762 0042: dt=129.472000, rms=0.660 (0.186%), neg=0, invalid=762 0043: dt=443.904000, rms=0.659 (0.097%), neg=0, invalid=762 0044: dt=443.904000, rms=0.659 (0.088%), neg=0, invalid=762 0045: dt=443.904000, rms=0.659 (-0.123%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0046: dt=131.947137, rms=0.661 (0.675%), neg=0, invalid=762 0047: dt=140.137931, rms=0.654 (0.970%), neg=0, invalid=762 0048: dt=68.392157, rms=0.651 (0.448%), neg=0, invalid=762 0049: dt=145.152000, rms=0.648 (0.554%), neg=0, invalid=762 0050: dt=36.288000, rms=0.646 (0.295%), neg=0, invalid=762 0051: dt=145.152000, rms=0.643 (0.412%), neg=0, invalid=762 0052: dt=89.281139, rms=0.641 (0.346%), neg=0, invalid=762 0053: dt=36.288000, rms=0.640 (0.136%), neg=0, invalid=762 0054: dt=36.288000, rms=0.639 (0.099%), neg=0, invalid=762 0055: dt=36.288000, rms=0.638 (0.163%), neg=0, invalid=762 0056: dt=36.288000, rms=0.637 (0.233%), neg=0, invalid=762 0057: dt=36.288000, rms=0.635 (0.292%), neg=0, invalid=762 0058: dt=36.288000, rms=0.633 (0.319%), neg=0, invalid=762 0059: dt=36.288000, rms=0.631 (0.327%), neg=0, invalid=762 0060: dt=36.288000, rms=0.629 (0.334%), neg=0, invalid=762 0061: dt=36.288000, rms=0.627 (0.339%), neg=0, invalid=762 0062: dt=36.288000, rms=0.625 (0.333%), neg=0, invalid=762 0063: dt=36.288000, rms=0.623 (0.301%), neg=0, invalid=762 0064: dt=36.288000, rms=0.621 (0.271%), neg=0, invalid=762 0065: dt=36.288000, rms=0.619 (0.252%), neg=0, invalid=762 0066: dt=36.288000, rms=0.618 (0.235%), neg=0, invalid=762 0067: dt=36.288000, rms=0.617 (0.216%), neg=0, invalid=762 0068: dt=36.288000, rms=0.615 (0.196%), neg=0, invalid=762 0069: dt=36.288000, rms=0.614 (0.177%), neg=0, invalid=762 0070: dt=36.288000, rms=0.613 (0.157%), neg=0, invalid=762 0071: dt=36.288000, rms=0.612 (0.151%), neg=0, invalid=762 0072: dt=36.288000, rms=0.612 (0.137%), neg=0, invalid=762 0073: dt=36.288000, rms=0.611 (0.130%), neg=0, invalid=762 0074: dt=36.288000, rms=0.610 (0.118%), neg=0, invalid=762 0075: dt=36.288000, rms=0.609 (0.113%), neg=0, invalid=762 0076: dt=145.152000, rms=0.609 (0.045%), neg=0, invalid=762 0077: dt=145.152000, rms=0.609 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.610, neg=0, invalid=762 0078: dt=73.375796, rms=0.607 (0.366%), neg=0, invalid=762 0079: dt=66.406015, rms=0.607 (0.129%), neg=0, invalid=762 0080: dt=66.406015, rms=0.606 (0.096%), neg=0, invalid=762 0081: dt=66.406015, rms=0.605 (0.108%), neg=0, invalid=762 0082: dt=66.406015, rms=0.605 (0.119%), neg=0, invalid=762 0083: dt=66.406015, rms=0.604 (0.089%), neg=0, invalid=762 0084: dt=66.406015, rms=0.604 (0.060%), neg=0, invalid=762 0085: dt=103.680000, rms=0.604 (0.021%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=762 0086: dt=4.800000, rms=0.623 (0.135%), neg=0, invalid=762 0087: dt=2.000000, rms=0.623 (0.007%), neg=0, invalid=762 0088: dt=2.000000, rms=0.623 (0.002%), neg=0, invalid=762 0089: dt=2.000000, rms=0.623 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.624, neg=0, invalid=762 0090: dt=-0.000098, rms=0.623 (0.083%), neg=0, invalid=762 0091: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0092: dt=5.317881, rms=0.662 (2.462%), neg=0, invalid=762 0093: dt=2.792453, rms=0.661 (0.103%), neg=0, invalid=762 0094: dt=2.792453, rms=0.661 (-0.047%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=762 0095: dt=0.000000, rms=0.661 (0.070%), neg=0, invalid=762 0096: dt=0.000000, rms=0.661 (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=0.713, neg=0, invalid=762 0097: dt=0.448000, rms=0.712 (0.223%), neg=0, invalid=762 0098: dt=0.768000, rms=0.711 (0.161%), neg=0, invalid=762 0099: dt=0.768000, rms=0.709 (0.159%), neg=0, invalid=762 0100: dt=0.768000, rms=0.709 (0.050%), neg=0, invalid=762 0101: dt=0.768000, rms=0.709 (-0.290%), neg=0, invalid=762 0102: dt=1.792000, rms=0.708 (0.141%), neg=0, invalid=762 0103: dt=0.448000, rms=0.708 (0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=762 0104: dt=1.536000, rms=0.707 (0.219%), neg=0, invalid=762 0105: dt=0.000000, rms=0.707 (0.001%), neg=0, invalid=762 0106: dt=0.100000, rms=0.707 (-0.006%), 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 0107: dt=0.910288, rms=0.651 (3.097%), neg=0, invalid=762 0108: dt=0.080000, rms=0.650 (0.154%), neg=0, invalid=762 0109: dt=0.080000, rms=0.650 (-0.078%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.650, neg=0, invalid=762 0110: dt=0.028000, rms=0.650 (0.090%), neg=0, invalid=762 0111: dt=0.004000, rms=0.650 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.21186 (25) Left_Lateral_Ventricle (4): linear fit = 1.21 x + 0.0 (1326 voxels, overlap=0.616) Left_Lateral_Ventricle (4): linear fit = 1.21 x + 0.0 (1326 voxels, peak = 24), gca=24.1 gca peak = 0.15565 (16) mri peak = 0.17512 (24) Right_Lateral_Ventricle (43): linear fit = 1.52 x + 0.0 (1027 voxels, overlap=0.373) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1027 voxels, peak = 24), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06541 (97) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (816 voxels, overlap=1.012) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (816 voxels, peak = 96), gca=96.0 gca peak = 0.20183 (93) mri peak = 0.07004 (104) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (768 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (768 voxels, peak = 99), gca=99.0 gca peak = 0.21683 (55) mri peak = 0.08532 (71) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (807 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (807 voxels, peak = 68), gca=68.5 gca peak = 0.30730 (58) mri peak = 0.07986 (72) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (897 voxels, overlap=0.025) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (897 voxels, peak = 73), gca=72.8 gca peak = 0.11430 (101) mri peak = 0.06889 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57268 voxels, overlap=0.937) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57268 voxels, peak = 102), gca=101.5 gca peak = 0.12076 (102) mri peak = 0.07405 (102) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (58310 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (58310 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.03758 (78) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (19258 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (19258 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.03387 (74) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (21088 voxels, overlap=0.039) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (21088 voxels, peak = 73), gca=73.4 gca peak = 0.14161 (67) mri peak = 0.12592 (79) Right_Caudate (50): linear fit = 1.16 x + 0.0 (960 voxels, overlap=0.049) Right_Caudate (50): linear fit = 1.16 x + 0.0 (960 voxels, peak = 78), gca=78.1 gca peak = 0.15243 (71) mri peak = 0.07493 (82) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1009 voxels, overlap=0.840) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1009 voxels, peak = 78), gca=78.5 gca peak = 0.13336 (57) mri peak = 0.03707 (57) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20094 voxels, overlap=0.903) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20094 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.04295 (63) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (22703 voxels, overlap=0.670) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (22703 voxels, peak = 66), gca=66.4 gca peak = 0.18181 (84) mri peak = 0.05989 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (8387 voxels, overlap=0.634) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (8387 voxels, peak = 94), gca=93.7 gca peak = 0.20573 (83) mri peak = 0.09958 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7479 voxels, overlap=0.322) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7479 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.09989 (75) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (462 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (462 voxels, peak = 74), gca=74.4 gca peak = 0.39313 (56) mri peak = 0.11241 (70) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (471 voxels, overlap=0.025) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (471 voxels, peak = 69), gca=68.6 gca peak = 0.14181 (85) mri peak = 0.04736 (93) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (4872 voxels, overlap=0.629) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (4872 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.06797 (92) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4032 voxels, overlap=0.542) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4032 voxels, peak = 92), gca=91.7 gca peak = 0.13399 (79) mri peak = 0.07205 (87) Left_Putamen (12): linear fit = 1.11 x + 0.0 (2429 voxels, overlap=0.602) Left_Putamen (12): linear fit = 1.11 x + 0.0 (2429 voxels, peak = 87), gca=87.3 gca peak = 0.14159 (79) mri peak = 0.08250 (80) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2356 voxels, overlap=0.759) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2356 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.08168 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10775 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10775 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.10836 (101) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1024 voxels, overlap=0.015) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1024 voxels, peak = 99), gca=99.3 gca peak = 0.12801 (89) mri peak = 0.08670 (98) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1097 voxels, overlap=0.429) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1097 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.20112 (33) Third_Ventricle (14): linear fit = 1.38 x + 0.0 (80 voxels, overlap=0.156) Third_Ventricle (14): linear fit = 1.38 x + 0.0 (80 voxels, peak = 32), gca=31.6 gca peak = 0.15061 (21) mri peak = 0.13069 (21) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (270 voxels, overlap=0.620) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (270 voxels, peak = 22), gca=22.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.27 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.29 x + 0.0 Left_Pallidum too bright - rescaling by 1.009 (from 1.065) to 99.9 (was 99.0) 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=0.660, neg=0, invalid=762 0112: dt=65.824710, rms=0.648 (1.732%), neg=0, invalid=762 0113: dt=32.368000, rms=0.648 (0.056%), neg=0, invalid=762 0114: dt=18.496000, rms=0.648 (0.009%), neg=0, invalid=762 0115: dt=18.496000, rms=0.648 (0.001%), neg=0, invalid=762 0116: dt=18.496000, rms=0.648 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0117: dt=295.936000, rms=0.643 (0.745%), neg=0, invalid=762 0118: dt=92.480000, rms=0.641 (0.278%), neg=0, invalid=762 0119: dt=369.920000, rms=0.640 (0.165%), neg=0, invalid=762 0120: dt=129.472000, rms=0.639 (0.278%), neg=0, invalid=762 0121: dt=129.472000, rms=0.638 (0.073%), neg=0, invalid=762 0122: dt=517.888000, rms=0.637 (0.250%), neg=0, invalid=762 0123: dt=92.480000, rms=0.636 (0.116%), neg=0, invalid=762 0124: dt=1479.680000, rms=0.633 (0.411%), neg=0, invalid=762 0125: dt=75.148387, rms=0.632 (0.247%), neg=0, invalid=762 0126: dt=92.480000, rms=0.632 (0.025%), neg=0, invalid=762 0127: dt=92.480000, rms=0.631 (0.028%), neg=0, invalid=762 0128: dt=92.480000, rms=0.631 (0.046%), neg=0, invalid=762 0129: dt=92.480000, rms=0.631 (0.064%), neg=0, invalid=762 0130: dt=92.480000, rms=0.630 (0.081%), neg=0, invalid=762 0131: dt=92.480000, rms=0.630 (0.099%), neg=0, invalid=762 0132: dt=92.480000, rms=0.629 (0.106%), neg=0, invalid=762 0133: dt=92.480000, rms=0.628 (0.106%), neg=0, invalid=762 0134: dt=92.480000, rms=0.628 (0.106%), neg=0, invalid=762 0135: dt=92.480000, rms=0.627 (0.101%), neg=0, invalid=762 0136: dt=92.480000, rms=0.626 (0.104%), neg=0, invalid=762 0137: dt=92.480000, rms=0.626 (0.103%), neg=0, invalid=762 0138: dt=92.480000, rms=0.625 (0.102%), neg=0, invalid=762 0139: dt=92.480000, rms=0.624 (0.091%), neg=0, invalid=762 0140: dt=92.480000, rms=0.624 (0.082%), neg=0, invalid=762 0141: dt=92.480000, rms=0.623 (0.080%), neg=0, invalid=762 0142: dt=92.480000, rms=0.623 (0.080%), neg=0, invalid=762 0143: dt=92.480000, rms=0.622 (0.078%), neg=0, invalid=762 0144: dt=92.480000, rms=0.622 (0.075%), neg=0, invalid=762 0145: dt=92.480000, rms=0.621 (0.072%), neg=0, invalid=762 0146: dt=92.480000, rms=0.621 (0.069%), neg=0, invalid=762 0147: dt=92.480000, rms=0.621 (0.067%), neg=0, invalid=762 0148: dt=92.480000, rms=0.620 (0.068%), neg=0, invalid=762 0149: dt=92.480000, rms=0.620 (0.067%), neg=0, invalid=762 0150: dt=92.480000, rms=0.619 (0.066%), neg=0, invalid=762 0151: dt=92.480000, rms=0.619 (0.063%), neg=0, invalid=762 0152: dt=92.480000, rms=0.619 (0.062%), neg=0, invalid=762 0153: dt=92.480000, rms=0.618 (0.061%), neg=0, invalid=762 0154: dt=92.480000, rms=0.618 (0.062%), neg=0, invalid=762 0155: dt=92.480000, rms=0.617 (0.058%), neg=0, invalid=762 0156: dt=92.480000, rms=0.617 (0.049%), neg=0, invalid=762 0157: dt=92.480000, rms=0.617 (0.048%), neg=0, invalid=762 0158: dt=92.480000, rms=0.617 (0.048%), neg=0, invalid=762 0159: dt=92.480000, rms=0.616 (0.055%), neg=0, invalid=762 0160: dt=92.480000, rms=0.616 (0.048%), neg=0, invalid=762 0161: dt=92.480000, rms=0.616 (0.046%), neg=0, invalid=762 0162: dt=92.480000, rms=0.615 (0.046%), neg=0, invalid=762 0163: dt=92.480000, rms=0.615 (0.048%), neg=0, invalid=762 0164: dt=92.480000, rms=0.615 (0.047%), neg=0, invalid=762 0165: dt=92.480000, rms=0.615 (0.046%), neg=0, invalid=762 0166: dt=92.480000, rms=0.614 (0.043%), neg=0, invalid=762 0167: dt=92.480000, rms=0.614 (0.041%), neg=0, invalid=762 0168: dt=92.480000, rms=0.614 (0.039%), neg=0, invalid=762 0169: dt=92.480000, rms=0.614 (0.032%), neg=0, invalid=762 0170: dt=92.480000, rms=0.613 (0.034%), neg=0, invalid=762 0171: dt=92.480000, rms=0.613 (0.034%), neg=0, invalid=762 0172: dt=92.480000, rms=0.613 (0.039%), neg=0, invalid=762 0173: dt=92.480000, rms=0.613 (0.034%), neg=0, invalid=762 0174: dt=92.480000, rms=0.612 (0.032%), neg=0, invalid=762 0175: dt=92.480000, rms=0.612 (0.035%), neg=0, invalid=762 0176: dt=92.480000, rms=0.612 (0.029%), neg=0, invalid=762 0177: dt=92.480000, rms=0.612 (0.027%), neg=0, invalid=762 0178: dt=92.480000, rms=0.612 (0.029%), neg=0, invalid=762 0179: dt=92.480000, rms=0.612 (0.028%), neg=0, invalid=762 0180: dt=92.480000, rms=0.611 (0.032%), neg=0, invalid=762 0181: dt=92.480000, rms=0.611 (0.028%), neg=0, invalid=762 0182: dt=92.480000, rms=0.611 (0.025%), neg=0, invalid=762 0183: dt=92.480000, rms=0.611 (0.023%), neg=0, invalid=762 0184: dt=92.480000, rms=0.611 (0.022%), neg=0, invalid=762 0185: dt=517.888000, rms=0.611 (0.028%), neg=0, invalid=762 0186: dt=32.368000, rms=0.611 (-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=0.612, neg=0, invalid=762 0187: dt=36.288000, rms=0.610 (0.214%), neg=0, invalid=762 0188: dt=145.152000, rms=0.607 (0.492%), neg=0, invalid=762 0189: dt=414.720000, rms=0.593 (2.400%), neg=0, invalid=762 0190: dt=48.372093, rms=0.590 (0.497%), neg=0, invalid=762 0191: dt=36.288000, rms=0.589 (0.052%), neg=0, invalid=762 0192: dt=145.152000, rms=0.588 (0.196%), neg=0, invalid=762 0193: dt=497.664000, rms=0.580 (1.333%), neg=0, invalid=762 0194: dt=49.142857, rms=0.578 (0.335%), neg=0, invalid=762 0195: dt=31.104000, rms=0.578 (0.015%), neg=0, invalid=762 0196: dt=31.104000, rms=0.578 (0.015%), neg=0, invalid=762 0197: dt=31.104000, rms=0.578 (0.027%), neg=0, invalid=762 0198: dt=31.104000, rms=0.578 (0.056%), neg=0, invalid=762 0199: dt=31.104000, rms=0.577 (0.120%), neg=0, invalid=762 0200: dt=31.104000, rms=0.576 (0.202%), neg=0, invalid=762 0201: dt=31.104000, rms=0.574 (0.256%), neg=0, invalid=762 0202: dt=31.104000, rms=0.573 (0.276%), neg=0, invalid=762 0203: dt=31.104000, rms=0.571 (0.265%), neg=0, invalid=762 0204: dt=31.104000, rms=0.570 (0.241%), neg=0, invalid=762 0205: dt=31.104000, rms=0.569 (0.211%), neg=0, invalid=762 0206: dt=31.104000, rms=0.568 (0.180%), neg=0, invalid=762 0207: dt=31.104000, rms=0.567 (0.152%), neg=0, invalid=762 0208: dt=31.104000, rms=0.566 (0.150%), neg=0, invalid=762 0209: dt=31.104000, rms=0.565 (0.156%), neg=0, invalid=762 0210: dt=31.104000, rms=0.564 (0.173%), neg=0, invalid=762 0211: dt=31.104000, rms=0.563 (0.177%), neg=0, invalid=762 0212: dt=31.104000, rms=0.562 (0.168%), neg=0, invalid=762 0213: dt=31.104000, rms=0.561 (0.157%), neg=0, invalid=762 0214: dt=31.104000, rms=0.561 (0.138%), neg=0, invalid=762 0215: dt=31.104000, rms=0.560 (0.117%), neg=0, invalid=762 0216: dt=31.104000, rms=0.559 (0.100%), neg=0, invalid=762 0217: dt=31.104000, rms=0.559 (0.016%), neg=0, invalid=762 0218: dt=31.104000, rms=0.559 (0.017%), neg=0, invalid=762 0219: dt=31.104000, rms=0.559 (0.023%), neg=0, invalid=762 0220: dt=31.104000, rms=0.559 (0.031%), neg=0, invalid=762 0221: dt=31.104000, rms=0.559 (0.042%), neg=0, invalid=762 0222: dt=31.104000, rms=0.558 (0.052%), neg=0, invalid=762 0223: dt=31.104000, rms=0.558 (0.059%), neg=0, invalid=762 0224: dt=31.104000, rms=0.558 (0.069%), neg=0, invalid=762 0225: dt=31.104000, rms=0.557 (0.072%), neg=0, invalid=762 0226: dt=31.104000, rms=0.557 (0.008%), neg=0, invalid=762 0227: dt=15.552000, rms=0.557 (0.005%), neg=0, invalid=762 0228: dt=2.268000, rms=0.557 (0.000%), neg=0, invalid=762 0229: dt=1.134000, rms=0.557 (0.000%), neg=0, invalid=762 0230: dt=0.567000, rms=0.557 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=762 0231: dt=145.152000, rms=0.554 (0.618%), neg=0, invalid=762 0232: dt=69.383178, rms=0.553 (0.204%), neg=0, invalid=762 0233: dt=103.680000, rms=0.553 (0.062%), neg=0, invalid=762 0234: dt=103.680000, rms=0.552 (0.122%), neg=0, invalid=762 0235: dt=36.288000, rms=0.552 (0.035%), neg=0, invalid=762 0236: dt=36.288000, rms=0.552 (0.028%), neg=0, invalid=762 0237: dt=36.288000, rms=0.551 (0.044%), neg=0, invalid=762 0238: dt=36.288000, rms=0.551 (0.063%), neg=0, invalid=762 0239: dt=36.288000, rms=0.551 (0.077%), neg=0, invalid=762 0240: dt=36.288000, rms=0.550 (0.084%), neg=0, invalid=762 0241: dt=36.288000, rms=0.550 (0.086%), neg=0, invalid=762 0242: dt=36.288000, rms=0.549 (0.082%), neg=0, invalid=762 0243: dt=36.288000, rms=0.549 (0.086%), neg=0, invalid=762 0244: dt=36.288000, rms=0.548 (0.087%), neg=0, invalid=762 0245: dt=36.288000, rms=0.548 (0.091%), neg=0, invalid=762 0246: dt=36.288000, rms=0.547 (0.097%), neg=0, invalid=762 0247: dt=36.288000, rms=0.547 (0.095%), neg=0, invalid=762 0248: dt=36.288000, rms=0.546 (0.091%), neg=0, invalid=762 0249: dt=36.288000, rms=0.546 (0.090%), neg=0, invalid=762 0250: dt=36.288000, rms=0.545 (0.092%), neg=0, invalid=762 0251: dt=36.288000, rms=0.545 (0.095%), neg=0, invalid=762 0252: dt=36.288000, rms=0.544 (0.103%), neg=0, invalid=762 0253: dt=36.288000, rms=0.544 (0.098%), neg=0, invalid=762 0254: dt=36.288000, rms=0.543 (0.088%), neg=0, invalid=762 0255: dt=36.288000, rms=0.543 (0.090%), neg=0, invalid=762 0256: dt=36.288000, rms=0.542 (0.078%), neg=0, invalid=762 0257: dt=36.288000, rms=0.542 (0.079%), neg=0, invalid=762 0258: dt=36.288000, rms=0.541 (0.078%), neg=0, invalid=762 0259: dt=36.288000, rms=0.541 (0.075%), neg=0, invalid=762 0260: dt=36.288000, rms=0.540 (0.075%), neg=0, invalid=762 0261: dt=36.288000, rms=0.540 (0.075%), neg=0, invalid=762 0262: dt=36.288000, rms=0.540 (0.073%), neg=0, invalid=762 0263: dt=36.288000, rms=0.539 (0.065%), neg=0, invalid=762 0264: dt=36.288000, rms=0.539 (0.065%), neg=0, invalid=762 0265: dt=36.288000, rms=0.539 (0.066%), neg=0, invalid=762 0266: dt=36.288000, rms=0.538 (0.059%), neg=0, invalid=762 0267: dt=36.288000, rms=0.538 (0.057%), neg=0, invalid=762 0268: dt=36.288000, rms=0.538 (0.061%), neg=0, invalid=762 0269: dt=36.288000, rms=0.537 (0.048%), neg=0, invalid=762 0270: dt=36.288000, rms=0.537 (0.047%), neg=0, invalid=762 0271: dt=36.288000, rms=0.537 (0.046%), neg=0, invalid=762 0272: dt=36.288000, rms=0.537 (0.044%), neg=0, invalid=762 0273: dt=36.288000, rms=0.536 (0.044%), neg=0, invalid=762 0274: dt=36.288000, rms=0.536 (0.047%), neg=0, invalid=762 0275: dt=36.288000, rms=0.536 (0.046%), neg=0, invalid=762 0276: dt=36.288000, rms=0.536 (0.044%), neg=0, invalid=762 0277: dt=36.288000, rms=0.535 (0.042%), neg=0, invalid=762 0278: dt=36.288000, rms=0.535 (0.039%), neg=0, invalid=762 0279: dt=36.288000, rms=0.535 (0.040%), neg=0, invalid=762 0280: dt=36.288000, rms=0.535 (0.038%), neg=0, invalid=762 0281: dt=36.288000, rms=0.535 (0.036%), neg=0, invalid=762 0282: dt=36.288000, rms=0.534 (0.036%), neg=0, invalid=762 0283: dt=36.288000, rms=0.534 (0.037%), neg=0, invalid=762 0284: dt=36.288000, rms=0.534 (0.036%), neg=0, invalid=762 0285: dt=36.288000, rms=0.534 (0.003%), neg=0, invalid=762 0286: dt=18.144000, rms=0.534 (0.003%), neg=0, invalid=762 0287: dt=2.268000, rms=0.534 (-0.001%), neg=0, invalid=762 0288: dt=2.268000, rms=0.534 (0.000%), neg=0, invalid=762 0289: dt=0.567000, rms=0.534 (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=0.542, neg=0, invalid=762 0290: dt=0.031250, rms=0.541 (0.056%), neg=0, invalid=762 0291: dt=0.002734, rms=0.541 (0.000%), neg=0, invalid=762 0292: dt=0.000684, rms=0.541 (0.000%), neg=0, invalid=762 0293: dt=0.000342, rms=0.541 (0.000%), neg=0, invalid=762 0294: dt=0.000171, rms=0.541 (0.000%), neg=0, invalid=762 0295: dt=0.000000, rms=0.541 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0296: dt=92.402367, rms=0.536 (1.110%), neg=0, invalid=762 0297: dt=11.200000, rms=0.534 (0.360%), neg=0, invalid=762 0298: dt=11.200000, rms=0.532 (0.245%), neg=0, invalid=762 0299: dt=2.800000, rms=0.532 (0.051%), neg=0, invalid=762 0300: dt=2.000000, rms=0.532 (0.035%), neg=0, invalid=762 0301: dt=0.125000, rms=0.532 (0.003%), neg=0, invalid=762 0302: dt=0.031250, rms=0.532 (0.001%), neg=0, invalid=762 0303: dt=0.000488, rms=0.532 (0.000%), neg=0, invalid=762 0304: dt=0.000000, rms=0.532 (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=0.550, neg=0, invalid=762 0305: dt=11.520000, rms=0.539 (1.909%), neg=0, invalid=762 0306: dt=0.252000, rms=0.539 (0.028%), neg=0, invalid=762 0307: dt=0.126000, rms=0.539 (0.013%), neg=0, invalid=762 0308: dt=0.063000, rms=0.539 (0.007%), neg=0, invalid=762 0309: dt=0.015750, rms=0.539 (0.001%), neg=0, invalid=762 0310: dt=0.003938, rms=0.539 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0311: dt=0.000630, rms=0.539 (0.051%), neg=0, invalid=762 0312: dt=0.000000, rms=0.539 (0.000%), neg=0, invalid=762 0313: dt=0.000018, rms=0.539 (0.000%), neg=0, invalid=762 0314: dt=0.000009, rms=0.539 (0.000%), neg=0, invalid=762 0315: dt=0.000001, rms=0.539 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.569, neg=0, invalid=762 0316: dt=1.888889, rms=0.567 (0.427%), neg=0, invalid=762 0317: dt=1.792000, rms=0.566 (0.104%), neg=0, invalid=762 0318: dt=1.280000, rms=0.566 (0.018%), neg=0, invalid=762 0319: dt=1.280000, rms=0.566 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=762 0320: dt=5.120000, rms=0.562 (0.773%), neg=0, invalid=762 0321: dt=0.448000, rms=0.562 (0.003%), neg=0, invalid=762 0322: dt=0.448000, rms=0.562 (0.002%), neg=0, invalid=762 0323: dt=0.448000, rms=0.562 (-0.001%), 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=0.536, neg=0, invalid=762 0324: dt=0.448000, rms=0.519 (3.103%), neg=0, invalid=762 0325: dt=0.448000, rms=0.514 (0.921%), neg=0, invalid=762 0326: dt=0.448000, rms=0.512 (0.539%), neg=0, invalid=762 0327: dt=0.448000, rms=0.510 (0.351%), neg=0, invalid=762 0328: dt=0.448000, rms=0.508 (0.265%), neg=0, invalid=762 0329: dt=0.448000, rms=0.507 (0.198%), neg=0, invalid=762 0330: dt=0.448000, rms=0.507 (0.163%), neg=0, invalid=762 0331: dt=0.448000, rms=0.506 (0.127%), neg=0, invalid=762 0332: dt=0.448000, rms=0.505 (0.112%), neg=0, invalid=762 0333: dt=0.448000, rms=0.505 (0.088%), neg=0, invalid=762 0334: dt=0.448000, rms=0.505 (0.083%), neg=0, invalid=762 0335: dt=0.448000, rms=0.504 (0.063%), neg=0, invalid=762 0336: dt=0.448000, rms=0.504 (0.062%), neg=0, invalid=762 0337: dt=0.448000, rms=0.504 (0.048%), neg=0, invalid=762 0338: dt=0.448000, rms=0.503 (0.049%), neg=0, invalid=762 0339: dt=0.448000, rms=0.503 (0.080%), neg=0, invalid=762 0340: dt=0.448000, rms=0.502 (0.098%), neg=0, invalid=762 0341: dt=0.448000, rms=0.502 (0.108%), neg=0, invalid=762 0342: dt=0.448000, rms=0.501 (0.105%), neg=0, invalid=762 0343: dt=0.448000, rms=0.501 (0.085%), neg=0, invalid=762 0344: dt=0.448000, rms=0.501 (0.062%), neg=0, invalid=762 0345: dt=0.448000, rms=0.500 (0.043%), neg=0, invalid=762 0346: dt=0.448000, rms=0.500 (-0.011%), neg=0, invalid=762 0347: dt=0.000004, rms=0.500 (0.000%), neg=0, invalid=762 0348: dt=0.000000, rms=0.500 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.501, neg=0, invalid=762 0349: dt=0.448000, rms=0.496 (0.931%), neg=0, invalid=762 0350: dt=0.448000, rms=0.496 (0.068%), neg=0, invalid=762 0351: dt=0.448000, rms=0.496 (0.011%), neg=0, invalid=762 0352: dt=0.448000, rms=0.496 (-0.011%), 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=0.493, neg=0, invalid=762 0353: dt=0.000000, rms=0.493 (0.064%), neg=0, invalid=762 0354: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0355: dt=129.472000, rms=0.492 (0.203%), neg=0, invalid=762 0356: dt=32.368000, rms=0.492 (0.004%), neg=0, invalid=762 0357: dt=32.368000, rms=0.492 (0.004%), neg=0, invalid=762 0358: dt=32.368000, rms=0.492 (0.007%), neg=0, invalid=762 0359: dt=32.368000, rms=0.492 (0.010%), neg=0, invalid=762 0360: dt=32.368000, rms=0.492 (0.017%), neg=0, invalid=762 0361: dt=32.368000, rms=0.492 (0.023%), neg=0, invalid=762 0362: dt=32.368000, rms=0.491 (0.024%), neg=0, invalid=762 0363: dt=32.368000, rms=0.491 (0.022%), neg=0, invalid=762 0364: dt=32.368000, rms=0.491 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.492, neg=0, invalid=762 0365: dt=9.072000, rms=0.491 (0.073%), neg=0, invalid=762 0366: dt=6.480000, rms=0.491 (0.005%), neg=0, invalid=762 0367: dt=6.480000, rms=0.491 (0.001%), neg=0, invalid=762 0368: dt=6.480000, rms=0.491 (-0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0369: dt=145.152000, rms=0.488 (0.722%), neg=0, invalid=762 0370: dt=36.288000, rms=0.487 (0.132%), neg=0, invalid=762 0371: dt=36.288000, rms=0.487 (0.083%), neg=0, invalid=762 0372: dt=36.288000, rms=0.486 (0.132%), neg=0, invalid=762 0373: dt=36.288000, rms=0.485 (0.179%), neg=0, invalid=762 0374: dt=36.288000, rms=0.484 (0.192%), neg=0, invalid=762 0375: dt=36.288000, rms=0.483 (0.205%), neg=0, invalid=762 0376: dt=36.288000, rms=0.483 (0.179%), neg=0, invalid=762 0377: dt=36.288000, rms=0.482 (0.161%), neg=0, invalid=762 0378: dt=36.288000, rms=0.481 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0379: dt=36.288000, rms=0.481 (0.119%), neg=0, invalid=762 0380: dt=36.288000, rms=0.480 (0.114%), neg=0, invalid=762 0381: dt=145.152000, rms=0.480 (0.068%), neg=0, invalid=762 0382: dt=145.152000, rms=0.480 (-0.139%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.481, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0383: dt=28.909657, rms=0.478 (0.464%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0384: dt=58.053097, rms=0.476 (0.529%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0385: dt=30.036810, rms=0.474 (0.397%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0386: dt=32.000000, rms=0.472 (0.357%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0387: dt=24.205128, rms=0.471 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0388: dt=24.205128, rms=0.470 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0389: dt=24.205128, rms=0.469 (0.249%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0390: dt=24.205128, rms=0.468 (0.305%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0391: dt=24.205128, rms=0.467 (0.264%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 3 iterations, nbhd size=0, neg = 0 0392: dt=24.205128, rms=0.465 (0.305%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 14 iterations, nbhd size=1, neg = 0 0393: dt=24.205128, rms=0.464 (0.219%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 11 iterations, nbhd size=1, neg = 0 0394: dt=24.205128, rms=0.463 (0.194%), neg=0, invalid=762 iter 0, gcam->neg = 34 after 10 iterations, nbhd size=0, neg = 0 0395: dt=24.205128, rms=0.463 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 13 iterations, nbhd size=1, neg = 0 0396: dt=24.205128, rms=0.462 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 9 iterations, nbhd size=0, neg = 0 0397: dt=24.205128, rms=0.461 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 21 iterations, nbhd size=1, neg = 0 0398: dt=24.205128, rms=0.461 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 20 iterations, nbhd size=1, neg = 0 0399: dt=24.205128, rms=0.461 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=0, neg = 0 0400: dt=25.600000, rms=0.460 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0401: dt=25.600000, rms=0.460 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 9 iterations, nbhd size=1, neg = 0 0402: dt=25.600000, rms=0.460 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0403: dt=25.600000, rms=0.459 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0404: dt=25.600000, rms=0.459 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0405: dt=25.600000, rms=0.459 (0.032%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0406: dt=48.744186, rms=0.454 (1.015%), neg=0, invalid=762 0407: dt=11.200000, rms=0.453 (0.303%), neg=0, invalid=762 0408: dt=44.800000, rms=0.452 (0.232%), neg=0, invalid=762 0409: dt=44.800000, rms=0.452 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0410: dt=4.032000, rms=0.463 (0.194%), neg=0, invalid=762 0411: dt=2.304000, rms=0.463 (0.020%), neg=0, invalid=762 0412: dt=2.304000, rms=0.463 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=762 0413: dt=8.583333, rms=0.461 (0.412%), neg=0, invalid=762 0414: dt=11.506849, rms=0.460 (0.216%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0415: dt=11.506849, rms=0.459 (0.221%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0416: dt=11.506849, rms=0.459 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 0417: dt=11.506849, rms=0.458 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=0, neg = 0 0418: dt=11.506849, rms=0.456 (0.410%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0419: dt=11.506849, rms=0.453 (0.685%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0420: dt=11.506849, rms=0.450 (0.728%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0421: dt=11.506849, rms=0.447 (0.480%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 0422: dt=11.506849, rms=0.447 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 5 iterations, nbhd size=0, neg = 0 0423: dt=11.506849, rms=0.447 (-0.147%), neg=0, invalid=762 0424: dt=0.000703, rms=0.447 (0.000%), neg=0, invalid=762 0425: dt=0.000000, rms=0.447 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0426: dt=0.000000, rms=0.455 (0.075%), neg=0, invalid=762 0427: dt=0.000000, rms=0.455 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0428: dt=0.000000, rms=0.455 (0.075%), neg=0, invalid=762 0429: dt=0.000000, rms=0.455 (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=0.442, neg=0, invalid=762 iter 0, gcam->neg = 1022 after 13 iterations, nbhd size=1, neg = 0 0430: dt=1.920892, rms=0.414 (6.222%), neg=0, invalid=762 0431: dt=0.000013, rms=0.414 (0.009%), neg=0, invalid=762 0432: dt=0.000013, rms=0.414 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0433: dt=0.028000, rms=0.414 (0.111%), neg=0, invalid=762 0434: dt=0.020000, rms=0.414 (0.001%), neg=0, invalid=762 0435: dt=0.020000, rms=0.414 (-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=0.402, neg=0, invalid=762 0436: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=762 0437: dt=0.000000, rms=0.402 (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=0.402, neg=0, invalid=762 0438: dt=0.025312, rms=0.402 (0.000%), neg=0, invalid=762 0439: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=762 0440: dt=15.552000, rms=0.402 (0.011%), neg=0, invalid=762 0441: dt=9.072000, rms=0.402 (0.002%), neg=0, invalid=762 0442: dt=9.072000, rms=0.402 (0.001%), neg=0, invalid=762 0443: dt=9.072000, rms=0.402 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.402, neg=0, invalid=762 0444: dt=9.600000, rms=0.402 (0.086%), neg=0, invalid=762 0445: dt=2.800000, rms=0.402 (0.010%), neg=0, invalid=762 0446: dt=2.800000, rms=0.402 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0447: dt=2.800000, rms=0.402 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=762 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0448: dt=68.622222, rms=0.399 (0.623%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 4 iterations, nbhd size=0, neg = 0 0449: dt=30.222222, rms=0.398 (0.303%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 2 iterations, nbhd size=0, neg = 0 0450: dt=32.000000, rms=0.398 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0451: dt=32.000000, rms=0.397 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 7 iterations, nbhd size=0, neg = 0 0452: dt=32.000000, rms=0.397 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 20 iterations, nbhd size=1, neg = 0 0453: dt=32.000000, rms=0.396 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 11 iterations, nbhd size=1, neg = 0 0454: dt=32.000000, rms=0.396 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 44 after 21 iterations, nbhd size=1, neg = 0 0455: dt=32.000000, rms=0.396 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0456: dt=38.400000, rms=0.395 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0457: dt=38.400000, rms=0.395 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 17 iterations, nbhd size=2, neg = 0 0458: dt=38.400000, rms=0.395 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0459: dt=38.400000, rms=0.394 (0.070%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 14 iterations, nbhd size=1, neg = 0 0460: dt=38.400000, rms=0.394 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0461: dt=38.400000, rms=0.394 (0.075%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 0462: dt=1.000000, rms=0.398 (0.003%), neg=0, invalid=762 0463: dt=0.144000, rms=0.398 (0.000%), neg=0, invalid=762 0464: dt=0.144000, rms=0.398 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0465: dt=9.000000, rms=0.397 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=0, neg = 0 0466: dt=15.733333, rms=0.397 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0467: dt=15.733333, rms=0.397 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 6 iterations, nbhd size=0, neg = 0 0468: dt=15.733333, rms=0.396 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 58 after 13 iterations, nbhd size=1, neg = 0 0469: dt=15.733333, rms=0.395 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 49 after 16 iterations, nbhd size=1, neg = 0 0470: dt=15.733333, rms=0.395 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 86 after 10 iterations, nbhd size=0, neg = 0 0471: dt=15.733333, rms=0.394 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 126 after 18 iterations, nbhd size=1, neg = 0 0472: dt=15.733333, rms=0.394 (0.090%), neg=0, invalid=762 iter 0, gcam->neg = 150 after 17 iterations, nbhd size=0, neg = 0 0473: dt=15.733333, rms=0.394 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0474: dt=4.032000, rms=0.394 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 17 iterations, nbhd size=1, neg = 0 0475: dt=4.032000, rms=0.394 (-0.024%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.400, neg=0, invalid=762 0476: dt=0.000050, rms=0.400 (0.000%), neg=0, invalid=762 0477: dt=0.000000, 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 0478: dt=0.000000, rms=0.400 (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=0.389, neg=0, invalid=762 iter 0, gcam->neg = 717 after 21 iterations, nbhd size=1, neg = 0 0479: dt=1.063975, rms=0.381 (2.095%), neg=0, invalid=762 0480: dt=0.000023, rms=0.381 (0.000%), neg=0, invalid=762 0481: dt=0.000023, rms=0.381 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.381, neg=0, invalid=762 0482: dt=0.096000, rms=0.381 (0.042%), neg=0, invalid=762 0483: dt=0.080000, rms=0.381 (0.017%), neg=0, invalid=762 0484: dt=0.080000, rms=0.381 (0.012%), neg=0, invalid=762 0485: dt=0.080000, rms=0.381 (-0.009%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 29 minutes and 17 seconds. mri_ca_register utimesec 12546.060000 mri_ca_register stimesec 11.240000 mri_ca_register ru_maxrss 1336176 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5440541 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62696 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 54 mri_ca_register ru_nivcsw 15536 FSRUNTIME@ mri_ca_register 3.4881 hours 1 threads #-------------------------------------- #@# SubCort Seg Sat Jun 2 13:38:19 EDT 2018 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/jianfeng/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 setenv SUBJECTS_DIR /home/jianfeng/freesurfer/subjects cd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/jianfeng/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/jianfeng/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 5.82 Atlas used for the 3D morph was /home/jianfeng/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 = 0.15303 (25) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1794 voxels, overlap=0.718) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1794 voxels, peak = 22), gca=22.5 gca peak = 0.17677 (13) mri peak = 0.16083 (24) Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (1297 voxels, overlap=0.314) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1297 voxels, peak = 23), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.14096 (97) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (603 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (603 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.11716 (104) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (596 voxels, overlap=0.752) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (596 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.11527 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (918 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (918 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.09619 (67) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (545 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (545 voxels, peak = 68), gca=67.6 gca peak = 0.07580 (103) mri peak = 0.07414 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32911 voxels, overlap=0.822) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32911 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.08344 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (24421 voxels, overlap=0.659) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (24421 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.03783 (77) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (23450 voxels, overlap=0.020) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (23450 voxels, peak = 75), gca=75.1 gca peak = 0.11620 (58) mri peak = 0.03779 (71) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (22417 voxels, overlap=0.174) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (22417 voxels, peak = 71), gca=71.1 gca peak = 0.30970 (66) mri peak = 0.17607 (79) Right_Caudate (50): linear fit = 1.17 x + 0.0 (727 voxels, overlap=0.016) Right_Caudate (50): linear fit = 1.17 x + 0.0 (727 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.11780 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (778 voxels, overlap=0.572) Left_Caudate (11): linear fit = 1.05 x + 0.0 (778 voxels, peak = 73), gca=72.8 gca peak = 0.13902 (56) mri peak = 0.04612 (63) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (20291 voxels, overlap=0.864) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (20291 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.05354 (68) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (22721 voxels, overlap=0.439) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (22721 voxels, peak = 66), gca=65.7 gca peak = 0.16765 (84) mri peak = 0.10315 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5245 voxels, overlap=0.238) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5245 voxels, peak = 93), gca=92.8 gca peak = 0.18739 (84) mri peak = 0.14589 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5422 voxels, overlap=0.326) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5422 voxels, peak = 90), gca=90.3 gca peak = 0.29869 (57) mri peak = 0.17578 (74) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (256 voxels, overlap=0.044) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (256 voxels, peak = 73), gca=73.2 gca peak = 0.33601 (57) mri peak = 0.15108 (70) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (410 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (410 voxels, peak = 70), gca=70.4 gca peak = 0.11131 (90) mri peak = 0.06538 (92) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (3214 voxels, overlap=0.667) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (3214 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.09958 (91) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3825 voxels, overlap=0.497) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3825 voxels, peak = 90), gca=90.1 gca peak = 0.08324 (81) mri peak = 0.10456 (85) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1565 voxels, overlap=0.499) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1565 voxels, peak = 88), gca=87.9 gca peak = 0.10360 (77) mri peak = 0.11677 (80) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2080 voxels, overlap=0.696) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2080 voxels, peak = 79), gca=78.9 gca peak = 0.08424 (78) mri peak = 0.08675 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9968 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9968 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.08581 (100) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1236 voxels, overlap=0.013) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1236 voxels, peak = 103), gca=102.8 gca peak = 0.14500 (87) mri peak = 0.08722 (98) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1035 voxels, overlap=0.476) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1035 voxels, peak = 97), gca=97.0 gca peak = 0.14975 (24) mri peak = 0.21359 (34) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (180 voxels, overlap=0.294) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (180 voxels, peak = 31), gca=30.6 gca peak = 0.19357 (14) mri peak = 0.21884 (20) Fourth_Ventricle (15): linear fit = 1.35 x + 0.0 (228 voxels, overlap=0.456) Fourth_Ventricle (15): linear fit = 1.35 x + 0.0 (228 voxels, peak = 19), gca=18.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) 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 1.24 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 Left_Pallidum too bright - rescaling by 0.978 (from 1.075) to 100.9 (was 103.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13944 (23) mri peak = 0.15303 (25) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (1794 voxels, overlap=0.857) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (1794 voxels, peak = 24), gca=24.5 gca peak = 0.13422 (19) mri peak = 0.16083 (24) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (1297 voxels, overlap=0.615) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (1297 voxels, peak = 22), gca=21.6 gca peak = 0.25604 (97) mri peak = 0.14096 (97) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (603 voxels, overlap=0.978) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (603 voxels, peak = 96), gca=95.5 gca peak = 0.14686 (100) mri peak = 0.11716 (104) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (596 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (596 voxels, peak = 102), gca=101.5 gca peak = 0.25435 (68) mri peak = 0.11527 (70) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (918 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (918 voxels, peak = 69), gca=69.0 gca peak = 0.22336 (68) mri peak = 0.09619 (67) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (545 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (545 voxels, peak = 72), gca=71.7 gca peak = 0.07841 (102) mri peak = 0.07414 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32911 voxels, overlap=0.804) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32911 voxels, peak = 102), gca=102.0 gca peak = 0.07854 (106) mri peak = 0.08344 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (24421 voxels, overlap=0.724) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (24421 voxels, peak = 106), gca=106.0 gca peak = 0.07489 (75) mri peak = 0.03783 (77) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (23450 voxels, overlap=0.935) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (23450 voxels, peak = 75), gca=75.0 gca peak = 0.09436 (71) mri peak = 0.03779 (71) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (22417 voxels, overlap=0.951) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (22417 voxels, peak = 73), gca=73.5 gca peak = 0.23086 (78) mri peak = 0.17607 (79) Right_Caudate (50): linear fit = 0.99 x + 0.0 (727 voxels, overlap=0.999) Right_Caudate (50): linear fit = 0.99 x + 0.0 (727 voxels, peak = 77), gca=76.8 gca peak = 0.15199 (72) mri peak = 0.11780 (79) Left_Caudate (11): linear fit = 1.02 x + 0.0 (778 voxels, overlap=0.840) Left_Caudate (11): linear fit = 1.02 x + 0.0 (778 voxels, peak = 74), gca=73.8 gca peak = 0.12459 (63) mri peak = 0.04612 (63) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20291 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20291 voxels, peak = 62), gca=62.1 gca peak = 0.12171 (66) mri peak = 0.05354 (68) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22721 voxels, overlap=0.962) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22721 voxels, peak = 65), gca=65.0 gca peak = 0.14173 (93) mri peak = 0.10315 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5245 voxels, overlap=0.938) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5245 voxels, peak = 93), gca=92.5 gca peak = 0.14841 (90) mri peak = 0.14589 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5422 voxels, overlap=0.858) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5422 voxels, peak = 90), gca=89.6 gca peak = 0.27832 (73) mri peak = 0.17578 (74) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (256 voxels, overlap=1.003) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (256 voxels, peak = 73), gca=73.0 gca peak = 0.33489 (70) mri peak = 0.15108 (70) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (410 voxels, overlap=0.997) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (410 voxels, peak = 70), gca=70.0 gca peak = 0.10126 (97) mri peak = 0.06538 (92) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3214 voxels, overlap=0.954) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3214 voxels, peak = 94), gca=93.6 gca peak = 0.10535 (90) mri peak = 0.09958 (91) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3825 voxels, overlap=0.890) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3825 voxels, peak = 90), gca=89.6 gca peak = 0.08289 (88) mri peak = 0.10456 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1565 voxels, overlap=0.824) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1565 voxels, peak = 88), gca=88.0 gca peak = 0.10149 (79) mri peak = 0.11677 (80) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2080 voxels, overlap=0.779) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2080 voxels, peak = 79), gca=79.0 gca peak = 0.08004 (86) mri peak = 0.08675 (83) Brain_Stem (16): linear fit = 0.96 x + 0.0 (9968 voxels, overlap=0.767) Brain_Stem (16): linear fit = 0.96 x + 0.0 (9968 voxels, peak = 83), gca=83.0 gca peak = 0.10477 (102) mri peak = 0.08581 (100) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1236 voxels, overlap=0.801) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1236 voxels, peak = 102), gca=102.0 gca peak = 0.14588 (95) mri peak = 0.08722 (98) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1035 voxels, overlap=0.931) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1035 voxels, peak = 95), gca=95.5 gca peak = 0.16783 (33) mri peak = 0.21359 (34) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (180 voxels, overlap=0.768) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (180 voxels, peak = 32), gca=31.5 gca peak = 0.15119 (20) mri peak = 0.21884 (20) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (228 voxels, overlap=0.633) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (228 voxels, peak = 19), gca=18.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17958 (37) gca peak Left_Thalamus = 0.64095 (103) gca peak CSF = 0.17638 (48) gca peak Left_Accumbens_area = 0.57343 (66) gca peak Left_undetermined = 0.96707 (27) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.20093 (28) gca peak Right_Accumbens_area = 0.31167 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14509 (37) gca peak Fifth_Ventricle = 0.86987 (41) gca peak WM_hypointensities = 0.08505 (76) gca peak non_WM_hypointensities = 0.07977 (77) gca peak Optic_Chiasm = 0.51752 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 Left_Pallidum too bright - rescaling by 0.994 (from 1.015) to 100.9 (was 101.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 53837 voxels changed in iteration 0 of unlikely voxel relabeling 287 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 54793 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 270 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 57861 changed. image ll: -2.069, PF=0.500 pass 2: 15627 changed. image ll: -2.069, PF=0.500 pass 3: 4618 changed. 