Mon Mar 29 23:54:23 UTC 2021 /out/out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-05 -sd /out/out/freesurfer subjid sub-05 setenv SUBJECTS_DIR /out/out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 83ec93b3099f 5.4.0-67-generic #75~18.04.1-Ubuntu SMP Tue Feb 23 19:17:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 65536 kbytes maxproc unlimited maxlocks unlimited maxsignal 62787 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16122748 7313776 2367360 968180 6441612 7141672 Swap: 31999996 740608 31259388 ######################################## 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: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-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: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-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: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-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: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-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: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-23:54:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-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 ####################################### #-------------------------------------------- #@# Tessellate rh Mon Mar 29 23:54:23 UTC 2021 /out/out/freesurfer/sub-05/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-): 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-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2 (out of 269407: 0.000742) 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 40: 1353 vertices, 1467 faces slice 50: 7724 vertices, 8005 faces slice 60: 17383 vertices, 17702 faces slice 70: 28430 vertices, 28827 faces slice 80: 40460 vertices, 40847 faces slice 90: 52012 vertices, 52378 faces slice 100: 64390 vertices, 64837 faces slice 110: 76406 vertices, 76828 faces slice 120: 87953 vertices, 88382 faces slice 130: 99073 vertices, 99461 faces slice 140: 109267 vertices, 109652 faces slice 150: 117984 vertices, 118301 faces slice 160: 126422 vertices, 126729 faces slice 170: 133599 vertices, 133875 faces slice 180: 139629 vertices, 139881 faces slice 190: 144470 vertices, 144685 faces slice 200: 146788 vertices, 146846 faces slice 210: 146788 vertices, 146846 faces slice 220: 146788 vertices, 146846 faces slice 230: 146788 vertices, 146846 faces slice 240: 146788 vertices, 146846 faces slice 250: 146788 vertices, 146846 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... 146788 voxel in cpt #1: X=-58 [v=146788,e=440538,f=293692] located at (27.494488, -18.912806, 24.708225) For the whole surface: X=-58 [v=146788,e=440538,f=293692] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Mon Mar 29 23:54:26 UTC 2021 /out/out/freesurfer/sub-05/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 rh Mon Mar 29 23:54:29 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.0 mm, total surface area = 79079 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.150 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.038 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 65.877978 mris_inflate stimesec 0.397702 mris_inflate ru_maxrss 236476 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 57792 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10328 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 79004 mris_inflate ru_nivcsw 89 #-------------------------------------------- #@# QSphere rh Mon Mar 29 23:54:41 UTC 2021 /out/out/freesurfer/sub-05/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 0.96 +- 0.56 (0.00-->6.65) (max @ vno 108922 --> 108923) face area 0.02 +- 0.03 (-0.13-->0.59) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.299... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.533, avgs=0 005/300: dt: 0.9000, rms radial error=176.272, avgs=0 010/300: dt: 0.9000, rms radial error=175.713, avgs=0 015/300: dt: 0.9000, rms radial error=174.978, avgs=0 020/300: dt: 0.9000, rms radial error=174.142, avgs=0 025/300: dt: 0.9000, rms radial error=173.253, avgs=0 030/300: dt: 0.9000, rms radial error=172.333, avgs=0 035/300: dt: 0.9000, rms radial error=171.398, avgs=0 040/300: dt: 0.9000, rms radial error=170.454, avgs=0 045/300: dt: 0.9000, rms radial error=169.507, avgs=0 050/300: dt: 0.9000, rms radial error=168.562, avgs=0 055/300: dt: 0.9000, rms radial error=167.620, avgs=0 060/300: dt: 0.9000, rms radial error=166.683, avgs=0 065/300: dt: 0.9000, rms radial error=165.751, avgs=0 070/300: dt: 0.9000, rms radial error=164.823, avgs=0 075/300: dt: 0.9000, rms radial error=163.901, avgs=0 080/300: dt: 0.9000, rms radial error=162.983, avgs=0 085/300: dt: 0.9000, rms radial error=162.071, avgs=0 090/300: dt: 0.9000, rms radial error=161.163, avgs=0 095/300: dt: 0.9000, rms radial error=160.260, avgs=0 100/300: dt: 0.9000, rms radial error=159.363, avgs=0 105/300: dt: 0.9000, rms radial error=158.470, avgs=0 110/300: dt: 0.9000, rms radial error=157.582, avgs=0 115/300: dt: 0.9000, rms radial error=156.699, avgs=0 120/300: dt: 0.9000, rms radial error=155.821, avgs=0 125/300: dt: 0.9000, rms radial error=154.947, avgs=0 130/300: dt: 0.9000, rms radial error=154.079, avgs=0 135/300: dt: 0.9000, rms radial error=153.215, avgs=0 140/300: dt: 0.9000, rms radial error=152.356, avgs=0 145/300: dt: 0.9000, rms radial error=151.502, avgs=0 150/300: dt: 0.9000, rms radial error=150.652, avgs=0 155/300: dt: 0.9000, rms radial error=149.807, avgs=0 160/300: dt: 0.9000, rms radial error=148.966, avgs=0 165/300: dt: 0.9000, rms radial error=148.131, avgs=0 170/300: dt: 0.9000, rms radial error=147.299, avgs=0 175/300: dt: 0.9000, rms radial error=146.472, avgs=0 180/300: dt: 0.9000, rms radial error=145.650, avgs=0 185/300: dt: 0.9000, rms radial error=144.832, avgs=0 190/300: dt: 0.9000, rms radial error=144.018, avgs=0 195/300: dt: 0.9000, rms radial error=143.210, avgs=0 200/300: dt: 0.9000, rms radial error=142.405, avgs=0 205/300: dt: 0.9000, rms radial error=141.605, avgs=0 210/300: dt: 0.9000, rms radial error=140.809, avgs=0 215/300: dt: 0.9000, rms radial error=140.018, avgs=0 220/300: dt: 0.9000, rms radial error=139.232, avgs=0 225/300: dt: 0.9000, rms radial error=138.449, avgs=0 230/300: dt: 0.9000, rms radial error=137.671, avgs=0 235/300: dt: 0.9000, rms radial error=136.897, avgs=0 240/300: dt: 0.9000, rms radial error=136.128, avgs=0 245/300: dt: 0.9000, rms radial error=135.363, avgs=0 250/300: dt: 0.9000, rms radial error=134.602, avgs=0 255/300: dt: 0.9000, rms radial error=133.845, avgs=0 260/300: dt: 0.9000, rms radial error=133.093, avgs=0 265/300: dt: 0.9000, rms radial error=132.344, avgs=0 270/300: dt: 0.9000, rms radial error=131.600, avgs=0 275/300: dt: 0.9000, rms radial error=130.860, avgs=0 280/300: dt: 0.9000, rms radial error=130.125, avgs=0 285/300: dt: 0.9000, rms radial error=129.393, avgs=0 290/300: dt: 0.9000, rms radial error=128.665, avgs=0 295/300: dt: 0.9000, rms radial error=127.942, avgs=0 300/300: dt: 0.9000, rms radial error=127.222, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17348.92 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 = 2963.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 314.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00714 epoch 4 (K=640.0), pass 1, starting sse = 21.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00763 final distance error %27.63 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 333.830025 mris_sphere stimesec 0.440514 mris_sphere ru_maxrss 236876 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 57825 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 144 mris_sphere ru_oublock 10328 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 86681 mris_sphere ru_nivcsw 449 FSRUNTIME@ mris_sphere 0.0206 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy rh Mon Mar 29 23:55:55 UTC 2021 /out/out/freesurfer/sub-05/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology rh Mon Mar 29 23:55:55 UTC 2021 mris_fix_topology -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-05 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=-58 (nv=146788, nf=293692, ne=440538, g=30) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 4822 ambiguous faces found in tessellation segmenting defects... 