2021��� 11��� 16��� ��������� 07:17:30 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1 /opt/freesurfer/bin/recon-all -s NC1 -i /home/siying/sharefolder/freesurfer_1/CON_1.nii.gz subjid NC1 setenv SUBJECTS_DIR /home/siying/sharefolder/piantoutong/freesurfer_1 FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 24719 maxlocks unlimited maxsignal 24719 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 6389640 705216 3851696 15376 1832728 5344100 Swap: 2206716 0 2206716 ######################################## 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: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:17:30-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/siying/sharefolder/piantoutong/freesurfer_1/NC1 mri_convert /home/siying/sharefolder/freesurfer_1/CON_1.nii.gz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig/001.mgz mri_convert.bin /home/siying/sharefolder/freesurfer_1/CON_1.nii.gz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/siying/sharefolder/freesurfer_1/CON_1.nii.gz... WARNING: hdr.dim[4] = 0 (nframes), setting to 1 TR=1300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999178, 0.030546, -0.0266626) j_ras = (-0.0310765, 0.999323, -0.0197139) k_ras = (0.0260424, 0.0205263, 0.99945) writing to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig/001.mgz... Started at 2021��� 11��� 16��� ��������� 07:17:30 CST Ended at 2021��� 11��� 16��� ��������� 07:17:34 CST #@#%# recon-all-run-time-hours 0.001 recon-all -s NC1 finished without error at 2021��� 11��� 16��� ��������� 07:17:34 CST New invocation of recon-all 2021��� 11��� 16��� ��������� 07:20:35 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1 /opt/freesurfer/bin/recon-all -s NC1 -all subjid NC1 setenv SUBJECTS_DIR /home/siying/sharefolder/piantoutong/freesurfer_1 FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 24719 maxlocks unlimited maxsignal 24719 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 6389640 706708 3346960 15376 2335972 5342552 Swap: 2206716 0 2206716 ######################################## 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: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/15-23:20:35-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor 2021��� 11��� 16��� ��������� 07:20:35 CST Found 1 runs /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig/001.mgz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/rawavg.mgz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1 mri_convert /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/rawavg.mgz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig.mgz --conform mri_convert.bin /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/rawavg.mgz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/rawavg.mgz... TR=1300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999178, 0.030546, -0.0266626) j_ras = (-0.0310765, 0.999323, -0.0197139) k_ras = (0.0260424, 0.0205263, 0.99945) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig.mgz... mri_add_xform_to_header -c /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/transforms/talairach.xfm /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig.mgz /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach 2021��� 11��� 16��� ��������� 07:20:42 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri /opt/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 siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 2021��� 11��� 16��� ��������� 07:20:43 CST 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.9464 /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9464/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9464/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.567e-10, 0) j_ras = (1.86265e-09, 0, -1) k_ras = (5.82077e-11, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9464/nu0.mnc... -------------------------------------------------------- Iteration 1 2021��� 11��� 16��� ��������� 07:20:46 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.9464/nu0.mnc ./tmp.mri_nu_correct.mni.9464/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9464/0/ -iterations 1000 -distance 50 [siying@siying-VM:/home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/] [2021-11-16 07:20:46] running: /opt/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.9464/0/ ./tmp.mri_nu_correct.mni.9464/nu0.mnc ./tmp.mri_nu_correct.mni.9464/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 53 CV of field change: 0.000975936 mri_convert ./tmp.mri_nu_correct.mni.9464/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9464/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.9464/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.567e-10, 0) j_ras = (1.86265e-09, 0, -1) k_ras = (5.82077e-11, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... 2021��� 11��� 16��� ��������� 07:22:00 CST 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 2021��� 11��� 16��� ��������� 07:22:00 CST Ended at 2021��� 11��� 16��� ��������� 07:22:21 CST talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection 2021��� 11��� 16��� ��������� 07:22:23 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7140, pval=0.4932 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/transforms/talairach_avi.log tal_QC_AZS /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/transforms/talairach_avi.log TalAviQA: 0.97982 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction 2021��� 11��� 16��� ��������� 07:22:23 CST mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri /opt/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 siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 2021��� 11��� 16��� ��������� 07:22:23 CST 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.10339 /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10339/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10339/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.567e-10, 0) j_ras = (1.86265e-09, 0, -1) k_ras = (5.82077e-11, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10339/nu0.mnc... -------------------------------------------------------- Iteration 1 2021��� 11��� 16��� ��������� 07:22:26 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.10339/nu0.mnc ./tmp.mri_nu_correct.mni.10339/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10339/0/ [siying@siying-VM:/home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/] [2021-11-16 07:22:26] running: /opt/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.10339/0/ ./tmp.mri_nu_correct.mni.10339/nu0.mnc ./tmp.mri_nu_correct.mni.10339/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00107339 -------------------------------------------------------- Iteration 2 2021��� 11��� 16��� ��������� 07:23:21 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.10339/nu1.mnc ./tmp.mri_nu_correct.mni.10339/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10339/1/ [siying@siying-VM:/home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/] [2021-11-16 07:23:21] running: /opt/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.10339/1/ ./tmp.mri_nu_correct.mni.10339/nu1.mnc ./tmp.mri_nu_correct.mni.10339/nu2.imp Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 28 CV of field change: 0.000971468 mri_binarize --i ./tmp.mri_nu_correct.mni.10339/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10339/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10339/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10339/ones.mgz sysname Linux hostname siying-VM machine x86_64 user siying input ./tmp.mri_nu_correct.mni.10339/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10339/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.10339/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10339/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10339/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.10339/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10339/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10339/input.mean.dat sysname Linux hostname siying-VM machine x86_64 user siying UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10339/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.10339/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10339/ones.mgz --i ./tmp.mri_nu_correct.mni.10339/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10339/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10339/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.10339/ones.mgz --i ./tmp.mri_nu_correct.mni.10339/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10339/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10339/output.mean.dat sysname Linux hostname siying-VM machine x86_64 user siying UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10339/ones.mgz Loading ./tmp.mri_nu_correct.mni.10339/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.10339/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10339/nu2.mnc ./tmp.mri_nu_correct.mni.10339/nu2.mnc mul .96305930821306201228 Saving result to './tmp.mri_nu_correct.mni.10339/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10339/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10339/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.10339/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.567e-10, 0) j_ras = (1.86265e-09, 0, -1) k_ras = (5.82077e-11, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 5 seconds. mapping ( 5, 104) to ( 3, 110) 2021��� 11��� 16��� ��������� 07:24:31 CST mri_nu_correct.mni done mri_add_xform_to_header -c /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization 2021��� 11��� 16��� ��������� 07:24:31 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 1.06923 0.03146 -0.07100 4.90837; 0.01741 0.98146 0.28065 -5.04463; 0.06100 -0.29120 1.05280 -74.33612; 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 = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 79 (79), valley at 39 (39) 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 77 (77), valley at 35 (35) csf peak at 39, setting threshold to 64 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 20 seconds. #-------------------------------------------- #@# Skull Stripping 2021��� 11��� 16��� ��������� 07:25:52 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_em_register -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /opt/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 '/opt/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=6.0 skull bounding box = (51, 41, 15) --> (210, 216, 215) using (104, 99, 115) as brain centroid... mean wm in atlas = 108, using box (84,77,90) --> (123, 120,139) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 4.1 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.311 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.311097 @ (0.000, 0.000, 0.000) max log p = -4.311097 @ (0.000, 0.000, 0.000) max log p = -4.274507 @ (-2.273, 2.273, -6.818) max log p = -4.249509 @ (1.136, -1.136, 1.136) max log p = -4.244206 @ (-1.705, -2.841, 0.568) max log p = -4.244206 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -1.7, -5.1): log p = -4.244 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.072, old_max_log_p =-4.244 (thresh=-4.2) 1.07500 0.00000 0.00000 -12.41963; 0.00000 1.19413 0.31997 -58.13785; 0.00000 -0.27532 1.02750 23.80746; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.066, old_max_log_p =-4.072 (thresh=-4.1) 1.07500 0.00000 0.00000 -12.41963; 0.00000 1.21985 0.18311 -45.05327; 0.00000 -0.10832 0.98094 14.34549; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.066, old_max_log_p =-4.066 (thresh=-4.1) 1.07500 0.00000 0.00000 -12.41963; 0.00000 1.21985 0.18311 -45.05327; 0.00000 -0.10832 0.98094 14.34549; 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=-3.982, old_max_log_p =-4.066 (thresh=-4.1) 1.05202 -0.06779 -0.05146 2.04823; 0.07163 1.21508 0.31471 -68.48975; 0.03510 -0.27902 0.98303 29.04615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.982, old_max_log_p =-3.982 (thresh=-4.0) 1.05202 -0.06779 -0.05146 2.04823; 0.07163 1.21508 0.31471 -68.48975; 0.03510 -0.27902 0.98303 29.04615; 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=-3.965, old_max_log_p =-3.982 (thresh=-4.0) 1.04981 -0.06990 -0.04331 2.14065; 0.07188 1.21935 0.31582 -69.23094; 0.02646 -0.27813 0.98227 30.15642; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.957, old_max_log_p =-3.965 (thresh=-4.0) 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.957, old_max_log_p =-3.957 (thresh=-4.0) 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 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 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.957 (old=-4.311) transform before final EM align: 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 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 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 1.05227 -0.07007 -0.04341 1.85298; 0.07188 1.21935 0.31582 -69.23094; 0.02655 -0.27911 0.98572 29.87226; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 763.281200 mri_em_register stimesec 1.492010 mri_em_register ru_maxrss 613920 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161747 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 551 mri_em_register ru_nivcsw 6424 registration took 12 minutes and 45 seconds. mri_watershed -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mri_watershed.dat -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=130 y=118 z=112 r=76 first estimation of the main basin volume: 1846104 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=148, y=105, z=75, Imax=255 CSF=19, 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=414719241 voxels, voxel volume =1.000 = 414719241 mmm3 = 414719.232 cm3 done. PostAnalyze...Basin Prior 1 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=121, z=107, r=9653 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=64 , nb = 42293 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1053903662 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=26 , nb = -1040841808 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=64 , nb = 1074032331 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=71 , nb = 1081117926 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=11 , nb = 1076506970 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 64, 51, 46, 71 after analyzing : 39, 51, 51, 56 RIGHT_CER before analyzing : 24, 39, 55, 77 after analyzing : 24, 49, 55, 56 LEFT_CER before analyzing : 26, 41, 54, 73 after analyzing : 26, 49, 54, 55 RIGHT_BRAIN before analyzing : 64, 51, 46, 71 after analyzing : 39, 51, 51, 56 LEFT_BRAIN before analyzing : 71, 52, 45, 71 after analyzing : 41, 52, 52, 56 OTHER before analyzing : 11, 33, 77, 91 after analyzing : 11, 62, 77, 69 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.322, std = 7.392 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.68, sigma = 4.03 after rotation: sse = 2.68, sigma = 4.03 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.93, its var is 4.26 before Erosion-Dilatation 0.62% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1681480 voxels, voxel volume = 1.000 mm3 = 1681480 mmm3 = 1681.480 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 13.695338 mri_watershed stimesec 0.253468 mri_watershed ru_maxrss 833000 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211746 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1184 