52870 voxels changed in iteration 0 of unlikely voxel relabeling 454 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5973 voxels changed in iteration 0 of unlikely voxel relabeling 67 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 4884 voxels changed in iteration 0 of unlikely voxel relabeling 44 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4505 voxels changed in iteration 0 of unlikely voxel relabeling 15 voxels changed in iteration 1 of unlikely voxel relabeling 1 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 4329.392000 mri_ca_label stimesec 1.488000 mri_ca_label ru_maxrss 2096992 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 694076 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 424 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 81 mri_ca_label ru_nivcsw 1846 auto-labeling took 72 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/transforms/cc_up.lta He_Aiqun_ReoT1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/transforms/cc_up.lta reading aseg from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aseg.auto_noCCseg.mgz reading norm from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/norm.mgz 14094 voxels in left wm, 19226 in right wm, xrange [127, 132] searching rotation angles z=[-6 8], y=[-7 7] searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 global minimum found at slice 129.6, rotations (0.39, 0.66) final transformation (x=129.6, yr=0.391, zr=0.662): 0.99991 -0.01155 0.00682 -1.39508; 0.01155 0.99993 0.00008 40.49928; -0.00682 0.00000 0.99998 7.88651; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 86 121 eigenvectors: 0.00033 -0.00725 0.99997; 0.15038 -0.98860 -0.00721; 0.98863 0.15038 0.00076; writing aseg with callosum to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Sat Jun 2 14:51:10 EDT 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Jun 2 14:51:10 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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... 188 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 80 (80), valley at 33 (33) csf peak at 40, setting threshold to 66 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 78 (78), valley at 32 (32) csf peak at 39, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 5 minutes and 16 seconds. #-------------------------------------------- #@# Mask BFS Sat Jun 2 14:56:30 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1319802 voxels in mask (pct= 7.87) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Jun 2 14:56:32 EDT 2018 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 (102.0): 102.4 +- 6.6 [79.0 --> 125.0] GM (75.0) : 72.8 +- 11.0 [30.0 --> 95.0] setting bottom of white matter range to 83.8 setting top of gray matter range to 94.7 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... 2849 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2345 filled 521 bright non-wm voxels segmented. 1598 diagonally connected voxels added... white matter segmentation took 2.2 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 0.74 minutes reading wm segmentation from wm.seg.mgz... 7 voxels added to wm to prevent paths from MTL structures to cortex 2738 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35208 voxels turned on, 35659 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 15 found - 15 modified | TOTAL: 22 pass 2 (xy-): 0 found - 15 modified | TOTAL: 22 pass 1 (yz+): 25 found - 25 modified | TOTAL: 47 pass 2 (yz+): 0 found - 25 modified | TOTAL: 47 pass 1 (yz-): 10 found - 10 modified | TOTAL: 57 pass 2 (yz-): 0 found - 10 modified | TOTAL: 57 pass 1 (xz+): 10 found - 10 modified | TOTAL: 67 pass 2 (xz+): 0 found - 10 modified | TOTAL: 67 pass 1 (xz-): 5 found - 5 modified | TOTAL: 72 pass 2 (xz-): 0 found - 5 modified | TOTAL: 72 Iteration Number : 1 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 (+++): 8 found - 8 modified | TOTAL: 14 pass 2 (+++): 0 found - 8 modified | TOTAL: 14 pass 1 (+++): 10 found - 10 modified | TOTAL: 24 pass 2 (+++): 0 found - 10 modified | TOTAL: 24 Iteration Number : 1 pass 1 (++): 55 found - 55 modified | TOTAL: 55 pass 2 (++): 0 found - 55 modified | TOTAL: 55 pass 1 (+-): 55 found - 55 modified | TOTAL: 110 pass 2 (+-): 0 found - 55 modified | TOTAL: 110 pass 1 (--): 46 found - 46 modified | TOTAL: 156 pass 2 (--): 0 found - 46 modified | TOTAL: 156 pass 1 (-+): 50 found - 50 modified | TOTAL: 206 pass 2 (-+): 0 found - 50 modified | TOTAL: 206 Iteration Number : 2 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+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 2 found - 2 modified | TOTAL: 10 pass 2 (xz-): 0 found - 2 modified | TOTAL: 10 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 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 = 315 (out of 479359: 0.065713) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Jun 2 14:59:32 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30092; -0.00808 0.00626 1.11665 -27.94269; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05497 0.00964 0.00978 -11.45190; -0.00860 1.16635 -0.01162 3.30092; -0.00808 0.00626 1.11665 -27.94269; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1199 (min = 350, max = 1400), aspect = 0.57 (min = 0.10, max = 0.75) no need to search using seed (126, 104, 113), TAL = (2.0, -15.0, 24.0) talairach voxel to voxel transform 0.94776 -0.00779 -0.00838 10.64522; 0.00705 0.85727 0.00886 -2.50137; 0.00682 -0.00486 0.89542 25.11471; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 104, 113) --> (2.0, -15.0, 24.0) done. writing output to filled.mgz... filling took 1.2 minutes talairach cc position changed to (2.00, -15.00, 24.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -15.00, 24.00) SRC: (111.25, 88.42, 126.53) search lh wm seed point around talairach space (-16.00, -15.00, 24.00), SRC: (145.37, 88.67, 126.77) 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 Sat Jun 2 15:00:43 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 2 found - 2 modified | TOTAL: 7 pass 2 (xz-): 0 found - 2 modified | TOTAL: 7 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 (-+): 2 found - 2 modified | TOTAL: 2 pass 2 (-+): 0 found - 2 modified | TOTAL: 2 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 = 9 (out of 226531: 0.003973) 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: 791 vertices, 877 faces slice 60: 5323 vertices, 5486 faces slice 70: 12001 vertices, 12245 faces slice 80: 19927 vertices, 20233 faces slice 90: 28529 vertices, 28864 faces slice 100: 38638 vertices, 39026 faces slice 110: 50232 vertices, 50622 faces slice 120: 61986 vertices, 62367 faces slice 130: 73059 vertices, 73456 faces slice 140: 83402 vertices, 83773 faces slice 150: 92773 vertices, 93084 faces slice 160: 100251 vertices, 100557 faces slice 170: 107644 vertices, 107912 faces slice 180: 113890 vertices, 114142 faces slice 190: 118761 vertices, 118961 faces slice 200: 120786 vertices, 120840 faces slice 210: 120786 vertices, 120840 faces slice 220: 120786 vertices, 120840 faces slice 230: 120786 vertices, 120840 faces slice 240: 120786 vertices, 120840 faces slice 250: 120786 vertices, 120840 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... 120786 voxel in cpt #1: X=-54 [v=120786,e=362520,f=241680] located at (-28.454548, -9.117116, 32.856548) For the whole surface: X=-54 [v=120786,e=362520,f=241680] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Jun 2 15:00:51 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 6 found - 6 modified | TOTAL: 7 pass 2 (yz+): 0 found - 6 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 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 = 13 (out of 237793: 0.005467) 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: 399 vertices, 446 faces slice 60: 3982 vertices, 4194 faces slice 70: 11199 vertices, 11434 faces slice 80: 19931 vertices, 20268 faces slice 90: 31017 vertices, 31410 faces slice 100: 41380 vertices, 41754 faces slice 110: 53700 vertices, 54128 faces slice 120: 65181 vertices, 65577 faces slice 130: 76590 vertices, 76969 faces slice 140: 86841 vertices, 87196 faces slice 150: 95962 vertices, 96278 faces slice 160: 103803 vertices, 104098 faces slice 170: 111024 vertices, 111295 faces slice 180: 117408 vertices, 117639 faces slice 190: 122529 vertices, 122751 faces slice 200: 124963 vertices, 125025 faces slice 210: 125012 vertices, 125056 faces slice 220: 125012 vertices, 125056 faces slice 230: 125012 vertices, 125056 faces slice 240: 125012 vertices, 125056 faces slice 250: 125012 vertices, 125056 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... 125012 voxel in cpt #1: X=-44 [v=125012,e=375168,f=250112] located at (26.781422, -9.276870, 33.295418) For the whole surface: X=-44 [v=125012,e=375168,f=250112] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Jun 2 15:00:59 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Sat Jun 2 15:01:06 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Sat Jun 2 15:01:12 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 43.6 mm, total surface area = 63928 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.047 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.044 (target=0.015) step 060: RMS=0.044 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 39.000000 mris_inflate stimesec 0.072000 mris_inflate ru_maxrss 159456 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19424 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8504 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 25 #-------------------------------------------- #@# Inflation1 rh Sat Jun 2 15:01:51 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.0 mm, total surface area = 66674 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 40.116000 mris_inflate stimesec 0.064000 mris_inflate ru_maxrss 164592 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 20239 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8800 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 56 #-------------------------------------------- #@# QSphere lh Sat Jun 2 15:02:32 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 1.05 +- 0.59 (0.00-->8.11) (max @ vno 40500 --> 41568) face area 0.03 +- 0.03 (-0.06-->1.11) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.329... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.073, avgs=0 005/300: dt: 0.9000, rms radial error=176.813, avgs=0 010/300: dt: 0.9000, rms radial error=176.253, avgs=0 015/300: dt: 0.9000, rms radial error=175.517, avgs=0 020/300: dt: 0.9000, rms radial error=174.678, avgs=0 025/300: dt: 0.9000, rms radial error=173.781, avgs=0 030/300: dt: 0.9000, rms radial error=172.852, avgs=0 035/300: dt: 0.9000, rms radial error=171.904, avgs=0 040/300: dt: 0.9000, rms radial error=170.951, avgs=0 045/300: dt: 0.9000, rms radial error=169.995, avgs=0 050/300: dt: 0.9000, rms radial error=169.040, avgs=0 055/300: dt: 0.9000, rms radial error=168.089, avgs=0 060/300: dt: 0.9000, rms radial error=167.145, avgs=0 065/300: dt: 0.9000, rms radial error=166.206, avgs=0 070/300: dt: 0.9000, rms radial error=165.271, avgs=0 075/300: dt: 0.9000, rms radial error=164.341, avgs=0 080/300: dt: 0.9000, rms radial error=163.415, avgs=0 085/300: dt: 0.9000, rms radial error=162.495, avgs=0 090/300: dt: 0.9000, rms radial error=161.579, avgs=0 095/300: dt: 0.9000, rms radial error=160.668, avgs=0 100/300: dt: 0.9000, rms radial error=159.763, avgs=0 105/300: dt: 0.9000, rms radial error=158.863, avgs=0 110/300: dt: 0.9000, rms radial error=157.967, avgs=0 115/300: dt: 0.9000, rms radial error=157.076, avgs=0 120/300: dt: 0.9000, rms radial error=156.191, avgs=0 125/300: dt: 0.9000, rms radial error=155.310, avgs=0 130/300: dt: 0.9000, rms radial error=154.434, avgs=0 135/300: dt: 0.9000, rms radial error=153.563, avgs=0 140/300: dt: 0.9000, rms radial error=152.697, avgs=0 145/300: dt: 0.9000, rms radial error=151.835, avgs=0 150/300: dt: 0.9000, rms radial error=150.978, avgs=0 155/300: dt: 0.9000, rms radial error=150.127, avgs=0 160/300: dt: 0.9000, rms radial error=149.282, avgs=0 165/300: dt: 0.9000, rms radial error=148.442, avgs=0 170/300: dt: 0.9000, rms radial error=147.606, avgs=0 175/300: dt: 0.9000, rms radial error=146.775, avgs=0 180/300: dt: 0.9000, rms radial error=145.948, avgs=0 185/300: dt: 0.9000, rms radial error=145.126, avgs=0 190/300: dt: 0.9000, rms radial error=144.309, avgs=0 195/300: dt: 0.9000, rms radial error=143.496, avgs=0 200/300: dt: 0.9000, rms radial error=142.688, avgs=0 205/300: dt: 0.9000, rms radial error=141.884, avgs=0 210/300: dt: 0.9000, rms radial error=141.084, avgs=0 215/300: dt: 0.9000, rms radial error=140.289, avgs=0 220/300: dt: 0.9000, rms radial error=139.499, avgs=0 225/300: dt: 0.9000, rms radial error=138.713, avgs=0 230/300: dt: 0.9000, rms radial error=137.931, avgs=0 235/300: dt: 0.9000, rms radial error=137.153, avgs=0 240/300: dt: 0.9000, rms radial error=136.380, avgs=0 245/300: dt: 0.9000, rms radial error=135.611, avgs=0 250/300: dt: 0.9000, rms radial error=134.847, avgs=0 255/300: dt: 0.9000, rms radial error=134.086, avgs=0 260/300: dt: 0.9000, rms radial error=133.330, avgs=0 265/300: dt: 0.9000, rms radial error=132.579, avgs=0 270/300: dt: 0.9000, rms radial error=131.831, avgs=0 275/300: dt: 0.9000, rms radial error=131.088, avgs=0 280/300: dt: 0.9000, rms radial error=130.348, avgs=0 285/300: dt: 0.9000, rms radial error=129.613, avgs=0 290/300: dt: 0.9000, rms radial error=128.882, avgs=0 295/300: dt: 0.9000, rms radial error=128.155, avgs=0 300/300: dt: 0.9000, rms radial error=127.433, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13825.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2196.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 3 (K=160.0), pass 1, starting sse = 211.53 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00747 epoch 4 (K=640.0), pass 1, starting sse = 13.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/13 = 0.00823 final distance error %24.77 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 257.100000 mris_sphere stimesec 0.036000 mris_sphere ru_maxrss 159680 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19438 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8504 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 119 FSRUNTIME@ mris_sphere 0.0714 hours 1 threads #-------------------------------------------- #@# QSphere rh Sat Jun 2 15:06:49 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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-->7.06) (max @ vno 92247 --> 92264) face area 0.03 +- 0.03 (-0.12-->0.77) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.332... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.407, avgs=0 005/300: dt: 0.9000, rms radial error=176.149, avgs=0 010/300: dt: 0.9000, rms radial error=175.593, avgs=0 015/300: dt: 0.9000, rms radial error=174.864, avgs=0 020/300: dt: 0.9000, rms radial error=174.033, avgs=0 025/300: dt: 0.9000, rms radial error=173.143, avgs=0 030/300: dt: 0.9000, rms radial error=172.221, avgs=0 035/300: dt: 0.9000, rms radial error=171.282, avgs=0 040/300: dt: 0.9000, rms radial error=170.334, avgs=0 045/300: dt: 0.9000, rms radial error=169.384, avgs=0 050/300: dt: 0.9000, rms radial error=168.434, avgs=0 055/300: dt: 0.9000, rms radial error=167.487, avgs=0 060/300: dt: 0.9000, rms radial error=166.546, avgs=0 065/300: dt: 0.9000, rms radial error=165.610, avgs=0 070/300: dt: 0.9000, rms radial error=164.680, avgs=0 075/300: dt: 0.9000, rms radial error=163.754, avgs=0 080/300: dt: 0.9000, rms radial error=162.834, avgs=0 085/300: dt: 0.9000, rms radial error=161.918, avgs=0 090/300: dt: 0.9000, rms radial error=161.007, avgs=0 095/300: dt: 0.9000, rms radial error=160.101, avgs=0 100/300: dt: 0.9000, rms radial error=159.199, avgs=0 105/300: dt: 0.9000, rms radial error=158.303, avgs=0 110/300: dt: 0.9000, rms radial error=157.411, avgs=0 115/300: dt: 0.9000, rms radial error=156.525, avgs=0 120/300: dt: 0.9000, rms radial error=155.643, avgs=0 125/300: dt: 0.9000, rms radial error=154.766, avgs=0 130/300: dt: 0.9000, rms radial error=153.893, avgs=0 135/300: dt: 0.9000, rms radial error=153.026, avgs=0 140/300: dt: 0.9000, rms radial error=152.163, avgs=0 145/300: dt: 0.9000, rms radial error=151.305, avgs=0 150/300: dt: 0.9000, rms radial error=150.452, avgs=0 155/300: dt: 0.9000, rms radial error=149.603, avgs=0 160/300: dt: 0.9000, rms radial error=148.759, avgs=0 165/300: dt: 0.9000, rms radial error=147.920, avgs=0 170/300: dt: 0.9000, rms radial error=147.086, avgs=0 175/300: dt: 0.9000, rms radial error=146.257, avgs=0 180/300: dt: 0.9000, rms radial error=145.432, avgs=0 185/300: dt: 0.9000, rms radial error=144.612, avgs=0 190/300: dt: 0.9000, rms radial error=143.796, avgs=0 195/300: dt: 0.9000, rms radial error=142.985, avgs=0 200/300: dt: 0.9000, rms radial error=142.178, avgs=0 205/300: dt: 0.9000, rms radial error=141.376, avgs=0 210/300: dt: 0.9000, rms radial error=140.578, avgs=0 215/300: dt: 0.9000, rms radial error=139.785, avgs=0 220/300: dt: 0.9000, rms radial error=138.996, avgs=0 225/300: dt: 0.9000, rms radial error=138.212, avgs=0 230/300: dt: 0.9000, rms radial error=137.432, avgs=0 235/300: dt: 0.9000, rms radial error=136.656, avgs=0 240/300: dt: 0.9000, rms radial error=135.885, avgs=0 245/300: dt: 0.9000, rms radial error=135.118, avgs=0 250/300: dt: 0.9000, rms radial error=134.355, avgs=0 255/300: dt: 0.9000, rms radial error=133.597, avgs=0 260/300: dt: 0.9000, rms radial error=132.843, avgs=0 265/300: dt: 0.9000, rms radial error=132.093, avgs=0 270/300: dt: 0.9000, rms radial error=131.348, avgs=0 275/300: dt: 0.9000, rms radial error=130.606, avgs=0 280/300: dt: 0.9000, rms radial error=129.869, avgs=0 285/300: dt: 0.9000, rms radial error=129.136, avgs=0 290/300: dt: 0.9000, rms radial error=128.407, avgs=0 295/300: dt: 0.9000, rms radial error=127.682, avgs=0 300/300: dt: 0.9000, rms radial error=126.962, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14240.82 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 = 2237.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 210.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/11 = 0.00904 epoch 4 (K=640.0), pass 1, starting sse = 13.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/13 = 0.00832 final distance error %24.57 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 268.468000 mris_sphere stimesec 0.068000 mris_sphere ru_maxrss 164864 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 20250 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 0 mris_sphere ru_nivcsw 122 FSRUNTIME@ mris_sphere 0.0746 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sat Jun 2 15:11:17 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Jun 2 15:11:17 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Jun 2 15:11:17 EDT 2018 mris_fix_topology -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 He_Aiqun_ReoT1 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=-54 (nv=120786, nf=241680, ne=362520, g=28) 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 9 iterations marking ambiguous vertices... 3971 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 9 31 defects to be corrected 0 vertices coincident reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4803 (-4.7401) -vertex loglikelihood: -6.2389 (-3.1194) -normal dot loglikelihood: -3.5772 (-3.5772) -quad curv loglikelihood: -6.4695 (-3.2348) Total Loglikelihood : -25.7659 CORRECTING DEFECT 0 (vertices=32, convex hull=61, v0=335) After retessellation of defect 0 (v0=335), euler #=-27 (118401,354325,235897) : difference with theory (-28) = -1 CORRECTING DEFECT 1 (vertices=15, convex hull=24, v0=4925) After retessellation of defect 1 (v0=4925), euler #=-26 (118403,354340,235911) : difference with theory (-27) = -1 CORRECTING DEFECT 2 (vertices=128, convex hull=109, v0=6512) After retessellation of defect 2 (v0=6512), euler #=-25 (118444,354505,236036) : difference with theory (-26) = -1 CORRECTING DEFECT 3 (vertices=52, convex hull=57, v0=9501) After retessellation of defect 3 (v0=9501), euler #=-24 (118453,354556,236079) : difference with theory (-25) = -1 CORRECTING DEFECT 4 (vertices=30, convex hull=66, v0=11515) After retessellation of defect 4 (v0=11515), euler #=-23 (118471,354635,236141) : difference with theory (-24) = -1 CORRECTING DEFECT 5 (vertices=75, convex hull=47, v0=11729) After retessellation of defect 5 (v0=11729), euler #=-22 (118482,354684,236180) : difference with theory (-23) = -1 CORRECTING DEFECT 6 (vertices=75, convex hull=41, v0=16091) After retessellation of defect 6 (v0=16091), euler #=-21 (118488,354717,236208) : difference with theory (-22) = -1 CORRECTING DEFECT 7 (vertices=62, convex hull=105, v0=22786) After retessellation of defect 7 (v0=22786), euler #=-20 (118532,354895,236343) : difference with theory (-21) = -1 CORRECTING DEFECT 8 (vertices=143, convex hull=165, v0=24731) After retessellation of defect 8 (v0=24731), euler #=-18 (118617,355223,236588) : difference with theory (-20) = -2 CORRECTING DEFECT 9 (vertices=19, convex hull=43, v0=25001) After retessellation of defect 9 (v0=25001), euler #=-17 (118627,355268,236624) : difference with theory (-19) = -2 CORRECTING DEFECT 10 (vertices=33, convex hull=67, v0=30356) After retessellation of defect 10 (v0=30356), euler #=-16 (118650,355363,236697) : difference with theory (-18) = -2 CORRECTING DEFECT 11 (vertices=35, convex hull=73, v0=40775) After retessellation of defect 11 (v0=40775), euler #=-15 (118667,355444,236762) : difference with theory (-17) = -2 CORRECTING DEFECT 12 (vertices=57, convex hull=47, v0=46075) After retessellation of defect 12 (v0=46075), euler #=-14 (118679,355495,236802) : difference with theory (-16) = -2 CORRECTING DEFECT 13 (vertices=72, convex hull=61, v0=62405) After retessellation of defect 13 (v0=62405), euler #=-13 (118703,355591,236875) : difference with theory (-15) = -2 CORRECTING DEFECT 14 (vertices=268, convex hull=58, v0=67106) After retessellation of defect 14 (v0=67106), euler #=-12 (118720,355670,236938) : difference with theory (-14) = -2 CORRECTING DEFECT 15 (vertices=32, convex hull=56, v0=74959) After retessellation of defect 15 (v0=74959), euler #=-11 (118729,355719,236979) : difference with theory (-13) = -2 CORRECTING DEFECT 16 (vertices=520, convex hull=318, v0=78942) After retessellation of defect 16 (v0=78942), euler #=-11 (118924,356482,237547) : difference with theory (-12) = -1 CORRECTING DEFECT 17 (vertices=32, convex hull=50, v0=80255) After retessellation of defect 17 (v0=80255), euler #=-10 (118940,356550,237600) : difference with theory (-11) = -1 CORRECTING DEFECT 18 (vertices=26, convex hull=55, v0=82617) After retessellation of defect 18 (v0=82617), euler #=-9 (118949,356596,237638) : difference with theory (-10) = -1 CORRECTING DEFECT 19 (vertices=109, convex hull=73, v0=84164) After retessellation of defect 19 (v0=84164), euler #=-8 (118956,356653,237689) : difference with theory (-9) = -1 CORRECTING DEFECT 20 (vertices=8, convex hull=35, v0=87041) After retessellation of defect 20 (v0=87041), euler #=-7 (118958,356671,237706) : difference with theory (-8) = -1 CORRECTING DEFECT 21 (vertices=34, convex hull=60, v0=87080) After retessellation of defect 21 (v0=87080), euler #=-6 (118967,356725,237752) : difference with theory (-7) = -1 CORRECTING DEFECT 22 (vertices=27, convex hull=54, v0=92050) After retessellation of defect 22 (v0=92050), euler #=-5 (118978,356779,237796) : difference with theory (-6) = -1 CORRECTING DEFECT 23 (vertices=49, convex hull=57, v0=94132) After retessellation of defect 23 (v0=94132), euler #=-5 (118987,356838,237846) : difference with theory (-5) = 0 CORRECTING DEFECT 24 (vertices=6, convex hull=28, v0=96551) After retessellation of defect 24 (v0=96551), euler #=-4 (118988,356848,237856) : difference with theory (-4) = 0 CORRECTING DEFECT 25 (vertices=7, convex hull=21, v0=99824) After retessellation of defect 25 (v0=99824), euler #=-3 (118991,356866,237872) : difference with theory (-3) = 0 CORRECTING DEFECT 26 (vertices=53, convex hull=29, v0=110240) After retessellation of defect 26 (v0=110240), euler #=-2 (118997,356894,237895) : difference with theory (-2) = 0 CORRECTING DEFECT 27 (vertices=286, convex hull=74, v0=110249) After retessellation of defect 27 (v0=110249), euler #=-1 (119028,357022,237993) : difference with theory (-1) = 0 CORRECTING DEFECT 28 (vertices=18, convex hull=20, v0=113659) After retessellation of defect 28 (v0=113659), euler #=0 (119029,357027,237998) : difference with theory (0) = 0 CORRECTING DEFECT 29 (vertices=23, convex hull=34, v0=113772) After retessellation of defect 29 (v0=113772), euler #=1 (119036,357060,238025) : difference with theory (1) = 0 CORRECTING DEFECT 30 (vertices=74, convex hull=98, v0=117816) After retessellation of defect 30 (v0=117816), euler #=2 (119067,357195,238130) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.04-->9.94) (max @ vno 82889 --> 88665) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.04-->9.94) (max @ vno 82889 --> 88665) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 112 mutations (38.0%), 183 crossovers (62.0%), 48 vertices were eliminated building final representation... 1719 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119067, nf=238130, ne=357195, g=0) writing corrected surface to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 18.7 minutes 0 defective edges removing intersecting faces 000: 170 intersecting 001: 5 intersecting mris_fix_topology utimesec 1124.144000 mris_fix_topology stimesec 0.136000 mris_fix_topology ru_maxrss 387436 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 48367 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 11208 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 6 mris_fix_topology ru_nivcsw 487 FSRUNTIME@ mris_fix_topology lh 0.3123 hours 1 threads #@# Fix Topology rh Sat Jun 2 15:30:02 EDT 2018 mris_fix_topology -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 He_Aiqun_ReoT1 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=-44 (nv=125012, nf=250112, ne=375168, g=23) 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 8 iterations marking ambiguous vertices... 4105 ambiguous faces found in tessellation segmenting defects... 