Thu Sep 2 11:29:51 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -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 1682364 2104704 189624 2114996 3713200 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: 2021/09/02-11:29:51-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: 2021/09/02-11:29:51-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: 2021/09/02-11:29:51-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: 2021/09/02-11:29:51-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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: 2021/09/02-11:29:52-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 rh Thu Sep 2 11:29:52 UTC 2021 /out/freesurfer/sub-M1215054/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 3 found - 3 modified | TOTAL: 4 pass 2 (yz-): 0 found - 3 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 2 found - 2 modified | TOTAL: 8 pass 2 (xz-): 0 found - 2 modified | TOTAL: 8 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 9 (out of 308204: 0.002920) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 1714 vertices, 1827 faces slice 50: 8332 vertices, 8615 faces slice 60: 18177 vertices, 18588 faces slice 70: 29456 vertices, 29864 faces slice 80: 41093 vertices, 41475 faces slice 90: 52429 vertices, 52803 faces slice 100: 64763 vertices, 65208 faces slice 110: 77768 vertices, 78199 faces slice 120: 90494 vertices, 90921 faces slice 130: 102608 vertices, 103051 faces slice 140: 114035 vertices, 114451 faces slice 150: 124847 vertices, 125254 faces slice 160: 133815 vertices, 134163 faces slice 170: 141789 vertices, 142110 faces slice 180: 148871 vertices, 149200 faces slice 190: 154899 vertices, 155150 faces slice 200: 158654 vertices, 158825 faces slice 210: 159490 vertices, 159564 faces slice 220: 159490 vertices, 159564 faces slice 230: 159490 vertices, 159564 faces slice 240: 159490 vertices, 159564 faces slice 250: 159490 vertices, 159564 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 159490 voxel in cpt #1: X=-74 [v=159490,e=478692,f=319128] located at (24.053514, -15.785993, 2.618910) For the whole surface: X=-74 [v=159490,e=478692,f=319128] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Sep 2 11:30:00 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Sep 2 11:30:08 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.7 mm, total surface area = 84496 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.042 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 52.197139 mris_inflate stimesec 0.794063 mris_inflate ru_maxrss 245212 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34814 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 29306 mris_inflate ru_nivcsw 196 #-------------------------------------------- #@# QSphere rh Thu Sep 2 11:30:32 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.93 +- 0.55 (0.00-->6.97) (max @ vno 102097 --> 102109) face area 0.02 +- 0.03 (-0.24-->0.53) == Number of threads available to mris_sphere for OpenMP = 3 == scaling brain by 0.288... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.092, avgs=0 005/300: dt: 0.9000, rms radial error=176.837, avgs=0 010/300: dt: 0.9000, rms radial error=176.283, avgs=0 015/300: dt: 0.9000, rms radial error=175.550, avgs=0 020/300: dt: 0.9000, rms radial error=174.716, avgs=0 025/300: dt: 0.9000, rms radial error=173.825, avgs=0 030/300: dt: 0.9000, rms radial error=172.902, avgs=0 035/300: dt: 0.9000, rms radial error=171.963, avgs=0 040/300: dt: 0.9000, rms radial error=171.016, avgs=0 045/300: dt: 0.9000, rms radial error=170.067, avgs=0 050/300: dt: 0.9000, rms radial error=169.119, avgs=0 055/300: dt: 0.9000, rms radial error=168.173, avgs=0 060/300: dt: 0.9000, rms radial error=167.232, avgs=0 065/300: dt: 0.9000, rms radial error=166.295, avgs=0 070/300: dt: 0.9000, rms radial error=165.362, avgs=0 075/300: dt: 0.9000, rms radial error=164.434, avgs=0 080/300: dt: 0.9000, rms radial error=163.511, avgs=0 085/300: dt: 0.9000, rms radial error=162.593, avgs=0 090/300: dt: 0.9000, rms radial error=161.680, avgs=0 095/300: dt: 0.9000, rms radial error=160.772, avgs=0 100/300: dt: 0.9000, rms radial error=159.869, avgs=0 105/300: dt: 0.9000, rms radial error=158.971, avgs=0 110/300: dt: 0.9000, rms radial error=158.079, avgs=0 115/300: dt: 0.9000, rms radial error=157.191, avgs=0 120/300: dt: 0.9000, rms radial error=156.308, avgs=0 125/300: dt: 0.9000, rms radial error=155.430, avgs=0 130/300: dt: 0.9000, rms radial error=154.557, avgs=0 135/300: dt: 0.9000, rms radial error=153.688, avgs=0 140/300: dt: 0.9000, rms radial error=152.824, avgs=0 145/300: dt: 0.9000, rms radial error=151.965, avgs=0 150/300: dt: 0.9000, rms radial error=151.111, avgs=0 155/300: dt: 0.9000, rms radial error=150.261, avgs=0 160/300: dt: 0.9000, rms radial error=149.416, avgs=0 165/300: dt: 0.9000, rms radial error=148.575, avgs=0 170/300: dt: 0.9000, rms radial error=147.739, avgs=0 175/300: dt: 0.9000, rms radial error=146.908, avgs=0 180/300: dt: 0.9000, rms radial error=146.081, avgs=0 185/300: dt: 0.9000, rms radial error=145.259, avgs=0 190/300: dt: 0.9000, rms radial error=144.441, avgs=0 195/300: dt: 0.9000, rms radial error=143.628, avgs=0 200/300: dt: 0.9000, rms radial error=142.820, avgs=0 205/300: dt: 0.9000, rms radial error=142.016, avgs=0 210/300: dt: 0.9000, rms radial error=141.217, avgs=0 215/300: dt: 0.9000, rms radial error=140.422, avgs=0 220/300: dt: 0.9000, rms radial error=139.632, avgs=0 225/300: dt: 0.9000, rms radial error=138.846, avgs=0 230/300: dt: 0.9000, rms radial error=138.065, avgs=0 235/300: dt: 0.9000, rms radial error=137.288, avgs=0 240/300: dt: 0.9000, rms radial error=136.515, avgs=0 245/300: dt: 0.9000, rms radial error=135.747, avgs=0 250/300: dt: 0.9000, rms radial error=134.982, avgs=0 255/300: dt: 0.9000, rms radial error=134.223, avgs=0 260/300: dt: 0.9000, rms radial error=133.467, avgs=0 265/300: dt: 0.9000, rms radial error=132.716, avgs=0 270/300: dt: 0.9000, rms radial error=131.969, avgs=0 275/300: dt: 0.9000, rms radial error=131.226, avgs=0 280/300: dt: 0.9000, rms radial error=130.487, avgs=0 285/300: dt: 0.9000, rms radial error=129.753, avgs=0 290/300: dt: 0.9000, rms radial error=129.022, avgs=0 295/300: dt: 0.9000, rms radial error=128.296, avgs=0 300/300: dt: 0.9000, rms radial error=127.574, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19076.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3322.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 364.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00397 epoch 4 (K=640.0), pass 1, starting sse = 27.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00581 final distance error %29.10 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 247.991201 mris_sphere stimesec 0.711294 mris_sphere ru_maxrss 245444 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 34833 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 29233 mris_sphere ru_nivcsw 1089 FSRUNTIME@ mris_sphere 0.0301 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy rh Thu Sep 2 11:32:20 UTC 2021 /out/freesurfer/sub-M1215054/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology rh Thu Sep 2 11:32:20 UTC 2021 mris_fix_topology -rusage /out/freesurfer/sub-M1215054/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-M1215054 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-74 (nv=159490, nf=319128, ne=478692, g=38) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 6966 ambiguous faces found in tessellation segmenting defects... 46 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 9 into 5 -merging segment 31 into 29 -merging segment 35 into 34 43 defects to be corrected 0 vertices coincident reading input surface /out/freesurfer/sub-M1215054/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0442 (-4.5221) -vertex loglikelihood: -5.8196 (-2.9098) -normal dot loglikelihood: -3.6734 (-3.6734) -quad curv loglikelihood: -5.8785 (-2.9393) Total Loglikelihood : -24.4157 CORRECTING DEFECT 0 (vertices=5, convex hull=14, v0=31204) After retessellation of defect 0 (v0=31204), euler #=-38 (155208,463892,308646) : difference with theory (-40) = -2 CORRECTING DEFECT 1 (vertices=81, convex hull=80, v0=31415) After retessellation of defect 1 (v0=31415), euler #=-37 (155225,463981,308719) : difference with theory (-39) = -2 CORRECTING DEFECT 2 (vertices=28, convex hull=83, v0=35512) After retessellation of defect 2 (v0=35512), euler #=-36 (155244,464072,308792) : difference with theory (-38) = -2 CORRECTING DEFECT 3 (vertices=44, convex hull=96, v0=39983) After retessellation of defect 3 (v0=39983), euler #=-35 (155276,464211,308900) : difference with theory (-37) = -2 CORRECTING DEFECT 4 (vertices=29, convex hull=33, v0=58221) After retessellation of defect 4 (v0=58221), euler #=-34 (155280,464234,308920) : difference with theory (-36) = -2 CORRECTING DEFECT 5 (vertices=792, convex hull=503, v0=60663) L defect detected... After retessellation of defect 5 (v0=60663), euler #=-34 (155485,465135,309616) : difference with theory (-35) = -1 CORRECTING DEFECT 6 (vertices=8, convex hull=25, v0=64346) After retessellation of defect 6 (v0=64346), euler #=-33 (155487,465146,309626) : difference with theory (-34) = -1 CORRECTING DEFECT 7 (vertices=42, convex hull=75, v0=66591) After retessellation of defect 7 (v0=66591), euler #=-32 (155514,465258,309712) : difference with theory (-33) = -1 CORRECTING DEFECT 8 (vertices=58, convex hull=71, v0=67593) After retessellation of defect 8 (v0=67593), euler #=-31 (155545,465380,309804) : difference with theory (-32) = -1 CORRECTING DEFECT 9 (vertices=28, convex hull=72, v0=77726) After retessellation of defect 9 (v0=77726), euler #=-30 (155560,465456,309866) : difference with theory (-31) = -1 CORRECTING DEFECT 10 (vertices=22, convex hull=36, v0=79571) After retessellation of defect 10 (v0=79571), euler #=-29 (155563,465474,309882) : difference with theory (-30) = -1 CORRECTING DEFECT 11 (vertices=5, convex hull=17, v0=80856) After retessellation of defect 11 (v0=80856), euler #=-28 (155564,465480,309888) : difference with theory (-29) = -1 CORRECTING DEFECT 12 (vertices=805, convex hull=571, v0=80898) L defect detected... After retessellation of defect 12 (v0=80898), euler #=-29 (155820,466557,310708) : difference with theory (-28) = 1 CORRECTING DEFECT 13 (vertices=518, convex hull=356, v0=92543) After retessellation of defect 13 (v0=92543), euler #=-28 (156006,467295,311261) : difference with theory (-27) = 1 CORRECTING DEFECT 14 (vertices=40, convex hull=32, v0=98690) After retessellation of defect 14 (v0=98690), euler #=-27 (156015,467330,311288) : difference with theory (-26) = 1 CORRECTING DEFECT 15 (vertices=384, convex hull=101, v0=107949) After retessellation of defect 15 (v0=107949), euler #=-26 (156048,467479,311405) : difference with theory (-25) = 1 CORRECTING DEFECT 16 (vertices=61, convex hull=36, v0=112731) After retessellation of defect 16 (v0=112731), euler #=-25 (156063,467541,311453) : difference with theory (-24) = 1 CORRECTING DEFECT 17 (vertices=113, convex hull=41, v0=112925) After retessellation of defect 17 (v0=112925), euler #=-24 (156077,467600,311499) : difference with theory (-23) = 1 CORRECTING DEFECT 18 (vertices=67, convex hull=97, v0=112928) After retessellation of defect 18 (v0=112928), euler #=-23 (156101,467714,311590) : difference with theory (-22) = 1 CORRECTING DEFECT 19 (vertices=47, convex hull=58, v0=113597) After retessellation of defect 19 (v0=113597), euler #=-22 (156121,467798,311655) : difference with theory (-21) = 1 CORRECTING DEFECT 20 (vertices=16, convex hull=21, v0=113659) After retessellation of defect 20 (v0=113659), euler #=-21 (156124,467812,311667) : difference with theory (-20) = 1 CORRECTING DEFECT 21 (vertices=45, convex hull=54, v0=114007) After retessellation of defect 21 (v0=114007), euler #=-20 (156133,467860,311707) : difference with theory (-19) = 1 CORRECTING DEFECT 22 (vertices=35, convex hull=52, v0=114531) After retessellation of defect 22 (v0=114531), euler #=-19 (156146,467919,311754) : difference with theory (-18) = 1 CORRECTING DEFECT 23 (vertices=40, convex hull=43, v0=115730) After retessellation of defect 23 (v0=115730), euler #=-18 (156158,467972,311796) : difference with theory (-17) = 1 CORRECTING DEFECT 24 (vertices=37, convex hull=34, v0=115779) After retessellation of defect 24 (v0=115779), euler #=-17 (156167,468011,311827) : difference with theory (-16) = 1 CORRECTING DEFECT 25 (vertices=152, convex hull=38, v0=118014) After retessellation of defect 25 (v0=118014), euler #=-16 (156181,468069,311872) : difference with theory (-15) = 1 CORRECTING DEFECT 26 (vertices=14, convex hull=19, v0=119272) After retessellation of defect 26 (v0=119272), euler #=-15 (156184,468084,311885) : difference with theory (-14) = 1 CORRECTING DEFECT 27 (vertices=23, convex hull=55, v0=119275) After retessellation of defect 27 (v0=119275), euler #=-14 (156193,468126,311919) : difference with theory (-13) = 1 CORRECTING DEFECT 28 (vertices=80, convex hull=73, v0=121317) After retessellation of defect 28 (v0=121317), euler #=-12 (156205,468196,311979) : difference with theory (-12) = 0 CORRECTING DEFECT 29 (vertices=33, convex hull=63, v0=121390) After retessellation of defect 29 (v0=121390), euler #=-11 (156217,468254,312026) : difference with theory (-11) = 0 CORRECTING DEFECT 30 (vertices=176, convex hull=205, v0=124687) After retessellation of defect 30 (v0=124687), euler #=-10 (156317,468655,312328) : difference with theory (-10) = 0 CORRECTING DEFECT 31 (vertices=80, convex hull=40, v0=125516) After retessellation of defect 31 (v0=125516), euler #=-9 (156326,468698,312363) : difference with theory (-9) = 0 CORRECTING DEFECT 32 (vertices=90, convex hull=68, v0=127585) After retessellation of defect 32 (v0=127585), euler #=-8 (156339,468775,312428) : difference with theory (-8) = 0 CORRECTING DEFECT 33 (vertices=55, convex hull=80, v0=140335) After retessellation of defect 33 (v0=140335), euler #=-7 (156348,468836,312481) : difference with theory (-7) = 0 CORRECTING DEFECT 34 (vertices=5, convex hull=20, v0=141538) After retessellation of defect 34 (v0=141538), euler #=-6 (156350,468849,312493) : difference with theory (-6) = 0 CORRECTING DEFECT 35 (vertices=30, convex hull=49, v0=145256) After retessellation of defect 35 (v0=145256), euler #=-5 (156359,468896,312532) : difference with theory (-5) = 0 CORRECTING DEFECT 36 (vertices=29, convex hull=71, v0=145577) After retessellation of defect 36 (v0=145577), euler #=-4 (156372,468965,312589) : difference with theory (-4) = 0 CORRECTING DEFECT 37 (vertices=5, convex hull=24, v0=147260) After retessellation of defect 37 (v0=147260), euler #=-3 (156373,468975,312599) : difference with theory (-3) = 0 CORRECTING DEFECT 38 (vertices=31, convex hull=70, v0=150822) After retessellation of defect 38 (v0=150822), euler #=-2 (156382,469029,312645) : difference with theory (-2) = 0 CORRECTING DEFECT 39 (vertices=12, convex hull=22, v0=153325) After retessellation of defect 39 (v0=153325), euler #=-1 (156383,469040,312656) : difference with theory (-1) = 0 CORRECTING DEFECT 40 (vertices=43, convex hull=84, v0=155115) After retessellation of defect 40 (v0=155115), euler #=0 (156398,469122,312724) : difference with theory (0) = 0 CORRECTING DEFECT 41 (vertices=30, convex hull=81, v0=158902) After retessellation of defect 41 (v0=158902), euler #=1 (156408,469184,312777) : difference with theory (1) = 0 CORRECTING DEFECT 42 (vertices=41, convex hull=78, v0=159203) After retessellation of defect 42 (v0=159203), euler #=2 (156435,469299,312866) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->11.40) (max @ vno 64174 --> 77723) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->11.40) (max @ vno 64174 --> 77723) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 147 mutations (35.1%), 272 crossovers (64.9%), 307 vertices were eliminated building final representation... 3055 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=156435, nf=312866, ne=469299, g=0) writing corrected surface to /out/freesurfer/sub-M1215054/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.8 minutes 0 defective edges removing intersecting faces 000: 294 intersecting 001: 2 intersecting mris_fix_topology utimesec 1307.998007 mris_fix_topology stimesec 0.570465 mris_fix_topology ru_maxrss 526772 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 63569 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 34134 mris_fix_topology ru_nivcsw 1419 FSRUNTIME@ mris_fix_topology rh 0.3631 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 156435 - 469299 + 312866 = 2 --> 0 holes F =2V-4: 312866 = 312870-4 (0) 2E=3F: 938598 = 938598 (0) total defect index = 0 /out/freesurfer/sub-M1215054/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 74 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Sep 2 11:54:15 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 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /out/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/rh.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-->5.11) (max @ vno 155333 --> 155358) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.68 +- 0.87 4090 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 = 93.2, mean outside = 78.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=84.0, 40 (40) missing vertices, mean dist 0.1 [0.6 (%44.1)->0.7 (%55.9))] %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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.24 (0.09-->6.02) (max @ vno 155333 --> 155358) face area 0.28 +- 0.13 (0.00-->5.08) mean absolute distance = 0.38 +- 0.66 3954 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2734280.0, rms=8.322 001: dt: 0.5000, sse=1566785.5, rms=5.587 (32.869%) 002: dt: 0.5000, sse=1079036.2, rms=3.887 (30.422%) 003: dt: 0.5000, sse=900660.9, rms=3.035 (21.932%) 004: dt: 0.5000, sse=835550.1, rms=2.659 (12.363%) 005: dt: 0.5000, sse=810986.9, rms=2.510 (5.632%) 006: dt: 0.5000, sse=804305.1, rms=2.451 (2.346%) rms = 2.42, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=798171.2, rms=2.416 (1.411%) 008: dt: 0.2500, sse=711361.9, rms=1.582 (34.515%) 009: dt: 0.2500, sse=700651.2, rms=1.453 (8.153%) rms = 1.42, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=697378.7, rms=1.421 (2.253%) rms = 1.40, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=695430.9, rms=1.398 (1.619%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.3, 42 (9) missing vertices, mean dist -0.2 [0.4 (%68.6)->0.3 (%31.4))] %73 local maxima, %23 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 0.89 +- 0.24 (0.08-->6.17) (max @ vno 155333 --> 155358) face area 0.34 +- 0.16 (0.00-->7.78) mean absolute distance = 0.30 +- 0.46 4843 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1191679.4, rms=3.709 012: dt: 0.5000, sse=932397.1, rms=2.221 (40.126%) 013: dt: 0.5000, sse=879017.6, rms=1.835 (17.358%) 014: dt: 0.5000, sse=870445.8, rms=1.745 (4.946%) rms = 1.84, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=834309.1, rms=1.369 (21.544%) 016: dt: 0.2500, sse=823385.9, rms=1.189 (13.139%) 017: dt: 0.2500, sse=819296.1, rms=1.132 (4.784%) rms = 1.10, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=819254.4, rms=1.102 (2.680%) rms = 1.08, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=813938.8, rms=1.080 (1.947%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.0, 43 (7) missing vertices, mean dist -0.1 [0.3 (%67.0)->0.2 (%33.0))] %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 +- 0.24 (0.06-->6.25) (max @ vno 155333 --> 155358) face area 0.34 +- 0.16 (0.00-->8.44) mean absolute distance = 0.27 +- 0.38 4512 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=953052.3, rms=2.558 020: dt: 0.5000, sse=848435.4, rms=1.642 (35.804%) 021: dt: 0.5000, sse=836997.2, rms=1.555 (5.348%) rms = 1.58, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=804231.9, rms=1.216 (21.779%) 023: dt: 0.2500, sse=793857.9, rms=1.049 (13.746%) rms = 1.03, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=792601.1, rms=1.025 (2.241%) rms = 1.01, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=790073.8, rms=1.006 (1.929%) 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 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.8, 55 (5) missing vertices, mean dist -0.1 [0.3 (%56.2)->0.2 (%43.8))] %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/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=807674.4, rms=1.463 026: dt: 0.5000, sse=792472.7, rms=1.169 (20.144%) rms = 1.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=770621.8, rms=0.933 (20.153%) rms = 0.89, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=783151.8, rms=0.886 (5.002%) rms = 0.84, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=765092.2, rms=0.841 (5.153%) positioning took 0.3 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7813 vertices erasing segment 0 (vno[0] = 43076) erasing segment 2 (vno[0] = 67818) erasing segment 3 (vno[0] = 85746) erasing segment 4 (vno[0] = 90536) erasing segment 5 (vno[0] = 97669) erasing segment 6 (vno[0] = 111022) erasing segment 7 (vno[0] = 111949) erasing segment 8 (vno[0] = 113915) erasing segment 9 (vno[0] = 114888) erasing segment 10 (vno[0] = 121084) erasing segment 11 (vno[0] = 131190) erasing segment 12 (vno[0] = 136778) erasing segment 13 (vno[0] = 156015) writing cortex label to /out/freesurfer/sub-M1215054/label/rh.cortex.label... writing curvature file /out/freesurfer/sub-M1215054/surf/rh.curv writing smoothed area to rh.area writing curvature file /out/freesurfer/sub-M1215054/surf/rh.area vertex spacing 0.88 +- 0.25 (0.02-->6.30) (max @ vno 155283 --> 155292) face area 0.33 +- 0.16 (0.00-->8.96) refinement took 3.1 minutes #-------------------------------------------- #@# Smooth2 rh Thu Sep 2 11:57:20 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Sep 2 11:57:27 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_inflate -rusage /out/freesurfer/sub-M1215054/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.9 mm, total surface area = 92932 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.172 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 42.239770 mris_inflate stimesec 0.604288 mris_inflate ru_maxrss 241184 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34226 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 30511 mris_inflate ru_nivcsw 198 #-------------------------------------------- #@# Curv .H and .K rh Thu Sep 2 11:57:47 UTC 2021 /out/freesurfer/sub-M1215054/surf mris_curvature -w rh.white.preaparc total integrated curvature = 3.649*4pi (45.851) --> -3 handles ICI = 192.1, FI = 1767.2, variation=28649.992 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 196 vertices thresholded to be in k1 ~ [-0.23 2.68], k2 ~ [-0.09 0.05] total integrated curvature = 0.563*4pi (7.077) --> 0 handles ICI = 1.6, FI = 12.1, variation=198.353 152 vertices thresholded to be in [-0.07 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 119 vertices thresholded to be in [-0.13 0.56] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats rh Thu Sep 2 11:58:46 UTC 2021 /out/freesurfer/sub-M1215054/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-M1215054 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-M1215054/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 253 ] Gb_filter = 0 WARN: S lookup min: -0.426216 WARN: S explicit min: 0.000000 vertex = 173 #-------------------------------------------- #@# Sphere rh Thu Sep 2 11:58:53 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_sphere -rusage /out/freesurfer/sub-M1215054/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 3 == scaling brain by 0.273... 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 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.94 pass 1: epoch 2 of 3 starting distance error %19.82 unfolding complete - removing small folds... starting distance error %19.72 removing remaining folds... final distance error %19.73 MRISunfold() return, current seed 1234 -01: dt=0.0000, 130 negative triangles 203: dt=0.9900, 130 negative triangles 204: dt=0.9900, 76 negative triangles 205: dt=0.9900, 67 negative triangles 206: dt=0.9900, 64 negative triangles 207: dt=0.9900, 58 negative triangles 208: dt=0.9900, 53 negative triangles 209: dt=0.9900, 45 negative triangles 210: dt=0.9900, 45 negative triangles 211: dt=0.9900, 46 negative triangles 212: dt=0.9900, 47 negative triangles 213: dt=0.9900, 52 negative triangles 214: dt=0.9900, 50 negative triangles 215: dt=0.9900, 48 negative triangles 216: dt=0.9900, 48 negative triangles 217: dt=0.9900, 52 negative triangles 218: dt=0.9900, 48 negative triangles 219: dt=0.9405, 57 negative triangles 220: dt=0.9405, 50 negative triangles 221: dt=0.9405, 52 negative triangles 222: dt=0.9405, 53 negative triangles 223: dt=0.9405, 50 negative triangles 224: dt=0.9405, 52 negative triangles 225: dt=0.9405, 50 negative triangles 226: dt=0.9405, 54 negative triangles 227: dt=0.9405, 54 negative triangles 228: dt=0.9405, 52 negative triangles 229: dt=0.8935, 53 negative triangles 230: dt=0.8935, 55 negative triangles 231: dt=0.8935, 53 negative triangles 232: dt=0.8935, 53 negative triangles 233: dt=0.8935, 52 negative triangles 234: dt=0.8935, 53 negative triangles 235: dt=0.8935, 54 negative triangles 236: dt=0.8935, 47 negative triangles 237: dt=0.8935, 47 negative triangles 238: dt=0.8935, 51 negative triangles 239: dt=0.8488, 49 negative triangles 240: dt=0.8488, 48 negative triangles 241: dt=0.8488, 42 negative triangles 242: dt=0.8488, 49 negative triangles 243: dt=0.8488, 43 negative triangles 244: dt=0.8488, 51 negative triangles 245: dt=0.8488, 44 negative triangles 246: dt=0.8488, 53 negative triangles 247: dt=0.8488, 46 negative triangles 248: dt=0.8488, 50 negative triangles 249: dt=0.8488, 49 negative triangles 250: dt=0.8488, 43 negative triangles 251: dt=0.8064, 51 negative triangles 252: dt=0.8064, 48 negative triangles 253: dt=0.8064, 44 negative triangles 254: dt=0.8064, 48 negative triangles 255: dt=0.8064, 44 negative triangles 256: dt=0.8064, 45 negative triangles 257: dt=0.8064, 49 negative triangles 258: dt=0.8064, 48 negative triangles 259: dt=0.8064, 46 negative triangles 260: dt=0.8064, 40 negative triangles 261: dt=0.8064, 44 negative triangles 262: dt=0.8064, 42 negative triangles 263: dt=0.8064, 41 negative triangles 264: dt=0.8064, 43 negative triangles 265: dt=0.8064, 41 negative triangles 266: dt=0.8064, 45 negative triangles 267: dt=0.8064, 41 negative triangles 268: dt=0.8064, 41 negative triangles 269: dt=0.8064, 41 negative triangles 270: dt=0.8064, 37 negative triangles 271: dt=0.8064, 40 negative triangles 272: dt=0.8064, 41 negative triangles 273: dt=0.8064, 38 negative triangles 274: dt=0.8064, 40 negative triangles 275: dt=0.8064, 35 negative triangles 276: dt=0.8064, 33 negative triangles 277: dt=0.8064, 34 negative triangles 278: dt=0.8064, 32 negative triangles 279: dt=0.8064, 31 negative triangles 280: dt=0.8064, 32 negative triangles 281: dt=0.8064, 30 negative triangles 282: dt=0.8064, 33 negative triangles 283: dt=0.8064, 28 negative triangles 284: dt=0.8064, 27 negative triangles 285: dt=0.8064, 25 negative triangles 286: dt=0.8064, 20 negative triangles 287: dt=0.8064, 18 negative triangles 288: dt=0.8064, 20 negative triangles 289: dt=0.8064, 22 negative triangles 290: dt=0.8064, 23 negative triangles 291: dt=0.8064, 20 negative triangles 292: dt=0.8064, 18 negative triangles 293: dt=0.8064, 16 negative triangles 294: dt=0.8064, 13 negative triangles 295: dt=0.8064, 13 negative triangles 296: dt=0.8064, 18 negative triangles 297: dt=0.8064, 15 negative triangles 298: dt=0.8064, 12 negative triangles 299: dt=0.8064, 14 negative triangles 300: dt=0.8064, 12 negative triangles 301: dt=0.8064, 11 negative triangles 302: dt=0.8064, 16 negative triangles 303: dt=0.8064, 13 negative triangles 304: dt=0.8064, 8 negative triangles 305: dt=0.8064, 12 negative triangles 306: dt=0.8064, 6 negative triangles 307: dt=0.8064, 5 negative triangles 308: dt=0.8064, 5 negative triangles 309: dt=0.8064, 5 negative triangles 310: dt=0.8064, 4 negative triangles 311: dt=0.8064, 5 negative triangles 312: dt=0.8064, 3 negative triangles 313: dt=0.8064, 2 negative triangles 314: dt=0.8064, 1 negative triangles 315: dt=0.8064, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.35 hours mris_sphere utimesec 3655.859850 mris_sphere stimesec 2.021520 mris_sphere ru_maxrss 336412 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 58096 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 41328 mris_sphere ru_nivcsw 9448 FSRUNTIME@ mris_sphere 0.3524 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Sep 2 12:20:01 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_register -curv -rusage /out/freesurfer/sub-M1215054/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.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.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=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 1 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 rh.sulc curvature mean = -0.000, std = 5.592 curvature mean = 0.016, std = 0.806 curvature mean = 0.024, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 8.00) sse = 286026.4, tmin=1.2036 d=16.00 min @ (4.00, 4.00, 0.00) sse = 238751.3, tmin=1.8516 d=8.00 min @ (0.00, -2.00, 0.00) sse = 234488.1, tmin=2.4728 d=4.00 min @ (1.00, 1.00, 0.00) sse = 231803.7, tmin=3.0893 d=2.00 min @ (-0.50, 0.00, -0.50) sse = 230720.5, tmin=3.7154 d=1.00 min @ (0.25, 0.00, 0.00) sse = 230706.4, tmin=4.3385 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 230668.8, tmin=5.0100 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 5.01 min curvature mean = -0.017, std = 0.820 curvature mean = 0.009, std = 0.945 curvature mean = -0.022, std = 0.829 curvature mean = 0.003, std = 0.978 curvature mean = -0.023, std = 0.830 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.032, std = 0.285 curvature mean = 0.030, std = 0.238 curvature mean = 0.069, std = 0.346 curvature mean = 0.027, std = 0.296 curvature mean = 0.039, std = 0.539 curvature mean = 0.027, std = 0.321 curvature mean = 0.020, std = 0.685 curvature mean = 0.027, std = 0.332 curvature mean = 0.006, std = 0.796 MRISregister() return, current seed 0 -01: dt=0.0000, 60 negative triangles 124: dt=0.9900, 60 negative triangles expanding nbhd size to 1 125: dt=0.9900, 66 negative triangles 126: dt=0.9900, 53 negative triangles 127: dt=0.9900, 47 negative triangles 128: dt=0.9900, 51 negative triangles 129: dt=0.9900, 43 negative triangles 130: dt=0.9900, 45 negative triangles 131: dt=0.9900, 44 negative triangles 132: dt=0.9900, 39 negative triangles 133: dt=0.9900, 37 negative triangles 134: dt=0.9900, 38 negative triangles 135: dt=0.9900, 36 negative triangles 136: dt=0.9900, 39 negative triangles 137: dt=0.9900, 39 negative triangles 138: dt=0.9900, 40 negative triangles 139: dt=0.9900, 39 negative triangles 140: dt=0.9900, 38 negative triangles 141: dt=0.9900, 40 negative triangles 142: dt=0.9900, 41 negative triangles 143: dt=0.9900, 37 negative triangles 144: dt=0.9900, 40 negative triangles 145: dt=0.9900, 34 negative triangles 146: dt=0.9900, 33 negative triangles 147: dt=0.9900, 37 negative triangles 148: dt=0.9900, 33 negative triangles 149: dt=0.9900, 34 negative triangles 150: dt=0.9900, 32 negative triangles 151: dt=0.9900, 31 negative triangles 152: dt=0.9900, 31 negative triangles 153: dt=0.9900, 31 negative triangles 154: dt=0.9900, 31 negative triangles 155: dt=0.9900, 27 negative triangles 156: dt=0.9900, 25 negative triangles 157: dt=0.9900, 27 negative triangles 158: dt=0.9900, 28 negative triangles 159: dt=0.9900, 28 negative triangles 160: dt=0.9900, 25 negative triangles 161: dt=0.9900, 24 negative triangles 162: dt=0.9900, 23 negative triangles 163: dt=0.9900, 19 negative triangles 164: dt=0.9900, 17 negative triangles 165: dt=0.9900, 16 negative triangles 166: dt=0.9900, 18 negative triangles 167: dt=0.9900, 20 negative triangles 168: dt=0.9900, 17 negative triangles 169: dt=0.9900, 16 negative triangles 170: dt=0.9900, 16 negative triangles 171: dt=0.9900, 15 negative triangles 172: dt=0.9900, 18 negative triangles 173: dt=0.9900, 17 negative triangles 174: dt=0.9900, 16 negative triangles 175: dt=0.9900, 13 negative triangles 176: dt=0.9900, 11 negative triangles 177: dt=0.9900, 11 negative triangles 178: dt=0.9900, 11 negative triangles 179: dt=0.9900, 9 negative triangles 180: dt=0.9900, 10 negative triangles 181: dt=0.9900, 8 negative triangles 182: dt=0.9900, 6 negative triangles 183: dt=0.9900, 7 negative triangles 184: dt=0.9900, 4 negative triangles 185: dt=0.9900, 6 negative triangles 186: dt=0.9900, 3 negative triangles 187: dt=0.9900, 2 negative triangles 188: dt=0.9900, 2 negative triangles 189: dt=0.9900, 1 negative triangles 190: dt=0.9900, 2 negative triangles 191: dt=0.9900, 2 negative triangles 192: dt=0.9900, 1 negative triangles 193: dt=0.9900, 2 negative triangles 194: dt=0.9900, 1 negative triangles 195: dt=0.9900, 1 negative triangles 196: dt=0.9900, 1 negative triangles 197: dt=0.9900, 2 negative triangles 198: dt=0.9900, 1 negative triangles 199: dt=0.9405, 1 negative triangles 200: dt=0.9405, 1 negative triangles 201: dt=0.9405, 1 negative triangles 202: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.64 hours mris_register utimesec 5885.125085 mris_register stimesec 4.975554 mris_register ru_maxrss 295244 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 40917 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 1224 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 48519 mris_register ru_nivcsw 16783 FSRUNTIME@ mris_register 0.6378 hours 1 threads #-------------------------------------------- #@# Jacobian white rh Thu Sep 2 12:58:18 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Sep 2 12:58:21 UTC 2021 /out/freesurfer/sub-M1215054/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Sep 2 12:58:24 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-M1215054 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1275 labels changed using aseg relabeling using gibbs priors... 000: 3104 changed, 156435 examined... 001: 736 changed, 13112 examined... 002: 184 changed, 4140 examined... 003: 54 changed, 1097 examined... 004: 28 changed, 350 examined... 005: 14 changed, 174 examined... 006: 6 changed, 73 examined... 007: 0 changed, 22 examined... 192 labels changed using aseg 000: 96 total segments, 57 labels (290 vertices) changed 001: 41 total segments, 2 labels (2 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1359 vertices marked for relabeling... 1359 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 14 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Sep 2 12:58:38 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 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /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/rh.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 = 93.2, mean outside = 78.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.02-->6.30) (max @ vno 155283 --> 155292) face area 0.32 +- 0.16 (0.00-->8.85) mean absolute distance = 0.61 +- 0.85 3402 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 39 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 5 with 187 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=83.9, 93 (92) missing vertices, mean dist 0.4 [0.7 (%17.6)->0.6 (%82.4))] %65 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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->6.62) (max @ vno 155292 --> 155283) face area 0.32 +- 0.15 (0.00-->7.34) mean absolute distance = 0.37 +- 0.65 3445 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2020045.0, rms=6.536 001: dt: 0.5000, sse=1214093.9, rms=4.005 (38.714%) 002: dt: 0.5000, sse=943986.6, rms=2.686 (32.940%) 003: dt: 0.5000, sse=869464.7, rms=2.213 (17.608%) 004: dt: 0.5000, sse=842099.3, rms=2.006 (9.347%) rms = 2.03, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=801606.9, rms=1.569 (21.804%) 006: dt: 0.2500, sse=784395.8, rms=1.338 (14.684%) 007: dt: 0.2500, sse=780087.6, rms=1.282 (4.216%) rms = 1.25, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=778167.6, rms=1.252 (2.338%) rms = 1.23, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=776624.1, rms=1.228 (1.890%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 39 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 155 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=86.2, 52 (28) missing vertices, mean dist -0.2 [0.4 (%68.4)->0.2 (%31.6))] %73 local maxima, %23 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 0.89 +- 0.24 (0.05-->6.74) (max @ vno 155292 --> 155283) face area 0.35 +- 0.17 (0.00-->8.63) mean absolute distance = 0.30 +- 0.47 4909 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1176135.4, rms=3.605 010: dt: 0.5000, sse=923450.7, rms=2.115 (41.321%) 011: dt: 0.5000, sse=870797.8, rms=1.692 (20.032%) 012: dt: 0.5000, sse=861516.3, rms=1.606 (5.034%) rms = 1.72, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=830308.7, rms=1.208 (24.796%) 014: dt: 0.2500, sse=820543.9, rms=1.035 (14.353%) rms = 1.02, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=825284.1, rms=1.017 (1.738%) rms = 1.00, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=835041.4, rms=0.995 (2.091%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 44 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 167 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 14 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 25.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=88.0, 39 (14) missing vertices, mean dist -0.2 [0.3 (%67.4)->0.2 (%32.6))] %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 0.88 +- 0.25 (0.05-->6.83) (max @ vno 155292 --> 155283) face area 0.34 +- 0.17 (0.00-->8.75) mean absolute distance = 0.27 +- 0.38 4492 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=973393.4, rms=2.549 017: dt: 0.5000, sse=844389.1, rms=1.606 (36.989%) 018: dt: 0.5000, sse=833538.2, rms=1.492 (7.115%) rms = 1.52, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=803203.5, rms=1.141 (23.497%) 020: dt: 0.2500, sse=792267.4, rms=0.962 (15.725%) rms = 0.94, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=792518.1, rms=0.945 (1.774%) rms = 0.92, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=788856.6, rms=0.920 (2.670%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 39 points - only 0.00% unknown deleting segment 2 with 19 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 188 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 19 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 25.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=88.8, 62 (12) missing vertices, mean dist -0.1 [0.3 (%56.4)->0.2 (%43.6))] %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/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=806103.2, rms=1.411 023: dt: 0.5000, sse=791406.9, rms=1.107 (21.505%) rms = 1.25, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=772237.4, rms=0.856 (22.710%) rms = 0.81, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=770435.9, rms=0.809 (5.502%) 026: dt: 0.1250, sse=768466.6, rms=0.758 (6.306%) rms = 0.74, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=766478.2, rms=0.736 (2.865%) positioning took 0.4 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7797 vertices erasing segment 0 (vno[0] = 44192) erasing segment 2 (vno[0] = 67818) erasing segment 3 (vno[0] = 88361) erasing segment 4 (vno[0] = 90536) erasing segment 5 (vno[0] = 97669) erasing segment 6 (vno[0] = 98005) erasing segment 7 (vno[0] = 111022) erasing segment 8 (vno[0] = 111949) erasing segment 9 (vno[0] = 113915) erasing segment 10 (vno[0] = 114888) erasing segment 11 (vno[0] = 121084) erasing segment 12 (vno[0] = 137496) erasing segment 13 (vno[0] = 156015) writing cortex label to /out/freesurfer/sub-M1215054/label/rh.cortex.label... writing curvature file /out/freesurfer/sub-M1215054/surf/rh.curv writing smoothed area to rh.area writing curvature file /out/freesurfer/sub-M1215054/surf/rh.area vertex spacing 0.88 +- 0.25 (0.02-->6.82) (max @ vno 155283 --> 155292) face area 0.33 +- 0.16 (0.00-->8.73) 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 39 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=63.1, 101 (101) missing vertices, mean dist 1.5 [0.0 (%0.0)->2.7 (%100.0))] % 8 local maxima, %43 large gradients and %45 min vals, 337 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=21681724.0, rms=26.417 001: dt: 0.0500, sse=19378992.0, rms=24.924 (5.654%) 002: dt: 0.0500, sse=17757592.0, rms=23.816 (4.445%) 003: dt: 0.0500, sse=16518046.0, rms=22.933 (3.709%) 004: dt: 0.0500, sse=15511958.0, rms=22.190 (3.239%) 005: dt: 0.0500, sse=14658023.0, rms=21.539 (2.932%) 006: dt: 0.0500, sse=13911698.0, rms=20.954 (2.717%) 007: dt: 0.0500, sse=13244273.0, rms=20.416 (2.566%) 008: dt: 0.0500, sse=12638881.0, rms=19.916 (2.450%) 009: dt: 0.0500, sse=12082061.0, rms=19.444 (2.368%) 010: dt: 0.0500, sse=11565459.0, rms=18.996 (2.304%) positioning took 0.6 minutes mean border=62.8, 72 (45) missing vertices, mean dist 1.2 [0.1 (%0.0)->2.2 (%100.0))] % 9 local maxima, %43 large gradients and %44 min vals, 306 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=12325077.0, rms=19.649 011: dt: 0.0500, sse=11835300.0, rms=19.229 (2.137%) 012: dt: 0.0500, sse=11375805.0, rms=18.827 (2.093%) 013: dt: 0.0500, sse=10942712.0, rms=18.439 (2.058%) 014: dt: 0.0500, sse=10533999.0, rms=18.066 (2.025%) 015: dt: 0.0500, sse=10147306.0, rms=17.705 (1.996%) 016: dt: 0.0500, sse=9782222.0, rms=17.358 (1.962%) 017: dt: 0.0500, sse=9437222.0, rms=17.023 (1.929%) 018: dt: 0.0500, sse=9110967.0, rms=16.700 (1.897%) 019: dt: 0.0500, sse=8801873.0, rms=16.388 (1.867%) 020: dt: 0.0500, sse=8508752.0, rms=16.087 (1.839%) positioning took 0.6 minutes mean border=62.7, 73 (33) missing vertices, mean dist 1.0 [0.1 (%0.8)->1.9 (%99.2))] % 9 local maxima, %43 large gradients and %44 min vals, 308 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=8600748.0, rms=16.187 021: dt: 0.0500, sse=8305756.5, rms=15.880 (1.898%) 022: dt: 0.0500, sse=8029744.0, rms=15.587 (1.845%) 023: dt: 0.0500, sse=7768327.5, rms=15.304 (1.814%) 024: dt: 0.0500, sse=7522417.0, rms=15.033 (1.770%) 025: dt: 0.0500, sse=7290332.0, rms=14.773 (1.732%) 026: dt: 0.0500, sse=7071535.0, rms=14.523 (1.691%) 027: dt: 0.0500, sse=6864236.5, rms=14.282 (1.658%) 028: dt: 0.0500, sse=6666324.0, rms=14.048 (1.637%) 029: dt: 0.0500, sse=6476204.5, rms=13.820 (1.626%) 030: dt: 0.0500, sse=6293458.0, rms=13.597 (1.615%) positioning took 0.6 minutes mean border=62.6, 90 (26) missing vertices, mean dist 0.8 [0.1 (%9.4)->1.7 (%90.6))] % 9 local maxima, %43 large gradients and %44 min vals, 306 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=6417307.5, rms=13.747 031: dt: 0.5000, sse=5092267.5, rms=12.026 (12.518%) 032: dt: 0.5000, sse=4198895.5, rms=10.704 (10.994%) 033: dt: 0.5000, sse=3461991.2, rms=9.476 (11.474%) 034: dt: 0.5000, sse=2938182.8, rms=8.490 (10.402%) 035: dt: 0.5000, sse=2541419.5, rms=7.658 (9.798%) 036: dt: 0.5000, sse=2237024.8, rms=6.948 (9.266%) 037: dt: 0.5000, sse=2008381.6, rms=6.367 (8.375%) 038: dt: 0.5000, sse=1842172.0, rms=5.903 (7.281%) 039: dt: 0.5000, sse=1722547.6, rms=5.550 (5.985%) 040: dt: 0.5000, sse=1659458.4, rms=5.348 (3.641%) 041: dt: 0.5000, sse=1601281.4, rms=5.160 (3.504%) 042: dt: 0.5000, sse=1586892.2, rms=5.107 (1.025%) 043: dt: 0.5000, sse=1552172.1, rms=4.993 (2.236%) rms = 4.98, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=1550444.2, rms=4.982 (0.216%) 045: dt: 0.2500, sse=1383739.9, rms=4.342 (12.862%) 046: dt: 0.2500, sse=1324807.0, rms=4.110 (5.340%) rms = 4.21, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=1282909.4, rms=3.932 (4.325%) 048: dt: 0.1250, sse=1226150.9, rms=3.677 (6.484%) 049: dt: 0.1250, sse=1212839.8, rms=3.615 (1.694%) rms = 3.60, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1209815.8, rms=3.600 (0.398%) positioning took 1.7 minutes mean border=61.8, 2702 (8) missing vertices, mean dist 0.1 [0.2 (%54.2)->0.5 (%45.8))] %16 local maxima, %36 large gradients and %42 min vals, 144 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=1523097.0, rms=4.284 rms = 4.97, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1376267.9, rms=3.653 (14.742%) rms = 3.73, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=1347629.2, rms=3.514 (3.784%) 053: dt: 0.1250, sse=1301141.8, rms=3.276 (6.783%) 054: dt: 0.1250, sse=1279619.9, rms=3.160 (3.524%) 055: dt: 0.1250, sse=1263003.2, rms=3.072 (2.813%) 056: dt: 0.1250, sse=1252196.2, rms=3.013 (1.897%) rms = 2.97, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1245072.2, rms=2.975 (1.277%) positioning took 0.8 minutes mean border=61.2, 3079 (8) missing vertices, mean dist 0.1 [0.2 (%52.3)->0.4 (%47.7))] %23 local maxima, %29 large gradients and %42 min vals, 200 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=1282643.2, rms=3.200 rms = 4.69, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1244728.9, rms=2.993 (6.453%) rms = 3.26, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1234633.0, rms=2.935 (1.928%) rms = 2.89, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1225665.8, rms=2.886 (1.695%) positioning took 0.4 minutes mean border=60.8, 5984 (7) missing vertices, mean dist 0.1 [0.2 (%50.5)->0.4 (%49.5))] %28 local maxima, %24 large gradients and %40 min vals, 209 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/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1252178.9, rms=3.023 rms = 4.41, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1225472.0, rms=2.872 (5.005%) rms = 3.09, time step reduction 2 of 3 to 0.125... 062: dt: 0.1250, sse=1215306.1, rms=2.812 (2.083%) 063: dt: 0.1250, sse=1202884.0, rms=2.743 (2.461%) rms = 2.73, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1201045.1, rms=2.735 (0.296%) positioning took 0.5 minutes writing curvature file /out/freesurfer/sub-M1215054/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /out/freesurfer/sub-M1215054/surf/rh.area.pial vertex spacing 0.98 +- 0.41 (0.08-->6.52) (max @ vno 59302 --> 58134) face area 0.38 +- 0.28 (0.00-->6.50) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 156435 vertices processed 25000 of 156435 vertices processed 50000 of 156435 vertices processed 75000 of 156435 vertices processed 100000 of 156435 vertices processed 125000 of 156435 vertices processed 150000 of 156435 vertices processed 0 of 156435 vertices processed 25000 of 156435 vertices processed 50000 of 156435 vertices processed 75000 of 156435 vertices processed 100000 of 156435 vertices processed 125000 of 156435 vertices processed 150000 of 156435 vertices processed thickness calculation complete, 341:759 truncations. 43640 vertices at 0 distance 117659 vertices at 1 distance 86483 vertices at 2 distance 34452 vertices at 3 distance 11692 vertices at 4 distance 3992 vertices at 5 distance 1383 vertices at 6 distance 475 vertices at 7 distance 183 vertices at 8 distance 86 vertices at 9 distance 71 vertices at 10 distance 48 vertices at 11 distance 45 vertices at 12 distance 40 vertices at 13 distance 26 vertices at 14 distance 9 vertices at 15 distance 12 vertices at 16 distance 17 vertices at 17 distance 12 vertices at 18 distance 5 vertices at 19 distance 16 vertices at 20 distance writing curvature file /out/freesurfer/sub-M1215054/surf/rh.thickness positioning took 9.6 minutes #-------------------------------------------- #@# Surf Volume rh Thu Sep 2 13:08:15 UTC 2021 /out/freesurfer/sub-M1215054/surf /out/freesurfer/sub-M1215054/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-M1215054 rh /out/freesurfer/sub-M1215054/surf/rh.volume masking with /out/freesurfer/sub-M1215054/label/rh.cortex.label Total face volume 260458 Total vertex volume 256508 (mask=0) #@# sub-M1215054 rh 256508 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 rh Thu Sep 2 13:08:24 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-M1215054 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 147 labels changed using aseg relabeling using gibbs priors... 000: 10047 changed, 156435 examined... 001: 2189 changed, 39584 examined... 002: 662 changed, 11622 examined... 003: 319 changed, 3761 examined... 004: 144 changed, 1779 examined... 005: 70 changed, 842 examined... 006: 34 changed, 389 examined... 007: 20 changed, 192 examined... 008: 7 changed, 112 examined... 009: 8 changed, 43 examined... 010: 2 changed, 45 examined... 011: 1 changed, 16 examined... 012: 0 changed, 6 examined... 62 labels changed using aseg 000: 319 total segments, 230 labels (3061 vertices) changed 001: 97 total segments, 10 labels (51 vertices) changed 002: 87 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... 900 vertices marked for relabeling... 900 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Sep 2 13:08:40 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-M1215054 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1855 labels changed using aseg relabeling using gibbs priors... 000: 2183 changed, 156435 examined... 001: 494 changed, 10092 examined... 002: 130 changed, 2744 examined... 003: 53 changed, 776 examined... 004: 23 changed, 310 examined... 005: 12 changed, 118 examined... 006: 9 changed, 73 examined... 007: 13 changed, 62 examined... 008: 10 changed, 60 examined... 009: 8 changed, 55 examined... 010: 5 changed, 45 examined... 011: 4 changed, 32 examined... 012: 4 changed, 13 examined... 013: 0 changed, 23 examined... 332 labels changed using aseg 000: 66 total segments, 33 labels (579 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 394 vertices marked for relabeling... 394 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# WM/GM Contrast rh Thu Sep 2 13:08:56 UTC 2021 /out/freesurfer/sub-M1215054/scripts pctsurfcon --s sub-M1215054 --rh-only Log file is /out/freesurfer/sub-M1215054/scripts/pctsurfcon.log Thu Sep 2 13:08:56 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 rh --noreshape --interp trilinear --projdist -1 --o /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20712/rh.wm.mgh --regheader sub-M1215054 --cortex srcvol = /out/freesurfer/sub-M1215054/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /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/rh.cortex.label Reading surface /out/freesurfer/sub-M1215054/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 61407 Masking with /out/freesurfer/sub-M1215054/label/rh.cortex.label Writing to /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20712/rh.wm.mgh Dim: 156435 1 1 mri_vol2surf --mov /out/freesurfer/sub-M1215054/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20712/rh.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 = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /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/rh.cortex.label Reading surface /out/freesurfer/sub-M1215054/surf/rh.white Done reading source surface Reading thickness /out/freesurfer/sub-M1215054/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 73410 Masking with /out/freesurfer/sub-M1215054/label/rh.cortex.label Writing to /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20712/rh.gm.mgh Dim: 156435 1 1 mri_concat /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20712/rh.wm.mgh /out/freesurfer/sub-M1215054/surf/tmp.pctsurfcon.20712/rh.gm.mgh --paired-diff-norm --mul 100 --o /out/freesurfer/sub-M1215054/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /out/freesurfer/sub-M1215054/surf/rh.w-g.pct.mgh mri_segstats --in /out/freesurfer/sub-M1215054/surf/rh.w-g.pct.mgh --annot sub-M1215054 rh aparc --sum /out/freesurfer/sub-M1215054/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /out/freesurfer/sub-M1215054/surf/rh.w-g.pct.mgh --annot sub-M1215054 rh aparc --sum /out/freesurfer/sub-M1215054/stats/rh.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/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /out/freesurfer/sub-M1215054/surf/rh.w-g.pct.mgh Vertex Area is 0.649429 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 11:29:51 UTC 2021 Ended at Thu Sep 2 13:09:12 UTC 2021 #@#%# recon-all-run-time-hours 1.656 recon-all -s sub-M1215054 finished without error at Thu Sep 2 13:09:12 UTC 2021 New invocation of recon-all Thu Sep 2 13:30:26 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -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 1683772 2036668 189624 2181624 3711540 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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:26-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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: 2021/09/02-13:30:27-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 rh Thu Sep 2 13:30:27 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-M1215054 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/rh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 260458 Total vertex volume 256508 (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 1671 1163 2834 2.575 0.434 0.104 0.019 11 1.3 bankssts 976 621 1896 2.474 0.707 0.136 0.023 16 0.8 caudalanteriorcingulate 4541 2909 7676 2.410 0.561 0.103 0.022 39 4.2 caudalmiddlefrontal 2712 1743 3400 1.864 0.459 0.153 0.039 41 4.3 cuneus 567 402 2016 4.003 0.660 0.111 0.023 3 0.6 entorhinal 4232 2922 9041 2.716 0.653 0.143 0.036 59 6.0 fusiform 8503 5601 15304 2.451 0.576 0.123 0.030 99 9.8 inferiorparietal 5086 3333 10428 2.723 0.690 0.121 0.032 63 6.5 inferiortemporal 1503 963 2969 2.557 0.912 0.129 0.032 21 1.8 isthmuscingulate 8482 5213 11229 2.050 0.606 0.133 0.034 104 11.9 lateraloccipital 5399 3529 9678 2.613 0.876 0.133 0.038 69 8.3 lateralorbitofrontal 6344 4171 9581 2.167 0.638 0.141 0.035 75 9.0 lingual 3263 2185 6554 2.633 0.721 0.141 0.039 64 5.1 medialorbitofrontal 5459 3628 11613 2.790 0.591 0.117 0.028 62 5.9 middletemporal 872 550 2145 3.308 0.806 0.102 0.026 7 0.7 parahippocampal 2461 1538 3535 2.128 0.524 0.117 0.024 20 2.3 paracentral 2728 1787 5346 2.655 0.596 0.117 0.030 33 3.6 parsopercularis 1346 838 2605 2.644 0.683 0.145 0.036 20 1.8 parsorbitalis 2214 1409 3996 2.576 0.660 0.116 0.024 23 2.1 parstriangularis 2871 1908 2556 1.498 0.345 0.138 0.032 32 3.7 pericalcarine 7559 4607 9619 1.966 0.678 0.105 0.024 65 7.4 postcentral 1907 1248 3608 2.493 0.778 0.132 0.027 27 2.1 posteriorcingulate 8414 5335 12653 2.335 0.579 0.114 0.026 68 8.8 precentral 6950 4664 11763 2.371 0.661 0.123 0.028 71 7.6 precuneus 714 430 1370 2.902 0.572 0.144 0.052 14 1.8 rostralanteriorcingulate 9420 6301 16606 2.294 0.582 0.138 0.037 137 14.0 rostralmiddlefrontal 12331 8145 23788 2.646 0.649 0.125 0.030 137 14.7 superiorfrontal 9460 5953 13212 2.073 0.498 0.117 0.027 96 10.3 superiorparietal 6883 4172 13214 2.875 0.694 0.101 0.025 65 6.6 superiortemporal 7772 4920 14582 2.752 0.588 0.122 0.029 88 9.0 supramarginal 534 329 866 2.243 0.667 0.169 0.064 13 1.6 frontalpole 618 412 1814 3.135 0.751 0.130 0.039 9 1.1 temporalpole 698 424 1101 2.286 0.540 0.123 0.038 7 0.9 transversetemporal 3701 2437 7856 3.269 0.780 0.118 0.036 34 6.2 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-M1215054 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input pial surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 260458 Total vertex volume 256508 (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 1671 1006 2834 2.575 0.434 0.107 0.027 20 1.8 bankssts 976 788 1896 2.474 0.707 0.136 0.030 22 1.0 caudalanteriorcingulate 4541 3453 7676 2.410 0.561 0.119 0.024 42 5.2 caudalmiddlefrontal 2712 2041 3400 1.864 0.459 0.133 0.033 31 3.7 cuneus 567 604 2016 4.003 0.660 0.162 0.035 9 0.9 entorhinal 4232 3615 9041 2.716 0.653 0.144 0.033 61 6.3 fusiform 8503 6819 15304 2.451 0.576 0.136 0.029 96 11.1 inferiorparietal 5086 4325 10428 2.723 0.690 0.138 0.028 59 6.8 inferiortemporal 1503 1246 2969 2.557 0.912 0.141 0.036 38 2.3 isthmuscingulate 8482 5911 11229 2.050 0.606 0.127 0.030 107 12.1 lateraloccipital 5399 3924 9678 2.613 0.876 0.137 0.035 78 8.7 lateralorbitofrontal 6344 4830 9581 2.167 0.638 0.135 0.035 97 9.8 lingual 3263 2743 6554 2.633 0.721 0.146 0.035 72 5.1 medialorbitofrontal 5459 4716 11613 2.790 0.591 0.133 0.027 51 7.1 middletemporal 872 709 2145 3.308 0.806 0.117 0.024 8 0.9 parahippocampal 2461 1803 3535 2.128 0.524 0.123 0.025 22 2.7 paracentral 2728 2289 5346 2.655 0.596 0.137 0.029 26 3.8 parsopercularis 1346 1169 2605 2.644 0.683 0.153 0.033 18 2.0 parsorbitalis 2214 1728 3996 2.576 0.660 0.132 0.030 35 3.0 parstriangularis 2871 1664 2556 1.498 0.345 0.111 0.026 34 3.3 pericalcarine 7559 5410 9619 1.966 0.678 0.111 0.023 67 7.9 postcentral 1907 1566 3608 2.493 0.778 0.149 0.034 32 2.8 posteriorcingulate 8414 5527 12653 2.335 0.579 0.111 0.029 156 11.5 precentral 6950 5154 11763 2.371 0.661 0.130 0.030 90 9.1 precuneus 714 561 1370 2.902 0.572 0.154 0.041 10 1.3 rostralanteriorcingulate 9420 8133 16606 2.294 0.582 0.161 0.036 129 16.7 rostralmiddlefrontal 12331 9579 23788 2.646 0.649 0.138 0.034 140 18.7 superiorfrontal 9460 6840 13212 2.073 0.498 0.120 0.025 91 10.5 superiorparietal 6883 5049 13214 2.875 0.694 0.119 0.027 70 8.8 superiortemporal 7772 5663 14582 2.752 0.588 0.124 0.030 90 10.4 supramarginal 534 450 866 2.243 0.667 0.189 0.049 9 1.4 frontalpole 618 731 1814 3.135 0.751 0.197 0.039 6 1.4 temporalpole 698 525 1101 2.286 0.540 0.117 0.028 4 0.8 transversetemporal 3701 2235 7856 3.269 0.780 0.133 0.037 69 6.0 insula #----------------------------------------- #@# Parcellation Stats 2 rh Thu Sep 2 13:31:53 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-M1215054 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/rh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 260458 Total vertex volume 256508 (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 1276 842 2010 2.180 0.555 0.142 0.040 16 2.2 G&S_frontomargin 1417 932 2332 2.369 0.710 0.136 0.033 17 1.8 G&S_occipital_inf 1489 856 2060 2.006 0.493 0.119 0.031 16 1.8 G&S_paracentral 1922 1212 3290 2.604 0.628 0.125 0.033 22 2.7 G&S_subcentral 1393 889 2647 2.451 0.706 0.159 0.058 32 3.4 G&S_transv_frontopol 3503 2277 6735 2.746 0.581 0.132 0.035 55 5.0 G&S_cingul-Ant 1424 980 2917 2.768 0.620 0.117 0.023 14 1.3 G&S_cingul-Mid-Ant 1477 995 2895 2.619 0.631 0.121 0.025 14 1.4 G&S_cingul-Mid-Post 692 465 1875 2.961 0.711 0.172 0.051 14 1.6 G_cingul-Post-dorsal 314 184 898 3.220 0.807 0.110 0.027 3 0.2 G_cingul-Post-ventral 2515 1610 3082 1.761 0.475 0.149 0.037 37 3.8 G_cuneus 2077 1286 4633 2.767 0.629 0.119 0.037 28 3.1 G_front_inf-Opercular 496 308 1005 2.345 0.556 0.151 0.039 9 0.8 G_front_inf-Orbital 921 539 2041 2.749 0.627 0.132 0.036 16 1.4 G_front_inf-Triangul 5276 3311 10819 2.420 0.611 0.140 0.039 90 8.7 G_front_middle 7907 5022 16134 2.631 0.671 0.134 0.035 103 10.7 G_front_sup 659 446 1620 3.361 0.719 0.130 0.037 8 0.9 G_Ins_lg&S_cent_ins 852 467 2425 3.535 0.917 0.114 0.047 12 1.6 G_insular_short 3254 2009 5647 2.380 0.625 0.137 0.034 47 4.3 G_occipital_middle 1752 999 2165 1.879 0.442 0.125 0.032 20 2.3 G_occipital_sup 1929 1288 4635 2.866 0.616 0.156 0.040 33 3.0 G_oc-temp_lat-fusifor 3974 2550 6450 2.111 0.668 0.143 0.038 51 5.9 G_oc-temp_med-Lingual 1305 849 4070 3.617 0.811 0.120 0.034 13 1.6 G_oc-temp_med-Parahip 3556 2165 7341 2.666 0.931 0.145 0.045 62 6.5 G_orbital 3361 2047 7598 2.658 0.553 0.134 0.041 57 4.9 G_pariet_inf-Angular 4201 2522 8770 2.877 0.620 0.127 0.033 58 5.7 G_pariet_inf-Supramar 3342 2056 5041 2.074 0.504 0.127 0.033 43 4.5 G_parietal_sup 2857 1561 3458 1.840 0.537 0.104 0.025 28 3.0 G_postcentral 3274 1843 5525 2.448 0.513 0.106 0.029 29 3.6 G_precentral 3105 1990 6120 2.446 0.614 0.128 0.033 39 4.0 G_precuneus 919 629 2367 2.670 0.765 0.154 0.054 25 2.3 G_rectus 412 263 687 2.534 0.943 0.079 0.030 4 0.2 G_subcallosal 593 346 1036 2.319 0.534 0.118 0.031 7 0.6 G_temp_sup-G_T_transv 2333 1277 5383 3.181 0.713 0.120 0.037 31 3.4 G_temp_sup-Lateral 869 585 2068 3.330 0.691 0.094 0.024 5 1.0 G_temp_sup-Plan_polar 1383 800 2436 2.637 0.478 0.104 0.032 14 1.5 G_temp_sup-Plan_tempo 2783 1731 6249 2.764 0.685 0.130 0.038 46 4.1 G_temporal_inf 3303 2115 8011 2.954 0.592 0.135 0.037 51 4.7 G_temporal_middle 383 263 446 2.170 0.447 0.103 0.018 2 0.3 Lat_Fis-ant-Horizont 329 216 621 3.084 0.607 0.103 0.013 2 0.2 Lat_Fis-ant-Vertical 1748 1182 2574 2.660 0.536 0.111 0.023 11 1.6 Lat_Fis-post 4319 2549 4731 1.805 0.543 0.138 0.040 57 7.3 Pole_occipital 1841 1268 4931 2.906 0.742 0.155 0.049 33 4.1 Pole_temporal 3064 2106 3644 1.946 0.784 0.140 0.031 33 4.1 S_calcarine 3107 2179 3165 1.688 0.485 0.118 0.025 22 3.2 S_central 1459 970 2076 2.115 0.547 0.120 0.026 15 1.3 S_cingul-Marginalis 688 475 1229 3.473 0.807 0.113 0.023 4 0.7 S_circular_insula_ant 1321 896 2215 3.072 0.727 0.082 0.025 5 2.0 S_circular_insula_inf 1644 1138 2763 3.057 0.426 0.102 0.018 8 1.2 S_circular_insula_sup 1310 940 2188 2.416 0.625 0.104 0.014 8 0.8 S_collat_transv_ant 523 373 588 2.030 0.460 0.157 0.034 6 0.8 S_collat_transv_post 1844 1277 2569 2.223 0.510 0.098 0.016 10 1.1 S_front_inf 2491 1751 3739 2.149 0.483 0.123 0.024 25 2.2 S_front_middle 3843 2631 5741 2.415 0.575 0.102 0.020 23 3.2 S_front_sup 679 460 861 2.393 0.453 0.132 0.029 6 0.8 S_interm_prim-Jensen 3421 2349 4803 2.154 0.466 0.112 0.022 26 2.9 S_intrapariet&P_trans 1067 746 1157 1.871 0.464 0.119 0.021 8 1.0 S_oc_middle&Lunatus 1549 1029 1780 1.991 0.427 0.108 0.025 11 1.5 S_oc_sup&transversal 634 440 1044 2.361 0.498 0.080 0.012 2 0.2 S_occipital_ant 895 629 1495 2.568 0.662 0.106 0.017 6 0.7 S_oc-temp_lat 1928 1313 3193 2.751 0.563 0.119 0.023 15 1.7 S_oc-temp_med&Lingual 428 300 577 2.225 0.462 0.117 0.020 3 0.4 S_orbital_lateral 893 637 1205 2.214 0.546 0.101 0.014 6 0.3 S_orbital_med-olfact 1915 1297 3115 2.561 0.659 0.138 0.037 21 2.9 S_orbital-H_Shaped 2558 1720 3269 2.114 0.603 0.115 0.023 20 2.4 S_parieto_occipital 1265 748 972 1.794 0.646 0.131 0.021 22 0.8 S_pericallosal 3247 2174 4278 2.253 0.558 0.101 0.019 18 2.4 S_postcentral 1672 1159 2668 2.451 0.485 0.114 0.020 14 1.4 S_precentral-inf-part 1669 1182 2130 2.131 0.462 0.109 0.018 10 1.3 S_precentral-sup-part 424 299 882 3.081 0.865 0.151 0.025 5 0.5 S_suborbital 1548 1067 2370 2.352 0.509 0.124 0.026 14 1.5 S_subparietal 1407 970 2044 2.456 0.549 0.109 0.019 9 1.1 S_temporal_inf 6622 4565 10457 2.476 0.477 0.095 0.015 38 4.1 S_temporal_sup 383 269 514 2.600 0.452 0.157 0.029 5 0.5 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 rh Thu Sep 2 13:32:39 UTC 2021 /out/freesurfer/sub-M1215054/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-M1215054 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/rh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 260458 Total vertex volume 256508 (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 1235 784 2512 2.553 0.723 0.137 0.024 20 1.0 caudalanteriorcingulate 4770 3061 7964 2.397 0.558 0.104 0.022 40 4.4 caudalmiddlefrontal 3272 2097 4069 1.872 0.468 0.146 0.036 45 4.8 cuneus 532 377 1914 4.016 0.602 0.110 0.023 3 0.6 entorhinal 3780 2617 7996 2.727 0.629 0.141 0.033 51 4.9 fusiform 8582 5631 15395 2.443 0.575 0.124 0.030 101 10.0 inferiorparietal 5509 3625 11405 2.711 0.709 0.124 0.033 69 7.6 inferiortemporal 1453 934 2875 2.598 0.897 0.123 0.027 17 1.4 isthmuscingulate 8544 5229 11151 2.033 0.601 0.134 0.035 106 12.1 lateraloccipital 5692 3701 10463 2.580 0.855 0.143 0.043 84 10.5 lateralorbitofrontal 6275 4129 9443 2.155 0.633 0.141 0.035 74 8.8 lingual 2368 1614 4929 2.620 0.810 0.136 0.040 47 3.8 medialorbitofrontal 6788 4552 14080 2.753 0.577 0.116 0.027 74 7.2 middletemporal 929 587 2259 3.308 0.815 0.101 0.025 7 0.7 parahippocampal 2560 1614 3743 2.130 0.525 0.117 0.024 20 2.4 paracentral 2966 1921 5868 2.706 0.584 0.119 0.031 37 3.9 parsopercularis 1272 802 2455 2.639 0.584 0.133 0.031 15 1.5 parsorbitalis 2107 1367 3603 2.514 0.651 0.116 0.024 21 2.1 parstriangularis 2804 1850 2482 1.490 0.333 0.136 0.032 30 3.6 pericalcarine 8450 5201 10749 1.988 0.672 0.109 0.025 76 8.6 postcentral 1991 1297 3713 2.466 0.786 0.134 0.031 30 2.5 posteriorcingulate 8119 5158 12448 2.356 0.581 0.114 0.027 66 8.5 precentral 7256 4826 12333 2.371 0.658 0.124 0.029 76 8.3 precuneus 974 593 1777 2.892 0.601 0.136 0.046 17 2.0 rostralanteriorcingulate 6561 4392 11305 2.275 0.549 0.137 0.035 93 9.1 rostralmiddlefrontal 15857 10449 29761 2.566 0.659 0.129 0.033 196 20.8 superiorfrontal 7718 4892 10974 2.087 0.491 0.116 0.027 77 8.2 superiorparietal 8523 5270 16827 2.880 0.678 0.104 0.026 81 8.6 superiortemporal 7288 4595 13574 2.761 0.585 0.120 0.028 80 8.3 supramarginal 698 425 1104 2.275 0.541 0.124 0.038 7 0.9 transversetemporal 3360 2221 7336 3.349 0.779 0.112 0.033 28 4.9 insula /out/freesurfer/sub-M1215054/label #-------------------------------------------- #@# BA_exvivo Labels rh Thu Sep 2 13:33:25 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 565 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 883 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7570 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 379 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4901 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 407 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4679 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 1603 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13859 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 1242 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 996 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6351 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 2684 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 7411 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 4403 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 12419 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 599 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2531 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 136 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1174 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-M1215054 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 835 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1025 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3055 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1778 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1457 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1554 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 858 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7817 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 479 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1491 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1374 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 1800 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 5032 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 2102 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5539 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 318 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-M1215054 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-M1215054 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-M1215054/surf/rh.white Reading target registration /out/freesurfer/sub-M1215054/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 156435 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 329 mri_label2label: Done mris_label2annot --s sub-M1215054 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /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 rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname 9e1e1df09144 machine x86_64 user root subject sub-M1215054 hemi rh 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/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 108401 unhit vertices Writing annot to /out/freesurfer/sub-M1215054/label/rh.BA_exvivo.annot mris_label2annot --s sub-M1215054 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /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 rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname 9e1e1df09144 machine x86_64 user root subject sub-M1215054 hemi rh 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/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 128939 unhit vertices Writing annot to /out/freesurfer/sub-M1215054/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-M1215054 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/rh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 260458 Total vertex volume 256508 (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 1237 606 1523 1.923 0.552 0.107 0.028 13 1.3 BA1_exvivo 4223 2715 5652 2.108 0.560 0.105 0.022 30 3.6 BA2_exvivo 1142 758 970 1.686 0.387 0.143 0.036 12 1.4 BA3a_exvivo 2197 1362 2193 1.515 0.439 0.103 0.024 19 2.5 BA3b_exvivo 1562 959 2305 2.168 0.455 0.099 0.021 9 1.3 BA4a_exvivo 1182 833 1568 2.022 0.475 0.116 0.026 8 1.3 BA4p_exvivo 9447 5915 15821 2.421 0.608 0.116 0.027 86 9.6 BA6_exvivo 4536 2960 7982 2.600 0.565 0.116 0.027 45 5.0 BA44_exvivo 4107 2670 7723 2.541 0.649 0.128 0.031 51 5.2 BA45_exvivo 5116 3239 5240 1.607 0.450 0.139 0.035 62 7.7 V1_exvivo 9873 6310 12989 2.005 0.587 0.145 0.038 128 15.2 V2_exvivo 2357 1573 3360 2.157 0.514 0.114 0.022 20 2.2 MT_exvivo 633 436 2147 3.852 0.806 0.129 0.041 9 0.9 perirhinal_exvivo 422 277 1317 3.756 0.535 0.124 0.033 4 0.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-M1215054 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /out/freesurfer/sub-M1215054/mri/wm.mgz... reading input surface /out/freesurfer/sub-M1215054/surf/rh.white... reading input pial surface /out/freesurfer/sub-M1215054/surf/rh.pial... reading input white surface /out/freesurfer/sub-M1215054/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 260458 Total vertex volume 256508 (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 1454060.000 836 421 927 1.760 0.479 0.109 0.027 9 0.9 BA1_exvivo 2423 1494 3235 2.039 0.524 0.092 0.018 14 1.8 BA2_exvivo 990 666 778 1.657 0.358 0.149 0.038 11 1.3 BA3a_exvivo 1665 1104 1547 1.407 0.324 0.099 0.020 13 1.5 BA3b_exvivo 985 559 1349 2.117 0.459 0.107 0.024 8 0.9 BA4a_exvivo 996 720 1322 1.993 0.485 0.112 0.025 6 1.0 BA4p_exvivo 5957 3667 9464 2.345 0.591 0.112 0.026 51 5.9 BA6_exvivo 1381 890 2833 2.632 0.614 0.128 0.038 19 2.4 BA44_exvivo 1139 705 2601 2.888 0.624 0.120 0.031 16 1.5 BA45_exvivo 4857 3092 4866 1.587 0.439 0.137 0.035 58 7.0 V1_exvivo 5338 3457 6873 1.908 0.547 0.154 0.042 77 9.3 V2_exvivo 298 210 481 2.035 0.597 0.109 0.021 2 0.3 MT_exvivo 344 233 1264 4.129 0.609 0.091 0.016 2 0.2 perirhinal_exvivo 287 215 857 3.961 0.510 0.112 0.018 1 0.2 entorhinal_exvivo Started at Thu Sep 2 13:30:25 UTC 2021 Ended at Thu Sep 2 13:40:18 UTC 2021 #@#%# recon-all-run-time-hours 0.165 recon-all -s sub-M1215054 finished without error at Thu Sep 2 13:40:18 UTC 2021