37 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 37 defects to be corrected 0 vertices coincident reading input surface /out/out/freesurfer/sub-05/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3009 (-4.6505) -vertex loglikelihood: -5.9888 (-2.9944) -normal dot loglikelihood: -3.5870 (-3.5870) -quad curv loglikelihood: -6.0926 (-3.0463) Total Loglikelihood : -24.9693 CORRECTING DEFECT 0 (vertices=167, convex hull=176, v0=2499) After retessellation of defect 0 (v0=2499), euler #=-34 (143945,430818,286839) : difference with theory (-34) = 0 CORRECTING DEFECT 1 (vertices=29, convex hull=59, v0=2959) After retessellation of defect 1 (v0=2959), euler #=-33 (143960,430887,286894) : difference with theory (-33) = 0 CORRECTING DEFECT 2 (vertices=33, convex hull=60, v0=13869) After retessellation of defect 2 (v0=13869), euler #=-32 (143972,430946,286942) : difference with theory (-32) = 0 CORRECTING DEFECT 3 (vertices=52, convex hull=70, v0=17129) After retessellation of defect 3 (v0=17129), euler #=-31 (143983,431006,286992) : difference with theory (-31) = 0 CORRECTING DEFECT 4 (vertices=9, convex hull=19, v0=19213) After retessellation of defect 4 (v0=19213), euler #=-30 (143984,431015,287001) : difference with theory (-30) = 0 CORRECTING DEFECT 5 (vertices=6, convex hull=32, v0=28008) After retessellation of defect 5 (v0=28008), euler #=-29 (143986,431034,287019) : difference with theory (-29) = 0 CORRECTING DEFECT 6 (vertices=24, convex hull=56, v0=41815) After retessellation of defect 6 (v0=41815), euler #=-28 (143996,431085,287061) : difference with theory (-28) = 0 CORRECTING DEFECT 7 (vertices=37, convex hull=32, v0=46404) After retessellation of defect 7 (v0=46404), euler #=-27 (143999,431107,287081) : difference with theory (-27) = 0 CORRECTING DEFECT 8 (vertices=483, convex hull=224, v0=57741) After retessellation of defect 8 (v0=57741), euler #=-26 (144080,431459,287353) : difference with theory (-26) = 0 CORRECTING DEFECT 9 (vertices=58, convex hull=84, v0=60504) After retessellation of defect 9 (v0=60504), euler #=-25 (144091,431529,287413) : difference with theory (-25) = 0 CORRECTING DEFECT 10 (vertices=93, convex hull=40, v0=62496) After retessellation of defect 10 (v0=62496), euler #=-24 (144105,431590,287461) : difference with theory (-24) = 0 CORRECTING DEFECT 11 (vertices=40, convex hull=56, v0=66685) After retessellation of defect 11 (v0=66685), euler #=-23 (144114,431640,287503) : difference with theory (-23) = 0 CORRECTING DEFECT 12 (vertices=81, convex hull=45, v0=67185) After retessellation of defect 12 (v0=67185), euler #=-22 (144123,431684,287539) : difference with theory (-22) = 0 CORRECTING DEFECT 13 (vertices=29, convex hull=52, v0=74885) After retessellation of defect 13 (v0=74885), euler #=-21 (144130,431723,287572) : difference with theory (-21) = 0 CORRECTING DEFECT 14 (vertices=18, convex hull=27, v0=75138) After retessellation of defect 14 (v0=75138), euler #=-20 (144131,431739,287588) : difference with theory (-20) = 0 CORRECTING DEFECT 15 (vertices=245, convex hull=140, v0=78517) After retessellation of defect 15 (v0=78517), euler #=-19 (144147,431865,287699) : difference with theory (-19) = 0 CORRECTING DEFECT 16 (vertices=279, convex hull=217, v0=82212) After retessellation of defect 16 (v0=82212), euler #=-18 (144213,432167,287936) : difference with theory (-18) = 0 CORRECTING DEFECT 17 (vertices=35, convex hull=30, v0=85238) After retessellation of defect 17 (v0=85238), euler #=-17 (144218,432197,287962) : difference with theory (-17) = 0 CORRECTING DEFECT 18 (vertices=33, convex hull=47, v0=94622) After retessellation of defect 18 (v0=94622), euler #=-16 (144228,432245,288001) : difference with theory (-16) = 0 CORRECTING DEFECT 19 (vertices=8, convex hull=14, v0=96733) After retessellation of defect 19 (v0=96733), euler #=-15 (144229,432251,288007) : difference with theory (-15) = 0 CORRECTING DEFECT 20 (vertices=83, convex hull=40, v0=98897) After retessellation of defect 20 (v0=98897), euler #=-14 (144234,432280,288032) : difference