31 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 31 defects to be corrected 0 vertices coincident reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2717 (-4.6358) -vertex loglikelihood: -6.1745 (-3.0872) -normal dot loglikelihood: -3.6596 (-3.6596) -quad curv loglikelihood: -6.5151 (-3.2575) Total Loglikelihood : -25.6208 CORRECTING DEFECT 0 (vertices=17, convex hull=58, v0=1512) After retessellation of defect 0 (v0=1512), euler #=-28 (122529,366560,244003) : difference with theory (-28) = 0 CORRECTING DEFECT 1 (vertices=71, convex hull=139, v0=6846) After retessellation of defect 1 (v0=6846), euler #=-27 (122575,366759,244157) : difference with theory (-27) = 0 CORRECTING DEFECT 2 (vertices=24, convex hull=67, v0=8626) After retessellation of defect 2 (v0=8626), euler #=-26 (122588,366822,244208) : difference with theory (-26) = 0 CORRECTING DEFECT 3 (vertices=19, convex hull=69, v0=18844) After retessellation of defect 3 (v0=18844), euler #=-25 (122600,366886,244261) : difference with theory (-25) = 0 CORRECTING DEFECT 4 (vertices=97, convex hull=103, v0=32085) After retessellation of defect 4 (v0=32085), euler #=-24 (122636,367035,244375) : difference with theory (-24) = 0 CORRECTING DEFECT 5 (vertices=9, convex hull=27, v0=36863) After retessellation of defect 5 (v0=36863), euler #=-23 (122636,367044,244385) : difference with theory (-23) = 0 CORRECTING DEFECT 6 (vertices=61, convex hull=29, v0=38286) After retessellation of defect 6 (v0=38286), euler #=-22 (122638,367060,244400) : difference with theory (-22) = 0 CORRECTING DEFECT 7 (vertices=33, convex hull=39, v0=43781) After retessellation of defect 7 (v0=43781), euler #=-21 (122642,367086,244423) : difference with theory (-21) = 0 CORRECTING DEFECT 8 (vertices=14, convex hull=23, v0=45974) After retessellation of defect 8 (v0=45974), euler #=-20 (122643,367099,244436) : difference with theory (-20) = 0 CORRECTING DEFECT 9 (vertices=26, convex hull=34, v0=50497) After retessellation of defect 9 (v0=50497), euler #=-19 (122650,367133,244464) : difference with theory (-19) = 0 CORRECTING DEFECT 10 (vertices=378, convex hull=372, v0=50662) After retessellation of defect 10 (v0=50662), euler #=-18 (122735,367565,244812) : difference with theory (-18) = 0 CORRECTING DEFECT 11 (vertices=245, convex hull=202, v0=58229) After retessellation of defect 11 (v0=58229), euler #=-17 (122800,367859,245042) : difference with theory (-17) = 0 CORRECTING DEFECT 12 (vertices=28, convex hull=63, v0=64449) After retessellation of defect 12 (v0=64449), euler #=-16 (122808,367909,245085) : difference with theory (-16) = 0 CORRECTING DEFECT 13 (vertices=27, convex hull=65, v0=72492) After retessellation of defect 13 (v0=72492), euler #=-15 (122822,367976,245139) : difference with theory (-15) = 0 CORRECTING DEFECT 14 (vertices=145, convex hull=70, v0=72973) After retessellation of defect 14 (v0=72973), euler #=-14 (122845,368075,245216) : difference with theory (-14) = 0 CORRECTING DEFECT 15 (vertices=27, convex hull=47, v0=74121) After retessellation of defect 15 (v0=74121), euler #=-13 (122851,368113,245249) : difference with theory (-13) = 0 CORRECTING DEFECT 16 (vertices=147, convex hull=136, v0=76557) After retessellation of defect 16 (v0=76557), euler #=-12 (122878,368256,245366) : difference with theory (-12) = 0 CORRECTING DEFECT 17 (vertices=112, convex hull=46, v0=78054) After retessellation of defect 17 (v0=78054), euler #=-11 (122894,368319,245414) : difference with theory (-11) = 0 CORRECTING DEFECT 18 (vertices=54, convex hull=49, v0=89546) After retessellation of defect 18 (v0=89546), euler #=-10 (122896,368346,245440) : difference with theory (-10) = 0 CORRECTING DEFECT 19 (vertices=36, convex hull=89, v0=91572) After retessellation of defect 19 (v0=91572), euler #=-9 (122907,368413,245497) : difference with theory (-9) = 0 CORRECTING DEFECT 20 (vertices=202, convex hull=63, v0=94955) After retessellation of defect 20 (v0=94955), euler #=-8 (122926,368493,245559) : difference with theory (-8) = 0 CORRECTING DEFECT 21 (vertices=99, convex hull=109, v0=95717) After retessellation of defect 21 (v0=95717), euler #=-7 (122958,368637,245672) : difference with theory (-7) = 0 CORRECTING DEFECT 22 (vertices=21, convex hull=33, v0=96643) After retessellation of defect 22 (v0=96643), euler #=-6 (122961,368662,245695) : difference with theory (-6) = 0 CORRECTING DEFECT 23 (vertices=49, convex hull=98, v0=103949) After retessellation of defect 23 (v0=103949), euler #=-5 (122996,368809,245808) : difference with theory (-5) = 0 CORRECTING DEFECT 24 (vertices=9, convex hull=18, v0=105777) After retessellation of defect 24 (v0=105777), euler #=-4 (122997,368818,245817) : difference with theory (-4) = 0 CORRECTING DEFECT 25 (vertices=45, convex hull=68, v0=109672) After retessellation of defect 25 (v0=109672), euler #=-3 (123010,368884,245871) : difference with theory (-3) = 0 CORRECTING DEFECT 26 (vertices=36, convex hull=67, v0=112433) After retessellation of defect 26 (v0=112433), euler #=-2 (123023,368949,245924) : difference with theory (-2) = 0 CORRECTING DEFECT 27 (vertices=377, convex hull=134, v0=113045) After retessellation of defect 27 (v0=113045), euler #=-1 (123072,369158,246085) : difference with theory (-1) = 0 CORRECTING DEFECT 28 (vertices=29, convex hull=26, v0=118448) After retessellation of defect 28 (v0=118448), euler #=0 (123075,369178,246103) : difference with theory (0) = 0 CORRECTING DEFECT 29 (vertices=24, convex hull=32, v0=121541) After retessellation of defect 29 (v0=121541), euler #=1 (123079,369200,246122) : difference with theory (1) = 0 CORRECTING DEFECT 30 (vertices=30, convex hull=74, v0=122902) After retessellation of defect 30 (v0=122902), euler #=2 (123097,369285,246190) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.11-->9.89) (max @ vno 120070 --> 124712) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.11-->9.89) (max @ vno 120070 --> 124712) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 107 mutations (34.5%), 203 crossovers (65.5%), 217 vertices were eliminated building final representation... 1915 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=123097, nf=246190, ne=369285, g=0) writing corrected surface to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 23.1 minutes 0 defective edges removing intersecting faces 000: 258 intersecting 001: 2 intersecting mris_fix_topology utimesec 1384.780000 mris_fix_topology stimesec 0.160000 mris_fix_topology ru_maxrss 397372 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 48817 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 11616 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 0 mris_fix_topology ru_nivcsw 795 FSRUNTIME@ mris_fix_topology rh 0.3847 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 119067 - 357195 + 238130 = 2 --> 0 holes F =2V-4: 238130 = 238134-4 (0) 2E=3F: 714390 = 714390 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 123097 - 369285 + 246190 = 2 --> 0 holes F =2V-4: 246190 = 246194-4 (0) 2E=3F: 738570 = 738570 (0) total defect index = 0 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 25 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 22 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Jun 2 15:53:17 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/filled.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/brain.finalsurfs.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/../mri/aseg.presurf.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... 18090 bright wm thresholded. 667 bright non-wm voxels segmented. reading original surface position from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.orig... computing class statistics... border white: 226209 voxels (1.35%) border gray 252885 voxels (1.51%) WM (98.0): 98.9 +- 7.2 [70.0 --> 110.0] GM (78.0) : 76.0 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.5 (was 70) setting MAX_BORDER_WHITE to 109.2 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 51.0 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->5.33) (max @ vno 78893 --> 118832) face area 0.28 +- 0.12 (0.00-->5.77) mean absolute distance = 0.82 +- 1.04 3512 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=102+-6.1, GM=74+-8.7 mean inside = 95.0, mean outside = 79.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=83.8, 97 (97) missing vertices, mean dist 0.3 [0.8 (%33.7)->0.9 (%66.3))] %46 local maxima, %50 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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 0.92 +- 0.26 (0.07-->7.21) (max @ vno 118832 --> 118836) face area 0.28 +- 0.13 (0.00-->4.56) mean absolute distance = 0.48 +- 0.82 4561 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2325669.8, rms=8.963 001: dt: 0.5000, sse=1453974.9, rms=6.555 (26.861%) 002: dt: 0.5000, sse=1054123.8, rms=5.024 (23.365%) 003: dt: 0.5000, sse=832103.8, rms=3.963 (21.113%) 004: dt: 0.5000, sse=712866.8, rms=3.255 (17.859%) 005: dt: 0.5000, sse=655737.8, rms=2.824 (13.250%) 006: dt: 0.5000, sse=629200.1, rms=2.599 (7.972%) 007: dt: 0.5000, sse=618724.6, rms=2.500 (3.782%) 008: dt: 0.5000, sse=611985.0, rms=2.438 (2.494%) rms = 2.43, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=610174.2, rms=2.425 (0.517%) 010: dt: 0.2500, sse=539448.1, rms=1.539 (36.562%) 011: dt: 0.2500, sse=532062.7, rms=1.394 (9.415%) rms = 1.35, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=527996.1, rms=1.350 (3.165%) 013: dt: 0.1250, sse=524626.0, rms=1.279 (5.207%) rms = 1.27, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=521908.1, rms=1.265 (1.094%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.2, 85 (28) missing vertices, mean dist -0.3 [0.6 (%66.5)->0.3 (%33.5))] %57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Preci, 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 0.90 +- 0.25 (0.11-->6.49) (max @ vno 118832 --> 118836) face area 0.35 +- 0.16 (0.00-->6.12) mean absolute distance = 0.39 +- 0.52 4336 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=978283.7, rms=4.058 015: dt: 0.5000, sse=778083.3, rms=2.747 (32.303%) 016: dt: 0.5000, sse=722975.4, rms=2.297 (16.408%) 017: dt: 0.5000, sse=702780.3, rms=2.154 (6.206%) rms = 2.14, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=703872.2, rms=2.139 (0.688%) 019: dt: 0.2500, sse=650483.6, rms=1.436 (32.874%) 020: dt: 0.2500, sse=638095.8, rms=1.267 (11.756%) rms = 1.24, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=637549.9, rms=1.240 (2.129%) 022: dt: 0.1250, sse=631714.5, rms=1.153 (6.992%) rms = 1.14, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=630906.2, rms=1.138 (1.376%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.1, 62 (6) missing vertices, mean dist -0.3 [0.4 (%75.3)->0.2 (%24.7))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Preci, 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 +- 0.25 (0.09-->6.10) (max @ vno 118832 --> 118836) face area 0.33 +- 0.16 (0.00-->5.89) mean absolute distance = 0.26 +- 0.39 3422 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=922142.7, rms=3.904 024: dt: 0.5000, sse=713804.3, rms=2.349 (39.813%) 025: dt: 0.5000, sse=671615.1, rms=1.982 (15.657%) rms = 1.97, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=680444.4, rms=1.970 (0.559%) 027: dt: 0.2500, sse=615492.6, rms=1.205 (38.831%) 028: dt: 0.2500, sse=625593.2, rms=1.109 (7.954%) rms = 1.12, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=610704.7, rms=1.065 (3.997%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.1, 50 (6) missing vertices, mean dist -0.1 [0.3 (%61.4)->0.2 (%38.6))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Preci, 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=644957.1, rms=1.830 030: dt: 0.5000, sse=632153.9, rms=1.472 (19.543%) rms = 1.71, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=594913.8, rms=1.044 (29.119%) rms = 1.03, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=596763.9, rms=1.027 (1.542%) 033: dt: 0.1250, sse=580612.2, rms=0.841 (18.106%) rms = 0.81, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=577616.2, rms=0.809 (3.872%) positioning took 0.7 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6437 vertices erasing segment 0 (vno[0] = 24902) erasing segment 2 (vno[0] = 51149) erasing segment 3 (vno[0] = 70279) erasing segment 4 (vno[0] = 72483) erasing segment 5 (vno[0] = 83732) erasing segment 6 (vno[0] = 84695) erasing segment 7 (vno[0] = 86695) erasing segment 8 (vno[0] = 86714) erasing segment 9 (vno[0] = 86758) erasing segment 10 (vno[0] = 87708) writing cortex label to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label... writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.area vertex spacing 0.88 +- 0.25 (0.04-->6.22) (max @ vno 118832 --> 118836) face area 0.33 +- 0.16 (0.00-->6.00) refinement took 6.0 minutes #-------------------------------------------- #@# Make White Surf rh Sat Jun 2 15:59:18 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/filled.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/brain.finalsurfs.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/../mri/aseg.presurf.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... 18090 bright wm thresholded. 667 bright non-wm voxels segmented. reading original surface position from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.orig... computing class statistics... border white: 226209 voxels (1.35%) border gray 252885 voxels (1.51%) WM (98.0): 98.9 +- 7.2 [70.0 --> 110.0] GM (78.0) : 76.0 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.5 (was 70) setting MAX_BORDER_WHITE to 109.2 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.0 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.05-->6.00) (max @ vno 123062 --> 123067) face area 0.28 +- 0.12 (0.00-->3.43) mean absolute distance = 0.80 +- 1.01 3512 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=102+-6.1, GM=75+-7.8 mean inside = 95.5, mean outside = 80.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.3, 58 (58) missing vertices, mean dist 0.3 [0.7 (%34.5)->0.8 (%65.5))] %47 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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 0.92 +- 0.25 (0.08-->5.57) (max @ vno 123062 --> 123067) face area 0.28 +- 0.13 (0.00-->3.46) mean absolute distance = 0.45 +- 0.78 4472 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2328613.2, rms=8.785 001: dt: 0.5000, sse=1373869.9, rms=6.104 (30.519%) 002: dt: 0.5000, sse=949452.3, rms=4.403 (27.859%) 003: dt: 0.5000, sse=761190.1, rms=3.381 (23.226%) 004: dt: 0.5000, sse=681405.9, rms=2.813 (16.781%) 005: dt: 0.5000, sse=646401.8, rms=2.550 (9.365%) 006: dt: 0.5000, sse=637743.1, rms=2.432 (4.609%) rms = 2.39, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=630102.1, rms=2.387 (1.872%) 008: dt: 0.2500, sse=559634.8, rms=1.516 (36.490%) 009: dt: 0.2500, sse=548152.8, rms=1.348 (11.085%) rms = 1.31, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=545675.1, rms=1.307 (3.020%) rms = 1.27, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=543768.5, rms=1.270 (2.843%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.7, 40 (10) missing vertices, mean dist -0.3 [0.6 (%66.9)->0.3 (%33.1))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Preci, 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 0.90 +- 0.24 (0.04-->5.31) (max @ vno 123062 --> 123067) face area 0.35 +- 0.16 (0.00-->4.62) mean absolute distance = 0.36 +- 0.50 3441 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1010505.2, rms=4.062 012: dt: 0.5000, sse=788150.8, rms=2.679 (34.038%) 013: dt: 0.5000, sse=739581.4, rms=2.282 (14.837%) 014: dt: 0.5000, sse=717952.1, rms=2.095 (8.205%) rms = 2.15, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=679944.1, rms=1.594 (23.910%) 016: dt: 0.2500, sse=661011.6, rms=1.312 (17.699%) 017: dt: 0.2500, sse=654435.8, rms=1.205 (8.154%) 018: dt: 0.2500, sse=653724.4, rms=1.154 (4.178%) rms = 1.12, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=650206.6, rms=1.121 (2.903%) rms = 1.09, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=648598.7, rms=1.093 (2.517%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.4, 36 (1) missing vertices, mean dist -0.2 [0.4 (%74.4)->0.2 (%25.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Preci, 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 +- 0.25 (0.05-->5.17) (max @ vno 123062 --> 123067) face area 0.33 +- 0.16 (0.00-->4.14) mean absolute distance = 0.26 +- 0.40 2854 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=912241.9, rms=3.678 021: dt: 0.5000, sse=703954.6, rms=2.118 (42.398%) 022: dt: 0.5000, sse=691850.4, rms=1.912 (9.732%) rms = 1.92, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=643161.0, rms=1.380 (27.851%) 024: dt: 0.2500, sse=627407.8, rms=1.077 (21.960%) rms = 1.03, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=626400.8, rms=1.028 (4.557%) rms = 0.99, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=620970.1, rms=0.988 (3.893%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=90.4, 56 (1) missing vertices, mean dist -0.1 [0.3 (%61.8)->0.2 (%38.2))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Preci, 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=655256.7, rms=1.750 027: dt: 0.5000, sse=626672.4, rms=1.246 (28.802%) rms = 1.54, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=605545.0, rms=0.918 (26.299%) 029: dt: 0.2500, sse=603319.9, rms=0.857 (6.704%) rms = 0.81, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=603057.9, rms=0.808 (5.648%) rms = 0.79, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=603172.6, rms=0.787 (2.675%) positioning took 0.7 minutes generating cortex label... 6 non-cortical segments detected only using segment with 6963 vertices erasing segment 1 (vno[0] = 61304) erasing segment 2 (vno[0] = 86926) erasing segment 3 (vno[0] = 88897) erasing segment 4 (vno[0] = 90712) erasing segment 5 (vno[0] = 95797) writing cortex label to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label... writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.area vertex spacing 0.88 +- 0.25 (0.04-->5.09) (max @ vno 123062 --> 123067) face area 0.33 +- 0.16 (0.00-->3.76) refinement took 5.9 minutes #-------------------------------------------- #@# Smooth2 lh Sat Jun 2 16:05:14 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Sat Jun 2 16:05:20 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Sat Jun 2 16:05:26 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_inflate -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.5 mm, total surface area = 70210 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 38.300000 mris_inflate stimesec 0.052000 mris_inflate ru_maxrss 157280 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19417 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9320 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 44 #-------------------------------------------- #@# Inflation2 rh Sat Jun 2 16:06:05 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_inflate -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.1 mm, total surface area = 72818 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.172 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 39.900000 mris_inflate stimesec 0.060000 mris_inflate ru_maxrss 162472 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19647 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9632 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 32 #-------------------------------------------- #@# Curv .H and .K lh Sat Jun 2 16:06:45 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf mris_curvature -w lh.white.preaparc total integrated curvature = 11.534*4pi (144.936) --> -11 handles ICI = 138.5, FI = 1468.2, variation=22884.987 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 135 vertices thresholded to be in k1 ~ [-0.33 4.35], k2 ~ [-0.29 0.13] total integrated curvature = 0.438*4pi (5.498) --> 1 handles ICI = 1.4, FI = 8.8, variation=153.256 127 vertices thresholded to be in [-0.11 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 80 vertices thresholded to be in [-0.18 0.88] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.025 done. #-------------------------------------------- #@# Curv .H and .K rh Sat Jun 2 16:08:24 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf mris_curvature -w rh.white.preaparc total integrated curvature = 11.786*4pi (148.108) --> -11 handles ICI = 140.4, FI = 1499.2, variation=23324.481 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 146 vertices thresholded to be in k1 ~ [-0.31 1.89], k2 ~ [-0.16 0.13] total integrated curvature = 0.453*4pi (5.694) --> 1 handles ICI = 1.4, FI = 8.3, variation=147.485 101 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 83 vertices thresholded to be in [-0.16 0.41] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Sat Jun 2 16:10:05 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm He_Aiqun_ReoT1 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 [ He_Aiqun_ReoT1/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 [ 191 ] Gb_filter = 0 WARN: S lookup min: -0.151324 WARN: S explicit min: 0.000000 vertex = 599 #----------------------------------------- #@# Curvature Stats rh Sat Jun 2 16:10:09 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm He_Aiqun_ReoT1 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 [ He_Aiqun_ReoT1/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 [ 221 ] Gb_filter = 0 WARN: S lookup min: -0.482806 WARN: S explicit min: 0.000000 vertex = 408 #-------------------------------------------- #@# Sphere lh Sat Jun 2 16:10:13 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_sphere -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 0.311... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=Preci, 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 %20.06 pass 1: epoch 2 of 3 starting distance error %20.02 unfolding complete - removing small folds... starting distance error %19.93 removing remaining folds... final distance error %19.96 MRISunfold() return, current seed 1234 -01: dt=0.0000, 125 negative triangles 283: dt=0.9900, 125 negative triangles 284: dt=0.9900, 61 negative triangles 285: dt=0.9900, 43 negative triangles 286: dt=0.9900, 33 negative triangles 287: dt=0.9900, 34 negative triangles 288: dt=0.9900, 26 negative triangles 289: dt=0.9900, 31 negative triangles 290: dt=0.9900, 23 negative triangles 291: dt=0.9900, 32 negative triangles 292: dt=0.9900, 32 negative triangles 293: dt=0.9900, 26 negative triangles 294: dt=0.9900, 25 negative triangles 295: dt=0.9900, 24 negative triangles 296: dt=0.9900, 24 negative triangles 297: dt=0.9900, 24 negative triangles 298: dt=0.9900, 23 negative triangles 299: dt=0.9900, 20 negative triangles 300: dt=0.9900, 19 negative triangles 301: dt=0.9900, 20 negative triangles 302: dt=0.9900, 19 negative triangles 303: dt=0.9900, 19 negative triangles 304: dt=0.9900, 17 negative triangles 305: dt=0.9900, 12 negative triangles 306: dt=0.9900, 14 negative triangles 307: dt=0.9900, 15 negative triangles 308: dt=0.9900, 16 negative triangles 309: dt=0.9900, 11 negative triangles 310: dt=0.9900, 15 negative triangles 311: dt=0.9900, 13 negative triangles 312: dt=0.9900, 14 negative triangles 313: dt=0.9900, 15 negative triangles 314: dt=0.9900, 15 negative triangles 315: dt=0.9900, 12 negative triangles 316: dt=0.9900, 18 negative triangles 317: dt=0.9900, 16 negative triangles 318: dt=0.9900, 13 negative triangles 319: dt=0.9405, 14 negative triangles 320: dt=0.9405, 10 negative triangles 321: dt=0.9405, 7 negative triangles 322: dt=0.9405, 13 negative triangles 323: dt=0.9405, 6 negative triangles 324: dt=0.9405, 12 negative triangles 325: dt=0.9405, 8 negative triangles 326: dt=0.9405, 5 negative triangles 327: dt=0.9405, 9 negative triangles 328: dt=0.9405, 9 negative triangles 329: dt=0.9405, 7 negative triangles 330: dt=0.9405, 6 negative triangles 331: dt=0.9405, 5 negative triangles 332: dt=0.9405, 3 negative triangles 333: dt=0.9405, 7 negative triangles 334: dt=0.9405, 1 negative triangles 335: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.07 hours mris_sphere utimesec 3836.992000 mris_sphere stimesec 0.368000 mris_sphere ru_maxrss 215328 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33766 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8384 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 6 mris_sphere ru_nivcsw 1620 FSRUNTIME@ mris_sphere 1.0659 hours 1 threads #-------------------------------------------- #@# Sphere rh Sat Jun 2 17:14:11 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_sphere -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 0.314... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=Preci, 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 %40.84 pass 1: epoch 2 of 3 starting distance error %19.89 unfolding complete - removing small folds... starting distance error %19.71 removing remaining folds... final distance error %19.74 MRISunfold() return, current seed 1234 -01: dt=0.0000, 132 negative triangles 134: dt=0.9900, 132 negative triangles 135: dt=0.9900, 71 negative triangles 136: dt=0.9900, 64 negative triangles 137: dt=0.9900, 57 negative triangles 138: dt=0.9900, 43 negative triangles 139: dt=0.9900, 40 negative triangles 140: dt=0.9900, 37 negative triangles 141: dt=0.9900, 40 negative triangles 142: dt=0.9900, 34 negative triangles 143: dt=0.9900, 30 negative triangles 144: dt=0.9900, 31 negative triangles 145: dt=0.9900, 28 negative triangles 146: dt=0.9900, 25 negative triangles 147: dt=0.9900, 28 negative triangles 148: dt=0.9900, 27 negative triangles 149: dt=0.9900, 29 negative triangles 150: dt=0.9900, 29 negative triangles 151: dt=0.9900, 28 negative triangles 152: dt=0.9900, 30 negative triangles 153: dt=0.9900, 27 negative triangles 154: dt=0.9900, 34 negative triangles 155: dt=0.9900, 31 negative triangles 156: dt=0.9405, 29 negative triangles 157: dt=0.9405, 28 negative triangles 158: dt=0.9405, 26 negative triangles 159: dt=0.9405, 29 negative triangles 160: dt=0.9405, 28 negative triangles 161: dt=0.9405, 28 negative triangles 162: dt=0.9405, 29 negative triangles 163: dt=0.9405, 30 negative triangles 164: dt=0.9405, 33 negative triangles 165: dt=0.9405, 34 negative triangles 166: dt=0.8935, 36 negative triangles 167: dt=0.8935, 36 negative triangles 168: dt=0.8935, 34 negative triangles 169: dt=0.8935, 29 negative triangles 170: dt=0.8935, 29 negative triangles 171: dt=0.8935, 31 negative triangles 172: dt=0.8935, 26 negative triangles 173: dt=0.8935, 24 negative triangles 174: dt=0.8935, 28 negative triangles 175: dt=0.8935, 29 negative triangles 176: dt=0.8935, 26 negative triangles 177: dt=0.8935, 27 negative triangles 178: dt=0.8935, 29 negative triangles 179: dt=0.8935, 29 negative triangles 180: dt=0.8935, 28 negative triangles 181: dt=0.8935, 27 negative triangles 182: dt=0.8935, 28 negative triangles 183: dt=0.8488, 27 negative triangles 184: dt=0.8488, 24 negative triangles 185: dt=0.8488, 29 negative triangles 186: dt=0.8488, 28 negative triangles 187: dt=0.8488, 28 negative triangles 188: dt=0.8488, 29 negative triangles 189: dt=0.8488, 28 negative triangles 190: dt=0.8488, 24 negative triangles 191: dt=0.8488, 26 negative triangles 192: dt=0.8488, 26 negative triangles 193: dt=0.8064, 26 negative triangles 194: dt=0.8064, 29 negative triangles 195: dt=0.8064, 28 negative triangles 196: dt=0.8064, 27 negative triangles 197: dt=0.8064, 26 negative triangles 198: dt=0.8064, 27 negative triangles 199: dt=0.8064, 25 negative triangles 200: dt=0.8064, 22 negative triangles 201: dt=0.8064, 21 negative triangles 202: dt=0.8064, 24 negative triangles 203: dt=0.8064, 21 negative triangles 204: dt=0.8064, 22 negative triangles 205: dt=0.8064, 22 negative triangles 206: dt=0.8064, 19 negative triangles 207: dt=0.8064, 23 negative triangles 208: dt=0.8064, 20 negative triangles 209: dt=0.8064, 20 negative triangles 210: dt=0.8064, 17 negative triangles 211: dt=0.8064, 22 negative triangles 212: dt=0.8064, 21 negative triangles 213: dt=0.8064, 22 negative triangles 214: dt=0.8064, 21 negative triangles 215: dt=0.8064, 21 negative triangles 216: dt=0.8064, 22 negative triangles 217: dt=0.8064, 21 negative triangles 218: dt=0.8064, 23 negative triangles 219: dt=0.8064, 22 negative triangles 220: dt=0.7660, 19 negative triangles 221: dt=0.7660, 14 negative triangles 222: dt=0.7660, 17 negative triangles 223: dt=0.7660, 14 negative triangles 224: dt=0.7660, 15 negative triangles 225: dt=0.7660, 13 negative triangles 226: dt=0.7660, 15 negative triangles 227: dt=0.7660, 15 negative triangles 228: dt=0.7660, 13 negative triangles 229: dt=0.7660, 14 negative triangles 230: dt=0.7660, 10 negative triangles 231: dt=0.7660, 10 negative triangles 232: dt=0.7660, 12 negative triangles 233: dt=0.7660, 8 negative triangles 234: dt=0.7660, 7 negative triangles 235: dt=0.7660, 7 negative triangles 236: dt=0.7660, 7 negative triangles 237: dt=0.7660, 7 negative triangles 238: dt=0.7660, 6 negative triangles 239: dt=0.7660, 9 negative triangles 240: dt=0.7660, 6 negative triangles 241: dt=0.7660, 4 negative triangles 242: dt=0.7660, 6 negative triangles 243: dt=0.7660, 2 negative triangles 244: dt=0.7660, 4 negative triangles 245: dt=0.7660, 2 negative triangles 246: dt=0.7660, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.65 hours mris_sphere utimesec 2329.580000 mris_sphere stimesec 0.272000 mris_sphere ru_maxrss 222112 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 34997 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8664 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 4 mris_sphere ru_nivcsw 1346 FSRUNTIME@ mris_sphere 0.6472 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Sat Jun 2 17:53:01 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_register -curv -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /home/jianfeng/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts cmdline mris_register -curv -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /home/jianfeng/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/jianfeng/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=Preci, 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=Preci, 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 = 5.331 curvature mean = 0.030, std = 0.818 curvature mean = 0.026, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 253452.9, tmin=1.2954 d=32.00 min @ (0.00, -8.00, 0.00) sse = 239138.5, tmin=2.6249 d=16.00 min @ (0.00, 4.00, -4.00) sse = 213398.0, tmin=3.9643 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 212308.3, tmin=6.7334 d=2.00 min @ (0.00, 0.50, 0.00) sse = 212234.9, tmin=8.1281 d=1.00 min @ (0.25, 0.00, -0.25) sse = 212097.5, tmin=9.5098 d=0.50 min @ (0.00, -0.25, 0.12) sse = 212090.5, tmin=10.8870 tol=1.0e+00, sigma=0.5, host=Preci, 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 10.89 min curvature mean = -0.001, std = 0.845 curvature mean = 0.009, std = 0.951 curvature mean = -0.002, std = 0.857 curvature mean = 0.003, std = 0.981 curvature mean = -0.003, std = 0.860 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.036, std = 0.300 curvature mean = 0.036, std = 0.249 curvature mean = 0.071, std = 0.367 curvature mean = 0.031, std = 0.309 curvature mean = 0.036, std = 0.555 curvature mean = 0.030, std = 0.336 curvature mean = 0.019, std = 0.691 curvature mean = 0.030, std = 0.348 curvature mean = 0.008, std = 0.788 MRISregister() return, current seed 0 -01: dt=0.0000, 111 negative triangles 104: dt=0.9900, 111 negative triangles expanding nbhd size to 1 105: dt=0.9900, 129 negative triangles 106: dt=0.9900, 120 negative triangles 107: dt=0.9900, 112 negative triangles 108: dt=0.9900, 116 negative triangles 109: dt=0.9900, 116 negative triangles 110: dt=0.9405, 111 negative triangles 111: dt=0.9405, 109 negative triangles 112: dt=0.9405, 112 negative triangles 113: dt=0.9405, 108 negative triangles 114: dt=0.9405, 104 negative triangles 115: dt=0.9405, 105 negative triangles 116: dt=0.9405, 103 negative triangles 117: dt=0.9405, 97 negative triangles 118: dt=0.9405, 93 negative triangles 119: dt=0.9405, 94 negative triangles 120: dt=0.9405, 94 negative triangles 121: dt=0.9405, 88 negative triangles 122: dt=0.9405, 94 negative triangles 123: dt=0.9405, 87 negative triangles 124: dt=0.9405, 86 negative triangles 125: dt=0.9405, 83 negative triangles 126: dt=0.9405, 83 negative triangles 127: dt=0.9405, 86 negative triangles 128: dt=0.9405, 82 negative triangles 129: dt=0.9405, 85 negative triangles 130: dt=0.9405, 80 negative triangles 131: dt=0.9405, 81 negative triangles 132: dt=0.9405, 83 negative triangles 133: dt=0.9405, 77 negative triangles 134: dt=0.9405, 73 negative triangles 135: dt=0.9405, 80 negative triangles 136: dt=0.9405, 74 negative triangles 137: dt=0.9405, 77 negative triangles 138: dt=0.9405, 71 negative triangles 139: dt=0.9405, 70 negative triangles 140: dt=0.9405, 66 negative triangles 141: dt=0.9405, 73 negative triangles 142: dt=0.9405, 69 negative triangles 143: dt=0.9405, 68 negative triangles 144: dt=0.9405, 73 negative triangles 145: dt=0.9405, 67 negative triangles 146: dt=0.9405, 67 negative triangles 147: dt=0.9405, 68 negative triangles 148: dt=0.9405, 66 negative triangles 149: dt=0.9405, 67 negative triangles 150: dt=0.8935, 66 negative triangles 151: dt=0.8935, 66 negative triangles 152: dt=0.8935, 70 negative triangles 153: dt=0.8935, 64 negative triangles 154: dt=0.8935, 63 negative triangles 155: dt=0.8935, 64 negative triangles 156: dt=0.8935, 65 negative triangles 157: dt=0.8935, 63 negative triangles 158: dt=0.8935, 61 negative triangles 159: dt=0.8935, 61 negative triangles 160: dt=0.8935, 60 negative triangles 161: dt=0.8935, 63 negative triangles 162: dt=0.8935, 61 negative triangles 163: dt=0.8935, 59 negative triangles 164: dt=0.8935, 59 negative triangles 165: dt=0.8935, 56 negative triangles 166: dt=0.8935, 59 negative triangles 167: dt=0.8935, 56 negative triangles 168: dt=0.8935, 60 negative triangles 169: dt=0.8935, 55 negative triangles 170: dt=0.8935, 54 negative triangles 171: dt=0.8935, 55 negative triangles 172: dt=0.8935, 49 negative triangles 173: dt=0.8935, 51 negative triangles 174: dt=0.8935, 51 negative triangles 175: dt=0.8935, 51 negative triangles 176: dt=0.8935, 49 negative triangles 177: dt=0.8935, 52 negative triangles 178: dt=0.8935, 52 negative triangles 179: dt=0.8935, 51 negative triangles 180: dt=0.8935, 49 negative triangles 181: dt=0.8935, 53 negative triangles 182: dt=0.8488, 49 negative triangles 183: dt=0.8488, 49 negative triangles 184: dt=0.8488, 54 negative triangles 185: dt=0.8488, 50 negative triangles 186: dt=0.8488, 50 negative triangles 187: dt=0.8488, 49 negative triangles 188: dt=0.8488, 53 negative triangles 189: dt=0.8488, 51 negative triangles 190: dt=0.8488, 51 negative triangles 191: dt=0.8488, 49 negative triangles 192: dt=0.8064, 51 negative triangles 193: dt=0.8064, 51 negative triangles 194: dt=0.8064, 49 negative triangles 195: dt=0.8064, 48 negative triangles 196: dt=0.8064, 47 negative triangles 197: dt=0.8064, 48 negative triangles 198: dt=0.8064, 46 negative triangles 199: dt=0.8064, 49 negative triangles 200: dt=0.8064, 45 negative triangles 201: dt=0.8064, 46 negative triangles 202: dt=0.8064, 45 negative triangles 203: dt=0.8064, 47 negative triangles 204: dt=0.8064, 44 negative triangles 205: dt=0.8064, 44 negative triangles 206: dt=0.8064, 45 negative triangles 207: dt=0.8064, 43 negative triangles 208: dt=0.8064, 44 negative triangles 209: dt=0.8064, 40 negative triangles 210: dt=0.8064, 39 negative triangles 211: dt=0.8064, 37 negative triangles 212: dt=0.8064, 39 negative triangles 213: dt=0.8064, 36 negative triangles 214: dt=0.8064, 36 negative triangles 215: dt=0.8064, 36 negative triangles 216: dt=0.8064, 35 negative triangles 217: dt=0.8064, 35 negative triangles 218: dt=0.8064, 36 negative triangles 219: dt=0.8064, 35 negative triangles 220: dt=0.8064, 32 negative triangles 221: dt=0.8064, 33 negative triangles 222: dt=0.8064, 31 negative triangles 223: dt=0.8064, 33 negative triangles 224: dt=0.8064, 31 negative triangles 225: dt=0.8064, 30 negative triangles 226: dt=0.8064, 25 negative triangles 227: dt=0.8064, 25 negative triangles 228: dt=0.8064, 28 negative triangles 229: dt=0.8064, 24 negative triangles 230: dt=0.8064, 23 negative triangles 231: dt=0.8064, 22 negative triangles 232: dt=0.8064, 23 negative triangles 233: dt=0.8064, 23 negative triangles 234: dt=0.8064, 21 negative triangles 235: dt=0.8064, 21 negative triangles 236: dt=0.8064, 20 negative triangles 237: dt=0.8064, 21 negative triangles 238: dt=0.8064, 16 negative triangles 239: dt=0.8064, 18 negative triangles 240: dt=0.8064, 17 negative triangles 241: dt=0.8064, 17 negative triangles 242: dt=0.8064, 18 negative triangles 243: dt=0.8064, 15 negative triangles 244: dt=0.8064, 14 negative triangles 245: dt=0.8064, 14 negative triangles 246: dt=0.8064, 14 negative triangles 247: dt=0.8064, 12 negative triangles 248: dt=0.8064, 12 negative triangles 249: dt=0.8064, 12 negative triangles 250: dt=0.8064, 13 negative triangles 251: dt=0.8064, 14 negative triangles 252: dt=0.8064, 12 negative triangles 253: dt=0.8064, 7 negative triangles 254: dt=0.8064, 6 negative triangles 255: dt=0.8064, 6 negative triangles 256: dt=0.8064, 8 negative triangles 257: dt=0.8064, 11 negative triangles 258: dt=0.8064, 4 negative triangles 259: dt=0.8064, 4 negative triangles 260: dt=0.8064, 4 negative triangles 261: dt=0.8064, 4 negative triangles 262: dt=0.8064, 7 negative triangles 263: dt=0.8064, 9 negative triangles 264: dt=0.8064, 6 negative triangles 265: dt=0.8064, 4 negative triangles 266: dt=0.8064, 2 negative triangles 267: dt=0.8064, 2 negative triangles 268: dt=0.8064, 2 negative triangles 269: dt=0.8064, 1 negative triangles 270: dt=0.8064, 1 negative triangles 271: dt=0.8064, 1 negative triangles 272: dt=0.8064, 1 negative triangles 273: dt=0.8064, 1 negative triangles 274: dt=0.8064, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.87 hours mris_register utimesec 3142.912000 mris_register stimesec 0.680000 mris_register ru_maxrss 211536 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 25601 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 8384 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 7 mris_register ru_nivcsw 1170 FSRUNTIME@ mris_register 0.8732 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Sat Jun 2 18:45:24 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_register -curv -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /home/jianfeng/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts cmdline mris_register -curv -rusage /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /home/jianfeng/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/jianfeng/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=Preci, 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=Preci, 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 = 5.425 curvature mean = 0.028, std = 0.814 curvature mean = 0.024, std = 0.871 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 341657.5, tmin=1.3516 d=32.00 min @ (-8.00, 0.00, -8.00) sse = 285944.8, tmin=2.7454 d=16.00 min @ (0.00, 4.00, 0.00) sse = 277952.8, tmin=4.1582 d=8.00 min @ (2.00, 0.00, 0.00) sse = 277773.2, tmin=5.5800 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 276620.1, tmin=7.0089 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 276385.2, tmin=8.4470 d=1.00 min @ (0.25, 0.25, 0.25) sse = 276339.9, tmin=9.8828 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 276327.2, tmin=11.3389 tol=1.0e+00, sigma=0.5, host=Preci, 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 11.34 min curvature mean = -0.008, std = 0.833 curvature mean = 0.009, std = 0.949 curvature mean = -0.014, std = 0.842 curvature mean = 0.003, std = 0.980 curvature mean = -0.016, std = 0.844 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.036, std = 0.291 curvature mean = 0.030, std = 0.241 curvature mean = 0.075, std = 0.368 curvature mean = 0.023, std = 0.302 curvature mean = 0.038, std = 0.558 curvature mean = 0.022, std = 0.329 curvature mean = 0.022, std = 0.693 curvature mean = 0.022, std = 0.341 curvature mean = 0.008, std = 0.794 MRISregister() return, current seed 0 -01: dt=0.0000, 94 negative triangles 109: dt=0.9900, 94 negative triangles 110: dt=0.9405, 116 negative triangles expanding nbhd size to 1 111: dt=0.9900, 106 negative triangles 112: dt=0.9900, 100 negative triangles 113: dt=0.9900, 88 negative triangles 114: dt=0.9900, 88 negative triangles 115: dt=0.9900, 87 negative triangles 116: dt=0.9900, 85 negative triangles 117: dt=0.9900, 88 negative triangles 118: dt=0.9900, 85 negative triangles 119: dt=0.9900, 81 negative triangles 120: dt=0.9900, 78 negative triangles 121: dt=0.9900, 75 negative triangles 122: dt=0.9900, 75 negative triangles 123: dt=0.9900, 77 negative triangles 124: dt=0.9900, 74 negative triangles 125: dt=0.9900, 67 negative triangles 126: dt=0.9900, 65 negative triangles 127: dt=0.9900, 60 negative triangles 128: dt=0.9900, 55 negative triangles 129: dt=0.9900, 57 negative triangles 130: dt=0.9900, 52 negative triangles 131: dt=0.9900, 50 negative triangles 132: dt=0.9900, 51 negative triangles 133: dt=0.9900, 48 negative triangles 134: dt=0.9900, 46 negative triangles 135: dt=0.9900, 43 negative triangles 136: dt=0.9900, 41 negative triangles 137: dt=0.9900, 37 negative triangles 138: dt=0.9900, 38 negative triangles 139: dt=0.9900, 35 negative triangles 140: dt=0.9900, 33 negative triangles 141: dt=0.9900, 30 negative triangles 142: dt=0.9900, 29 negative triangles 143: dt=0.9900, 27 negative triangles 144: dt=0.9900, 25 negative triangles 145: dt=0.9900, 27 negative triangles 146: dt=0.9900, 26 negative triangles 147: dt=0.9900, 22 negative triangles 148: dt=0.9900, 24 negative triangles 149: dt=0.9900, 26 negative triangles 150: dt=0.9900, 23 negative triangles 151: dt=0.9900, 24 negative triangles 152: dt=0.9900, 20 negative triangles 153: dt=0.9900, 21 negative triangles 154: dt=0.9900, 25 negative triangles 155: dt=0.9900, 23 negative triangles 156: dt=0.9900, 23 negative triangles 157: dt=0.9900, 19 negative triangles 158: dt=0.9900, 19 negative triangles 159: dt=0.9900, 21 negative triangles 160: dt=0.9900, 20 negative triangles 161: dt=0.9900, 20 negative triangles 162: dt=0.9900, 18 negative triangles 163: dt=0.9900, 17 negative triangles 164: dt=0.9900, 18 negative triangles 165: dt=0.9900, 18 negative triangles 166: dt=0.9900, 21 negative triangles 167: dt=0.9900, 18 negative triangles 168: dt=0.9900, 16 negative triangles 169: dt=0.9900, 16 negative triangles 170: dt=0.9900, 17 negative triangles 171: dt=0.9900, 21 negative triangles 172: dt=0.9900, 17 negative triangles 173: dt=0.9900, 17 negative triangles 174: dt=0.9900, 19 negative triangles 175: dt=0.9900, 16 negative triangles 176: dt=0.9900, 13 negative triangles 177: dt=0.9900, 14 negative triangles 178: dt=0.9900, 13 negative triangles 179: dt=0.9900, 15 negative triangles 180: dt=0.9900, 17 negative triangles 181: dt=0.9900, 16 negative triangles 182: dt=0.9900, 11 negative triangles 183: dt=0.9900, 10 negative triangles 184: dt=0.9900, 12 negative triangles 185: dt=0.9900, 12 negative triangles 186: dt=0.9900, 9 negative triangles 187: dt=0.9900, 9 negative triangles 188: dt=0.9900, 10 negative triangles 189: dt=0.9900, 8 negative triangles 190: dt=0.9900, 7 negative triangles 191: dt=0.9900, 5 negative triangles 192: dt=0.9900, 6 negative triangles 193: dt=0.9900, 7 negative triangles 194: dt=0.9900, 5 negative triangles 195: dt=0.9900, 5 negative triangles 196: dt=0.9900, 2 negative triangles 197: dt=0.9900, 4 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 1 negative triangles 200: dt=0.9900, 1 negative triangles 201: dt=0.9900, 1 negative triangles 202: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.09 hours mris_register utimesec 3907.348000 mris_register stimesec 0.920000 mris_register ru_maxrss 216680 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 24810 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 8664 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 4 mris_register ru_nivcsw 1776 FSRUNTIME@ mris_register 1.0856 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Sat Jun 2 19:50:32 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Sat Jun 2 19:50:34 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Sat Jun 2 19:50:36 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mrisp_paint -a 5 /home/jianfeng/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/jianfeng/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Sat Jun 2 19:50:38 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mrisp_paint -a 5 /home/jianfeng/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/jianfeng/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sat Jun 2 19:50:40 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 He_Aiqun_ReoT1 lh ../surf/lh.sphere.reg /home/jianfeng/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/jianfeng/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... 885 labels changed using aseg relabeling using gibbs priors... 000: 2835 changed, 119067 examined... 001: 680 changed, 12000 examined... 002: 185 changed, 3703 examined... 003: 61 changed, 1094 examined... 004: 28 changed, 347 examined... 005: 13 changed, 160 examined... 006: 7 changed, 93 examined... 007: 3 changed, 44 examined... 008: 1 changed, 18 examined... 009: 1 changed, 7 examined... 010: 0 changed, 7 examined... 229 labels changed using aseg 000: 101 total segments, 56 labels (232 vertices) changed 001: 46 total segments, 2 labels (2 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1356 vertices marked for relabeling... 1356 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc rh Sat Jun 2 19:50:56 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 He_Aiqun_ReoT1 rh ../surf/rh.sphere.reg /home/jianfeng/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/jianfeng/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... 800 labels changed using aseg relabeling using gibbs priors... 000: 2509 changed, 123097 examined... 001: 568 changed, 10767 examined... 002: 125 changed, 3208 examined... 003: 41 changed, 766 examined... 004: 13 changed, 270 examined... 005: 5 changed, 88 examined... 006: 4 changed, 31 examined... 007: 1 changed, 23 examined... 008: 1 changed, 7 examined... 009: 0 changed, 7 examined... 155 labels changed using aseg 000: 86 total segments, 48 labels (201 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1111 vertices marked for relabeling... 1111 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat Jun 2 19:51:12 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/filled.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/brain.finalsurfs.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/../mri/aseg.presurf.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... 18090 bright wm thresholded. 