Mon Mar 29 23:54:23 UTC 2021 /out/out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -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 7318504 2362956 968180 6441288 7137272 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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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: 2021/03/29-23:54:24-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 lh Mon Mar 29 23:54:24 UTC 2021 /out/out/freesurfer/sub-05/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 269319: 0.002228) 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: 2093 vertices, 2243 faces slice 50: 9587 vertices, 9885 faces slice 60: 19186 vertices, 19522 faces slice 70: 30002 vertices, 30410 faces slice 80: 41666 vertices, 42073 faces slice 90: 53151 vertices, 53514 faces slice 100: 65104 vertices, 65501 faces slice 110: 76838 vertices, 77229 faces slice 120: 88064 vertices, 88456 faces slice 130: 98771 vertices, 99160 faces slice 140: 108537 vertices, 108880 faces slice 150: 116497 vertices, 116780 faces slice 160: 124285 vertices, 124573 faces slice 170: 131574 vertices, 131867 faces slice 180: 137684 vertices, 137899 faces slice 190: 142292 vertices, 142468 faces slice 200: 144579 vertices, 144625 faces slice 210: 144604 vertices, 144638 faces slice 220: 144604 vertices, 144638 faces slice 230: 144604 vertices, 144638 faces slice 240: 144604 vertices, 144638 faces slice 250: 144604 vertices, 144638 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... 144604 voxel in cpt #1: X=-34 [v=144604,e=433914,f=289276] located at (-26.141636, -20.108150, 22.990637) For the whole surface: X=-34 [v=144604,e=433914,f=289276] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Mar 29 23:54:26 UTC 2021 /out/out/freesurfer/sub-05/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... #-------------------------------------------- #@# Inflation1 lh Mon Mar 29 23:54:29 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 77882 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.149 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.038 (target=0.015) step 050: RMS=0.037 (target=0.015) step 055: RMS=0.036 (target=0.015) step 060: RMS=0.035 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 65.640298 mris_inflate stimesec 0.522038 mris_inflate ru_maxrss 233304 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 56923 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10176 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 97979 mris_inflate ru_nivcsw 93 #-------------------------------------------- #@# QSphere lh Mon Mar 29 23:54:41 UTC 2021 /out/out/freesurfer/sub-05/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 0.95 +- 0.57 (0.00-->6.13) (max @ vno 66991 --> 66999) face area 0.02 +- 0.03 (-0.18-->0.61) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.573, avgs=0 005/300: dt: 0.9000, rms radial error=176.313, avgs=0 010/300: dt: 0.9000, rms radial error=175.754, avgs=0 015/300: dt: 0.9000, rms radial error=175.020, avgs=0 020/300: dt: 0.9000, rms radial error=174.184, avgs=0 025/300: dt: 0.9000, rms radial error=173.291, avgs=0 030/300: dt: 0.9000, rms radial error=172.371, avgs=0 035/300: dt: 0.9000, rms radial error=171.435, avgs=0 040/300: dt: 0.9000, rms radial error=170.490, avgs=0 045/300: dt: 0.9000, rms radial error=169.544, avgs=0 050/300: dt: 0.9000, rms radial error=168.598, avgs=0 055/300: dt: 0.9000, rms radial error=167.655, avgs=0 060/300: dt: 0.9000, rms radial error=166.715, avgs=0 065/300: dt: 0.9000, rms radial error=165.779, avgs=0 070/300: dt: 0.9000, rms radial error=164.848, avgs=0 075/300: dt: 0.9000, rms radial error=163.921, avgs=0 080/300: dt: 0.9000, rms radial error=163.000, avgs=0 085/300: dt: 0.9000, rms radial error=162.084, avgs=0 090/300: dt: 0.9000, rms radial error=161.174, avgs=0 095/300: dt: 0.9000, rms radial error=160.268, avgs=0 100/300: dt: 0.9000, rms radial error=159.368, avgs=0 105/300: dt: 0.9000, rms radial error=158.472, avgs=0 110/300: dt: 0.9000, rms radial error=157.581, avgs=0 115/300: dt: 0.9000, rms radial error=156.695, avgs=0 120/300: dt: 0.9000, rms radial error=155.814, avgs=0 125/300: dt: 0.9000, rms radial error=154.937, avgs=0 130/300: dt: 0.9000, rms radial error=154.065, avgs=0 135/300: dt: 0.9000, rms radial error=153.197, avgs=0 140/300: dt: 0.9000, rms radial error=152.335, avgs=0 145/300: dt: 0.9000, rms radial error=151.477, avgs=0 150/300: dt: 0.9000, rms radial error=150.624, avgs=0 155/300: dt: 0.9000, rms radial error=149.775, avgs=0 160/300: dt: 0.9000, rms radial error=148.932, avgs=0 165/300: dt: 0.9000, rms radial error=148.093, avgs=0 170/300: dt: 0.9000, rms radial error=147.259, avgs=0 175/300: dt: 0.9000, rms radial error=146.430, avgs=0 180/300: dt: 0.9000, rms radial error=145.606, avgs=0 185/300: dt: 0.9000, rms radial error=144.786, avgs=0 190/300: dt: 0.9000, rms radial error=143.971, avgs=0 195/300: dt: 0.9000, rms radial error=143.160, avgs=0 200/300: dt: 0.9000, rms radial error=142.354, avgs=0 205/300: dt: 0.9000, rms radial error=141.552, avgs=0 210/300: dt: 0.9000, rms radial error=140.755, avgs=0 215/300: dt: 0.9000, rms radial error=139.962, avgs=0 220/300: dt: 0.9000, rms radial error=139.173, avgs=0 225/300: dt: 0.9000, rms radial error=138.389, avgs=0 230/300: dt: 0.9000, rms radial error=137.610, avgs=0 235/300: dt: 0.9000, rms radial error=136.834, avgs=0 240/300: dt: 0.9000, rms radial error=136.063, avgs=0 245/300: dt: 0.9000, rms radial error=135.296, avgs=0 250/300: dt: 0.9000, rms radial error=134.534, avgs=0 255/300: dt: 0.9000, rms radial error=133.775, avgs=0 260/300: dt: 0.9000, rms radial error=133.021, avgs=0 265/300: dt: 0.9000, rms radial error=132.271, avgs=0 270/300: dt: 0.9000, rms radial error=131.526, avgs=0 275/300: dt: 0.9000, rms radial error=130.784, avgs=0 280/300: dt: 0.9000, rms radial error=130.047, avgs=0 285/300: dt: 0.9000, rms radial error=129.314, avgs=0 290/300: dt: 0.9000, rms radial error=128.585, avgs=0 295/300: dt: 0.9000, rms radial error=127.861, avgs=0 300/300: dt: 0.9000, rms radial error=127.140, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17122.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2950.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 318.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00859 epoch 4 (K=640.0), pass 1, starting sse = 19.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/20 = 0.01157 final distance error %28.23 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 355.020906 mris_sphere stimesec 0.488298 mris_sphere ru_maxrss 233600 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 56957 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 128 mris_sphere ru_oublock 10176 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 91357 mris_sphere ru_nivcsw 500 FSRUNTIME@ mris_sphere 0.0214 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Mar 29 23:55:58 UTC 2021 /out/out/freesurfer/sub-05/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Mon Mar 29 23:55:58 UTC 2021 mris_fix_topology -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-05 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=-34 (nv=144604, nf=289276, ne=433914, g=18) 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 10 iterations marking ambiguous vertices... 3334 ambiguous faces found in tessellation segmenting defects... 28 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 24 -merging segment 23 into 24 26 defects to be corrected 0 vertices coincident reading input surface /out/out/freesurfer/sub-05/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2542 (-4.6271) -vertex loglikelihood: -5.9800 (-2.9900) -normal dot loglikelihood: -3.6441 (-3.6441) -quad curv loglikelihood: -6.3349 (-3.1675) Total Loglikelihood : -25.2132 CORRECTING DEFECT 0 (vertices=86, convex hull=66, v0=5043) After retessellation of defect 0 (v0=5043), euler #=-25 (142619,427173,284529) : difference with theory (-23) = 2 CORRECTING DEFECT 1 (vertices=6, convex hull=31, v0=14238) After retessellation of defect 1 (v0=14238), euler #=-24 (142621,427188,284543) : difference with theory (-22) = 2 CORRECTING DEFECT 2 (vertices=71, convex hull=94, v0=16366) After retessellation of defect 2 (v0=16366), euler #=-23 (142659,427340,284658) : difference with theory (-21) = 2 CORRECTING DEFECT 3 (vertices=25, convex hull=39, v0=47550) After retessellation of defect 3 (v0=47550), euler #=-22 (142661,427358,284675) : difference with theory (-20) = 2 CORRECTING DEFECT 4 (vertices=655, convex hull=278, v0=58572) After retessellation of defect 4 (v0=58572), euler #=-21 (142761,427796,285014) : difference with theory (-19) = 2 CORRECTING DEFECT 5 (vertices=18, convex hull=28, v0=58629) After retessellation of defect 5 (v0=58629), euler #=-20 (142765,427817,285032) : difference with theory (-18) = 2 CORRECTING DEFECT 6 (vertices=13, convex hull=20, v0=61951) After retessellation of defect 6 (v0=61951), euler #=-19 (142767,427830,285044) : difference with theory (-17) = 2 CORRECTING DEFECT 7 (vertices=5, convex hull=12, v0=89541) After retessellation of defect 7 (v0=89541), euler #=-18 (142767,427832,285047) : difference with theory (-16) = 2 CORRECTING DEFECT 8 (vertices=44, convex hull=38, v0=92806) After retessellation of defect 8 (v0=92806), euler #=-17 (142777,427874,285080) : difference with theory (-15) = 2 CORRECTING DEFECT 9 (vertices=38, convex hull=52, v0=93274) After retessellation of defect 9 (v0=93274), euler #=-16 (142781,427907,285110) : difference with theory (-14) = 2 CORRECTING DEFECT 10 (vertices=77, convex hull=96, v0=100540) After retessellation of defect 10 (v0=100540), euler #=-15 (142818,428059,285226) : difference with theory (-13) = 2 CORRECTING DEFECT 11 (vertices=6, convex hull=32, v0=100826) After retessellation of defect 11 (v0=100826), euler #=-14 (142820,428073,285239) : difference with theory (-12) = 2 CORRECTING DEFECT 12 (vertices=45, convex hull=25, v0=105415) After retessellation of defect 12 (v0=105415), euler #=-13 (142828,428103,285262) : difference with theory (-11) = 2 CORRECTING DEFECT 13 (vertices=6, convex hull=32, v0=105476) After retessellation of defect 13 (v0=105476), euler #=-12 (142830,428117,285275) : difference with theory (-10) = 2 CORRECTING DEFECT 14 (vertices=52, convex hull=82, v0=107063) After retessellation of defect 14 (v0=107063), euler #=-11 (142861,428245,285373) : difference with theory (-9) = 2 CORRECTING DEFECT 15 (vertices=29, convex hull=19, v0=107232) After retessellation of defect 15 (v0=107232), euler #=-10 (142864,428256,285382) : difference with theory (-8) = 2 CORRECTING DEFECT 16 (vertices=8, convex hull=22, v0=107332) After retessellation of defect 16 (v0=107332), euler #=-9 (142866,428267,285392) : difference with theory (-7) = 2 CORRECTING DEFECT 17 (vertices=103, convex hull=34, v0=111908) After retessellation of defect 17 (v0=111908), euler #=-8 (142870,428288,285410) : difference with theory (-6) = 2 CORRECTING DEFECT 18 (vertices=45, convex hull=31, v0=113555) After retessellation of defect 18 (v0=113555), euler #=-7 (142876,428316,285433) : difference with theory (-5) = 2 CORRECTING DEFECT 19 (vertices=35, convex hull=95, v0=115657) After retessellation of defect 19 (v0=115657), euler #=-6 (142898,428418,285514) : difference with theory (-4) = 2 CORRECTING DEFECT 20 (vertices=76, convex hull=99, v0=115727) After retessellation of defect 20 (v0=115727), euler #=-5 (142927,428549,285617) : difference with theory (-3) = 2 CORRECTING DEFECT 21 (vertices=25, convex hull=60, v0=117203) After retessellation of defect 21 (v0=117203), euler #=-4 (142936,428602,285662) : difference with theory (-2) = 2 CORRECTING DEFECT 22 (vertices=42, convex hull=41, v0=118829) After retessellation of defect 22 (v0=118829), euler #=-3 (142944,428639,285692) : difference with theory (-1) = 2 CORRECTING DEFECT 23 (vertices=462, convex hull=291, v0=120372) After retessellation of defect 23 (v0=120372), euler #=0 (143018,429011,285993) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=17, convex hull=39, v0=139490) After retessellation of defect 24 (v0=139490), euler #=1 (143025,429045,286021) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=19, convex hull=57, v0=140231) After retessellation of defect 25 (v0=140231), euler #=2 (143034,429096,286064) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.09-->10.24) (max @ vno 121780 --> 128716) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.09-->10.24) (max @ vno 121780 --> 128716) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 103 mutations (38.3%), 166 crossovers (61.7%), 126 vertices were eliminated building final representation... 1570 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=143034, nf=286064, ne=429096, g=0) writing corrected surface to /out/out/freesurfer/sub-05/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 10.3 minutes 0 defective edges removing intersecting faces 000: 258 intersecting 001: 33 intersecting 002: 7 intersecting mris_fix_topology utimesec 625.567781 mris_fix_topology stimesec 0.087996 mris_fix_topology ru_maxrss 457692 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 114342 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13472 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 359 mris_fix_topology ru_nivcsw 2486 FSRUNTIME@ mris_fix_topology lh 0.1719 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 143034 - 429096 + 286064 = 2 --> 0 holes F =2V-4: 286064 = 286068-4 (0) 2E=3F: 858192 = 858192 (0) total defect index = 0 /out/out/freesurfer/sub-05/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 49 intersecting 001: 21 intersecting 002: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Mar 30 00:06:20 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 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 /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/lh.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 64.7 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 55.5 (was 40) setting MAX_GRAY to 97.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.02-->4.64) (max @ vno 119630 --> 121794) face area 0.28 +- 0.12 (0.00-->7.17) mean absolute distance = 0.64 +- 0.80 4213 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=74+-6.1 mean inside = 96.4, mean outside = 79.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=83.7, 129 (129) missing vertices, mean dist 0.3 [0.5 (%35.6)->0.7 (%64.4))] %72 local maxima, %24 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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.24 (0.03-->4.62) (max @ vno 119630 --> 121794) face area 0.28 +- 0.13 (0.00-->5.48) mean absolute distance = 0.32 +- 0.47 3070 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2775236.2, rms=8.879 001: dt: 0.5000, sse=1586467.9, rms=6.043 (31.944%) 002: dt: 0.5000, sse=1121535.9, rms=4.449 (26.371%) 003: dt: 0.5000, sse=932472.2, rms=3.603 (19.022%) 004: dt: 0.5000, sse=849309.4, rms=3.155 (12.433%) 005: dt: 0.5000, sse=819546.1, rms=2.968 (5.936%) 006: dt: 0.5000, sse=803579.4, rms=2.872 (3.241%) rms = 2.84, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=801240.3, rms=2.843 (0.991%) 008: dt: 0.2500, sse=673770.2, rms=1.719 (39.549%) 009: dt: 0.2500, sse=650082.2, rms=1.479 (13.936%) 010: dt: 0.2500, sse=645656.5, rms=1.413 (4.475%) rms = 1.37, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=643607.1, rms=1.374 (2.757%) rms = 1.34, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=640045.0, rms=1.337 (2.727%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.1, 102 (41) missing vertices, mean dist -0.2 [0.3 (%80.5)->0.2 (%19.5))] %84 local maxima, %12 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 (0.10-->4.53) (max @ vno 119630 --> 121794) face area 0.35 +- 0.16 (0.00-->6.46) mean absolute distance = 0.21 +- 0.33 3113 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1270470.1, rms=4.466 013: dt: 0.5000, sse=925733.5, rms=2.711 (39.296%) 014: dt: 0.5000, sse=900105.4, rms=2.555 (5.752%) 015: dt: 0.5000, sse=885150.7, rms=2.477 (3.042%) rms = 2.68, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=796035.1, rms=1.661 (32.951%) 017: dt: 0.2500, sse=767433.8, rms=1.275 (23.271%) 018: dt: 0.2500, sse=760890.7, rms=1.170 (8.232%) rms = 1.15, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=760781.1, rms=1.151 (1.593%) rms = 1.12, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=756187.8, rms=1.119 (2.747%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.9, 85 (24) missing vertices, mean dist -0.1 [0.2 (%71.7)->0.2 (%28.3))] %89 local maxima, % 6 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 0.90 +- 0.24 (0.06-->4.64) (max @ vno 110610 --> 111434) face area 0.34 +- 0.15 (0.00-->6.12) mean absolute distance = 0.18 +- 0.28 3053 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=892653.8, rms=2.637 021: dt: 0.5000, sse=819692.0, rms=2.044 (22.483%) rms = 2.24, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=763265.2, rms=1.432 (29.954%) 023: dt: 0.2500, sse=741849.2, rms=1.133 (20.888%) 024: dt: 0.2500, sse=733775.2, rms=1.049 (7.406%) rms = 1.05, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=733647.0, rms=1.046 (0.255%) rms = 1.02, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=731340.4, rms=1.017 (2.805%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.5, 97 (14) missing vertices, mean dist -0.0 [0.2 (%55.7)->0.2 (%44.3))] %91 local maxima, % 5 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/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=738656.4, rms=1.248 rms = 1.22, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=736924.2, rms=1.220 (2.222%) 028: dt: 0.2500, sse=720451.0, rms=0.952 (21.986%) 029: dt: 0.2500, sse=713368.3, rms=0.837 (12.066%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.81, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=711435.9, rms=0.811 (3.118%) positioning took 0.2 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7330 vertices erasing segment 0 (vno[0] = 43503) erasing segment 1 (vno[0] = 48254) erasing segment 3 (vno[0] = 60527) erasing segment 4 (vno[0] = 64144) erasing segment 5 (vno[0] = 86006) erasing segment 6 (vno[0] = 104280) erasing segment 7 (vno[0] = 104510) erasing segment 8 (vno[0] = 105071) erasing segment 9 (vno[0] = 106090) erasing segment 10 (vno[0] = 111473) erasing segment 11 (vno[0] = 112219) erasing segment 12 (vno[0] = 120091) erasing segment 13 (vno[0] = 142848) writing cortex label to /out/out/freesurfer/sub-05/label/lh.cortex.label... writing curvature file /out/out/freesurfer/sub-05/surf/lh.curv writing smoothed area to lh.area writing curvature file /out/out/freesurfer/sub-05/surf/lh.area vertex spacing 0.89 +- 0.24 (0.04-->4.79) (max @ vno 110610 --> 111434) face area 0.33 +- 0.15 (0.00-->5.91) refinement took 2.4 minutes #-------------------------------------------- #@# Smooth2 lh Tue Mar 30 00:08:47 UTC 2021 /out/out/freesurfer/sub-05/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... #-------------------------------------------- #@# Inflation2 lh Tue Mar 30 00:08:49 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_inflate -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.7 mm, total surface area = 87679 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.170 (target=0.015) step 005: RMS=0.120 (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=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.1 minutes mris_inflate utimesec 49.816932 mris_inflate stimesec 0.380863 mris_inflate ru_maxrss 230276 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 56313 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 296 mris_inflate ru_oublock 11184 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 75828 mris_inflate ru_nivcsw 87 #-------------------------------------------- #@# Curv .H and .K lh Tue Mar 30 00:08:58 UTC 2021 /out/out/freesurfer/sub-05/surf mris_curvature -w lh.white.preaparc total integrated curvature = 12.922*4pi (162.379) --> -12 handles ICI = 155.8, FI = 1733.0, variation=26739.075 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 175 vertices thresholded to be in k1 ~ [-0.28 2.69], k2 ~ [-0.10 0.11] total integrated curvature = 0.557*4pi (6.996) --> 0 handles ICI = 1.4, FI = 10.2, variation=167.565 134 vertices thresholded to be in [-0.05 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 106 vertices thresholded to be in [-0.13 0.54] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Tue Mar 30 00:09:37 UTC 2021 /out/out/freesurfer/sub-05/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-05 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-05/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 254 ] Gb_filter = 0 WARN: S lookup min: -0.655524 WARN: S explicit min: 0.000000 vertex = 768 #-------------------------------------------- #@# Sphere lh Tue Mar 30 00:09:39 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_sphere -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.279... 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 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.79 pass 1: epoch 2 of 3 starting distance error %20.66 unfolding complete - removing small folds... starting distance error %20.57 removing remaining folds... final distance error %20.59 MRISunfold() return, current seed 1234 -01: dt=0.0000, 213 negative triangles 177: dt=0.9900, 213 negative triangles 178: dt=0.9900, 120 negative triangles 179: dt=0.9900, 106 negative triangles 180: dt=0.9900, 88 negative triangles 181: dt=0.9900, 94 negative triangles 182: dt=0.9900, 83 negative triangles 183: dt=0.9900, 76 negative triangles 184: dt=0.9900, 69 negative triangles 185: dt=0.9900, 79 negative triangles 186: dt=0.9900, 71 negative triangles 187: dt=0.9900, 76 negative triangles 188: dt=0.9900, 70 negative triangles 189: dt=0.9900, 78 negative triangles 190: dt=0.9900, 64 negative triangles 191: dt=0.9900, 64 negative triangles 192: dt=0.9900, 69 negative triangles 193: dt=0.9900, 63 negative triangles 194: dt=0.9900, 60 negative triangles 195: dt=0.9900, 55 negative triangles 196: dt=0.9900, 51 negative triangles 197: dt=0.9900, 58 negative triangles 198: dt=0.9900, 54 negative triangles 199: dt=0.9900, 45 negative triangles 200: dt=0.9900, 42 negative triangles 201: dt=0.9900, 42 negative triangles 202: dt=0.9900, 33 negative triangles 203: dt=0.9900, 36 negative triangles 204: dt=0.9900, 36 negative triangles 205: dt=0.9900, 37 negative triangles 206: dt=0.9900, 26 negative triangles 207: dt=0.9900, 26 negative triangles 208: dt=0.9900, 27 negative triangles 209: dt=0.9900, 22 negative triangles 210: dt=0.9900, 22 negative triangles 211: dt=0.9900, 17 negative triangles 212: dt=0.9900, 15 negative triangles 213: dt=0.9900, 9 negative triangles 214: dt=0.9900, 13 negative triangles 215: dt=0.9900, 10 negative triangles 216: dt=0.9900, 9 negative triangles 217: dt=0.9900, 6 negative triangles 218: dt=0.9900, 4 negative triangles 219: dt=0.9900, 8 negative triangles 220: dt=0.9900, 7 negative triangles 221: dt=0.9900, 7 negative triangles 222: dt=0.9900, 5 negative triangles 223: dt=0.9900, 2 negative triangles 224: dt=0.9900, 6 negative triangles 225: dt=0.9900, 5 negative triangles 226: dt=0.9900, 5 negative triangles 227: dt=0.9900, 6 negative triangles 228: dt=0.9900, 4 negative triangles 229: dt=0.9900, 6 negative triangles 230: dt=0.9900, 3 negative triangles 231: dt=0.9900, 3 negative triangles 232: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.14 hours mris_sphere utimesec 3535.515359 mris_sphere stimesec 0.924123 mris_sphere ru_maxrss 311460 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 78132 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10064 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 109258 mris_sphere ru_nivcsw 4034 FSRUNTIME@ mris_sphere 0.1425 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue Mar 30 00:18:12 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_register -curv -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /out/out/freesurfer/sub-05/scripts cmdline mris_register -curv -rusage /out/out/freesurfer/sub-05/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=83ec9, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=83ec9, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.604 curvature mean = 0.035, std = 0.819 curvature mean = 0.021, std = 0.858 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 352576.6, tmin=0.4633 d=32.00 min @ (-8.00, -8.00, 8.00) sse = 233683.3, tmin=0.9310 d=8.00 min @ (0.00, 2.00, 0.00) sse = 231250.7, tmin=1.8726 d=4.00 min @ (0.00, -1.00, 0.00) sse = 229637.8, tmin=2.3441 d=2.00 min @ (0.50, 0.50, 0.00) sse = 229204.9, tmin=2.8176 d=0.50 min @ (0.00, -0.12, -0.12) sse = 229156.5, tmin=3.7697 tol=1.0e+00, sigma=0.5, host=83ec9, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 3.77 min curvature mean = -0.006, std = 0.826 curvature mean = 0.008, std = 0.947 curvature mean = -0.011, std = 0.836 curvature mean = 0.003, std = 0.978 curvature mean = -0.013, std = 0.838 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.029, std = 0.301 curvature mean = 0.037, std = 0.248 curvature mean = 0.069, std = 0.326 curvature mean = 0.033, std = 0.307 curvature mean = 0.038, std = 0.501 curvature mean = 0.032, std = 0.335 curvature mean = 0.021, std = 0.633 curvature mean = 0.032, std = 0.347 curvature mean = 0.008, std = 0.740 MRISregister() return, current seed 0 -01: dt=0.0000, 70 negative triangles 116: dt=0.9900, 70 negative triangles expanding nbhd size to 1 117: dt=0.9900, 90 negative triangles 118: dt=0.9900, 68 negative triangles 119: dt=0.9900, 66 negative triangles 120: dt=0.9900, 59 negative triangles 121: dt=0.9900, 51 negative triangles 122: dt=0.9900, 49 negative triangles 123: dt=0.9900, 42 negative triangles 124: dt=0.9900, 36 negative triangles 125: dt=0.9900, 35 negative triangles 126: dt=0.9900, 33 negative triangles 127: dt=0.9900, 26 negative triangles 128: dt=0.9900, 24 negative triangles 129: dt=0.9900, 15 negative triangles 130: dt=0.9900, 16 negative triangles 131: dt=0.9900, 13 negative triangles 132: dt=0.9900, 4 negative triangles 133: dt=0.9900, 6 negative triangles 134: dt=0.9900, 5 negative triangles 135: dt=0.9900, 2 negative triangles 136: dt=0.9900, 2 negative triangles 137: dt=0.9900, 2 negative triangles 138: dt=0.9900, 2 negative triangles 139: dt=0.9900, 1 negative triangles 140: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.26 hours mris_register utimesec 5045.922991 mris_register stimesec 1.144467 mris_register ru_maxrss 283876 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 69664 mris_register ru_majflt 19 mris_register ru_nswap 0 mris_register ru_inblock 7984 mris_register ru_oublock 10064 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 105034 mris_register ru_nivcsw 7170 FSRUNTIME@ mris_register 0.2638 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue Mar 30 00:34:02 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Mar 30 00:34:03 UTC 2021 /out/out/freesurfer/sub-05/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Mar 30 00:34:04 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1622 labels changed using aseg relabeling using gibbs priors... 000: 3329 changed, 143034 examined... 001: 788 changed, 13892 examined... 002: 174 changed, 4344 examined... 003: 70 changed, 1053 examined... 004: 23 changed, 406 examined... 005: 6 changed, 142 examined... 006: 3 changed, 40 examined... 007: 1 changed, 18 examined... 008: 1 changed, 7 examined... 009: 0 changed, 7 examined... 239 labels changed using aseg 000: 127 total segments, 82 labels (427 vertices) changed 001: 41 total segments, 3 labels (21 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1930 vertices marked for relabeling... 1930 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 6 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Mar 30 00:34:10 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-05 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /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/lh.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 64.7 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 55.5 (was 40) setting MAX_GRAY to 97.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=74+-6.1 mean inside = 96.4, mean outside = 79.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.24 (0.04-->4.79) (max @ vno 110610 --> 111434) face area 0.33 +- 0.15 (0.00-->5.88) mean absolute distance = 0.58 +- 0.77 3322 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 82 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 13 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=83.4, 213 (213) missing vertices, mean dist 0.4 [0.9 (%9.9)->0.5 (%90.1))] %68 local maxima, %28 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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.12-->4.52) (max @ vno 110610 --> 111434) face area 0.33 +- 0.15 (0.00-->5.89) mean absolute distance = 0.33 +- 0.46 3371 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2201292.2, rms=7.421 001: dt: 0.5000, sse=1204544.9, rms=4.293 (42.157%) 002: dt: 0.5000, sse=927919.6, rms=2.973 (30.740%) 003: dt: 0.5000, sse=880892.6, rms=2.691 (9.472%) 004: dt: 0.5000, sse=849184.9, rms=2.477 (7.983%) rms = 2.61, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=773699.3, rms=1.774 (28.377%) 006: dt: 0.2500, sse=747502.6, rms=1.452 (18.121%) 007: dt: 0.2500, sse=740689.6, rms=1.356 (6.658%) rms = 1.33, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=739351.0, rms=1.332 (1.776%) rms = 1.30, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=737180.4, rms=1.296 (2.673%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 58 points - only 0.00% unknown deleting segment 6 with 26 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown mean border=87.0, 95 (42) missing vertices, mean dist -0.2 [0.4 (%81.9)->0.2 (%18.1))] %84 local maxima, %12 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 (0.05-->4.52) (max @ vno 110610 --> 111434) face area 0.35 +- 0.16 (0.00-->6.25) mean absolute distance = 0.21 +- 0.34 3119 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1295841.0, rms=4.528 010: dt: 0.5000, sse=929775.6, rms=2.642 (41.639%) 011: dt: 0.5000, sse=895877.8, rms=2.444 (7.490%) 012: dt: 0.5000, sse=887176.5, rms=2.392 (2.132%) rms = 2.60, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=800377.3, rms=1.571 (34.311%) 014: dt: 0.2500, sse=772642.7, rms=1.185 (24.600%) 015: dt: 0.2500, sse=768234.7, rms=1.097 (7.456%) rms = 1.09, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=768260.6, rms=1.090 (0.629%) rms = 1.06, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=765033.9, rms=1.064 (2.353%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 66 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 14 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown mean border=88.9, 61 (19) missing vertices, mean dist -0.1 [0.2 (%72.3)->0.2 (%27.7))] %89 local maxima, % 6 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 0.90 +- 0.24 (0.08-->4.37) (max @ vno 110610 --> 111434) face area 0.34 +- 0.16 (0.00-->5.93) mean absolute distance = 0.18 +- 0.28 3137 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=896951.8, rms=2.630 018: dt: 0.5000, sse=832673.1, rms=2.029 (22.880%) rms = 2.22, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=763774.8, rms=1.411 (30.434%) 020: dt: 0.2500, sse=752824.6, rms=1.095 (22.410%) 021: dt: 0.2500, sse=737256.5, rms=1.014 (7.437%) rms = 1.01, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=736919.9, rms=1.012 (0.156%) rms = 0.98, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=734445.9, rms=0.981 (3.051%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 25 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 70 points - only 0.00% unknown deleting segment 3 with 25 points - only 0.00% unknown deleting segment 4 with 21 points - only 0.00% unknown mean border=89.4, 79 (17) missing vertices, mean dist -0.0 [0.2 (%56.0)->0.2 (%44.0))] %91 local maxima, % 5 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/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=741220.1, rms=1.224 rms = 1.20, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=741646.7, rms=1.204 (1.643%) 025: dt: 0.2500, sse=722792.2, rms=0.923 (23.357%) 026: dt: 0.2500, sse=716438.8, rms=0.813 (11.957%) rms = 0.85, time step reduction 2 of 3 to 0.125... rms = 0.79, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=714577.9, rms=0.788 (2.998%) positioning took 0.2 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7332 vertices erasing segment 0 (vno[0] = 43488) erasing segment 1 (vno[0] = 48254) erasing segment 3 (vno[0] = 64144) erasing segment 4 (vno[0] = 86006) erasing segment 5 (vno[0] = 104280) erasing segment 6 (vno[0] = 104510) erasing segment 7 (vno[0] = 105071) erasing segment 8 (vno[0] = 106090) erasing segment 9 (vno[0] = 111473) erasing segment 10 (vno[0] = 112219) writing cortex label to /out/out/freesurfer/sub-05/label/lh.cortex.label... writing curvature file /out/out/freesurfer/sub-05/surf/lh.curv writing smoothed area to lh.area writing curvature file /out/out/freesurfer/sub-05/surf/lh.area vertex spacing 0.89 +- 0.25 (0.04-->4.42) (max @ vno 110610 --> 111434) face area 0.34 +- 0.16 (0.00-->5.80) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 0.00% unknown removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=62.4, 219 (219) missing vertices, mean dist 1.9 [1.4 (%0.0)->2.9 (%100.0))] %15 local maxima, %46 large gradients and %35 min vals, 611 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=83ec9, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21883274.0, rms=27.794 001: dt: 0.0500, sse=19273962.0, rms=26.027 (6.357%) 002: dt: 0.0500, sse=17421322.0, rms=24.696 (5.115%) 003: dt: 0.0500, sse=16014203.0, rms=23.634 (4.298%) 004: dt: 0.0500, sse=14885131.0, rms=22.747 (3.755%) 005: dt: 0.0500, sse=13944212.0, rms=21.980 (3.372%) 006: dt: 0.0500, sse=13137208.0, rms=21.300 (3.094%) 007: dt: 0.0500, sse=12429537.0, rms=20.685 (2.886%) 008: dt: 0.0500, sse=11799407.0, rms=20.122 (2.723%) 009: dt: 0.0500, sse=11231634.0, rms=19.600 (2.591%) 010: dt: 0.0500, sse=10715668.0, rms=19.114 (2.481%) positioning took 0.5 minutes mean border=62.2, 124 (88) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.4 (%100.0))] %16 local maxima, %45 large gradients and %35 min vals, 572 gradients ignored tol=1.0e-04, sigma=2.0, host=83ec9, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11434349.0, rms=19.783 011: dt: 0.0500, sse=10959052.0, rms=19.340 (2.239%) 012: dt: 0.0500, sse=10521792.0, rms=18.924 (2.154%) 013: dt: 0.0500, sse=10118169.0, rms=18.531 (2.077%) 014: dt: 0.0500, sse=9744892.0, rms=18.160 (2.002%) 015: dt: 0.0500, sse=9398399.0, rms=17.808 (1.935%) 016: dt: 0.0500, sse=9076592.0, rms=17.476 (1.869%) 017: dt: 0.0500, sse=8777297.0, rms=17.160 (1.805%) 018: dt: 0.0500, sse=8498572.0, rms=16.861 (1.743%) 019: dt: 0.0500, sse=8238128.5, rms=16.577 (1.687%) 020: dt: 0.0500, sse=7994883.0, rms=16.306 (1.630%) positioning took 0.5 minutes mean border=62.1, 110 (56) missing vertices, mean dist 1.4 [0.1 (%0.5)->2.1 (%99.5))] %17 local maxima, %45 large gradients and %34 min vals, 550 gradients ignored tol=1.0e-04, sigma=2.0, host=83ec9, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8120478.0, rms=16.451 021: dt: 0.0500, sse=7888330.5, rms=16.191 (1.579%) 022: dt: 0.0500, sse=7671009.5, rms=15.944 (1.526%) 023: dt: 0.0500, sse=7466672.0, rms=15.708 (1.480%) 024: dt: 0.0500, sse=7274939.0, rms=15.483 (1.431%) 025: dt: 0.0500, sse=7094252.0, rms=15.268 (1.389%) 026: dt: 0.0500, sse=6923469.0, rms=15.062 (1.350%) 027: dt: 0.0500, sse=6761325.0, rms=14.863 (1.317%) 028: dt: 0.0500, sse=6607007.0, rms=14.672 (1.288%) 029: dt: 0.0500, sse=6459415.5, rms=14.486 (1.265%) 030: dt: 0.0500, sse=6318011.5, rms=14.306 (1.243%) positioning took 0.5 minutes mean border=62.0, 118 (45) missing vertices, mean dist 1.2 [0.1 (%5.3)->1.9 (%94.7))] %17 local maxima, %46 large gradients and %34 min vals, 529 gradients ignored tol=1.0e-04, sigma=2.0, host=83ec9, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6416563.5, rms=14.432 031: dt: 0.5000, sse=5400912.5, rms=13.077 (9.386%) 032: dt: 0.5000, sse=4636103.5, rms=11.949 (8.623%) 033: dt: 0.5000, sse=4023432.0, rms=10.962 (8.266%) 034: dt: 0.5000, sse=3520885.2, rms=10.074 (8.097%) 035: dt: 0.5000, sse=3104325.2, rms=9.274 (7.943%) 036: dt: 0.5000, sse=2731122.5, rms=8.491 (8.442%) 037: dt: 0.5000, sse=2391848.5, rms=7.714 (9.149%) 038: dt: 0.5000, sse=2086878.0, rms=6.941 (10.019%) 039: dt: 0.5000, sse=1829791.5, rms=6.219 (10.406%) 040: dt: 0.5000, sse=1631667.1, rms=5.598 (9.988%) 041: dt: 0.5000, sse=1486012.8, rms=5.098 (8.934%) 042: dt: 0.5000, sse=1391676.5, rms=4.740 (7.009%) 043: dt: 0.5000, sse=1332617.9, rms=4.506 (4.947%) 044: dt: 0.5000, sse=1292246.1, rms=4.335 (3.796%) 045: dt: 0.5000, sse=1264779.0, rms=4.217 (2.708%) 046: dt: 0.5000, sse=1245201.2, rms=4.129 (2.089%) rms = 4.09, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1235244.6, rms=4.087 (1.034%) 048: dt: 0.2500, sse=1146332.5, rms=3.610 (11.658%) 049: dt: 0.2500, sse=1120948.1, rms=3.478 (3.667%) rms = 3.49, time step reduction 2 of 3 to 0.125... rms = 3.43, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1113168.8, rms=3.434 (1.269%) positioning took 1.2 minutes mean border=60.8, 1941 (25) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.5 (%55.7))] %33 local maxima, %31 large gradients and %30 min vals, 237 gradients ignored tol=1.0e-04, sigma=1.0, host=83ec9, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1494067.2, rms=4.201 051: dt: 0.5000, sse=1409768.9, rms=3.821 (9.041%) 052: dt: 0.5000, sse=1336296.2, rms=3.474 (9.084%) rms = 3.65, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1250769.6, rms=2.932 (15.598%) 054: dt: 0.2500, sse=1225156.8, rms=2.745 (6.403%) rms = 2.75, time step reduction 2 of 3 to 0.125... 055: dt: 0.1250, sse=1216293.5, rms=2.679 (2.378%) 056: dt: 0.1250, sse=1203117.6, rms=2.580 (3.722%) rms = 2.54, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1198098.1, rms=2.542 (1.445%) positioning took 0.6 minutes mean border=59.8, 2242 (22) missing vertices, mean dist 0.1 [0.2 (%37.8)->0.3 (%62.2))] %48 local maxima, %18 large gradients and %29 min vals, 232 gradients ignored tol=1.0e-04, sigma=0.5, host=83ec9, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1267942.1, rms=3.023 rms = 3.22, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1231416.2, rms=2.780 (8.053%) 059: dt: 0.2500, sse=1208790.2, rms=2.621 (5.731%) rms = 2.61, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1206166.6, rms=2.608 (0.498%) 061: dt: 0.1250, sse=1190560.4, rms=2.488 (4.577%) rms = 2.44, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1184245.5, rms=2.444 (1.766%) positioning took 0.4 minutes mean border=59.2, 4519 (21) missing vertices, mean dist 0.0 [0.2 (%41.5)->0.2 (%58.5))] %51 local maxima, %13 large gradients and %28 min vals, 206 gradients ignored tol=1.0e-04, sigma=0.2, host=83ec9, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /out/out/freesurfer/sub-05/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1199288.5, rms=2.564 rms = 2.86, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1185463.0, rms=2.457 (4.164%) rms = 2.42, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=1179053.8, rms=2.420 (1.489%) 065: dt: 0.1250, sse=1172068.1, rms=2.361 (2.458%) rms = 2.33, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1167877.2, rms=2.334 (1.156%) positioning took 0.4 minutes writing curvature file /out/out/freesurfer/sub-05/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /out/out/freesurfer/sub-05/surf/lh.area.pial vertex spacing 1.03 +- 0.46 (0.04-->6.69) (max @ vno 98489 --> 98490) face area 0.42 +- 0.33 (0.00-->6.55) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 143034 vertices processed 25000 of 143034 vertices processed 50000 of 143034 vertices processed 75000 of 143034 vertices processed 100000 of 143034 vertices processed 125000 of 143034 vertices processed 0 of 143034 vertices processed 25000 of 143034 vertices processed 50000 of 143034 vertices processed 75000 of 143034 vertices processed 100000 of 143034 vertices processed 125000 of 143034 vertices processed thickness calculation complete, 922:2239 truncations. 33298 vertices at 0 distance 96947 vertices at 1 distance 85435 vertices at 2 distance 38128 vertices at 3 distance 13552 vertices at 4 distance 4519 vertices at 5 distance 1592 vertices at 6 distance 612 vertices at 7 distance 268 vertices at 8 distance 129 vertices at 9 distance 82 vertices at 10 distance 55 vertices at 11 distance 30 vertices at 12 distance 20 vertices at 13 distance 14 vertices at 14 distance 8 vertices at 15 distance 19 vertices at 16 distance 19 vertices at 17 distance 15 vertices at 18 distance 11 vertices at 19 distance 21 vertices at 20 distance writing curvature file /out/out/freesurfer/sub-05/surf/lh.thickness positioning took 7.2 minutes #-------------------------------------------- #@# Surf Volume lh Tue Mar 30 00:41:23 UTC 2021 /out/out/freesurfer/sub-05/surf /out/out/freesurfer/sub-05/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-05 lh /out/out/freesurfer/sub-05/surf/lh.volume masking with /out/out/freesurfer/sub-05/label/lh.cortex.label Total face volume 304702 Total vertex volume 301212 (mask=0) #@# sub-05 lh 301212 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 lh Tue Mar 30 00:41:25 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 5 labels changed using aseg relabeling using gibbs priors... 000: 8955 changed, 143034 examined... 001: 2145 changed, 35149 examined... 002: 598 changed, 11181 examined... 003: 249 changed, 3409 examined... 004: 89 changed, 1388 examined... 005: 31 changed, 493 examined... 006: 19 changed, 177 examined... 007: 13 changed, 114 examined... 008: 8 changed, 68 examined... 009: 5 changed, 42 examined... 010: 4 changed, 27 examined... 011: 0 changed, 13 examined... 0 labels changed using aseg 000: 249 total segments, 166 labels (2068 vertices) changed 001: 99 total segments, 16 labels (56 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1266 vertices marked for relabeling... 1266 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 8 seconds. #----------------------------------------- #@# Cortical Parc 3 lh Tue Mar 30 00:41:33 UTC 2021 /out/out/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1384 labels changed using aseg relabeling using gibbs priors... 000: 2066 changed, 143034 examined... 001: 509 changed, 9499 examined... 002: 127 changed, 2891 examined... 003: 53 changed, 781 examined... 004: 16 changed, 321 examined... 005: 9 changed, 106 examined... 006: 2 changed, 56 examined... 007: 0 changed, 14 examined... 176 labels changed using aseg 000: 56 total segments, 23 labels (147 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 970 vertices marked for relabeling... 970 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 6 seconds. #----------------------------------------- #@# WM/GM Contrast lh Tue Mar 30 00:41:39 UTC 2021 /out/out/freesurfer/sub-05/scripts pctsurfcon --s sub-05 --lh-only Log file is /out/out/freesurfer/sub-05/scripts/pctsurfcon.log Tue Mar 30 00:41:39 UTC 2021 setenv SUBJECTS_DIR /out/out/freesurfer cd /out/out/freesurfer/sub-05/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ 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 FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /out/out/freesurfer/sub-05/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /out/out/freesurfer/sub-05/surf/tmp.pctsurfcon.19351/lh.wm.mgh --regheader sub-05 --cortex srcvol = /out/out/freesurfer/sub-05/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /out/out/freesurfer/sub-05/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99947 -0.03141 -0.00873 0.00000; -0.00873 -0.00027 0.99996 -0.00002; 0.03141 -0.99951 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /out/out/freesurfer/sub-05/label/lh.cortex.label Reading surface /out/out/freesurfer/sub-05/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 78452 Masking with /out/out/freesurfer/sub-05/label/lh.cortex.label Writing to /out/out/freesurfer/sub-05/surf/tmp.pctsurfcon.19351/lh.wm.mgh Dim: 143034 1 1 mri_vol2surf --mov /out/out/freesurfer/sub-05/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /out/out/freesurfer/sub-05/surf/tmp.pctsurfcon.19351/lh.gm.mgh --projfrac 0.3 --regheader sub-05 --cortex srcvol = /out/out/freesurfer/sub-05/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /out/out/freesurfer/sub-05/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99947 -0.03141 -0.00873 0.00000; -0.00873 -0.00027 0.99996 -0.00002; 0.03141 -0.99951 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /out/out/freesurfer/sub-05/label/lh.cortex.label Reading surface /out/out/freesurfer/sub-05/surf/lh.white Done reading source surface Reading thickness /out/out/freesurfer/sub-05/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 94066 Masking with /out/out/freesurfer/sub-05/label/lh.cortex.label Writing to /out/out/freesurfer/sub-05/surf/tmp.pctsurfcon.19351/lh.gm.mgh Dim: 143034 1 1 mri_concat /out/out/freesurfer/sub-05/surf/tmp.pctsurfcon.19351/lh.wm.mgh /out/out/freesurfer/sub-05/surf/tmp.pctsurfcon.19351/lh.gm.mgh --paired-diff-norm --mul 100 --o /out/out/freesurfer/sub-05/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /out/out/freesurfer/sub-05/surf/lh.w-g.pct.mgh mri_segstats --in /out/out/freesurfer/sub-05/surf/lh.w-g.pct.mgh --annot sub-05 lh aparc --sum /out/out/freesurfer/sub-05/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /out/out/freesurfer/sub-05/surf/lh.w-g.pct.mgh --annot sub-05 lh aparc --sum /out/out/freesurfer/sub-05/stats/lh.w-g.pct.stats --snr sysname Linux hostname 83ec93b3099f machine x86_64 user root UseRobust 0 Constructing seg from annotation Reading annotation /out/out/freesurfer/sub-05/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /out/out/freesurfer/sub-05/surf/lh.w-g.pct.mgh Vertex Area is 0.66868 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up Started at Mon Mar 29 23:54:23 UTC 2021 Ended at Tue Mar 30 00:41:42 UTC 2021 #@#%# recon-all-run-time-hours 0.789 recon-all -s sub-05 finished without error at Tue Mar 30 00:41:42 UTC 2021