with theory (-14) = 0 CORRECTING DEFECT 21 (vertices=49, convex hull=100, v0=106938) After retessellation of defect 21 (v0=106938), euler #=-13 (144250,432369,288106) : difference with theory (-13) = 0 CORRECTING DEFECT 22 (vertices=62, convex hull=60, v0=107083) After retessellation of defect 22 (v0=107083), euler #=-12 (144260,432422,288150) : difference with theory (-12) = 0 CORRECTING DEFECT 23 (vertices=79, convex hull=85, v0=111175) After retessellation of defect 23 (v0=111175), euler #=-11 (144290,432548,288247) : difference with theory (-11) = 0 CORRECTING DEFECT 24 (vertices=27, convex hull=43, v0=113790) After retessellation of defect 24 (v0=113790), euler #=-10 (144292,432571,288269) : difference with theory (-10) = 0 CORRECTING DEFECT 25 (vertices=52, convex hull=94, v0=116280) After retessellation of defect 25 (v0=116280), euler #=-9 (144302,432642,288331) : difference with theory (-9) = 0 CORRECTING DEFECT 26 (vertices=11, convex hull=27, v0=117870) After retessellation of defect 26 (v0=117870), euler #=-8 (144303,432653,288342) : difference with theory (-8) = 0 CORRECTING DEFECT 27 (vertices=34, convex hull=80, v0=119533) After retessellation of defect 27 (v0=119533), euler #=-7 (144326,432755,288422) : difference with theory (-7) = 0 CORRECTING DEFECT 28 (vertices=5, convex hull=20, v0=120337) After retessellation of defect 28 (v0=120337), euler #=-6 (144327,432763,288430) : difference with theory (-6) = 0 CORRECTING DEFECT 29 (vertices=39, convex hull=89, v0=130572) After retessellation of defect 29 (v0=130572), euler #=-5 (144346,432855,288504) : difference with theory (-5) = 0 CORRECTING DEFECT 30 (vertices=32, convex hull=62, v0=132301) After retessellation of defect 30 (v0=132301), euler #=-4 (144363,432928,288561) : difference with theory (-4) = 0 CORRECTING DEFECT 31 (vertices=66, convex hull=87, v0=133560) After retessellation of defect 31 (v0=133560), euler #=-3 (144394,433056,288659) : difference with theory (-3) = 0 CORRECTING DEFECT 32 (vertices=20, convex hull=56, v0=134731) After retessellation of defect 32 (v0=134731), euler #=-2 (144405,433108,288701) : difference with theory (-2) = 0 CORRECTING DEFECT 33 (vertices=442, convex hull=65, v0=136698) After retessellation of defect 33 (v0=136698), euler #=-1 (144423,433192,288768) : difference with theory (-1) = 0 CORRECTING DEFECT 34 (vertices=57, convex hull=84, v0=139940) After retessellation of defect 34 (v0=139940), euler #=0 (144450,433310,288860) : difference with theory (0) = 0 CORRECTING DEFECT 35 (vertices=29, convex hull=66, v0=144689) After retessellation of defect 35 (v0=144689), euler #=1 (144463,433373,288911) : difference with theory (1) = 0 CORRECTING DEFECT 36 (vertices=53, convex hull=33, v0=146138) After retessellation of defect 36 (v0=146138), euler #=2 (144467,433395,288930) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.06-->13.04) (max @ vno 57468 --> 60727) 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 (0.06-->13.04) (max @ vno 57468 --> 60727) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 140 mutations (37.0%), 238 crossovers (63.0%), 274 vertices were eliminated building final representation... 2321 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=144467, nf=288930, ne=433395, g=0) writing corrected surface to /out/out/freesurfer/sub-05/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.6 minutes 0 defective edges removing intersecting faces 000: 322 intersecting 001: 7 intersecting mris_fix_topology utimesec 765.002245 mris_fix_topology stimesec 0.095985 mris_fix_topology ru_maxrss 461540 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 115161 mris_fix_topology ru_majflt 13 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 2600 mris_fix_topology ru_oublock 13616 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 339 mris_fix_topology ru_nivcsw 874 FSRUNTIME@ mris_fix_topology rh 0.2104 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 144467 - 433395 + 288930 = 2 --> 0 holes F =2V-4: 288930 = 288934-4 (0) 2E=3F: 866790 = 866790 (0) total defect index = 0 /out/out/freesurfer/sub-05/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 32 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Mar 30 00:08:35 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-05 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 /out/out/freesurfer/sub-05/mri/filled.mgz... reading volume /out/out/freesurfer/sub-05/mri/brain.finalsurfs.mgz... reading volume /out/out/freesurfer/sub-05/mri/../mri/aseg.presurf.mgz... reading volume /out/out/freesurfer/sub-05/mri/wm.mgz... 22324 bright wm thresholded. 