667 bright non-wm voxels segmented. reading original surface position from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.orig... computing class statistics... border white: 226209 voxels (1.35%) border gray 252885 voxels (1.51%) WM (98.0): 98.9 +- 7.2 [70.0 --> 110.0] GM (78.0) : 76.0 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.5 (was 70) setting MAX_BORDER_WHITE to 109.2 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 51.0 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=74+-8.7 mean inside = 95.0, mean outside = 79.6 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 +- 0.25 (0.04-->6.22) (max @ vno 118832 --> 118836) face area 0.32 +- 0.16 (0.00-->5.95) mean absolute distance = 0.85 +- 1.03 2622 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 6 with 46 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 55 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=83.9, 136 (136) missing vertices, mean dist 0.5 [1.4 (%12.9)->0.8 (%87.1))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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 0.91 +- 0.26 (0.11-->7.23) (max @ vno 118832 --> 118836) face area 0.32 +- 0.16 (0.00-->5.74) mean absolute distance = 0.47 +- 0.78 3914 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1918571.2, rms=7.733 001: dt: 0.5000, sse=1111456.8, rms=4.941 (36.109%) 002: dt: 0.5000, sse=809133.5, rms=3.360 (32.003%) 003: dt: 0.5000, sse=719240.5, rms=2.737 (18.541%) 004: dt: 0.5000, sse=675720.8, rms=2.379 (13.081%) rms = 2.36, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=674637.6, rms=2.363 (0.660%) 006: dt: 0.2500, sse=612784.1, rms=1.600 (32.287%) 007: dt: 0.2500, sse=604956.4, rms=1.482 (7.396%) rms = 1.44, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=607795.3, rms=1.437 (2.989%) 009: dt: 0.1250, sse=598050.6, rms=1.368 (4.862%) rms = 1.35, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=597076.9, rms=1.348 (1.463%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown deleting segment 2 with 24 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 27 points - only 0.00% unknown deleting segment 5 with 11 points - only 9.09% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 17 points - only 47.06% unknown mean border=86.2, 47 (18) missing vertices, mean dist -0.3 [0.6 (%64.4)->0.2 (%35.6))] %57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Preci, 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 0.89 +- 0.25 (0.06-->6.44) (max @ vno 118832 --> 118836) face area 0.35 +- 0.17 (0.00-->6.74) mean absolute distance = 0.39 +- 0.52 4266 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=940257.5, rms=3.858 011: dt: 0.5000, sse=760732.0, rms=2.658 (31.110%) 012: dt: 0.5000, sse=705714.6, rms=2.170 (18.368%) 013: dt: 0.5000, sse=693906.8, rms=2.061 (5.033%) rms = 2.02, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=687928.0, rms=2.020 (1.956%) 015: dt: 0.2500, sse=642219.8, rms=1.344 (33.471%) 016: dt: 0.2500, sse=633550.9, rms=1.182 (12.087%) rms = 1.19, time step reduction 2 of 3 to 0.125... rms = 1.15, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=631026.1, rms=1.145 (3.058%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 2 with 21 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 49 points - only 0.00% unknown deleting segment 6 with 11 points - only 9.09% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=89.1, 49 (7) missing vertices, mean dist -0.3 [0.4 (%75.3)->0.2 (%24.7))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Preci, 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 +- 0.25 (0.06-->6.02) (max @ vno 118832 --> 118836) face area 0.33 +- 0.17 (0.00-->6.28) mean absolute distance = 0.26 +- 0.38 3257 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=922784.8, rms=3.903 018: dt: 0.5000, sse=708405.4, rms=2.340 (40.051%) 019: dt: 0.5000, sse=670288.4, rms=1.996 (14.705%) rms = 1.98, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=669219.5, rms=1.981 (0.759%) 021: dt: 0.2500, sse=616355.2, rms=1.204 (39.195%) 022: dt: 0.2500, sse=609202.9, rms=1.111 (7.724%) rms = 1.10, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=608915.2, rms=1.098 (1.162%) 024: dt: 0.1250, sse=602370.4, rms=0.989 (9.985%) rms = 0.98, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=601694.8, rms=0.978 (1.035%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 25 points - only 0.00% unknown deleting segment 2 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 65 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 11 points - only 9.09% unknown deleting segment 7 with 13 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown mean border=90.1, 68 (6) missing vertices, mean dist -0.1 [0.3 (%61.5)->0.2 (%38.5))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Preci, 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=635055.9, rms=1.769 026: dt: 0.5000, sse=623975.4, rms=1.413 (20.109%) rms = 1.58, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=589886.0, rms=1.012 (28.417%) rms = 0.97, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=587342.7, rms=0.974 (3.743%) 029: dt: 0.1250, sse=579197.2, rms=0.811 (16.678%) rms = 0.78, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=577610.6, rms=0.784 (3.338%) positioning took 0.7 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6471 vertices erasing segment 0 (vno[0] = 24902) erasing segment 2 (vno[0] = 51149) erasing segment 3 (vno[0] = 69214) erasing segment 4 (vno[0] = 72483) erasing segment 5 (vno[0] = 84695) erasing segment 6 (vno[0] = 86695) erasing segment 7 (vno[0] = 86758) erasing segment 8 (vno[0] = 87708) writing cortex label to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label... writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.area vertex spacing 0.88 +- 0.26 (0.04-->6.11) (max @ vno 118832 --> 118836) face area 0.33 +- 0.16 (0.00-->6.50) 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 10 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=59.7, 110 (110) missing vertices, mean dist 1.9 [0.7 (%0.0)->2.6 (%100.0))] %19 local maxima, %50 large gradients and %26 min vals, 143 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=Preci, 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=22602530.0, rms=31.152 001: dt: 0.0500, sse=20554754.0, rms=29.670 (4.756%) 002: dt: 0.0500, sse=19092714.0, rms=28.565 (3.724%) 003: dt: 0.0500, sse=17963028.0, rms=27.681 (3.095%) 004: dt: 0.0500, sse=17036830.0, rms=26.935 (2.697%) 005: dt: 0.0500, sse=16247031.0, rms=26.281 (2.426%) 006: dt: 0.0500, sse=15553394.0, rms=25.694 (2.236%) 007: dt: 0.0500, sse=14930981.0, rms=25.155 (2.098%) 008: dt: 0.0500, sse=14362592.0, rms=24.652 (1.998%) 009: dt: 0.0500, sse=13838273.0, rms=24.179 (1.918%) 010: dt: 0.0500, sse=13349257.0, rms=23.730 (1.859%) positioning took 1.1 minutes mean border=59.6, 92 (65) missing vertices, mean dist 1.5 [0.1 (%0.1)->2.0 (%99.9))] %20 local maxima, %50 large gradients and %25 min vals, 126 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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=14004137.0, rms=24.326 011: dt: 0.0500, sse=13543411.0, rms=23.905 (1.729%) 012: dt: 0.0500, sse=13108806.0, rms=23.502 (1.689%) 013: dt: 0.0500, sse=12697068.0, rms=23.113 (1.655%) 014: dt: 0.0500, sse=12305138.0, rms=22.736 (1.629%) 015: dt: 0.0500, sse=11933079.0, rms=22.373 (1.598%) 016: dt: 0.0500, sse=11578595.0, rms=22.021 (1.573%) 017: dt: 0.0500, sse=11240138.0, rms=21.680 (1.550%) 018: dt: 0.0500, sse=10918669.0, rms=21.350 (1.519%) 019: dt: 0.0500, sse=10611557.0, rms=21.031 (1.496%) 020: dt: 0.0500, sse=10318046.0, rms=20.721 (1.474%) positioning took 1.1 minutes mean border=59.4, 91 (54) missing vertices, mean dist 1.2 [0.1 (%0.9)->1.7 (%99.1))] %20 local maxima, %50 large gradients and %25 min vals, 116 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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=10423205.0, rms=20.835 021: dt: 0.0500, sse=10132302.0, rms=20.525 (1.489%) 022: dt: 0.0500, sse=9855044.0, rms=20.225 (1.462%) 023: dt: 0.0500, sse=9587533.0, rms=19.931 (1.453%) 024: dt: 0.0500, sse=9332653.0, rms=19.647 (1.426%) 025: dt: 0.0500, sse=9089290.0, rms=19.372 (1.401%) 026: dt: 0.0500, sse=8856189.0, rms=19.104 (1.380%) 027: dt: 0.0500, sse=8630948.0, rms=18.842 (1.372%) 028: dt: 0.0500, sse=8411926.0, rms=18.584 (1.372%) 029: dt: 0.0500, sse=8197394.5, rms=18.327 (1.381%) 030: dt: 0.0500, sse=7987978.5, rms=18.073 (1.387%) positioning took 1.1 minutes mean border=59.3, 103 (42) missing vertices, mean dist 1.0 [0.1 (%9.7)->1.5 (%90.3))] %21 local maxima, %50 large gradients and %25 min vals, 114 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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=8097042.0, rms=18.204 031: dt: 0.5000, sse=6596326.0, rms=16.284 (10.547%) 032: dt: 0.5000, sse=5369466.0, rms=14.521 (10.826%) 033: dt: 0.5000, sse=4344706.5, rms=12.870 (11.370%) 034: dt: 0.5000, sse=3452113.2, rms=11.228 (12.757%) 035: dt: 0.5000, sse=2750501.0, rms=9.750 (13.168%) 036: dt: 0.5000, sse=2190563.2, rms=8.378 (14.071%) 037: dt: 0.5000, sse=1812425.9, rms=7.314 (12.701%) 038: dt: 0.5000, sse=1553193.0, rms=6.476 (11.453%) 039: dt: 0.5000, sse=1420074.5, rms=6.008 (7.223%) 040: dt: 0.5000, sse=1323491.0, rms=5.633 (6.239%) 041: dt: 0.5000, sse=1282218.0, rms=5.473 (2.841%) 042: dt: 0.5000, sse=1242052.2, rms=5.301 (3.150%) rms = 5.26, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1230521.0, rms=5.258 (0.810%) 044: dt: 0.2500, sse=1032482.8, rms=4.283 (18.549%) 045: dt: 0.2500, sse=986491.4, rms=4.037 (5.741%) rms = 4.03, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=985784.8, rms=4.027 (0.234%) 047: dt: 0.1250, sse=929569.5, rms=3.696 (8.236%) 048: dt: 0.1250, sse=920052.8, rms=3.638 (1.556%) rms = 3.64, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=919689.6, rms=3.635 (0.082%) positioning took 2.6 minutes mean border=58.0, 1259 (13) missing vertices, mean dist 0.1 [0.1 (%47.4)->0.4 (%52.6))] %34 local maxima, %38 large gradients and %22 min vals, 66 gradients ignored tol=1.0e-04, sigma=1.0, host=Preci, 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=1188598.2, rms=4.377 rms = 4.76, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=1057294.5, rms=3.636 (16.930%) 051: dt: 0.2500, sse=992301.6, rms=3.202 (11.943%) rms = 3.21, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=971600.8, rms=3.050 (4.753%) 053: dt: 0.1250, sse=941487.6, rms=2.815 (7.677%) 054: dt: 0.1250, sse=929200.7, rms=2.716 (3.520%) rms = 2.67, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=922930.9, rms=2.667 (1.826%) positioning took 1.1 minutes mean border=57.0, 1369 (12) missing vertices, mean dist 0.1 [0.1 (%47.8)->0.3 (%52.2))] %48 local maxima, %25 large gradients and %21 min vals, 77 gradients ignored tol=1.0e-04, sigma=0.5, host=Preci, 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=987681.6, rms=3.202 rms = 4.00, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=932293.4, rms=2.787 (12.951%) 057: dt: 0.2500, sse=915915.7, rms=2.657 (4.672%) rms = 2.74, time step reduction 2 of 3 to 0.125... 058: dt: 0.1250, sse=909280.1, rms=2.599 (2.191%) 059: dt: 0.1250, sse=900834.6, rms=2.526 (2.780%) rms = 2.49, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=896605.2, rms=2.492 (1.349%) positioning took 1.0 minutes mean border=56.3, 2430 (10) missing vertices, mean dist 0.0 [0.1 (%50.3)->0.3 (%49.7))] %52 local maxima, %21 large gradients and %21 min vals, 84 gradients ignored tol=1.0e-04, sigma=0.2, host=Preci, 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=915680.8, rms=2.650 rms = 3.40, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=894463.0, rms=2.461 (7.143%) rms = 2.43, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=889403.2, rms=2.428 (1.342%) 063: dt: 0.1250, sse=881300.5, rms=2.349 (3.260%) rms = 2.31, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=876601.0, rms=2.309 (1.667%) positioning took 0.8 minutes writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.area.pial vertex spacing 0.99 +- 0.41 (0.08-->9.25) (max @ vno 118832 --> 118836) face area 0.39 +- 0.29 (0.00-->7.64) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119067 vertices processed 25000 of 119067 vertices processed 50000 of 119067 vertices processed 75000 of 119067 vertices processed 100000 of 119067 vertices processed 0 of 119067 vertices processed 25000 of 119067 vertices processed 50000 of 119067 vertices processed 75000 of 119067 vertices processed 100000 of 119067 vertices processed thickness calculation complete, 159:349 truncations. 36411 vertices at 0 distance 92479 vertices at 1 distance 64474 vertices at 2 distance 23734 vertices at 3 distance 7331 vertices at 4 distance 1988 vertices at 5 distance 581 vertices at 6 distance 203 vertices at 7 distance 56 vertices at 8 distance 31 vertices at 9 distance 22 vertices at 10 distance 11 vertices at 11 distance 14 vertices at 12 distance 20 vertices at 13 distance 10 vertices at 14 distance 3 vertices at 15 distance 1 vertices at 16 distance 5 vertices at 17 distance 7 vertices at 18 distance 0 vertices at 19 distance 7 vertices at 20 distance writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.thickness positioning took 16.9 minutes #-------------------------------------------- #@# Make Pial Surf rh Sat Jun 2 20:08:06 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/filled.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/brain.finalsurfs.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/../mri/aseg.presurf.mgz... reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... 18090 bright wm thresholded. 667 bright non-wm voxels segmented. reading original surface position from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.orig... computing class statistics... border white: 226209 voxels (1.35%) border gray 252885 voxels (1.51%) WM (98.0): 98.9 +- 7.2 [70.0 --> 110.0] GM (78.0) : 76.0 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.5 (was 70) setting MAX_BORDER_WHITE to 109.2 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.0 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=75+-7.8 mean inside = 95.5, 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 +- 0.25 (0.04-->5.09) (max @ vno 123062 --> 123067) face area 0.32 +- 0.15 (0.00-->3.72) mean absolute distance = 0.80 +- 0.98 2564 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 158 points - only 0.00% unknown deleting segment 3 with 39 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown mean border=84.4, 100 (100) missing vertices, mean dist 0.5 [1.3 (%12.7)->0.7 (%87.3))] %45 local maxima, %50 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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 0.92 +- 0.26 (0.06-->4.80) (max @ vno 123062 --> 123067) face area 0.32 +- 0.15 (0.00-->4.04) mean absolute distance = 0.44 +- 0.77 3531 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1905096.1, rms=7.499 001: dt: 0.5000, sse=1085526.2, rms=4.658 (37.880%) 002: dt: 0.5000, sse=805378.2, rms=3.141 (32.582%) 003: dt: 0.5000, sse=721803.2, rms=2.561 (18.441%) 004: dt: 0.5000, sse=688839.6, rms=2.274 (11.223%) rms = 2.25, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=688563.8, rms=2.251 (0.991%) 006: dt: 0.2500, sse=626433.3, rms=1.491 (33.764%) 007: dt: 0.2500, sse=618793.0, rms=1.355 (9.139%) rms = 1.31, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=615668.8, rms=1.309 (3.426%) rms = 1.27, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=615407.8, rms=1.273 (2.728%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 113 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown mean border=86.7, 31 (9) missing vertices, mean dist -0.3 [0.6 (%64.3)->0.2 (%35.7))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Preci, 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 0.89 +- 0.25 (0.08-->4.69) (max @ vno 123062 --> 123067) face area 0.35 +- 0.17 (0.00-->4.56) mean absolute distance = 0.36 +- 0.50 3521 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=968233.1, rms=3.818 010: dt: 0.5000, sse=771840.5, rms=2.527 (33.801%) 011: dt: 0.5000, sse=726581.2, rms=2.118 (16.191%) 012: dt: 0.5000, sse=710495.6, rms=1.981 (6.495%) rms = 2.03, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=672006.2, rms=1.468 (25.904%) 014: dt: 0.2500, sse=658486.4, rms=1.181 (19.538%) 015: dt: 0.2500, sse=651417.4, rms=1.095 (7.246%) rms = 1.07, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=650945.8, rms=1.068 (2.513%) rms = 1.04, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=649791.3, rms=1.037 (2.835%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 118 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown mean border=89.4, 51 (6) missing vertices, mean dist -0.2 [0.4 (%74.6)->0.2 (%25.4))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Preci, 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 +- 0.25 (0.06-->4.81) (max @ vno 89776 --> 88856) face area 0.33 +- 0.17 (0.00-->3.92) mean absolute distance = 0.26 +- 0.39 3366 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=917323.8, rms=3.684 018: dt: 0.5000, sse=707428.1, rms=2.117 (42.532%) 019: dt: 0.5000, sse=700283.9, rms=1.894 (10.523%) rms = 1.90, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=645613.2, rms=1.363 (28.045%) 021: dt: 0.2500, sse=628629.2, rms=1.056 (22.502%) 022: dt: 0.2500, sse=628015.0, rms=1.002 (5.191%) rms = 0.98, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=645480.8, rms=0.982 (1.953%) rms = 0.96, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=622680.1, rms=0.958 (2.483%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 125 points - only 0.00% unknown deleting segment 1 with 48 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown mean border=90.5, 63 (4) missing vertices, mean dist -0.1 [0.3 (%61.8)->0.2 (%38.2))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Preci, 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=656833.5, rms=1.735 025: dt: 0.5000, sse=632874.5, rms=1.234 (28.858%) rms = 1.52, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=607856.6, rms=0.898 (27.277%) 027: dt: 0.2500, sse=604999.9, rms=0.834 (7.083%) 028: dt: 0.2500, sse=602222.6, rms=0.783 (6.119%) rms = 0.81, time step reduction 2 of 3 to 0.125... rms = 0.77, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=599662.2, rms=0.768 (1.904%) positioning took 0.7 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6965 vertices erasing segment 1 (vno[0] = 61304) erasing segment 2 (vno[0] = 75094) erasing segment 3 (vno[0] = 86926) erasing segment 4 (vno[0] = 88897) erasing segment 5 (vno[0] = 90712) erasing segment 6 (vno[0] = 95797) writing cortex label to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label... writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.area vertex spacing 0.88 +- 0.26 (0.05-->4.88) (max @ vno 88856 --> 89776) face area 0.33 +- 0.16 (0.00-->3.56) 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 17 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=60.6, 112 (112) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.5 (%100.0))] %20 local maxima, %50 large gradients and %26 min vals, 147 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=Preci, 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=22523286.0, rms=30.583 001: dt: 0.0500, sse=20444348.0, rms=29.099 (4.852%) 002: dt: 0.0500, sse=18959458.0, rms=27.991 (3.808%) 003: dt: 0.0500, sse=17814500.0, rms=27.105 (3.164%) 004: dt: 0.0500, sse=16878374.0, rms=26.359 (2.753%) 005: dt: 0.0500, sse=16081906.0, rms=25.707 (2.473%) 006: dt: 0.0500, sse=15383243.0, rms=25.121 (2.279%) 007: dt: 0.0500, sse=14757637.0, rms=24.585 (2.136%) 008: dt: 0.0500, sse=14188126.0, rms=24.086 (2.029%) 009: dt: 0.0500, sse=13663332.0, rms=23.617 (1.948%) 010: dt: 0.0500, sse=13175136.0, rms=23.172 (1.884%) positioning took 1.1 minutes mean border=60.4, 94 (74) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.0 (%100.0))] %21 local maxima, %49 large gradients and %25 min vals, 125 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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=13945225.0, rms=23.866 011: dt: 0.0500, sse=13485560.0, rms=23.452 (1.735%) 012: dt: 0.0500, sse=13052533.0, rms=23.055 (1.693%) 013: dt: 0.0500, sse=12643303.0, rms=22.674 (1.655%) 014: dt: 0.0500, sse=12255772.0, rms=22.306 (1.621%) 015: dt: 0.0500, sse=11887849.0, rms=21.951 (1.590%) 016: dt: 0.0500, sse=11538491.0, rms=21.609 (1.559%) 017: dt: 0.0500, sse=11206439.0, rms=21.279 (1.529%) 018: dt: 0.0500, sse=10890332.0, rms=20.960 (1.501%) 019: dt: 0.0500, sse=10588974.0, rms=20.650 (1.475%) 020: dt: 0.0500, sse=10301889.0, rms=20.351 (1.448%) positioning took 1.1 minutes mean border=60.2, 94 (62) missing vertices, mean dist 1.2 [0.1 (%0.8)->1.7 (%99.2))] %21 local maxima, %49 large gradients and %25 min vals, 138 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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=10444408.0, rms=20.503 021: dt: 0.0500, sse=10160663.0, rms=20.205 (1.452%) 022: dt: 0.0500, sse=9890293.0, rms=19.917 (1.424%) 023: dt: 0.0500, sse=9630440.0, rms=19.637 (1.409%) 024: dt: 0.0500, sse=9382481.0, rms=19.365 (1.383%) 025: dt: 0.0500, sse=9145828.0, rms=19.102 (1.358%) 026: dt: 0.0500, sse=8919674.0, rms=18.847 (1.334%) 027: dt: 0.0500, sse=8701845.0, rms=18.599 (1.320%) 028: dt: 0.0500, sse=8490072.0, rms=18.353 (1.318%) 029: dt: 0.0500, sse=8284203.0, rms=18.112 (1.316%) 030: dt: 0.0500, sse=8084199.0, rms=17.874 (1.313%) positioning took 1.1 minutes mean border=60.0, 104 (55) missing vertices, mean dist 1.0 [0.1 (%9.6)->1.5 (%90.4))] %21 local maxima, %49 large gradients and %24 min vals, 130 gradients ignored tol=1.0e-04, sigma=2.0, host=Preci, 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=8212129.5, rms=18.024 031: dt: 0.5000, sse=6755578.0, rms=16.205 (10.090%) 032: dt: 0.5000, sse=5586650.0, rms=14.578 (10.043%) 033: dt: 0.5000, sse=4564265.0, rms=12.992 (10.878%) 034: dt: 0.5000, sse=3697468.5, rms=11.471 (11.706%) 035: dt: 0.5000, sse=2993884.2, rms=10.072 (12.196%) 036: dt: 0.5000, sse=2431570.2, rms=8.791 (12.718%) 037: dt: 0.5000, sse=2019890.5, rms=7.724 (12.143%) 038: dt: 0.5000, sse=1732340.6, rms=6.875 (10.991%) 039: dt: 0.5000, sse=1563224.2, rms=6.327 (7.966%) 040: dt: 0.5000, sse=1449489.0, rms=5.924 (6.368%) 041: dt: 0.5000, sse=1388145.8, rms=5.699 (3.804%) 042: dt: 0.5000, sse=1331881.5, rms=5.478 (3.869%) 043: dt: 0.5000, sse=1309443.1, rms=5.392 (1.574%) 044: dt: 0.5000, sse=1279785.2, rms=5.269 (2.280%) rms = 5.25, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1275363.2, rms=5.254 (0.295%) 046: dt: 0.2500, sse=1086169.9, rms=4.356 (17.088%) 047: dt: 0.2500, sse=1038119.2, rms=4.113 (5.579%) rms = 4.13, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1016947.6, rms=3.996 (2.830%) 049: dt: 0.1250, sse=988178.9, rms=3.832 (4.122%) rms = 3.80, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=982159.6, rms=3.797 (0.911%) positioning took 2.9 minutes mean border=58.5, 1426 (29) missing vertices, mean dist 0.1 [0.1 (%45.8)->0.4 (%54.2))] %35 local maxima, %37 large gradients and %22 min vals, 68 gradients ignored tol=1.0e-04, sigma=1.0, host=Preci, 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=1336920.4, rms=4.801 rms = 4.84, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1188911.5, rms=4.073 (15.170%) 052: dt: 0.2500, sse=1090175.5, rms=3.500 (14.060%) 053: dt: 0.2500, sse=1072708.6, rms=3.396 (2.981%) 054: dt: 0.2500, sse=1059202.6, rms=3.313 (2.443%) rms = 3.28, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1053901.6, rms=3.282 (0.940%) 056: dt: 0.1250, sse=989966.6, rms=2.818 (14.142%) 057: dt: 0.1250, sse=980578.9, rms=2.747 (2.498%) rms = 2.73, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=977782.9, rms=2.726 (0.764%) positioning took 1.4 minutes mean border=57.4, 1444 (27) missing vertices, mean dist 0.1 [0.1 (%46.1)->0.3 (%53.9))] %48 local maxima, %25 large gradients and %21 min vals, 88 gradients ignored tol=1.0e-04, sigma=0.5, host=Preci, 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=1065010.6, rms=3.367 rms = 4.05, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1000202.9, rms=2.918 (13.322%) 060: dt: 0.2500, sse=979432.0, rms=2.760 (5.413%) rms = 2.80, time step reduction 2 of 3 to 0.125... 061: dt: 0.1250, sse=972718.6, rms=2.705 (1.987%) 062: dt: 0.1250, sse=963138.4, rms=2.628 (2.846%) rms = 2.60, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=958793.8, rms=2.595 (1.262%) positioning took 1.1 minutes mean border=56.6, 2597 (27) missing vertices, mean dist 0.1 [0.1 (%48.4)->0.2 (%51.6))] %53 local maxima, %20 large gradients and %21 min vals, 87 gradients ignored tol=1.0e-04, sigma=0.2, host=Preci, 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=984415.9, rms=2.801 rms = 3.45, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=961581.0, rms=2.614 (6.664%) 065: dt: 0.2500, sse=953655.4, rms=2.559 (2.103%) rms = 2.62, time step reduction 2 of 3 to 0.125... rms = 2.52, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=949361.1, rms=2.521 (1.495%) positioning took 0.7 minutes writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.area.pial vertex spacing 1.00 +- 0.41 (0.09-->6.58) (max @ vno 79100 --> 79084) face area 0.39 +- 0.29 (0.00-->7.58) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 123097 vertices processed 25000 of 123097 vertices processed 50000 of 123097 vertices processed 75000 of 123097 vertices processed 100000 of 123097 vertices processed 0 of 123097 vertices processed 25000 of 123097 vertices processed 50000 of 123097 vertices processed 75000 of 123097 vertices processed 100000 of 123097 vertices processed thickness calculation complete, 470:782 truncations. 