mri_watershed ru_nivcsw 74 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration 2021��� 11��� 16��� ��������� 07:38:52 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_em_register -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/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 '/opt/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=28.1 skull bounding box = (61, 59, 30) --> (197, 206, 195) using (106, 108, 113) as brain centroid... mean wm in atlas = 107, using box (89,90,93) --> (122, 126,133) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.6 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -3.810 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.765278 @ (0.000, 0.000, 0.000) max log p = -3.753176 @ (-4.545, -4.545, -4.545) max log p = -3.689498 @ (2.273, 2.273, -2.273) max log p = -3.686956 @ (1.136, 1.136, 1.136) max log p = -3.672464 @ (-0.568, -1.705, -1.705) max log p = -3.672464 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -2.8, -7.4): log p = -3.672 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.538, old_max_log_p =-3.672 (thresh=-3.7) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.03837 0.27823 -31.42005; 0.00000 -0.25882 0.96593 35.56806; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.538, old_max_log_p =-3.538 (thresh=-3.5) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.03837 0.27823 -31.42005; 0.00000 -0.25882 0.96593 35.56806; 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=-3.343, old_max_log_p =-3.538 (thresh=-3.5) 1.01311 -0.06414 -0.01719 4.04554; 0.07027 1.02712 0.30909 -46.19951; -0.00234 -0.29807 0.97426 37.79154; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.343, old_max_log_p =-3.343 (thresh=-3.3) 1.01311 -0.06414 -0.01719 4.04554; 0.07027 1.02712 0.30909 -46.19951; -0.00234 -0.29807 0.97426 37.79154; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.333, old_max_log_p =-3.343 (thresh=-3.3) 1.01480 -0.05813 -0.00673 1.99070; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.323, old_max_log_p =-3.333 (thresh=-3.3) 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.323, old_max_log_p =-3.323 (thresh=-3.3) 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 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 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.323 (old=-3.810) transform before final EM align: 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 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 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 565.828533 mri_em_register stimesec 1.348220 mri_em_register ru_maxrss 603236 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162496 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 774 mri_em_register ru_nivcsw 2259 registration took 9 minutes and 28 seconds. #-------------------------------------- #@# CA Normalize 2021��� 11��� 16��� ��������� 07:48:20 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/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 '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.0 skull bounding box = (61, 59, 30) --> (197, 206, 195) using (106, 108, 113) as brain centroid... mean wm in atlas = 107, using box (89,90,93) --> (122, 126,133) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.6 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246344 sample points... INFO: compute sample coordinates transform 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 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 (130, 58, 34) --> (196, 169, 194) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 2 of 8042 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 59, 32) --> (131, 165, 195) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 3 of 9124 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (133, 146, 63) --> (182, 184, 116) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 333 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 61) --> (132, 186, 117) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 293 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 131, 97) --> (150, 196, 127) Brain_Stem: limiting intensities to 90.0 --> 132.0 0 of 529 (0.0%) samples deleted using 18321 total control points for intensity normalization... bias field = 0.976 +- 0.055 129 of 18316 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 58, 34) --> (196, 169, 194) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 4 of 8261 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 59, 32) --> (131, 165, 195) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 5 of 9389 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (133, 146, 63) --> (182, 184, 116) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 27 of 434 (6.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 61) --> (132, 186, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 348 (4.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 131, 97) --> (150, 196, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 74 of 664 (11.1%) samples deleted using 19096 total control points for intensity normalization... bias field = 1.014 +- 0.040 117 of 18901 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 58, 34) --> (196, 169, 194) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 5 of 8351 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 59, 32) --> (131, 165, 195) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 12 of 9371 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (133, 146, 63) --> (182, 184, 116) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 106 of 456 (23.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 61) --> (132, 186, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 203 of 386 (52.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 131, 97) --> (150, 196, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 226 of 664 (34.0%) samples deleted using 19228 total control points for intensity normalization... bias field = 1.009 +- 0.033 91 of 18549 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 55 seconds. #-------------------------------------- #@# CA Reg 2021��� 11��� 16��� ��������� 07:49:16 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_ca_register -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/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 '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.12 (predicted orig area = 7.2) 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=0.824, neg=0, invalid=762 0001: dt=221.504442, rms=0.739 (10.294%), neg=0, invalid=762 0002: dt=161.549474, rms=0.716 (3.072%), neg=0, invalid=762 0003: dt=228.977778, rms=0.706 (1.409%), neg=0, invalid=762 0004: dt=161.655172, rms=0.700 (0.900%), neg=0, invalid=762 0005: dt=221.952000, rms=0.696 (0.514%), neg=0, invalid=762 0006: dt=129.472000, rms=0.693 (0.409%), neg=0, invalid=762 0007: dt=517.888000, rms=0.689 (0.615%), neg=0, invalid=762 0008: dt=129.472000, rms=0.687 (0.263%), neg=0, invalid=762 0009: dt=517.888000, rms=0.685 (0.323%), neg=0, invalid=762 0010: dt=110.976000, rms=0.684 (0.200%), neg=0, invalid=762 0011: dt=110.976000, rms=0.683 (0.070%), neg=0, invalid=762 0012: dt=110.976000, rms=0.683 (0.115%), neg=0, invalid=762 0013: dt=110.976000, rms=0.682 (0.146%), neg=0, invalid=762 0014: dt=110.976000, rms=0.680 (0.166%), neg=0, invalid=762 0015: dt=110.976000, rms=0.679 (0.189%), neg=0, invalid=762 0016: dt=110.976000, rms=0.678 (0.176%), neg=0, invalid=762 0017: dt=110.976000, rms=0.677 (0.128%), neg=0, invalid=762 0018: dt=110.976000, rms=0.676 (0.099%), neg=0, invalid=762 0019: dt=110.976000, rms=0.676 (0.072%), neg=0, invalid=762 0020: dt=1775.616000, rms=0.675 (0.155%), neg=0, invalid=762 0021: dt=221.952000, rms=0.674 (0.163%), neg=0, invalid=762 0022: dt=73.984000, rms=0.674 (0.009%), neg=0, invalid=762 0023: dt=73.984000, rms=0.674 (0.017%), neg=0, invalid=762 0024: dt=73.984000, rms=0.673 (0.017%), neg=0, invalid=762 0025: dt=73.984000, rms=0.673 (0.013%), neg=0, invalid=762 0026: dt=73.984000, rms=0.673 (0.017%), neg=0, invalid=762 0027: dt=73.984000, rms=0.673 (0.046%), neg=0, invalid=762 0028: dt=73.984000, rms=0.673 (0.041%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=762 0029: dt=295.936000, rms=0.670 (0.460%), neg=0, invalid=762 0030: dt=129.472000, rms=0.670 (0.074%), neg=0, invalid=762 0031: dt=129.472000, rms=0.669 (0.033%), neg=0, invalid=762 0032: dt=129.472000, rms=0.669 (0.043%), neg=0, invalid=762 0033: dt=129.472000, rms=0.669 (0.074%), neg=0, invalid=762 0034: dt=129.472000, rms=0.668 (0.085%), neg=0, invalid=762 0035: dt=129.472000, rms=0.667 (0.108%), neg=0, invalid=762 0036: dt=129.472000, rms=0.667 (0.113%), neg=0, invalid=762 0037: dt=129.472000, rms=0.666 (0.115%), neg=0, invalid=762 0038: dt=129.472000, rms=0.665 (0.092%), neg=0, invalid=762 0039: dt=129.472000, rms=0.665 (0.068%), neg=0, invalid=762 0040: dt=517.888000, rms=0.664 (0.077%), neg=0, invalid=762 0041: dt=73.984000, rms=0.664 (0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 0042: dt=103.680000, rms=0.664 (0.822%), neg=0, invalid=762 0043: dt=276.136861, rms=0.649 (2.301%), neg=0, invalid=762 0044: dt=48.000000, rms=0.645 (0.583%), neg=0, invalid=762 0045: dt=145.152000, rms=0.643 (0.331%), neg=0, invalid=762 0046: dt=216.421053, rms=0.636 (0.994%), neg=0, invalid=762 0047: dt=36.288000, rms=0.634 (0.322%), neg=0, invalid=762 0048: dt=36.288000, rms=0.634 (0.076%), neg=0, invalid=762 0049: dt=36.288000, rms=0.633 (0.076%), neg=0, invalid=762 0050: dt=36.288000, rms=0.632 (0.141%), neg=0, invalid=762 0051: dt=36.288000, rms=0.631 (0.223%), neg=0, invalid=762 0052: dt=36.288000, rms=0.629 (0.343%), neg=0, invalid=762 0053: dt=36.288000, rms=0.626 (0.413%), neg=0, invalid=762 0054: dt=36.288000, rms=0.624 (0.413%), neg=0, invalid=762 0055: dt=36.288000, rms=0.621 (0.385%), neg=0, invalid=762 0056: dt=36.288000, rms=0.619 (0.332%), neg=0, invalid=762 0057: dt=36.288000, rms=0.617 (0.309%), neg=0, invalid=762 0058: dt=36.288000, rms=0.615 (0.306%), neg=0, invalid=762 0059: dt=36.288000, rms=0.613 (0.314%), neg=0, invalid=762 0060: dt=36.288000, rms=0.612 (0.307%), neg=0, invalid=762 0061: dt=36.288000, rms=0.610 (0.277%), neg=0, invalid=762 0062: dt=36.288000, rms=0.608 (0.232%), neg=0, invalid=762 0063: dt=36.288000, rms=0.607 (0.203%), neg=0, invalid=762 0064: dt=36.288000, rms=0.606 (0.187%), neg=0, invalid=762 0065: dt=36.288000, rms=0.605 (0.159%), neg=0, invalid=762 0066: dt=36.288000, rms=0.604 (0.143%), neg=0, invalid=762 0067: dt=36.288000, rms=0.604 (0.117%), neg=0, invalid=762 0068: dt=36.288000, rms=0.603 (0.109%), neg=0, invalid=762 0069: dt=145.152000, rms=0.602 (0.072%), neg=0, invalid=762 0070: dt=145.152000, rms=0.602 (-0.185%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=762 0071: dt=109.629630, rms=0.600 (0.523%), neg=0, invalid=762 0072: dt=82.944000, rms=0.599 (0.134%), neg=0, invalid=762 0073: dt=82.944000, rms=0.599 (0.077%), neg=0, invalid=762 0074: dt=82.944000, rms=0.598 (0.108%), neg=0, invalid=762 0075: dt=82.944000, rms=0.597 (0.094%), neg=0, invalid=762 0076: dt=82.944000, rms=0.597 (0.018%), neg=0, invalid=762 0077: dt=36.288000, rms=0.597 (0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=762 0078: dt=11.200000, rms=0.621 (0.309%), neg=0, invalid=762 0079: dt=6.400000, rms=0.621 (0.032%), neg=0, invalid=762 0080: dt=6.400000, rms=0.621 (0.014%), neg=0, invalid=762 0081: dt=6.400000, rms=0.621 (-0.040%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0082: dt=2.800000, rms=0.621 (0.132%), neg=0, invalid=762 0083: dt=2.400000, rms=0.621 (0.005%), neg=0, invalid=762 0084: dt=2.400000, rms=0.621 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.677, neg=0, invalid=762 0085: dt=5.565657, rms=0.665 (1.843%), neg=0, invalid=762 0086: dt=4.764706, rms=0.664 (0.201%), neg=0, invalid=762 0087: dt=4.764706, rms=0.664 (0.007%), neg=0, invalid=762 0088: dt=4.764706, rms=0.664 (-0.250%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0089: dt=0.000000, rms=0.664 (0.109%), neg=0, invalid=762 0090: dt=0.000000, rms=0.664 (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=0.710, neg=0, invalid=762 0091: dt=0.000000, rms=0.709 (0.095%), neg=0, invalid=762 0092: dt=0.000000, rms=0.709 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.710, neg=0, invalid=762 0093: dt=0.112000, rms=0.709 (0.105%), neg=0, invalid=762 0094: dt=0.112000, rms=0.709 (0.003%), neg=0, invalid=762 0095: dt=0.112000, rms=0.709 (0.001%), neg=0, invalid=762 0096: dt=0.112000, rms=0.709 (-0.014%), 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=0.637, neg=0, invalid=762 0097: dt=0.751366, rms=0.622 (2.281%), neg=0, invalid=762 0098: dt=0.064000, rms=0.622 (0.106%), neg=0, invalid=762 0099: dt=0.064000, rms=0.622 (-0.052%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0100: dt=0.028000, rms=0.621 (0.136%), neg=0, invalid=762 0101: dt=0.003000, rms=0.621 (0.003%), neg=0, invalid=762 0102: dt=0.003000, rms=0.621 (0.000%), neg=0, invalid=762 0103: dt=0.003000, rms=0.621 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10917 (30) Left_Lateral_Ventricle (4): linear fit = 1.68 x + 0.0 (1116 voxels, overlap=0.244) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1116 voxels, peak = 34), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.16628 (31) Right_Lateral_Ventricle (43): linear fit = 1.85 x + 0.0 (885 voxels, overlap=0.165) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (885 voxels, peak = 30), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09932 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (1030 voxels, overlap=0.609) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (1030 voxels, peak = 101), gca=101.3 gca peak = 0.20183 (93) mri peak = 0.07785 (103) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (874 voxels, overlap=0.964) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (874 voxels, peak = 101), gca=100.9 gca peak = 0.21683 (55) mri peak = 0.08893 (74) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1250 voxels, overlap=0.014) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1250 voxels, peak = 71), gca=71.2 gca peak = 0.30730 (58) mri peak = 0.07710 (72) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1110 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1110 voxels, peak = 73), gca=72.8 gca peak = 0.11430 (101) mri peak = 0.16444 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (77644 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (77644 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.13209 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (78509 voxels, overlap=0.353) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (78509 voxels, peak = 108), gca=107.6 gca peak = 0.14995 (59) mri peak = 0.03431 (67) Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (37595 voxels, overlap=0.157) Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (37595 voxels, peak = 69), gca=69.3 gca peak = 0.15082 (58) mri peak = 0.04185 (69) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (38686 voxels, overlap=0.050) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (38686 voxels, peak = 69), gca=69.3 gca peak = 0.14161 (67) mri peak = 0.08523 (86) Right_Caudate (50): linear fit = 1.23 x + 0.0 (949 voxels, overlap=0.012) Right_Caudate (50): linear fit = 1.23 x + 0.0 (949 voxels, peak = 82), gca=82.1 gca peak = 0.15243 (71) mri peak = 0.07863 (87) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1160 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1160 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.04706 (71) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (30091 voxels, overlap=0.086) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (30091 voxels, peak = 70), gca=70.4 gca peak = 0.13252 (56) mri peak = 0.04950 (68) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (34725 voxels, overlap=0.014) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (34725 voxels, peak = 71), gca=70.8 gca peak = 0.18181 (84) mri peak = 0.11069 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10555 voxels, overlap=0.566) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10555 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.12285 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8942 voxels, overlap=0.814) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8942 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.09958 (76) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (491 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (491 voxels, peak = 75), gca=75.0 gca peak = 0.39313 (56) mri peak = 0.10448 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (575 voxels, overlap=0.028) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (575 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.07275 (99) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5985 voxels, overlap=0.174) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5985 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.07277 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4916 voxels, overlap=0.422) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4916 voxels, peak = 93), gca=93.4 gca peak = 0.13399 (79) mri peak = 0.05792 (96) Left_Putamen (12): linear fit = 1.22 x + 0.0 (2754 voxels, overlap=0.011) Left_Putamen (12): linear fit = 1.22 x + 0.0 (2754 voxels, peak = 96), gca=96.0 gca peak = 0.14159 (79) mri peak = 0.07301 (93) Right_Putamen (51): linear fit = 1.20 x + 0.0 (2812 voxels, overlap=0.050) Right_Putamen (51): linear fit = 1.20 x + 0.0 (2812 voxels, peak = 94), gca=94.4 gca peak = 0.10025 (80) mri peak = 0.10320 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12821 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12821 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.09423 (98) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1187 voxels, overlap=0.183) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1187 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.11377 (98) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1486 voxels, overlap=0.160) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1486 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.19298 (28) Fourth_Ventricle (15): linear fit = 1.37 x + 0.0 (528 voxels, overlap=0.312) Fourth_Ventricle (15): linear fit = 1.37 x + 0.0 (528 voxels, peak = 29), gca=28.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak 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 1.25 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.45 x + 0.0 Left_Putamen too bright - rescaling by 0.995 (from 1.215) to 95.5 (was 96.0) Right_Putamen too bright - rescaling by 1.011 (from 1.195) to 95.5 (was 94.4) 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=0.611, neg=0, invalid=762 0104: dt=85.718710, rms=0.598 (2.072%), neg=0, invalid=762 0105: dt=92.480000, rms=0.597 (0.200%), neg=0, invalid=762 0106: dt=129.472000, rms=0.596 (0.198%), neg=0, invalid=762 0107: dt=517.888000, rms=0.593 (0.466%), neg=0, invalid=762 0108: dt=517.888000, rms=0.590 (0.533%), neg=0, invalid=762 0109: dt=295.936000, rms=0.588 (0.266%), neg=0, invalid=762 0110: dt=32.368000, rms=0.588 (0.014%), neg=0, invalid=762 0111: dt=32.368000, rms=0.588 (0.004%), neg=0, invalid=762 0112: dt=32.368000, rms=0.588 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=762 0113: dt=369.920000, rms=0.585 (0.533%), neg=0, invalid=762 0114: dt=110.976000, rms=0.585 (0.053%), neg=0, invalid=762 0115: dt=443.904000, rms=0.585 (0.099%), neg=0, invalid=762 0116: dt=129.472000, rms=0.584 (0.060%), neg=0, invalid=762 0117: dt=369.920000, rms=0.584 (0.106%), neg=0, invalid=762 0118: dt=92.480000, rms=0.583 (0.043%), neg=0, invalid=762 0119: dt=92.480000, rms=0.583 (0.024%), neg=0, invalid=762 0120: dt=92.480000, rms=0.583 (0.038%), neg=0, invalid=762 0121: dt=92.480000, rms=0.583 (0.053%), neg=0, invalid=762 0122: dt=92.480000, rms=0.582 (0.065%), neg=0, invalid=762 0123: dt=92.480000, rms=0.582 (0.073%), neg=0, invalid=762 0124: dt=92.480000, rms=0.581 (0.084%), neg=0, invalid=762 0125: dt=92.480000, rms=0.581 (0.087%), neg=0, invalid=762 0126: dt=92.480000, rms=0.580 (0.085%), neg=0, invalid=762 0127: dt=92.480000, rms=0.580 (0.080%), neg=0, invalid=762 0128: dt=92.480000, rms=0.579 (0.075%), neg=0, invalid=762 0129: dt=92.480000, rms=0.579 (0.073%), neg=0, invalid=762 0130: dt=92.480000, rms=0.579 (0.072%), neg=0, invalid=762 0131: dt=92.480000, rms=0.578 (0.065%), neg=0, invalid=762 0132: dt=92.480000, rms=0.578 (0.060%), neg=0, invalid=762 0133: dt=92.480000, rms=0.578 (0.056%), neg=0, invalid=762 0134: dt=92.480000, rms=0.577 (0.055%), neg=0, invalid=762 0135: dt=92.480000, rms=0.577 (0.063%), neg=0, invalid=762 0136: dt=92.480000, rms=0.577 (0.062%), neg=0, invalid=762 0137: dt=92.480000, rms=0.576 (0.063%), neg=0, invalid=762 0138: dt=92.480000, rms=0.576 (0.056%), neg=0, invalid=762 0139: dt=92.480000, rms=0.576 (0.050%), neg=0, invalid=762 0140: dt=92.480000, rms=0.575 (0.046%), neg=0, invalid=762 0141: dt=92.480000, rms=0.575 (0.039%), neg=0, invalid=762 0142: dt=92.480000, rms=0.575 (0.036%), neg=0, invalid=762 0143: dt=92.480000, rms=0.575 (0.036%), neg=0, invalid=762 0144: dt=92.480000, rms=0.575 (0.029%), neg=0, invalid=762 0145: dt=92.480000, rms=0.574 (0.034%), neg=0, invalid=762 0146: dt=92.480000, rms=0.574 (0.037%), neg=0, invalid=762 0147: dt=92.480000, rms=0.574 (0.034%), neg=0, invalid=762 0148: dt=92.480000, rms=0.574 (0.028%), neg=0, invalid=762 0149: dt=92.480000, rms=0.574 (0.033%), neg=0, invalid=762 0150: dt=92.480000, rms=0.573 (0.033%), neg=0, invalid=762 0151: dt=92.480000, rms=0.573 (0.033%), neg=0, invalid=762 0152: dt=92.480000, rms=0.573 (0.025%), neg=0, invalid=762 0153: dt=92.480000, rms=0.573 (0.030%), neg=0, invalid=762 0154: dt=92.480000, rms=0.573 (0.021%), neg=0, invalid=762 0155: dt=92.480000, rms=0.573 (0.024%), neg=0, invalid=762 0156: dt=92.480000, rms=0.572 (0.025%), neg=0, invalid=762 0157: dt=92.480000, rms=0.572 (0.022%), neg=0, invalid=762 0158: dt=92.480000, rms=0.572 (0.022%), neg=0, invalid=762 0159: dt=92.480000, rms=0.572 (0.019%), neg=0, invalid=762 0160: dt=1183.744000, rms=0.572 (0.026%), neg=0, invalid=762 0161: dt=32.368000, rms=0.572 (0.001%), neg=0, invalid=762 0162: dt=32.368000, rms=0.572 (0.002%), neg=0, invalid=762 0163: dt=32.368000, rms=0.572 (0.000%), neg=0, invalid=762 0164: dt=32.368000, rms=0.572 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.573, neg=0, invalid=762 0165: dt=93.866667, rms=0.571 (0.357%), neg=0, invalid=762 0166: dt=331.776000, rms=0.563 (1.401%), neg=0, invalid=762 0167: dt=49.870130, rms=0.560 (0.462%), neg=0, invalid=762 0168: dt=145.152000, rms=0.558 (0.325%), neg=0, invalid=762 0169: dt=145.152000, rms=0.555 (0.541%), neg=0, invalid=762 0170: dt=36.288000, rms=0.554 (0.169%), neg=0, invalid=762 0171: dt=82.944000, rms=0.554 (0.119%), neg=0, invalid=762 0172: dt=145.152000, rms=0.552 (0.342%), neg=0, invalid=762 0173: dt=36.288000, rms=0.551 (0.107%), neg=0, invalid=762 0174: dt=145.152000, rms=0.550 (0.160%), neg=0, invalid=762 0175: dt=103.680000, rms=0.549 (0.264%), neg=0, invalid=762 0176: dt=36.288000, rms=0.548 (0.095%), neg=0, invalid=762 0177: dt=145.152000, rms=0.547 (0.144%), neg=0, invalid=762 0178: dt=124.416000, rms=0.546 (0.230%), neg=0, invalid=762 0179: dt=36.288000, rms=0.546 (0.085%), neg=0, invalid=762 0180: dt=103.680000, rms=0.545 (0.067%), neg=0, invalid=762 0181: dt=145.152000, rms=0.544 (0.229%), neg=0, invalid=762 0182: dt=36.288000, rms=0.544 (0.058%), neg=0, invalid=762 0183: dt=145.152000, rms=0.543 (0.092%), neg=0, invalid=762 0184: dt=145.152000, rms=0.542 (0.195%), neg=0, invalid=762 0185: dt=36.288000, rms=0.542 (0.055%), neg=0, invalid=762 0186: dt=145.152000, rms=0.542 (0.081%), neg=0, invalid=762 0187: dt=124.416000, rms=0.541 (0.160%), neg=0, invalid=762 0188: dt=36.288000, rms=0.540 (0.039%), neg=0, invalid=762 0189: dt=36.288000, rms=0.540 (0.020%), neg=0, invalid=762 0190: dt=36.288000, rms=0.540 (0.043%), neg=0, invalid=762 0191: dt=36.288000, rms=0.540 (0.076%), neg=0, invalid=762 0192: dt=36.288000, rms=0.539 (0.111%), neg=0, invalid=762 0193: dt=36.288000, rms=0.539 (0.112%), neg=0, invalid=762 0194: dt=36.288000, rms=0.538 (0.119%), neg=0, invalid=762 0195: dt=36.288000, rms=0.537 (0.112%), neg=0, invalid=762 0196: dt=36.288000, rms=0.537 (0.111%), neg=0, invalid=762 0197: dt=36.288000, rms=0.536 (0.125%), neg=0, invalid=762 0198: dt=36.288000, rms=0.535 (0.135%), neg=0, invalid=762 0199: dt=36.288000, rms=0.535 (0.127%), neg=0, invalid=762 0200: dt=36.288000, rms=0.534 (0.112%), neg=0, invalid=762 0201: dt=36.288000, rms=0.533 (0.103%), neg=0, invalid=762 0202: dt=36.288000, rms=0.533 (0.107%), neg=0, invalid=762 0203: dt=36.288000, rms=0.532 (0.102%), neg=0, invalid=762 0204: dt=36.288000, rms=0.532 (0.108%), neg=0, invalid=762 0205: dt=36.288000, rms=0.531 (0.098%), neg=0, invalid=762 0206: dt=36.288000, rms=0.531 (0.090%), neg=0, invalid=762 0207: dt=36.288000, rms=0.530 (0.084%), neg=0, invalid=762 0208: dt=36.288000, rms=0.530 (0.082%), neg=0, invalid=762 0209: dt=36.288000, rms=0.529 (0.082%), neg=0, invalid=762 0210: dt=36.288000, rms=0.529 (0.080%), neg=0, invalid=762 0211: dt=36.288000, rms=0.529 (0.085%), neg=0, invalid=762 0212: dt=36.288000, rms=0.528 (0.074%), neg=0, invalid=762 0213: dt=36.288000, rms=0.528 (0.076%), neg=0, invalid=762 0214: dt=36.288000, rms=0.527 (0.068%), neg=0, invalid=762 0215: dt=36.288000, rms=0.527 (0.064%), neg=0, invalid=762 0216: dt=36.288000, rms=0.527 (0.060%), neg=0, invalid=762 0217: dt=36.288000, rms=0.526 (0.060%), neg=0, invalid=762 0218: dt=36.288000, rms=0.526 (0.065%), neg=0, invalid=762 0219: dt=36.288000, rms=0.526 (0.069%), neg=0, invalid=762 0220: dt=36.288000, rms=0.525 (0.061%), neg=0, invalid=762 0221: dt=36.288000, rms=0.525 (0.052%), neg=0, invalid=762 0222: dt=36.288000, rms=0.525 (0.053%), neg=0, invalid=762 0223: dt=36.288000, rms=0.525 (0.053%), neg=0, invalid=762 0224: dt=36.288000, rms=0.524 (0.050%), neg=0, invalid=762 0225: dt=36.288000, rms=0.524 (0.052%), neg=0, invalid=762 0226: dt=36.288000, rms=0.524 (0.044%), neg=0, invalid=762 0227: dt=36.288000, rms=0.524 (0.044%), neg=0, invalid=762 0228: dt=36.288000, rms=0.523 (0.049%), neg=0, invalid=762 0229: dt=36.288000, rms=0.523 (0.036%), neg=0, invalid=762 0230: dt=36.288000, rms=0.523 (0.034%), neg=0, invalid=762 0231: dt=36.288000, rms=0.523 (0.035%), neg=0, invalid=762 0232: dt=36.288000, rms=0.523 (0.045%), neg=0, invalid=762 0233: dt=36.288000, rms=0.522 (0.043%), neg=0, invalid=762 0234: dt=36.288000, rms=0.522 (0.037%), neg=0, invalid=762 0235: dt=36.288000, rms=0.522 (0.035%), neg=0, invalid=762 0236: dt=36.288000, rms=0.522 (0.035%), neg=0, invalid=762 0237: dt=36.288000, rms=0.522 (0.031%), neg=0, invalid=762 0238: dt=36.288000, rms=0.521 (0.032%), neg=0, invalid=762 0239: dt=36.288000, rms=0.521 (0.035%), neg=0, invalid=762 0240: dt=36.288000, rms=0.521 (0.033%), neg=0, invalid=762 0241: dt=36.288000, rms=0.521 (0.033%), neg=0, invalid=762 0242: dt=36.288000, rms=0.521 (0.025%), neg=0, invalid=762 0243: dt=36.288000, rms=0.521 (0.032%), neg=0, invalid=762 0244: dt=36.288000, rms=0.520 (0.031%), neg=0, invalid=762 0245: dt=36.288000, rms=0.520 (0.026%), neg=0, invalid=762 0246: dt=36.288000, rms=0.520 (0.029%), neg=0, invalid=762 0247: dt=36.288000, rms=0.520 (0.023%), neg=0, invalid=762 0248: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=762 0249: dt=36.288000, rms=0.520 (0.026%), neg=0, invalid=762 0250: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=762 0251: dt=36.288000, rms=0.519 (0.021%), neg=0, invalid=762 0252: dt=36.288000, rms=0.519 (0.026%), neg=0, invalid=762 0253: dt=36.288000, rms=0.519 (0.026%), neg=0, invalid=762 0254: dt=36.288000, rms=0.519 (0.026%), neg=0, invalid=762 0255: dt=36.288000, rms=0.519 (0.032%), neg=0, invalid=762 0256: dt=36.288000, rms=0.519 (0.024%), neg=0, invalid=762 0257: dt=36.288000, rms=0.519 (0.022%), neg=0, invalid=762 0258: dt=145.152000, rms=0.519 (0.012%), neg=0, invalid=762 0259: dt=145.152000, rms=0.519 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=762 0260: dt=145.152000, rms=0.517 (0.446%), neg=0, invalid=762 0261: dt=62.208000, rms=0.516 (0.119%), neg=0, invalid=762 0262: dt=145.152000, rms=0.515 (0.112%), neg=0, invalid=762 0263: dt=82.944000, rms=0.515 (0.065%), neg=0, invalid=762 0264: dt=62.208000, rms=0.515 (0.029%), neg=0, invalid=762 0265: dt=62.208000, rms=0.515 (0.045%), neg=0, invalid=762 0266: dt=62.208000, rms=0.514 (0.054%), neg=0, invalid=762 0267: dt=62.208000, rms=0.514 (0.071%), neg=0, invalid=762 0268: dt=62.208000, rms=0.514 (0.056%), neg=0, invalid=762 0269: dt=62.208000, rms=0.513 (0.075%), neg=0, invalid=762 0270: dt=62.208000, rms=0.513 (0.077%), neg=0, invalid=762 0271: dt=62.208000, rms=0.513 (0.064%), neg=0, invalid=762 0272: dt=62.208000, rms=0.512 (0.062%), neg=0, invalid=762 0273: dt=62.208000, rms=0.512 (0.055%), neg=0, invalid=762 0274: dt=62.208000, rms=0.512 (0.063%), neg=0, invalid=762 0275: dt=62.208000, rms=0.512 (0.049%), neg=0, invalid=762 0276: dt=62.208000, rms=0.511 (0.045%), neg=0, invalid=762 0277: dt=62.208000, rms=0.511 (0.040%), neg=0, invalid=762 0278: dt=62.208000, rms=0.511 (0.042%), neg=0, invalid=762 0279: dt=62.208000, rms=0.511 (0.055%), neg=0, invalid=762 0280: dt=62.208000, rms=0.510 (0.052%), neg=0, invalid=762 0281: dt=62.208000, rms=0.510 (0.044%), neg=0, invalid=762 0282: dt=62.208000, rms=0.510 (0.043%), neg=0, invalid=762 0283: dt=62.208000, rms=0.510 (0.045%), neg=0, invalid=762 0284: dt=62.208000, rms=0.509 (0.037%), neg=0, invalid=762 0285: dt=62.208000, rms=0.509 (0.027%), neg=0, invalid=762 0286: dt=62.208000, rms=0.509 (0.029%), neg=0, invalid=762 0287: dt=62.208000, rms=0.509 (0.031%), neg=0, invalid=762 0288: dt=62.208000, rms=0.509 (0.034%), neg=0, invalid=762 0289: dt=62.208000, rms=0.509 (0.035%), neg=0, invalid=762 0290: dt=62.208000, rms=0.509 (0.035%), neg=0, invalid=762 0291: dt=62.208000, rms=0.508 (0.038%), neg=0, invalid=762 0292: dt=62.208000, rms=0.508 (0.028%), neg=0, invalid=762 0293: dt=62.208000, rms=0.508 (0.027%), neg=0, invalid=762 0294: dt=62.208000, rms=0.508 (0.026%), neg=0, invalid=762 0295: dt=62.208000, rms=0.508 (0.035%), neg=0, invalid=762 0296: dt=62.208000, rms=0.508 (0.035%), neg=0, invalid=762 0297: dt=62.208000, rms=0.507 (0.032%), neg=0, invalid=762 0298: dt=62.208000, rms=0.507 (0.033%), neg=0, invalid=762 0299: dt=62.208000, rms=0.507 (0.033%), neg=0, invalid=762 0300: dt=62.208000, rms=0.507 (0.022%), neg=0, invalid=762 0301: dt=62.208000, rms=0.507 (0.025%), neg=0, invalid=762 0302: dt=62.208000, rms=0.507 (0.024%), neg=0, invalid=762 0303: dt=62.208000, rms=0.507 (0.030%), neg=0, invalid=762 0304: dt=62.208000, rms=0.506 (0.027%), neg=0, invalid=762 0305: dt=62.208000, rms=0.506 (0.021%), neg=0, invalid=762 0306: dt=62.208000, rms=0.506 (0.026%), neg=0, invalid=762 0307: dt=62.208000, rms=0.506 (0.024%), neg=0, invalid=762 0308: dt=62.208000, rms=0.506 (0.021%), neg=0, invalid=762 0309: dt=82.944000, rms=0.506 (0.003%), neg=0, invalid=762 0310: dt=82.944000, rms=0.506 (0.003%), neg=0, invalid=762 0311: dt=82.944000, rms=0.506 (0.001%), neg=0, invalid=762 0312: dt=82.944000, rms=0.506 (0.008%), neg=0, invalid=762 0313: dt=82.944000, rms=0.506 (0.012%), neg=0, invalid=762 0314: dt=82.944000, rms=0.506 (0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0315: dt=19.200000, rms=0.513 (0.210%), neg=0, invalid=762 0316: dt=44.800000, rms=0.511 (0.214%), neg=0, invalid=762 0317: dt=44.800000, rms=0.509 (0.441%), neg=0, invalid=762 0318: dt=102.400000, rms=0.507 (0.455%), neg=0, invalid=762 0319: dt=38.400000, rms=0.505 (0.422%), neg=0, invalid=762 0320: dt=38.400000, rms=0.503 (0.287%), neg=0, invalid=762 0321: dt=38.400000, rms=0.502 (0.165%), neg=0, invalid=762 0322: dt=44.800000, rms=0.501 (0.257%), neg=0, invalid=762 0323: dt=25.600000, rms=0.501 (0.122%), neg=0, invalid=762 0324: dt=44.800000, rms=0.499 (0.238%), neg=0, invalid=762 0325: dt=25.600000, rms=0.499 (0.067%), neg=0, invalid=762 0326: dt=38.400000, rms=0.498 (0.172%), neg=0, invalid=762 0327: dt=2.800000, rms=0.498 (0.010%), neg=0, invalid=762 0328: dt=0.175000, rms=0.498 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=762 0329: dt=62.197183, rms=0.495 (0.787%), neg=0, invalid=762 0330: dt=28.755245, rms=0.493 (0.315%), neg=0, invalid=762 0331: dt=38.400000, rms=0.492 (0.166%), neg=0, invalid=762 0332: dt=32.000000, rms=0.492 (0.122%), neg=0, invalid=762 0333: dt=32.000000, rms=0.491 (0.105%), neg=0, invalid=762 0334: dt=32.000000, rms=0.491 (0.110%), neg=0, invalid=762 0335: dt=32.000000, rms=0.490 (0.105%), neg=0, invalid=762 0336: dt=32.000000, rms=0.490 (0.085%), neg=0, invalid=762 0337: dt=32.000000, rms=0.489 (0.090%), neg=0, invalid=762 0338: dt=25.600000, rms=0.489 (0.078%), neg=0, invalid=762 0339: dt=44.800000, rms=0.488 (0.075%), neg=0, invalid=762 0340: dt=25.600000, rms=0.488 (0.086%), neg=0, invalid=762 0341: dt=44.800000, rms=0.488 (0.075%), neg=0, invalid=762 0342: dt=25.600000, rms=0.487 (0.078%), neg=0, invalid=762 0343: dt=38.400000, rms=0.487 (0.070%), neg=0, invalid=762 0344: dt=25.600000, rms=0.487 (0.046%), neg=0, invalid=762 0345: dt=25.600000, rms=0.486 (0.061%), neg=0, invalid=762 0346: dt=25.600000, rms=0.486 (0.083%), neg=0, invalid=762 0347: dt=25.600000, rms=0.485 (0.137%), neg=0, invalid=762 0348: dt=25.600000, rms=0.485 (0.138%), neg=0, invalid=762 0349: dt=25.600000, rms=0.484 (0.166%), neg=0, invalid=762 0350: dt=25.600000, rms=0.483 (0.165%), neg=0, invalid=762 0351: dt=25.600000, rms=0.482 (0.190%), neg=0, invalid=762 0352: dt=25.600000, rms=0.481 (0.188%), neg=0, invalid=762 0353: dt=25.600000, rms=0.480 (0.176%), neg=0, invalid=762 0354: dt=25.600000, rms=0.480 (0.150%), neg=0, invalid=762 0355: dt=25.600000, rms=0.479 (0.186%), neg=0, invalid=762 0356: dt=25.600000, rms=0.478 (0.171%), neg=0, invalid=762 0357: dt=25.600000, rms=0.477 (0.147%), neg=0, invalid=762 0358: dt=25.600000, rms=0.477 (0.136%), neg=0, invalid=762 0359: dt=25.600000, rms=0.476 (0.142%), neg=0, invalid=762 0360: dt=25.600000, rms=0.475 (0.126%), neg=0, invalid=762 0361: dt=25.600000, rms=0.475 (0.105%), neg=0, invalid=762 0362: dt=25.600000, rms=0.474 (0.092%), neg=0, invalid=762 0363: dt=25.600000, rms=0.474 (0.082%), neg=0, invalid=762 0364: dt=25.600000, rms=0.474 (0.096%), neg=0, invalid=762 0365: dt=25.600000, rms=0.473 (0.070%), neg=0, invalid=762 0366: dt=25.600000, rms=0.473 (0.056%), neg=0, invalid=762 0367: dt=25.600000, rms=0.473 (0.062%), neg=0, invalid=762 0368: dt=25.600000, rms=0.472 (0.058%), neg=0, invalid=762 0369: dt=25.600000, rms=0.472 (0.044%), neg=0, invalid=762 0370: dt=25.600000, rms=0.472 (0.052%), neg=0, invalid=762 0371: dt=25.600000, rms=0.472 (0.042%), neg=0, invalid=762 0372: dt=25.600000, rms=0.471 (0.051%), neg=0, invalid=762 0373: dt=25.600000, rms=0.471 (0.036%), neg=0, invalid=762 0374: dt=25.600000, rms=0.471 (0.040%), neg=0, invalid=762 0375: dt=25.600000, rms=0.471 (0.036%), neg=0, invalid=762 0376: dt=25.600000, rms=0.471 (0.042%), neg=0, invalid=762 0377: dt=25.600000, rms=0.471 (0.033%), neg=0, invalid=762 0378: dt=25.600000, rms=0.470 (0.032%), neg=0, invalid=762 0379: dt=25.600000, rms=0.470 (0.037%), neg=0, invalid=762 0380: dt=25.600000, rms=0.470 (0.014%), neg=0, invalid=762 0381: dt=25.600000, rms=0.470 (0.042%), neg=0, invalid=762 0382: dt=25.600000, rms=0.470 (0.040%), neg=0, invalid=762 0383: dt=25.600000, rms=0.470 (0.029%), neg=0, invalid=762 0384: dt=25.600000, rms=0.470 (0.014%), neg=0, invalid=762 0385: dt=25.600000, rms=0.469 (0.034%), neg=0, invalid=762 0386: dt=25.600000, rms=0.469 (0.036%), neg=0, invalid=762 0387: dt=25.600000, rms=0.469 (0.021%), neg=0, invalid=762 0388: dt=25.600000, rms=0.469 (0.022%), neg=0, invalid=762 0389: dt=25.600000, rms=0.469 (0.012%), neg=0, invalid=762 0390: dt=25.600000, rms=0.469 (0.018%), neg=0, invalid=762 0391: dt=11.200000, rms=0.469 (0.002%), neg=0, invalid=762 0392: dt=11.200000, rms=0.469 (0.000%), neg=0, invalid=762 0393: dt=11.200000, rms=0.469 (-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=0.487, neg=0, invalid=762 0394: dt=0.000000, rms=0.487 (0.066%), neg=0, invalid=762 0395: dt=0.000000, rms=0.487 (0.000%), neg=0, invalid=762 0396: dt=0.150000, rms=0.487 (-0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=762 0397: dt=0.000000, rms=0.487 (0.066%), neg=0, invalid=762 0398: dt=0.000000, rms=0.487 (0.000%), neg=0, invalid=762 0399: dt=0.150000, rms=0.487 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 0400: dt=1.280000, rms=0.521 (0.607%), neg=0, invalid=762 0401: dt=0.192000, rms=0.520 (0.007%), neg=0, invalid=762 0402: dt=0.192000, rms=0.520 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=762 0403: dt=0.448000, rms=0.520 (0.117%), neg=0, invalid=762 0404: dt=0.320000, rms=0.520 (0.014%), neg=0, invalid=762 0405: dt=0.320000, rms=0.520 (-0.007%), 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=0.480, neg=0, invalid=762 0406: dt=0.448000, rms=0.469 (2.374%), neg=0, invalid=762 0407: dt=0.448000, rms=0.467 (0.464%), neg=0, invalid=762 0408: dt=0.448000, rms=0.465 (0.274%), neg=0, invalid=762 0409: dt=0.500000, rms=0.464 (0.179%), neg=0, invalid=762 0410: dt=0.448000, rms=0.464 (0.111%), neg=0, invalid=762 0411: dt=0.448000, rms=0.464 (0.085%), neg=0, invalid=762 0412: dt=0.448000, rms=0.463 (0.060%), neg=0, invalid=762 0413: dt=0.448000, rms=0.463 (0.048%), neg=0, invalid=762 0414: dt=0.448000, rms=0.463 (0.039%), neg=0, invalid=762 0415: dt=0.448000, rms=0.463 (0.069%), neg=0, invalid=762 0416: dt=0.448000, rms=0.462 (0.071%), neg=0, invalid=762 0417: dt=0.448000, rms=0.462 (0.074%), neg=0, invalid=762 0418: dt=0.448000, rms=0.462 (0.056%), neg=0, invalid=762 0419: dt=0.448000, rms=0.461 (0.031%), neg=0, invalid=762 0420: dt=0.448000, rms=0.461 (0.011%), neg=0, invalid=762 0421: dt=0.448000, rms=0.461 (-0.009%), neg=0, invalid=762 0422: dt=0.000016, rms=0.461 (0.000%), neg=0, invalid=762 0423: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=762 0424: dt=0.448000, rms=0.458 (0.772%), neg=0, invalid=762 0425: dt=0.448000, rms=0.458 (0.100%), neg=0, invalid=762 0426: dt=0.448000, rms=0.458 (0.032%), neg=0, invalid=762 0427: dt=0.448000, rms=0.458 (0.015%), neg=0, invalid=762 0428: dt=0.448000, rms=0.457 (0.012%), neg=0, invalid=762 0429: dt=0.224000, rms=0.457 (0.004%), neg=0, invalid=762 0430: dt=0.256000, rms=0.457 (0.004%), neg=0, invalid=762 0431: dt=0.112000, rms=0.457 (-0.004%), 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=0.456, neg=0, invalid=762 0432: dt=0.000000, rms=0.455 (0.082%), neg=0, invalid=762 0433: 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 0434: dt=129.472000, rms=0.455 (0.095%), neg=0, invalid=762 0435: dt=129.472000, rms=0.455 (0.010%), neg=0, invalid=762 0436: dt=129.472000, rms=0.455 (0.015%), neg=0, invalid=762 0437: dt=129.472000, rms=0.455 (0.006%), neg=0, invalid=762 0438: dt=129.472000, rms=0.455 (0.022%), neg=0, invalid=762 0439: dt=129.472000, rms=0.455 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0440: dt=0.000000, rms=0.455 (0.081%), neg=0, invalid=762 0441: 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=0.455, neg=0, invalid=762 0442: dt=248.832000, rms=0.454 (0.391%), neg=0, invalid=762 0443: dt=36.288000, rms=0.453 (0.121%), neg=0, invalid=762 0444: dt=36.288000, rms=0.453 (0.039%), neg=0, invalid=762 0445: dt=36.288000, rms=0.453 (0.054%), neg=0, invalid=762 0446: dt=36.288000, rms=0.452 (0.074%), neg=0, invalid=762 0447: dt=36.288000, rms=0.452 (0.078%), neg=0, invalid=762 0448: dt=36.288000, rms=0.452 (0.089%), neg=0, invalid=762 0449: dt=36.288000, rms=0.451 (0.084%), neg=0, invalid=762 0450: dt=36.288000, rms=0.451 (0.077%), neg=0, invalid=762 0451: dt=82.944000, rms=0.451 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0452: dt=11.200000, rms=0.450 (0.211%), neg=0, invalid=762 0453: dt=25.600000, rms=0.450 (0.112%), neg=0, invalid=762 0454: dt=25.600000, rms=0.449 (0.208%), neg=0, invalid=762 0455: dt=25.600000, rms=0.448 (0.187%), neg=0, invalid=762 0456: dt=25.600000, rms=0.448 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0457: dt=25.600000, rms=0.447 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0458: dt=25.600000, rms=0.446 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 10 iterations, nbhd size=1, neg = 0 0459: dt=25.600000, rms=0.445 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0460: dt=25.600000, rms=0.444 (0.247%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0461: dt=25.600000, rms=0.443 (0.237%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0462: dt=25.600000, rms=0.442 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0463: dt=25.600000, rms=0.442 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0464: dt=25.600000, rms=0.441 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0465: dt=44.800000, rms=0.441 (0.187%), neg=0, invalid=762 0466: dt=19.200000, rms=0.441 (0.017%), neg=0, invalid=762 0467: dt=19.200000, rms=0.440 (0.036%), neg=0, invalid=762 0468: dt=19.200000, rms=0.440 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0469: dt=19.200000, rms=0.440 (0.040%), neg=0, invalid=762 0470: dt=19.200000, rms=0.440 (0.021%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 0471: dt=61.400000, rms=0.436 (0.997%), neg=0, invalid=762 0472: dt=22.284123, rms=0.435 (0.289%), neg=0, invalid=762 0473: dt=38.400000, rms=0.434 (0.163%), neg=0, invalid=762 0474: dt=38.400000, rms=0.434 (-0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.442, neg=0, invalid=762 0475: dt=5.161290, rms=0.441 (0.217%), neg=0, invalid=762 0476: dt=3.456000, rms=0.441 (0.038%), neg=0, invalid=762 0477: dt=3.456000, rms=0.441 (0.011%), neg=0, invalid=762 0478: dt=3.456000, rms=0.441 (-0.048%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=762 0479: dt=14.995169, rms=0.438 (0.688%), neg=0, invalid=762 0480: dt=20.383562, rms=0.436 (0.401%), neg=0, invalid=762 0481: dt=10.848485, rms=0.435 (0.202%), neg=0, invalid=762 0482: dt=10.848485, rms=0.435 (0.179%), neg=0, invalid=762 0483: dt=10.848485, rms=0.434 (0.209%), neg=0, invalid=762 0484: dt=10.848485, rms=0.433 (0.253%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0485: dt=10.848485, rms=0.432 (0.225%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0486: dt=10.848485, rms=0.431 (0.273%), neg=0, invalid=762 0487: dt=10.848485, rms=0.430 (0.205%), neg=0, invalid=762 0488: dt=10.848485, rms=0.429 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0489: dt=10.848485, rms=0.428 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0490: dt=10.848485, rms=0.428 (0.101%), neg=0, invalid=762 0491: dt=4.032000, rms=0.428 (0.012%), neg=0, invalid=762 0492: dt=4.032000, rms=0.428 (0.009%), neg=0, invalid=762 0493: dt=4.032000, rms=0.428 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0494: dt=0.000000, rms=0.433 (0.089%), neg=0, invalid=762 0495: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0496: dt=0.000000, rms=0.433 (0.089%), neg=0, invalid=762 0497: dt=0.000000, rms=0.433 (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=0.425, neg=0, invalid=762 iter 0, gcam->neg = 277 after 12 iterations, nbhd size=1, neg = 0 0498: dt=1.953717, rms=0.406 (4.397%), neg=0, invalid=762 0499: dt=0.028000, rms=0.406 (0.025%), neg=0, invalid=762 0500: dt=0.028000, rms=0.406 (0.002%), neg=0, invalid=762 0501: dt=0.028000, rms=0.406 (-0.030%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0502: dt=0.064000, rms=0.406 (0.145%), neg=0, invalid=762 0503: dt=0.001750, rms=0.406 (0.000%), neg=0, invalid=762 0504: dt=0.001750, rms=0.406 (-0.000%), 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=0.396, neg=0, invalid=762 0505: dt=0.000000, rms=0.396 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=762 0506: dt=0.000000, rms=0.396 (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=0.396, neg=0, invalid=762 0507: dt=0.000000, rms=0.396 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=762 0508: dt=20.736000, rms=0.396 (0.009%), neg=0, invalid=762 0509: dt=19.200000, rms=0.396 (0.003%), neg=0, invalid=762 0510: dt=19.200000, rms=0.396 (0.002%), neg=0, invalid=762 0511: dt=19.200000, rms=0.396 (-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=0.396, neg=0, invalid=762 0512: dt=8.000000, rms=0.396 (0.037%), neg=0, invalid=762 0513: dt=2.800000, rms=0.396 (0.004%), neg=0, invalid=762 0514: dt=2.800000, rms=0.396 (0.001%), neg=0, invalid=762 0515: dt=2.800000, rms=0.396 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=762 0516: dt=68.507042, rms=0.394 (0.511%), neg=0, invalid=762 0517: dt=23.689922, rms=0.393 (0.255%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0518: dt=44.800000, rms=0.393 (0.131%), neg=0, invalid=762 0519: dt=44.800000, rms=0.392 (0.057%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0520: dt=44.800000, rms=0.391 (0.255%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0521: dt=44.800000, rms=0.391 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0522: dt=44.800000, rms=0.390 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0523: dt=44.800000, rms=0.390 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0524: dt=44.800000, rms=0.389 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0525: dt=44.800000, rms=0.389 (0.085%), neg=0, invalid=762 0526: dt=19.200000, rms=0.389 (0.033%), neg=0, invalid=762 0527: dt=19.200000, rms=0.389 (0.006%), neg=0, invalid=762 0528: dt=19.200000, rms=0.389 (0.009%), neg=0, invalid=762 0529: dt=19.200000, rms=0.389 (0.013%), neg=0, invalid=762 0530: dt=19.200000, rms=0.389 (0.013%), neg=0, invalid=762 0531: dt=19.200000, rms=0.389 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=762 0532: dt=0.054000, rms=0.392 (0.000%), neg=0, invalid=762 0533: dt=0.003938, rms=0.392 (0.000%), neg=0, invalid=762 0534: dt=0.003938, rms=0.392 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=762 0535: dt=7.809524, rms=0.392 (0.074%), neg=0, invalid=762 0536: dt=11.520000, rms=0.392 (0.051%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0537: dt=11.520000, rms=0.391 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0538: dt=11.520000, rms=0.391 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0539: dt=11.520000, rms=0.391 (0.063%), neg=0, invalid=762 0540: dt=11.520000, rms=0.390 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 13 iterations, nbhd size=1, neg = 0 0541: dt=11.520000, rms=0.390 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 12 iterations, nbhd size=1, neg = 0 0542: dt=11.520000, rms=0.389 (0.191%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 5 iterations, nbhd size=0, neg = 0 0543: dt=11.520000, rms=0.388 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 13 iterations, nbhd size=1, neg = 0 0544: dt=11.520000, rms=0.388 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 12 iterations, nbhd size=1, neg = 0 0545: dt=11.520000, rms=0.388 (-0.076%), neg=0, invalid=762 0546: dt=0.000984, rms=0.388 (0.000%), neg=0, invalid=762 0547: dt=0.000563, rms=0.388 (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=0.394, neg=0, invalid=762 0548: dt=0.000000, rms=0.394 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 0549: dt=0.000040, rms=0.394 (0.000%), neg=0, invalid=762 0550: dt=0.000000, rms=0.394 (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=0.385, neg=0, invalid=762 iter 0, gcam->neg = 342 after 14 iterations, nbhd size=1, neg = 0 0551: dt=1.280000, rms=0.378 (1.767%), neg=0, invalid=762 0552: dt=0.000023, rms=0.378 (0.000%), neg=0, invalid=762 0553: dt=0.000023, rms=0.378 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.378, neg=0, invalid=762 0554: dt=0.096000, rms=0.378 (0.047%), neg=0, invalid=762 0555: dt=0.064000, rms=0.378 (0.011%), neg=0, invalid=762 0556: dt=0.064000, rms=0.378 (0.002%), neg=0, invalid=762 0557: dt=0.064000, rms=0.378 (-0.029%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 49 minutes and 12 seconds. mri_ca_register utimesec 6539.855459 mri_ca_register stimesec 6.317246 mri_ca_register ru_maxrss 1341324 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5673966 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4422 mri_ca_register ru_nivcsw 61988 FSRUNTIME@ mri_ca_register 1.8199 hours 1 threads #-------------------------------------- #@# SubCort Seg 2021��� 11��� 16��� ��������� 09:38:27 CST mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname siying-VM machine x86_64 setenv SUBJECTS_DIR /home/siying/sharefolder/piantoutong/freesurfer_1 cd /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/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 /opt/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 7.15 Atlas used for the 3D morph was /opt/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 = 0.10345 (28) Left_Lateral_Ventricle (4): linear fit = 1.42 x + 0.0 (643 voxels, overlap=0.187) Left_Lateral_Ventricle (4): linear fit = 1.42 x + 0.0 (643 voxels, peak = 28), gca=28.5 gca peak = 0.17677 (13) mri peak = 0.13402 (31) Right_Lateral_Ventricle (43): linear fit = 2.15 x + 0.0 (589 voxels, overlap=0.176) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (589 voxels, peak = 28), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.23447 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (789 voxels, overlap=0.016) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (789 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.25949 (104) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (723 voxels, overlap=0.018) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (723 voxels, peak = 105), gca=105.1 gca peak = 0.24553 (55) mri peak = 0.11719 (75) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (1153 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (1153 voxels, peak = 72), gca=72.3 gca peak = 0.30264 (59) mri peak = 0.11826 (78) Left_Hippocampus (17): linear fit = 1.32 x + 0.0 (1053 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.32 x + 0.0 (1053 voxels, peak = 78), gca=77.6 gca peak = 0.07580 (103) mri peak = 0.18651 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (64288 voxels, overlap=0.545) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (64288 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.14540 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (64800 voxels, overlap=0.465) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (64800 voxels, peak = 108), gca=107.6 gca peak = 0.09712 (58) mri peak = 0.04276 (67) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (47369 voxels, overlap=0.447) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (47369 voxels, peak = 69), gca=68.7 gca peak = 0.11620 (58) mri peak = 0.04942 (69) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (42485 voxels, overlap=0.223) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (42485 voxels, peak = 69), gca=69.3 gca peak = 0.30970 (66) mri peak = 0.14260 (86) Right_Caudate (50): linear fit = 1.26 x + 0.0 (805 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.26 x + 0.0 (805 voxels, peak = 83), gca=83.5 gca peak = 0.15280 (69) mri peak = 0.11920 (89) Left_Caudate (11): linear fit = 1.17 x + 0.0 (719 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.17 x + 0.0 (719 voxels, peak = 81), gca=81.1 gca peak = 0.13902 (56) mri peak = 0.05819 (71) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (31616 voxels, overlap=0.132) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (31616 voxels, peak = 69), gca=68.6 gca peak = 0.14777 (55) mri peak = 0.06668 (71) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (33216 voxels, overlap=0.039) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (33216 voxels, peak = 68), gca=68.5 gca peak = 0.16765 (84) mri peak = 0.16974 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8263 voxels, overlap=0.530) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8263 voxels, peak = 88), gca=87.8 gca peak = 0.18739 (84) mri peak = 0.18487 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8074 voxels, overlap=0.555) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8074 voxels, peak = 88), gca=87.8 gca peak = 0.29869 (57) mri peak = 0.13830 (76) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (563 voxels, overlap=0.044) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (563 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.13701 (73) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (562 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (562 voxels, peak = 74), gca=73.8 gca peak = 0.11131 (90) mri peak = 0.08012 (97) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5081 voxels, overlap=0.529) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5081 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.09387 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4827 voxels, overlap=0.426) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4827 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.07833 (97) Left_Putamen (12): linear fit = 1.22 x + 0.0 (2021 voxels, overlap=0.013) Left_Putamen (12): linear fit = 1.22 x + 0.0 (2021 voxels, peak = 98), gca=98.4 gca peak = 0.10360 (77) mri peak = 0.08780 (94) Right_Putamen (51): linear fit = 1.21 x + 0.0 (2312 voxels, overlap=0.099) Right_Putamen (51): linear fit = 1.21 x + 0.0 (2312 voxels, peak = 93), gca=92.8 gca peak = 0.08424 (78) mri peak = 0.09469 (88) Brain_Stem (16): linear fit = 1.08 x + 0.0 (14267 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.08 x + 0.0 (14267 voxels, peak = 84), gca=83.9 gca peak = 0.12631 (89) mri peak = 0.10296 (96) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1791 voxels, overlap=0.389) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1791 voxels, peak = 97), gca=96.6 gca peak = 0.14500 (87) mri peak = 0.10865 (96) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1886 voxels, overlap=0.175) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1886 voxels, peak = 95), gca=95.3 gca peak = 0.14975 (24) mri peak = 0.14806 (28) gca peak = 0.19357 (14) mri peak = 0.16465 (30) Fourth_Ventricle (15): linear fit = 1.83 x + 0.0 (202 voxels, overlap=0.172) Fourth_Ventricle (15): linear fit = 1.83 x + 0.0 (202 voxels, peak = 26), gca=25.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.27 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.46 x + 0.0 Left_Putamen too bright - rescaling by 0.970 (from 1.215) to 95.5 (was 98.4) Left_Pallidum too bright - rescaling by 0.979 (from 1.095) to 102.9 (was 105.1) Right_Pallidum too bright - rescaling by 1.008 (from 1.075) to 102.9 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15429 (26) mri peak = 0.10345 (28) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (643 voxels, overlap=0.781) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (643 voxels, peak = 25), gca=24.6 gca peak = 0.13981 (19) mri peak = 0.13402 (31) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (589 voxels, overlap=0.370) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (589 voxels, peak = 27), gca=26.7 gca peak = 0.23856 (103) mri peak = 0.23447 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (789 voxels, overlap=0.998) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (789 voxels, peak = 102), gca=102.5 gca peak = 0.14483 (101) mri peak = 0.25949 (104) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (723 voxels, overlap=0.706) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (723 voxels, peak = 103), gca=102.5 gca peak = 0.23483 (73) mri peak = 0.11719 (75) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1153 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1153 voxels, peak = 73), gca=73.0 gca peak = 0.28085 (74) mri peak = 0.11826 (78) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1053 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1053 voxels, peak = 74), gca=74.0 gca peak = 0.07794 (104) mri peak = 0.18651 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (64288 voxels, overlap=0.598) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (64288 voxels, peak = 104), gca=104.0 gca peak = 0.07684 (108) mri peak = 0.14540 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (64800 voxels, overlap=0.630) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (64800 voxels, peak = 108), gca=108.0 gca peak = 0.08212 (69) mri peak = 0.04276 (67) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (47369 voxels, overlap=0.962) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (47369 voxels, peak = 68), gca=68.0 gca peak = 0.09971 (69) mri peak = 0.04942 (69) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (42485 voxels, overlap=0.954) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (42485 voxels, peak = 68), gca=68.0 gca peak = 0.21450 (83) mri peak = 0.14260 (86) Right_Caudate (50): linear fit = 1.00 x + 0.0 (805 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (805 voxels, peak = 83), gca=83.0 gca peak = 0.14950 (91) mri peak = 0.11920 (89) Left_Caudate (11): linear fit = 0.99 x + 0.0 (719 voxels, overlap=0.920) Left_Caudate (11): linear fit = 0.99 x + 0.0 (719 voxels, peak = 90), gca=89.6 gca peak = 0.11773 (68) mri peak = 0.05819 (71) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31616 voxels, overlap=0.989) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31616 voxels, peak = 68), gca=68.0 gca peak = 0.12593 (68) mri peak = 0.06668 (71) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (33216 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (33216 voxels, peak = 68), gca=68.0 gca peak = 0.15161 (88) mri peak = 0.16974 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8263 voxels, overlap=0.840) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8263 voxels, peak = 89), gca=89.3 gca peak = 0.16906 (88) mri peak = 0.18487 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8074 voxels, overlap=0.845) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8074 voxels, peak = 88), gca=87.6 gca peak = 0.29354 (75) mri peak = 0.13830 (76) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (563 voxels, overlap=0.989) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (563 voxels, peak = 76), gca=76.1 gca peak = 0.24004 (72) mri peak = 0.13701 (73) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (562 voxels, overlap=0.996) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (562 voxels, peak = 72), gca=72.0 gca peak = 0.09897 (96) mri peak = 0.08012 (97) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5081 voxels, overlap=0.896) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5081 voxels, peak = 97), gca=97.4 gca peak = 0.10417 (90) mri peak = 0.09387 (94) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4827 voxels, overlap=0.937) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4827 voxels, peak = 91), gca=91.3 gca peak = 0.08058 (95) mri peak = 0.07833 (97) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2021 voxels, overlap=0.800) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2021 voxels, peak = 99), gca=99.3 gca peak = 0.07997 (91) mri peak = 0.08780 (94) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2312 voxels, overlap=0.916) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2312 voxels, peak = 90), gca=89.6 gca peak = 0.08924 (84) mri peak = 0.09469 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14267 voxels, overlap=0.738) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14267 voxels, peak = 84), gca=83.6 gca peak = 0.11005 (96) mri peak = 0.10296 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1791 voxels, overlap=0.800) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1791 voxels, peak = 96), gca=95.5 gca peak = 0.13793 (95) mri peak = 0.10865 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1886 voxels, overlap=0.793) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1886 voxels, peak = 95), gca=95.5 gca peak = 0.12657 (37) mri peak = 0.14806 (28) gca peak = 0.14735 (22) mri peak = 0.16465 (30) Fourth_Ventricle (15): linear fit = 1.21 x + 0.0 (202 voxels, overlap=0.416) Fourth_Ventricle (15): linear fit = 1.21 x + 0.0 (202 voxels, peak = 27), gca=26.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.13460 (42) gca peak Left_Thalamus = 0.36646 (106) gca peak Third_Ventricle = 0.12657 (37) gca peak CSF = 0.17072 (53) gca peak Left_Accumbens_area = 0.74115 (73) gca peak Left_undetermined = 0.96707 (33) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12606 (35) gca peak Right_Inf_Lat_Vent = 0.19792 (30) gca peak Right_Accumbens_area = 0.31943 (82) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (45) gca peak WM_hypointensities = 0.07978 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.68770 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.18 x + 0.0 Left_Putamen too bright - rescaling by 0.961 (from 1.045) to 95.4 (was 99.3) Left_Pallidum too bright - rescaling by 1.003 (from 1.015) to 102.8 (was 102.5) Right_Pallidum too bright - rescaling by 1.003 (from 0.995) to 102.8 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 49557 voxels changed in iteration 0 of unlikely voxel relabeling 314 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 47831 gm and wm labels changed (%30 to gray, %70 to white out of all changed labels) 290 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 61202 changed. image ll: -2.100, PF=0.500 pass 2: 15291 changed. image ll: -2.099, PF=0.500 pass 3: 4595 changed. 