28 bright non-wm voxels segmented. reading original surface position from /out/out/freesurfer/sub-05/surf/rh.orig... computing class statistics... border white: 266449 voxels (1.59%) border gray 300678 voxels (1.79%) WM (101.0): 100.4 +- 7.5 [70.0 --> 110.0] GM (77.0) : 76.3 +- 9.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.7 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 56.5 (was 40) setting MAX_GRAY to 97.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.04-->4.86) (max @ vno 60784 --> 144010) face area 0.28 +- 0.12 (0.00-->3.83) mean absolute distance = 0.64 +- 0.82 3876 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=105+-4.3, GM=75+-6.1 mean inside = 96.7, mean outside = 79.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.9, 52 (52) missing vertices, mean dist 0.2 [0.5 (%38.5)->0.7 (%61.5))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=83ec9, 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 0.91 +- 0.24 (0.06-->6.04) (max @ vno 57468 --> 58610) face area 0.28 +- 0.13 (0.00-->3.72) mean absolute distance = 0.34 +- 0.51 3488 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2786556.8, rms=8.856 001: dt: 0.5000, sse=1553174.0, rms=5.895 (33.433%) 002: dt: 0.5000, sse=1085162.2, rms=4.244 (28.012%) 003: dt: 0.5000, sse=914749.0, rms=3.441 (18.913%) 004: dt: 0.5000, sse=839291.5, rms=3.042 (11.594%) 005: dt: 0.5000, sse=814445.5, rms=2.891 (4.980%) 006: dt: 0.5000, sse=806066.4, rms=2.814 (2.663%) rms = 2.80, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=801701.5, rms=2.799 (0.515%) 008: dt: 0.2500, sse=673785.8, rms=1.679 (40.030%) 009: dt: 0.2500, sse=653778.1, rms=1.440 (14.240%) 010: dt: 0.2500, sse=651785.4, rms=1.383 (3.930%) rms = 1.35, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=647178.8, rms=1.347 (2.620%) rms = 1.31, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=644565.9, rms=1.311 (2.666%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.1, 42 (9) missing vertices, mean dist -0.2 [0.4 (%78.3)->0.2 (%21.7))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=83ec9, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.11-->6.46) (max @ vno 57468 --> 58610) face area 0.35 +- 0.16 (0.00-->5.16) mean absolute distance = 0.22 +- 0.38 3036 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1282029.9, rms=4.474 013: dt: 0.5000, sse=932558.9, rms=2.719 (39.232%) 014: dt: 0.5000, sse=899503.7, rms=2.514 (7.534%) 015: dt: 0.5000, sse=891892.2, rms=2.453 (2.438%) rms = 2.61, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=800817.2, rms=1.647 (32.831%) 017: dt: 0.2500, sse=770664.7, rms=1.251 (24.088%) 018: dt: 0.2500, sse=762696.6, rms=1.138 (9.005%) rms = 1.12, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=761684.2, rms=1.117 (1.843%) rms = 1.08, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=759050.7, rms=1.081 (3.201%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.9, 48 (3) missing vertices, mean dist -0.1 [0.2 (%70.7)->0.2 (%29.3))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=83ec9, 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 0.89 +- 0.24 (0.07-->6.52) (max @ vno 57468 --> 58610) face area 0.34 +- 0.15 (0.00-->5.14) mean absolute distance = 0.18 +- 0.31 3080 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=880746.2, rms=2.517 021: dt: 0.5000, sse=811967.2, rms=1.934 (23.146%) rms = 2.16, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=758373.7, rms=1.355 (29.945%) 023: dt: 0.2500, sse=740557.1, rms=1.072 (20.885%) 024: dt: 0.2500, sse=735261.9, rms=1.009 (5.832%) rms = 1.01, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=734893.4, rms=1.007 (0.241%) rms = 0.98, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=733096.5, rms=0.981 (2.628%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.5, 73 (3) missing vertices, mean dist -0.0 [0.2 (%54.9)->0.2 (%45.