37624 vertices at 0 distance 95257 vertices at 1 distance 66229 vertices at 2 distance 24525 vertices at 3 distance 7461 vertices at 4 distance 2219 vertices at 5 distance 741 vertices at 6 distance 315 vertices at 7 distance 142 vertices at 8 distance 84 vertices at 9 distance 69 vertices at 10 distance 52 vertices at 11 distance 34 vertices at 12 distance 32 vertices at 13 distance 20 vertices at 14 distance 14 vertices at 15 distance 10 vertices at 16 distance 17 vertices at 17 distance 9 vertices at 18 distance 2 vertices at 19 distance 8 vertices at 20 distance writing curvature file /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.thickness positioning took 17.7 minutes #-------------------------------------------- #@# Surf Volume lh Sat Jun 2 20:25:50 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 lh /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.volume masking with /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label Total face volume 195731 Total vertex volume 193097 (mask=0) #@# He_Aiqun_ReoT1 lh 193097 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sat Jun 2 20:25:53 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 rh /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.volume masking with /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label Total face volume 209210 Total vertex volume 205398 (mask=0) #@# He_Aiqun_ReoT1 rh 205398 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sat Jun 2 20:25:57 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 SUBJECTS_DIR is /home/jianfeng/freesurfer/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 = 269 writing volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/ribbon.mgz mris_volmask took 14.16 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sat Jun 2 20:40:07 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 195731 Total vertex volume 193097 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1608 1103 2296 2.238 0.435 0.112 0.020 15 1.4 bankssts 711 424 1281 2.737 0.511 0.120 0.020 11 0.5 caudalanteriorcingulate 2661 1748 4786 2.611 0.541 0.108 0.018 20 1.9 caudalmiddlefrontal 1734 1128 2444 1.922 0.486 0.152 0.036 33 2.7 cuneus 633 454 1703 2.980 0.678 0.139 0.039 9 0.9 entorhinal 4132 2882 8706 2.669 0.576 0.135 0.030 53 5.0 fusiform 5840 3615 9179 2.321 0.555 0.133 0.033 88 7.8 inferiorparietal 4654 3111 9549 2.643 0.743 0.140 0.038 81 8.3 inferiortemporal 1203 784 2070 2.268 0.963 0.146 0.037 24 1.6 isthmuscingulate 7282 4492 10204 2.006 0.555 0.129 0.028 96 8.3 lateraloccipital 2867 1945 5574 2.490 0.625 0.126 0.031 36 3.6 lateralorbitofrontal 3983 2642 5465 1.941 0.547 0.137 0.029 62 4.8 lingual 2515 1750 4658 2.327 0.688 0.142 0.042 51 3.5 medialorbitofrontal 4604 3054 8395 2.424 0.738 0.138 0.038 68 7.7 middletemporal 843 546 1716 2.799 0.730 0.094 0.016 6 0.5 parahippocampal 1775 1066 2831 2.486 0.586 0.095 0.021 13 1.5 paracentral 2339 1405 4027 2.472 0.468 0.094 0.025 25 2.6 parsopercularis 784 512 1979 2.821 0.619 0.138 0.032 13 1.0 parsorbitalis 1796 1113 2930 2.300 0.500 0.104 0.024 19 1.8 parstriangularis 1716 1208 2140 1.830 0.491 0.133 0.032 21 2.3 pericalcarine 5982 3499 7934 2.095 0.626 0.100 0.022 48 5.5 postcentral 1349 909 2418 2.455 0.838 0.153 0.034 26 2.0 posteriorcingulate 6676 3922 10965 2.612 0.530 0.096 0.020 53 5.8 precentral 4161 2887 7543 2.497 0.557 0.139 0.029 57 5.0 precuneus 1029 673 1931 2.603 0.626 0.125 0.031 14 1.2 rostralanteriorcingulate 7233 4560 12609 2.397 0.562 0.132 0.029 105 8.9 rostralmiddlefrontal 9114 5806 18767 2.797 0.545 0.121 0.028 105 10.2 superiorfrontal 6667 4337 9745 2.033 0.507 0.122 0.024 82 6.4 superiorparietal 5582 3761 10092 2.468 0.666 0.115 0.026 57 6.3 superiortemporal 6458 4101 9945 2.291 0.600 0.126 0.031 73 8.4 supramarginal 318 213 931 2.833 0.511 0.163 0.057 7 0.6 frontalpole 526 362 1521 2.784 0.706 0.144 0.049 11 1.2 temporalpole 680 430 990 2.404 0.541 0.145 0.023 9 0.5 transversetemporal 2792 1947 5746 3.149 0.784 0.121 0.025 22 3.1 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 He_Aiqun_ReoT1 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 195731 Total vertex volume 193097 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1608 938 2296 2.238 0.435 0.103 0.027 32 1.6 bankssts 711 546 1281 2.737 0.511 0.130 0.027 10 0.8 caudalanteriorcingulate 2661 1918 4786 2.611 0.541 0.112 0.020 30 2.2 caudalmiddlefrontal 1734 1428 2444 1.922 0.486 0.148 0.033 25 2.7 cuneus 633 700 1703 2.980 0.678 0.153 0.031 8 0.9 entorhinal 4132 3597 8706 2.669 0.576 0.145 0.033 60 6.1 fusiform 5840 4312 9179 2.321 0.555 0.133 0.030 72 7.8 inferiorparietal 4654 3950 9549 2.643 0.743 0.141 0.031 131 6.3 inferiortemporal 1203 982 2070 2.268 0.963 0.174 0.050 22 3.0 isthmuscingulate 7282 5588 10204 2.006 0.555 0.132 0.027 97 8.9 lateraloccipital 2867 2439 5574 2.490 0.625 0.152 0.032 48 4.1 lateralorbitofrontal 3983 3137 5465 1.941 0.547 0.134 0.029 50 5.2 lingual 2515 2223 4658 2.327 0.688 0.157 0.037 41 4.2 medialorbitofrontal 4604 3785 8395 2.424 0.738 0.128 0.029 52 6.2 middletemporal 843 704 1716 2.799 0.730 0.121 0.025 8 0.9 parahippocampal 1775 1261 2831 2.486 0.586 0.091 0.016 12 1.3 paracentral 2339 1762 4027 2.472 0.468 0.108 0.019 26 2.0 parsopercularis 784 852 1979 2.821 0.619 0.189 0.038 10 1.3 parsorbitalis 1796 1385 2930 2.300 0.500 0.124 0.020 19 1.7 parstriangularis 1716 1131 2140 1.830 0.491 0.136 0.031 26 2.4 pericalcarine 5982 4264 7934 2.095 0.626 0.103 0.018 42 4.6 postcentral 1349 1057 2418 2.455 0.838 0.151 0.035 37 1.8 posteriorcingulate 6676 4445 10965 2.612 0.530 0.093 0.016 68 4.4 precentral 4161 3157 7543 2.497 0.557 0.139 0.034 72 5.3 precuneus 1029 843 1931 2.603 0.626 0.151 0.036 15 1.7 rostralanteriorcingulate 7233 5802 12609 2.397 0.562 0.146 0.032 88 10.3 rostralmiddlefrontal 9114 7310 18767 2.797 0.545 0.129 0.028 115 11.0 superiorfrontal 6667 5242 9745 2.033 0.507 0.134 0.024 87 6.7 superiorparietal 5582 4286 10092 2.468 0.666 0.113 0.023 54 5.5 superiortemporal 6458 4642 9945 2.291 0.600 0.122 0.025 75 7.3 supramarginal 318 427 931 2.833 0.511 0.240 0.057 5 0.7 frontalpole 526 666 1521 2.784 0.706 0.184 0.034 5 0.8 temporalpole 680 419 990 2.404 0.541 0.095 0.018 5 0.4 transversetemporal 2792 1699 5746 3.149 0.784 0.120 0.029 45 3.5 insula #----------------------------------------- #@# Parcellation Stats rh Sat Jun 2 20:41:25 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 209210 Total vertex volume 205398 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1150 826 1767 2.262 0.394 0.098 0.016 7 0.7 bankssts 846 518 1739 2.753 0.800 0.126 0.018 12 0.6 caudalanteriorcingulate 3026 1999 5716 2.546 0.585 0.115 0.023 28 2.8 caudalmiddlefrontal 2213 1361 2856 1.903 0.475 0.143 0.032 34 3.1 cuneus 588 435 2042 3.680 0.676 0.130 0.026 5 0.6 entorhinal 3736 2606 8572 2.927 0.628 0.129 0.025 49 3.7 fusiform 8628 5310 14542 2.425 0.518 0.118 0.029 103 10.1 inferiorparietal 5112 3455 11076 2.649 0.733 0.137 0.037 84 8.4 inferiortemporal 1037 673 1931 2.341 0.912 0.135 0.033 18 1.1 isthmuscingulate 7476 4604 10611 2.150 0.529 0.130 0.029 103 8.8 lateraloccipital 2910 1994 5649 2.490 0.587 0.125 0.028 38 3.5 lateralorbitofrontal 4136 2570 6030 2.216 0.705 0.133 0.033 55 5.8 lingual 2733 1748 4983 2.443 0.605 0.120 0.030 36 3.3 medialorbitofrontal 5515 3593 9425 2.369 0.690 0.134 0.038 85 9.4 middletemporal 807 531 1876 3.033 0.748 0.089 0.013 5 0.4 parahippocampal 1852 1123 3071 2.596 0.661 0.113 0.025 16 2.1 paracentral 1661 1065 2990 2.498 0.451 0.113 0.022 19 1.4 parsopercularis 848 596 2150 2.532 0.711 0.159 0.041 18 1.5 parsorbitalis 2111 1363 3778 2.350 0.526 0.132 0.037 33 3.4 parstriangularis 1900 1249 1943 1.670 0.395 0.125 0.026 20 2.0 pericalcarine 5679 3428 8070 2.084 0.651 0.104 0.021 50 5.0 postcentral 1244 827 2753 2.866 0.654 0.131 0.028 18 1.5 posteriorcingulate 6291 3864 10639 2.499 0.621 0.097 0.017 42 4.2 precentral 4637 3208 8163 2.414 0.597 0.136 0.030 61 5.7 precuneus 814 529 2084 3.142 0.548 0.134 0.027 12 0.9 rostralanteriorcingulate 7163 4879 12489 2.143 0.586 0.136 0.031 123 9.1 rostralmiddlefrontal 8705 5601 17517 2.719 0.543 0.119 0.026 119 9.4 superiorfrontal 6695 4250 10270 2.195 0.511 0.120 0.023 77 6.2 superiorparietal 5575 3735 10625 2.454 0.659 0.109 0.024 62 6.0 superiortemporal 5687 3588 8642 2.306 0.558 0.117 0.027 60 6.4 supramarginal 385 264 1009 2.538 0.653 0.162 0.037 10 0.5 frontalpole 654 471 2872 3.908 0.569 0.172 0.045 15 1.6 temporalpole 472 282 785 2.482 0.303 0.098 0.015 4 0.3 transversetemporal 3291 2206 6667 3.103 0.835 0.113 0.024 31 3.0 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 He_Aiqun_ReoT1 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 209210 Total vertex volume 205398 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1150 729 1767 2.262 0.394 0.105 0.020 10 1.0 bankssts 846 691 1739 2.753 0.800 0.140 0.029 48 0.9 caudalanteriorcingulate 3026 2388 5716 2.546 0.585 0.125 0.023 30 3.0 caudalmiddlefrontal 2213 1713 2856 1.903 0.475 0.136 0.029 23 2.8 cuneus 588 632 2042 3.680 0.676 0.154 0.035 12 0.9 entorhinal 3736 3249 8572 2.927 0.628 0.129 0.025 46 4.2 fusiform 8628 6562 14542 2.425 0.518 0.126 0.026 94 10.1 inferiorparietal 5112 4587 11076 2.649 0.733 0.153 0.033 102 8.2 inferiortemporal 1037 904 1931 2.341 0.912 0.152 0.042 19 1.9 isthmuscingulate 7476 5360 10611 2.150 0.529 0.127 0.033 149 12.6 lateraloccipital 2910 2533 5649 2.490 0.587 0.151 0.038 49 3.9 lateralorbitofrontal 4136 3028 6030 2.216 0.705 0.121 0.029 45 5.2 lingual 2733 2321 4983 2.443 0.605 0.158 0.036 41 4.4 medialorbitofrontal 5515 4383 9425 2.369 0.690 0.127 0.026 66 6.5 middletemporal 807 685 1876 3.033 0.748 0.114 0.020 8 0.7 parahippocampal 1852 1262 3071 2.596 0.661 0.107 0.021 20 1.7 paracentral 1661 1319 2990 2.498 0.451 0.126 0.022 17 1.6 parsopercularis 848 1076 2150 2.532 0.711 0.229 0.047 15 2.0 parsorbitalis 2111 1818 3778 2.350 0.526 0.159 0.029 32 2.6 parstriangularis 1900 1173 1943 1.670 0.395 0.116 0.026 31 2.2 pericalcarine 5679 4359 8070 2.084 0.651 0.114 0.020 48 4.9 postcentral 1244 1051 2753 2.866 0.654 0.157 0.038 50 1.8 posteriorcingulate 6291 4591 10639 2.499 0.621 0.102 0.016 50 4.3 precentral 4637 3443 8163 2.414 0.597 0.134 0.033 68 6.8 precuneus 814 799 2084 3.142 0.548 0.154 0.032 15 1.1 rostralanteriorcingulate 7163 6496 12489 2.143 0.586 0.164 0.032 99 10.2 rostralmiddlefrontal 8705 6980 17517 2.719 0.543 0.128 0.025 93 9.0 superiorfrontal 6695 5052 10270 2.195 0.511 0.125 0.024 90 6.4 superiorparietal 5575 4784 10625 2.454 0.659 0.125 0.022 45 5.4 superiortemporal 5687 3886 8642 2.306 0.558 0.111 0.023 61 5.4 supramarginal 385 507 1009 2.538 0.653 0.208 0.039 5 0.5 frontalpole 654 933 2872 3.908 0.569 0.204 0.032 6 1.1 temporalpole 472 344 785 2.482 0.303 0.096 0.017 2 0.3 transversetemporal 3291 1985 6667 3.103 0.835 0.115 0.025 47 3.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat Jun 2 20:42:47 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 He_Aiqun_ReoT1 lh ../surf/lh.sphere.reg /home/jianfeng/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/jianfeng/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... 24 labels changed using aseg relabeling using gibbs priors... 000: 7877 changed, 119067 examined... 001: 1738 changed, 30735 examined... 002: 490 changed, 9232 examined... 003: 205 changed, 2784 examined... 004: 100 changed, 1210 examined... 005: 52 changed, 574 examined... 006: 34 changed, 306 examined... 007: 14 changed, 182 examined... 008: 5 changed, 87 examined... 009: 3 changed, 27 examined... 010: 3 changed, 25 examined... 011: 0 changed, 15 examined... 7 labels changed using aseg 000: 227 total segments, 139 labels (1941 vertices) changed 001: 97 total segments, 9 labels (38 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 839 vertices marked for relabeling... 839 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Sat Jun 2 20:43:07 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 He_Aiqun_ReoT1 rh ../surf/rh.sphere.reg /home/jianfeng/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/jianfeng/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... 11 labels changed using aseg relabeling using gibbs priors... 000: 8075 changed, 123097 examined... 001: 1877 changed, 31872 examined... 002: 579 changed, 9893 examined... 003: 200 changed, 3358 examined... 004: 83 changed, 1169 examined... 005: 39 changed, 497 examined... 006: 19 changed, 234 examined... 007: 8 changed, 106 examined... 008: 4 changed, 49 examined... 009: 1 changed, 21 examined... 010: 1 changed, 5 examined... 011: 0 changed, 6 examined... 6 labels changed using aseg 000: 243 total segments, 158 labels (2347 vertices) changed 001: 94 total segments, 9 labels (37 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 730 vertices marked for relabeling... 730 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Jun 2 20:43:29 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 195731 Total vertex volume 193097 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 908 617 1647 2.300 0.593 0.155 0.042 13 1.8 G&S_frontomargin 1544 1043 2723 2.223 0.634 0.140 0.026 21 1.7 G&S_occipital_inf 1383 728 2214 2.501 0.565 0.102 0.025 13 1.3 G&S_paracentral 1522 904 2527 2.523 0.546 0.127 0.039 22 3.1 G&S_subcentral 631 428 1466 2.517 0.520 0.164 0.049 13 1.2 G&S_transv_frontopol 2158 1442 3933 2.615 0.504 0.123 0.025 28 2.1 G&S_cingul-Ant 996 688 1916 2.675 0.458 0.103 0.016 7 0.6 G&S_cingul-Mid-Ant 1145 776 2262 2.738 0.688 0.130 0.023 13 1.1 G&S_cingul-Mid-Post 512 343 1352 2.822 0.965 0.184 0.064 13 1.3 G_cingul-Post-dorsal 240 163 493 2.651 0.707 0.177 0.036 6 0.4 G_cingul-Post-ventral 1697 1079 2601 1.960 0.539 0.153 0.042 31 3.2 G_cuneus 1155 644 2398 2.728 0.405 0.100 0.035 18 1.8 G_front_inf-Opercular 316 193 782 2.682 0.418 0.137 0.025 5 0.4 G_front_inf-Orbital 1065 574 1978 2.525 0.454 0.109 0.032 16 1.5 G_front_inf-Triangul 4122 2348 8529 2.662 0.574 0.125 0.027 64 4.9 G_front_middle 6449 3899 14098 2.891 0.546 0.127 0.033 89 8.4 G_front_sup 550 392 1359 3.493 0.880 0.133 0.034 6 0.7 G_Ins_lg&S_cent_ins 531 338 1802 3.777 0.675 0.116 0.024 6 0.6 G_insular_short 2311 1236 4026 2.468 0.535 0.125 0.036 39 3.4 G_occipital_middle 1432 789 1933 2.061 0.451 0.126 0.028 24 1.5 G_occipital_sup 1899 1241 4473 2.848 0.571 0.139 0.031 29 2.5 G_oc-temp_lat-fusifor 2833 1778 4048 1.930 0.566 0.150 0.034 55 4.0 G_oc-temp_med-Lingual 1206 808 3095 3.030 0.692 0.119 0.031 12 1.3 G_oc-temp_med-Parahip 2016 1323 4863 2.635 0.646 0.138 0.039 37 3.2 G_orbital 2695 1614 5045 2.442 0.599 0.143 0.038 55 4.0 G_pariet_inf-Angular 3147 1855 5158 2.371 0.655 0.133 0.039 43 5.1 G_pariet_inf-Supramar 2383 1599 4524 2.180 0.594 0.135 0.027 41 2.7 G_parietal_sup 2263 1152 3311 2.258 0.546 0.095 0.023 18 2.2 G_postcentral 2609 1253 4674 2.881 0.438 0.090 0.020 24 1.9 G_precentral 2084 1408 4440 2.480 0.573 0.155 0.034 42 3.0 G_precuneus 841 570 1928 2.370 0.693 0.156 0.045 21 1.6 G_rectus 560 366 1034 2.518 0.885 0.139 0.084 14 1.0 G_subcallosal 476 287 776 2.389 0.497 0.126 0.022 5 0.3 G_temp_sup-G_T_transv 1951 1256 4026 2.415 0.826 0.147 0.044 34 3.8 G_temp_sup-Lateral 453 345 1092 2.646 0.496 0.084 0.012 2 0.2 G_temp_sup-Plan_polar 1407 870 2244 2.423 0.659 0.124 0.034 15 1.9 G_temp_sup-Plan_tempo 2336 1489 5331 2.713 0.875 0.156 0.056 54 6.2 G_temporal_inf 3002 1942 5819 2.334 0.856 0.149 0.048 54 6.6 G_temporal_middle 274 187 289 1.739 0.297 0.097 0.008 1 0.1 Lat_Fis-ant-Horizont 349 236 454 2.131 0.337 0.074 0.010 1 0.1 Lat_Fis-ant-Vertical 1271 850 1698 2.356 0.655 0.107 0.019 7 1.0 Lat_Fis-post 2095 1187 2196 1.702 0.389 0.132 0.034 33 3.0 Pole_occipital 1307 929 3655 2.863 0.659 0.148 0.042 29 2.4 Pole_temporal 2086 1540 2563 1.911 0.606 0.122 0.027 21 2.3 S_calcarine 2837 1955 3338 1.888 0.645 0.094 0.015 13 1.9 S_central 877 610 1289 2.304 0.533 0.100 0.014 5 0.6 S_cingul-Marginalis 377 263 560 2.534 0.460 0.084 0.012 1 0.2 S_circular_insula_ant 1198 838 1760 2.512 0.524 0.091 0.012 6 0.6 S_circular_insula_inf 1511 1050 2244 2.625 0.436 0.104 0.018 7 1.2 S_circular_insula_sup 826 595 1409 2.757 0.488 0.100 0.013 4 0.5 S_collat_transv_ant 428 295 441 1.793 0.351 0.123 0.019 4 0.3 S_collat_transv_post 2040 1386 3059 2.239 0.374 0.103 0.018 16 1.4 S_front_inf 1159 796 1476 2.134 0.440 0.131 0.027 13 1.3 S_front_middle 2170 1471 3415 2.477 0.453 0.101 0.018 14 1.5 S_front_sup 575 387 664 2.033 0.400 0.139 0.025 6 0.7 S_interm_prim-Jensen 2645 1845 3073 1.842 0.392 0.109 0.016 20 1.9 S_intrapariet&P_trans 977 695 1144 1.842 0.468 0.122 0.023 7 0.9 S_oc_middle&Lunatus 1012 664 1118 1.810 0.361 0.118 0.020 9 0.9 S_oc_sup&transversal 683 467 849 2.054 0.412 0.129 0.022 6 0.6 S_occipital_ant 812 554 1486 2.558 0.437 0.145 0.031 13 1.0 S_oc-temp_lat 1815 1321 2832 2.348 0.485 0.108 0.018 12 1.3 S_oc-temp_med&Lingual 461 333 546 1.809 0.348 0.137 0.029 4 0.5 S_orbital_lateral 413 316 679 2.382 0.997 0.135 0.019 4 0.3 S_orbital_med-olfact 962 665 1768 2.562 0.689 0.125 0.025 8 1.0 S_orbital-H_Shaped 1414 963 2012 2.305 0.494 0.114 0.020 11 1.2 S_parieto_occipital 963 562 700 1.687 0.623 0.126 0.022 20 0.6 S_pericallosal 2802 1810 3628 2.165 0.442 0.105 0.020 21 2.4 S_postcentral 1492 1042 2208 2.331 0.425 0.097 0.014 8 0.9 S_precentral-inf-part 1137 773 1812 2.631 0.472 0.110 0.017 9 0.8 S_precentral-sup-part 543 413 829 2.150 0.515 0.133 0.017 5 0.4 S_suborbital 725 534 1293 2.734 0.451 0.141 0.034 8 1.0 S_subparietal 1617 1154 2129 2.269 0.368 0.124 0.020 13 1.5 S_temporal_inf 5195 3649 8048 2.383 0.456 0.116 0.020 46 4.4 S_temporal_sup 283 190 515 3.024 0.474 0.134 0.015 3 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Sat Jun 2 20:44:11 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 209210 Total vertex volume 205398 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 861 603 1259 1.852 0.576 0.135 0.025 14 0.9 G&S_frontomargin 1461 903 2085 2.234 0.555 0.122 0.023 20 1.3 G&S_occipital_inf 1200 681 1886 2.313 0.602 0.113 0.023 11 1.2 G&S_paracentral 1404 920 2783 2.701 0.546 0.140 0.029 21 1.6 G&S_subcentral 1066 710 2391 2.450 0.547 0.156 0.037 25 1.5 G&S_transv_frontopol 2791 1866 5422 2.702 0.563 0.113 0.023 24 2.7 G&S_cingul-Ant 1142 761 2266 2.765 0.596 0.119 0.018 11 0.8 G&S_cingul-Mid-Ant 1074 727 2272 2.976 0.522 0.114 0.027 8 1.1 G&S_cingul-Mid-Post 407 276 1322 3.188 0.539 0.151 0.037 7 0.7 G_cingul-Post-dorsal 261 160 689 2.926 0.772 0.160 0.055 6 0.6 G_cingul-Post-ventral 2039 1247 2667 1.863 0.503 0.150 0.034 35 2.9 G_cuneus 1429 868 2761 2.581 0.449 0.125 0.028 21 1.8 G_front_inf-Opercular 320 202 722 2.562 0.446 0.132 0.028 6 0.4 G_front_inf-Orbital 1066 658 2270 2.493 0.562 0.149 0.052 23 2.4 G_front_inf-Triangul 3582 2304 8083 2.567 0.638 0.138 0.032 75 4.8 G_front_middle 5858 3512 13424 2.913 0.558 0.125 0.031 106 7.8 G_front_sup 513 370 1271 3.207 0.717 0.122 0.029 6 0.5 G_Ins_lg&S_cent_ins 699 402 1777 3.417 0.877 0.121 0.031 12 0.9 G_insular_short 3224 1734 5526 2.488 0.534 0.127 0.036 53 4.4 G_occipital_middle 1452 837 2142 2.206 0.473 0.128 0.026 19 1.7 G_occipital_sup 1901 1215 4501 2.976 0.637 0.140 0.031 33 2.5 G_oc-temp_lat-fusifor 2672 1570 4023 2.214 0.654 0.131 0.035 35 3.7 G_oc-temp_med-Lingual 1158 783 3801 3.608 0.662 0.121 0.028 11 1.2 G_oc-temp_med-Parahip 2012 1357 5107 2.638 0.633 0.143 0.041 43 3.5 G_orbital 3209 1811 5987 2.517 0.612 0.127 0.038 48 5.3 G_pariet_inf-Angular 2625 1590 4441 2.276 0.564 0.126 0.036 38 4.0 G_pariet_inf-Supramar 2067 1254 3789 2.344 0.595 0.129 0.028 33 2.4 G_parietal_sup 2177 1124 3361 2.230 0.553 0.094 0.021 20 1.9 G_postcentral 2557 1329 5228 2.884 0.482 0.088 0.017 17 1.7 G_precentral 1982 1390 4441 2.577 0.573 0.158 0.039 38 3.1 G_precuneus 874 559 1978 2.469 0.570 0.139 0.044 19 1.6 G_rectus 190 131 441 2.946 0.807 0.096 0.021 1 0.1 G_subcallosal 384 227 711 2.579 0.261 0.084 0.013 3 0.2 G_temp_sup-G_T_transv 1934 1294 4360 2.511 0.820 0.149 0.041 37 3.7 G_temp_sup-Lateral 815 582 2157 3.233 0.761 0.101 0.021 6 0.6 G_temp_sup-Plan_polar 863 577 1472 2.310 0.500 0.095 0.018 7 0.5 G_temp_sup-Plan_tempo 2797 1812 7216 2.806 0.836 0.160 0.053 66 6.7 G_temporal_inf 3460 2175 6135 2.279 0.779 0.146 0.051 68 8.1 G_temporal_middle 314 223 392 2.099 0.383 0.088 0.013 1 0.1 Lat_Fis-ant-Horizont 157 122 195 1.973 0.309 0.122 0.016 1 0.1 Lat_Fis-ant-Vertical 1464 983 1999 2.459 0.554 0.105 0.016 8 1.0 Lat_Fis-post 3096 1825 4125 1.998 0.520 0.133 0.033 46 4.4 Pole_occipital 1534 1115 5426 3.341 0.778 0.155 0.035 31 2.5 Pole_temporal 1870 1248 2026 1.794 0.610 0.124 0.026 20 1.9 S_calcarine 2613 1807 2818 1.749 0.527 0.089 0.014 10 1.5 S_central 857 613 1302 2.526 0.475 0.119 0.020 6 0.8 S_cingul-Marginalis 485 338 751 2.681 0.578 0.085 0.013 1 0.3 S_circular_insula_ant 1301 873 2057 2.746 0.856 0.081 0.010 5 0.6 S_circular_insula_inf 1294 881 1925 2.511 0.387 0.102 0.017 6 1.0 S_circular_insula_sup 970 692 1690 2.619 0.402 0.090 0.010 4 0.4 S_collat_transv_ant 330 248 424 2.265 0.458 0.154 0.029 4 0.4 S_collat_transv_post 1904 1324 2735 2.129 0.412 0.110 0.020 14 1.4 S_front_inf 1926 1349 2742 1.905 0.548 0.126 0.027 20 2.1 S_front_middle 1886 1322 2847 2.329 0.419 0.106 0.018 10 1.5 S_front_sup 460 300 558 2.308 0.683 0.108 0.018 3 0.4 S_interm_prim-Jensen 2810 1913 3558 2.061 0.426 0.106 0.016 19 1.8 S_intrapariet&P_trans 1046 711 1195 2.011 0.353 0.114 0.022 7 1.0 S_oc_middle&Lunatus 1193 784 1656 2.240 0.481 0.117 0.025 10 1.1 S_oc_sup&transversal 1061 752 1715 2.383 0.559 0.134 0.025 13 1.1 S_occipital_ant 966 704 1649 2.528 0.423 0.117 0.018 7 0.7 S_oc-temp_lat 1697 1238 2823 2.646 0.635 0.104 0.015 10 1.1 S_oc-temp_med&Lingual 388 266 503 1.844 0.461 0.160 0.033 5 0.6 S_orbital_lateral 639 424 813 2.029 0.610 0.100 0.014 4 0.3 S_orbital_med-olfact 1005 719 1892 2.515 0.587 0.132 0.028 11 1.3 S_orbital-H_Shaped 2275 1527 3028 2.181 0.506 0.109 0.019 18 1.8 S_parieto_occipital 1137 677 1004 2.023 0.681 0.133 0.020 25 0.7 S_pericallosal 2167 1493 2937 2.051 0.482 0.117 0.021 21 1.7 S_postcentral 1349 927 2101 2.315 0.422 0.109 0.017 10 1.0 S_precentral-inf-part 926 639 1332 2.303 0.535 0.104 0.016 6 0.6 S_precentral-sup-part 365 256 449 1.955 0.320 0.130 0.024 3 0.4 S_suborbital 771 543 1139 2.097 0.519 0.125 0.025 7 0.7 S_subparietal 1338 933 1964 2.467 0.515 0.124 0.020 11 1.2 S_temporal_inf 6338 4378 9272 2.269 0.414 0.103 0.018 47 4.7 S_temporal_sup 118 83 192 2.170 0.272 0.045 0.005 0 0.0 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Sat Jun 2 20:44:53 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 He_Aiqun_ReoT1 lh ../surf/lh.sphere.reg /home/jianfeng/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/jianfeng/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... 1191 labels changed using aseg relabeling using gibbs priors... 000: 1746 changed, 119067 examined... 001: 403 changed, 8265 examined... 002: 110 changed, 2264 examined... 003: 52 changed, 646 examined... 004: 25 changed, 311 examined... 005: 7 changed, 152 examined... 006: 7 changed, 51 examined... 007: 6 changed, 45 examined... 008: 1 changed, 36 examined... 009: 0 changed, 7 examined... 143 labels changed using aseg 000: 49 total segments, 16 labels (191 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 560 vertices marked for relabeling... 560 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Sat Jun 2 20:45:10 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 He_Aiqun_ReoT1 rh ../surf/rh.sphere.reg /home/jianfeng/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/jianfeng/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... 1075 labels changed using aseg relabeling using gibbs priors... 000: 1809 changed, 123097 examined... 001: 434 changed, 8363 examined... 002: 127 changed, 2487 examined... 003: 48 changed, 766 examined... 004: 28 changed, 276 examined... 005: 26 changed, 152 examined... 006: 12 changed, 117 examined... 007: 11 changed, 56 examined... 008: 10 changed, 47 examined... 009: 6 changed, 42 examined... 010: 3 changed, 22 examined... 011: 3 changed, 13 examined... 012: 4 changed, 17 examined... 013: 5 changed, 24 examined... 014: 5 changed, 22 examined... 015: 2 changed, 25 examined... 016: 0 changed, 14 examined... 231 labels changed using aseg 000: 51 total segments, 18 labels (215 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 457 vertices marked for relabeling... 457 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Sat Jun 2 20:45:27 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 195731 Total vertex volume 193097 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1452 912 2573 2.692 0.494 0.116 0.024 19 1.3 caudalanteriorcingulate 2812 1835 5090 2.621 0.532 0.108 0.018 22 2.0 caudalmiddlefrontal 2281 1479 3213 1.965 0.479 0.142 0.032 38 3.2 cuneus 569 415 1628 3.031 0.691 0.142 0.038 8 0.9 entorhinal 3811 2634 7866 2.636 0.591 0.133 0.028 48 4.4 fusiform 6209 3872 9931 2.310 0.564 0.136 0.033 97 8.5 inferiorparietal 4560 3075 9648 2.691 0.719 0.137 0.037 75 7.6 inferiortemporal 1220 796 2149 2.332 0.929 0.145 0.034 23 1.6 isthmuscingulate 7204 4417 10142 2.017 0.551 0.129 0.029 95 8.4 lateraloccipital 3153 2120 6403 2.590 0.771 0.138 0.036 47 4.6 lateralorbitofrontal 4108 2718 5512 1.913 0.546 0.137 0.030 64 5.1 lingual 1985 1410 4006 2.329 0.702 0.145 0.045 45 2.9 medialorbitofrontal 6043 4067 10651 2.400 0.701 0.139 0.036 90 9.9 middletemporal 899 584 1813 2.788 0.713 0.096 0.017 6 0.6 parahippocampal 2109 1267 3436 2.532 0.581 0.097 0.020 16 1.8 paracentral 2077 1265 3648 2.496 0.475 0.100 0.028 24 2.5 parsopercularis 774 514 1633 2.575 0.644 0.120 0.021 9 0.6 parsorbitalis 2240 1389 3555 2.307 0.484 0.099 0.022 21 2.1 parstriangularis 1724 1208 2158 1.847 0.482 0.131 0.031 21 2.1 pericalcarine 6673 3951 8753 2.106 0.626 0.103 0.022 55 6.4 postcentral 1517 1010 2828 2.513 0.872 0.149 0.033 27 2.2 posteriorcingulate 6579 3873 10782 2.615 0.527 0.097 0.020 52 6.0 precentral 4002 2762 7504 2.524 0.552 0.141 0.030 58 4.8 precuneus 1543 991 2902 2.608 0.660 0.120 0.029 20 1.6 rostralanteriorcingulate 5472 3400 9977 2.473 0.576 0.130 0.029 80 6.7 rostralmiddlefrontal 9596 6148 19192 2.699 0.568 0.125 0.029 118 11.4 superiorfrontal 5531 3625 8194 2.028 0.516 0.119 0.023 68 5.1 superiorparietal 7282 4905 13196 2.462 0.654 0.117 0.028 78 8.6 superiortemporal 5802 3664 8727 2.281 0.600 0.123 0.031 61 7.5 supramarginal 658 419 960 2.379 0.519 0.146 0.024 8 0.5 transversetemporal 2274 1577 5028 3.094 0.725 0.111 0.021 16 2.0 insula #----------------------------------------- #@# Parcellation Stats 3 rh Sat Jun 2 20:46:07 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 209210 Total vertex volume 205398 (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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 958 593 1950 2.756 0.770 0.127 0.018 14 0.7 caudalanteriorcingulate 3074 2032 5703 2.531 0.569 0.115 0.023 28 2.8 caudalmiddlefrontal 2603 1619 3316 1.916 0.485 0.142 0.031 39 3.3 cuneus 524 388 1842 3.652 0.671 0.130 0.029 4 0.6 entorhinal 3432 2376 7622 2.901 0.618 0.125 0.024 43 3.2 fusiform 8598 5272 14378 2.421 0.516 0.119 0.030 103 10.4 inferiorparietal 5376 3678 12037 2.696 0.752 0.139 0.037 88 8.9 inferiortemporal 993 648 1861 2.331 0.909 0.133 0.033 17 1.0 isthmuscingulate 7469 4591 10666 2.146 0.536 0.132 0.029 105 9.1 lateraloccipital 3417 2350 6690 2.503 0.691 0.132 0.032 51 4.7 lateralorbitofrontal 4085 2552 5941 2.214 0.709 0.133 0.032 53 5.6 lingual 2071 1329 3902 2.384 0.641 0.125 0.033 32 2.7 medialorbitofrontal 6647 4376 11467 2.394 0.661 0.129 0.035 97 10.3 middletemporal 856 567 2001 3.054 0.769 0.088 0.013 5 0.4 parahippocampal 1902 1144 3233 2.619 0.688 0.112 0.024 16 2.1 paracentral 1935 1205 3368 2.490 0.459 0.115 0.028 24 2.3 parsopercularis 816 557 1752 2.427 0.541 0.129 0.029 12 1.0 parsorbitalis 2008 1339 3592 2.303 0.534 0.131 0.033 29 2.7 parstriangularis 1908 1247 1977 1.686 0.402 0.127 0.028 22 2.2 pericalcarine 6193 3770 8556 2.069 0.639 0.109 0.022 56 5.9 postcentral 1291 856 2809 2.865 0.647 0.132 0.029 19 1.5 posteriorcingulate 6140 3779 10390 2.488 0.619 0.098 0.017 42 4.1 precentral 4735 3269 8449 2.405 0.599 0.131 0.030 60 5.7 precuneus 1005 653 2338 3.059 0.557 0.128 0.026 13 1.0 rostralanteriorcingulate 5259 3593 9713 2.182 0.641 0.136 0.031 92 7.0 rostralmiddlefrontal 11076 7174 21796 2.626 0.568 0.122 0.026 157 12.1 superiorfrontal 5634 3530 8721 2.216 0.505 0.117 0.022 66 5.0 superiorparietal 6988 4746 14512 2.562 0.773 0.113 0.026 82 7.9 superiortemporal 5337 3373 8278 2.333 0.567 0.113 0.026 54 5.6 supramarginal 486 290 807 2.481 0.305 0.098 0.015 4 0.3 transversetemporal 2760 1860 5731 3.108 0.815 0.112 0.021 26 2.3 insula #----------------------------------------- #@# WM/GM Contrast lh Sat Jun 2 20:46:48 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts pctsurfcon --s He_Aiqun_ReoT1 --lh-only Log file is /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts/pctsurfcon.log Sat Jun 2 20:46:48 EDT 2018 setenv SUBJECTS_DIR /home/jianfeng/freesurfer/subjects cd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts /home/jianfeng/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux Precision-WorkStation-T3500 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/jianfeng/freesurfer mri_vol2surf --mov /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19865/lh.wm.mgh --regheader He_Aiqun_ReoT1 --cortex srcvol = /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00839 0.99871 0.05014 -0.00002; 0.99962 -0.00706 -0.02658 0.00001; -0.02620 0.05035 -0.99839 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label Reading surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 = 66444 Masking with /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label Writing to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19865/lh.wm.mgh Dim: 119067 1 1 mri_vol2surf --mov /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19865/lh.gm.mgh --projfrac 0.3 --regheader He_Aiqun_ReoT1 --cortex srcvol = /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00839 0.99871 0.05014 -0.00002; 0.99962 -0.00706 -0.02658 0.00001; -0.02620 0.05035 -0.99839 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label Reading surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Done reading source surface Reading thickness /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 = 80738 Masking with /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.cortex.label Writing to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19865/lh.gm.mgh Dim: 119067 1 1 mri_concat /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19865/lh.wm.mgh /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19865/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.w-g.pct.mgh mri_segstats --in /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.w-g.pct.mgh --annot He_Aiqun_ReoT1 lh aparc --sum /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.w-g.pct.mgh --annot He_Aiqun_ReoT1 lh aparc --sum /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/stats/lh.w-g.pct.stats --snr sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng UseRobust 0 Constructing seg from annotation Reading annotation /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.w-g.pct.mgh Vertex Area is 0.64562 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 Sat Jun 2 20:46:55 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts pctsurfcon --s He_Aiqun_ReoT1 --rh-only Log file is /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts/pctsurfcon.log Sat Jun 2 20:46:55 EDT 2018 setenv SUBJECTS_DIR /home/jianfeng/freesurfer/subjects cd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/scripts /home/jianfeng/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux Precision-WorkStation-T3500 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/jianfeng/freesurfer mri_vol2surf --mov /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19920/rh.wm.mgh --regheader He_Aiqun_ReoT1 --cortex srcvol = /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00839 0.99871 0.05014 -0.00002; 0.99962 -0.00706 -0.02658 0.00001; -0.02620 0.05035 -0.99839 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label Reading surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 = 69481 Masking with /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label Writing to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19920/rh.wm.mgh Dim: 123097 1 1 mri_vol2surf --mov /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19920/rh.gm.mgh --projfrac 0.3 --regheader He_Aiqun_ReoT1 --cortex srcvol = /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00839 0.99871 0.05014 -0.00002; 0.99962 -0.00706 -0.02658 0.00001; -0.02620 0.05035 -0.99839 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label Reading surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Done reading source surface Reading thickness /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 = 83762 Masking with /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.cortex.label Writing to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19920/rh.gm.mgh Dim: 123097 1 1 mri_concat /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19920/rh.wm.mgh /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/tmp.pctsurfcon.19920/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.w-g.pct.mgh mri_segstats --in /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.w-g.pct.mgh --annot He_Aiqun_ReoT1 rh aparc --sum /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.w-g.pct.mgh --annot He_Aiqun_ReoT1 rh aparc --sum /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/stats/rh.w-g.pct.stats --snr sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng UseRobust 0 Constructing seg from annotation Reading annotation /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.w-g.pct.mgh Vertex Area is 0.647057 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 Sat Jun 2 20:47:02 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 4999 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2913 voxels changed to hypointensity... 7809 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sat Jun 2 20:47:29 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 mri_aparc2aseg --s He_Aiqun_ReoT1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/jianfeng/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/jianfeng/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/jianfeng/freesurfer/subjects subject He_Aiqun_ReoT1 outvol /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading lh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial Loading lh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading rh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial Loading rh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 5.82 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 39 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 74 rescaling Left_Putamen from 80 --> 88 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 19 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 49 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 102 rescaling Right_Cerebral_Cortex from 58 --> 73 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 69 rescaling Right_Amygdala from 55 --> 70 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 77 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 = 396346 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 101 changed. pass 2: 13 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Sat Jun 2 20:53:38 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 mri_aparc2aseg --s He_Aiqun_ReoT1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/jianfeng/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/jianfeng/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/jianfeng/freesurfer/subjects subject He_Aiqun_ReoT1 outvol /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading lh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial Loading lh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading rh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial Loading rh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 5.82 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 39 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 74 rescaling Left_Putamen from 80 --> 88 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 19 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 49 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 102 rescaling Right_Cerebral_Cortex from 58 --> 73 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 69 rescaling Right_Amygdala from 55 --> 70 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 77 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 = 396178 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 101 changed. pass 2: 13 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sat Jun 2 20:59:49 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 mri_aparc2aseg --s He_Aiqun_ReoT1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/jianfeng/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/jianfeng/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/jianfeng/freesurfer/subjects subject He_Aiqun_ReoT1 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading lh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial Loading lh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading rh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial Loading rh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 5.82 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 39 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 74 rescaling Left_Putamen from 80 --> 88 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 19 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 49 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 102 rescaling Right_Cerebral_Cortex from 58 --> 73 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 69 rescaling Right_Amygdala from 55 --> 70 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 77 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 = 396178 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 101 changed. pass 2: 13 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Sat Jun 2 21:05:53 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sat Jun 2 21:05:53 EDT 2018 setenv SUBJECTS_DIR /home/jianfeng/freesurfer/subjects cd /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri /home/jianfeng/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 Precision-WorkStation-T3500 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 Precision-WorkStation-T3500 machine x86_64 user jianfeng 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 Sat Jun 2 21:05:53 EDT 2018 Ended at Sat Jun 2 21:06:01 EDT 2018 Apas2aseg-Run-Time-Sec 8 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sat Jun 2 21:06:01 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 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/jianfeng/freesurfer/ASegStatsLUT.txt --subject He_Aiqun_ReoT1 $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/jianfeng/freesurfer/ASegStatsLUT.txt --subject He_Aiqun_ReoT1 sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng UseRobust 0 atlas_icv (eTIV) = 1397872 mm^3 (det: 1.393622 ) Computing euler number orig.nofix lheno = -54, rheno = -44 orig.nofix lhholes = 28, rhholes = 23 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 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 Sat Jun 2 21:10:10 EDT 2018 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1 mri_aparc2aseg --s He_Aiqun_ReoT1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/jianfeng/freesurfer/subjects subject He_Aiqun_ReoT1 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aparc+aseg.mgz Reading lh white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading lh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial Loading lh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading rh pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial Loading rh annotations from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/ribbon.mgz Loading filled from /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 6820 vertices from left hemi Ripped 7520 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/aseg.mgz Loading Ctx Seg File /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 = 779594 Used brute-force search on 63 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1064.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 5.000000 Fixing Parahip RH WM Found 6 clusters 0 k 1188.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 4.000000 5 k 2.000000 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 He_Aiqun_ReoT1 --surf-wm-vol --ctab /home/jianfeng/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 He_Aiqun_ReoT1 --surf-wm-vol --ctab /home/jianfeng/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname Precision-WorkStation-T3500 machine x86_64 user jianfeng UseRobust 0 atlas_icv (eTIV) = 1397872 mm^3 (det: 1.393622 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label #-------------------------------------------- #@# BA_exvivo Labels lh Sat Jun 2 21:21:39 EDT 2018 mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 239 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4368 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4175 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 225 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5996 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4179 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 657 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14246 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4509 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 651 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4073 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 1102 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5743 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 2095 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10209 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 369 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2387 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1351 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1259 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1094 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1537 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2053 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2396 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1581 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 334 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7369 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2033 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1424 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 711 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4116 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 1002 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 608 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 496 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 119067 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 475 mri_label2label: Done mris_label2annot --s He_Aiqun_ReoT1 --hemi lh --ctab /home/jianfeng/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/jianfeng/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label cmdline mris_label2annot --s He_Aiqun_ReoT1 --hemi lh --ctab /home/jianfeng/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 Precision-WorkStation-T3500 machine x86_64 user jianfeng subject He_Aiqun_ReoT1 hemi lh SUBJECTS_DIR /home/jianfeng/freesurfer/subjects ColorTable /home/jianfeng/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 81825 unhit vertices Writing annot to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/lh.BA_exvivo.annot mris_label2annot --s He_Aiqun_ReoT1 --hemi lh --ctab /home/jianfeng/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/jianfeng/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label cmdline mris_label2annot --s He_Aiqun_ReoT1 --hemi lh --ctab /home/jianfeng/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 Precision-WorkStation-T3500 machine x86_64 user jianfeng subject He_Aiqun_ReoT1 hemi lh SUBJECTS_DIR /home/jianfeng/freesurfer/subjects ColorTable /home/jianfeng/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 97009 unhit vertices Writing annot to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 195731 Total vertex volume 193097 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/jianfeng/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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1085 510 1539 2.260 0.486 0.106 0.030 11 1.2 BA1_exvivo 3779 2333 5283 2.206 0.496 0.101 0.021 31 3.1 BA2_exvivo 956 659 917 1.708 0.459 0.133 0.025 8 1.0 BA3a_exvivo 2194 1340 2512 1.803 0.559 0.100 0.022 15 2.1 BA3b_exvivo 1455 791 2473 2.725 0.539 0.091 0.022 10 1.3 BA4a_exvivo 1150 713 1895 2.621 0.493 0.073 0.013 4 0.5 BA4p_exvivo 8102 4791 15680 2.823 0.531 0.109 0.024 85 8.5 BA6_exvivo 2041 1316 3676 2.460 0.418 0.104 0.027 23 2.5 BA44_exvivo 2943 1750 4966 2.399 0.515 0.109 0.025 35 3.3 BA45_exvivo 3151 2104 4030 1.808 0.502 0.132 0.036 44 4.7 V1_exvivo 7357 4601 9275 1.870 0.496 0.138 0.031 113 9.3 V2_exvivo 1931 1294 3431 2.296 0.531 0.143 0.029 28 2.6 MT_exvivo 529 335 1609 3.356 0.563 0.112 0.029 5 0.6 perirhinal_exvivo 569 459 1426 2.927 0.699 0.138 0.033 9 0.7 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 He_Aiqun_ReoT1 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 195731 Total vertex volume 193097 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/jianfeng/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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 720 295 1044 2.413 0.505 0.104 0.028 8 0.8 BA1_exvivo 1500 868 2179 2.278 0.488 0.075 0.014 8 0.7 BA2_exvivo 826 563 764 1.705 0.455 0.134 0.026 7 0.9 BA3a_exvivo 1318 879 1345 1.501 0.366 0.083 0.012 5 0.7 BA3b_exvivo 1408 778 2404 2.720 0.526 0.086 0.020 9 1.3 BA4a_exvivo 943 609 1567 2.590 0.514 0.082 0.014 4 0.5 BA4p_exvivo 4588 2626 8518 2.830 0.552 0.106 0.023 44 4.4 BA6_exvivo 1288 827 2297 2.418 0.437 0.102 0.031 16 1.9 BA44_exvivo 1226 611 2005 2.523 0.484 0.104 0.031 18 1.6 BA45_exvivo 3355 2250 4333 1.802 0.490 0.132 0.035 47 4.9 V1_exvivo 3775 2348 4507 1.778 0.441 0.147 0.033 69 5.2 V2_exvivo 512 333 792 2.153 0.507 0.131 0.026 6 0.6 MT_exvivo 283 170 902 3.482 0.525 0.106 0.025 2 0.3 perirhinal_exvivo 316 249 652 2.877 0.670 0.134 0.024 4 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sat Jun 2 21:27:15 EDT 2018 mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4226 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 259 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6946 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4052 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 171 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4693 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5912 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 386 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12642 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 458 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7370 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 682 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 1177 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5904 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 1917 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9933 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 951 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2883 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1120 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 822 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 976 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2768 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1723 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1425 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1536 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 199 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7158 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1080 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1391 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 781 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4013 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 906 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4343 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 756 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject He_Aiqun_ReoT1 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/jianfeng/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = He_Aiqun_ReoT1 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 /home/jianfeng/freesurfer/subjects FREESURFER_HOME /home/jianfeng/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/jianfeng/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white Reading target registration /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 123097 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 325 mri_label2label: Done mris_label2annot --s He_Aiqun_ReoT1 --hemi rh --ctab /home/jianfeng/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/jianfeng/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label cmdline mris_label2annot --s He_Aiqun_ReoT1 --hemi rh --ctab /home/jianfeng/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 Precision-WorkStation-T3500 machine x86_64 user jianfeng subject He_Aiqun_ReoT1 hemi rh SUBJECTS_DIR /home/jianfeng/freesurfer/subjects ColorTable /home/jianfeng/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 86978 unhit vertices Writing annot to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label/rh.BA_exvivo.annot mris_label2annot --s He_Aiqun_ReoT1 --hemi rh --ctab /home/jianfeng/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/jianfeng/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 /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/label cmdline mris_label2annot --s He_Aiqun_ReoT1 --hemi rh --ctab /home/jianfeng/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 Precision-WorkStation-T3500 machine x86_64 user jianfeng subject He_Aiqun_ReoT1 hemi rh SUBJECTS_DIR /home/jianfeng/freesurfer/subjects ColorTable /home/jianfeng/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 102675 unhit vertices Writing annot to /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/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 He_Aiqun_ReoT1 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 209210 Total vertex volume 205398 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/jianfeng/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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 1002 440 1522 2.443 0.497 0.100 0.027 11 1.1 BA1_exvivo 2637 1755 3889 2.083 0.492 0.107 0.020 23 2.0 BA2_exvivo 936 647 831 1.570 0.404 0.127 0.022 7 0.8 BA3a_exvivo 1795 1098 2300 1.799 0.594 0.087 0.017 11 1.2 BA3b_exvivo 1316 746 2196 2.548 0.608 0.089 0.017 9 1.0 BA4a_exvivo 1111 711 1639 2.321 0.538 0.079 0.014 4 0.6 BA4p_exvivo 6520 4070 13348 2.800 0.603 0.105 0.020 50 5.5 BA6_exvivo 2816 1905 5058 2.420 0.449 0.123 0.022 33 2.5 BA44_exvivo 3710 2397 6704 2.328 0.539 0.130 0.035 56 5.3 BA45_exvivo 3590 2175 4338 1.846 0.529 0.127 0.033 47 4.8 V1_exvivo 7001 4365 9547 2.074 0.599 0.141 0.032 100 9.6 V2_exvivo 2765 1798 4403 2.332 0.492 0.127 0.030 36 3.3 MT_exvivo 556 389 1941 3.637 0.624 0.111 0.021 4 0.5 perirhinal_exvivo 364 280 1095 3.610 0.666 0.126 0.023 4 0.3 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 He_Aiqun_ReoT1 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/mri/wm.mgz... reading input surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... reading input pial surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.pial... reading input white surface /home/jianfeng/freesurfer/subjects/He_Aiqun_ReoT1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 209210 Total vertex volume 205398 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/jianfeng/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) = 1397872 mm^3 (det: 1.393622 ) lhCtxGM: 192613.226 192147.000 diff= 466.2 pctdiff= 0.242 rhCtxGM: 205441.622 204928.000 diff= 513.6 pctdiff= 0.250 lhCtxWM: 186993.423 187358.000 diff= -364.6 pctdiff=-0.195 rhCtxWM: 197101.083 197813.000 diff= -711.9 pctdiff=-0.361 SubCortGMVol 48996.000 SupraTentVol 847749.354 (845616.000) diff=2133.354 pctdiff=0.252 SupraTentVolNotVent 833382.354 (831249.000) diff=2133.354 pctdiff=0.256 BrainSegVol 971430.000 (968745.000) diff=2685.000 pctdiff=0.276 BrainSegVolNotVent 953192.000 (952885.354) diff=306.646 pctdiff=0.032 BrainSegVolNotVent 953192.000 CerebellumVol 121733.000 VentChorVol 14367.000 3rd4th5thCSF 3871.000 CSFVol 1186.000, OptChiasmVol 210.000 MaskVol 1342522.000 717 300 1053 2.350 0.533 0.101 0.028 9 0.8 BA1_exvivo 1591 1056 2375 2.053 0.516 0.102 0.017 13 1.2 BA2_exvivo 827 581 658 1.492 0.288 0.133 0.021 7 0.7 BA3a_exvivo 1405 886 1503 1.604 0.441 0.077 0.012 6 0.7 BA3b_exvivo 833 438 1387 2.638 0.733 0.122 0.033 9 1.3 BA4a_exvivo 942 600 1403 2.395 0.549 0.076 0.015 3 0.6 BA4p_exvivo 4212 2529 8754 2.844 0.576 0.100 0.019 31 3.2 BA6_exvivo 704 490 1418 2.419 0.428 0.138 0.024 12 0.7 BA44_exvivo 1055 654 1991 2.374 0.561 0.136 0.047 18 2.2 BA45_exvivo 3404 2055 4016 1.837 0.520 0.126 0.033 44 4.5 V1_exvivo 3749 2262 4954 2.011 0.576 0.146 0.035 58 5.6 V2_exvivo 384 263 690 2.315 0.489 0.134 0.034 5 0.5 MT_exvivo 334 231 1177 3.662 0.623 0.108 0.020 2 0.2 perirhinal_exvivo 265 197 669 3.586 0.688 0.132 0.019 2 0.2 entorhinal_exvivo Started at Sat Jun 2 09:08:26 EDT 2018 Ended at Sat Jun 2 21:32:57 EDT 2018 #@#%# recon-all-run-time-hours 12.409 recon-all -s He_Aiqun_ReoT1 finished without error at Sat Jun 2 21:32:57 EDT 2018