37864 voxels changed in iteration 0 of unlikely voxel relabeling 206 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7451 voxels changed in iteration 0 of unlikely voxel relabeling 158 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5908 voxels changed in iteration 0 of unlikely voxel relabeling 46 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 4875 voxels changed in iteration 0 of unlikely voxel relabeling 18 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 2181.191341 mri_ca_label stimesec 1.993820 mri_ca_label ru_maxrss 2114972 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 797393 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 4106 mri_ca_label ru_nivcsw 41556 auto-labeling took 36 minutes and 25 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/transforms/cc_up.lta NC1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/transforms/cc_up.lta reading aseg from /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/aseg.auto_noCCseg.mgz reading norm from /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/norm.mgz 85078 voxels in left wm, 48493 in right wm, xrange [124, 137] searching rotation angles z=[-3 11], y=[-7 7] searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.8 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.3 searching scale 1 Z rot 10.5 global minimum found at slice 128.0, rotations (-0.81, 3.76) final transformation (x=128.0, yr=-0.814, zr=3.760): 0.99775 -0.06558 -0.01417 8.64800; 0.06558 0.99785 -0.00093 14.92926; 0.01420 0.00000 0.99990 22.19308; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 127 cc center is found at 127 105 104 eigenvectors: 0.00054 -0.00216 1.00000; -0.14716 -0.98911 -0.00206; 0.98911 -0.14716 -0.00085; writing aseg with callosum to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg 2021��� 11��� 16��� ��������� 10:15:44 CST cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 2021��� 11��� 16��� ��������� 10:15:44 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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... 380 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 110 gm peak at 81 (81), valley at 42 (42) csf peak at 41, setting threshold to 67 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 79 (79), valley at 40 (40) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 12 seconds. #-------------------------------------------- #@# Mask BFS 2021��� 11��� 16��� ��������� 10:17:57 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1661333 voxels in mask (pct= 9.90) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation 2021��� 11��� 16��� ��������� 10:17:58 CST 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): 101.6 +- 7.1 [79.0 --> 125.0] GM (75.0) : 73.7 +- 11.0 [30.0 --> 95.0] setting bottom of white matter range to 84.7 setting top of gray matter range to 95.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 3555 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3258 filled 1812 bright non-wm voxels segmented. 2871 diagonally connected voxels added... white matter segmentation took 1.1 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 0.29 minutes reading wm segmentation from wm.seg.mgz... 49 voxels added to wm to prevent paths from MTL structures to cortex 2908 additional wm voxels added 0 additional wm voxels added SEG EDIT: 28991 voxels turned on, 74304 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 17 found - 17 modified | TOTAL: 33 pass 2 (xy-): 0 found - 17 modified | TOTAL: 33 pass 1 (yz+): 18 found - 18 modified | TOTAL: 51 pass 2 (yz+): 0 found - 18 modified | TOTAL: 51 pass 1 (yz-): 19 found - 19 modified | TOTAL: 70 pass 2 (yz-): 0 found - 19 modified | TOTAL: 70 pass 1 (xz+): 14 found - 14 modified | TOTAL: 84 pass 2 (xz+): 0 found - 14 modified | TOTAL: 84 pass 1 (xz-): 12 found - 12 modified | TOTAL: 96 pass 2 (xz-): 0 found - 12 modified | TOTAL: 96 Iteration Number : 1 pass 1 (+++): 22 found - 22 modified | TOTAL: 22 pass 2 (+++): 0 found - 22 modified | TOTAL: 22 pass 1 (+++): 13 found - 13 modified | TOTAL: 35 pass 2 (+++): 0 found - 13 modified | TOTAL: 35 pass 1 (+++): 10 found - 10 modified | TOTAL: 45 pass 2 (+++): 0 found - 10 modified | TOTAL: 45 pass 1 (+++): 12 found - 12 modified | TOTAL: 57 pass 2 (+++): 0 found - 12 modified | TOTAL: 57 Iteration Number : 1 pass 1 (++): 53 found - 53 modified | TOTAL: 53 pass 2 (++): 0 found - 53 modified | TOTAL: 53 pass 1 (+-): 45 found - 45 modified | TOTAL: 98 pass 2 (+-): 0 found - 45 modified | TOTAL: 98 pass 1 (--): 50 found - 50 modified | TOTAL: 148 pass 2 (--): 0 found - 50 modified | TOTAL: 148 pass 1 (-+): 52 found - 52 modified | TOTAL: 200 pass 2 (-+): 0 found - 52 modified | TOTAL: 200 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 2 found - 2 modified | TOTAL: 13 pass 2 (xz+): 0 found - 2 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 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 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 Iteration Number : 4 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 : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 376 (out of 647989: 0.058026) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill 2021��� 11��� 16��� ��������� 10:19:25 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01837 -0.05834 -0.00676 1.55180; 0.06216 1.03245 0.30190 -45.48323; -0.01004 -0.28876 0.97572 37.05373; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1022 (min = 350, max = 1400), aspect = 0.40 (min = 0.10, max = 0.75) no need to search using seed (125, 107, 91), TAL = (3.0, -37.0, 21.0) talairach voxel to voxel transform 0.97866 0.05264 -0.00951 1.22778; -0.05694 0.88837 -0.27527 50.69387; -0.00678 0.26345 0.94332 -22.96037; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 107, 91) --> (3.0, -37.0, 21.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (3.00, -37.00, 21.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -37.00, 21.00) SRC: (110.71, 114.61, 90.35) search lh wm seed point around talairach space (-15.00, -37.00, 21.00), SRC: (145.94, 112.56, 90.10) 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 2021��� 11��� 16��� ��������� 10:19:50 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 3 found - 3 modified | TOTAL: 8 pass 2 (xz+): 0 found - 3 modified | TOTAL: 8 pass 1 (xz-): 2 found - 2 modified | TOTAL: 10 pass 2 (xz-): 0 found - 2 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 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 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 = 12 (out of 306547: 0.003915) 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 40: 1214 vertices, 1328 faces slice 50: 7852 vertices, 8140 faces slice 60: 17695 vertices, 18058 faces slice 70: 29427 vertices, 29860 faces slice 80: 41333 vertices, 41712 faces slice 90: 52739 vertices, 53132 faces slice 100: 64971 vertices, 65400 faces slice 110: 77708 vertices, 78156 faces slice 120: 89752 vertices, 90208 faces slice 130: 101540 vertices, 101997 faces slice 140: 111928 vertices, 112301 faces slice 150: 121058 vertices, 121438 faces slice 160: 128958 vertices, 129254 faces slice 170: 135340 vertices, 135612 faces slice 180: 140951 vertices, 141195 faces slice 190: 144945 vertices, 145092 faces slice 200: 145422 vertices, 145482 faces slice 210: 145422 vertices, 145482 faces slice 220: 145422 vertices, 145482 faces slice 230: 145422 vertices, 145482 faces slice 240: 145422 vertices, 145482 faces slice 250: 145422 vertices, 145482 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... 145422 voxel in cpt #1: X=-60 [v=145422,e=436446,f=290964] located at (-28.044863, -21.196716, 17.423519) For the whole surface: X=-60 [v=145422,e=436446,f=290964] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh 2021��� 11��� 16��� ��������� 10:19:54 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 318142: 0.001572) 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 30: 60 vertices, 76 faces slice 40: 4560 vertices, 4795 faces slice 50: 13194 vertices, 13536 faces slice 60: 24301 vertices, 24704 faces slice 70: 36085 vertices, 36517 faces slice 80: 47757 vertices, 48126 faces slice 90: 59006 vertices, 59397 faces slice 100: 71465 vertices, 71881 faces slice 110: 83686 vertices, 84120 faces slice 120: 95030 vertices, 95465 faces slice 130: 106756 vertices, 107169 faces slice 140: 116700 vertices, 117055 faces slice 150: 125535 vertices, 125868 faces slice 160: 133294 vertices, 133588 faces slice 170: 139658 vertices, 139931 faces slice 180: 145603 vertices, 145839 faces slice 190: 149647 vertices, 149791 faces slice 200: 150400 vertices, 150450 faces slice 210: 150400 vertices, 150450 faces slice 220: 150400 vertices, 150450 faces slice 230: 150400 vertices, 150450 faces slice 240: 150400 vertices, 150450 faces slice 250: 150400 vertices, 150450 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... 150400 voxel in cpt #1: X=-50 [v=150400,e=451350,f=300900] located at (26.633511, -23.953403, 13.336756) For the whole surface: X=-50 [v=150400,e=451350,f=300900] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh 2021��� 11��� 16��� ��������� 10:19:58 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 2021��� 11��� 16��� ��������� 10:20:02 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 2021��� 11��� 16��� ��������� 10:20:05 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.4 mm, total surface area = 76964 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.054 (target=0.015) step 035: RMS=0.051 (target=0.015) step 040: RMS=0.048 (target=0.015) step 045: RMS=0.046 (target=0.015) step 050: RMS=0.045 (target=0.015) step 055: RMS=0.045 (target=0.015) step 060: RMS=0.044 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 25.575572 mris_inflate stimesec 0.048164 mris_inflate ru_maxrss 190356 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 46045 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2601 mris_inflate ru_nivcsw 44 #-------------------------------------------- #@# Inflation1 rh 2021��� 11��� 16��� ��������� 10:20:31 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.2 mm, total surface area = 79871 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.041 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 26.756061 mris_inflate stimesec 0.120251 mris_inflate ru_maxrss 196604 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 47618 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2673 mris_inflate ru_nivcsw 132 #-------------------------------------------- #@# QSphere lh 2021��� 11��� 16��� ��������� 10:20:58 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 0.96 +- 0.56 (0.00-->6.64) (max @ vno 104681 --> 105727) face area 0.03 +- 0.03 (-0.18-->0.67) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.594, avgs=0 005/300: dt: 0.9000, rms radial error=175.336, avgs=0 010/300: dt: 0.9000, rms radial error=174.784, avgs=0 015/300: dt: 0.9000, rms radial error=174.059, avgs=0 020/300: dt: 0.9000, rms radial error=173.233, avgs=0 025/300: dt: 0.9000, rms radial error=172.348, avgs=0 030/300: dt: 0.9000, rms radial error=171.432, avgs=0 035/300: dt: 0.9000, rms radial error=170.498, avgs=0 040/300: dt: 0.9000, rms radial error=169.555, avgs=0 045/300: dt: 0.9000, rms radial error=168.609, avgs=0 050/300: dt: 0.9000, rms radial error=167.664, avgs=0 055/300: dt: 0.9000, rms radial error=166.720, avgs=0 060/300: dt: 0.9000, rms radial error=165.780, avgs=0 065/300: dt: 0.9000, rms radial error=164.844, avgs=0 070/300: dt: 0.9000, rms radial error=163.912, avgs=0 075/300: dt: 0.9000, rms radial error=162.984, avgs=0 080/300: dt: 0.9000, rms radial error=162.062, avgs=0 085/300: dt: 0.9000, rms radial error=161.144, avgs=0 090/300: dt: 0.9000, rms radial error=160.230, avgs=0 095/300: dt: 0.9000, rms radial error=159.321, avgs=0 100/300: dt: 0.9000, rms radial error=158.417, avgs=0 105/300: dt: 0.9000, rms radial error=157.518, avgs=0 110/300: dt: 0.9000, rms radial error=156.623, avgs=0 115/300: dt: 0.9000, rms radial error=155.736, avgs=0 120/300: dt: 0.9000, rms radial error=154.859, avgs=0 125/300: dt: 0.9000, rms radial error=153.987, avgs=0 130/300: dt: 0.9000, rms radial error=153.120, avgs=0 135/300: dt: 0.9000, rms radial error=152.258, avgs=0 140/300: dt: 0.9000, rms radial error=151.402, avgs=0 145/300: dt: 0.9000, rms radial error=150.550, avgs=0 150/300: dt: 0.9000, rms radial error=149.702, avgs=0 155/300: dt: 0.9000, rms radial error=148.860, avgs=0 160/300: dt: 0.9000, rms radial error=148.022, avgs=0 165/300: dt: 0.9000, rms radial error=147.190, avgs=0 170/300: dt: 0.9000, rms radial error=146.361, avgs=0 175/300: dt: 0.9000, rms radial error=145.538, avgs=0 180/300: dt: 0.9000, rms radial error=144.718, avgs=0 185/300: dt: 0.9000, rms radial error=143.904, avgs=0 190/300: dt: 0.9000, rms radial error=143.095, avgs=0 195/300: dt: 0.9000, rms radial error=142.290, avgs=0 200/300: dt: 0.9000, rms radial error=141.489, avgs=0 205/300: dt: 0.9000, rms radial error=140.693, avgs=0 210/300: dt: 0.9000, rms radial error=139.901, avgs=0 215/300: dt: 0.9000, rms radial error=139.114, avgs=0 220/300: dt: 0.9000, rms radial error=138.331, avgs=0 225/300: dt: 0.9000, rms radial error=137.553, avgs=0 230/300: dt: 0.9000, rms radial error=136.779, avgs=0 235/300: dt: 0.9000, rms radial error=136.009, avgs=0 240/300: dt: 0.9000, rms radial error=135.243, avgs=0 245/300: dt: 0.9000, rms radial error=134.482, avgs=0 250/300: dt: 0.9000, rms radial error=133.725, avgs=0 255/300: dt: 0.9000, rms radial error=132.972, avgs=0 260/300: dt: 0.9000, rms radial error=132.224, avgs=0 265/300: dt: 0.9000, rms radial error=131.479, avgs=0 270/300: dt: 0.9000, rms radial error=130.739, avgs=0 275/300: dt: 0.9000, rms radial error=130.003, avgs=0 280/300: dt: 0.9000, rms radial error=129.271, avgs=0 285/300: dt: 0.9000, rms radial error=128.543, avgs=0 290/300: dt: 0.9000, rms radial error=127.819, avgs=0 295/300: dt: 0.9000, rms radial error=127.099, avgs=0 300/300: dt: 0.9000, rms radial error=126.383, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16833.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2779.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 3 (K=160.0), pass 1, starting sse = 285.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00424 epoch 4 (K=640.0), pass 1, starting sse = 25.