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=83ec9, 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 /out/out/freesurfer/sub-05/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=740418.8, rms=1.226 rms = 1.21, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=740649.4, rms=1.213 (1.054%) 028: dt: 0.2500, sse=721566.3, rms=0.921 (24.064%) 029: dt: 0.2500, sse=714919.1, rms=0.804 (12.741%) rms = 0.84, time step reduction 2 of 3 to 0.125... rms = 0.78, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=713638.8, rms=0.782 (2.681%) positioning took 0.3 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7072 vertices erasing segment 0 (vno[0] = 41040) erasing segment 2 (vno[0] = 80349) erasing segment 3 (vno[0] = 97884) erasing segment 4 (vno[0] = 101980) erasing segment 5 (vno[0] = 105050) erasing segment 6 (vno[0] = 106050) erasing segment 7 (vno[0] = 106092) erasing segment 8 (vno[0] = 107960) erasing segment 9 (vno[0] = 109973) erasing segment 10 (vno[0] = 123053) erasing segment 11 (vno[0] = 127887) erasing segment 12 (vno[0] = 127919) writing cortex label to /out/out/freesurfer/sub-05/label/rh.cortex.label... writing curvature file /out/out/freesurfer/sub-05/surf/rh.curv writing smoothed area to rh.area writing curvature file /out/out/freesurfer/sub-05/surf/rh.area vertex spacing 0.89 +- 0.24 (0.04-->6.58) (max @ vno 57468 --> 58610) face area 0.33 +- 0.15 (0.00-->5.23) refinement took 2.8 minutes #-------------------------------------------- #@# Smooth2 rh Tue Mar 30 00:11:24 UTC 2021 /out/out/freesurfer/sub-05/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 rh Tue Mar 30 00:11:27 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_inflate -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.0 mm, total surface area = 88337 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.169 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (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=0.022 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 81.278355 mris_inflate stimesec 0.432033 mris_inflate ru_maxrss 233308 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 56918 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11304 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 78554 mris_inflate ru_nivcsw 156 #-------------------------------------------- #@# Curv .H and .K rh Tue Mar 30 00:11:44 UTC 2021 /out/out/freesurfer/sub-05/surf mris_curvature -w rh.white.preaparc total integrated curvature = 5.997*4pi (75.356) --> -5 handles ICI = 149.3, FI = 1763.1, variation=27005.341 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 212 vertices thresholded to be in k1 ~ [-3.13 0.25], k2 ~ [-0.20 0.11] total integrated curvature = 0.456*4pi (5.731) --> 1 handles ICI = 1.4, FI = 10.4, variation=169.926 173 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 108 vertices thresholded to be in [-0.37 0.13] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats rh Tue Mar 30 00:12:34 UTC 2021 /out/out/freesurfer/sub-05/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-05 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-05/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 280 ] Gb_filter = 0 WARN: S lookup min: -0.239260 WARN: S explicit min: 0.000000 vertex = 548 #-------------------------------------------- #@# Sphere rh Tue Mar 30 00:12:37 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_sphere -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.281... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=83ec9, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 Segmentation fault (core dumped) Linux 83ec93b3099f 5.4.0-67-generic #75~18.04.1-Ubuntu SMP Tue Feb 23 19:17:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-05 exited with ERRORS at Tue Mar 30 00:18:13 UTC 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting