Thu Sep 2 10:14:13 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 3 -subjid sub-M1215054 -sd /out/freesurfer subjid sub-M1215054 setenv SUBJECTS_DIR /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 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 23036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5902064 1686372 2199252 189624 2016440 3708196 Swap: 2097152 332800 1764352 ######################################## 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: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:13-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:14-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-10:14:15-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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 Thu Sep 2 10:14:15 UTC 2021 /out/freesurfer/sub-M1215054/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 3 found - 3 modified | TOTAL: 6 pass 2 (xz-): 0 found - 3 modified | TOTAL: 6 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 = 6 (out of 309623: 0.001938) 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: 1633 vertices, 1760 faces slice 50: 7342 vertices, 7573 faces slice 60: 15829 vertices, 16177 faces slice 70: 26097 vertices, 26476 faces slice 80: 36732 vertices, 37093 faces slice 90: 48439 vertices, 48839 faces slice 100: 60359 vertices, 60808 faces slice 110: 73672 vertices, 74082 faces slice 120: 86630 vertices, 87088 faces slice 130: 98833 vertices, 99300 faces slice 140: 110629 vertices, 111081 faces slice 150: 121556 vertices, 121964 faces slice 160: 130822 vertices, 131189 faces slice 170: 139428 vertices, 139755 faces slice 180: 146718 vertices, 147025 faces slice 190: 152913 vertices, 153173 faces slice 200: 157015 vertices, 157189 faces slice 210: 158136 vertices, 158204 faces slice 220: 158136 vertices, 158204 faces slice 230: 158136 vertices, 158204 faces slice 240: 158136 vertices, 158204 faces slice 250: 158136 vertices, 158204 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... 158136 voxel in cpt #1: X=-68 [v=158136,e=474612,f=316408] located at (-30.883841, -13.469337, 2.857243) For the whole surface: X=-68 [v=158136,e=474612,f=316408] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Sep 2 10:14:24 UTC 2021 /out/freesurfer/sub-M1215054/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 Thu Sep 2 10:14:32 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.3 mm, total surface area = 83252 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.043 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 43.459601 mris_inflate stimesec 0.534670 mris_inflate ru_maxrss 243120 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34825 mris_inflate ru_majflt 4 mris_inflate ru_nswap 0 mris_inflate ru_inblock 600 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 28874 mris_inflate ru_nivcsw 159 #-------------------------------------------- #@# QSphere lh Thu Sep 2 10:14:52 UTC 2021 /out/freesurfer/sub-M1215054/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 0.92 +- 0.54 (0.00-->8.14) (max @ vno 57375 --> 57376) face area 0.02 +- 0.03 (-0.20-->0.82) == Number of threads available to mris_sphere for OpenMP = 3 == scaling brain by 0.285... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.520, avgs=0 005/300: dt: 0.9000, rms radial error=177.258, avgs=0 010/300: dt: 0.9000, rms radial error=176.695, avgs=0 015/300: dt: 0.9000, rms radial error=175.957, avgs=0 020/300: dt: 0.9000, rms radial error=175.116, avgs=0 025/300: dt: 0.9000, rms radial error=174.216, avgs=0 030/300: dt: 0.9000, rms radial error=173.289, avgs=0 035/300: dt: 0.9000, rms radial error=172.345, avgs=0 040/300: dt: 0.9000, rms radial error=171.395, avgs=0 045/300: dt: 0.9000, rms radial error=170.441, avgs=0 050/300: dt: 0.9000, rms radial error=169.489, avgs=0 055/300: dt: 0.9000, rms radial error=168.540, avgs=0 060/300: dt: 0.9000, rms radial error=167.594, avgs=0 065/300: dt: 0.9000, rms radial error=166.652, avgs=0 070/300: dt: 0.9000, rms radial error=165.717, avgs=0 075/300: dt: 0.9000, rms radial error=164.786, avgs=0 080/300: dt: 0.9000, rms radial error=163.861, avgs=0 085/300: dt: 0.9000, rms radial error=162.940, avgs=0 090/300: dt: 0.9000, rms radial error=162.025, avgs=0 095/300: dt: 0.9000, rms radial error=161.114, avgs=0 100/300: dt: 0.9000, rms radial error=160.209, avgs=0 105/300: dt: 0.9000, rms radial error=159.309, avgs=0 110/300: dt: 0.9000, rms radial error=158.413, avgs=0 115/300: dt: 0.9000, rms radial error=157.523, avgs=0 120/300: dt: 0.9000, rms radial error=156.638, avgs=0 125/300: dt: 0.9000, rms radial error=155.757, avgs=0 130/300: dt: 0.9000, rms radial error=154.881, avgs=0 135/300: dt: 0.9000, rms radial error=154.011, avgs=0 140/300: dt: 0.9000, rms radial error=153.145, avgs=0 145/300: dt: 0.9000, rms radial error=152.283, avgs=0 150/300: dt: 0.9000, rms radial error=151.427, avgs=0 155/300: dt: 0.9000, rms radial error=150.575, avgs=0 160/300: dt: 0.9000, rms radial error=149.728, avgs=0 165/300: dt: 0.9000, rms radial error=148.886, avgs=0 170/300: dt: 0.9000, rms radial error=148.048, avgs=0 175/300: dt: 0.9000, rms radial error=147.215, avgs=0 180/300: dt: 0.9000, rms radial error=146.387, avgs=0 185/300: dt: 0.9000, rms radial error=145.563, avgs=0 190/300: dt: 0.9000, rms radial error=144.744, avgs=0 195/300: dt: 0.9000, rms radial error=143.930, avgs=0 200/300: dt: 0.9000, rms radial error=143.120, avgs=0 205/300: dt: 0.9000, rms radial error=142.315, avgs=0 210/300: dt: 0.9000, rms radial error=141.514, avgs=0 215/300: dt: 0.9000, rms radial error=140.718, avgs=0 220/300: dt: 0.9000, rms radial error=139.926, avgs=0 225/300: dt: 0.9000, rms radial error=139.139, avgs=0 230/300: dt: 0.9000, rms radial error=138.356, avgs=0 235/300: dt: 0.9000, rms radial error=137.577, avgs=0 240/300: dt: 0.9000, rms radial error=136.803, avgs=0 245/300: dt: 0.9000, rms radial error=136.033, avgs=0 250/300: dt: 0.9000, rms radial error=135.268, avgs=0 255/300: dt: 0.9000, rms radial error=134.506, avgs=0 260/300: dt: 0.9000, rms radial error=133.749, avgs=0 265/300: dt: 0.9000, rms radial error=132.996, avgs=0 270/300: dt: 0.9000, rms radial error=132.248, avgs=0 275/300: dt: 0.9000, rms radial error=131.503, avgs=0 280/300: dt: 0.9000, rms radial error=130.763, avgs=0 285/300: dt: 0.9000, rms radial error=130.027, avgs=0 290/300: dt: 0.9000, rms radial error=129.295, avgs=0 295/300: dt: 0.9000, rms radial error=128.567, avgs=0 300/300: dt: 0.9000, rms radial error=127.844, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18995.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 3347.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 372.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00452 epoch 4 (K=640.0), pass 1, starting sse = 26.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00725 final distance error %28.82 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 231.997910 mris_sphere stimesec 0.592061 mris_sphere ru_maxrss 243496 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 34338 mris_sphere ru_majflt 9 mris_sphere ru_nswap 0 mris_sphere ru_inblock 976 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 31171 mris_sphere ru_nivcsw 1051 FSRUNTIME@ mris_sphere 0.0282 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Thu Sep 2 10:16:34 UTC 2021 /out/freesurfer/sub-M1215054/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Thu Sep 2 10:16:34 UTC 2021 mris_fix_topology -rusage /out/freesurfer/sub-M1215054/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-M1215054 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=-68 (nv=158136, nf=316408, ne=474612, g=35) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 7204 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 32 defects to be corrected 0 vertices coincident reading input surface /out/freesurfer/sub-M1215054/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8877 (-4.4438) -vertex loglikelihood: -5.7506 (-2.8753) -normal dot loglikelihood: -3.5640 (-3.5640) -quad curv loglikelihood: -6.1536 (-3.0768) Total Loglikelihood : -24.3558 CORRECTING DEFECT 0 (vertices=101, convex hull=142, v0=1573) After retessellation of defect 0 (v0=1573), euler #=-28 (153891,460410,306491) : difference with theory (-29) = -1 CORRECTING DEFECT 1 (vertices=20, convex hull=52, v0=16848) After retessellation of defect 1 (v0=16848), euler #=-27 (153901,460458,306530) : difference with theory (-28) = -1 CORRECTING DEFECT 2 (vertices=44, convex hull=85, v0=20214) After retessellation of defect 2 (v0=20214), euler #=-26 (153927,460572,306619) : difference with theory (-27) = -1 CORRECTING DEFECT 3 (vertices=42, convex hull=71, v0=22932) After retessellation of defect 3 (v0=22932), euler #=-25 (153949,460666,306692) : difference with theory (-26) = -1 CORRECTING DEFECT 4 (vertices=90, convex hull=88, v0=36381) After retessellation of defect 4 (v0=36381), euler #=-24 (153963,460744,306757) : difference with theory (-25) = -1 CORRECTING DEFECT 5 (vertices=13, convex hull=27, v0=56256) After retessellation of defect 5 (v0=56256), euler #=-23 (153965,460757,306769) : difference with theory (-24) = -1 CORRECTING DEFECT 6 (vertices=47, convex hull=52, v0=57214) After retessellation of defect 6 (v0=57214), euler #=-22 (153983,460830,306825) : difference with theory (-23) = -1 CORRECTING DEFECT 7 (vertices=39, convex hull=73, v0=60087) After retessellation of defect 7 (v0=60087), euler #=-21 (154009,460937,306907) : difference with theory (-22) = -1 CORRECTING DEFECT 8 (vertices=76, convex hull=36, v0=63932) After retessellation of defect 8 (v0=63932), euler #=-20 (154019,460981,306942) : difference with theory (-21) = -1 CORRECTING DEFECT 9 (vertices=22, convex hull=47, v0=77075) After retessellation of defect 9 (v0=77075), euler #=-19 (154029,461029,306981) : difference with theory (-20) = -1 CORRECTING DEFECT 10 (vertices=1154, convex hull=508, v0=79836) L defect detected... After retessellation of defect 10 (v0=79836), euler #=-18 (154332,462206,307856) : difference with theory (-19) = -1 CORRECTING DEFECT 11 (vertices=6, convex hull=19, v0=83604) After retessellation of defect 11 (v0=83604), euler #=-17 (154333,462214,307864) : difference with theory (-18) = -1 CORRECTING DEFECT 12 (vertices=22, convex hull=36, v0=88118) After retessellation of defect 12 (v0=88118), euler #=-16 (154349,462274,307909) : difference with theory (-17) = -1 CORRECTING DEFECT 13 (vertices=229, convex hull=78, v0=94662) After retessellation of defect 13 (v0=94662), euler #=-16 (154370,462379,307993) : difference with theory (-16) = 0 CORRECTING DEFECT 14 (vertices=34, convex hull=75, v0=97622) After retessellation of defect 14 (v0=97622), euler #=-15 (154387,462465,308063) : difference with theory (-15) = 0 CORRECTING DEFECT 15 (vertices=30, convex hull=33, v0=98586) After retessellation of defect 15 (v0=98586), euler #=-14 (154389,462484,308081) : difference with theory (-14) = 0 CORRECTING DEFECT 16 (vertices=5, convex hull=21, v0=98623) After retessellation of defect 16 (v0=98623), euler #=-13 (154390,462490,308087) : difference with theory (-13) = 0 CORRECTING DEFECT 17 (vertices=29, convex hull=40, v0=100959) After retessellation of defect 17 (v0=100959), euler #=-12 (154395,462522,308115) : difference with theory (-12) = 0 CORRECTING DEFECT 18 (vertices=394, convex hull=123, v0=100975) After retessellation of defect 18 (v0=100975), euler #=-11 (154466,462793,308316) : difference with theory (-11) = 0 CORRECTING DEFECT 19 (vertices=136, convex hull=89, v0=103257) After retessellation of defect 19 (v0=103257), euler #=-10 (154489,462903,308404) : difference with theory (-10) = 0 CORRECTING DEFECT 20 (vertices=96, convex hull=87, v0=106731) After retessellation of defect 20 (v0=106731), euler #=-9 (154523,463042,308510) : difference with theory (-9) = 0 CORRECTING DEFECT 21 (vertices=317, convex hull=111, v0=108978) After retessellation of defect 21 (v0=108978), euler #=-8 (154534,463122,308580) : difference with theory (-8) = 0 CORRECTING DEFECT 22 (vertices=380, convex hull=179, v0=111469) After retessellation of defect 22 (v0=111469), euler #=-7 (154609,463430,308814) : difference with theory (-7) = 0 CORRECTING DEFECT 23 (vertices=69, convex hull=79, v0=112428) After retessellation of defect 23 (v0=112428), euler #=-6 (154633,463537,308898) : difference with theory (-6) = 0 CORRECTING DEFECT 24 (vertices=57, convex hull=37, v0=127825) After retessellation of defect 24 (v0=127825), euler #=-5 (154640,463572,308927) : difference with theory (-5) = 0 CORRECTING DEFECT 25 (vertices=38, convex hull=66, v0=130701) After retessellation of defect 25 (v0=130701), euler #=-4 (154653,463640,308983) : difference with theory (-4) = 0 CORRECTING DEFECT 26 (vertices=501, convex hull=352, v0=135225) After retessellation of defect 26 (v0=135225), euler #=-3 (154808,464287,309476) : difference with theory (-3) = 0 CORRECTING DEFECT 27 (vertices=94, convex hull=108, v0=145178) After retessellation of defect 27 (v0=145178), euler #=-2 (154819,464370,309549) : difference with theory (-2) = 0 CORRECTING DEFECT 28 (vertices=24, convex hull=20, v0=149227) After retessellation of defect 28 (v0=149227), euler #=-1 (154820,464378,309557) : difference with theory (-1) = 0 CORRECTING DEFECT 29 (vertices=45, convex hull=69, v0=152803) After retessellation of defect 29 (v0=152803), euler #=0 (154847,464486,309639) : difference with theory (0) = 0 CORRECTING DEFECT 30 (vertices=45, convex hull=64, v0=157025) After retessellation of defect 30 (v0=157025), euler #=1 (154864,464561,309698) : difference with theory (1) = 0 CORRECTING DEFECT 31 (vertices=52, convex hull=66, v0=157752) After retessellation of defect 31 (v0=157752), euler #=2 (154876,464622,309748) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.05-->11.53) (max @ vno 108860 --> 117062) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.05-->11.53) (max @ vno 108860 --> 117062) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 116 mutations (33.7%), 228 crossovers (66.3%), 251 vertices were eliminated building final representation... 3260 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=154876, nf=309748, ne=464622, g=0) writing corrected surface to /out/freesurfer/sub-M1215054/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.9 minutes 0 defective edges removing intersecting faces 000: 469 intersecting 001: 17 intersecting mris_fix_topology utimesec 951.944409 mris_fix_topology stimesec 0.620674 mris_fix_topology ru_maxrss 514896 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56566 mris_fix_topology ru_majflt 9 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 872 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 33840 mris_fix_topology ru_nivcsw 83 FSRUNTIME@ mris_fix_topology lh 0.2643 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 154876 - 464622 + 309748 = 2 --> 0 holes F =2V-4: 309748 = 309752-4 (0) 2E=3F: 929244 = 929244 (0) total defect index = 0 /out/freesurfer/sub-M1215054/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 135 intersecting 001: 8 intersecting 002: 6 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Sep 2 10:32:35 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-M1215054 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/freesurfer/sub-M1215054/mri/filled.mgz... reading volume /out/freesurfer/sub-M1215054/mri/brain.finalsurfs.mgz... reading volume /out/freesurfer/sub-M1215054/mri/../mri/aseg.presurf.mgz... reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... 15229 bright wm thresholded. 811 bright non-wm voxels segmented. reading original surface position from /out/freesurfer/sub-M1215054/surf/lh.orig... computing class statistics... border white: 294175 voxels (1.75%) border gray 325043 voxels (1.94%) WM (96.0): 97.2 +- 7.3 [70.0 --> 110.0] GM (76.0) : 75.8 +- 8.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.5 (was 70) setting MAX_BORDER_WHITE to 107.3 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 56.0 (was 40) setting MAX_GRAY to 92.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->6.24) (max @ vno 154135 --> 154247) face area 0.28 +- 0.13 (0.00-->5.37) mean absolute distance = 0.69 +- 0.86 4303 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=100+-5.2, GM=73+-6.1 mean inside = 93.1, mean outside = 78.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=84.2, 84 (84) missing vertices, mean dist 0.1 [0.6 (%45.1)->0.8 (%54.9))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=9e1e1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.08-->6.01) (max @ vno 154135 --> 154247) face area 0.28 +- 0.13 (0.00-->5.87) mean absolute distance = 0.36 +- 0.63 3891 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2501323.0, rms=7.903 001: dt: 0.5000, sse=1458488.5, rms=5.300 (32.933%) 002: dt: 0.5000, sse=1026261.3, rms=3.708 (30.042%) 003: dt: 0.5000, sse=866131.8, rms=2.901 (21.772%) 004: dt: 0.5000, sse=805093.7, rms=2.530 (12.792%) 005: dt: 0.5000, sse=781478.2, rms=2.366 (6.465%) 006: dt: 0.5000, sse=773361.0, rms=2.307 (2.488%) rms = 2.29, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=772133.2, rms=2.288 (0.824%) 008: dt: 0.2500, sse=687922.4, rms=1.388 (39.336%) 009: dt: 0.2500, sse=674971.0, rms=1.238 (10.789%) rms = 1.21, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=673007.4, rms=1.210 (2.330%) rms = 1.18, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=671434.1, rms=1.181 (2.342%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.2, 80 (31) missing vertices, mean dist -0.2 [0.4 (%67.3)->0.2 (%32.7))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=9e1e1, 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-->6.06) (max @ vno 80613 --> 154302) face area 0.35 +- 0.16 (0.00-->8.42) mean absolute distance = 0.30 +- 0.46 4711 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1119613.5, rms=3.378 012: dt: 0.5000, sse=910072.7, rms=1.986 (41.206%) 013: dt: 0.5000, sse=856916.1, rms=1.652 (16.823%) 014: dt: 0.5000, sse=851543.4, rms=1.601 (3.068%) rms = 1.68, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=821789.4, rms=1.214 (24.174%) 016: dt: 0.2500, sse=811122.8, rms=1.040 (14.318%) rms = 1.02, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=810554.4, rms=1.018 (2.098%) rms = 1.00, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=808475.9, rms=0.997 (2.117%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.9, 63 (19) missing vertices, mean dist -0.1 [0.3 (%66.1)->0.2 (%33.9))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=9e1e1, 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 (0.08-->6.08) (max @ vno 91264 --> 154219) face area 0.34 +- 0.16 (0.00-->8.61) mean absolute distance = 0.27 +- 0.38 4509 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=941775.4, rms=2.483 019: dt: 0.5000, sse=838108.7, rms=1.566 (36.930%) 020: dt: 0.5000, sse=824933.5, rms=1.443 (7.872%) rms = 1.48, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=798767.6, rms=1.124 (22.108%) 022: dt: 0.2500, sse=789674.1, rms=0.968 (13.824%) rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=788099.4, rms=0.953 (1.584%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 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 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=88.6, 77 (17) missing vertices, mean dist -0.1 [0.3 (%56.1)->0.2 (%43.9))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=9e1e1, 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/freesurfer/sub-M1215054/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=806805.1, rms=1.442 024: dt: 0.5000, sse=788898.0, rms=1.119 (22.402%) rms = 1.32, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=770594.6, rms=0.870 (22.272%) rms = 0.83, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=768165.6, rms=0.827 (4.989%) 027: dt: 0.1250, sse=762486.6, rms=0.773 (6.434%) rms = 0.76, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=761473.6, rms=0.756 (2.279%) positioning took 0.4 minutes generating cortex label... 12 non-cortical segments detected only using segment with 7521 vertices erasing segment 0 (vno[0] = 36234) erasing segment 2 (vno[0] = 75560) erasing segment 3 (vno[0] = 80671) erasing segment 4 (vno[0] = 90142) erasing segment 5 (vno[0] = 96426) erasing segment 6 (vno[0] = 103195) erasing segment 7 (vno[0] = 105343) erasing segment 8 (vno[0] = 107806) erasing segment 9 (vno[0] = 107811) erasing segment 10 (vno[0] = 108776) erasing segment 11 (vno[0] = 114188) writing cortex label to /out/freesurfer/sub-M1215054/label/lh.cortex.label... writing curvature file /out/freesurfer/sub-M1215054/surf/lh.curv writing smoothed area to lh.area writing curvature file /out/freesurfer/sub-M1215054/surf/lh.area vertex spacing 0.89 +- 0.25 (0.04-->6.12) (max @ vno 80613 --> 154302) face area 0.33 +- 0.16 (0.00-->8.70) refinement took 3.0 minutes #-------------------------------------------- #@# Smooth2 lh Thu Sep 2 10:35:37 UTC 2021 /out/freesurfer/sub-M1215054/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 Thu Sep 2 10:35:44 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_inflate -rusage /out/freesurfer/sub-M1215054/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.4 mm, total surface area = 92763 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 43.160211 mris_inflate stimesec 0.464631 mris_inflate ru_maxrss 238480 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34164 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 336 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 31022 mris_inflate ru_nivcsw 91 #-------------------------------------------- #@# Curv .H and .K lh Thu Sep 2 10:36:05 UTC 2021 /out/freesurfer/sub-M1215054/surf mris_curvature -w lh.white.preaparc total integrated curvature = -7.846*4pi (-98.591) --> 9 handles ICI = 190.7, FI = 1806.4, variation=29317.869 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 237 vertices thresholded to be in k1 ~ [-0.26 0.26], k2 ~ [-0.11 0.06] total integrated curvature = 0.504*4pi (6.334) --> 0 handles ICI = 1.6, FI = 10.7, variation=180.450 148 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 187 vertices thresholded to be in [-0.15 0.13] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Thu Sep 2 10:37:03 UTC 2021 /out/freesurfer/sub-M1215054/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-M1215054 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-M1215054/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 [ 314 ] Gb_filter = 0 WARN: S lookup min: -0.027532 WARN: S explicit min: 0.000000 vertex = 738 #-------------------------------------------- #@# Sphere lh Thu Sep 2 10:37:09 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_sphere -rusage /out/freesurfer/sub-M1215054/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 = 3 == scaling brain by 0.267... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=9e1e1, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.83 pass 1: epoch 2 of 3 starting distance error %19.79 unfolding complete - removing small folds... starting distance error %19.74 removing remaining folds... final distance error %19.75 MRISunfold() return, current seed 1234 -01: dt=0.0000, 145 negative triangles 182: dt=0.9900, 145 negative triangles 183: dt=0.9900, 73 negative triangles 184: dt=0.9900, 66 negative triangles 185: dt=0.9900, 48 negative triangles 186: dt=0.9900, 26 negative triangles 187: dt=0.9900, 17 negative triangles 188: dt=0.9900, 25 negative triangles 189: dt=0.9900, 20 negative triangles 190: dt=0.9900, 18 negative triangles 191: dt=0.9900, 12 negative triangles 192: dt=0.9900, 15 negative triangles 193: dt=0.9900, 10 negative triangles 194: dt=0.9900, 6 negative triangles 195: dt=0.9900, 9 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 11 negative triangles 198: dt=0.9900, 5 negative triangles 199: dt=0.9900, 3 negative triangles 200: dt=0.9900, 3 negative triangles 201: dt=0.9900, 5 negative triangles 202: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.29 hours mris_sphere utimesec 3052.659149 mris_sphere stimesec 1.971814 mris_sphere ru_maxrss 332204 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 56912 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 38164 mris_sphere ru_nivcsw 8966 FSRUNTIME@ mris_sphere 0.2949 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Thu Sep 2 10:54:51 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_register -curv -rusage /out/freesurfer/sub-M1215054/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/freesurfer/sub-M1215054/scripts cmdline mris_register -curv -rusage /out/freesurfer/sub-M1215054/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=9e1e1, 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=9e1e1, 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 = 5.650 curvature mean = 0.015, std = 0.814 curvature mean = 0.023, std = 0.858 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 402719.9, tmin=0.5898 d=32.00 min @ (0.00, 8.00, 8.00) sse = 232388.2, tmin=1.1771 d=16.00 min @ (4.00, 0.00, 0.00) sse = 224963.0, tmin=1.7746 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 217454.9, tmin=2.3705 d=2.00 min @ (0.50, 0.00, 0.00) sse = 217320.9, tmin=3.5700 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 217218.0, tmin=4.1691 d=0.50 min @ (0.00, -0.12, 0.00) sse = 217184.8, tmin=4.7749 tol=1.0e+00, sigma=0.5, host=9e1e1, 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 4.77 min curvature mean = -0.011, std = 0.827 curvature mean = 0.009, std = 0.946 curvature mean = -0.016, std = 0.835 curvature mean = 0.003, std = 0.978 curvature mean = -0.019, std = 0.836 curvature mean = 0.000, std = 0.991 2 Reading smoothwm curvature mean = -0.031, std = 0.272 curvature mean = 0.033, std = 0.245 curvature mean = 0.068, std = 0.366 curvature mean = 0.031, std = 0.303 curvature mean = 0.036, std = 0.571 curvature mean = 0.030, std = 0.329 curvature mean = 0.020, std = 0.724 curvature mean = 0.030, std = 0.340 curvature mean = 0.008, std = 0.833 MRISregister() return, current seed 0 -01: dt=0.0000, 19 negative triangles 120: dt=0.9900, 19 negative triangles expanding nbhd size to 1 121: dt=0.9900, 21 negative triangles 122: dt=0.9900, 15 negative triangles 123: dt=0.9900, 15 negative triangles 124: dt=0.9900, 12 negative triangles 125: dt=0.9900, 15 negative triangles 126: dt=0.9900, 11 negative triangles 127: dt=0.9900, 14 negative triangles 128: dt=0.9900, 9 negative triangles 129: dt=0.9900, 10 negative triangles 130: dt=0.9900, 9 negative triangles 131: dt=0.9900, 9 negative triangles 132: dt=0.9900, 7 negative triangles 133: dt=0.9900, 8 negative triangles 134: dt=0.9900, 5 negative triangles 135: dt=0.9900, 5 negative triangles 136: dt=0.9900, 7 negative triangles 137: dt=0.9900, 3 negative triangles 138: dt=0.9900, 4 negative triangles 139: dt=0.9900, 1 negative triangles 140: dt=0.9900, 1 negative triangles 141: dt=0.9900, 2 negative triangles 142: dt=0.9900, 1 negative triangles 143: dt=0.9900, 1 negative triangles 144: dt=0.9900, 1 negative triangles 145: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.41 hours mris_register utimesec 3493.959040 mris_register stimesec 3.192027 mris_register ru_maxrss 296620 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 39353 mris_register ru_majflt 11 mris_register ru_nswap 0 mris_register ru_inblock 4936 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 49272 mris_register ru_nivcsw 11419 FSRUNTIME@ mris_register 0.4115 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Thu Sep 2 11:19:32 UTC 2021 /out/freesurfer/sub-M1215054/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 Thu Sep 2 11:19:36 UTC 2021 /out/freesurfer/sub-M1215054/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 Thu Sep 2 11:19:39 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-M1215054 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... 1423 labels changed using aseg relabeling using gibbs priors... 000: 3432 changed, 154876 examined... 001: 788 changed, 14328 examined... 002: 208 changed, 4322 examined... 003: 75 changed, 1196 examined... 004: 33 changed, 425 examined... 005: 17 changed, 205 examined... 006: 8 changed, 94 examined... 007: 3 changed, 38 examined... 008: 0 changed, 14 examined... 302 labels changed using aseg 000: 113 total segments, 71 labels (221 vertices) changed 001: 45 total segments, 5 labels (12 vertices) changed 002: 40 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... 1997 vertices marked for relabeling... 1997 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Sep 2 11:19:52 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-M1215054 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/freesurfer/sub-M1215054/mri/filled.mgz... reading volume /out/freesurfer/sub-M1215054/mri/brain.finalsurfs.mgz... reading volume /out/freesurfer/sub-M1215054/mri/../mri/aseg.presurf.mgz... reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... 15229 bright wm thresholded. 811 bright non-wm voxels segmented. reading original surface position from /out/freesurfer/sub-M1215054/surf/lh.orig... computing class statistics... border white: 294175 voxels (1.75%) border gray 325043 voxels (1.94%) WM (96.0): 97.2 +- 7.3 [70.0 --> 110.0] GM (76.0) : 75.8 +- 8.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.5 (was 70) setting MAX_BORDER_WHITE to 107.3 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 56.0 (was 40) setting MAX_GRAY to 92.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100+-5.2, GM=73+-6.1 mean inside = 93.1, mean outside = 78.6 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.04-->6.12) (max @ vno 80613 --> 154302) face area 0.33 +- 0.16 (0.00-->8.59) mean absolute distance = 0.60 +- 0.86 3228 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 0.00% unknown deleting segment 1 with 99 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 8 points - only 0.00% unknown deleting segment 7 with 90 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 22 points - only 0.00% unknown deleting segment 11 with 23 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group mean border=84.1, 105 (101) missing vertices, mean dist 0.3 [0.7 (%18.3)->0.6 (%81.7))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=9e1e1, 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 (0.10-->6.17) (max @ vno 91264 --> 154219) face area 0.33 +- 0.16 (0.00-->7.08) mean absolute distance = 0.36 +- 0.64 3585 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1867697.0, rms=6.161 001: dt: 0.5000, sse=1161918.1, rms=3.798 (38.344%) 002: dt: 0.5000, sse=927394.8, rms=2.589 (31.849%) 003: dt: 0.5000, sse=862887.9, rms=2.153 (16.816%) 004: dt: 0.5000, sse=837468.6, rms=1.959 (9.038%) rms = 2.00, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=799649.9, rms=1.529 (21.956%) 006: dt: 0.2500, sse=784132.4, rms=1.311 (14.208%) 007: dt: 0.2500, sse=780618.1, rms=1.259 (3.966%) rms = 1.24, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=779245.1, rms=1.237 (1.820%) rms = 1.21, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=777739.6, rms=1.211 (2.048%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 0.00% unknown deleting segment 1 with 113 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown deleting segment 5 with 53 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown deleting segment 10 with 31 points - only 12.90% unknown mean border=86.1, 72 (25) missing vertices, mean dist -0.2 [0.4 (%67.0)->0.2 (%33.0))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=9e1e1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.03-->6.41) (max @ vno 91264 --> 154219) face area 0.35 +- 0.17 (0.00-->8.46) mean absolute distance = 0.30 +- 0.47 4743 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1118441.6, rms=3.333 010: dt: 0.5000, sse=903056.8, rms=1.973 (40.793%) 011: dt: 0.5000, sse=863294.0, rms=1.620 (17.890%) rms = 1.57, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=861796.4, rms=1.573 (2.896%) 013: dt: 0.2500, sse=824072.4, rms=1.092 (30.612%) 014: dt: 0.2500, sse=820321.8, rms=1.028 (5.800%) rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=819197.8, rms=1.018 (1.049%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown deleting segment 1 with 115 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown deleting segment 4 with 91 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 22 points - only 0.00% unknown deleting segment 9 with 31 points - only 12.90% unknown deleting segment 10 with 14 points - only 0.00% unknown mean border=87.9, 77 (17) missing vertices, mean dist -0.2 [0.3 (%66.2)->0.2 (%33.8))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=9e1e1, 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 +- 0.25 (0.09-->6.58) (max @ vno 91264 --> 154219) face area 0.34 +- 0.17 (0.00-->8.71) mean absolute distance = 0.27 +- 0.38 4526 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=946589.8, rms=2.487 016: dt: 0.5000, sse=840260.2, rms=1.566 (37.057%) 017: dt: 0.5000, sse=828053.8, rms=1.446 (7.649%) rms = 1.50, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=802256.0, rms=1.119 (22.598%) 019: dt: 0.2500, sse=794028.2, rms=0.970 (13.295%) rms = 0.96, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=792948.5, rms=0.963 (0.796%) rms = 0.93, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=790881.9, rms=0.933 (3.059%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 119 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 94 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 21 points - only 0.00% unknown deleting segment 8 with 31 points - only 12.90% unknown deleting segment 9 with 19 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown mean border=88.6, 95 (16) missing vertices, mean dist -0.1 [0.3 (%55.9)->0.2 (%44.1))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=9e1e1, 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/freesurfer/sub-M1215054/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=808841.1, rms=1.432 022: dt: 0.5000, sse=786314.1, rms=1.077 (24.802%) rms = 1.22, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=771255.4, rms=0.854 (20.663%) rms = 0.82, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=769601.6, rms=0.823 (3.658%) 025: dt: 0.1250, sse=766931.7, rms=0.766 (6.921%) rms = 0.75, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=764410.1, rms=0.750 (2.107%) positioning took 0.4 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7509 vertices erasing segment 0 (vno[0] = 36219) erasing segment 2 (vno[0] = 75560) erasing segment 3 (vno[0] = 80671) erasing segment 4 (vno[0] = 90142) erasing segment 5 (vno[0] = 96422) erasing segment 6 (vno[0] = 103195) erasing segment 7 (vno[0] = 105343) erasing segment 8 (vno[0] = 107806) erasing segment 9 (vno[0] = 107811) erasing segment 10 (vno[0] = 108776) erasing segment 11 (vno[0] = 114188) erasing segment 12 (vno[0] = 116093) writing cortex label to /out/freesurfer/sub-M1215054/label/lh.cortex.label... writing curvature file /out/freesurfer/sub-M1215054/surf/lh.curv writing smoothed area to lh.area writing curvature file /out/freesurfer/sub-M1215054/surf/lh.area vertex spacing 0.89 +- 0.26 (0.04-->6.59) (max @ vno 91264 --> 154219) face area 0.33 +- 0.17 (0.00-->8.63) 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 57 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=63.2, 96 (96) missing vertices, mean dist 1.5 [0.7 (%0.0)->2.7 (%100.0))] % 9 local maxima, %42 large gradients and %44 min vals, 379 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=9e1e1, 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=21017016.0, rms=26.111 001: dt: 0.0500, sse=18839476.0, rms=24.670 (5.518%) 002: dt: 0.0500, sse=17293870.0, rms=23.594 (4.362%) 003: dt: 0.0500, sse=16104769.0, rms=22.731 (3.657%) 004: dt: 0.0500, sse=15133468.0, rms=22.002 (3.211%) 005: dt: 0.0500, sse=14308231.0, rms=21.362 (2.908%) 006: dt: 0.0500, sse=13585531.0, rms=20.785 (2.699%) 007: dt: 0.0500, sse=12939009.0, rms=20.255 (2.549%) 008: dt: 0.0500, sse=12350218.0, rms=19.760 (2.443%) 009: dt: 0.0500, sse=11807956.0, rms=19.293 (2.364%) 010: dt: 0.0500, sse=11304114.0, rms=18.849 (2.303%) positioning took 0.6 minutes mean border=63.0, 92 (48) missing vertices, mean dist 1.2 [0.2 (%0.0)->2.2 (%100.0))] %10 local maxima, %43 large gradients and %44 min vals, 343 gradients ignored tol=1.0e-04, sigma=2.0, host=9e1e1, 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=12008643.0, rms=19.466 011: dt: 0.0500, sse=11532850.0, rms=19.050 (2.135%) 012: dt: 0.0500, sse=11086281.0, rms=18.652 (2.092%) 013: dt: 0.0500, sse=10665303.0, rms=18.268 (2.057%) 014: dt: 0.0500, sse=10267561.0, rms=17.898 (2.026%) 015: dt: 0.0500, sse=9891102.0, rms=17.540 (1.998%) 016: dt: 0.0500, sse=9535146.0, rms=17.195 (1.967%) 017: dt: 0.0500, sse=9198562.0, rms=16.862 (1.936%) 018: dt: 0.0500, sse=8879723.0, rms=16.541 (1.907%) 019: dt: 0.0500, sse=8577576.0, rms=16.230 (1.878%) 020: dt: 0.0500, sse=8291791.5, rms=15.931 (1.845%) positioning took 0.6 minutes mean border=62.8, 118 (40) missing vertices, mean dist 1.0 [0.1 (%0.8)->1.9 (%99.2))] %10 local maxima, %43 large gradients and %44 min vals, 324 gradients ignored tol=1.0e-04, sigma=2.0, host=9e1e1, 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=8418457.0, rms=16.069 021: dt: 0.0500, sse=8134370.5, rms=15.768 (1.872%) 022: dt: 0.0500, sse=7867290.0, rms=15.480 (1.828%) 023: dt: 0.0500, sse=7614138.5, rms=15.202 (1.798%) 024: dt: 0.0500, sse=7375613.0, rms=14.935 (1.757%) 025: dt: 0.0500, sse=7150911.0, rms=14.679 (1.715%) 026: dt: 0.0500, sse=6939112.0, rms=14.433 (1.674%) 027: dt: 0.0500, sse=6738761.5, rms=14.197 (1.638%) 028: dt: 0.0500, sse=6547708.5, rms=13.967 (1.615%) 029: dt: 0.0500, sse=6364557.5, rms=13.744 (1.600%) 030: dt: 0.0500, sse=6189019.5, rms=13.526 (1.584%) positioning took 0.6 minutes mean border=62.7, 148 (33) missing vertices, mean dist 0.8 [0.1 (%9.9)->1.7 (%90.1))] %10 local maxima, %43 large gradients and %43 min vals, 312 gradients ignored tol=1.0e-04, sigma=2.0, host=9e1e1, 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=6290793.0, rms=13.651 031: dt: 0.5000, sse=5003625.5, rms=11.953 (12.443%) 032: dt: 0.5000, sse=4129026.0, rms=10.637 (11.010%) 033: dt: 0.5000, sse=3443264.5, rms=9.479 (10.888%) 034: dt: 0.5000, sse=2928027.2, rms=8.498 (10.341%) 035: dt: 0.5000, sse=2519590.2, rms=7.633 (10.187%) 036: dt: 0.5000, sse=2218734.5, rms=6.922 (9.311%) 037: dt: 0.5000, sse=1974469.9, rms=6.289 (9.143%) 038: dt: 0.5000, sse=1807956.6, rms=5.814 (7.552%) 039: dt: 0.5000, sse=1679565.2, rms=5.424 (6.717%) 040: dt: 0.5000, sse=1604320.4, rms=5.176 (4.569%) 041: dt: 0.5000, sse=1543394.2, rms=4.971 (3.966%) 042: dt: 0.5000, sse=1519444.9, rms=4.883 (1.757%) 043: dt: 0.5000, sse=1484434.4, rms=4.761 (2.508%) rms = 4.73, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=1477962.4, rms=4.735 (0.549%) 045: dt: 0.2500, sse=1335927.4, rms=4.149 (12.364%) 046: dt: 0.2500, sse=1286202.1, rms=3.942 (4.994%) rms = 4.01, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=1255832.9, rms=3.807 (3.437%) 048: dt: 0.1250, sse=1216501.1, rms=3.623 (4.826%) rms = 3.58, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1206596.6, rms=3.575 (1.317%) positioning took 1.6 minutes mean border=61.9, 2565 (14) missing vertices, mean dist 0.1 [0.2 (%53.5)->0.6 (%46.5))] %16 local maxima, %37 large gradients and %41 min vals, 184 gradients ignored tol=1.0e-04, sigma=1.0, host=9e1e1, 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=1474250.9, rms=4.093 rms = 4.59, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=1349930.1, rms=3.528 (13.804%) rms = 3.50, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=1345524.9, rms=3.498 (0.850%) 052: dt: 0.1250, sse=1263538.8, rms=3.065 (12.365%) 053: dt: 0.1250, sse=1234953.8, rms=2.906 (5.211%) rms = 2.86, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1226243.2, rms=2.856 (1.715%) positioning took 0.5 minutes mean border=61.4, 3072 (10) missing vertices, mean dist 0.1 [0.2 (%52.1)->0.4 (%47.9))] %24 local maxima, %30 large gradients and %40 min vals, 185 gradients ignored tol=1.0e-04, sigma=0.5, host=9e1e1, 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=1258795.9, rms=3.073 rms = 4.28, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1224628.2, rms=2.878 (6.343%) rms = 3.06, time step reduction 2 of 3 to 0.125... rms = 2.83, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1216695.0, rms=2.830 (1.658%) positioning took 0.3 minutes mean border=61.0, 5639 (8) missing vertices, mean dist 0.1 [0.2 (%48.9)->0.4 (%51.1))] %29 local maxima, %25 large gradients and %39 min vals, 244 gradients ignored tol=1.0e-04, sigma=0.2, host=9e1e1, 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/freesurfer/sub-M1215054/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1244380.4, rms=2.985 rms = 3.90, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1214969.1, rms=2.815 (5.696%) rms = 2.91, time step reduction 2 of 3 to 0.125... 058: dt: 0.1250, sse=1206003.2, rms=2.760 (1.936%) 059: dt: 0.1250, sse=1191455.8, rms=2.674 (3.113%) rms = 2.64, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1186008.8, rms=2.644 (1.142%) positioning took 0.5 minutes writing curvature file /out/freesurfer/sub-M1215054/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /out/freesurfer/sub-M1215054/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.05-->8.04) (max @ vno 154302 --> 80613) face area 0.38 +- 0.29 (0.00-->10.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 154876 vertices processed 25000 of 154876 vertices processed 50000 of 154876 vertices processed 75000 of 154876 vertices processed 100000 of 154876 vertices processed 125000 of 154876 vertices processed 150000 of 154876 vertices processed 0 of 154876 vertices processed 25000 of 154876 vertices processed 50000 of 154876 vertices processed 75000 of 154876 vertices processed 100000 of 154876 vertices processed 125000 of 154876 vertices processed 150000 of 154876 vertices processed thickness calculation complete, 475:794 truncations. 42559 vertices at 0 distance 114910 vertices at 1 distance 86610 vertices at 2 distance 35307 vertices at 3 distance 11884 vertices at 4 distance 3874 vertices at 5 distance 1340 vertices at 6 distance 517 vertices at 7 distance 221 vertices at 8 distance 126 vertices at 9 distance 72 vertices at 10 distance 45 vertices at 11 distance 32 vertices at 12 distance 35 vertices at 13 distance 32 vertices at 14 distance 25 vertices at 15 distance 17 vertices at 16 distance 6 vertices at 17 distance 7 vertices at 18 distance 6 vertices at 19 distance 7 vertices at 20 distance writing curvature file /out/freesurfer/sub-M1215054/surf/lh.thickness positioning took 9.0 minutes #-------------------------------------------- #@# Surf Volume lh Thu Sep 2 11:28:52 UTC 2021 /out/freesurfer/sub-M1215054/surf /out/freesurfer/sub-M1215054/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-M1215054 lh /out/freesurfer/sub-M1215054/surf/lh.volume masking with /out/freesurfer/sub-M1215054/label/lh.cortex.label Total face volume 258613 Total vertex volume 255203 (mask=0) #@# sub-M1215054 lh 255203 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 lh Thu Sep 2 11:29:01 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-M1215054 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... 48 labels changed using aseg relabeling using gibbs priors... 000: 10024 changed, 154876 examined... 001: 2367 changed, 39132 examined... 002: 693 changed, 12146 examined... 003: 301 changed, 3861 examined... 004: 122 changed, 1718 examined... 005: 56 changed, 681 examined... 006: 36 changed, 328 examined... 007: 22 changed, 200 examined... 008: 8 changed, 119 examined... 009: 4 changed, 47 examined... 010: 3 changed, 21 examined... 011: 1 changed, 15 examined... 012: 0 changed, 7 examined... 6 labels changed using aseg 000: 305 total segments, 216 labels (2987 vertices) changed 001: 100 total segments, 12 labels (52 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1264 vertices marked for relabeling... 1264 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Cortical Parc 3 lh Thu Sep 2 11:29:19 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-M1215054 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... 1470 labels changed using aseg relabeling using gibbs priors... 000: 2131 changed, 154876 examined... 001: 503 changed, 9882 examined... 002: 153 changed, 2845 examined... 003: 73 changed, 908 examined... 004: 40 changed, 411 examined... 005: 24 changed, 198 examined... 006: 16 changed, 127 examined... 007: 16 changed, 81 examined... 008: 12 changed, 75 examined... 009: 9 changed, 54 examined... 010: 6 changed, 54 examined... 011: 5 changed, 38 examined... 012: 2 changed, 27 examined... 013: 1 changed, 12 examined... 014: 1 changed, 7 examined... 015: 1 changed, 7 examined... 016: 2 changed, 7 examined... 017: 1 changed, 10 examined... 018: 1 changed, 7 examined... 019: 1 changed, 7 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 0 changed, 7 examined... 307 labels changed using aseg 000: 50 total segments, 17 labels (180 vertices) changed 001: 35 total segments, 2 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 700 vertices marked for relabeling... 700 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# WM/GM Contrast lh Thu Sep 2 11:29:33 UTC 2021 /out/freesurfer/sub-M1215054/scripts pctsurfcon --s sub-M1215054 --lh-only Log file is /out/freesurfer/sub-M1215054/scripts/pctsurfcon.log Thu Sep 2 11:29:33 UTC 2021 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-M1215054/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /out/freesurfer/sub-M1215054/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20022/lh.wm.mgh --regheader sub-M1215054 --cortex srcvol = /out/freesurfer/sub-M1215054/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/freesurfer/sub-M1215054/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99961 -0.00367 0.02770 -0.00002; 0.02794 -0.13125 0.99096 -0.00003; -0.00000 -0.99134 -0.13130 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /out/freesurfer/sub-M1215054/label/lh.cortex.label Reading surface /out/freesurfer/sub-M1215054/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 = 61807 Masking with /out/freesurfer/sub-M1215054/label/lh.cortex.label Writing to /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20022/lh.wm.mgh Dim: 154876 1 1 mri_vol2surf --mov /out/freesurfer/sub-M1215054/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20022/lh.gm.mgh --projfrac 0.3 --regheader sub-M1215054 --cortex srcvol = /out/freesurfer/sub-M1215054/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/freesurfer/sub-M1215054/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99961 -0.00367 0.02770 -0.00002; 0.02794 -0.13125 0.99096 -0.00003; -0.00000 -0.99134 -0.13130 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /out/freesurfer/sub-M1215054/label/lh.cortex.label Reading surface /out/freesurfer/sub-M1215054/surf/lh.white Done reading source surface Reading thickness /out/freesurfer/sub-M1215054/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 = 73370 Masking with /out/freesurfer/sub-M1215054/label/lh.cortex.label Writing to /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20022/lh.gm.mgh Dim: 154876 1 1 mri_concat /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20022/lh.wm.mgh /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20022/lh.gm.mgh --paired-diff-norm --mul 100 --o /out/freesurfer/sub-M1215054/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/freesurfer/sub-M1215054/surf/lh.w-g.pct.mgh mri_segstats --in /out/freesurfer/sub-M1215054/surf/lh.w-g.pct.mgh --annot sub-M1215054 lh aparc --sum /out/freesurfer/sub-M1215054/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/freesurfer/sub-M1215054/surf/lh.w-g.pct.mgh --annot sub-M1215054 lh aparc --sum /out/freesurfer/sub-M1215054/stats/lh.w-g.pct.stats --snr sysname Linux hostname 9e1e1df09144 machine x86_64 user root UseRobust 0 Constructing seg from annotation Reading annotation /out/freesurfer/sub-M1215054/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/freesurfer/sub-M1215054/surf/lh.w-g.pct.mgh Vertex Area is 0.656973 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 Thu Sep 2 10:14:13 UTC 2021 Ended at Thu Sep 2 11:29:49 UTC 2021 #@#%# recon-all-run-time-hours 1.260 recon-all -s sub-M1215054 finished without error at Thu Sep 2 11:29:49 UTC 2021 New invocation of recon-all Thu Sep 2 13:20:23 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -nohyporelabel -openmp 3 -subjid sub-M1215054 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon subjid sub-M1215054 setenv SUBJECTS_DIR /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 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 23036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5902064 1683560 2040988 189624 2177516 3711868 Swap: 2097152 332800 1764352 ######################################## 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: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:23-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:20:24-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: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 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 ####################################### #----------------------------------------- #@# Parcellation Stats lh Thu Sep 2 13:20:24 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-M1215054 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/lh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 258613 Total vertex volume 255203 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 1600 1091 2672 2.659 0.547 0.106 0.020 11 1.3 bankssts 900 556 1671 2.664 0.806 0.138 0.018 14 0.6 caudalanteriorcingulate 3932 2541 7013 2.586 0.526 0.120 0.030 38 4.5 caudalmiddlefrontal 2681 1735 3142 1.773 0.383 0.153 0.040 37 4.2 cuneus 932 627 2405 3.379 0.969 0.113 0.035 9 1.3 entorhinal 4729 3125 9126 2.632 0.640 0.137 0.037 63 6.7 fusiform 7261 4883 12948 2.393 0.617 0.125 0.028 79 8.2 inferiorparietal 5248 3410 11047 2.876 0.726 0.134 0.036 69 7.7 inferiortemporal 1583 1034 2813 2.480 0.753 0.127 0.034 20 1.7 isthmuscingulate 8007 5090 10719 2.039 0.546 0.137 0.034 97 11.1 lateraloccipital 5289 3474 9620 2.686 0.829 0.134 0.036 74 7.6 lateralorbitofrontal 5628 3714 7812 1.972 0.629 0.138 0.034 69 7.7 lingual 3247 2232 6327 2.590 0.805 0.131 0.035 43 4.6 medialorbitofrontal 4966 3291 10387 2.698 0.594 0.124 0.030 63 5.8 middletemporal 1282 849 2858 3.106 0.868 0.119 0.027 15 1.2 parahippocampal 1900 1160 2526 2.067 0.559 0.102 0.020 13 1.5 paracentral 2688 1801 4993 2.473 0.542 0.108 0.023 28 2.3 parsopercularis 1237 780 2554 2.624 0.581 0.148 0.038 19 1.9 parsorbitalis 2227 1440 3774 2.382 0.546 0.124 0.026 25 2.3 parstriangularis 2092 1492 1904 1.471 0.439 0.138 0.032 42 2.7 pericalcarine 8261 5049 10837 2.003 0.695 0.117 0.028 83 9.3 postcentral 1761 1165 3151 2.475 0.802 0.141 0.035 31 2.5 posteriorcingulate 7951 4992 12623 2.388 0.597 0.114 0.027 68 8.3 precentral 7528 5098 12220 2.368 0.595 0.135 0.030 88 9.2 precuneus 1658 1068 3241 2.605 0.887 0.135 0.040 31 2.4 rostralanteriorcingulate 9958 6751 18473 2.378 0.617 0.140 0.039 142 16.0 rostralmiddlefrontal 12041 8030 24071 2.731 0.656 0.122 0.029 125 13.4 superiorfrontal 9106 5962 13253 2.058 0.505 0.119 0.027 89 9.5 superiorparietal 7380 4678 13803 2.660 0.706 0.111 0.031 71 9.6 superiortemporal 7951 5210 14931 2.562 0.632 0.125 0.031 88 9.7 supramarginal 487 303 865 2.216 0.642 0.160 0.060 11 1.4 frontalpole 745 502 1926 2.931 0.913 0.128 0.038 9 1.3 temporalpole 826 543 1165 2.031 0.440 0.122 0.029 7 1.0 transversetemporal 3856 2597 8298 3.274 0.753 0.123 0.034 40 5.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-M1215054 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input pial surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 258613 Total vertex volume 255203 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 1600 940 2672 2.659 0.547 0.106 0.028 18 2.0 bankssts 900 668 1671 2.664 0.806 0.144 0.031 36 1.0 caudalanteriorcingulate 3932 2930 7013 2.586 0.526 0.121 0.025 44 4.4 caudalmiddlefrontal 2681 1924 3142 1.773 0.383 0.133 0.033 36 3.9 cuneus 932 808 2405 3.379 0.969 0.145 0.036 16 1.6 entorhinal 4729 3784 9126 2.632 0.640 0.138 0.032 66 6.9 fusiform 7261 5871 12948 2.393 0.617 0.136 0.029 74 9.7 inferiorparietal 5248 4164 11047 2.876 0.726 0.138 0.033 73 8.3 inferiortemporal 1583 1249 2813 2.480 0.753 0.147 0.038 30 2.7 isthmuscingulate 8007 5615 10719 2.039 0.546 0.123 0.030 102 11.0 lateraloccipital 5289 3799 9620 2.686 0.829 0.127 0.031 71 7.2 lateralorbitofrontal 5628 4337 7812 1.972 0.629 0.134 0.032 88 8.3 lingual 3247 2762 6327 2.590 0.805 0.149 0.035 49 5.2 medialorbitofrontal 4966 4362 10387 2.698 0.594 0.141 0.030 53 7.1 middletemporal 1282 1082 2858 3.106 0.868 0.126 0.029 14 1.5 parahippocampal 1900 1308 2526 2.067 0.559 0.104 0.021 21 1.7 paracentral 2688 2214 4993 2.473 0.542 0.130 0.024 23 3.0 parsopercularis 1237 1174 2554 2.624 0.581 0.166 0.042 16 2.4 parsorbitalis 2227 1709 3774 2.382 0.546 0.137 0.028 25 2.8 parstriangularis 2092 1199 1904 1.471 0.439 0.099 0.027 25 2.2 pericalcarine 8261 5923 10837 2.003 0.695 0.119 0.026 79 9.4 postcentral 1761 1347 3151 2.475 0.802 0.146 0.040 46 2.7 posteriorcingulate 7951 5606 12623 2.388 0.597 0.109 0.025 129 9.8 precentral 7528 5353 12220 2.368 0.595 0.126 0.030 88 9.1 precuneus 1658 1330 3241 2.605 0.887 0.163 0.047 41 3.1 rostralanteriorcingulate 9958 8576 18473 2.378 0.617 0.161 0.037 129 17.7 rostralmiddlefrontal 12041 9461 24071 2.731 0.656 0.133 0.030 154 16.4 superiorfrontal 9106 6870 13253 2.058 0.505 0.128 0.028 91 10.8 superiorparietal 7380 5562 13803 2.660 0.706 0.123 0.030 130 9.9 superiortemporal 7951 6277 14931 2.562 0.632 0.133 0.030 115 10.3 supramarginal 487 472 865 2.216 0.642 0.183 0.042 6 1.0 frontalpole 745 825 1926 2.931 0.913 0.181 0.042 10 1.6 temporalpole 826 657 1165 2.031 0.440 0.127 0.029 6 1.1 transversetemporal 3856 2365 8298 3.274 0.753 0.129 0.037 70 6.5 insula #----------------------------------------- #@# Parcellation Stats 2 lh Thu Sep 2 13:21:54 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-M1215054 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/lh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 258613 Total vertex volume 255203 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 1465 971 2459 2.189 0.649 0.154 0.051 24 3.2 G&S_frontomargin 1185 774 2028 2.283 0.659 0.133 0.037 14 1.7 G&S_occipital_inf 1447 806 1710 1.875 0.509 0.103 0.024 11 1.5 G&S_paracentral 1829 1146 3530 2.695 0.607 0.135 0.037 23 2.6 G&S_subcentral 913 636 1928 2.445 0.596 0.173 0.062 22 2.4 G&S_transv_frontopol 2764 1867 5816 2.807 0.624 0.133 0.032 38 3.4 G&S_cingul-Ant 1224 845 2429 2.948 0.539 0.122 0.021 11 0.9 G&S_cingul-Mid-Ant 1306 897 2456 2.603 0.622 0.132 0.035 17 1.9 G&S_cingul-Mid-Post 684 433 1836 3.103 0.655 0.149 0.040 11 1.0 G_cingul-Post-dorsal 317 206 536 2.322 0.666 0.155 0.060 5 0.7 G_cingul-Post-ventral 2332 1484 2814 1.725 0.406 0.153 0.041 34 3.6 G_cuneus 1354 921 2963 2.568 0.630 0.129 0.032 18 1.7 G_front_inf-Opercular 594 351 1251 2.685 0.644 0.142 0.033 10 0.9 G_front_inf-Orbital 1532 886 2946 2.502 0.548 0.131 0.032 24 1.9 G_front_inf-Triangul 5881 3824 13184 2.620 0.595 0.147 0.043 97 10.7 G_front_middle 8463 5484 17882 2.761 0.688 0.127 0.032 97 10.7 G_front_sup 879 579 1842 3.089 0.719 0.154 0.052 14 1.9 G_Ins_lg&S_cent_ins 924 563 2666 3.688 0.830 0.133 0.043 15 1.6 G_insular_short 2759 1742 4824 2.292 0.515 0.143 0.035 42 3.9 G_occipital_middle 1651 1012 2240 2.005 0.400 0.124 0.032 17 2.0 G_occipital_sup 1857 1182 3944 2.755 0.603 0.152 0.042 31 3.2 G_oc-temp_lat-fusifor 4155 2652 5925 1.934 0.646 0.147 0.038 58 6.5 G_oc-temp_med-Lingual 1870 1242 4764 3.273 0.902 0.126 0.033 23 2.0 G_oc-temp_med-Parahip 3288 2090 6640 2.584 0.841 0.151 0.046 62 6.3 G_orbital 3209 2106 6895 2.568 0.721 0.133 0.034 43 4.3 G_pariet_inf-Angular 3951 2462 8602 2.692 0.685 0.132 0.042 58 6.4 G_pariet_inf-Supramar 3622 2361 5988 2.081 0.526 0.128 0.033 47 4.6 G_parietal_sup 3703 2045 4879 2.006 0.644 0.115 0.031 42 4.5 G_postcentral 3231 1794 5603 2.509 0.568 0.102 0.026 28 3.2 G_precentral 3790 2546 7280 2.325 0.574 0.150 0.036 58 5.6 G_precuneus 1220 833 2706 2.583 0.860 0.145 0.046 22 2.2 G_rectus 740 484 1392 2.632 0.999 0.101 0.042 7 1.0 G_subcallosal 627 410 1012 2.076 0.491 0.136 0.038 7 1.0 G_temp_sup-G_T_transv 2542 1462 5681 2.789 0.812 0.127 0.042 32 4.4 G_temp_sup-Lateral 854 565 2144 3.233 0.923 0.073 0.029 4 1.3 G_temp_sup-Plan_polar 1409 951 2560 2.406 0.547 0.118 0.022 13 1.2 G_temp_sup-Plan_tempo 2796 1718 6709 2.922 0.786 0.147 0.047 51 5.2 G_temporal_inf 2741 1751 6720 2.780 0.642 0.138 0.037 47 4.1 G_temporal_middle 313 219 492 2.513 0.327 0.099 0.016 2 0.1 Lat_Fis-ant-Horizont 357 270 515 2.159 0.468 0.098 0.015 2 0.1 Lat_Fis-ant-Vertical 1310 906 1819 2.614 0.468 0.118 0.023 9 1.2 Lat_Fis-post 2356 1408 2590 1.802 0.525 0.150 0.040 35 4.1 Pole_occipital 1779 1152 4245 2.790 0.839 0.143 0.047 28 3.7 Pole_temporal 2773 2022 3086 1.815 0.714 0.138 0.030 49 3.6 S_calcarine 3525 2450 3855 1.801 0.561 0.119 0.028 27 3.5 S_central 938 641 1229 2.146 0.413 0.104 0.018 7 0.6 S_cingul-Marginalis 707 480 1255 3.168 0.491 0.079 0.010 2 0.3 S_circular_insula_ant 1395 967 2336 2.974 0.709 0.093 0.015 6 0.8 S_circular_insula_inf 1933 1349 3230 2.935 0.582 0.102 0.018 9 1.4 S_circular_insula_sup 1399 994 2261 2.514 0.572 0.111 0.020 9 1.2 S_collat_transv_ant 567 383 577 2.019 0.342 0.158 0.045 7 1.0 S_collat_transv_post 2597 1798 3724 2.197 0.477 0.104 0.020 16 2.0 S_front_inf 1611 1121 2386 2.206 0.501 0.124 0.033 18 1.7 S_front_middle 3224 2184 5144 2.524 0.522 0.107 0.021 23 2.4 S_front_sup 449 306 582 2.409 0.613 0.123 0.019 4 0.4 S_interm_prim-Jensen 3441 2287 4519 2.134 0.463 0.111 0.021 25 2.9 S_intrapariet&P_trans 1165 799 1310 1.897 0.413 0.107 0.020 7 0.9 S_oc_middle&Lunatus 1338 932 1705 2.083 0.487 0.109 0.019 7 1.1 S_oc_sup&transversal 688 490 790 1.995 0.412 0.131 0.024 6 0.7 S_occipital_ant 585 404 1094 2.768 0.623 0.097 0.016 3 0.4 S_oc-temp_lat 2037 1447 3249 2.516 0.645 0.119 0.025 18 1.9 S_oc-temp_med&Lingual 439 307 513 1.814 0.513 0.139 0.028 4 0.6 S_orbital_lateral 661 541 1071 2.454 0.785 0.127 0.021 6 0.4 S_orbital_med-olfact 1951 1277 3331 2.719 0.791 0.125 0.029 20 2.1 S_orbital-H_Shaped 3024 1995 3856 2.197 0.615 0.118 0.024 26 2.8 S_parieto_occipital 1371 824 1094 1.830 0.576 0.132 0.023 27 0.9 S_pericallosal 3461 2342 4391 2.050 0.553 0.111 0.022 24 3.1 S_postcentral 1819 1248 2691 2.394 0.527 0.116 0.023 15 1.6 S_precentral-inf-part 1082 760 1466 2.271 0.547 0.110 0.017 7 0.8 S_precentral-sup-part 843 566 1306 2.542 0.885 0.124 0.020 9 0.8 S_suborbital 1484 1029 2110 2.452 0.613 0.119 0.025 10 1.5 S_subparietal 1953 1329 2975 2.695 0.563 0.108 0.018 12 1.5 S_temporal_inf 6596 4535 10795 2.536 0.526 0.111 0.022 52 5.7 S_temporal_sup 663 442 830 2.279 0.521 0.100 0.013 5 0.4 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 lh Thu Sep 2 13:22:37 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-M1215054 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/lh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 258613 Total vertex volume 255203 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 1790 1130 3730 2.871 0.741 0.133 0.022 27 1.5 caudalanteriorcingulate 4153 2696 7459 2.590 0.528 0.120 0.030 40 4.6 caudalmiddlefrontal 3693 2386 4416 1.827 0.419 0.141 0.035 45 5.0 cuneus 764 525 2003 3.366 0.904 0.110 0.030 7 0.7 entorhinal 4276 2856 7974 2.625 0.593 0.138 0.035 55 5.8 fusiform 7568 5093 13519 2.371 0.610 0.125 0.028 82 8.7 inferiorparietal 5425 3471 11661 2.861 0.776 0.133 0.039 74 8.6 inferiortemporal 1569 1024 2835 2.522 0.756 0.128 0.034 20 1.8 isthmuscingulate 7955 5027 10650 2.041 0.549 0.137 0.034 96 10.9 lateraloccipital 5756 3788 10545 2.628 0.870 0.139 0.041 88 9.5 lateralorbitofrontal 5717 3787 7915 1.966 0.623 0.140 0.034 71 7.9 lingual 2795 1907 5660 2.631 0.861 0.127 0.035 37 3.8 medialorbitofrontal 6475 4317 12764 2.703 0.581 0.124 0.028 75 7.3 middletemporal 1329 882 2984 3.114 0.883 0.124 0.029 17 1.3 parahippocampal 2255 1386 3129 2.140 0.587 0.103 0.022 15 2.0 paracentral 2493 1669 4610 2.477 0.551 0.111 0.024 27 2.3 parsopercularis 1342 835 2555 2.702 0.567 0.125 0.028 15 1.6 parsorbitalis 2771 1788 4537 2.309 0.542 0.119 0.025 29 2.7 parstriangularis 2115 1503 1916 1.469 0.436 0.138 0.032 42 2.8 pericalcarine 9176 5640 12144 2.042 0.706 0.118 0.028 90 10.3 postcentral 1873 1251 3276 2.446 0.780 0.141 0.036 32 2.6 posteriorcingulate 7891 4945 12596 2.402 0.596 0.114 0.027 67 8.3 precentral 7333 4950 12051 2.367 0.597 0.136 0.031 87 9.0 precuneus 2093 1370 4119 2.684 0.797 0.138 0.038 36 2.8 rostralanteriorcingulate 7142 4833 13251 2.408 0.599 0.141 0.038 99 11.1 rostralmiddlefrontal 13297 8964 26184 2.627 0.660 0.129 0.033 157 17.4 superiorfrontal 7363 4856 11003 2.078 0.505 0.118 0.027 73 7.7 superiorparietal 9336 6020 18124 2.700 0.731 0.112 0.031 90 11.9 superiortemporal 7144 4683 13318 2.558 0.633 0.125 0.032 78 8.8 supramarginal 823 541 1154 2.034 0.434 0.122 0.029 7 1.0 transversetemporal 3230 2161 7120 3.324 0.707 0.119 0.029 32 3.7 insula /out/freesurfer/sub-M1215054/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Sep 2 13:23:20 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 967 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 5096 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 1191 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 253 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4330 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 916 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6899 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 486 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6270 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 369 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4439 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 1571 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15160 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 454 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4635 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 965 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4387 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 1663 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6304 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 3693 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11807 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 385 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 345 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1635 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-M1215054 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 404 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1603 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 260 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1274 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 526 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2618 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1569 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2251 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 231 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2550 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1646 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 589 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7624 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 366 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1517 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 1206 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 1657 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4991 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 600 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 619 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/lh.white Reading target registration /out/freesurfer/sub-M1215054/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 154876 Number of reverse mapping hits = 155 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 605 mri_label2label: Done mris_label2annot --s sub-M1215054 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /out/freesurfer/sub-M1215054/label cmdline mris_label2annot --s sub-M1215054 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname 9e1e1df09144 machine x86_64 user root subject sub-M1215054 hemi lh SUBJECTS_DIR /out/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /out/freesurfer/sub-M1215054/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 108084 unhit vertices Writing annot to /out/freesurfer/sub-M1215054/label/lh.BA_exvivo.annot mris_label2annot --s sub-M1215054 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /out/freesurfer/sub-M1215054/label cmdline mris_label2annot --s sub-M1215054 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname 9e1e1df09144 machine x86_64 user root subject sub-M1215054 hemi lh SUBJECTS_DIR /out/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /out/freesurfer/sub-M1215054/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 127347 unhit vertices Writing annot to /out/freesurfer/sub-M1215054/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-M1215054 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/lh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 258613 Total vertex volume 255203 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 1562 824 1987 2.000 0.655 0.108 0.029 17 1.9 BA1_exvivo 4828 3098 6806 2.139 0.652 0.116 0.029 43 5.4 BA2_exvivo 1139 804 1097 1.736 0.446 0.142 0.044 11 1.5 BA3a_exvivo 3011 1851 3782 1.858 0.719 0.115 0.028 30 3.5 BA3b_exvivo 1746 972 2444 2.274 0.498 0.100 0.022 12 1.7 BA4a_exvivo 1371 914 1878 2.196 0.508 0.108 0.023 9 1.3 BA4p_exvivo 9821 6173 17625 2.558 0.622 0.113 0.026 89 9.6 BA6_exvivo 2344 1610 4385 2.472 0.499 0.120 0.026 24 2.3 BA44_exvivo 3563 2300 5969 2.256 0.568 0.123 0.027 43 3.8 BA45_exvivo 3935 2624 3893 1.533 0.459 0.141 0.034 67 5.7 V1_exvivo 9482 6116 12053 1.931 0.545 0.150 0.039 127 14.9 V2_exvivo 1994 1317 3268 2.339 0.593 0.125 0.029 21 2.3 MT_exvivo 913 581 2299 3.462 0.810 0.112 0.033 10 1.1 perirhinal_exvivo 1083 713 2285 2.897 0.843 0.129 0.036 15 1.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-M1215054 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/lh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/lh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 258613 Total vertex volume 255203 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 1108 554 1348 1.920 0.587 0.116 0.035 15 1.6 BA1_exvivo 2310 1429 3313 2.064 0.548 0.117 0.027 22 2.4 BA2_exvivo 926 663 859 1.657 0.388 0.143 0.045 10 1.1 BA3a_exvivo 1754 1162 1685 1.444 0.307 0.099 0.017 11 1.2 BA3b_exvivo 1748 1011 2438 2.241 0.519 0.103 0.022 13 1.6 BA4a_exvivo 1103 743 1475 2.156 0.483 0.114 0.027 7 1.2 BA4p_exvivo 5175 3145 8706 2.484 0.615 0.113 0.027 48 5.6 BA6_exvivo 1462 1014 2658 2.395 0.460 0.115 0.023 14 1.3 BA44_exvivo 1406 852 2690 2.433 0.575 0.121 0.032 19 1.7 BA45_exvivo 4224 2786 4204 1.546 0.457 0.140 0.035 72 6.2 V1_exvivo 4754 3092 5893 1.895 0.523 0.159 0.041 69 8.1 V2_exvivo 514 350 896 2.326 0.576 0.118 0.024 6 0.4 MT_exvivo 471 304 1378 3.708 0.763 0.091 0.030 4 0.4 perirhinal_exvivo 574 396 1324 3.081 0.720 0.141 0.033 8 0.7 entorhinal_exvivo Started at Thu Sep 2 13:20:23 UTC 2021 Ended at Thu Sep 2 13:30:21 UTC 2021 #@#%# recon-all-run-time-hours 0.166 recon-all -s sub-M1215054 finished without error at Thu Sep 2 13:30:22 UTC 2021