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/10 = 0.00797 final distance error %26.38 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 149.595170 mris_sphere stimesec 0.072190 mris_sphere ru_maxrss 190652 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 46057 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2605 mris_sphere ru_nivcsw 1904 FSRUNTIME@ mris_sphere 0.0416 hours 1 threads #-------------------------------------------- #@# QSphere rh 2021��� 11��� 16��� ��������� 10:23:28 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 0.94 +- 0.56 (0.00-->6.39) (max @ vno 62597 --> 63942) face area 0.02 +- 0.03 (-0.10-->0.52) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.958, avgs=0 005/300: dt: 0.9000, rms radial error=175.695, avgs=0 010/300: dt: 0.9000, rms radial error=175.129, avgs=0 015/300: dt: 0.9000, rms radial error=174.386, avgs=0 020/300: dt: 0.9000, rms radial error=173.552, avgs=0 025/300: dt: 0.9000, rms radial error=172.664, avgs=0 030/300: dt: 0.9000, rms radial error=171.743, avgs=0 035/300: dt: 0.9000, rms radial error=170.806, avgs=0 040/300: dt: 0.9000, rms radial error=169.861, avgs=0 045/300: dt: 0.9000, rms radial error=168.913, avgs=0 050/300: dt: 0.9000, rms radial error=167.966, avgs=0 055/300: dt: 0.9000, rms radial error=167.026, avgs=0 060/300: dt: 0.9000, rms radial error=166.092, avgs=0 065/300: dt: 0.9000, rms radial error=165.163, avgs=0 070/300: dt: 0.9000, rms radial error=164.238, avgs=0 075/300: dt: 0.9000, rms radial error=163.318, avgs=0 080/300: dt: 0.9000, rms radial error=162.403, avgs=0 085/300: dt: 0.9000, rms radial error=161.492, avgs=0 090/300: dt: 0.9000, rms radial error=160.587, avgs=0 095/300: dt: 0.9000, rms radial error=159.686, avgs=0 100/300: dt: 0.9000, rms radial error=158.790, avgs=0 105/300: dt: 0.9000, rms radial error=157.899, avgs=0 110/300: dt: 0.9000, rms radial error=157.014, avgs=0 115/300: dt: 0.9000, rms radial error=156.132, avgs=0 120/300: dt: 0.9000, rms radial error=155.257, avgs=0 125/300: dt: 0.9000, rms radial error=154.387, avgs=0 130/300: dt: 0.9000, rms radial error=153.523, avgs=0 135/300: dt: 0.9000, rms radial error=152.663, avgs=0 140/300: dt: 0.9000, rms radial error=151.809, avgs=0 145/300: dt: 0.9000, rms radial error=150.958, avgs=0 150/300: dt: 0.9000, rms radial error=150.113, avgs=0 155/300: dt: 0.9000, rms radial error=149.272, avgs=0 160/300: dt: 0.9000, rms radial error=148.435, avgs=0 165/300: dt: 0.9000, rms radial error=147.601, avgs=0 170/300: dt: 0.9000, rms radial error=146.772, avgs=0 175/300: dt: 0.9000, rms radial error=145.947, avgs=0 180/300: dt: 0.9000, rms radial error=145.127, avgs=0 185/300: dt: 0.9000, rms radial error=144.311, avgs=0 190/300: dt: 0.9000, rms radial error=143.499, avgs=0 195/300: dt: 0.9000, rms radial error=142.692, avgs=0 200/300: dt: 0.9000, rms radial error=141.890, avgs=0 205/300: dt: 0.9000, rms radial error=141.092, avgs=0 210/300: dt: 0.9000, rms radial error=140.298, avgs=0 215/300: dt: 0.9000, rms radial error=139.509, avgs=0 220/300: dt: 0.9000, rms radial error=138.724, avgs=0 225/300: dt: 0.9000, rms radial error=137.943, avgs=0 230/300: dt: 0.9000, rms radial error=137.167, avgs=0 235/300: dt: 0.9000, rms radial error=136.395, avgs=0 240/300: dt: 0.9000, rms radial error=135.628, avgs=0 245/300: dt: 0.9000, rms radial error=134.864, avgs=0 250/300: dt: 0.9000, rms radial error=134.105, avgs=0 255/300: dt: 0.9000, rms radial error=133.351, avgs=0 260/300: dt: 0.9000, rms radial error=132.600, avgs=0 265/300: dt: 0.9000, rms radial error=131.854, avgs=0 270/300: dt: 0.9000, rms radial error=131.112, avgs=0 275/300: dt: 0.9000, rms radial error=130.374, avgs=0 280/300: dt: 0.9000, rms radial error=129.640, avgs=0 285/300: dt: 0.9000, rms radial error=128.910, avgs=0 290/300: dt: 0.9000, rms radial error=128.184, avgs=0 295/300: dt: 0.9000, rms radial error=127.463, avgs=0 300/300: dt: 0.9000, rms radial error=126.745, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17687.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3015.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 334.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00418 epoch 4 (K=640.0), pass 1, starting sse = 28.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00654 final distance error %28.50 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 163.462672 mris_sphere stimesec 0.064330 mris_sphere ru_maxrss 196924 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 47631 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2684 mris_sphere ru_nivcsw 578 FSRUNTIME@ mris_sphere 0.0455 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh 2021��� 11��� 16��� ��������� 10:26:12 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh 2021��� 11��� 16��� ��������� 10:26:12 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh 2021��� 11��� 16��� ��������� 10:26:12 CST mris_fix_topology -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 NC1 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=-60 (nv=145422, nf=290964, ne=436446, g=31) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 11954 ambiguous faces found in tessellation segmenting defects... 24 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 24 defects to be corrected 0 vertices coincident reading input surface /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7933 (-4.3967) -vertex loglikelihood: -5.6360 (-2.8180) -normal dot loglikelihood: -3.6059 (-3.6059) -quad curv loglikelihood: -5.9861 (-2.9931) Total Loglikelihood : -24.0214 CORRECTING DEFECT 0 (vertices=101, convex hull=113, v0=9343) After retessellation of defect 0 (v0=9343), euler #=-20 (138886,415454,276548) : difference with theory (-21) = -1 CORRECTING DEFECT 1 (vertices=498, convex hull=192, v0=12153) After retessellation of defect 1 (v0=12153), euler #=-19 (139010,415914,276885) : difference with theory (-20) = -1 CORRECTING DEFECT 2 (vertices=47, convex hull=67, v0=32836) After retessellation of defect 2 (v0=32836), euler #=-18 (139040,416033,276975) : difference with theory (-19) = -1 CORRECTING DEFECT 3 (vertices=28, convex hull=39, v0=44219) After retessellation of defect 3 (v0=44219), euler #=-17 (139047,416067,277003) : difference with theory (-18) = -1 CORRECTING DEFECT 4 (vertices=20, convex hull=56, v0=45138) After retessellation of defect 4 (v0=45138), euler #=-16 (139056,416114,277042) : difference with theory (-17) = -1 CORRECTING DEFECT 5 (vertices=3432, convex hull=461, v0=46434) XL defect detected... After retessellation of defect 5 (v0=46434), euler #=-16 (139156,416651,277479) : difference with theory (-16) = 0 CORRECTING DEFECT 6 (vertices=8, convex hull=23, v0=64224) After retessellation of defect 6 (v0=64224), euler #=-15 (139158,416666,277493) : difference with theory (-15) = 0 CORRECTING DEFECT 7 (vertices=394, convex hull=335, v0=71439) After retessellation of defect 7 (v0=71439), euler #=-14 (139312,417300,277974) : difference with theory (-14) = 0 CORRECTING DEFECT 8 (vertices=94, convex hull=74, v0=74975) After retessellation of defect 8 (v0=74975), euler #=-13 (139351,417450,278086) : difference with theory (-13) = 0 CORRECTING DEFECT 9 (vertices=1180, convex hull=551, v0=84562) XL defect detected... After retessellation of defect 9 (v0=84562), euler #=-12 (139766,419001,279223) : difference with theory (-12) = 0 CORRECTING DEFECT 10 (vertices=13, convex hull=34, v0=86958) After retessellation of defect 10 (v0=86958), euler #=-11 (139771,419025,279243) : difference with theory (-11) = 0 CORRECTING DEFECT 11 (vertices=22, convex hull=53, v0=87163) After retessellation of defect 11 (v0=87163), euler #=-10 (139781,419078,279287) : difference with theory (-10) = 0 CORRECTING DEFECT 12 (vertices=111, convex hull=82, v0=93283) After retessellation of defect 12 (v0=93283), euler #=-9 (139809,419204,279386) : difference with theory (-9) = 0 CORRECTING DEFECT 13 (vertices=5, convex hull=13, v0=96261) After retessellation of defect 13 (v0=96261), euler #=-8 (139810,419210,279392) : difference with theory (-8) = 0 CORRECTING DEFECT 14 (vertices=34, convex hull=54, v0=96410) After retessellation of defect 14 (v0=96410), euler #=-7 (139825,419272,279440) : difference with theory (-7) = 0 CORRECTING DEFECT 15 (vertices=22, convex hull=47, v0=102343) After retessellation of defect 15 (v0=102343), euler #=-6 (139837,419324,279481) : difference with theory (-6) = 0 CORRECTING DEFECT 16 (vertices=40, convex hull=32, v0=103253) After retessellation of defect 16 (v0=103253), euler #=-5 (139842,419349,279502) : difference with theory (-5) = 0 CORRECTING DEFECT 17 (vertices=285, convex hull=85, v0=104634) After retessellation of defect 17 (v0=104634), euler #=-4 (139877,419492,279611) : difference with theory (-4) = 0 CORRECTING DEFECT 18 (vertices=67, convex hull=29, v0=105108) After retessellation of defect 18 (v0=105108), euler #=-3 (139882,419516,279631) : difference with theory (-3) = 0 CORRECTING DEFECT 19 (vertices=25, convex hull=50, v0=111898) After retessellation of defect 19 (v0=111898), euler #=-2 (139897,419583,279684) : difference with theory (-2) = 0 CORRECTING DEFECT 20 (vertices=30, convex hull=72, v0=117352) After retessellation of defect 20 (v0=117352), euler #=-1 (139906,419638,279731) : difference with theory (-1) = 0 CORRECTING DEFECT 21 (vertices=20, convex hull=31, v0=118786) After retessellation of defect 21 (v0=118786), euler #=0 (139909,419658,279749) : difference with theory (0) = 0 CORRECTING DEFECT 22 (vertices=44, convex hull=71, v0=142571) After retessellation of defect 22 (v0=142571), euler #=1 (139927,419741,279815) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=62, convex hull=91, v0=144032) After retessellation of defect 23 (v0=144032), euler #=2 (139950,419844,279896) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.04-->9.85) (max @ vno 68900 --> 73412) 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 (0.04-->9.85) (max @ vno 68900 --> 73412) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 78 mutations (35.5%), 142 crossovers (64.5%), 555 vertices were eliminated building final representation... 5472 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139950, nf=279896, ne=419844, g=0) writing corrected surface to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.2 minutes 0 defective edges removing intersecting faces 000: 342 intersecting 001: 4 intersecting mris_fix_topology utimesec 1029.261768 mris_fix_topology stimesec 0.188160 mris_fix_topology ru_maxrss 462788 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 120019 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 4303 mris_fix_topology ru_nivcsw 1472 FSRUNTIME@ mris_fix_topology lh 0.2862 hours 1 threads #@# Fix Topology rh 2021��� 11��� 16��� ��������� 10:43:22 CST mris_fix_topology -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 NC1 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=-50 (nv=150400, nf=300900, ne=451350, g=26) 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... 9743 ambiguous faces found in tessellation segmenting defects... 30 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 6 29 defects to be corrected 0 vertices coincident reading input surface /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8233 (-4.4116) -vertex loglikelihood: -5.7171 (-2.8586) -normal dot loglikelihood: -3.6616 (-3.6616) -quad curv loglikelihood: -6.0412 (-3.0206) Total Loglikelihood : -24.2432 CORRECTING DEFECT 0 (vertices=10, convex hull=24, v0=20452) After retessellation of defect 0 (v0=20452), euler #=-26 (144913,433491,288552) : difference with theory (-26) = 0 CORRECTING DEFECT 1 (vertices=29, convex hull=79, v0=43938) After retessellation of defect 1 (v0=43938), euler #=-25 (144930,433572,288617) : difference with theory (-25) = 0 CORRECTING DEFECT 2 (vertices=2901, convex hull=670, v0=53466) XL defect detected... After retessellation of defect 2 (v0=53466), euler #=-25 (144952,434000,289023) : difference with theory (-24) = 1 CORRECTING DEFECT 3 (vertices=33, convex hull=78, v0=61398) After retessellation of defect 3 (v0=61398), euler #=-24 (144961,434057,289072) : difference with theory (-23) = 1 CORRECTING DEFECT 4 (vertices=497, convex hull=241, v0=62486) After retessellation of defect 4 (v0=62486), euler #=-23 (145004,434303,289276) : difference with theory (-22) = 1 CORRECTING DEFECT 5 (vertices=8, convex hull=36, v0=66186) After retessellation of defect 5 (v0=66186), euler #=-22 (145008,434325,289295) : difference with theory (-21) = 1 CORRECTING DEFECT 6 (vertices=123, convex hull=152, v0=66634) After retessellation of defect 6 (v0=66634), euler #=-20 (145057,434544,289467) : difference with theory (-20) = 0 CORRECTING DEFECT 7 (vertices=67, convex hull=94, v0=84737) After retessellation of defect 7 (v0=84737), euler #=-19 (145092,434689,289578) : difference with theory (-19) = 0 CORRECTING DEFECT 8 (vertices=881, convex hull=332, v0=86849) After retessellation of defect 8 (v0=86849), euler #=-18 (145140,434994,289836) : difference with theory (-18) = 0 CORRECTING DEFECT 9 (vertices=121, convex hull=147, v0=92785) After retessellation of defect 9 (v0=92785), euler #=-17 (145203,435252,290032) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=44, convex hull=50, v0=92799) After retessellation of defect 10 (v0=92799), euler #=-16 (145216,435310,290078) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=11, convex hull=27, v0=96709) After retessellation of defect 11 (v0=96709), euler #=-15 (145218,435325,290092) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=26, convex hull=41, v0=102949) After retessellation of defect 12 (v0=102949), euler #=-14 (145227,435366,290125) : difference with theory (-14) = 0 CORRECTING DEFECT 13 (vertices=15, convex hull=30, v0=104780) After retessellation of defect 13 (v0=104780), euler #=-13 (145228,435383,290142) : difference with theory (-13) = 0 CORRECTING DEFECT 14 (vertices=28, convex hull=67, v0=106435) After retessellation of defect 14 (v0=106435), euler #=-12 (145242,435451,290197) : difference with theory (-12) = 0 CORRECTING DEFECT 15 (vertices=103, convex hull=46, v0=107559) After retessellation of defect 15 (v0=107559), euler #=-11 (145256,435514,290247) : difference with theory (-11) = 0 CORRECTING DEFECT 16 (vertices=41, convex hull=26, v0=107614) After retessellation of defect 16 (v0=107614), euler #=-10 (145263,435546,290273) : difference with theory (-10) = 0 CORRECTING DEFECT 17 (vertices=24, convex hull=21, v0=108057) After retessellation of defect 17 (v0=108057), euler #=-9 (145266,435567,290292) : difference with theory (-9) = 0 CORRECTING DEFECT 18 (vertices=8, convex hull=30, v0=112760) After retessellation of defect 18 (v0=112760), euler #=-8 (145268,435581,290305) : difference with theory (-8) = 0 CORRECTING DEFECT 19 (vertices=72, convex hull=43, v0=113816) After retessellation of defect 19 (v0=113816), euler #=-7 (145271,435610,290332) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=12, convex hull=25, v0=116288) After retessellation of defect 20 (v0=116288), euler #=-6 (145272,435620,290342) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=38, convex hull=62, v0=121177) After retessellation of defect 21 (v0=121177), euler #=-5 (145294,435711,290412) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=45, convex hull=65, v0=125369) After retessellation of defect 22 (v0=125369), euler #=-4 (145310,435782,290468) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=47, convex hull=51, v0=127685) After retessellation of defect 23 (v0=127685), euler #=-3 (145317,435826,290506) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=197, convex hull=116, v0=135999) After retessellation of defect 24 (v0=135999), euler #=-2 (145359,436001,290640) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=10, convex hull=17, v0=145599) After retessellation of defect 25 (v0=145599), euler #=-1 (145360,436010,290649) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=26, convex hull=63, v0=145813) After retessellation of defect 26 (v0=145813), euler #=0 (145371,436069,290698) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=30, convex hull=31, v0=146646) After retessellation of defect 27 (v0=146646), euler #=1 (145374,436090,290717) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=38, convex hull=71, v0=147439) After retessellation of defect 28 (v0=147439), euler #=2 (145383,436143,290762) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.14-->14.07) (max @ vno 67483 --> 80906) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.14-->14.07) (max @ vno 67483 --> 80906) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 114 mutations (37.1%), 193 crossovers (62.9%), 906 vertices were eliminated building final representation... 5017 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=145383, nf=290762, ne=436143, g=0) writing corrected surface to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 20.6 minutes 0 defective edges removing intersecting faces 000: 363 intersecting 001: 13 intersecting mris_fix_topology utimesec 1237.423162 mris_fix_topology stimesec 0.204100 mris_fix_topology ru_maxrss 482472 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 123929 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 4433 mris_fix_topology ru_nivcsw 1664 FSRUNTIME@ mris_fix_topology rh 0.3440 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 139950 - 419844 + 279896 = 2 --> 0 holes F =2V-4: 279896 = 279900-4 (0) 2E=3F: 839688 = 839688 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 145383 - 436143 + 290762 = 2 --> 0 holes F =2V-4: 290762 = 290766-4 (0) 2E=3F: 872286 = 872286 (0) total defect index = 0 /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 121 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 50 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh 2021��� 11��� 16��� ��������� 11:04:08 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs NC1 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/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/filled.mgz... reading volume /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/brain.finalsurfs.mgz... reading volume /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/../mri/aseg.presurf.mgz... reading volume /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/wm.mgz... 18797 bright wm thresholded. 2066 bright non-wm voxels segmented. reading original surface position from /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.orig... computing class statistics... border white: 280485 voxels (1.67%) border gray 309102 voxels (1.84%) WM (100.0): 100.2 +- 6.7 [70.0 --> 110.0] GM (80.0) : 79.0 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.9 (was 70) setting MAX_BORDER_WHITE to 110.7 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 56.9 (was 40) setting MAX_GRAY to 97.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.51) (max @ vno 138895 --> 138897) face area 0.28 +- 0.13 (0.00-->6.35) mean absolute distance = 0.75 +- 0.98 3282 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=104+-4.3, GM=77+-7.0 mean inside = 96.7, mean outside = 82.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=86.7, 100 (100) missing vertices, mean dist 0.2 [0.7 (%39.3)->0.8 (%60.7))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=siyin, 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 +- 0.25 (0.05-->5.17) (max @ vno 138894 --> 138897) face area 0.28 +- 0.13 (0.00-->6.66) mean absolute distance = 0.36 +- 0.68 3106 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2277432.0, rms=7.974 001: dt: 0.5000, sse=1396517.1, rms=5.591 (29.884%) 002: dt: 0.5000, sse=992649.6, rms=4.038 (27.781%) 003: dt: 0.5000, sse=814234.8, rms=3.111 (22.958%) 004: dt: 0.5000, sse=733176.9, rms=2.580 (17.076%) 005: dt: 0.5000, sse=704469.6, rms=2.350 (8.884%) 006: dt: 0.5000, sse=690646.3, rms=2.237 (4.822%) rms = 2.21, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=687565.2, rms=2.211 (1.188%) 008: dt: 0.2500, sse=619571.0, rms=1.387 (37.240%) 009: dt: 0.2500, sse=612096.1, rms=1.267 (8.683%) rms = 1.24, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=610258.6, rms=1.241 (2.062%) rms = 1.22, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=609008.4, rms=1.220 (1.643%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.5, 80 (40) missing vertices, mean dist -0.2 [0.4 (%67.1)->0.3 (%32.9))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=siyin, 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 0.91 +- 0.24 (0.08-->5.14) (max @ vno 138894 --> 138897) face area 0.35 +- 0.16 (0.00-->8.62) mean absolute distance = 0.29 +- 0.46 3679 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1012307.1, rms=3.355 012: dt: 0.5000, sse=818883.9, rms=2.026 (39.618%) 013: dt: 0.5000, sse=783182.4, rms=1.689 (16.597%) 014: dt: 0.5000, sse=771065.6, rms=1.561 (7.614%) rms = 1.63, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=750701.5, rms=1.244 (20.314%) 016: dt: 0.2500, sse=742119.2, rms=1.095 (11.973%) rms = 1.06, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=740180.2, rms=1.064 (2.790%) rms = 1.05, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=739973.9, rms=1.048 (1.518%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=90.2, 78 (31) missing vertices, mean dist -0.1 [0.3 (%69.1)->0.2 (%30.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=siyin, 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 0.90 +- 0.24 (0.09-->4.99) (max @ vno 138894 --> 138897) face area 0.35 +- 0.16 (0.00-->8.37) mean absolute distance = 0.24 +- 0.36 3075 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=870816.4, rms=2.554 019: dt: 0.5000, sse=766523.1, rms=1.592 (37.664%) 020: dt: 0.5000, sse=753025.1, rms=1.462 (8.148%) rms = 1.42, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=747086.2, rms=1.416 (3.142%) 022: dt: 0.2500, sse=722614.5, rms=1.003 (29.193%) rms = 0.96, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=720531.0, rms=0.963 (3.980%) rms = 0.95, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=720073.1, rms=0.951 (1.189%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.9, 88 (26) missing vertices, mean dist -0.1 [0.3 (%57.6)->0.2 (%42.4))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=siyin, 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/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=729896.9, rms=1.335 025: dt: 0.5000, sse=707191.7, rms=0.959 (28.156%) rms = 1.17, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=699733.8, rms=0.811 (15.476%) rms = 0.78, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=698340.2, rms=0.785 (3.199%) rms = 0.77, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=697392.9, rms=0.774 (1.339%) positioning took 0.3 minutes generating cortex label... 3 non-cortical segments detected only using segment with 7900 vertices erasing segment 1 (vno[0] = 93524) erasing segment 2 (vno[0] = 99586) writing cortex label to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/label/lh.cortex.label... writing curvature file /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->4.94) (max @ vno 139572 --> 139762) face area 0.34 +- 0.16 (0.00-->7.99) refinement took 2.9 minutes #-------------------------------------------- #@# Make White Surf rh 2021��� 11��� 16��� ��������� 11:07:03 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs NC1 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/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/filled.mgz... reading volume /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/brain.finalsurfs.mgz... reading volume /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/../mri/aseg.presurf.mgz... reading volume /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/mri/wm.mgz... 18797 bright wm thresholded. 2066 bright non-wm voxels segmented. reading original surface position from /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/rh.orig... computing class statistics... border white: 280485 voxels (1.67%) border gray 309102 voxels (1.84%) WM (100.0): 100.2 +- 6.7 [70.0 --> 110.0] GM (80.0) : 79.0 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.9 (was 70) setting MAX_BORDER_WHITE to 110.7 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 56.9 (was 40) setting MAX_GRAY to 97.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.73) (max @ vno 67483 --> 80906) face area 0.28 +- 0.13 (0.00-->8.54) mean absolute distance = 0.77 +- 1.02 3334 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=104+-5.2, GM=77+-7.0 mean inside = 96.7, mean outside = 82.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.2, 94 (94) missing vertices, mean dist 0.2 [0.7 (%41.8)->0.8 (%58.2))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=siyin, 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 (0.13-->5.68) (max @ vno 67483 --> 80906) face area 0.28 +- 0.13 (0.00-->5.24) mean absolute distance = 0.39 +- 0.72 3760 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2480471.0, rms=8.217 001: dt: 0.5000, sse=1517357.2, rms=5.791 (29.526%) 002: dt: 0.5000, sse=1081932.0, rms=4.245 (26.697%) 003: dt: 0.5000, sse=891601.8, rms=3.343 (21.258%) 004: dt: 0.5000, sse=799716.7, rms=2.810 (15.944%) 005: dt: 0.5000, sse=764345.6, rms=2.545 (9.403%) 006: dt: 0.5000, sse=744812.4, rms=2.424 (4.777%) 007: dt: 0.5000, sse=737802.5, rms=2.359 (2.695%) rms = 2.31, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=731222.6, rms=2.310 (2.063%) 009: dt: 0.2500, sse=664161.5, rms=1.597 (30.877%) 010: dt: 0.2500, sse=652709.9, rms=1.448 (9.331%) rms = 1.42, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=650689.9, rms=1.425 (1.599%) rms = 1.39, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=648049.9, rms=1.392 (2.254%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.0, 54 (21) missing vertices, mean dist -0.2 [0.5 (%65.0)->0.3 (%35.0))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=siyin, 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 0.91 +- 0.24 (0.02-->5.49) (max @ vno 67483 --> 80906) face area 0.35 +- 0.16 (0.00-->6.04) mean absolute distance = 0.31 +- 0.48 3732 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1088846.0, rms=3.537 013: dt: 0.5000, sse=882256.9, rms=2.267 (35.906%) 014: dt: 0.5000, sse=834941.6, rms=1.886 (16.786%) 015: dt: 0.5000, sse=822442.9, rms=1.768 (6.267%) rms = 1.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=799481.8, rms=1.491 (15.664%) 017: dt: 0.2500, sse=788412.1, rms=1.334 (10.565%) rms = 1.30, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=785686.1, rms=1.298 (2.666%) rms = 1.27, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=784665.5, rms=1.274 (1.870%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.7, 53 (11) missing vertices, mean dist -0.2 [0.3 (%69.1)->0.2 (%30.9))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=siyin, 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 0.90 +- 0.24 (0.07-->5.44) (max @ vno 67483 --> 80906) face area 0.34 +- 0.16 (0.00-->6.50) mean absolute distance = 0.25 +- 0.38 3751 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=925895.7, rms=2.716 020: dt: 0.5000, sse=808256.9, rms=1.742 (35.852%) 021: dt: 0.5000, sse=791439.4, rms=1.593 (8.552%) rms = 1.56, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=798649.3, rms=1.561 (2.022%) 023: dt: 0.2500, sse=764209.5, rms=1.200 (23.104%) rms = 1.15, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=758372.6, rms=1.155 (3.804%) rms = 1.14, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=757388.1, rms=1.145 (0.882%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... 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 mean border=91.4, 52 (6) missing vertices, mean dist -0.1 [0.3 (%57.9)->0.2 (%42.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=siyin, 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/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=771145.8, rms=1.534 026: dt: 0.5000, sse=748278.1, rms=1.219 (20.544%) rms = 1.33, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=735999.3, rms=1.045 (14.293%) rms = 1.02, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=734953.9, rms=1.021 (2.295%) rms = 0.97, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=731290.0, rms=0.975 (4.547%) positioning took 0.3 minutes generating cortex label... 5 non-cortical segments detected only using segment with 7666 vertices erasing segment 1 (vno[0] = 63494) erasing segment 2 (vno[0] = 105845) erasing segment 3 (vno[0] = 106824) erasing segment 4 (vno[0] = 106826) writing cortex label to /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/label/rh.cortex.label... writing curvature file /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/rh.area vertex spacing 0.89 +- 0.25 (0.07-->5.36) (max @ vno 67483 --> 78638) face area 0.34 +- 0.16 (0.00-->5.82) refinement took 3.1 minutes #-------------------------------------------- #@# Smooth2 lh 2021��� 11��� 16��� ��������� 11:10:08 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 2021��� 11��� 16��� ��������� 11:10:12 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/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 2021��� 11��� 16��� ��������� 11:10:15 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_inflate -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.7 mm, total surface area = 85957 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 25.072268 mris_inflate stimesec 0.076280 mris_inflate ru_maxrss 183708 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 44365 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2678 mris_inflate ru_nivcsw 37 #-------------------------------------------- #@# Inflation2 rh 2021��� 11��� 16��� ��������� 11:10:40 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/scripts mris_inflate -rusage /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.4 mm, total surface area = 88621 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.175 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 25.970417 mris_inflate stimesec 0.064402 mris_inflate ru_maxrss 190624 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 46079 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2778 mris_inflate ru_nivcsw 49 #-------------------------------------------- #@# Curv .H and .K lh 2021��� 11��� 16��� ��������� 11:11:07 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf mris_curvature -w lh.white.preaparc total integrated curvature = 1.039*4pi (13.062) --> 0 handles ICI = 160.8, FI = 1656.3, variation=26210.273 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 Linux siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NC1 exited with ERRORS at 2021��� 11��� 16��� ��������� 11:11:08 CST To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all 2021��� 11��� 17��� ��������� 08:39:49 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1 /opt/freesurfer/bin/recon-all -s NC1 -qcache subjid NC1 setenv SUBJECTS_DIR /home/siying/sharefolder/piantoutong/freesurfer_1 FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 24719 maxlocks unlimited maxsignal 24719 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 6389640 729068 3319196 15376 2341376 5319904 Swap: 2206716 0 2206716 ######################################## 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: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-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: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:49-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:50-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/17-00:39:50-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: siying Machine: siying-VM Platform: Linux PlatformVersion: 4.15.0-142-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage 2021��� 11��� 17��� ��������� 08:39:50 CST /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf mris_preproc --s NC1 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 ERROR: cannot find /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.thickness Linux siying-VM 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NC1 exited with ERRORS at 2021��� 11��� 17��� ��������� 08:39:50 CST To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting