Fri Sep 9 12:54:22 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 /opt/HCP/HCPpipelines/FreeSurfer/custom/recon-all.v6.hires -subjid FM0001 -sd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w -all -i /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -emregmask /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T2w_acpc_dc_restore.nii.gz -T2pial -parallel -openmp 8 -conf2hires subjid FM0001 setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w FREESURFER_HOME /opt/freesurfer/freesurfer-6.0 Actual FREESURFER_HOME /opt/freesurfer/freesurfer-6.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 6553600 kbytes vmemoryuse unlimited descriptors 32768 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 2060439 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 527908240 82774056 265523816 1605300 179610368 441294372 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 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: 2022/09/09-17:54:23-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 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: 2022/09/09-17:54:23-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 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: 2022/09/09-17:54:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 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: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 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: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/09/09-17:54:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: moana004 Machine: acn179 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/freesurfer-6.0/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/freesurfer-6.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 mri_convert /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/001.mgz mri_convert.bin /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz... TR=1820.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Sep 9 12:54:32 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 mri_convert --no_scale 1 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T2w_acpc_dc_restore.nii.gz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T2w_acpc_dc_restore.nii.gz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T2w_acpc_dc_restore.nii.gz... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Sep 9 12:54:35 CDT 2022 Found 1 runs /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig/001.mgz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 mri_convert /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz --conform mri_convert.bin /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz... TR=1820.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz... mri_add_xform_to_header -c /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/transforms/talairach.xfm /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz INFO: extension is mgz mri_vol2vol --mov /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_brain.nii.gz --targ /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz --regheader --interp nearest --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/extern.emreg.mask.mgz movvol /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/T1w_acpc_dc_restore_brain.nii.gz targvol /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz outvol /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/extern.emreg.mask.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1662818360 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -37.00000; 0.00000 0.00000 1.00000 -19.00000; 0.00000 -1.00000 0.00000 219.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done #-------------------------------------------- #@# Talairach Fri Sep 9 12:54:44 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Fri Sep 9 12:54:44 CDT 2022 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.768102 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.768102/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.768102/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1820.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.768102/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Sep 9 12:54:45 CDT 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.768102/nu0.mnc ./tmp.mri_nu_correct.mni.768102/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.768102/0/ -iterations 1000 -distance 50 [moana004@acn179:/home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/] [2022-09-09 12:54:45] running: /opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.768102/0/ ./tmp.mri_nu_correct.mni.768102/nu0.mnc ./tmp.mri_nu_correct.mni.768102/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.000967147 mri_convert ./tmp.mri_nu_correct.mni.768102/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.768102/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.768102/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Fri Sep 9 12:55:43 CDT 2022 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Fri Sep 9 12:55:44 CDT 2022 Ended at Fri Sep 9 12:56:05 CDT 2022 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Sep 9 12:56:07 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7600, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/freesurfer-6.0/bin/extract_talairach_avi_QA.awk /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/transforms/talairach_avi.log tal_QC_AZS /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/transforms/talairach_avi.log TalAviQA: 0.97375 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Sep 9 12:56:07 CDT 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Fri Sep 9 12:56:07 CDT 2022 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.769130 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.769130/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.769130/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1820.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.769130/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Sep 9 12:56:08 CDT 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.769130/nu0.mnc ./tmp.mri_nu_correct.mni.769130/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.769130/0/ [moana004@acn179:/home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/] [2022-09-09 12:56:08] running: /opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.769130/0/ ./tmp.mri_nu_correct.mni.769130/nu0.mnc ./tmp.mri_nu_correct.mni.769130/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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of field change: 0.00095802 -------------------------------------------------------- Iteration 2 Fri Sep 9 12:56:45 CDT 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.769130/nu1.mnc ./tmp.mri_nu_correct.mni.769130/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.769130/1/ [moana004@acn179:/home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/] [2022-09-09 12:56:45] running: /opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.769130/1/ ./tmp.mri_nu_correct.mni.769130/nu1.mnc ./tmp.mri_nu_correct.mni.769130/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000977301 mri_binarize --i ./tmp.mri_nu_correct.mni.769130/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.769130/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.769130/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.769130/ones.mgz sysname Linux hostname acn179 machine x86_64 user moana004 input ./tmp.mri_nu_correct.mni.769130/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.769130/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.769130/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.769130/sum.junk --avgwf ./tmp.mri_nu_correct.mni.769130/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.769130/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.769130/sum.junk --avgwf ./tmp.mri_nu_correct.mni.769130/input.mean.dat sysname Linux hostname acn179 machine x86_64 user moana004 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.769130/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.769130/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.769130/ones.mgz --i ./tmp.mri_nu_correct.mni.769130/nu2.mnc --sum ./tmp.mri_nu_correct.mni.769130/sum.junk --avgwf ./tmp.mri_nu_correct.mni.769130/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.769130/ones.mgz --i ./tmp.mri_nu_correct.mni.769130/nu2.mnc --sum ./tmp.mri_nu_correct.mni.769130/sum.junk --avgwf ./tmp.mri_nu_correct.mni.769130/output.mean.dat sysname Linux hostname acn179 machine x86_64 user moana004 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.769130/ones.mgz Loading ./tmp.mri_nu_correct.mni.769130/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.769130/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.769130/nu2.mnc ./tmp.mri_nu_correct.mni.769130/nu2.mnc mul .94373402502802792712 Saving result to './tmp.mri_nu_correct.mni.769130/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.769130/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.769130/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.769130/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping (17, 197) to ( 3, 110) Fri Sep 9 12:57:30 CDT 2022 mri_nu_correct.mni done mri_add_xform_to_header -c /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Sep 9 12:57:30 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.07186 0.02736 -0.03742 0.77650; -0.04039 1.12659 0.02160 5.67676; -0.00249 -0.03746 1.21613 -1.68230; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 21 Starting OpenSpline(): npoints = 21 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 71 (71), valley at 50 (50) csf peak at 36, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 69 (69), valley at 37 (37) csf peak at 35, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 7 seconds. #-------------------------------------------- #@# Skull Stripping Fri Sep 9 12:58:38 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_em_register -mask extern.emreg.mask.mgz nu.mgz /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_externmask.lta using MR volume extern.emreg.mask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach_with_externmask.log reading '/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.5 (494 zeros) ************************************************ spacing=8, using 2252 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2252, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.1 skull bounding box = (60, 82, 44) --> (191, 188, 207) using (104, 117, 126) as brain centroid... mean wm in atlas = 107, using box (88,104,106) --> (120, 129,146) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 5.7 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.720 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.382063 @ (-9.091, -27.273, -9.091) max log p = -4.110503 @ (13.636, 4.545, -4.545) max log p = -4.057929 @ (-2.273, -2.273, 2.273) max log p = -4.048830 @ (1.136, -1.136, -1.136) max log p = -4.021152 @ (-2.841, -0.568, -3.977) max log p = -4.021152 @ (0.000, 0.000, 0.000) Found translation: (0.6, -26.7, -16.5): log p = -4.021 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.867, old_max_log_p =-4.021 (thresh=-4.0) 1.06580 0.14032 0.00000 -28.21948; -0.14032 1.06580 0.00000 -11.10800; 0.00000 0.00000 1.07500 -25.62140; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.832, old_max_log_p =-3.867 (thresh=-3.9) 1.07500 -0.00000 0.00000 -9.87345; 0.00000 1.15563 0.00000 -41.43144; 0.00000 0.00000 1.07500 -25.62140; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.786, old_max_log_p =-3.832 (thresh=-3.8) 1.07500 -0.00000 0.00000 -9.87345; 0.00000 1.14574 -0.14032 -22.94894; 0.00000 0.13953 0.98587 -34.15927; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.786, old_max_log_p =-3.786 (thresh=-3.8) 1.07500 -0.00000 0.00000 -9.87345; 0.00000 1.14574 -0.14032 -22.94894; 0.00000 0.13953 0.98587 -34.15927; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.717, old_max_log_p =-3.786 (thresh=-3.8) 1.05395 0.03394 -0.03093 -8.14820; -0.03039 1.19693 -0.00994 -42.10180; 0.03836 -0.01185 1.05182 -24.14618; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.717, old_max_log_p =-3.717 (thresh=-3.7) 1.05395 0.03394 -0.03093 -8.14820; -0.03039 1.19693 -0.00994 -42.10180; 0.03836 -0.01185 1.05182 -24.14618; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.681, old_max_log_p =-3.717 (thresh=-3.7) 1.05119 0.00379 -0.04680 -0.76937; -0.00636 1.19513 -0.06239 -38.12460; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.675, old_max_log_p =-3.681 (thresh=-3.7) 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.675, old_max_log_p =-3.675 (thresh=-3.7) 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2252 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; nsamples 2252 Quasinewton: input matrix 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.675 (old=-4.720) transform before final EM align: 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 246344 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; nsamples 246344 Quasinewton: input matrix 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000 final transform: 1.05366 0.00380 -0.04691 -1.06822; -0.00638 1.19793 -0.06254 -38.49354; 0.05437 0.04714 1.05065 -34.68155; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_externmask.lta... mri_em_register utimesec 1575.551870 mri_em_register stimesec 2.272107 mri_em_register ru_maxrss 596512 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 498296 mri_em_register ru_majflt 4 mri_em_register ru_nswap 0 mri_em_register ru_inblock 26826 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 205 mri_em_register ru_nivcsw 1249 registration took 3 minutes and 31 seconds. mri_watershed -T1 -brain_atlas /opt/freesurfer/freesurfer-6.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_externmask.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=134 z=128 r=69 first estimation of the main basin volume: 1424350 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=147, y=117, z=96, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=8828358551 voxels, voxel volume =1.000 = 8828358551 mmm3 = 8828358.656 cm3 done. PostAnalyze...Basin Prior 15 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=138, z=122, r=9556 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45494 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1036638834 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1044423848 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1058205442 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1077595060 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 1065651316 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 9, 45, 67 after analyzing : 5, 33, 45, 41 RIGHT_CER before analyzing : 14, 21, 42, 74 after analyzing : 14, 35, 42, 44 LEFT_CER before analyzing : 26, 31, 38, 66 after analyzing : 26, 35, 38, 42 RIGHT_BRAIN before analyzing : 4, 7, 45, 67 after analyzing : 4, 32, 45, 40 LEFT_BRAIN before analyzing : 5, 10, 45, 66 after analyzing : 5, 33, 45, 41 OTHER before analyzing : 37, 69, 83, 95 after analyzing : 37, 78, 83, 82 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.645, std = 7.907 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.97, sigma = 10.43 after rotation: sse = 5.97, sigma = 10.43 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.50, its var is 9.47 before Erosion-Dilatation 5.35% of inacurate vertices after Erosion-Dilatation 8.26% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...47 iterations mri_strip_skull: done peeling brain Brain Size = 1597423 voxels, voxel volume = 1.000 mm3 = 1597423 mmm3 = 1597.423 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 31.972044 mri_watershed stimesec 0.823056 mri_watershed ru_maxrss 820500 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 353941 mri_watershed ru_majflt 4 mri_watershed ru_nswap 0 mri_watershed ru_inblock 37428 mri_watershed ru_oublock 2560 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 11494 mri_watershed ru_nivcsw 26 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Sep 9 13:02:23 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=23.1 skull bounding box = (59, 81, 43) --> (192, 188, 208) using (103, 117, 126) as brain centroid... mean wm in atlas = 107, using box (87,104,106) --> (119, 130,146) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 5.7 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.416 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.047739 @ (-9.091, -27.273, -9.091) max log p = -3.776872 @ (13.636, 4.545, -4.545) max log p = -3.728310 @ (-2.273, -2.273, 2.273) max log p = -3.709166 @ (-1.136, 3.409, -1.136) max log p = -3.685518 @ (-0.568, -0.568, 1.705) max log p = -3.684330 @ (-0.852, -0.852, -1.420) Found translation: (-0.3, -23.0, -12.2): log p = -3.684 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.581, old_max_log_p =-3.684 (thresh=-3.7) 1.00000 0.00000 0.00000 -0.28409; 0.00000 1.15000 0.00000 -44.35657; 0.00000 0.00000 1.00000 -12.21591; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.581, old_max_log_p =-3.581 (thresh=-3.6) 1.00000 0.00000 0.00000 -0.28409; 0.00000 1.15000 0.00000 -44.35657; 0.00000 0.00000 1.00000 -12.21591; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.437, old_max_log_p =-3.581 (thresh=-3.6) 1.05582 -0.03567 -0.03568 2.02781; 0.03456 1.12646 0.03343 -47.57691; 0.03458 -0.03688 1.05582 -19.87043; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.437, old_max_log_p =-3.437 (thresh=-3.4) 1.05582 -0.03567 -0.03568 2.02781; 0.03456 1.12646 0.03343 -47.57691; 0.03458 -0.03688 1.05582 -19.87043; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.389, old_max_log_p =-3.437 (thresh=-3.4) 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.389, old_max_log_p =-3.389 (thresh=-3.4) 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.389 (old=-4.416) transform before final EM align: 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.9 tol 0.000000 final transform: 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1450.018975 mri_em_register stimesec 1.665089 mri_em_register ru_maxrss 599036 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 504988 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 248 mri_em_register ru_nivcsw 1435 registration took 3 minutes and 22 seconds. #-------------------------------------- #@# CA Normalize Fri Sep 9 13:05:46 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=23.1 skull bounding box = (59, 81, 43) --> (192, 188, 208) using (103, 117, 126) as brain centroid... mean wm in atlas = 107, using box (87,104,106) --> (119, 130,146) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 5.7 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246344 sample points... INFO: compute sample coordinates transform 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 80, 45) --> (188, 186, 204) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 90 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 81, 46) --> (128, 188, 205) Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 86 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 157, 65) --> (173, 193, 117) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 3 of 8 (37.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 157, 64) --> (125, 194, 120) Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 6 of 13 (46.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 150, 98) --> (143, 212, 129) Brain_Stem: limiting intensities to 107.0 --> 132.0 0 of 30 (0.0%) samples deleted using 227 total control points for intensity normalization... bias field = 0.924 +- 0.102 0 of 218 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 80, 45) --> (188, 186, 204) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 186 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 81, 46) --> (128, 188, 205) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 152 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 157, 65) --> (173, 193, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 75 (17.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 157, 64) --> (125, 194, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 48 (18.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 150, 98) --> (143, 212, 129) Brain_Stem: limiting intensities to 88.0 --> 132.0 19 of 106 (17.9%) samples deleted using 567 total control points for intensity normalization... bias field = 0.982 +- 0.090 0 of 519 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 80, 45) --> (188, 186, 204) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 306 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 81, 46) --> (128, 188, 205) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 288 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 157, 65) --> (173, 193, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 62 of 133 (46.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 157, 64) --> (125, 194, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 28 of 63 (44.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 150, 98) --> (143, 212, 129) Brain_Stem: limiting intensities to 88.0 --> 132.0 40 of 139 (28.8%) samples deleted using 929 total control points for intensity normalization... bias field = 1.001 +- 0.062 0 of 792 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 54 seconds. #-------------------------------------- #@# CA Reg Fri Sep 9 13:06:39 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_ca_register -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.26 (predicted orig area = 6.4) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.786, neg=0, invalid=762 0001: dt=292.753880, rms=0.730 (7.220%), neg=0, invalid=762 0002: dt=152.087527, rms=0.710 (2.648%), neg=0, invalid=762 0003: dt=443.904000, rms=0.701 (1.374%), neg=0, invalid=762 0004: dt=110.976000, rms=0.696 (0.599%), neg=0, invalid=762 0005: dt=887.808000, rms=0.689 (1.044%), neg=0, invalid=762 0006: dt=129.472000, rms=0.687 (0.353%), neg=0, invalid=762 0007: dt=517.888000, rms=0.684 (0.320%), neg=0, invalid=762 0008: dt=129.472000, rms=0.684 (0.131%), neg=0, invalid=762 0009: dt=129.472000, rms=0.683 (0.103%), neg=0, invalid=762 0010: dt=129.472000, rms=0.682 (0.159%), neg=0, invalid=762 0011: dt=129.472000, rms=0.681 (0.184%), neg=0, invalid=762 0012: dt=129.472000, rms=0.679 (0.204%), neg=0, invalid=762 0013: dt=129.472000, rms=0.678 (0.224%), neg=0, invalid=762 0014: dt=129.472000, rms=0.676 (0.240%), neg=0, invalid=762 0015: dt=129.472000, rms=0.674 (0.232%), neg=0, invalid=762 0016: dt=129.472000, rms=0.673 (0.219%), neg=0, invalid=762 0017: dt=129.472000, rms=0.672 (0.188%), neg=0, invalid=762 0018: dt=129.472000, rms=0.670 (0.180%), neg=0, invalid=762 0019: dt=129.472000, rms=0.669 (0.160%), neg=0, invalid=762 0020: dt=129.472000, rms=0.668 (0.143%), neg=0, invalid=762 0021: dt=129.472000, rms=0.668 (0.112%), neg=0, invalid=762 0022: dt=129.472000, rms=0.667 (0.106%), neg=0, invalid=762 0023: dt=517.888000, rms=0.666 (0.076%), neg=0, invalid=762 0024: dt=517.888000, rms=0.666 (-0.590%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0025: dt=129.472000, rms=0.666 (0.195%), neg=0, invalid=762 0026: dt=517.888000, rms=0.665 (0.156%), neg=0, invalid=762 0027: dt=517.888000, rms=0.665 (-0.346%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 0028: dt=104.831541, rms=0.663 (0.953%), neg=0, invalid=762 0029: dt=176.872727, rms=0.653 (1.485%), neg=0, invalid=762 0030: dt=65.129412, rms=0.648 (0.701%), neg=0, invalid=762 0031: dt=172.088889, rms=0.643 (0.759%), neg=0, invalid=762 0032: dt=62.000000, rms=0.640 (0.506%), neg=0, invalid=762 0033: dt=145.152000, rms=0.637 (0.541%), neg=0, invalid=762 0034: dt=36.288000, rms=0.635 (0.296%), neg=0, invalid=762 0035: dt=248.832000, rms=0.632 (0.454%), neg=0, invalid=762 0036: dt=85.333333, rms=0.629 (0.400%), neg=0, invalid=762 0037: dt=36.288000, rms=0.628 (0.228%), neg=0, invalid=762 0038: dt=36.288000, rms=0.627 (0.087%), neg=0, invalid=762 0039: dt=36.288000, rms=0.626 (0.141%), neg=0, invalid=762 0040: dt=36.288000, rms=0.625 (0.207%), neg=0, invalid=762 0041: dt=36.288000, rms=0.623 (0.268%), neg=0, invalid=762 0042: dt=36.288000, rms=0.622 (0.290%), neg=0, invalid=762 0043: dt=36.288000, rms=0.620 (0.303%), neg=0, invalid=762 0044: dt=36.288000, rms=0.618 (0.308%), neg=0, invalid=762 0045: dt=36.288000, rms=0.616 (0.308%), neg=0, invalid=762 0046: dt=36.288000, rms=0.614 (0.304%), neg=0, invalid=762 0047: dt=36.288000, rms=0.612 (0.311%), neg=0, invalid=762 0048: dt=36.288000, rms=0.610 (0.297%), neg=0, invalid=762 0049: dt=36.288000, rms=0.609 (0.269%), neg=0, invalid=762 0050: dt=36.288000, rms=0.607 (0.243%), neg=0, invalid=762 0051: dt=36.288000, rms=0.606 (0.219%), neg=0, invalid=762 0052: dt=36.288000, rms=0.605 (0.215%), neg=0, invalid=762 0053: dt=36.288000, rms=0.603 (0.190%), neg=0, invalid=762 0054: dt=36.288000, rms=0.602 (0.167%), neg=0, invalid=762 0055: dt=36.288000, rms=0.601 (0.155%), neg=0, invalid=762 0056: dt=36.288000, rms=0.601 (0.137%), neg=0, invalid=762 0057: dt=36.288000, rms=0.600 (0.137%), neg=0, invalid=762 0058: dt=36.288000, rms=0.599 (0.129%), neg=0, invalid=762 0059: dt=36.288000, rms=0.598 (0.112%), neg=0, invalid=762 0060: dt=36.288000, rms=0.598 (0.095%), neg=0, invalid=762 0061: dt=5.184000, rms=0.598 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=762 0062: dt=124.416000, rms=0.596 (0.385%), neg=0, invalid=762 0063: dt=36.288000, rms=0.595 (0.088%), neg=0, invalid=762 0064: dt=36.288000, rms=0.595 (0.028%), neg=0, invalid=762 0065: dt=36.288000, rms=0.595 (0.045%), neg=0, invalid=762 0066: dt=36.288000, rms=0.595 (0.035%), neg=0, invalid=762 0067: dt=36.288000, rms=0.595 (0.048%), neg=0, invalid=762 0068: dt=36.288000, rms=0.594 (0.043%), neg=0, invalid=762 0069: dt=145.152000, rms=0.594 (0.055%), neg=0, invalid=762 0070: dt=20.736000, rms=0.594 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.615, neg=0, invalid=762 0071: dt=2.000000, rms=0.615 (0.083%), neg=0, invalid=762 0072: dt=0.300000, rms=0.615 (0.003%), neg=0, invalid=762 0073: dt=0.300000, rms=0.615 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=762 0074: dt=0.000586, rms=0.615 (0.078%), neg=0, invalid=762 0075: dt=0.000000, rms=0.615 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.677, neg=0, invalid=762 0076: dt=5.306590, rms=0.657 (2.851%), neg=0, invalid=762 0077: dt=2.931034, rms=0.657 (0.139%), neg=0, invalid=762 0078: dt=2.931034, rms=0.657 (-0.043%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.657, neg=0, invalid=762 0079: dt=0.000000, rms=0.657 (0.065%), neg=0, invalid=762 0080: dt=0.000000, rms=0.657 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.713, neg=0, invalid=762 0081: dt=1.039344, rms=0.709 (0.473%), neg=0, invalid=762 0082: dt=1.933824, rms=0.705 (0.664%), neg=0, invalid=762 0083: dt=1.024000, rms=0.704 (0.091%), neg=0, invalid=762 0084: dt=1.024000, rms=0.703 (0.181%), neg=0, invalid=762 0085: dt=1.024000, rms=0.702 (0.090%), neg=0, invalid=762 0086: dt=1.024000, rms=0.702 (-0.219%), neg=0, invalid=762 0087: dt=0.000000, rms=0.702 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=762 0088: dt=1.024000, rms=0.702 (0.128%), neg=0, invalid=762 0089: dt=0.768000, rms=0.702 (0.015%), neg=0, invalid=762 0090: dt=0.768000, rms=0.702 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0091: dt=0.867235, rms=0.651 (2.821%), neg=0, invalid=762 0092: dt=0.080000, rms=0.650 (0.138%), neg=0, invalid=762 0093: dt=0.080000, rms=0.650 (-0.084%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0094: dt=0.028000, rms=0.650 (0.084%), neg=0, invalid=762 0095: dt=0.005000, rms=0.650 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12259 (18) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (986 voxels, overlap=0.718) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (986 voxels, peak = 19), gca=18.7 gca peak = 0.15565 (16) mri peak = 0.11921 (18) Right_Lateral_Ventricle (43): linear fit = 1.15 x + 0.0 (759 voxels, overlap=0.896) Right_Lateral_Ventricle (43): linear fit = 1.15 x + 0.0 (759 voxels, peak = 18), gca=18.5 gca peak = 0.26829 (96) mri peak = 0.07028 (97) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (832 voxels, overlap=0.745) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (832 voxels, peak = 98), gca=98.4 gca peak = 0.20183 (93) mri peak = 0.07392 (97) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (726 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (726 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.08163 (64) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (757 voxels, overlap=0.506) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (757 voxels, peak = 62), gca=62.4 gca peak = 0.30730 (58) mri peak = 0.07792 (63) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (768 voxels, overlap=0.562) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (768 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.08403 (105) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (60620 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (60620 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.07707 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60721 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60721 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.04136 (64) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (22642 voxels, overlap=0.775) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (22642 voxels, peak = 63), gca=63.4 gca peak = 0.15082 (58) mri peak = 0.03895 (65) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (22315 voxels, overlap=0.385) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (22315 voxels, peak = 68), gca=67.6 gca peak = 0.14161 (67) mri peak = 0.07726 (78) Right_Caudate (50): linear fit = 1.16 x + 0.0 (942 voxels, overlap=0.205) Right_Caudate (50): linear fit = 1.16 x + 0.0 (942 voxels, peak = 78), gca=78.1 gca peak = 0.15243 (71) mri peak = 0.09961 (79) Left_Caudate (11): linear fit = 1.03 x + 0.0 (901 voxels, overlap=0.837) Left_Caudate (11): linear fit = 1.03 x + 0.0 (901 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.04640 (65) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (15686 voxels, overlap=0.647) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (15686 voxels, peak = 66), gca=66.4 gca peak = 0.13252 (56) mri peak = 0.03987 (68) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (15674 voxels, overlap=0.093) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (15674 voxels, peak = 67), gca=67.5 gca peak = 0.18181 (84) mri peak = 0.07636 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7522 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7522 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.06816 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (5796 voxels, overlap=0.581) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (5796 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.10448 (65) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (467 voxels, overlap=0.500) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (467 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.11215 (63) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (533 voxels, overlap=0.052) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (533 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.06497 (89) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5301 voxels, overlap=0.920) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5301 voxels, peak = 87), gca=87.1 gca peak = 0.11978 (83) mri peak = 0.06777 (93) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4550 voxels, overlap=0.651) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4550 voxels, peak = 90), gca=90.1 gca peak = 0.13399 (79) mri peak = 0.04767 (82) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2058 voxels, overlap=0.869) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2058 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.06091 (88) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2196 voxels, overlap=0.665) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2196 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.08651 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10809 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10809 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07857 (89) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (934 voxels, overlap=0.571) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (934 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.08252 (92) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1183 voxels, overlap=0.668) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1183 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 0.26667 (24) gca peak = 0.15061 (21) mri peak = 0.16709 (19) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (319 voxels, overlap=0.721) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (319 voxels, peak = 18), gca=18.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0096: dt=110.976000, rms=0.642 (1.567%), neg=0, invalid=762 0097: dt=221.952000, rms=0.638 (0.629%), neg=0, invalid=762 0098: dt=110.976000, rms=0.637 (0.142%), neg=0, invalid=762 0099: dt=443.904000, rms=0.634 (0.464%), neg=0, invalid=762 0100: dt=73.984000, rms=0.633 (0.132%), neg=0, invalid=762 0101: dt=887.808000, rms=0.631 (0.358%), neg=0, invalid=762 0102: dt=129.472000, rms=0.629 (0.267%), neg=0, invalid=762 0103: dt=55.488000, rms=0.629 (0.026%), neg=0, invalid=762 0104: dt=55.488000, rms=0.629 (0.012%), neg=0, invalid=762 0105: dt=55.488000, rms=0.629 (0.022%), neg=0, invalid=762 0106: dt=55.488000, rms=0.629 (0.038%), neg=0, invalid=762 0107: dt=55.488000, rms=0.628 (0.062%), neg=0, invalid=762 0108: dt=55.488000, rms=0.628 (0.077%), neg=0, invalid=762 0109: dt=55.488000, rms=0.627 (0.080%), neg=0, invalid=762 0110: dt=55.488000, rms=0.627 (0.075%), neg=0, invalid=762 0111: dt=55.488000, rms=0.626 (0.070%), neg=0, invalid=762 0112: dt=55.488000, rms=0.626 (0.067%), neg=0, invalid=762 0113: dt=55.488000, rms=0.626 (0.064%), neg=0, invalid=762 0114: dt=55.488000, rms=0.625 (0.065%), neg=0, invalid=762 0115: dt=55.488000, rms=0.625 (0.063%), neg=0, invalid=762 0116: dt=55.488000, rms=0.624 (0.060%), neg=0, invalid=762 0117: dt=55.488000, rms=0.624 (0.052%), neg=0, invalid=762 0118: dt=55.488000, rms=0.624 (0.045%), neg=0, invalid=762 0119: dt=55.488000, rms=0.624 (0.039%), neg=0, invalid=762 0120: dt=55.488000, rms=0.623 (0.039%), neg=0, invalid=762 0121: dt=55.488000, rms=0.623 (0.037%), neg=0, invalid=762 0122: dt=55.488000, rms=0.623 (0.039%), neg=0, invalid=762 0123: dt=55.488000, rms=0.623 (0.040%), neg=0, invalid=762 0124: dt=55.488000, rms=0.622 (0.040%), neg=0, invalid=762 0125: dt=55.488000, rms=0.622 (0.040%), neg=0, invalid=762 0126: dt=55.488000, rms=0.622 (0.038%), neg=0, invalid=762 0127: dt=55.488000, rms=0.622 (0.042%), neg=0, invalid=762 0128: dt=55.488000, rms=0.621 (0.038%), neg=0, invalid=762 0129: dt=55.488000, rms=0.621 (0.040%), neg=0, invalid=762 0130: dt=55.488000, rms=0.621 (0.038%), neg=0, invalid=762 0131: dt=55.488000, rms=0.621 (0.037%), neg=0, invalid=762 0132: dt=55.488000, rms=0.620 (0.034%), neg=0, invalid=762 0133: dt=55.488000, rms=0.620 (0.031%), neg=0, invalid=762 0134: dt=55.488000, rms=0.620 (0.029%), neg=0, invalid=762 0135: dt=55.488000, rms=0.620 (0.031%), neg=0, invalid=762 0136: dt=55.488000, rms=0.620 (0.032%), neg=0, invalid=762 0137: dt=55.488000, rms=0.619 (0.033%), neg=0, invalid=762 0138: dt=55.488000, rms=0.619 (0.033%), neg=0, invalid=762 0139: dt=55.488000, rms=0.619 (0.029%), neg=0, invalid=762 0140: dt=55.488000, rms=0.619 (0.028%), neg=0, invalid=762 0141: dt=55.488000, rms=0.619 (0.025%), neg=0, invalid=762 0142: dt=55.488000, rms=0.619 (0.024%), neg=0, invalid=762 0143: dt=4734.976000, rms=0.618 (0.166%), neg=0, invalid=762 0144: dt=73.984000, rms=0.617 (0.074%), neg=0, invalid=762 0145: dt=32.368000, rms=0.617 (0.002%), neg=0, invalid=762 0146: dt=32.368000, rms=0.617 (0.002%), neg=0, invalid=762 0147: dt=32.368000, rms=0.617 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=762 0148: dt=295.936000, rms=0.616 (0.198%), neg=0, invalid=762 0149: dt=129.472000, rms=0.616 (0.083%), neg=0, invalid=762 0150: dt=517.888000, rms=0.615 (0.088%), neg=0, invalid=762 0151: dt=92.480000, rms=0.615 (0.033%), neg=0, invalid=762 0152: dt=92.480000, rms=0.615 (0.004%), neg=0, invalid=762 0153: dt=92.480000, rms=0.615 (0.010%), neg=0, invalid=762 0154: dt=92.480000, rms=0.615 (0.016%), neg=0, invalid=762 0155: dt=92.480000, rms=0.615 (0.025%), neg=0, invalid=762 0156: dt=92.480000, rms=0.614 (0.028%), neg=0, invalid=762 0157: dt=92.480000, rms=0.614 (0.029%), neg=0, invalid=762 0158: dt=92.480000, rms=0.614 (0.025%), neg=0, invalid=762 0159: dt=92.480000, rms=0.614 (0.022%), neg=0, invalid=762 0160: dt=92.480000, rms=0.614 (0.023%), neg=0, invalid=762 0161: dt=92.480000, rms=0.614 (0.022%), neg=0, invalid=762 0162: dt=2071.552000, rms=0.613 (0.068%), neg=0, invalid=762 0163: dt=92.480000, rms=0.613 (0.017%), neg=0, invalid=762 0164: dt=92.480000, rms=0.613 (0.001%), neg=0, invalid=762 0165: dt=92.480000, rms=0.613 (0.001%), neg=0, invalid=762 0166: dt=92.480000, rms=0.613 (0.005%), neg=0, invalid=762 0167: dt=92.480000, rms=0.613 (0.015%), neg=0, invalid=762 0168: dt=92.480000, rms=0.613 (0.021%), neg=0, invalid=762 0169: dt=92.480000, rms=0.613 (0.019%), neg=0, invalid=762 0170: dt=0.000000, rms=0.613 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.614, neg=0, invalid=762 0171: dt=145.152000, rms=0.609 (0.786%), neg=0, invalid=762 0172: dt=202.720812, rms=0.601 (1.206%), neg=0, invalid=762 0173: dt=57.690141, rms=0.598 (0.561%), neg=0, invalid=762 0174: dt=145.152000, rms=0.595 (0.512%), neg=0, invalid=762 0175: dt=62.208000, rms=0.593 (0.318%), neg=0, invalid=762 0176: dt=145.152000, rms=0.590 (0.473%), neg=0, invalid=762 0177: dt=36.288000, rms=0.589 (0.225%), neg=0, invalid=762 0178: dt=497.664000, rms=0.584 (0.806%), neg=0, invalid=762 0179: dt=75.259259, rms=0.581 (0.623%), neg=0, invalid=762 0180: dt=36.288000, rms=0.580 (0.184%), neg=0, invalid=762 0181: dt=331.776000, rms=0.578 (0.275%), neg=0, invalid=762 0182: dt=66.444944, rms=0.576 (0.373%), neg=0, invalid=762 0183: dt=62.208000, rms=0.575 (0.095%), neg=0, invalid=762 0184: dt=331.776000, rms=0.573 (0.336%), neg=0, invalid=762 0185: dt=36.288000, rms=0.572 (0.240%), neg=0, invalid=762 0186: dt=103.680000, rms=0.572 (0.064%), neg=0, invalid=762 0187: dt=124.416000, rms=0.571 (0.176%), neg=0, invalid=762 0188: dt=36.288000, rms=0.570 (0.071%), neg=0, invalid=762 0189: dt=331.776000, rms=0.569 (0.175%), neg=0, invalid=762 0190: dt=67.738832, rms=0.568 (0.251%), neg=0, invalid=762 0191: dt=36.288000, rms=0.567 (0.040%), neg=0, invalid=762 0192: dt=36.288000, rms=0.567 (0.030%), neg=0, invalid=762 0193: dt=36.288000, rms=0.567 (0.055%), neg=0, invalid=762 0194: dt=36.288000, rms=0.566 (0.089%), neg=0, invalid=762 0195: dt=36.288000, rms=0.566 (0.116%), neg=0, invalid=762 0196: dt=36.288000, rms=0.565 (0.135%), neg=0, invalid=762 0197: dt=36.288000, rms=0.564 (0.150%), neg=0, invalid=762 0198: dt=36.288000, rms=0.563 (0.150%), neg=0, invalid=762 0199: dt=36.288000, rms=0.563 (0.152%), neg=0, invalid=762 0200: dt=36.288000, rms=0.562 (0.157%), neg=0, invalid=762 0201: dt=36.288000, rms=0.561 (0.154%), neg=0, invalid=762 0202: dt=36.288000, rms=0.560 (0.157%), neg=0, invalid=762 0203: dt=36.288000, rms=0.559 (0.154%), neg=0, invalid=762 0204: dt=36.288000, rms=0.558 (0.145%), neg=0, invalid=762 0205: dt=36.288000, rms=0.557 (0.137%), neg=0, invalid=762 0206: dt=36.288000, rms=0.557 (0.133%), neg=0, invalid=762 0207: dt=36.288000, rms=0.557 (0.020%), neg=0, invalid=762 0208: dt=36.288000, rms=0.556 (0.030%), neg=0, invalid=762 0209: dt=36.288000, rms=0.556 (0.040%), neg=0, invalid=762 0210: dt=36.288000, rms=0.556 (0.048%), neg=0, invalid=762 0211: dt=36.288000, rms=0.556 (0.015%), neg=0, invalid=762 0212: dt=36.288000, rms=0.556 (0.026%), neg=0, invalid=762 0213: dt=9.072000, rms=0.556 (0.003%), neg=0, invalid=762 0214: dt=4.536000, rms=0.556 (0.001%), neg=0, invalid=762 0215: dt=2.268000, rms=0.556 (0.001%), neg=0, invalid=762 0216: dt=1.134000, rms=0.556 (0.000%), neg=0, invalid=762 0217: dt=0.567000, rms=0.556 (0.000%), neg=0, invalid=762 0218: dt=0.070875, rms=0.556 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.556, neg=0, invalid=762 0219: dt=145.152000, rms=0.552 (0.701%), neg=0, invalid=762 0220: dt=82.944000, rms=0.552 (0.107%), neg=0, invalid=762 0221: dt=145.152000, rms=0.551 (0.160%), neg=0, invalid=762 0222: dt=36.288000, rms=0.551 (0.058%), neg=0, invalid=762 0223: dt=331.776000, rms=0.550 (0.124%), neg=0, invalid=762 0224: dt=62.208000, rms=0.549 (0.158%), neg=0, invalid=762 0225: dt=36.288000, rms=0.549 (0.020%), neg=0, invalid=762 0226: dt=36.288000, rms=0.549 (0.018%), neg=0, invalid=762 0227: dt=36.288000, rms=0.549 (0.035%), neg=0, invalid=762 0228: dt=36.288000, rms=0.548 (0.048%), neg=0, invalid=762 0229: dt=36.288000, rms=0.548 (0.059%), neg=0, invalid=762 0230: dt=36.288000, rms=0.548 (0.065%), neg=0, invalid=762 0231: dt=36.288000, rms=0.547 (0.073%), neg=0, invalid=762 0232: dt=36.288000, rms=0.547 (0.077%), neg=0, invalid=762 0233: dt=36.288000, rms=0.546 (0.078%), neg=0, invalid=762 0234: dt=36.288000, rms=0.546 (0.080%), neg=0, invalid=762 0235: dt=36.288000, rms=0.545 (0.081%), neg=0, invalid=762 0236: dt=36.288000, rms=0.545 (0.078%), neg=0, invalid=762 0237: dt=36.288000, rms=0.545 (0.076%), neg=0, invalid=762 0238: dt=36.288000, rms=0.544 (0.074%), neg=0, invalid=762 0239: dt=36.288000, rms=0.544 (0.074%), neg=0, invalid=762 0240: dt=36.288000, rms=0.543 (0.077%), neg=0, invalid=762 0241: dt=36.288000, rms=0.543 (0.079%), neg=0, invalid=762 0242: dt=36.288000, rms=0.543 (0.082%), neg=0, invalid=762 0243: dt=36.288000, rms=0.542 (0.081%), neg=0, invalid=762 0244: dt=36.288000, rms=0.542 (0.080%), neg=0, invalid=762 0245: dt=36.288000, rms=0.541 (0.082%), neg=0, invalid=762 0246: dt=36.288000, rms=0.541 (0.083%), neg=0, invalid=762 0247: dt=36.288000, rms=0.540 (0.077%), neg=0, invalid=762 0248: dt=36.288000, rms=0.540 (0.071%), neg=0, invalid=762 0249: dt=36.288000, rms=0.540 (0.012%), neg=0, invalid=762 0250: dt=36.288000, rms=0.540 (0.019%), neg=0, invalid=762 0251: dt=36.288000, rms=0.540 (0.023%), neg=0, invalid=762 0252: dt=36.288000, rms=0.540 (0.027%), neg=0, invalid=762 0253: dt=36.288000, rms=0.539 (0.032%), neg=0, invalid=762 0254: dt=36.288000, rms=0.539 (0.031%), neg=0, invalid=762 0255: dt=36.288000, rms=0.539 (0.007%), neg=0, invalid=762 0256: dt=36.288000, rms=0.539 (0.011%), neg=0, invalid=762 0257: dt=36.288000, rms=0.539 (0.020%), neg=0, invalid=762 0258: dt=36.288000, rms=0.539 (0.021%), neg=0, invalid=762 0259: dt=36.288000, rms=0.539 (0.027%), neg=0, invalid=762 0260: dt=36.288000, rms=0.539 (0.031%), neg=0, invalid=762 0261: dt=18.144000, rms=0.539 (0.003%), neg=0, invalid=762 0262: dt=4.536000, rms=0.539 (-0.000%), neg=0, invalid=762 0263: dt=6.480000, rms=0.539 (0.001%), neg=0, invalid=762 0264: dt=0.567000, rms=0.539 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0265: dt=44.800000, rms=0.541 (0.752%), neg=0, invalid=762 0266: dt=101.917655, rms=0.533 (1.513%), neg=0, invalid=762 0267: dt=21.344503, rms=0.530 (0.687%), neg=0, invalid=762 0268: dt=172.547564, rms=0.524 (1.085%), neg=0, invalid=762 0269: dt=24.363636, rms=0.519 (0.870%), neg=0, invalid=762 0270: dt=38.400000, rms=0.518 (0.299%), neg=0, invalid=762 0271: dt=25.600000, rms=0.517 (0.131%), neg=0, invalid=762 0272: dt=44.800000, rms=0.516 (0.220%), neg=0, invalid=762 0273: dt=2.800000, rms=0.516 (0.020%), neg=0, invalid=762 0274: dt=2.800000, rms=0.516 (0.024%), neg=0, invalid=762 0275: dt=0.350000, rms=0.516 (0.008%), neg=0, invalid=762 0276: dt=0.175000, rms=0.516 (0.001%), neg=0, invalid=762 0277: dt=0.043750, rms=0.516 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0278: dt=54.577778, rms=0.512 (0.799%), neg=0, invalid=762 0279: dt=25.600000, rms=0.510 (0.354%), neg=0, invalid=762 0280: dt=44.800000, rms=0.509 (0.209%), neg=0, invalid=762 0281: dt=25.600000, rms=0.508 (0.163%), neg=0, invalid=762 0282: dt=38.400000, rms=0.508 (0.133%), neg=0, invalid=762 0283: dt=25.600000, rms=0.507 (0.119%), neg=0, invalid=762 0284: dt=32.000000, rms=0.507 (0.114%), neg=0, invalid=762 0285: dt=25.600000, rms=0.506 (0.092%), neg=0, invalid=762 0286: dt=38.400000, rms=0.506 (0.106%), neg=0, invalid=762 0287: dt=25.600000, rms=0.505 (0.093%), neg=0, invalid=762 0288: dt=32.000000, rms=0.505 (0.088%), neg=0, invalid=762 0289: dt=11.200000, rms=0.504 (0.051%), neg=0, invalid=762 0290: dt=2.800000, rms=0.504 (0.013%), neg=0, invalid=762 0291: dt=0.350000, rms=0.504 (0.001%), neg=0, invalid=762 0292: dt=0.175000, rms=0.504 (0.001%), neg=0, invalid=762 0293: dt=0.087500, rms=0.504 (0.001%), neg=0, invalid=762 0294: dt=0.043750, rms=0.504 (0.000%), neg=0, invalid=762 0295: dt=0.002734, rms=0.504 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0296: dt=0.000000, rms=0.521 (0.081%), neg=0, invalid=762 0297: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762 0298: dt=0.150000, rms=0.521 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0299: dt=0.000000, rms=0.521 (0.081%), neg=0, invalid=762 0300: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762 0301: dt=0.150000, rms=0.521 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.556, neg=0, invalid=762 0302: dt=1.536000, rms=0.553 (0.597%), neg=0, invalid=762 0303: dt=0.384000, rms=0.553 (0.012%), neg=0, invalid=762 0304: dt=0.384000, rms=0.553 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0305: dt=1.280000, rms=0.552 (0.205%), neg=0, invalid=762 0306: dt=0.112000, rms=0.552 (0.000%), neg=0, invalid=762 0307: dt=0.112000, rms=0.552 (-0.001%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.513, neg=0, invalid=762 0308: dt=0.448000, rms=0.499 (2.809%), neg=0, invalid=762 0309: dt=0.448000, rms=0.495 (0.656%), neg=0, invalid=762 0310: dt=0.448000, rms=0.493 (0.393%), neg=0, invalid=762 0311: dt=0.448000, rms=0.492 (0.246%), neg=0, invalid=762 0312: dt=0.448000, rms=0.491 (0.182%), neg=0, invalid=762 0313: dt=0.448000, rms=0.491 (0.130%), neg=0, invalid=762 0314: dt=0.448000, rms=0.490 (0.110%), neg=0, invalid=762 0315: dt=0.448000, rms=0.490 (0.082%), neg=0, invalid=762 0316: dt=0.448000, rms=0.489 (0.072%), neg=0, invalid=762 0317: dt=0.448000, rms=0.489 (0.053%), neg=0, invalid=762 0318: dt=0.448000, rms=0.489 (0.053%), neg=0, invalid=762 0319: dt=0.448000, rms=0.489 (0.034%), neg=0, invalid=762 0320: dt=0.448000, rms=0.488 (0.041%), neg=0, invalid=762 0321: dt=0.448000, rms=0.488 (0.061%), neg=0, invalid=762 0322: dt=0.448000, rms=0.488 (0.070%), neg=0, invalid=762 0323: dt=0.448000, rms=0.487 (0.081%), neg=0, invalid=762 0324: dt=0.224000, rms=0.487 (0.007%), neg=0, invalid=762 0325: dt=0.224000, rms=0.487 (0.006%), neg=0, invalid=762 0326: dt=0.112000, rms=0.487 (0.003%), neg=0, invalid=762 0327: dt=0.112000, rms=0.487 (0.001%), neg=0, invalid=762 0328: dt=0.112000, rms=0.487 (0.002%), neg=0, invalid=762 0329: dt=0.112000, rms=0.487 (0.004%), neg=0, invalid=762 0330: dt=0.112000, rms=0.487 (0.003%), neg=0, invalid=762 0331: dt=0.112000, rms=0.487 (0.004%), neg=0, invalid=762 0332: dt=0.112000, rms=0.487 (0.008%), neg=0, invalid=762 0333: dt=0.112000, rms=0.487 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=762 0334: dt=0.250000, rms=0.484 (0.642%), neg=0, invalid=762 0335: dt=0.384000, rms=0.483 (0.396%), neg=0, invalid=762 0336: dt=0.448000, rms=0.482 (0.096%), neg=0, invalid=762 0337: dt=0.448000, rms=0.482 (0.010%), neg=0, invalid=762 0338: dt=0.448000, rms=0.482 (0.006%), neg=0, invalid=762 0339: dt=0.448000, rms=0.482 (0.004%), neg=0, invalid=762 0340: dt=0.448000, rms=0.482 (0.001%), neg=0, invalid=762 0341: dt=0.384000, rms=0.482 (0.003%), neg=0, invalid=762 0342: dt=0.320000, rms=0.482 (0.002%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0343: dt=0.000000, rms=0.480 (0.099%), neg=0, invalid=762 0344: dt=0.000000, rms=0.480 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0345: dt=295.936000, rms=0.479 (0.155%), neg=0, invalid=762 0346: dt=73.984000, rms=0.479 (0.011%), neg=0, invalid=762 0347: dt=73.984000, rms=0.479 (0.010%), neg=0, invalid=762 0348: dt=73.984000, rms=0.479 (0.014%), neg=0, invalid=762 0349: dt=73.984000, rms=0.479 (0.011%), neg=0, invalid=762 0350: dt=73.984000, rms=0.479 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0351: dt=9.072000, rms=0.479 (0.107%), neg=0, invalid=762 0352: dt=9.072000, rms=0.479 (0.003%), neg=0, invalid=762 0353: dt=9.072000, rms=0.479 (0.001%), neg=0, invalid=762 0354: dt=9.072000, rms=0.479 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0355: dt=145.152000, rms=0.477 (0.579%), neg=0, invalid=762 0356: dt=36.288000, rms=0.477 (0.072%), neg=0, invalid=762 0357: dt=36.288000, rms=0.476 (0.047%), neg=0, invalid=762 0358: dt=36.288000, rms=0.476 (0.081%), neg=0, invalid=762 0359: dt=36.288000, rms=0.475 (0.105%), neg=0, invalid=762 0360: dt=36.288000, rms=0.475 (0.121%), neg=0, invalid=762 0361: dt=36.288000, rms=0.474 (0.126%), neg=0, invalid=762 0362: dt=36.288000, rms=0.474 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0363: dt=36.288000, rms=0.473 (0.102%), neg=0, invalid=762 0364: dt=103.680000, rms=0.473 (0.025%), neg=0, invalid=762 0365: dt=103.680000, rms=0.473 (0.002%), neg=0, invalid=762 0366: dt=103.680000, rms=0.473 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=0, neg = 0 0367: dt=103.680000, rms=0.472 (0.151%), neg=0, invalid=762 0368: dt=103.680000, rms=0.472 (0.112%), neg=0, invalid=762 0369: dt=103.680000, rms=0.471 (0.061%), neg=0, invalid=762 0370: dt=36.288000, rms=0.471 (0.079%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0371: dt=36.288000, rms=0.471 (0.003%), neg=0, invalid=762 0372: dt=36.288000, rms=0.471 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0373: dt=36.288000, rms=0.471 (0.014%), neg=0, invalid=762 0374: dt=36.288000, rms=0.471 (0.015%), neg=0, invalid=762 0375: dt=36.288000, rms=0.471 (0.025%), neg=0, invalid=762 0376: dt=36.288000, rms=0.471 (0.027%), neg=0, invalid=762 0377: dt=36.288000, rms=0.470 (0.025%), neg=0, invalid=762 0378: dt=36.288000, rms=0.470 (0.032%), neg=0, invalid=762 0379: dt=36.288000, rms=0.470 (0.034%), neg=0, invalid=762 0380: dt=36.288000, rms=0.470 (0.033%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0381: dt=25.600000, rms=0.469 (0.339%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 12 iterations, nbhd size=1, neg = 0 0382: dt=91.534884, rms=0.468 (0.384%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0383: dt=38.400000, rms=0.466 (0.386%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0384: dt=32.000000, rms=0.464 (0.300%), neg=0, invalid=762 0385: dt=25.600000, rms=0.464 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0386: dt=25.600000, rms=0.463 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=0, neg = 0 0387: dt=25.600000, rms=0.462 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0388: dt=25.600000, rms=0.461 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 0389: dt=25.600000, rms=0.460 (0.256%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=0, neg = 0 0390: dt=25.600000, rms=0.459 (0.221%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0391: dt=25.600000, rms=0.458 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=0, neg = 0 0392: dt=25.600000, rms=0.457 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 5 iterations, nbhd size=0, neg = 0 0393: dt=25.600000, rms=0.456 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 5 iterations, nbhd size=0, neg = 0 0394: dt=25.600000, rms=0.455 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=0, neg = 0 0395: dt=25.600000, rms=0.454 (0.191%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 0396: dt=25.600000, rms=0.453 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 3 iterations, nbhd size=0, neg = 0 0397: dt=25.600000, rms=0.453 (0.160%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0398: dt=25.600000, rms=0.452 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 5 iterations, nbhd size=0, neg = 0 0399: dt=25.600000, rms=0.452 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0400: dt=25.600000, rms=0.451 (0.094%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0401: dt=32.000000, rms=0.451 (0.048%), neg=0, invalid=762 0402: dt=32.000000, rms=0.451 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0403: dt=56.615385, rms=0.448 (0.772%), neg=0, invalid=762 0404: dt=25.212121, rms=0.447 (0.280%), neg=0, invalid=762 0405: dt=32.000000, rms=0.446 (0.131%), neg=0, invalid=762 0406: dt=32.000000, rms=0.446 (0.082%), neg=0, invalid=762 0407: dt=32.000000, rms=0.445 (0.198%), neg=0, invalid=762 0408: dt=32.000000, rms=0.444 (0.081%), neg=0, invalid=762 0409: dt=32.000000, rms=0.444 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0410: dt=32.000000, rms=0.443 (0.023%), neg=0, invalid=762 0411: dt=32.000000, rms=0.443 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0412: dt=32.000000, rms=0.443 (-0.017%), neg=0, invalid=762 0413: dt=32.000000, rms=0.443 (0.055%), neg=0, invalid=762 0414: dt=11.200000, rms=0.443 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0415: dt=0.000068, rms=0.449 (0.113%), neg=0, invalid=762 0416: dt=0.000000, rms=0.449 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0417: dt=1.008000, rms=0.449 (0.124%), neg=0, invalid=762 0418: dt=1.008000, rms=0.449 (0.004%), neg=0, invalid=762 0419: dt=1.008000, rms=0.449 (0.001%), neg=0, invalid=762 0420: dt=1.008000, rms=0.449 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=762 0421: dt=1.024000, rms=0.461 (0.304%), neg=0, invalid=762 0422: dt=0.256000, rms=0.461 (0.005%), neg=0, invalid=762 0423: dt=0.256000, rms=0.461 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=762 0424: dt=1.280000, rms=0.460 (0.259%), neg=0, invalid=762 0425: dt=0.448000, rms=0.460 (0.013%), neg=0, invalid=762 0426: dt=0.448000, rms=0.460 (-0.004%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 iter 0, gcam->neg = 734 after 16 iterations, nbhd size=1, neg = 0 0427: dt=2.268856, rms=0.420 (6.698%), neg=0, invalid=762 0428: dt=0.080000, rms=0.419 (0.074%), neg=0, invalid=762 0429: dt=0.080000, rms=0.419 (-0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0430: dt=0.080000, rms=0.419 (0.190%), neg=0, invalid=762 0431: dt=0.000000, rms=0.419 (-0.002%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0432: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0433: dt=27.744000, rms=0.405 (0.002%), neg=0, invalid=762 0434: dt=6.936000, rms=0.405 (0.000%), neg=0, invalid=762 0435: dt=6.936000, rms=0.405 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0436: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0437: dt=36.288000, rms=0.405 (0.030%), neg=0, invalid=762 0438: dt=103.680000, rms=0.405 (0.030%), neg=0, invalid=762 0439: dt=103.680000, rms=0.404 (0.046%), neg=0, invalid=762 0440: dt=103.680000, rms=0.404 (0.036%), neg=0, invalid=762 0441: dt=103.680000, rms=0.404 (0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0442: dt=9.600000, rms=0.405 (0.041%), neg=0, invalid=762 0443: dt=6.400000, rms=0.405 (0.008%), neg=0, invalid=762 0444: dt=6.400000, rms=0.405 (0.001%), neg=0, invalid=762 0445: dt=6.400000, rms=0.405 (-0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0446: dt=86.032787, rms=0.402 (0.658%), neg=0, invalid=762 0447: dt=22.294294, rms=0.401 (0.297%), neg=0, invalid=762 0448: dt=44.800000, rms=0.400 (0.100%), neg=0, invalid=762 0449: dt=44.800000, rms=0.400 (0.018%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0450: dt=44.800000, rms=0.399 (0.272%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0451: dt=44.800000, rms=0.398 (0.258%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0452: dt=44.800000, rms=0.397 (0.203%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0453: dt=44.800000, rms=0.397 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0454: dt=44.800000, rms=0.396 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0455: dt=44.800000, rms=0.395 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0456: dt=44.800000, rms=0.395 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0457: dt=44.800000, rms=0.394 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0458: dt=11.200000, rms=0.394 (0.060%), neg=0, invalid=762 0459: dt=32.000000, rms=0.394 (0.016%), neg=0, invalid=762 0460: dt=32.000000, rms=0.394 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=762 0461: dt=0.432000, rms=0.399 (0.001%), neg=0, invalid=762 0462: dt=0.093750, rms=0.399 (0.000%), neg=0, invalid=762 0463: dt=0.093750, rms=0.399 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.399, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0464: dt=4.000000, rms=0.399 (0.033%), neg=0, invalid=762 0465: dt=2.304000, rms=0.399 (0.006%), neg=0, invalid=762 0466: dt=2.304000, rms=0.399 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0467: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0468: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.393, neg=0, invalid=762 iter 0, gcam->neg = 428 after 19 iterations, nbhd size=1, neg = 0 0469: dt=1.135965, rms=0.386 (1.824%), neg=0, invalid=762 0470: dt=0.000027, rms=0.386 (0.000%), neg=0, invalid=762 0471: dt=0.000027, rms=0.386 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=762 0472: dt=0.112000, rms=0.385 (0.110%), neg=0, invalid=762 0473: dt=0.112000, rms=0.385 (0.064%), neg=0, invalid=762 0474: dt=0.112000, rms=0.385 (0.054%), neg=0, invalid=762 0475: dt=0.112000, rms=0.385 (0.043%), neg=0, invalid=762 0476: dt=0.112000, rms=0.385 (-0.024%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 10 minutes and 21 seconds. mri_ca_register utimesec 5821.525568 mri_ca_register stimesec 14.594771 mri_ca_register ru_maxrss 1328876 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 18205752 mri_ca_register ru_majflt 5 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 740 mri_ca_register ru_oublock 62864 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 60607 mri_ca_register ru_nivcsw 13326 FSRUNTIME@ mri_ca_register 1.1726 hours 8 threads #-------------------------------------- #@# SubCort Seg Fri Sep 9 14:17:01 CDT 2022 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname acn179 machine x86_64 setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 8 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.36 Atlas used for the 3D morph was /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.12102 (18) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (876 voxels, overlap=0.894) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (876 voxels, peak = 19), gca=19.3 gca peak = 0.17677 (13) mri peak = 0.12085 (21) Right_Lateral_Ventricle (43): linear fit = 1.27 x + 0.0 (543 voxels, overlap=0.630) Right_Lateral_Ventricle (43): linear fit = 1.27 x + 0.0 (543 voxels, peak = 17), gca=16.6 gca peak = 0.28129 (95) mri peak = 0.10307 (97) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (402 voxels, overlap=1.018) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (402 voxels, peak = 98), gca=98.3 gca peak = 0.16930 (96) mri peak = 0.08315 (99) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (450 voxels, overlap=0.991) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (450 voxels, peak = 101), gca=101.3 gca peak = 0.24553 (55) mri peak = 0.08832 (64) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1019 voxels, overlap=0.482) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1019 voxels, peak = 64), gca=63.5 gca peak = 0.30264 (59) mri peak = 0.08892 (63) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (861 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (861 voxels, peak = 66), gca=65.8 gca peak = 0.07580 (103) mri peak = 0.09212 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (43043 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (43043 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.08242 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (45381 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (45381 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04720 (65) Left_Cerebral_Cortex (3): linear fit = 1.11 x + 0.0 (21835 voxels, overlap=0.722) Left_Cerebral_Cortex (3): linear fit = 1.11 x + 0.0 (21835 voxels, peak = 64), gca=64.1 gca peak = 0.11620 (58) mri peak = 0.04122 (66) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (22971 voxels, overlap=0.656) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (22971 voxels, peak = 68), gca=67.6 gca peak = 0.30970 (66) mri peak = 0.09581 (79) Right_Caudate (50): linear fit = 1.17 x + 0.0 (839 voxels, overlap=0.021) Right_Caudate (50): linear fit = 1.17 x + 0.0 (839 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.10999 (79) Left_Caudate (11): linear fit = 1.04 x + 0.0 (839 voxels, overlap=0.678) Left_Caudate (11): linear fit = 1.04 x + 0.0 (839 voxels, peak = 72), gca=72.1 gca peak = 0.13902 (56) mri peak = 0.05485 (66) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (15390 voxels, overlap=0.797) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (15390 voxels, peak = 65), gca=64.7 gca peak = 0.14777 (55) mri peak = 0.05287 (65) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (17291 voxels, overlap=0.439) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (17291 voxels, peak = 66), gca=65.7 gca peak = 0.16765 (84) mri peak = 0.09344 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5206 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5206 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.10119 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4713 voxels, overlap=0.672) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4713 voxels, peak = 90), gca=90.3 gca peak = 0.29869 (57) mri peak = 0.11332 (67) Left_Amygdala (18): linear fit = 1.14 x + 0.0 (501 voxels, overlap=0.988) Left_Amygdala (18): linear fit = 1.14 x + 0.0 (501 voxels, peak = 65), gca=65.3 gca peak = 0.33601 (57) mri peak = 0.09091 (64) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (593 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (593 voxels, peak = 65), gca=64.7 gca peak = 0.11131 (90) mri peak = 0.07017 (89) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4411 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4411 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.07172 (92) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4539 voxels, overlap=0.680) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4539 voxels, peak = 90), gca=90.1 gca peak = 0.08324 (81) mri peak = 0.05744 (87) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1140 voxels, overlap=0.636) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1140 voxels, peak = 89), gca=88.7 gca peak = 0.10360 (77) mri peak = 0.06355 (84) Right_Putamen (51): linear fit = 1.11 x + 0.0 (1301 voxels, overlap=0.636) Right_Putamen (51): linear fit = 1.11 x + 0.0 (1301 voxels, peak = 85), gca=85.1 gca peak = 0.08424 (78) mri peak = 0.08334 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11913 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11913 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.07610 (88) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1402 voxels, overlap=0.693) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1402 voxels, peak = 95), gca=94.8 gca peak = 0.14500 (87) mri peak = 0.07164 (98) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1429 voxels, overlap=0.843) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1429 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.21538 (24) gca peak = 0.19357 (14) mri peak = 0.14332 (20) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (377 voxels, overlap=0.841) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (377 voxels, peak = 17), gca=16.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.14 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.14 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14850 (20) mri peak = 0.12102 (18) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (876 voxels, overlap=0.909) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (876 voxels, peak = 19), gca=19.3 gca peak = 0.16187 (16) mri peak = 0.12085 (21) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (543 voxels, overlap=0.693) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (543 voxels, peak = 16), gca=16.2 gca peak = 0.28607 (99) mri peak = 0.10307 (97) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (402 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (402 voxels, peak = 99), gca=99.5 gca peak = 0.15758 (101) mri peak = 0.08315 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (450 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (450 voxels, peak = 102), gca=101.5 gca peak = 0.24834 (64) mri peak = 0.08832 (64) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1019 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1019 voxels, peak = 63), gca=63.0 gca peak = 0.30360 (63) mri peak = 0.08892 (63) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (861 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (861 voxels, peak = 62), gca=62.1 gca peak = 0.07615 (105) mri peak = 0.09212 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43043 voxels, overlap=0.755) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43043 voxels, peak = 105), gca=105.0 gca peak = 0.07820 (106) mri peak = 0.08242 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45381 voxels, overlap=0.811) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45381 voxels, peak = 106), gca=106.0 gca peak = 0.08775 (63) mri peak = 0.04720 (65) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (21835 voxels, overlap=0.964) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (21835 voxels, peak = 63), gca=63.0 gca peak = 0.09798 (68) mri peak = 0.04122 (66) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (22971 voxels, overlap=0.973) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (22971 voxels, peak = 67), gca=67.0 gca peak = 0.23089 (78) mri peak = 0.09581 (79) Right_Caudate (50): linear fit = 1.00 x + 0.0 (839 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.00 x + 0.0 (839 voxels, peak = 78), gca=78.0 gca peak = 0.15387 (72) mri peak = 0.10999 (79) Left_Caudate (11): linear fit = 0.99 x + 0.0 (839 voxels, overlap=0.999) Left_Caudate (11): linear fit = 0.99 x + 0.0 (839 voxels, peak = 71), gca=70.9 gca peak = 0.12436 (65) mri peak = 0.05485 (66) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (15390 voxels, overlap=0.996) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (15390 voxels, peak = 64), gca=64.0 gca peak = 0.12227 (66) mri peak = 0.05287 (65) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17291 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17291 voxels, peak = 65), gca=65.0 gca peak = 0.15744 (86) mri peak = 0.09344 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5206 voxels, overlap=0.962) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5206 voxels, peak = 86), gca=85.6 gca peak = 0.14841 (90) mri peak = 0.10119 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4713 voxels, overlap=0.963) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4713 voxels, peak = 90), gca=89.6 gca peak = 0.28278 (65) mri peak = 0.11332 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (501 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (501 voxels, peak = 65), gca=65.0 gca peak = 0.32511 (65) mri peak = 0.09091 (64) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (593 voxels, overlap=0.997) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (593 voxels, peak = 65), gca=65.0 gca peak = 0.11211 (90) mri peak = 0.07017 (89) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4411 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4411 voxels, peak = 89), gca=88.7 gca peak = 0.10410 (90) mri peak = 0.07172 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4539 voxels, overlap=0.945) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4539 voxels, peak = 90), gca=89.6 gca peak = 0.07569 (91) mri peak = 0.05744 (87) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1140 voxels, overlap=0.945) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1140 voxels, peak = 91), gca=90.5 gca peak = 0.07634 (86) mri peak = 0.06355 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1301 voxels, overlap=0.987) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1301 voxels, peak = 86), gca=85.6 gca peak = 0.07899 (86) mri peak = 0.08334 (84) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11913 voxels, overlap=0.809) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11913 voxels, peak = 86), gca=86.0 gca peak = 0.11809 (95) mri peak = 0.07610 (88) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1402 voxels, overlap=0.831) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1402 voxels, peak = 95), gca=94.5 gca peak = 0.17060 (92) mri peak = 0.07164 (98) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1429 voxels, overlap=0.932) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1429 voxels, peak = 91), gca=90.6 gca peak = 0.16742 (29) mri peak = 0.21538 (24) gca peak = 0.17387 (17) mri peak = 0.14332 (20) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (377 voxels, overlap=0.776) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (377 voxels, peak = 17), gca=17.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16626 (36) gca peak Left_Thalamus = 0.36646 (103) gca peak Third_Ventricle = 0.16742 (29) gca peak CSF = 0.19178 (41) gca peak Left_Accumbens_area = 0.73510 (65) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.18678 (27) gca peak Right_Accumbens_area = 0.29776 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14531 (37) gca peak Fifth_Ventricle = 0.53896 (36) gca peak WM_hypointensities = 0.07588 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70613 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 55383 voxels changed in iteration 0 of unlikely voxel relabeling 315 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 46178 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 372 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 60208 changed. image ll: -2.083, PF=0.500 pass 2: 13754 changed. image ll: -2.082, PF=0.500 pass 3: 3448 changed. 35788 voxels changed in iteration 0 of unlikely voxel relabeling 303 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6269 voxels changed in iteration 0 of unlikely voxel relabeling 106 voxels changed in iteration 1 of unlikely voxel relabeling 13 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5232 voxels changed in iteration 0 of unlikely voxel relabeling 83 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 4187 voxels changed in iteration 0 of unlikely voxel relabeling 21 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2009.354119 mri_ca_label stimesec 3.592080 mri_ca_label ru_maxrss 2124756 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 5693903 mri_ca_label ru_majflt 7 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 856 mri_ca_label ru_oublock 456 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 716 mri_ca_label ru_nivcsw 1267 auto-labeling took 32 minutes and 50 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/transforms/cc_up.lta FM0001 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/transforms/cc_up.lta reading aseg from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aseg.auto_noCCseg.mgz reading norm from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/norm.mgz 27619 voxels in left wm, 55483 in right wm, xrange [120, 130] searching rotation angles z=[-7 7], y=[-9 5] searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 global minimum found at slice 126.0, rotations (-1.91, 0.39) final transformation (x=126.0, yr=-1.914, zr=0.386): 0.99942 -0.00673 -0.03340 7.01655; 0.00673 0.99998 -0.00022 3.18245; 0.03340 -0.00000 0.99944 0.85998; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 124 123 eigenvectors: -0.00001 0.00488 0.99999; 0.20484 -0.97878 0.00478; 0.97880 0.20484 -0.00099; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aseg.auto.mgz... corpus callosum segmentation took 0.3 minutes #-------------------------------------- #@# Merge ASeg Fri Sep 9 14:50:09 CDT 2022 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Sep 9 14:50:09 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1169 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 70 (70), valley at 34 (34) csf peak at 10, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 74 (74), valley at 33 (33) csf peak at 10, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 36 seconds. #-------------------------------------------- #@# Mask BFS Fri Sep 9 14:51:46 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1502655 voxels in mask (pct= 8.96) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Sep 9 14:51:47 CDT 2022 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.5 +- 6.2 [79.0 --> 125.0] GM (72.0) : 70.4 +- 9.4 [30.0 --> 95.0] setting bottom of white matter range to 79.7 setting top of gray matter range to 89.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 8012 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4042 filled 13 bright non-wm voxels segmented. 4021 diagonally connected voxels added... white matter segmentation took 0.9 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.27 minutes reading wm segmentation from wm.seg.mgz... 186 voxels added to wm to prevent paths from MTL structures to cortex 1944 additional wm voxels added 0 additional wm voxels added SEG EDIT: 28957 voxels turned on, 38709 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 12 found - 12 modified | TOTAL: 24 pass 2 (xy-): 0 found - 12 modified | TOTAL: 24 pass 1 (yz+): 23 found - 23 modified | TOTAL: 47 pass 2 (yz+): 0 found - 23 modified | TOTAL: 47 pass 1 (yz-): 17 found - 17 modified | TOTAL: 64 pass 2 (yz-): 0 found - 17 modified | TOTAL: 64 pass 1 (xz+): 10 found - 10 modified | TOTAL: 74 pass 2 (xz+): 0 found - 10 modified | TOTAL: 74 pass 1 (xz-): 15 found - 15 modified | TOTAL: 89 pass 2 (xz-): 0 found - 15 modified | TOTAL: 89 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 20 found - 20 modified | TOTAL: 33 pass 2 (+++): 0 found - 20 modified | TOTAL: 33 pass 1 (+++): 8 found - 8 modified | TOTAL: 41 pass 2 (+++): 0 found - 8 modified | TOTAL: 41 pass 1 (+++): 18 found - 18 modified | TOTAL: 59 pass 2 (+++): 0 found - 18 modified | TOTAL: 59 Iteration Number : 1 pass 1 (++): 81 found - 81 modified | TOTAL: 81 pass 2 (++): 0 found - 81 modified | TOTAL: 81 pass 1 (+-): 167 found - 167 modified | TOTAL: 248 pass 2 (+-): 0 found - 167 modified | TOTAL: 248 pass 1 (--): 76 found - 76 modified | TOTAL: 324 pass 2 (--): 0 found - 76 modified | TOTAL: 324 pass 1 (-+): 122 found - 122 modified | TOTAL: 446 pass 2 (-+): 0 found - 122 modified | TOTAL: 446 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 8 found - 8 modified | TOTAL: 13 pass 2 (xy-): 0 found - 8 modified | TOTAL: 13 pass 1 (yz+): 7 found - 7 modified | TOTAL: 20 pass 2 (yz+): 0 found - 7 modified | TOTAL: 20 pass 1 (yz-): 7 found - 7 modified | TOTAL: 27 pass 2 (yz-): 0 found - 7 modified | TOTAL: 27 pass 1 (xz+): 7 found - 7 modified | TOTAL: 34 pass 2 (xz+): 0 found - 7 modified | TOTAL: 34 pass 1 (xz-): 1 found - 1 modified | TOTAL: 35 pass 2 (xz-): 0 found - 1 modified | TOTAL: 35 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 0 found - 0 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 634 (out of 572068: 0.110826) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Sep 9 14:52:59 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05482 -0.02639 -0.03571 1.79343; 0.02453 1.12860 -0.00947 -41.01125; 0.03593 0.00923 1.05506 -27.84492; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 995 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (128, 111, 94), TAL = (0.0, -34.0, 17.0) talairach voxel to voxel transform 0.94643 0.02187 0.03223 0.09708; -0.02084 0.88551 0.00724 36.55479; -0.03204 -0.00849 0.94665 26.06849; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (128, 111, 94) --> (0.0, -34.0, 17.0) done. writing output to filled.mgz... filling took 0.3 minutes talairach cc position changed to (0.00, -34.00, 17.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(18.00, -34.00, 17.00) SRC: (109.66, 133.23, 110.59) search lh wm seed point around talairach space (-18.00, -34.00, 17.00), SRC: (143.73, 132.48, 109.43) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Sep 9 14:53:18 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 2 found - 2 modified | TOTAL: 10 pass 2 (xz+): 0 found - 2 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 23 (out of 275386: 0.008352) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1341 vertices, 1464 faces slice 60: 7761 vertices, 8043 faces slice 70: 16445 vertices, 16820 faces slice 80: 27483 vertices, 27892 faces slice 90: 39232 vertices, 39655 faces slice 100: 50235 vertices, 50639 faces slice 110: 62975 vertices, 63418 faces slice 120: 75903 vertices, 76359 faces slice 130: 88596 vertices, 89039 faces slice 140: 100531 vertices, 100972 faces slice 150: 111451 vertices, 111789 faces slice 160: 120191 vertices, 120540 faces slice 170: 128348 vertices, 128680 faces slice 180: 135692 vertices, 136005 faces slice 190: 141985 vertices, 142245 faces slice 200: 146282 vertices, 146482 faces slice 210: 147406 vertices, 147472 faces slice 220: 147406 vertices, 147472 faces slice 230: 147406 vertices, 147472 faces slice 240: 147406 vertices, 147472 faces slice 250: 147406 vertices, 147472 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 147406 voxel in cpt #1: X=-66 [v=147406,e=442416,f=294944] located at (-25.623041, -9.122037, -6.379347) For the whole surface: X=-66 [v=147406,e=442416,f=294944] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri Sep 9 14:53:22 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 2 found - 2 modified | TOTAL: 4 pass 2 (-+): 0 found - 2 modified | TOTAL: 4 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 = 13 (out of 277456: 0.004685) 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 50: 441 vertices, 489 faces slice 60: 3971 vertices, 4184 faces slice 70: 11078 vertices, 11324 faces slice 80: 20204 vertices, 20541 faces slice 90: 31657 vertices, 32063 faces slice 100: 44807 vertices, 45204 faces slice 110: 56929 vertices, 57350 faces slice 120: 70309 vertices, 70789 faces slice 130: 83483 vertices, 83963 faces slice 140: 96756 vertices, 97237 faces slice 150: 108439 vertices, 108854 faces slice 160: 118442 vertices, 118787 faces slice 170: 126854 vertices, 127193 faces slice 180: 134939 vertices, 135268 faces slice 190: 141581 vertices, 141840 faces slice 200: 146486 vertices, 146715 faces slice 210: 148592 vertices, 148646 faces slice 220: 148592 vertices, 148646 faces slice 230: 148592 vertices, 148646 faces slice 240: 148592 vertices, 148646 faces slice 250: 148592 vertices, 148646 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... 148592 voxel in cpt #1: X=-54 [v=148592,e=445938,f=297292] located at (29.817326, -4.514025, -5.690353) For the whole surface: X=-54 [v=148592,e=445938,f=297292] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Sep 9 14:53:27 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Sep 9 14:53:27 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 942905 of (942905 942908) to complete... Waiting for PID 942908 of (942905 942908) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... 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... PIDs (942905 942908) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Sep 9 14:53:31 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Sep 9 14:53:31 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 942968 of (942968 942971) to complete... Waiting for PID 942971 of (942968 942971) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 75782 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 73.985832 mris_inflate stimesec 0.953317 mris_inflate ru_maxrss 235252 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 234897 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 502 mris_inflate ru_oublock 10384 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 98215 mris_inflate ru_nivcsw 1833 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.6 mm, total surface area = 76352 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.159 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.040 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 67.958244 mris_inflate stimesec 1.229542 mris_inflate ru_maxrss 237036 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 207777 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10464 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 94924 mris_inflate ru_nivcsw 530 PIDs (942968 942971) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Sep 9 14:53:48 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Sep 9 14:53:48 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 943038 of (943038 943041) to complete... Waiting for PID 943041 of (943038 943041) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.55 (0.00-->7.91) (max @ vno 51022 --> 51023) face area 0.02 +- 0.03 (-0.20-->1.13) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.307... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.672, avgs=0 005/300: dt: 0.9000, rms radial error=176.413, avgs=0 010/300: dt: 0.9000, rms radial error=175.856, avgs=0 015/300: dt: 0.9000, rms radial error=175.125, avgs=0 020/300: dt: 0.9000, rms radial error=174.292, avgs=0 025/300: dt: 0.9000, rms radial error=173.401, avgs=0 030/300: dt: 0.9000, rms radial error=172.477, avgs=0 035/300: dt: 0.9000, rms radial error=171.535, avgs=0 040/300: dt: 0.9000, rms radial error=170.586, avgs=0 045/300: dt: 0.9000, rms radial error=169.634, avgs=0 050/300: dt: 0.9000, rms radial error=168.685, avgs=0 055/300: dt: 0.9000, rms radial error=167.737, avgs=0 060/300: dt: 0.9000, rms radial error=166.794, avgs=0 065/300: dt: 0.9000, rms radial error=165.857, avgs=0 070/300: dt: 0.9000, rms radial error=164.924, avgs=0 075/300: dt: 0.9000, rms radial error=163.997, avgs=0 080/300: dt: 0.9000, rms radial error=163.075, avgs=0 085/300: dt: 0.9000, rms radial error=162.158, avgs=0 090/300: dt: 0.9000, rms radial error=161.246, avgs=0 095/300: dt: 0.9000, rms radial error=160.339, avgs=0 100/300: dt: 0.9000, rms radial error=159.436, avgs=0 105/300: dt: 0.9000, rms radial error=158.539, avgs=0 110/300: dt: 0.9000, rms radial error=157.647, avgs=0 115/300: dt: 0.9000, rms radial error=156.759, avgs=0 120/300: dt: 0.9000, rms radial error=155.876, avgs=0 125/300: dt: 0.9000, rms radial error=154.999, avgs=0 130/300: dt: 0.9000, rms radial error=154.125, avgs=0 135/300: dt: 0.9000, rms radial error=153.257, avgs=0 140/300: dt: 0.9000, rms radial error=152.393, avgs=0 145/300: dt: 0.9000, rms radial error=151.535, avgs=0 150/300: dt: 0.9000, rms radial error=150.680, avgs=0 155/300: dt: 0.9000, rms radial error=149.831, avgs=0 160/300: dt: 0.9000, rms radial error=148.986, avgs=0 165/300: dt: 0.9000, rms radial error=148.146, avgs=0 170/300: dt: 0.9000, rms radial error=147.311, avgs=0 175/300: dt: 0.9000, rms radial error=146.481, avgs=0 180/300: dt: 0.9000, rms radial error=145.655, avgs=0 185/300: dt: 0.9000, rms radial error=144.834, avgs=0 190/300: dt: 0.9000, rms radial error=144.017, avgs=0 195/300: dt: 0.9000, rms radial error=143.205, avgs=0 200/300: dt: 0.9000, rms radial error=142.398, avgs=0 205/300: dt: 0.9000, rms radial error=141.595, avgs=0 210/300: dt: 0.9000, rms radial error=140.797, avgs=0 215/300: dt: 0.9000, rms radial error=140.003, avgs=0 220/300: dt: 0.9000, rms radial error=139.214, avgs=0 225/300: dt: 0.9000, rms radial error=138.429, avgs=0 230/300: dt: 0.9000, rms radial error=137.648, avgs=0 235/300: dt: 0.9000, rms radial error=136.872, avgs=0 240/300: dt: 0.9000, rms radial error=136.100, avgs=0 245/300: dt: 0.9000, rms radial error=135.333, avgs=0 250/300: dt: 0.9000, rms radial error=134.570, avgs=0 255/300: dt: 0.9000, rms radial error=133.811, avgs=0 260/300: dt: 0.9000, rms radial error=133.056, avgs=0 265/300: dt: 0.9000, rms radial error=132.306, avgs=0 270/300: dt: 0.9000, rms radial error=131.560, avgs=0 275/300: dt: 0.9000, rms radial error=130.818, avgs=0 280/300: dt: 0.9000, rms radial error=130.080, avgs=0 285/300: dt: 0.9000, rms radial error=129.346, avgs=0 290/300: dt: 0.9000, rms radial error=128.616, avgs=0 295/300: dt: 0.9000, rms radial error=127.891, avgs=0 300/300: dt: 0.9000, rms radial error=127.169, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17390.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2956.93 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 = 317.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00454 epoch 4 (K=640.0), pass 1, starting sse = 25.35 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00661 final distance error %27.35 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 411.346360 mris_sphere stimesec 1.898187 mris_sphere ru_maxrss 235480 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 613301 mris_sphere ru_majflt 4 mris_sphere ru_nswap 0 mris_sphere ru_inblock 514 mris_sphere ru_oublock 10408 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 135377 mris_sphere ru_nivcsw 2266 FSRUNTIME@ mris_sphere 0.0284 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.54 (0.00-->7.66) (max @ vno 54003 --> 55248) face area 0.02 +- 0.03 (-0.11-->0.78) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.307... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.781, avgs=0 005/300: dt: 0.9000, rms radial error=176.521, avgs=0 010/300: dt: 0.9000, rms radial error=175.963, avgs=0 015/300: dt: 0.9000, rms radial error=175.230, avgs=0 020/300: dt: 0.9000, rms radial error=174.396, avgs=0 025/300: dt: 0.9000, rms radial error=173.505, avgs=0 030/300: dt: 0.9000, rms radial error=172.582, avgs=0 035/300: dt: 0.9000, rms radial error=171.643, avgs=0 040/300: dt: 0.9000, rms radial error=170.695, avgs=0 045/300: dt: 0.9000, rms radial error=169.745, avgs=0 050/300: dt: 0.9000, rms radial error=168.796, avgs=0 055/300: dt: 0.9000, rms radial error=167.849, avgs=0 060/300: dt: 0.9000, rms radial error=166.906, avgs=0 065/300: dt: 0.9000, rms radial error=165.968, avgs=0 070/300: dt: 0.9000, rms radial error=165.035, avgs=0 075/300: dt: 0.9000, rms radial error=164.107, avgs=0 080/300: dt: 0.9000, rms radial error=163.184, avgs=0 085/300: dt: 0.9000, rms radial error=162.267, avgs=0 090/300: dt: 0.9000, rms radial error=161.355, avgs=0 095/300: dt: 0.9000, rms radial error=160.448, avgs=0 100/300: dt: 0.9000, rms radial error=159.546, avgs=0 105/300: dt: 0.9000, rms radial error=158.649, avgs=0 110/300: dt: 0.9000, rms radial error=157.757, avgs=0 115/300: dt: 0.9000, rms radial error=156.869, avgs=0 120/300: dt: 0.9000, rms radial error=155.987, avgs=0 125/300: dt: 0.9000, rms radial error=155.109, avgs=0 130/300: dt: 0.9000, rms radial error=154.236, avgs=0 135/300: dt: 0.9000, rms radial error=153.368, avgs=0 140/300: dt: 0.9000, rms radial error=152.505, avgs=0 145/300: dt: 0.9000, rms radial error=151.646, avgs=0 150/300: dt: 0.9000, rms radial error=150.792, avgs=0 155/300: dt: 0.9000, rms radial error=149.943, avgs=0 160/300: dt: 0.9000, rms radial error=149.098, avgs=0 165/300: dt: 0.9000, rms radial error=148.258, avgs=0 170/300: dt: 0.9000, rms radial error=147.423, avgs=0 175/300: dt: 0.9000, rms radial error=146.592, avgs=0 180/300: dt: 0.9000, rms radial error=145.766, avgs=0 185/300: dt: 0.9000, rms radial error=144.945, avgs=0 190/300: dt: 0.9000, rms radial error=144.128, avgs=0 195/300: dt: 0.9000, rms radial error=143.317, avgs=0 200/300: dt: 0.9000, rms radial error=142.510, avgs=0 205/300: dt: 0.9000, rms radial error=141.707, avgs=0 210/300: dt: 0.9000, rms radial error=140.909, avgs=0 215/300: dt: 0.9000, rms radial error=140.116, avgs=0 220/300: dt: 0.9000, rms radial error=139.327, avgs=0 225/300: dt: 0.9000, rms radial error=138.542, avgs=0 230/300: dt: 0.9000, rms radial error=137.761, avgs=0 235/300: dt: 0.9000, rms radial error=136.985, avgs=0 240/300: dt: 0.9000, rms radial error=136.213, avgs=0 245/300: dt: 0.9000, rms radial error=135.446, avgs=0 250/300: dt: 0.9000, rms radial error=134.683, avgs=0 255/300: dt: 0.9000, rms radial error=133.923, avgs=0 260/300: dt: 0.9000, rms radial error=133.169, avgs=0 265/300: dt: 0.9000, rms radial error=132.418, avgs=0 270/300: dt: 0.9000, rms radial error=131.672, avgs=0 275/300: dt: 0.9000, rms radial error=130.929, avgs=0 280/300: dt: 0.9000, rms radial error=130.191, avgs=0 285/300: dt: 0.9000, rms radial error=129.457, avgs=0 290/300: dt: 0.9000, rms radial error=128.727, avgs=0 295/300: dt: 0.9000, rms radial error=128.001, avgs=0 300/300: dt: 0.9000, rms radial error=127.279, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17499.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=40.0), pass 1, starting sse = 2942.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 298.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00584 epoch 4 (K=640.0), pass 1, starting sse = 19.12 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/16 = 0.00821 final distance error %25.17 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 494.387007 mris_sphere stimesec 0.998428 mris_sphere ru_maxrss 237264 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 299420 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10488 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 149536 mris_sphere ru_nivcsw 3255 FSRUNTIME@ mris_sphere 0.0346 hours 1 threads PIDs (943038 943041) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Fri Sep 9 14:55:52 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri Sep 9 14:55:52 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri Sep 9 14:55:53 CDT 2022 mris_fix_topology -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 FM0001 lh #@# Fix Topology rh Fri Sep 9 14:55:53 CDT 2022 mris_fix_topology -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 FM0001 rh Waiting for PID 943382 of (943382 943385) to complete... Waiting for PID 943385 of (943382 943385) to complete... mris_fix_topology -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 FM0001 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-66 (nv=147406, nf=294944, ne=442416, g=34) 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... 7213 ambiguous faces found in tessellation segmenting defects... 38 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 1 37 defects to be corrected 0 vertices coincident reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2751 (-4.6375) -vertex loglikelihood: -6.2282 (-3.1141) -normal dot loglikelihood: -3.5914 (-3.5914) -quad curv loglikelihood: -6.2687 (-3.1343) Total Loglikelihood : -25.3634 CORRECTING DEFECT 0 (vertices=270, convex hull=144, v0=127) After retessellation of defect 0 (v0=127), euler #=-35 (143194,428197,284968) : difference with theory (-34) = 1 CORRECTING DEFECT 1 (vertices=946, convex hull=615, v0=2548) L defect detected... After retessellation of defect 1 (v0=2548), euler #=-33 (143324,428910,285553) : difference with theory (-33) = 0 CORRECTING DEFECT 2 (vertices=29, convex hull=55, v0=4015) After retessellation of defect 2 (v0=4015), euler #=-32 (143333,428958,285593) : difference with theory (-32) = 0 CORRECTING DEFECT 3 (vertices=8, convex hull=16, v0=9418) After retessellation of defect 3 (v0=9418), euler #=-31 (143333,428964,285600) : difference with theory (-31) = 0 CORRECTING DEFECT 4 (vertices=438, convex hull=222, v0=49878) After retessellation of defect 4 (v0=49878), euler #=-30 (143370,429186,285786) : difference with theory (-30) = 0 CORRECTING DEFECT 5 (vertices=158, convex hull=170, v0=60391) After retessellation of defect 5 (v0=60391), euler #=-29 (143455,429522,286038) : difference with theory (-29) = 0 CORRECTING DEFECT 6 (vertices=23, convex hull=59, v0=61195) After retessellation of defect 6 (v0=61195), euler #=-28 (143467,429581,286086) : difference with theory (-28) = 0 CORRECTING DEFECT 7 (vertices=17, convex hull=26, v0=70457) After retessellation of defect 7 (v0=70457), euler #=-27 (143471,429601,286103) : difference with theory (-27) = 0 CORRECTING DEFECT 8 (vertices=725, convex hull=336, v0=71861) After retessellation of defect 8 (v0=71861), euler #=-26 (143558,430022,286438) : difference with theory (-26) = 0 CORRECTING DEFECT 9 (vertices=51, convex hull=88, v0=73360) After retessellation of defect 9 (v0=73360), euler #=-25 (143583,430133,286525) : difference with theory (-25) = 0 CORRECTING DEFECT 10 (vertices=18, convex hull=30, v0=74376) After retessellation of defect 10 (v0=74376), euler #=-24 (143586,430149,286539) : difference with theory (-24) = 0 CORRECTING DEFECT 11 (vertices=59, convex hull=26, v0=79957) After retessellation of defect 11 (v0=79957), euler #=-23 (143594,430182,286565) : difference with theory (-23) = 0 CORRECTING DEFECT 12 (vertices=23, convex hull=42, v0=83706) After retessellation of defect 12 (v0=83706), euler #=-22 (143603,430223,286598) : difference with theory (-22) = 0 CORRECTING DEFECT 13 (vertices=34, convex hull=54, v0=84388) After retessellation of defect 13 (v0=84388), euler #=-21 (143620,430300,286659) : difference with theory (-21) = 0 CORRECTING DEFECT 14 (vertices=33, convex hull=74, v0=88394) After retessellation of defect 14 (v0=88394), euler #=-20 (143635,430376,286721) : difference with theory (-20) = 0 CORRECTING DEFECT 15 (vertices=27, convex hull=70, v0=88554) After retessellation of defect 15 (v0=88554), euler #=-19 (143645,430433,286769) : difference with theory (-19) = 0 CORRECTING DEFECT 16 (vertices=9, convex hull=17, v0=90810) After retessellation of defect 16 (v0=90810), euler #=-18 (143645,430440,286777) : difference with theory (-18) = 0 CORRECTING DEFECT 17 (vertices=26, convex hull=21, v0=95870) After retessellation of defect 17 (v0=95870), euler #=-17 (143648,430454,286789) : difference with theory (-17) = 0 CORRECTING DEFECT 18 (vertices=67, convex hull=70, v0=96568) After retessellation of defect 18 (v0=96568), euler #=-16 (143677,430574,286881) : difference with theory (-16) = 0 CORRECTING DEFECT 19 (vertices=35, convex hull=29, v0=98917) After retessellation of defect 19 (v0=98917), euler #=-15 (143686,430609,286908) : difference with theory (-15) = 0 CORRECTING DEFECT 20 (vertices=11, convex hull=34, v0=101416) After retessellation of defect 20 (v0=101416), euler #=-14 (143690,430630,286926) : difference with theory (-14) = 0 CORRECTING DEFECT 21 (vertices=16, convex hull=25, v0=102387) After retessellation of defect 21 (v0=102387), euler #=-13 (143692,430643,286938) : difference with theory (-13) = 0 CORRECTING DEFECT 22 (vertices=595, convex hull=222, v0=102448) After retessellation of defect 22 (v0=102448), euler #=-12 (143746,430912,287154) : difference with theory (-12) = 0 CORRECTING DEFECT 23 (vertices=55, convex hull=35, v0=102835) After retessellation of defect 23 (v0=102835), euler #=-11 (143752,430943,287180) : difference with theory (-11) = 0 CORRECTING DEFECT 24 (vertices=14, convex hull=18, v0=107169) After retessellation of defect 24 (v0=107169), euler #=-10 (143756,430959,287193) : difference with theory (-10) = 0 CORRECTING DEFECT 25 (vertices=11, convex hull=23, v0=108272) After retessellation of defect 25 (v0=108272), euler #=-9 (143760,430976,287207) : difference with theory (-9) = 0 CORRECTING DEFECT 26 (vertices=43, convex hull=47, v0=109370) After retessellation of defect 26 (v0=109370), euler #=-8 (143780,431055,287267) : difference with theory (-8) = 0 CORRECTING DEFECT 27 (vertices=7, convex hull=19, v0=110833) After retessellation of defect 27 (v0=110833), euler #=-7 (143780,431061,287274) : difference with theory (-7) = 0 CORRECTING DEFECT 28 (vertices=31, convex hull=85, v0=111094) After retessellation of defect 28 (v0=111094), euler #=-6 (143801,431156,287349) : difference with theory (-6) = 0 CORRECTING DEFECT 29 (vertices=31, convex hull=74, v0=114874) After retessellation of defect 29 (v0=114874), euler #=-5 (143813,431221,287403) : difference with theory (-5) = 0 CORRECTING DEFECT 30 (vertices=34, convex hull=62, v0=117240) After retessellation of defect 30 (v0=117240), euler #=-4 (143832,431301,287465) : difference with theory (-4) = 0 CORRECTING DEFECT 31 (vertices=228, convex hull=207, v0=121754) After retessellation of defect 31 (v0=121754), euler #=-3 (143931,431704,287770) : difference with theory (-3) = 0 CORRECTING DEFECT 32 (vertices=82, convex hull=38, v0=132020) After retessellation of defect 32 (v0=132020), euler #=-2 (143939,431742,287801) : difference with theory (-2) = 0 CORRECTING DEFECT 33 (vertices=29, convex hull=55, v0=137857) After retessellation of defect 33 (v0=137857), euler #=-1 (143953,431806,287852) : difference with theory (-1) = 0 CORRECTING DEFECT 34 (vertices=56, convex hull=67, v0=138976) After retessellation of defect 34 (v0=138976), euler #=0 (143967,431877,287910) : difference with theory (0) = 0 CORRECTING DEFECT 35 (vertices=8, convex hull=35, v0=139660) After retessellation of defect 35 (v0=139660), euler #=1 (143968,431888,287921) : difference with theory (1) = 0 CORRECTING DEFECT 36 (vertices=15, convex hull=34, v0=143759) After retessellation of defect 36 (v0=143759), euler #=2 (143971,431907,287938) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.05-->13.67) (max @ vno 22538 --> 34259) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.05-->13.67) (max @ vno 22538 --> 34259) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 118 mutations (34.8%), 221 crossovers (65.2%), 576 vertices were eliminated building final representation... 3435 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=143971, nf=287938, ne=431907, g=0) writing corrected surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 23.9 minutes 0 defective edges removing intersecting faces 000: 392 intersecting 001: 26 intersecting mris_fix_topology utimesec 1442.804743 mris_fix_topology stimesec 0.942051 mris_fix_topology ru_maxrss 483020 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 1140719 mris_fix_topology ru_majflt 3 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 514 mris_fix_topology ru_oublock 13728 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 8643 mris_fix_topology ru_nivcsw 594 FSRUNTIME@ mris_fix_topology lh 0.3977 hours 1 threads mris_fix_topology -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 FM0001 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=-54 (nv=148592, nf=297292, ne=445938, g=28) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 4640 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 14 -merging segment 19 into 14 -merging segment 25 into 22 36 defects to be corrected 0 vertices coincident reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2890 (-4.6445) -vertex loglikelihood: -6.1740 (-3.0870) -normal dot loglikelihood: -3.6362 (-3.6362) -quad curv loglikelihood: -6.6387 (-3.3193) Total Loglikelihood : -25.7378 CORRECTING DEFECT 0 (vertices=10, convex hull=16, v0=2405) After retessellation of defect 0 (v0=2405), euler #=-36 (145814,436402,290552) : difference with theory (-33) = 3 CORRECTING DEFECT 1 (vertices=13, convex hull=28, v0=8892) After retessellation of defect 1 (v0=8892), euler #=-35 (145816,436417,290566) : difference with theory (-32) = 3 CORRECTING DEFECT 2 (vertices=36, convex hull=88, v0=15256) After retessellation of defect 2 (v0=15256), euler #=-34 (145836,436513,290643) : difference with theory (-31) = 3 CORRECTING DEFECT 3 (vertices=98, convex hull=48, v0=21180) After retessellation of defect 3 (v0=21180), euler #=-33 (145844,436560,290683) : difference with theory (-30) = 3 CORRECTING DEFECT 4 (vertices=39, convex hull=58, v0=25768) After retessellation of defect 4 (v0=25768), euler #=-32 (145867,436651,290752) : difference with theory (-29) = 3 CORRECTING DEFECT 5 (vertices=29, convex hull=63, v0=25832) After retessellation of defect 5 (v0=25832), euler #=-31 (145886,436733,290816) : difference with theory (-28) = 3 CORRECTING DEFECT 6 (vertices=51, convex hull=32, v0=31651) After retessellation of defect 6 (v0=31651), euler #=-30 (145888,436753,290835) : difference with theory (-27) = 3 CORRECTING DEFECT 7 (vertices=7, convex hull=23, v0=35246) After retessellation of defect 7 (v0=35246), euler #=-29 (145890,436765,290846) : difference with theory (-26) = 3 CORRECTING DEFECT 8 (vertices=6, convex hull=25, v0=39416) After retessellation of defect 8 (v0=39416), euler #=-28 (145892,436778,290858) : difference with theory (-25) = 3 CORRECTING DEFECT 9 (vertices=32, convex hull=66, v0=41076) After retessellation of defect 9 (v0=41076), euler #=-27 (145910,436856,290919) : difference with theory (-24) = 3 CORRECTING DEFECT 10 (vertices=24, convex hull=43, v0=48845) After retessellation of defect 10 (v0=48845), euler #=-26 (145928,436927,290973) : difference with theory (-23) = 3 CORRECTING DEFECT 11 (vertices=25, convex hull=33, v0=51423) After retessellation of defect 11 (v0=51423), euler #=-25 (145931,436948,290992) : difference with theory (-22) = 3 CORRECTING DEFECT 12 (vertices=271, convex hull=164, v0=51511) After retessellation of defect 12 (v0=51511), euler #=-24 (146028,437316,291264) : difference with theory (-21) = 3 CORRECTING DEFECT 13 (vertices=30, convex hull=62, v0=51597) After retessellation of defect 13 (v0=51597), euler #=-23 (146044,437388,291321) : difference with theory (-20) = 3 CORRECTING DEFECT 14 (vertices=251, convex hull=263, v0=56624) normal vector of length zero at vertex 146529 with 3 faces normal vector of length zero at vertex 146529 with 3 faces normal vector of length zero at vertex 146529 with 3 faces normal vector of length zero at vertex 146529 with 3 faces After retessellation of defect 14 (v0=56624), euler #=-20 (146098,437693,291575) : difference with theory (-19) = 1 CORRECTING DEFECT 15 (vertices=36, convex hull=31, v0=59489) After retessellation of defect 15 (v0=59489), euler #=-19 (146100,437710,291591) : difference with theory (-18) = 1 CORRECTING DEFECT 16 (vertices=27, convex hull=50, v0=60729) After retessellation of defect 16 (v0=60729), euler #=-18 (146115,437779,291646) : difference with theory (-17) = 1 CORRECTING DEFECT 17 (vertices=29, convex hull=86, v0=64794) After retessellation of defect 17 (v0=64794), euler #=-17 (146124,437840,291699) : difference with theory (-16) = 1 CORRECTING DEFECT 18 (vertices=35, convex hull=26, v0=70270) After retessellation of defect 18 (v0=70270), euler #=-16 (146127,437858,291715) : difference with theory (-15) = 1 CORRECTING DEFECT 19 (vertices=21, convex hull=26, v0=74162) After retessellation of defect 19 (v0=74162), euler #=-15 (146128,437870,291727) : difference with theory (-14) = 1 CORRECTING DEFECT 20 (vertices=817, convex hull=324, v0=76380) After retessellation of defect 20 (v0=76380), euler #=-13 (146197,438262,292052) : difference with theory (-13) = 0 CORRECTING DEFECT 21 (vertices=45, convex hull=47, v0=89320) After retessellation of defect 21 (v0=89320), euler #=-12 (146219,438346,292115) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=15, convex hull=19, v0=91188) After retessellation of defect 22 (v0=91188), euler #=-11 (146221,438358,292126) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=539, convex hull=240, v0=98911) After retessellation of defect 23 (v0=98911), euler #=-10 (146305,438725,292410) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=48, convex hull=34, v0=102662) After retessellation of defect 24 (v0=102662), euler #=-9 (146316,438769,292444) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=46, convex hull=96, v0=102830) After retessellation of defect 25 (v0=102830), euler #=-8 (146348,438904,292548) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=32, convex hull=61, v0=104721) After retessellation of defect 26 (v0=104721), euler #=-7 (146357,438956,292592) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=6, convex hull=21, v0=105867) After retessellation of defect 27 (v0=105867), euler #=-6 (146358,438965,292601) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=9, convex hull=24, v0=109206) After retessellation of defect 28 (v0=109206), euler #=-5 (146359,438975,292611) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=11, convex hull=27, v0=110471) After retessellation of defect 29 (v0=110471), euler #=-4 (146360,438987,292623) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=25, convex hull=68, v0=112777) After retessellation of defect 30 (v0=112777), euler #=-3 (146376,439062,292683) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=22, convex hull=42, v0=114481) After retessellation of defect 31 (v0=114481), euler #=-2 (146385,439104,292717) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=19, convex hull=25, v0=120166) After retessellation of defect 32 (v0=120166), euler #=-1 (146385,439113,292727) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=8, convex hull=24, v0=131709) After retessellation of defect 33 (v0=131709), euler #=0 (146388,439129,292741) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=35, convex hull=57, v0=139356) After retessellation of defect 34 (v0=139356), euler #=1 (146400,439187,292788) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=31, convex hull=23, v0=139818) After retessellation of defect 35 (v0=139818), euler #=2 (146402,439200,292800) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.22 (0.03-->5.63) (max @ vno 54744 --> 146421) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.22 (0.03-->5.63) (max @ vno 54744 --> 146421) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 149 mutations (36.1%), 264 crossovers (63.9%), 252 vertices were eliminated building final representation... 2190 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146402, nf=292800, ne=439200, g=0) writing corrected surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.4 minutes 0 defective edges removing intersecting faces 000: 282 intersecting 001: 4 intersecting mris_fix_topology utimesec 1051.803109 mris_fix_topology stimesec 2.078071 mris_fix_topology ru_maxrss 468240 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 1012609 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 226 mris_fix_topology ru_oublock 13928 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 6675 mris_fix_topology ru_nivcsw 7237 FSRUNTIME@ mris_fix_topology rh 0.2899 hours 1 threads PIDs (943382 943385) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 143971 - 431907 + 287938 = 2 --> 0 holes F =2V-4: 287938 = 287942-4 (0) 2E=3F: 863814 = 863814 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 146402 - 439200 + 292800 = 2 --> 0 holes F =2V-4: 292800 = 292804-4 (0) 2E=3F: 878400 = 878400 (0) total defect index = 0 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 96 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 38 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Sep 9 15:19:53 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs FM0001 lh #-------------------------------------------- #@# Make White Surf rh Fri Sep 9 15:19:53 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs FM0001 rh Waiting for PID 956089 of (956089 956092) to complete... Waiting for PID 956092 of (956089 956092) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs FM0001 lh using white.preaparc as white matter name... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/filled.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/brain.finalsurfs.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/../mri/aseg.presurf.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... 32379 bright wm thresholded. 123 bright non-wm voxels segmented. reading original surface position from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.orig... computing class statistics... border white: 277660 voxels (1.65%) border gray 299649 voxels (1.79%) WM (98.0): 98.0 +- 8.3 [70.0 --> 110.0] GM (74.0) : 72.6 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.9 (was 70) setting MAX_BORDER_WHITE to 110.3 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 50.7 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.02-->5.94) (max @ vno 50951 --> 53373) face area 0.27 +- 0.13 (0.00-->8.04) mean absolute distance = 0.76 +- 1.05 3912 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=102+-7.0, GM=71+-7.0 mean inside = 93.7, mean outside = 76.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.9, 83 (83) missing vertices, mean dist 0.1 [0.8 (%40.4)->0.7 (%59.6))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.09-->5.79) (max @ vno 50951 --> 53373) face area 0.27 +- 0.13 (0.00-->6.43) mean absolute distance = 0.39 +- 0.67 4284 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2923371.2, rms=9.162 001: dt: 0.5000, sse=1644478.4, rms=6.242 (31.873%) 002: dt: 0.5000, sse=1139362.4, rms=4.578 (26.657%) 003: dt: 0.5000, sse=950254.4, rms=3.760 (17.860%) 004: dt: 0.5000, sse=870807.5, rms=3.358 (10.692%) 005: dt: 0.5000, sse=843557.3, rms=3.224 (3.985%) 006: dt: 0.5000, sse=828981.8, rms=3.136 (2.742%) rms = 3.13, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=828333.8, rms=3.134 (0.072%) 008: dt: 0.2500, sse=686251.5, rms=2.041 (34.862%) 009: dt: 0.2500, sse=656421.3, rms=1.754 (14.076%) 010: dt: 0.2500, sse=652704.3, rms=1.698 (3.213%) rms = 1.66, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=649985.5, rms=1.662 (2.099%) rms = 1.62, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=645101.2, rms=1.619 (2.615%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.6, 103 (38) missing vertices, mean dist -0.2 [0.4 (%69.2)->0.3 (%30.8))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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 +- 0.25 (0.06-->5.69) (max @ vno 50951 --> 53373) face area 0.34 +- 0.16 (0.00-->8.25) mean absolute distance = 0.29 +- 0.43 4100 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1196344.0, rms=4.204 013: dt: 0.5000, sse=921759.9, rms=2.774 (34.003%) rms = 2.85, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=838759.4, rms=2.171 (21.762%) 015: dt: 0.2500, sse=792474.2, rms=1.753 (19.217%) 016: dt: 0.2500, sse=778188.4, rms=1.582 (9.771%) 017: dt: 0.2500, sse=774696.9, rms=1.512 (4.400%) rms = 1.47, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=770059.7, rms=1.471 (2.735%) rms = 1.43, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=764772.6, rms=1.432 (2.638%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.7, 116 (34) missing vertices, mean dist -0.1 [0.3 (%68.3)->0.2 (%31.7))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.06-->5.62) (max @ vno 50951 --> 53373) face area 0.33 +- 0.16 (0.00-->8.40) mean absolute distance = 0.25 +- 0.36 3383 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=939595.7, rms=2.979 020: dt: 0.5000, sse=865586.6, rms=2.457 (17.527%) rms = 2.74, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=780812.8, rms=1.743 (29.069%) 022: dt: 0.2500, sse=785938.4, rms=1.418 (18.654%) 023: dt: 0.2500, sse=749845.9, rms=1.338 (5.651%) rms = 1.33, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=743581.9, rms=1.326 (0.830%) rms = 1.29, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=740631.8, rms=1.286 (3.029%) 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 mean border=87.5, 141 (28) missing vertices, mean dist -0.1 [0.3 (%55.3)->0.2 (%44.7))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=759730.8, rms=1.623 rms = 1.59, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=760262.4, rms=1.592 (1.954%) 027: dt: 0.2500, sse=732297.9, rms=1.275 (19.889%) 028: dt: 0.2500, sse=713804.9, rms=1.056 (17.200%) rms = 1.15, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=711047.4, rms=1.013 (4.101%) positioning took 0.3 minutes generating cortex label... 5 non-cortical segments detected only using segment with 6910 vertices erasing segment 1 (vno[0] = 99432) erasing segment 2 (vno[0] = 101777) erasing segment 3 (vno[0] = 101790) erasing segment 4 (vno[0] = 103940) writing cortex label to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label... writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.area vertex spacing 0.88 +- 0.25 (0.02-->5.51) (max @ vno 52081 --> 59703) face area 0.33 +- 0.16 (0.00-->8.20) 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... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=58.5, 147 (147) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.7 (%100.0))] %18 local maxima, %42 large gradients and %36 min vals, 152 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=acn17, 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=23744258.0, rms=28.900 001: dt: 0.0500, sse=21064530.0, rms=27.176 (5.964%) 002: dt: 0.0500, sse=19024652.0, rms=25.787 (5.113%) 003: dt: 0.0500, sse=17439200.0, rms=24.653 (4.399%) 004: dt: 0.0500, sse=16167946.0, rms=23.704 (3.849%) 005: dt: 0.0500, sse=15115866.0, rms=22.889 (3.438%) 006: dt: 0.0500, sse=14226786.0, rms=22.177 (3.112%) 007: dt: 0.0500, sse=13454324.0, rms=21.539 (2.877%) 008: dt: 0.0500, sse=12772679.0, rms=20.959 (2.689%) 009: dt: 0.0500, sse=12162324.0, rms=20.427 (2.541%) 010: dt: 0.0500, sse=11611239.0, rms=19.934 (2.414%) positioning took 0.6 minutes mean border=58.1, 105 (63) missing vertices, mean dist 1.3 [0.1 (%0.2)->2.1 (%99.8))] %19 local maxima, %42 large gradients and %34 min vals, 142 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=12739182.0, rms=20.891 011: dt: 0.0500, sse=12225206.0, rms=20.442 (2.149%) 012: dt: 0.0500, sse=11753826.0, rms=20.022 (2.058%) 013: dt: 0.0500, sse=11318460.0, rms=19.625 (1.981%) 014: dt: 0.0500, sse=10915435.0, rms=19.251 (1.908%) 015: dt: 0.0500, sse=10541385.0, rms=18.896 (1.840%) 016: dt: 0.0500, sse=10193034.0, rms=18.560 (1.779%) 017: dt: 0.0500, sse=9866032.0, rms=18.239 (1.731%) 018: dt: 0.0500, sse=9557904.0, rms=17.931 (1.689%) 019: dt: 0.0500, sse=9266646.0, rms=17.635 (1.652%) 020: dt: 0.0500, sse=8990776.0, rms=17.350 (1.617%) positioning took 0.5 minutes mean border=58.0, 122 (48) missing vertices, mean dist 1.1 [0.1 (%3.1)->1.8 (%96.9))] %20 local maxima, %42 large gradients and %34 min vals, 127 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=9091542.0, rms=17.448 021: dt: 0.0500, sse=8822877.0, rms=17.168 (1.609%) 022: dt: 0.0500, sse=8568451.0, rms=16.897 (1.574%) 023: dt: 0.0500, sse=8324543.5, rms=16.634 (1.558%) 024: dt: 0.0500, sse=8092429.5, rms=16.380 (1.530%) 025: dt: 0.0500, sse=7870827.0, rms=16.133 (1.506%) 026: dt: 0.0500, sse=7658587.0, rms=15.893 (1.487%) 027: dt: 0.0500, sse=7454532.5, rms=15.659 (1.474%) 028: dt: 0.0500, sse=7256372.5, rms=15.428 (1.475%) 029: dt: 0.0500, sse=7063947.5, rms=15.200 (1.476%) 030: dt: 0.0500, sse=6877046.0, rms=14.976 (1.477%) positioning took 0.6 minutes mean border=57.9, 175 (40) missing vertices, mean dist 0.9 [0.1 (%10.8)->1.6 (%89.2))] %20 local maxima, %43 large gradients and %34 min vals, 112 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=6963109.5, rms=15.067 031: dt: 0.5000, sse=5607494.0, rms=13.340 (11.460%) 032: dt: 0.5000, sse=4590713.5, rms=11.875 (10.988%) 033: dt: 0.5000, sse=3767186.0, rms=10.542 (11.218%) 034: dt: 0.5000, sse=3107412.8, rms=9.333 (11.472%) 035: dt: 0.5000, sse=2591716.0, rms=8.268 (11.411%) 036: dt: 0.5000, sse=2196149.8, rms=7.345 (11.169%) 037: dt: 0.5000, sse=1891052.9, rms=6.548 (10.840%) 038: dt: 0.5000, sse=1685363.5, rms=5.947 (9.181%) 039: dt: 0.5000, sse=1552270.5, rms=5.528 (7.054%) 040: dt: 0.5000, sse=1473626.4, rms=5.257 (4.894%) 041: dt: 0.5000, sse=1427288.5, rms=5.097 (3.049%) 042: dt: 0.5000, sse=1397098.5, rms=4.983 (2.228%) 043: dt: 0.5000, sse=1375285.4, rms=4.906 (1.559%) 044: dt: 0.5000, sse=1362739.0, rms=4.854 (1.046%) rms = 4.81, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1350099.9, rms=4.810 (0.919%) 046: dt: 0.2500, sse=1201584.5, rms=4.150 (13.713%) 047: dt: 0.2500, sse=1153767.4, rms=3.936 (5.163%) rms = 3.94, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1139847.2, rms=3.867 (1.751%) 049: dt: 0.1250, sse=1121219.9, rms=3.772 (2.463%) rms = 3.76, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1118870.9, rms=3.759 (0.349%) positioning took 1.6 minutes mean border=56.3, 2408 (17) missing vertices, mean dist 0.1 [0.2 (%40.5)->0.4 (%59.5))] %32 local maxima, %33 large gradients and %30 min vals, 84 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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=1530295.6, rms=4.728 051: dt: 0.5000, sse=1451960.6, rms=4.438 (6.127%) 052: dt: 0.5000, sse=1393466.5, rms=4.226 (4.775%) rms = 4.44, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1229035.4, rms=3.390 (19.783%) 054: dt: 0.2500, sse=1184328.6, rms=3.119 (8.010%) rms = 3.10, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1181817.0, rms=3.104 (0.468%) 056: dt: 0.1250, sse=1139910.8, rms=2.833 (8.730%) rms = 2.79, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1132696.9, rms=2.788 (1.607%) positioning took 0.7 minutes mean border=55.3, 2511 (13) missing vertices, mean dist 0.1 [0.2 (%39.7)->0.3 (%60.3))] %43 local maxima, %22 large gradients and %30 min vals, 76 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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=1209037.2, rms=3.270 rms = 3.95, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1153437.0, rms=2.935 (10.231%) 059: dt: 0.2500, sse=1142252.9, rms=2.867 (2.333%) rms = 2.87, time step reduction 2 of 3 to 0.125... rms = 2.82, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1135645.6, rms=2.822 (1.574%) positioning took 0.4 minutes mean border=54.7, 4739 (13) missing vertices, mean dist 0.0 [0.2 (%45.1)->0.2 (%54.9))] %47 local maxima, %17 large gradients and %29 min vals, 74 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, 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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1151271.6, rms=2.928 rms = 3.55, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1128189.0, rms=2.775 (5.201%) rms = 2.73, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1118734.8, rms=2.731 (1.609%) 063: dt: 0.1250, sse=1109023.2, rms=2.660 (2.602%) rms = 2.63, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1103721.2, rms=2.629 (1.156%) positioning took 0.4 minutes writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.area.pial vertex spacing 0.98 +- 0.42 (0.07-->6.65) (max @ vno 95057 --> 95056) face area 0.38 +- 0.29 (0.00-->8.19) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 143971 vertices processed 25000 of 143971 vertices processed 50000 of 143971 vertices processed 75000 of 143971 vertices processed 100000 of 143971 vertices processed 125000 of 143971 vertices processed 0 of 143971 vertices processed 25000 of 143971 vertices processed 50000 of 143971 vertices processed 75000 of 143971 vertices processed 100000 of 143971 vertices processed 125000 of 143971 vertices processed thickness calculation complete, 391:611 truncations. 30175 vertices at 0 distance 97474 vertices at 1 distance 92361 vertices at 2 distance 39575 vertices at 3 distance 12151 vertices at 4 distance 3579 vertices at 5 distance 1156 vertices at 6 distance 405 vertices at 7 distance 164 vertices at 8 distance 94 vertices at 9 distance 65 vertices at 10 distance 54 vertices at 11 distance 44 vertices at 12 distance 30 vertices at 13 distance 12 vertices at 14 distance 8 vertices at 15 distance 13 vertices at 16 distance 14 vertices at 17 distance 14 vertices at 18 distance 4 vertices at 19 distance 10 vertices at 20 distance writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.thickness positioning took 8.9 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs FM0001 rh using white.preaparc as white matter name... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/filled.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/brain.finalsurfs.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/../mri/aseg.presurf.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... 32379 bright wm thresholded. 123 bright non-wm voxels segmented. reading original surface position from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.orig... computing class statistics... border white: 277660 voxels (1.65%) border gray 299649 voxels (1.79%) WM (98.0): 98.0 +- 8.3 [70.0 --> 110.0] GM (74.0) : 72.6 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.9 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 50.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->4.01) (max @ vno 145981 --> 146025) face area 0.27 +- 0.12 (0.00-->3.60) mean absolute distance = 0.76 +- 1.05 3905 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=103+-7.8, GM=71+-7.8 mean inside = 93.5, mean outside = 76.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=82.6, 97 (97) missing vertices, mean dist 0.1 [0.8 (%42.6)->0.7 (%57.4))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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 0.90 +- 0.25 (0.08-->4.60) (max @ vno 146025 --> 146016) face area 0.27 +- 0.13 (0.00-->4.56) mean absolute distance = 0.40 +- 0.67 4576 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2821625.5, rms=8.840 001: dt: 0.5000, sse=1583415.9, rms=5.983 (32.319%) 002: dt: 0.5000, sse=1103863.1, rms=4.348 (27.322%) 003: dt: 0.5000, sse=929535.2, rms=3.565 (18.020%) 004: dt: 0.5000, sse=856339.4, rms=3.207 (10.031%) 005: dt: 0.5000, sse=838461.8, rms=3.096 (3.481%) 006: dt: 0.5000, sse=840881.1, rms=3.035 (1.940%) rms = 3.03, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=838148.1, rms=3.028 (0.245%) 008: dt: 0.2500, sse=689476.5, rms=1.968 (35.024%) 009: dt: 0.2500, sse=660487.6, rms=1.697 (13.762%) 010: dt: 0.2500, sse=658408.6, rms=1.646 (2.961%) rms = 1.62, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=653483.8, rms=1.618 (1.738%) rms = 1.58, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=650941.0, rms=1.583 (2.141%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=85.1, 113 (45) missing vertices, mean dist -0.2 [0.5 (%68.3)->0.3 (%31.7))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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 (0.04-->4.92) (max @ vno 145981 --> 57292) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.30 +- 0.44 4028 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1175317.8, rms=4.044 013: dt: 0.5000, sse=928382.0, rms=2.705 (33.111%) rms = 2.72, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=843585.5, rms=2.137 (20.991%) 015: dt: 0.2500, sse=800942.4, rms=1.711 (19.951%) 016: dt: 0.2500, sse=781827.6, rms=1.530 (10.571%) 017: dt: 0.2500, sse=774786.6, rms=1.455 (4.863%) rms = 1.42, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=771509.9, rms=1.418 (2.583%) rms = 1.38, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=769041.9, rms=1.380 (2.649%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.1, 108 (34) missing vertices, mean dist -0.1 [0.3 (%67.9)->0.2 (%32.1))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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-->5.54) (max @ vno 145981 --> 57292) face area 0.33 +- 0.16 (0.00-->5.93) mean absolute distance = 0.25 +- 0.36 3668 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=948520.6, rms=2.967 020: dt: 0.5000, sse=876050.1, rms=2.338 (21.223%) rms = 2.59, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=784699.8, rms=1.685 (27.921%) 022: dt: 0.2500, sse=773336.4, rms=1.372 (18.577%) 023: dt: 0.2500, sse=748572.7, rms=1.299 (5.292%) rms = 1.29, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=758653.4, rms=1.288 (0.861%) rms = 1.25, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=745510.8, rms=1.252 (2.815%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=87.8, 120 (30) missing vertices, mean dist -0.1 [0.3 (%56.0)->0.2 (%44.0))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=765841.9, rms=1.612 026: dt: 0.5000, sse=757217.9, rms=1.528 (5.200%) rms = 2.18, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=722904.8, rms=1.085 (28.997%) rms = 1.04, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=742127.1, rms=1.041 (4.074%) 029: dt: 0.1250, sse=717454.4, rms=0.972 (6.576%) rms = 0.96, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=713727.5, rms=0.956 (1.661%) positioning took 0.4 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7077 vertices erasing segment 0 (vno[0] = 39178) erasing segment 2 (vno[0] = 84099) erasing segment 3 (vno[0] = 96979) erasing segment 4 (vno[0] = 99332) erasing segment 5 (vno[0] = 100431) erasing segment 6 (vno[0] = 101628) erasing segment 7 (vno[0] = 104680) erasing segment 8 (vno[0] = 104701) erasing segment 9 (vno[0] = 105723) erasing segment 10 (vno[0] = 123914) writing cortex label to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label... writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.area vertex spacing 0.88 +- 0.25 (0.04-->5.80) (max @ vno 57292 --> 145981) face area 0.32 +- 0.16 (0.00-->6.32) 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... removing 1 vertex label from ripped group removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=59.0, 161 (161) missing vertices, mean dist 1.6 [1.8 (%0.0)->2.7 (%100.0))] %17 local maxima, %39 large gradients and %41 min vals, 173 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=acn17, 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=24091516.0, rms=28.866 001: dt: 0.0500, sse=21420956.0, rms=27.177 (5.853%) 002: dt: 0.0500, sse=19411168.0, rms=25.832 (4.947%) 003: dt: 0.0500, sse=17851366.0, rms=24.738 (4.235%) 004: dt: 0.0500, sse=16603212.0, rms=23.826 (3.686%) 005: dt: 0.0500, sse=15571156.0, rms=23.045 (3.279%) 006: dt: 0.0500, sse=14694337.0, rms=22.360 (2.974%) 007: dt: 0.0500, sse=13932357.0, rms=21.747 (2.742%) 008: dt: 0.0500, sse=13258900.0, rms=21.190 (2.560%) 009: dt: 0.0500, sse=12654229.0, rms=20.677 (2.420%) 010: dt: 0.0500, sse=12105915.0, rms=20.201 (2.303%) positioning took 0.6 minutes mean border=58.6, 102 (42) missing vertices, mean dist 1.3 [0.1 (%0.3)->2.2 (%99.7))] %19 local maxima, %40 large gradients and %38 min vals, 170 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=13285376.0, rms=21.171 011: dt: 0.0500, sse=12773309.0, rms=20.737 (2.048%) 012: dt: 0.0500, sse=12301201.0, rms=20.329 (1.967%) 013: dt: 0.0500, sse=11863637.0, rms=19.944 (1.897%) 014: dt: 0.0500, sse=11457404.0, rms=19.579 (1.830%) 015: dt: 0.0500, sse=11078505.0, rms=19.232 (1.771%) 016: dt: 0.0500, sse=10724237.0, rms=18.902 (1.716%) 017: dt: 0.0500, sse=10390915.0, rms=18.586 (1.671%) 018: dt: 0.0500, sse=10076066.0, rms=18.283 (1.632%) 019: dt: 0.0500, sse=9778466.0, rms=17.991 (1.595%) 020: dt: 0.0500, sse=9496023.0, rms=17.710 (1.563%) positioning took 0.6 minutes mean border=58.5, 139 (38) missing vertices, mean dist 1.1 [0.1 (%2.7)->1.8 (%97.3))] %19 local maxima, %40 large gradients and %38 min vals, 167 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=9590489.0, rms=17.800 021: dt: 0.0500, sse=9315742.0, rms=17.523 (1.554%) 022: dt: 0.0500, sse=9054766.0, rms=17.256 (1.523%) 023: dt: 0.0500, sse=8804274.0, rms=16.996 (1.507%) 024: dt: 0.0500, sse=8565406.0, rms=16.744 (1.482%) 025: dt: 0.0500, sse=8336923.5, rms=16.500 (1.461%) 026: dt: 0.0500, sse=8117993.5, rms=16.262 (1.441%) 027: dt: 0.0500, sse=7906358.0, rms=16.028 (1.435%) 028: dt: 0.0500, sse=7700532.5, rms=15.798 (1.437%) 029: dt: 0.0500, sse=7500261.5, rms=15.571 (1.440%) 030: dt: 0.0500, sse=7305273.5, rms=15.346 (1.443%) positioning took 0.7 minutes mean border=58.4, 206 (37) missing vertices, mean dist 0.9 [0.1 (%10.1)->1.6 (%89.9))] %19 local maxima, %40 large gradients and %38 min vals, 129 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=7392481.5, rms=15.437 031: dt: 0.5000, sse=5966704.0, rms=13.695 (11.279%) 032: dt: 0.5000, sse=4865275.5, rms=12.175 (11.102%) 033: dt: 0.5000, sse=3973998.0, rms=10.792 (11.361%) 034: dt: 0.5000, sse=3250587.0, rms=9.518 (11.805%) 035: dt: 0.5000, sse=2687536.0, rms=8.395 (11.794%) 036: dt: 0.5000, sse=2259349.8, rms=7.426 (11.540%) 037: dt: 0.5000, sse=1937835.9, rms=6.609 (11.010%) 038: dt: 0.5000, sse=1720980.6, rms=5.991 (9.353%) 039: dt: 0.5000, sse=1583085.4, rms=5.565 (7.102%) 040: dt: 0.5000, sse=1497451.8, rms=5.280 (5.130%) 041: dt: 0.5000, sse=1440508.4, rms=5.084 (3.714%) 042: dt: 0.5000, sse=1409739.2, rms=4.970 (2.229%) 043: dt: 0.5000, sse=1385973.2, rms=4.886 (1.704%) 044: dt: 0.5000, sse=1371027.6, rms=4.827 (1.209%) rms = 4.78, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1359703.8, rms=4.784 (0.873%) 046: dt: 0.2500, sse=1214539.2, rms=4.150 (13.262%) 047: dt: 0.2500, sse=1168763.1, rms=3.949 (4.833%) rms = 3.95, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1154313.8, rms=3.879 (1.773%) 049: dt: 0.1250, sse=1135288.2, rms=3.784 (2.466%) rms = 3.77, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1132535.4, rms=3.769 (0.400%) positioning took 1.8 minutes mean border=57.0, 2774 (16) missing vertices, mean dist 0.1 [0.2 (%42.5)->0.5 (%57.5))] %29 local maxima, %32 large gradients and %34 min vals, 57 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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=1545540.0, rms=4.746 051: dt: 0.5000, sse=1488303.1, rms=4.549 (4.140%) 052: dt: 0.5000, sse=1412276.5, rms=4.267 (6.205%) rms = 4.49, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1254604.4, rms=3.492 (18.155%) 054: dt: 0.2500, sse=1211628.0, rms=3.246 (7.066%) rms = 3.24, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1210672.2, rms=3.239 (0.213%) 056: dt: 0.1250, sse=1166931.8, rms=2.973 (8.209%) rms = 2.93, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1159366.2, rms=2.928 (1.526%) positioning took 0.7 minutes mean border=56.1, 2765 (13) missing vertices, mean dist 0.1 [0.2 (%41.3)->0.3 (%58.7))] %39 local maxima, %22 large gradients and %33 min vals, 68 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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=1222711.6, rms=3.306 rms = 3.90, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1176880.5, rms=3.040 (8.036%) 059: dt: 0.2500, sse=1165732.4, rms=2.979 (2.020%) rms = 2.99, time step reduction 2 of 3 to 0.125... rms = 2.94, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1159413.0, rms=2.938 (1.375%) positioning took 0.4 minutes mean border=55.6, 5254 (10) missing vertices, mean dist 0.0 [0.2 (%45.9)->0.2 (%54.1))] %43 local maxima, %18 large gradients and %32 min vals, 69 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, 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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1170942.0, rms=3.007 rms = 3.55, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1149469.1, rms=2.872 (4.480%) rms = 2.83, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1140426.0, rms=2.834 (1.345%) 063: dt: 0.1250, sse=1129920.8, rms=2.760 (2.587%) rms = 2.73, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1124660.1, rms=2.731 (1.049%) positioning took 0.5 minutes writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.area.pial vertex spacing 0.97 +- 0.41 (0.04-->7.45) (max @ vno 58543 --> 145947) face area 0.38 +- 0.29 (0.00-->8.29) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146402 vertices processed 25000 of 146402 vertices processed 50000 of 146402 vertices processed 75000 of 146402 vertices processed 100000 of 146402 vertices processed 125000 of 146402 vertices processed 0 of 146402 vertices processed 25000 of 146402 vertices processed 50000 of 146402 vertices processed 75000 of 146402 vertices processed 100000 of 146402 vertices processed 125000 of 146402 vertices processed thickness calculation complete, 451:878 truncations. 30885 vertices at 0 distance 98484 vertices at 1 distance 92290 vertices at 2 distance 40340 vertices at 3 distance 13272 vertices at 4 distance 4389 vertices at 5 distance 1513 vertices at 6 distance 509 vertices at 7 distance 208 vertices at 8 distance 94 vertices at 9 distance 44 vertices at 10 distance 46 vertices at 11 distance 25 vertices at 12 distance 21 vertices at 13 distance 18 vertices at 14 distance 19 vertices at 15 distance 15 vertices at 16 distance 16 vertices at 17 distance 7 vertices at 18 distance 9 vertices at 19 distance 12 vertices at 20 distance writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.thickness positioning took 9.8 minutes PIDs (956089 956092) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Fri Sep 9 15:29:40 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Fri Sep 9 15:29:40 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 957172 of (957172 957175) to complete... Waiting for PID 957175 of (957172 957175) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... 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... PIDs (957172 957175) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Fri Sep 9 15:29:44 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_inflate -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Fri Sep 9 15:29:44 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_inflate -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 957234 of (957234 957237) to complete... Waiting for PID 957237 of (957234 957237) to complete... mris_inflate -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.8 mm, total surface area = 84827 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.180 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (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 0.2 minutes mris_inflate utimesec 57.649709 mris_inflate stimesec 1.230530 mris_inflate ru_maxrss 229980 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 170728 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11264 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 87476 mris_inflate ru_nivcsw 550 mris_inflate -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.8 mm, total surface area = 85490 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.180 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (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 0.2 minutes mris_inflate utimesec 60.483962 mris_inflate stimesec 1.282738 mris_inflate ru_maxrss 233708 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 134225 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11456 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 83452 mris_inflate ru_nivcsw 393 PIDs (957234 957237) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Fri Sep 9 15:29:57 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Fri Sep 9 15:29:57 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf mris_curvature -w rh.white.preaparc 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 cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf reconbatchjobs /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 957367 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957370 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957373 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957376 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957379 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957382 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957385 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957388 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957391 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957394 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957397 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... Waiting for PID 957400 of (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 48.443*4pi (608.749) --> -47 handles ICI = 242.7, FI = 2190.3, variation=34821.908 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 205 vertices thresholded to be in k1 ~ [-0.17 0.28], k2 ~ [-0.09 0.06] total integrated curvature = 0.570*4pi (7.158) --> 0 handles ICI = 1.5, FI = 8.4, variation=149.824 126 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 149 vertices thresholded to be in [-0.12 0.13] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.021 done. mris_curvature -w rh.white.preaparc total integrated curvature = 39.087*4pi (491.180) --> -38 handles ICI = 244.0, FI = 2100.9, variation=33963.000 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 174 vertices thresholded to be in k1 ~ [-0.23 0.44], k2 ~ [-0.09 0.06] total integrated curvature = 0.586*4pi (7.362) --> 0 handles ICI = 1.5, FI = 9.1, variation=157.250 116 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 161 vertices thresholded to be in [-0.12 0.21] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023 done. PIDs (957367 957370 957373 957376 957379 957382 957385 957388 957391 957394 957397 957400) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Fri Sep 9 15:30:49 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm FM0001 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ FM0001/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 258 ] Gb_filter = 0 WARN: S lookup min: -0.977251 WARN: S explicit min: 0.000000 vertex = 169 #----------------------------------------- #@# Curvature Stats rh Fri Sep 9 15:30:52 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm FM0001 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 [ FM0001/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 [ 285 ] Gb_filter = 0 WARN: S lookup min: -0.245079 WARN: S explicit min: 0.000000 vertex = 20 #-------------------------------------------- #@# Sphere lh Fri Sep 9 15:30:56 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_sphere -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Fri Sep 9 15:30:56 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_sphere -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 957641 of (957641 957651) to complete... Waiting for PID 957651 of (957641 957651) to complete... mris_sphere -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.290... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=acn17, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.79 pass 1: epoch 2 of 3 starting distance error %19.83 unfolding complete - removing small folds... starting distance error %19.79 removing remaining folds... final distance error %19.80 MRISunfold() return, current seed 1234 -01: dt=0.0000, 188 negative triangles 186: dt=0.9900, 188 negative triangles 187: dt=0.9900, 92 negative triangles 188: dt=0.9900, 75 negative triangles 189: dt=0.9900, 61 negative triangles 190: dt=0.9900, 60 negative triangles 191: dt=0.9900, 48 negative triangles 192: dt=0.9900, 42 negative triangles 193: dt=0.9900, 44 negative triangles 194: dt=0.9900, 36 negative triangles 195: dt=0.9900, 29 negative triangles 196: dt=0.9900, 30 negative triangles 197: dt=0.9900, 27 negative triangles 198: dt=0.9900, 22 negative triangles 199: dt=0.9900, 25 negative triangles 200: dt=0.9900, 17 negative triangles 201: dt=0.9900, 14 negative triangles 202: dt=0.9900, 18 negative triangles 203: dt=0.9900, 14 negative triangles 204: dt=0.9900, 10 negative triangles 205: dt=0.9900, 12 negative triangles 206: dt=0.9900, 5 negative triangles 207: dt=0.9900, 6 negative triangles 208: dt=0.9900, 4 negative triangles 209: dt=0.9900, 6 negative triangles 210: dt=0.9900, 4 negative triangles 211: dt=0.9900, 3 negative triangles 212: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.11 hours mris_sphere utimesec 2541.213818 mris_sphere stimesec 3.574213 mris_sphere ru_maxrss 317640 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 1697537 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10152 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 115580 mris_sphere ru_nivcsw 17270 FSRUNTIME@ mris_sphere 0.1062 hours 1 threads mris_sphere -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=acn17, 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 %20.18 pass 1: epoch 2 of 3 starting distance error %20.10 unfolding complete - removing small folds... starting distance error %20.05 removing remaining folds... final distance error %20.06 MRISunfold() return, current seed 1234 -01: dt=0.0000, 285 negative triangles 187: dt=0.9900, 285 negative triangles 188: dt=0.9900, 152 negative triangles 189: dt=0.9900, 110 negative triangles 190: dt=0.9900, 95 negative triangles 191: dt=0.9900, 74 negative triangles 192: dt=0.9900, 72 negative triangles 193: dt=0.9900, 68 negative triangles 194: dt=0.9900, 59 negative triangles 195: dt=0.9900, 57 negative triangles 196: dt=0.9900, 56 negative triangles 197: dt=0.9900, 40 negative triangles 198: dt=0.9900, 36 negative triangles 199: dt=0.9900, 33 negative triangles 200: dt=0.9900, 27 negative triangles 201: dt=0.9900, 24 negative triangles 202: dt=0.9900, 25 negative triangles 203: dt=0.9900, 11 negative triangles 204: dt=0.9900, 18 negative triangles 205: dt=0.9900, 11 negative triangles 206: dt=0.9900, 18 negative triangles 207: dt=0.9900, 12 negative triangles 208: dt=0.9900, 12 negative triangles 209: dt=0.9900, 12 negative triangles 210: dt=0.9900, 5 negative triangles 211: dt=0.9900, 7 negative triangles 212: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.11 hours mris_sphere utimesec 2645.811504 mris_sphere stimesec 3.874577 mris_sphere ru_maxrss 322756 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 1611625 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10320 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 118379 mris_sphere ru_nivcsw 113397 FSRUNTIME@ mris_sphere 0.1087 hours 1 threads PIDs (957641 957651) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Fri Sep 9 15:37:27 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_register -curv -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Fri Sep 9 15:37:27 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_register -curv -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/freesurfer-6.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 958365 of (958365 958368) to complete... Waiting for PID 958368 of (958365 958368) to complete... mris_register -curv -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts cmdline mris_register -curv -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=acn17, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=acn17, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 5.400 curvature mean = 0.029, std = 0.814 curvature mean = 0.022, std = 0.855 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 323962.5, tmin=0.4672 d=32.00 min @ (8.00, 8.00, -8.00) sse = 253397.8, tmin=0.9381 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 213049.3, tmin=1.4236 d=8.00 min @ (0.00, 0.00, 2.00) sse = 201609.0, tmin=1.9022 d=4.00 min @ (0.00, 1.00, 0.00) sse = 199393.7, tmin=2.3754 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 198489.6, tmin=2.8586 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 198422.6, tmin=3.3437 d=0.50 min @ (0.12, 0.12, 0.00) sse = 198360.4, tmin=3.8300 tol=1.0e+00, sigma=0.5, host=acn17, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 3.83 min curvature mean = -0.003, std = 0.833 curvature mean = 0.008, std = 0.944 curvature mean = -0.007, std = 0.843 curvature mean = 0.003, std = 0.978 curvature mean = -0.008, std = 0.845 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.025, std = 0.316 curvature mean = 0.036, std = 0.248 curvature mean = 0.058, std = 0.309 curvature mean = 0.033, std = 0.305 curvature mean = 0.030, std = 0.489 curvature mean = 0.033, std = 0.331 curvature mean = 0.014, std = 0.628 curvature mean = 0.033, std = 0.343 curvature mean = 0.004, std = 0.737 MRISregister() return, current seed 0 -01: dt=0.0000, 34 negative triangles 112: dt=0.9900, 34 negative triangles expanding nbhd size to 1 113: dt=0.9900, 50 negative triangles 114: dt=0.9900, 33 negative triangles 115: dt=0.9900, 33 negative triangles 116: dt=0.9900, 29 negative triangles 117: dt=0.9900, 27 negative triangles 118: dt=0.9900, 24 negative triangles 119: dt=0.9900, 22 negative triangles 120: dt=0.9900, 18 negative triangles 121: dt=0.9900, 15 negative triangles 122: dt=0.9900, 17 negative triangles 123: dt=0.9900, 14 negative triangles 124: dt=0.9900, 9 negative triangles 125: dt=0.9900, 9 negative triangles 126: dt=0.9900, 9 negative triangles 127: dt=0.9900, 7 negative triangles 128: dt=0.9900, 6 negative triangles 129: dt=0.9900, 7 negative triangles 130: dt=0.9900, 6 negative triangles 131: dt=0.9900, 5 negative triangles 132: dt=0.9900, 6 negative triangles 133: dt=0.9900, 4 negative triangles 134: dt=0.9900, 4 negative triangles 135: dt=0.9900, 5 negative triangles 136: dt=0.9900, 4 negative triangles 137: dt=0.9900, 4 negative triangles 138: dt=0.9900, 5 negative triangles 139: dt=0.9900, 3 negative triangles 140: dt=0.9900, 3 negative triangles 141: dt=0.9900, 2 negative triangles 142: dt=0.9900, 3 negative triangles 143: dt=0.9900, 3 negative triangles 144: dt=0.9900, 1 negative triangles 145: dt=0.9900, 2 negative triangles 146: dt=0.9900, 1 negative triangles 147: dt=0.9900, 4 negative triangles 148: dt=0.9900, 2 negative triangles 149: dt=0.9900, 2 negative triangles 150: dt=0.9900, 2 negative triangles 151: dt=0.9900, 3 negative triangles 152: dt=0.9900, 2 negative triangles 153: dt=0.9900, 2 negative triangles 154: dt=0.9405, 1 negative triangles 155: dt=0.9405, 1 negative triangles 156: dt=0.9405, 3 negative triangles 157: dt=0.9405, 1 negative triangles 158: dt=0.9405, 2 negative triangles 159: dt=0.9405, 2 negative triangles 160: dt=0.9405, 1 negative triangles 161: dt=0.9405, 1 negative triangles 162: dt=0.9405, 3 negative triangles 163: dt=0.9405, 1 negative triangles 164: dt=0.8935, 1 negative triangles 165: dt=0.8935, 2 negative triangles 166: dt=0.8935, 1 negative triangles 167: dt=0.8935, 1 negative triangles 168: dt=0.8935, 1 negative triangles 169: dt=0.8935, 1 negative triangles 170: dt=0.8935, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.25 hours mris_register utimesec 4292.533973 mris_register stimesec 6.286213 mris_register ru_maxrss 283228 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 2119955 mris_register ru_majflt 4 mris_register ru_nswap 0 mris_register ru_inblock 6208 mris_register ru_oublock 10200 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 122553 mris_register ru_nivcsw 62739 FSRUNTIME@ mris_register 0.2472 hours 1 threads mris_register -curv -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/freesurfer-6.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts cmdline mris_register -curv -rusage /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/freesurfer-6.0/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/freesurfer-6.0/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=acn17, 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=acn17, 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 = 5.460 curvature mean = 0.032, std = 0.802 curvature mean = 0.024, std = 0.855 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 309430.2, tmin=0.4969 d=32.00 min @ (-8.00, -8.00, 8.00) sse = 297426.6, tmin=1.0212 d=16.00 min @ (0.00, 4.00, -4.00) sse = 225863.5, tmin=1.5414 d=8.00 min @ (2.00, 0.00, 0.00) sse = 218467.2, tmin=2.0543 d=4.00 min @ (0.00, 1.00, 0.00) sse = 215515.4, tmin=2.5573 d=2.00 min @ (0.00, 0.00, 0.50) sse = 215004.5, tmin=3.0582 d=0.50 min @ (0.00, -0.12, 0.00) sse = 214971.9, tmin=4.1012 tol=1.0e+00, sigma=0.5, host=acn17, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 4.10 min curvature mean = -0.003, std = 0.825 curvature mean = 0.009, std = 0.945 curvature mean = -0.007, std = 0.834 curvature mean = 0.004, std = 0.978 curvature mean = -0.011, std = 0.834 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.028, std = 0.419 curvature mean = 0.035, std = 0.239 curvature mean = 0.050, std = 0.239 curvature mean = 0.030, std = 0.298 curvature mean = 0.026, std = 0.373 curvature mean = 0.029, std = 0.325 curvature mean = 0.015, std = 0.479 curvature mean = 0.029, std = 0.337 curvature mean = 0.006, std = 0.570 MRISregister() return, current seed 0 -01: dt=0.0000, 92 negative triangles 114: dt=0.9900, 92 negative triangles expanding nbhd size to 1 115: dt=0.9900, 106 negative triangles 116: dt=0.9900, 83 negative triangles 117: dt=0.9900, 80 negative triangles 118: dt=0.9900, 79 negative triangles 119: dt=0.9900, 76 negative triangles 120: dt=0.9900, 75 negative triangles 121: dt=0.9900, 71 negative triangles 122: dt=0.9900, 60 negative triangles 123: dt=0.9900, 55 negative triangles 124: dt=0.9900, 64 negative triangles 125: dt=0.9900, 58 negative triangles 126: dt=0.9900, 53 negative triangles 127: dt=0.9900, 53 negative triangles 128: dt=0.9900, 50 negative triangles 129: dt=0.9900, 49 negative triangles 130: dt=0.9900, 51 negative triangles 131: dt=0.9900, 43 negative triangles 132: dt=0.9900, 44 negative triangles 133: dt=0.9900, 39 negative triangles 134: dt=0.9900, 39 negative triangles 135: dt=0.9900, 38 negative triangles 136: dt=0.9900, 35 negative triangles 137: dt=0.9900, 34 negative triangles 138: dt=0.9900, 30 negative triangles 139: dt=0.9900, 27 negative triangles 140: dt=0.9900, 24 negative triangles 141: dt=0.9900, 24 negative triangles 142: dt=0.9900, 26 negative triangles 143: dt=0.9900, 28 negative triangles 144: dt=0.9900, 20 negative triangles 145: dt=0.9900, 22 negative triangles 146: dt=0.9900, 19 negative triangles 147: dt=0.9900, 19 negative triangles 148: dt=0.9900, 21 negative triangles 149: dt=0.9900, 25 negative triangles 150: dt=0.9900, 20 negative triangles 151: dt=0.9900, 20 negative triangles 152: dt=0.9900, 17 negative triangles 153: dt=0.9900, 17 negative triangles 154: dt=0.9900, 18 negative triangles 155: dt=0.9900, 18 negative triangles 156: dt=0.9900, 18 negative triangles 157: dt=0.9900, 18 negative triangles 158: dt=0.9900, 19 negative triangles 159: dt=0.9900, 19 negative triangles 160: dt=0.9900, 16 negative triangles 161: dt=0.9900, 16 negative triangles 162: dt=0.9900, 14 negative triangles 163: dt=0.9900, 14 negative triangles 164: dt=0.9900, 14 negative triangles 165: dt=0.9900, 14 negative triangles 166: dt=0.9900, 16 negative triangles 167: dt=0.9900, 18 negative triangles 168: dt=0.9900, 15 negative triangles 169: dt=0.9900, 12 negative triangles 170: dt=0.9900, 11 negative triangles 171: dt=0.9900, 10 negative triangles 172: dt=0.9900, 11 negative triangles 173: dt=0.9900, 7 negative triangles 174: dt=0.9900, 6 negative triangles 175: dt=0.9900, 3 negative triangles 176: dt=0.9900, 8 negative triangles 177: dt=0.9900, 4 negative triangles 178: dt=0.9900, 2 negative triangles 179: dt=0.9900, 3 negative triangles 180: dt=0.9900, 3 negative triangles 181: dt=0.9900, 2 negative triangles 182: dt=0.9900, 2 negative triangles 183: dt=0.9900, 2 negative triangles 184: dt=0.9900, 4 negative triangles 185: dt=0.9900, 2 negative triangles 186: dt=0.9900, 2 negative triangles 187: dt=0.9900, 4 negative triangles 188: dt=0.9405, 4 negative triangles 189: dt=0.9405, 5 negative triangles 190: dt=0.9405, 2 negative triangles 191: dt=0.9405, 7 negative triangles 192: dt=0.9405, 2 negative triangles 193: dt=0.9405, 4 negative triangles 194: dt=0.9405, 1 negative triangles 195: dt=0.9405, 2 negative triangles 196: dt=0.9405, 4 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.25 hours mris_register utimesec 4340.971861 mris_register stimesec 9.018727 mris_register ru_maxrss 288532 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 3364785 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5582 mris_register ru_oublock 10368 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 171402 mris_register ru_nivcsw 47430 FSRUNTIME@ mris_register 0.2545 hours 1 threads PIDs (958365 958368) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri Sep 9 15:52:44 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Sep 9 15:52:44 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 959964 of (959964 959967) to complete... Waiting for PID 959967 of (959964 959967) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white 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 PIDs (959964 959967) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri Sep 9 15:52:45 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mrisp_paint -a 5 /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Fri Sep 9 15:52:45 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mrisp_paint -a 5 /opt/freesurfer/freesurfer-6.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 960026 of (960026 960029) to complete... Waiting for PID 960029 of (960026 960029) to complete... mrisp_paint -a 5 /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /opt/freesurfer/freesurfer-6.0/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/freesurfer-6.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (960026 960029) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri Sep 9 15:52:47 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 lh ../surf/lh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Fri Sep 9 15:52:47 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 rh ../surf/rh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 960087 of (960087 960090) to complete... Waiting for PID 960090 of (960087 960090) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 lh ../surf/lh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/freesurfer-6.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1316 labels changed using aseg relabeling using gibbs priors... 000: 3238 changed, 143971 examined... 001: 787 changed, 13658 examined... 002: 180 changed, 4357 examined... 003: 50 changed, 1121 examined... 004: 15 changed, 287 examined... 005: 4 changed, 85 examined... 006: 0 changed, 24 examined... 249 labels changed using aseg 000: 139 total segments, 93 labels (279 vertices) changed 001: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2012 vertices marked for relabeling... 2012 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 rh ../surf/rh.sphere.reg /opt/freesurfer/freesurfer-6.0/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/freesurfer-6.0/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... 997 labels changed using aseg relabeling using gibbs priors... 000: 2921 changed, 146402 examined... 001: 726 changed, 12671 examined... 002: 173 changed, 4148 examined... 003: 49 changed, 1027 examined... 004: 11 changed, 285 examined... 005: 5 changed, 69 examined... 006: 6 changed, 32 examined... 007: 4 changed, 37 examined... 008: 0 changed, 26 examined... 169 labels changed using aseg 000: 102 total segments, 65 labels (269 vertices) changed 001: 41 total segments, 4 labels (4 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1851 vertices marked for relabeling... 1851 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 10 seconds. PIDs (960087 960090) completed and logs appended. conf2hires --threads 8 --T2 --s FM0001 --trilin Fri Sep 9 15:52:57 CDT 2022 setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts /opt/HCP/HCPpipelines/FreeSurfer/custom/conf2hires --threads 8 --T2 --s FM0001 --trilin freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id$ usedev = usedev CONF2HIRES_USEDEV 0 MMnormSigma 8 CopyBiasFromConf 0 Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux pid 960155 #=============================== mri_convert rawavg.mgz rawavg.cmdc0.mgz --conform-dc --conform_min mri_convert.bin rawavg.mgz rawavg.cmdc0.mgz --conform-dc --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rawavg.mgz... TR=1820.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping DC 0 2 1 ostr LAS, width 256, size 1 K --------------- 1.00000 0.00000 0.00000 37.00000; 0.00000 0.00000 -1.00000 219.00000; 0.00000 1.00000 0.00000 19.00000; 0.00000 0.00000 0.00000 1.00000; Kinv --------------- 1.00000 0.00000 0.00000 -37.00000; 0.00000 0.00000 1.00000 -19.00000; 0.00000 -1.00000 0.00000 219.00000; 0.00000 0.00000 0.00000 1.00000; Smri --------------- -1.00000 0.00000 0.00000 90.00000; 0.00000 1.00000 0.00000 -126.00000; 0.00000 0.00000 1.00000 -72.00000; 0.00000 0.00000 0.00000 1.00000; Stemp --------------- -1.00000 0.00000 0.00000 127.00000; 0.00000 0.00000 1.00000 -145.00000; 0.00000 -1.00000 0.00000 147.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------- changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to rawavg.cmdc0.mgz... #=============================== mri_vol2vol --mov rawavg.mgz --targ rawavg.cmdc0.mgz --regheader --o rawavg.cmdc.mgz --interp cubic movvol rawavg.mgz targvol rawavg.cmdc0.mgz outvol rawavg.cmdc.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp cubic (5) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1662866627 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -37.00000; 0.00000 0.00000 1.00000 -19.00000; 0.00000 -1.00000 0.00000 219.00000; 0.00000 0.00000 0.00000 1.00000; Resampling MRItoBSpline degree 3 Output registration matrix is identity mri_vol2vol done #=============================== tkregister2_cmdl --noedit --mov orig.mgz --targ rawavg.cmdc.mgz --regheader --reg transforms/conf2rawavg.dat --ltaout transforms/conf2rawavg.lta tkregister_tcl /opt/freesurfer/freesurfer-6.0/tktools/tkregister2.tcl target volume rawavg.cmdc.mgz movable volume orig.mgz reg file transforms/conf2rawavg.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 INFO: loading target rawavg.cmdc.mgz Ttarg: -------------------- -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; INFO: loading movable orig.mgz Tmov: -------------------- -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; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; #=============================== tkregister2_cmdl --noedit --mov rawavg.cmdc.mgz --targ orig.mgz --regheader --reg transforms/rawavg2conf.dat --ltaout transforms/rawavg2conf.lta tkregister_tcl /opt/freesurfer/freesurfer-6.0/tktools/tkregister2.tcl target volume orig.mgz movable volume rawavg.cmdc.mgz reg file transforms/rawavg2conf.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 INFO: loading target orig.mgz Ttarg: -------------------- -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; INFO: loading movable rawavg.cmdc.mgz Tmov: -------------------- -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; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; #=============================== mri_vol2vol --mov wm.mgz --targ rawavg.cmdc.mgz --interp nearest --o rawavg.wm.mgz --regheader movvol wm.mgz targvol rawavg.cmdc.mgz outvol rawavg.wm.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1663510326 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done #=============================== mri_vol2vol --mov filled.mgz --targ rawavg.cmdc.mgz --interp nearest --o rawavg.filled.mgz --regheader movvol filled.mgz targvol rawavg.cmdc.mgz outvol rawavg.filled.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1663303539 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done #=============================== mri_vol2vol --mov aseg.presurf.mgz --targ rawavg.cmdc.mgz --interp nearest --o rawavg.aseg.presurf.mgz --regheader movvol aseg.presurf.mgz targvol rawavg.cmdc.mgz outvol rawavg.aseg.presurf.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1663186399 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov brain.finalsurfs.mgz --targ rawavg.cmdc.mgz --interp nearest --o rawavg.brain.fs.mgz --regheader movvol brain.finalsurfs.mgz targvol rawavg.cmdc.mgz outvol rawavg.brain.fs.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1662877341 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Fri Sep 9 15:53:13 CDT 2022 #=============================== mri_surf2surf --s FM0001 --hemi lh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg Reading header for rawavg.cmdc.mgz Source registration surface changed to white.preaparc Target registration surface changed to white.preaparc $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi lh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = white.preaparc.rawavg trgtype = srcsurfreg = white.preaparc trgsurfreg = white.preaparc srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.preaparc Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.preaparc Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data Fri Sep 9 15:53:16 CDT 2022 #=============================== mri_surf2surf --s FM0001 --hemi rh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg Reading header for rawavg.cmdc.mgz Source registration surface changed to white.preaparc Target registration surface changed to white.preaparc $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi rh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = white.preaparc.rawavg trgtype = srcsurfreg = white.preaparc trgsurfreg = white.preaparc srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.preaparc Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.preaparc Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data Computing bias field from rawavg mri_normalize -sigma 8 -erode 1 -min_dist 1 -surface ../surf/lh.white.preaparc.rawavg identity.nofile -surface ../surf/rh.white.preaparc.rawavg identity.nofile rawavg.cmdc.mgz rawavg.norm.mgz using Gaussian smoothing of bias field, sigma=8.000 eroding interior of surface 1 times retaining nonmaximum suppressed points that are at least 1.000mm from the boundary reading from rawavg.cmdc.mgz... computing distance transform computing distance transform computing nonmaximum suppression building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=8.000 writing normalized volume to rawavg.norm.mgz mri_mask rawavg.norm.mgz rawavg.brain.fs.mgz rawavg.brain.finalsurfs.mgz DoAbs = 0 Writing masked volume to rawavg.brain.finalsurfs.mgz...done. mri_vol2vol --mov rawavg.brain.finalsurfs.mgz --targ orig.mgz --regheader --o rawavg.brain.finalsurfs.conf.mgz --interp nearest movvol rawavg.brain.finalsurfs.mgz targvol orig.mgz outvol rawavg.brain.finalsurfs.conf.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1662912777 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Fri Sep 9 15:53:52 CDT 2022 #=============================== cp /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.thickness /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.bak.thickness #=============================== mris_make_surfaces -aseg rawavg.aseg.presurf -filled rawavg.filled -wm rawavg.wm -T1 rawavg.brain.finalsurfs -orig white.preaparc.rawavg -orig_white white.preaparc.rawavg -white white.rawavg -pial woT2.pial.rawavg FM0001 lh using rawavg.filled as filled name using rawavg.wm as filled name reading original vertex positions from white.preaparc.rawavg using white.rawavg as white matter name... writing pial surface to file named woT2.pial.rawavg using aseg volume rawavg.aseg.presurf to prevent surfaces crossing the midline using rawavg.brain.finalsurfs as T1 volume... using white.preaparc.rawavg starting white location... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.filled.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.brain.finalsurfs.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.aseg.presurf.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.wm.mgz... 244777 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.preaparc.rawavg... computing class statistics... border white: 277660 voxels (1.65%) border gray 299649 voxels (1.79%) WM (103.0): 102.5 +- 7.2 [70.0 --> 110.0] GM (79.0) : 78.3 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.4 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 56.7 (was 40) setting MAX_GRAY to 101.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) changing type of input wm volume to UCHAR... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=78+-6.1 mean inside = 101.1, mean outside = 84.2 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc.rawavg... 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-->5.51) (max @ vno 52081 --> 59703) face area 0.33 +- 0.16 (0.00-->8.17) mean absolute distance = 0.68 +- 0.95 3112 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 176 points - only 0.00% unknown mean border=87.1, 145 (145) missing vertices, mean dist 0.3 [1.6 (%11.4)->0.6 (%88.6))] %58 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.05-->5.76) (max @ vno 52081 --> 59703) face area 0.33 +- 0.16 (0.00-->8.15) mean absolute distance = 0.35 +- 0.62 3297 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2102582.8, rms=7.165 001: dt: 0.5000, sse=1142340.8, rms=4.079 (43.073%) 002: dt: 0.5000, sse=925681.9, rms=2.999 (26.477%) 003: dt: 0.5000, sse=901795.9, rms=2.894 (3.499%) 004: dt: 0.5000, sse=877478.1, rms=2.753 (4.882%) rms = 2.89, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=793647.1, rms=2.046 (25.657%) 006: dt: 0.2500, sse=760782.6, rms=1.706 (16.653%) 007: dt: 0.2500, sse=754175.9, rms=1.622 (4.916%) rms = 1.61, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=753447.4, rms=1.607 (0.908%) rms = 1.57, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=755705.5, rms=1.574 (2.049%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 13 points - only 0.00% unknown deleting segment 2 with 131 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=89.5, 97 (46) missing vertices, mean dist -0.2 [0.4 (%68.5)->0.2 (%31.5))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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 +- 0.25 (0.03-->5.92) (max @ vno 52081 --> 59703) face area 0.34 +- 0.17 (0.00-->8.81) mean absolute distance = 0.27 +- 0.40 3536 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1072690.4, rms=3.600 010: dt: 0.5000, sse=867739.7, rms=2.368 (34.223%) rms = 2.45, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=804252.2, rms=1.848 (21.983%) 012: dt: 0.2500, sse=772221.5, rms=1.502 (18.720%) 013: dt: 0.2500, sse=763447.6, rms=1.393 (7.213%) rms = 1.36, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=761266.1, rms=1.363 (2.191%) rms = 1.33, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=759717.4, rms=1.332 (2.275%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 19 points - only 0.00% unknown deleting segment 2 with 142 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=91.5, 110 (37) missing vertices, mean dist -0.1 [0.3 (%70.1)->0.2 (%29.9))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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 +- 0.26 (0.07-->6.03) (max @ vno 52081 --> 59703) face area 0.33 +- 0.17 (0.00-->8.77) mean absolute distance = 0.23 +- 0.33 3505 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=906248.8, rms=2.770 016: dt: 0.5000, sse=836959.4, rms=2.237 (19.259%) rms = 2.46, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=769119.9, rms=1.618 (27.670%) 018: dt: 0.2500, sse=744783.5, rms=1.324 (18.150%) 019: dt: 0.2500, sse=739680.1, rms=1.263 (4.582%) rms = 1.26, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=739446.9, rms=1.260 (0.300%) rms = 1.23, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=736237.1, rms=1.228 (2.516%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 161 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 31 points - only 29.03% unknown mean border=92.2, 135 (29) missing vertices, mean dist -0.1 [0.2 (%56.9)->0.2 (%43.1))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.rawavg... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=749420.9, rms=1.515 022: dt: 0.5000, sse=744840.2, rms=1.407 (7.094%) rms = 2.07, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=714255.1, rms=1.025 (27.145%) rms = 1.02, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=713742.6, rms=1.018 (0.714%) 025: dt: 0.1250, sse=707698.4, rms=0.952 (6.500%) rms = 0.94, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=706539.4, rms=0.935 (1.709%) positioning took 0.3 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6916 vertices erasing segment 1 (vno[0] = 87118) erasing segment 2 (vno[0] = 89382) erasing segment 3 (vno[0] = 99432) erasing segment 4 (vno[0] = 101777) erasing segment 5 (vno[0] = 101790) erasing segment 6 (vno[0] = 103933) writing cortex label to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label... writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.area vertex spacing 0.88 +- 0.26 (0.02-->6.07) (max @ vno 52081 --> 59703) face area 0.33 +- 0.17 (0.00-->8.39) 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... removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=64.7, 119 (119) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.7 (%100.0))] %19 local maxima, %41 large gradients and %37 min vals, 202 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=acn17, 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=21774994.0, rms=27.639 001: dt: 0.0500, sse=19290896.0, rms=25.968 (6.046%) 002: dt: 0.0500, sse=17406750.0, rms=24.625 (5.172%) 003: dt: 0.0500, sse=15955993.0, rms=23.538 (4.413%) 004: dt: 0.0500, sse=14807314.0, rms=22.641 (3.813%) 005: dt: 0.0500, sse=13863334.0, rms=21.876 (3.380%) 006: dt: 0.0500, sse=13065238.0, rms=21.207 (3.056%) 007: dt: 0.0500, sse=12374972.0, rms=20.611 (2.810%) 008: dt: 0.0500, sse=11766680.0, rms=20.071 (2.619%) 009: dt: 0.0500, sse=11222969.0, rms=19.576 (2.467%) 010: dt: 0.0500, sse=10731069.0, rms=19.117 (2.345%) positioning took 0.6 minutes mean border=64.3, 101 (47) missing vertices, mean dist 1.3 [0.1 (%0.3)->2.1 (%99.7))] %21 local maxima, %41 large gradients and %35 min vals, 179 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=11916977.0, rms=20.166 011: dt: 0.0500, sse=11457870.0, rms=19.751 (2.059%) 012: dt: 0.0500, sse=11036817.0, rms=19.362 (1.968%) 013: dt: 0.0500, sse=10647550.0, rms=18.996 (1.893%) 014: dt: 0.0500, sse=10287547.0, rms=18.650 (1.819%) 015: dt: 0.0500, sse=9952994.0, rms=18.324 (1.753%) 016: dt: 0.0500, sse=9640869.0, rms=18.013 (1.694%) 017: dt: 0.0500, sse=9347183.0, rms=17.716 (1.650%) 018: dt: 0.0500, sse=9069582.0, rms=17.430 (1.612%) 019: dt: 0.0500, sse=8806509.0, rms=17.155 (1.578%) 020: dt: 0.0500, sse=8556751.0, rms=16.890 (1.547%) positioning took 0.6 minutes mean border=64.2, 124 (37) missing vertices, mean dist 1.1 [0.1 (%3.6)->1.8 (%96.4))] %21 local maxima, %41 large gradients and %34 min vals, 171 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=8673551.0, rms=17.008 021: dt: 0.0500, sse=8428360.0, rms=16.745 (1.545%) 022: dt: 0.0500, sse=8195555.5, rms=16.492 (1.514%) 023: dt: 0.0500, sse=7971257.5, rms=16.244 (1.504%) 024: dt: 0.0500, sse=7757184.0, rms=16.003 (1.479%) 025: dt: 0.0500, sse=7552533.0, rms=15.770 (1.457%) 026: dt: 0.0500, sse=7356618.5, rms=15.544 (1.437%) 027: dt: 0.0500, sse=7167836.5, rms=15.322 (1.425%) 028: dt: 0.0500, sse=6984502.5, rms=15.104 (1.425%) 029: dt: 0.0500, sse=6806632.0, rms=14.889 (1.423%) 030: dt: 0.0500, sse=6633788.0, rms=14.677 (1.424%) positioning took 0.6 minutes mean border=64.1, 187 (30) missing vertices, mean dist 0.9 [0.1 (%11.7)->1.6 (%88.3))] %21 local maxima, %41 large gradients and %34 min vals, 141 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=6727336.5, rms=14.778 031: dt: 0.5000, sse=5468132.0, rms=13.146 (11.042%) 032: dt: 0.5000, sse=4532526.5, rms=11.782 (10.379%) 033: dt: 0.5000, sse=3769305.2, rms=10.542 (10.521%) 034: dt: 0.5000, sse=3147698.5, rms=9.406 (10.773%) 035: dt: 0.5000, sse=2637010.0, rms=8.363 (11.090%) 036: dt: 0.5000, sse=2229135.5, rms=7.422 (11.258%) 037: dt: 0.5000, sse=1914975.8, rms=6.611 (10.929%) 038: dt: 0.5000, sse=1693789.0, rms=5.967 (9.731%) 039: dt: 0.5000, sse=1557467.4, rms=5.541 (7.148%) 040: dt: 0.5000, sse=1472666.8, rms=5.250 (5.248%) 041: dt: 0.5000, sse=1422246.1, rms=5.076 (3.320%) 042: dt: 0.5000, sse=1392372.4, rms=4.962 (2.250%) 043: dt: 0.5000, sse=1373202.1, rms=4.894 (1.362%) 044: dt: 0.5000, sse=1360086.4, rms=4.840 (1.100%) rms = 4.81, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1351751.2, rms=4.812 (0.582%) 046: dt: 0.2500, sse=1207477.4, rms=4.172 (13.293%) 047: dt: 0.2500, sse=1163202.8, rms=3.976 (4.709%) rms = 3.98, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1150395.9, rms=3.913 (1.584%) 049: dt: 0.1250, sse=1133586.0, rms=3.827 (2.196%) rms = 3.82, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1131736.8, rms=3.816 (0.281%) positioning took 1.6 minutes mean border=62.5, 2550 (15) missing vertices, mean dist 0.1 [0.2 (%39.8)->0.4 (%60.2))] %35 local maxima, %29 large gradients and %30 min vals, 84 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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=1554750.8, rms=4.818 051: dt: 0.5000, sse=1452269.0, rms=4.438 (7.904%) 052: dt: 0.5000, sse=1396614.1, rms=4.238 (4.496%) rms = 4.42, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1237141.8, rms=3.431 (19.049%) 054: dt: 0.2500, sse=1192632.9, rms=3.164 (7.770%) rms = 3.13, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1187698.0, rms=3.134 (0.941%) 056: dt: 0.1250, sse=1148857.8, rms=2.885 (7.955%) rms = 2.84, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1142295.9, rms=2.844 (1.431%) positioning took 0.7 minutes mean border=61.5, 2646 (13) missing vertices, mean dist 0.1 [0.2 (%38.4)->0.3 (%61.6))] %46 local maxima, %18 large gradients and %30 min vals, 91 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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=1217708.2, rms=3.320 rms = 3.97, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1160318.0, rms=2.981 (10.230%) 059: dt: 0.2500, sse=1149057.8, rms=2.914 (2.244%) rms = 2.91, time step reduction 2 of 3 to 0.125... rms = 2.87, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1142499.6, rms=2.870 (1.506%) positioning took 0.4 minutes mean border=60.9, 5012 (12) missing vertices, mean dist 0.0 [0.2 (%44.6)->0.2 (%55.4))] %50 local maxima, %15 large gradients and %29 min vals, 88 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, 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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.woT2.pial.rawavg... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1156916.4, rms=2.965 rms = 3.53, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1133573.5, rms=2.813 (5.111%) rms = 2.77, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1123681.2, rms=2.766 (1.662%) 063: dt: 0.1250, sse=1113500.0, rms=2.692 (2.684%) rms = 2.66, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1108376.9, rms=2.663 (1.073%) positioning took 0.4 minutes writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.07-->5.93) (max @ vno 94078 --> 95116) face area 0.38 +- 0.29 (0.00-->8.27) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 143971 vertices processed 25000 of 143971 vertices processed 50000 of 143971 vertices processed 75000 of 143971 vertices processed 100000 of 143971 vertices processed 125000 of 143971 vertices processed 0 of 143971 vertices processed 25000 of 143971 vertices processed 50000 of 143971 vertices processed 75000 of 143971 vertices processed 100000 of 143971 vertices processed 125000 of 143971 vertices processed thickness calculation complete, 311:488 truncations. 31351 vertices at 0 distance 99428 vertices at 1 distance 91041 vertices at 2 distance 38337 vertices at 3 distance 11801 vertices at 4 distance 3476 vertices at 5 distance 1169 vertices at 6 distance 401 vertices at 7 distance 149 vertices at 8 distance 72 vertices at 9 distance 49 vertices at 10 distance 43 vertices at 11 distance 41 vertices at 12 distance 16 vertices at 13 distance 10 vertices at 14 distance 9 vertices at 15 distance 7 vertices at 16 distance 14 vertices at 17 distance 7 vertices at 18 distance 3 vertices at 19 distance 4 vertices at 20 distance writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.thickness positioning took 8.7 minutes #=============================== mri_surf2surf --s FM0001 --hemi lh --sval-xyz white.rawavg --surfreg white.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval white.rawavg.conf Reading header for orig.mgz Source registration surface changed to white.rawavg Target registration surface changed to white.rawavg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi lh --sval-xyz white.rawavg --surfreg white.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval white.rawavg.conf sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = white.rawavg.conf trgtype = srcsurfreg = white.rawavg trgsurfreg = white.rawavg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.rawavg Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.rawavg Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data #=============================== mri_surf2surf --s FM0001 --hemi lh --sval-xyz woT2.pial.rawavg --surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval woT2.pial.rawavg.conf Reading header for orig.mgz Source registration surface changed to woT2.pial.rawavg Target registration surface changed to woT2.pial.rawavg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi lh --sval-xyz woT2.pial.rawavg --surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval woT2.pial.rawavg.conf sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = woT2.pial.rawavg.conf trgtype = srcsurfreg = woT2.pial.rawavg trgsurfreg = woT2.pial.rawavg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.woT2.pial.rawavg Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.woT2.pial.rawavg Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri Fri Sep 9 16:02:38 CDT 2022 #=============================== cp /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.thickness /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.bak.thickness #=============================== mris_make_surfaces -aseg rawavg.aseg.presurf -filled rawavg.filled -wm rawavg.wm -T1 rawavg.brain.finalsurfs -orig white.preaparc.rawavg -orig_white white.preaparc.rawavg -white white.rawavg -pial woT2.pial.rawavg FM0001 rh using rawavg.filled as filled name using rawavg.wm as filled name reading original vertex positions from white.preaparc.rawavg using white.rawavg as white matter name... writing pial surface to file named woT2.pial.rawavg using aseg volume rawavg.aseg.presurf to prevent surfaces crossing the midline using rawavg.brain.finalsurfs as T1 volume... using white.preaparc.rawavg starting white location... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.filled.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.brain.finalsurfs.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.aseg.presurf.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.wm.mgz... 244777 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.preaparc.rawavg... computing class statistics... border white: 277660 voxels (1.65%) border gray 299649 voxels (1.79%) WM (103.0): 102.5 +- 7.2 [70.0 --> 110.0] GM (79.0) : 78.3 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.4 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 56.7 (was 40) setting MAX_GRAY to 101.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) changing type of input wm volume to UCHAR... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=78+-7.0 mean inside = 101.1, mean outside = 84.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc.rawavg... 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 (0.04-->5.80) (max @ vno 57292 --> 145981) face area 0.32 +- 0.15 (0.00-->6.28) mean absolute distance = 0.68 +- 0.95 3302 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 72 points - only 0.00% unknown deleting segment 5 with 66 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown mean border=87.6, 156 (156) missing vertices, mean dist 0.3 [1.4 (%12.2)->0.6 (%87.8))] %62 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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 0.90 +- 0.25 (0.07-->5.92) (max @ vno 145981 --> 57292) face area 0.32 +- 0.16 (0.00-->6.15) mean absolute distance = 0.35 +- 0.62 3643 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2055313.4, rms=6.968 001: dt: 0.5000, sse=1137933.2, rms=4.003 (42.547%) 002: dt: 0.5000, sse=919763.1, rms=2.921 (27.038%) 003: dt: 0.5000, sse=897424.2, rms=2.803 (4.028%) 004: dt: 0.5000, sse=872353.7, rms=2.657 (5.223%) rms = 2.80, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=792782.8, rms=1.984 (25.330%) 006: dt: 0.2500, sse=771536.4, rms=1.663 (16.179%) 007: dt: 0.2500, sse=757243.2, rms=1.589 (4.454%) rms = 1.57, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=755398.3, rms=1.570 (1.159%) rms = 1.54, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=752618.1, rms=1.540 (1.908%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 60 points - only 0.00% unknown deleting segment 1 with 60 points - only 0.00% unknown mean border=89.8, 111 (58) missing vertices, mean dist -0.2 [0.4 (%67.5)->0.2 (%32.5))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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 0.88 +- 0.25 (0.05-->6.19) (max @ vno 146025 --> 146016) face area 0.34 +- 0.16 (0.00-->6.97) mean absolute distance = 0.28 +- 0.41 4235 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1063038.2, rms=3.508 010: dt: 0.5000, sse=870192.9, rms=2.328 (33.635%) rms = 2.33, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=811589.2, rms=1.839 (21.016%) 012: dt: 0.2500, sse=780114.9, rms=1.488 (19.048%) 013: dt: 0.2500, sse=770266.0, rms=1.374 (7.706%) rms = 1.34, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=769169.4, rms=1.337 (2.686%) rms = 1.31, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=767280.6, rms=1.307 (2.210%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 50 points - only 0.00% unknown deleting segment 2 with 69 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown mean border=91.7, 105 (42) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.2 (%30.5))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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 (0.06-->6.42) (max @ vno 146025 --> 146016) face area 0.33 +- 0.16 (0.00-->7.16) mean absolute distance = 0.23 +- 0.34 3867 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=916014.1, rms=2.754 016: dt: 0.5000, sse=832188.4, rms=2.127 (22.766%) rms = 2.31, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=775201.2, rms=1.564 (26.461%) 018: dt: 0.2500, sse=749638.2, rms=1.290 (17.517%) 019: dt: 0.2500, sse=746308.8, rms=1.237 (4.169%) rms = 1.23, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=744664.7, rms=1.231 (0.415%) rms = 1.20, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=743166.1, rms=1.202 (2.373%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 69 points - only 0.00% unknown deleting segment 1 with 62 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown mean border=92.4, 119 (34) missing vertices, mean dist -0.1 [0.3 (%57.3)->0.2 (%42.7))] %89 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.rawavg... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=757193.6, rms=1.513 022: dt: 0.5000, sse=745216.2, rms=1.347 (10.921%) rms = 1.96, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=718852.2, rms=1.000 (25.790%) rms = 0.99, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=718115.1, rms=0.989 (1.123%) 025: dt: 0.1250, sse=715094.1, rms=0.933 (5.659%) rms = 0.92, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=711671.7, rms=0.921 (1.228%) positioning took 0.3 minutes generating cortex label... 9 non-cortical segments detected only using segment with 7088 vertices erasing segment 1 (vno[0] = 84099) erasing segment 2 (vno[0] = 99332) erasing segment 3 (vno[0] = 99350) erasing segment 4 (vno[0] = 100431) erasing segment 5 (vno[0] = 101628) erasing segment 6 (vno[0] = 104680) erasing segment 7 (vno[0] = 104701) erasing segment 8 (vno[0] = 105723) writing cortex label to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label... writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.area vertex spacing 0.88 +- 0.26 (0.04-->6.32) (max @ vno 145981 --> 146015) face area 0.32 +- 0.16 (0.00-->6.95) 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 12 points - only 0.00% unknown removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=65.2, 151 (151) missing vertices, mean dist 1.6 [1.5 (%0.0)->2.7 (%100.0))] %18 local maxima, %38 large gradients and %41 min vals, 202 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=acn17, 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=21935322.0, rms=27.508 001: dt: 0.0500, sse=19467986.0, rms=25.869 (5.958%) 002: dt: 0.0500, sse=17616450.0, rms=24.567 (5.033%) 003: dt: 0.0500, sse=16194455.0, rms=23.518 (4.270%) 004: dt: 0.0500, sse=15062120.0, rms=22.648 (3.700%) 005: dt: 0.0500, sse=14131215.0, rms=21.906 (3.274%) 006: dt: 0.0500, sse=13344857.0, rms=21.260 (2.951%) 007: dt: 0.0500, sse=12663508.0, rms=20.683 (2.712%) 008: dt: 0.0500, sse=12062138.0, rms=20.161 (2.527%) 009: dt: 0.0500, sse=11522872.0, rms=19.680 (2.384%) 010: dt: 0.0500, sse=11034668.0, rms=19.235 (2.264%) positioning took 0.6 minutes mean border=64.7, 112 (49) missing vertices, mean dist 1.3 [0.1 (%0.3)->2.1 (%99.7))] %20 local maxima, %38 large gradients and %38 min vals, 179 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=12283414.0, rms=20.313 011: dt: 0.0500, sse=11826616.0, rms=19.910 (1.984%) 012: dt: 0.0500, sse=11406284.0, rms=19.532 (1.900%) 013: dt: 0.0500, sse=11016959.0, rms=19.175 (1.829%) 014: dt: 0.0500, sse=10655495.0, rms=18.837 (1.761%) 015: dt: 0.0500, sse=10318249.0, rms=18.516 (1.703%) 016: dt: 0.0500, sse=10003240.0, rms=18.211 (1.646%) 017: dt: 0.0500, sse=9706163.0, rms=17.919 (1.604%) 018: dt: 0.0500, sse=9424942.0, rms=17.638 (1.569%) 019: dt: 0.0500, sse=9158305.0, rms=17.367 (1.535%) 020: dt: 0.0500, sse=8905072.0, rms=17.106 (1.504%) positioning took 0.6 minutes mean border=64.6, 140 (39) missing vertices, mean dist 1.1 [0.1 (%3.1)->1.8 (%96.9))] %20 local maxima, %38 large gradients and %38 min vals, 161 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=9008565.0, rms=17.207 021: dt: 0.0500, sse=8760448.0, rms=16.949 (1.502%) 022: dt: 0.0500, sse=8524572.0, rms=16.700 (1.471%) 023: dt: 0.0500, sse=8297905.0, rms=16.456 (1.457%) 024: dt: 0.0500, sse=8081796.0, rms=16.221 (1.430%) 025: dt: 0.0500, sse=7874977.0, rms=15.992 (1.409%) 026: dt: 0.0500, sse=7676560.0, rms=15.770 (1.391%) 027: dt: 0.0500, sse=7485187.0, rms=15.552 (1.380%) 028: dt: 0.0500, sse=7299139.0, rms=15.338 (1.380%) 029: dt: 0.0500, sse=7118268.0, rms=15.126 (1.380%) 030: dt: 0.0500, sse=6942277.0, rms=14.917 (1.381%) positioning took 0.6 minutes mean border=64.6, 193 (37) missing vertices, mean dist 0.9 [0.1 (%11.0)->1.6 (%89.0))] %20 local maxima, %38 large gradients and %38 min vals, 135 gradients ignored tol=1.0e-04, sigma=2.0, host=acn17, 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=7003878.5, rms=14.979 031: dt: 0.5000, sse=5711046.5, rms=13.355 (10.840%) 032: dt: 0.5000, sse=4718424.0, rms=11.953 (10.496%) 033: dt: 0.5000, sse=3906709.8, rms=10.674 (10.703%) 034: dt: 0.5000, sse=3230009.2, rms=9.472 (11.263%) 035: dt: 0.5000, sse=2688698.2, rms=8.390 (11.421%) 036: dt: 0.5000, sse=2258003.8, rms=7.414 (11.628%) 037: dt: 0.5000, sse=1932918.6, rms=6.587 (11.161%) 038: dt: 0.5000, sse=1709280.1, rms=5.946 (9.728%) 039: dt: 0.5000, sse=1568546.5, rms=5.509 (7.354%) 040: dt: 0.5000, sse=1475638.2, rms=5.194 (5.709%) 041: dt: 0.5000, sse=1423218.5, rms=5.013 (3.497%) 042: dt: 0.5000, sse=1386081.4, rms=4.873 (2.789%) 043: dt: 0.5000, sse=1366563.1, rms=4.803 (1.439%) 044: dt: 0.5000, sse=1345126.6, rms=4.718 (1.771%) rms = 4.69, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1338338.5, rms=4.694 (0.500%) 046: dt: 0.2500, sse=1196960.6, rms=4.061 (13.477%) 047: dt: 0.2500, sse=1153432.9, rms=3.867 (4.789%) rms = 3.88, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1140706.2, rms=3.804 (1.635%) 049: dt: 0.1250, sse=1124534.8, rms=3.720 (2.200%) rms = 3.71, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1123303.5, rms=3.712 (0.214%) positioning took 1.7 minutes mean border=63.1, 2824 (17) missing vertices, mean dist 0.1 [0.2 (%41.7)->0.4 (%58.3))] %31 local maxima, %29 large gradients and %34 min vals, 70 gradients ignored tol=1.0e-04, sigma=1.0, host=acn17, 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=1545216.1, rms=4.740 051: dt: 0.5000, sse=1459747.5, rms=4.432 (6.480%) 052: dt: 0.5000, sse=1388351.2, rms=4.165 (6.038%) rms = 4.38, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1237135.0, rms=3.399 (18.386%) 054: dt: 0.2500, sse=1194517.4, rms=3.146 (7.438%) rms = 3.12, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1190360.9, rms=3.121 (0.795%) 056: dt: 0.1250, sse=1151309.4, rms=2.874 (7.923%) rms = 2.83, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1144835.9, rms=2.834 (1.385%) positioning took 0.7 minutes mean border=62.3, 2729 (12) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.3 (%59.8))] %42 local maxima, %19 large gradients and %33 min vals, 103 gradients ignored tol=1.0e-04, sigma=0.5, host=acn17, 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=1211005.1, rms=3.244 rms = 3.82, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1164688.6, rms=2.970 (8.454%) 059: dt: 0.2500, sse=1153887.2, rms=2.908 (2.085%) rms = 2.92, time step reduction 2 of 3 to 0.125... rms = 2.87, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1148189.2, rms=2.870 (1.308%) positioning took 0.4 minutes mean border=61.7, 5392 (12) missing vertices, mean dist 0.0 [0.2 (%45.2)->0.2 (%54.8))] %46 local maxima, %15 large gradients and %32 min vals, 83 gradients ignored tol=1.0e-04, sigma=0.2, host=acn17, 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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.woT2.pial.rawavg... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1164244.1, rms=2.968 rms = 3.49, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1142629.6, rms=2.830 (4.645%) rms = 2.79, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1132673.1, rms=2.786 (1.569%) 063: dt: 0.1250, sse=1122666.5, rms=2.715 (2.566%) rms = 2.69, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1117816.8, rms=2.688 (0.992%) positioning took 0.5 minutes writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.area.pial vertex spacing 0.97 +- 0.41 (0.07-->8.10) (max @ vno 94455 --> 94456) face area 0.38 +- 0.29 (0.00-->6.92) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146402 vertices processed 25000 of 146402 vertices processed 50000 of 146402 vertices processed 75000 of 146402 vertices processed 100000 of 146402 vertices processed 125000 of 146402 vertices processed 0 of 146402 vertices processed 25000 of 146402 vertices processed 50000 of 146402 vertices processed 75000 of 146402 vertices processed 100000 of 146402 vertices processed 125000 of 146402 vertices processed thickness calculation complete, 466:713 truncations. 31913 vertices at 0 distance 100851 vertices at 1 distance 91101 vertices at 2 distance 39226 vertices at 3 distance 12665 vertices at 4 distance 4099 vertices at 5 distance 1449 vertices at 6 distance 471 vertices at 7 distance 196 vertices at 8 distance 66 vertices at 9 distance 33 vertices at 10 distance 26 vertices at 11 distance 21 vertices at 12 distance 18 vertices at 13 distance 14 vertices at 14 distance 19 vertices at 15 distance 9 vertices at 16 distance 7 vertices at 17 distance 7 vertices at 18 distance 11 vertices at 19 distance 12 vertices at 20 distance writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.thickness positioning took 8.9 minutes #=============================== mri_surf2surf --s FM0001 --hemi rh --sval-xyz white.rawavg --surfreg white.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval white.rawavg.conf Reading header for orig.mgz Source registration surface changed to white.rawavg Target registration surface changed to white.rawavg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi rh --sval-xyz white.rawavg --surfreg white.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval white.rawavg.conf sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = white.rawavg.conf trgtype = srcsurfreg = white.rawavg trgsurfreg = white.rawavg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.rawavg Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.rawavg Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data #=============================== mri_surf2surf --s FM0001 --hemi rh --sval-xyz woT2.pial.rawavg --surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval woT2.pial.rawavg.conf Reading header for orig.mgz Source registration surface changed to woT2.pial.rawavg Target registration surface changed to woT2.pial.rawavg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi rh --sval-xyz woT2.pial.rawavg --surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval woT2.pial.rawavg.conf sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = woT2.pial.rawavg.conf trgtype = srcsurfreg = woT2.pial.rawavg trgsurfreg = woT2.pial.rawavg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.woT2.pial.rawavg Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.woT2.pial.rawavg Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri Fri Sep 9 16:11:35 CDT 2022 #=============================== bbregister --s FM0001 --mov orig/T2raw.mgz --lta transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc --proj-abs 1.5 --threads 8 tmp transforms/tmp.bbregister.962467 Log file is transforms/T2raw.auto.dat.log Fri Sep 9 16:11:35 CDT 2022 setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /opt/freesurfer/freesurfer-6.0/bin/bbregister --s FM0001 --mov orig/T2raw.mgz --lta transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc --proj-abs 1.5 --threads 8 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/freesurfer-6.0 mri_convert orig/T2raw.mgz transforms/tmp.bbregister.962467/template.nii mri_convert.bin orig/T2raw.mgz transforms/tmp.bbregister.962467/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig/T2raw.mgz... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to transforms/tmp.bbregister.962467/template.nii... mri_coreg --s FM0001 --mov transforms/tmp.bbregister.962467/template.nii --regdat transforms/tmp.bbregister.962467/reg.init.dat --reg transforms/tmp.bbregister.962467/mri_coreg.lta --nthreads 8 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri cmdline mri_coreg --s FM0001 --mov transforms/tmp.bbregister.962467/template.nii --regdat transforms/tmp.bbregister.962467/reg.init.dat --reg transforms/tmp.bbregister.962467/mri_coreg.lta --nthreads 8 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname acn179 machine x86_64 user moana004 dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov transforms/tmp.bbregister.962467/template.nii Reading in ref brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters 0.0000 0.0000 -1.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 8 movsat = 1882.1899 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0535702923 nhits = 111114 out of 16777216, Percent Overlap: 42.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -1.00000; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 1.00000 0.00000 0.00000 -37.00000; 0.00000 0.00000 1.00000 -19.00000; 0.00000 -1.00000 0.00000 218.00000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0416432 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0535702705 #@# 4 188 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0535703 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.053570 #@# 4 195 -0.05567 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0535756 #@# 4 196 -0.06567 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0535758 #@# 4 204 -0.06567 0.16518 -1.00000 0.00000 0.00000 0.00000 -1.0536084 #@# 4 208 -0.06567 0.16518 0.00000 0.00000 0.00000 0.00000 -1.0537341 #@# 4 212 -0.06567 0.16518 -0.38197 0.00000 0.00000 0.00000 -1.0538834 #@# 4 213 -0.06567 0.16518 -0.42340 0.00000 0.00000 0.00000 -1.0538902 #@# 4 215 -0.06567 0.16518 -0.47389 0.00000 0.00000 0.00000 -1.0538939 #@# 4 217 -0.06567 0.16518 -0.45564 0.00000 0.00000 0.00000 -1.0538949 #@# 4 225 -0.06567 0.16518 -0.45564 -0.10577 0.00000 0.00000 -1.0539058 #@# 4 226 -0.06567 0.16518 -0.45564 -0.11577 0.00000 0.00000 -1.0539061 #@# 4 227 -0.06567 0.16518 -0.45564 -0.12806 0.00000 0.00000 -1.0539066 #@# 4 230 -0.06567 0.16518 -0.45564 -0.15536 0.00000 0.00000 -1.0539072 #@# 4 232 -0.06567 0.16518 -0.45564 -0.14536 0.00000 0.00000 -1.0539083 #@# 4 248 -0.06567 0.16518 -0.45564 -0.14536 0.00000 0.05276 -1.0539117 #@# 4 258 -0.07441 0.18717 -0.38315 -0.16472 0.00000 0.05978 -1.0539187 powell nthiter 1: fret = -1.053919 #@# 4 269 -0.04328 0.18717 -0.38315 -0.16472 0.00000 0.05978 -1.0539204 #@# 4 279 -0.05328 0.20240 -0.38315 -0.16472 0.00000 0.05978 -1.0539206 #@# 4 291 -0.05328 0.20240 -0.38315 -0.16472 0.00000 0.07378 -1.0539209 #@# 4 308 -0.05328 0.20240 -0.38315 -0.16472 -0.01000 0.07378 -1.0539210 #@# 4 318 -0.05394 0.20405 -0.37771 -0.16617 -0.01000 0.07430 -1.0539222 Powell done niters total = 1 OptTimeSec 1.4 sec OptTimeMin 0.02 min nEvals 319 Final parameters -0.05393674 0.20405276 -0.37770966 -0.16617213 -0.01000000 0.07430480 Final cost -1.053922198659220 --------------------------------- mri_coreg utimesec 75.064412 mri_coreg stimesec 0.298131 mri_coreg ru_maxrss 419268 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 259253 mri_coreg ru_majflt 21 mri_coreg ru_nswap 0 mri_coreg ru_inblock 3278 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 1451 mri_coreg ru_nivcsw 105 Final RefRAS-to-MovRAS 1.00000 0.00130 -0.00017 -0.05394; -0.00130 0.99999 -0.00290 0.20405; 0.00017 0.00290 1.00000 -0.37771; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 1.00000 -0.00017 -0.00130 -36.73225; 0.00130 0.00290 0.99999 -19.38631; -0.00017 -1.00000 0.00290 218.22279; 0.00000 0.00000 0.00000 1.00000; Final parameters -0.0539 0.2041 -0.3777 -0.1662 -0.0100 0.0743 nhits = 111088 out of 16777216, Percent Overlap: 42.4 mri_coreg RunTimeSec 21.1 sec To check run: tkregisterfv --mov transforms/tmp.bbregister.962467/template.nii --targ brainmask.mgz --reg transforms/tmp.bbregister.962467/mri_coreg.lta --s FM0001 --surfs mri_coreg done mri_segreg --mov transforms/tmp.bbregister.962467/template.nii --init-reg transforms/tmp.bbregister.962467/reg.init.dat --out-reg transforms/tmp.bbregister.962467/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white.preaparc --gm-proj-abs 1.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_segreg --mov transforms/tmp.bbregister.962467/template.nii --init-reg transforms/tmp.bbregister.962467/reg.init.dat --out-reg transforms/tmp.bbregister.962467/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white.preaparc --gm-proj-abs 1.5 --gm-gt-wm 0.5 sysname Linux hostname acn179 machine x86_64 user moana004 movvol transforms/tmp.bbregister.962467/template.nii regfile transforms/tmp.bbregister.962467/reg.init.dat subject FM0001 dof 6 outregfile transforms/tmp.bbregister.962467/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white.preaparc GMProjAbs 1.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1663078763 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.00000 0.00130 -0.00017 -0.07931; 0.00017 0.00290 1.00000 -0.42725; 0.00130 -0.99999 0.00290 -0.15033; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white.preaparc surf GM Proj: 0 0.500000 1.500000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white.preaparc surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.997208 1 -25.0 -25.0 25.0 0.961288 2 -25.0 25.0 -25.0 0.963423 3 -25.0 25.0 25.0 1.009335 4 25.0 -25.0 -25.0 0.972106 5 25.0 -25.0 25.0 0.971587 6 25.0 25.0 -25.0 0.993123 7 25.0 25.0 25.0 0.996372 REL: 8 0.082757 7.864442 0.983055 rel = 0.0841839 Initial costs ---------------- Number of surface hits 2752 WM Intensity 476.6059 +/- 78.9247 Ctx Intensity 637.7533 +/- 96.6087 Pct Contrast 28.8872 +/- 17.3992 Cost 0.0828 RelCost 0.0842 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9110 0.9110 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8947 0.8947 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8733 0.8733 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8056 0.8056 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8053 0.8053 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.7896 0.7896 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7887 0.7887 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7073 0.7073 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5943 0.5943 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.5526 0.5526 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.4988 0.4988 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0828 0.0828 0.0 Brute Force -------------------------- Min cost was 0.082757 Number of iterations 729 Search time 0.796000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.082757 7 0.171 0.000 0.000 0.000 0.000 0.000 0.0802766041 9 0.134 0.000 0.000 0.000 0.000 0.000 0.0799939406 11 0.113 0.000 0.000 0.000 0.000 0.000 0.0798968187 12 0.111 0.000 0.000 0.000 0.000 0.000 0.0798932266 14 0.108 0.000 0.000 0.000 0.000 0.000 0.0798916811 22 0.108 0.382 0.000 0.000 0.000 0.000 0.0709417284 23 0.108 0.378 0.000 0.000 0.000 0.000 0.0708911940 24 0.108 0.312 0.000 0.000 0.000 0.000 0.0706616438 26 0.108 0.333 0.000 0.000 0.000 0.000 0.0706075974 37 0.108 0.333 0.055 0.000 0.000 0.000 0.0703236208 38 0.108 0.333 0.057 0.000 0.000 0.000 0.0703202384 39 0.108 0.333 0.068 0.000 0.000 0.000 0.0703152733 41 0.108 0.333 0.065 0.000 0.000 0.000 0.0703131934 42 0.108 0.333 0.064 0.000 0.000 0.000 0.0703130923 50 0.108 0.333 0.064 -0.149 0.000 0.000 0.0691349663 51 0.108 0.333 0.064 -0.148 0.000 0.000 0.0691226822 52 0.108 0.333 0.064 -0.112 0.000 0.000 0.0689420674 55 0.108 0.333 0.064 -0.109 0.000 0.000 0.0689377712 56 0.108 0.333 0.064 -0.107 0.000 0.000 0.0689362953 67 0.108 0.333 0.064 -0.107 0.019 0.000 0.0688921768 68 0.108 0.333 0.064 -0.107 0.018 0.000 0.0688876165 69 0.108 0.333 0.064 -0.107 0.013 0.000 0.0688817885 71 0.108 0.333 0.064 -0.107 0.014 0.000 0.0688805055 72 0.108 0.333 0.064 -0.107 0.015 0.000 0.0688801954 83 0.108 0.333 0.064 -0.107 0.015 0.032 0.0688232508 84 0.108 0.333 0.064 -0.107 0.015 0.027 0.0688183388 85 0.108 0.333 0.064 -0.107 0.015 0.025 0.0688179102 87 0.108 0.333 0.064 -0.107 0.015 0.026 0.0688178783 95 0.128 0.393 0.076 -0.126 0.018 0.030 0.0687900549 96 0.123 0.379 0.073 -0.122 0.017 0.029 0.0687562878 97 0.119 0.367 0.071 -0.118 0.017 0.028 0.0687372979 99 0.118 0.362 0.070 -0.116 0.017 0.028 0.0687351088 powell nthiter 1: fret = 0.068735 113 0.123 0.362 0.070 -0.116 0.017 0.028 0.0687270885 114 0.122 0.362 0.070 -0.116 0.017 0.028 0.0687268255 126 0.122 0.362 0.070 -0.116 0.017 0.020 0.0687227882 127 0.122 0.362 0.070 -0.116 0.017 0.022 0.0687225721 135 0.122 0.362 0.196 -0.116 0.017 0.022 0.0682753435 137 0.122 0.362 0.294 -0.116 0.017 0.022 0.0670062270 139 0.122 0.362 0.275 -0.116 0.017 0.022 0.0669176396 141 0.122 0.362 0.277 -0.116 0.017 0.022 0.0669147103 151 0.122 0.362 0.277 -0.244 0.017 0.022 0.0659056437 152 0.122 0.362 0.277 -0.237 0.017 0.022 0.0658654977 153 0.122 0.362 0.277 -0.214 0.017 0.022 0.0657670686 155 0.122 0.362 0.277 -0.201 0.017 0.022 0.0657478146 156 0.122 0.362 0.277 -0.200 0.017 0.022 0.0657470047 158 0.122 0.362 0.277 -0.197 0.017 0.022 0.0657463608 167 0.122 0.362 0.277 -0.197 0.041 0.022 0.0654935934 169 0.122 0.362 0.277 -0.197 0.046 0.022 0.0654601262 170 0.122 0.362 0.277 -0.197 0.058 0.022 0.0654516155 171 0.122 0.362 0.277 -0.197 0.053 0.022 0.0654390251 180 0.133 0.397 0.284 -0.208 0.054 0.025 0.0650153537 182 0.134 0.400 0.285 -0.209 0.054 0.025 0.0650132843 184 0.134 0.399 0.284 -0.209 0.054 0.025 0.0650128696 186 0.134 0.399 0.284 -0.209 0.054 0.025 0.0650128532 powell nthiter 2: fret = 0.065013 196 0.148 0.399 0.284 -0.209 0.054 0.025 0.0648772858 197 0.154 0.399 0.284 -0.209 0.054 0.025 0.0648725786 198 0.152 0.399 0.284 -0.209 0.054 0.025 0.0648708901 212 0.152 0.399 0.284 -0.209 0.054 0.028 0.0648683036 213 0.152 0.399 0.284 -0.209 0.054 0.029 0.0648679287 222 0.152 0.399 0.254 -0.209 0.054 0.029 0.0640553590 223 0.152 0.399 0.240 -0.209 0.054 0.029 0.0640321043 224 0.152 0.399 0.245 -0.209 0.054 0.029 0.0640076813 233 0.152 0.399 0.245 -0.260 0.054 0.029 0.0639472343 234 0.152 0.399 0.245 -0.241 0.054 0.029 0.0638852532 235 0.152 0.399 0.245 -0.239 0.054 0.029 0.0638829944 236 0.152 0.399 0.245 -0.236 0.054 0.029 0.0638826008 238 0.152 0.399 0.245 -0.237 0.054 0.029 0.0638824010 245 0.152 0.399 0.245 -0.237 0.041 0.029 0.0638042855 258 0.152 0.400 0.245 -0.237 0.041 0.030 0.0638040084 powell nthiter 3: fret = 0.063804 271 0.156 0.400 0.245 -0.237 0.041 0.030 0.0638039925 273 0.155 0.400 0.245 -0.237 0.041 0.030 0.0638025956 274 0.154 0.400 0.245 -0.237 0.041 0.030 0.0638023871 284 0.154 0.400 0.245 -0.237 0.041 0.033 0.0638013557 285 0.154 0.400 0.245 -0.237 0.041 0.032 0.0638011642 295 0.154 0.400 0.236 -0.237 0.041 0.032 0.0637809151 296 0.154 0.400 0.239 -0.237 0.041 0.032 0.0637752274 297 0.154 0.400 0.240 -0.237 0.041 0.032 0.0637750325 306 0.154 0.400 0.240 -0.238 0.041 0.032 0.0637737743 307 0.154 0.400 0.240 -0.241 0.041 0.032 0.0637730035 316 0.154 0.400 0.240 -0.241 0.040 0.032 0.0637720440 328 0.154 0.400 0.240 -0.241 0.040 0.032 0.0637718973 338 0.154 0.400 0.239 -0.242 0.040 0.033 0.0637709303 345 0.154 0.400 0.239 -0.242 0.040 0.033 0.0637709257 powell nthiter 4: fret = 0.063771 356 0.152 0.400 0.239 -0.242 0.040 0.033 0.0637693691 378 0.153 0.402 0.239 -0.243 0.040 0.033 0.0637692027 379 0.153 0.402 0.239 -0.242 0.040 0.033 0.0637690659 380 0.153 0.402 0.239 -0.242 0.040 0.033 0.0637689599 389 0.153 0.402 0.239 -0.240 0.040 0.033 0.0637684604 406 0.153 0.402 0.238 -0.241 0.040 0.034 0.0637681839 409 0.153 0.402 0.238 -0.241 0.040 0.034 0.0637680659 412 0.153 0.402 0.238 -0.241 0.040 0.034 0.0637680257 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.999417 1 -25.0 -25.0 25.0 0.968658 2 -25.0 25.0 -25.0 0.969084 3 -25.0 25.0 25.0 1.014510 4 25.0 -25.0 -25.0 0.981236 5 25.0 -25.0 25.0 0.961956 6 25.0 25.0 -25.0 0.988431 7 25.0 25.0 25.0 0.975910 REL: 8 0.063768 7.859203 0.982400 rel = 0.0649104 Number of iterations 4 Min cost was 0.063768 Number of FunctionCalls 416 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.441000 sec Parameters at optimum (transmm) 0.15303 0.40203 0.23803 Parameters at optimum (rotdeg) -0.24111 0.03997 0.03365 Final costs ---------------- Number of surface hits 2752 WM Intensity 476.0443 +/- 79.2796 Ctx Intensity 642.2956 +/- 97.6608 Pct Contrast 29.7218 +/- 16.8238 Cost 0.0638 RelCost 0.0842 Reg at min cost was 1.00000 0.00060 -0.00076 0.07387; 0.00076 -0.00131 1.00000 -0.02590; 0.00060 -1.00000 -0.00131 0.08956; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to transforms/tmp.bbregister.962467/bbr.pass1.dat, type = 14 Original Reg 1.00000 0.00130 -0.00017 -0.07931; 0.00017 0.00290 1.00000 -0.42725; 0.00130 -0.99999 0.00290 -0.15033; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 0.00070 0.00059 -0.15318; -0.00059 0.00421 -0.00000 -0.40135; 0.00070 0.00000 0.00421 -0.23989; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.552175 Computing change in rh position Surface-RMS-Diff-mm 0.546897 0.137480 0.855251 mri_segreg done mri_segreg --mov transforms/tmp.bbregister.962467/template.nii --init-reg transforms/tmp.bbregister.962467/bbr.pass1.dat --out-reg transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1.5 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param transforms/T2raw.auto.dat.param --surf white.preaparc --brute -0.1 0.1 0.1 --cur-reg transforms/tmp.bbregister.962467/reg.curopt.dat --gm-proj-abs 1.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_segreg --mov transforms/tmp.bbregister.962467/template.nii --init-reg transforms/tmp.bbregister.962467/bbr.pass1.dat --out-reg transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1.5 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param transforms/T2raw.auto.dat.param --surf white.preaparc --brute -0.1 0.1 0.1 --cur-reg transforms/tmp.bbregister.962467/reg.curopt.dat --gm-proj-abs 1.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname acn179 machine x86_64 user moana004 movvol transforms/tmp.bbregister.962467/template.nii regfile transforms/tmp.bbregister.962467/bbr.pass1.dat subject FM0001 dof 6 outregfile transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white.preaparc GMProjAbs 1.500000 WMProjAbs 1.500000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1662782114 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.00000 0.00060 -0.00076 0.07387; 0.00076 -0.00131 1.00000 -0.02590; 0.00060 -1.00000 -0.00131 0.08956; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white.preaparc surf GM Proj: 0 0.500000 1.500000 WM Proj: 0 0.500000 1.500000 Projecting RH Surfs Loading rh.white.preaparc surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.992710 1 -25.0 -25.0 25.0 0.963775 2 -25.0 25.0 -25.0 0.992987 3 -25.0 25.0 25.0 1.009576 4 25.0 -25.0 -25.0 0.968733 5 25.0 -25.0 25.0 0.975643 6 25.0 25.0 -25.0 1.001215 7 25.0 25.0 25.0 1.003881 REL: 8 0.050361 7.908520 0.988565 rel = 0.0509435 Initial costs ---------------- Number of surface hits 275745 WM Intensity 469.8523 +/- 69.1948 Ctx Intensity 643.3006 +/- 96.7257 Pct Contrast 30.9052 +/- 15.8431 Cost 0.0504 RelCost 0.0509 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0569 0.0569 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0550 0.0550 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0546 0.0546 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0542 0.0542 0.0 83 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.1000 0.0540 0.0540 0.0 86 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.1000 0.0540 0.0540 0.0 92 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.0538 0.0538 0.0 164 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0537 0.0537 0.0 167 -0.1000 0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0531 0.0531 0.0 407 0.0000 0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0528 0.0528 0.0 409 0.0000 0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0523 0.0523 0.0 410 0.0000 0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0517 0.0517 0.0 650 0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0514 0.0514 0.0 Brute Force -------------------------- Min cost was 0.051417 Number of iterations 729 Search time 1.052000 sec Parameters at best (transmm, rotdeg) 0.100 0.100 -0.100 -0.100 -0.100 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0.1 2 -0.1 3 -0.1 4 -0.1 5 0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.051623 7 -0.028 0.100 -0.100 -0.100 -0.100 0.100 0.0510280967 8 -0.018 0.100 -0.100 -0.100 -0.100 0.100 0.0510235673 9 -0.017 0.100 -0.100 -0.100 -0.100 0.100 0.0510234575 19 -0.016 -0.018 -0.100 -0.100 -0.100 0.100 0.0507006844 20 -0.016 -0.002 -0.100 -0.100 -0.100 0.100 0.0506975715 21 -0.016 -0.007 -0.100 -0.100 -0.100 0.100 0.0506967802 22 -0.016 -0.008 -0.100 -0.100 -0.100 0.100 0.0506967697 30 -0.016 -0.008 -0.111 -0.100 -0.100 0.100 0.0506596748 31 -0.016 -0.008 -0.178 -0.100 -0.100 0.100 0.0506310571 33 -0.016 -0.008 -0.151 -0.100 -0.100 0.100 0.0506057584 42 -0.016 -0.008 -0.151 0.037 -0.100 0.100 0.0503204234 43 -0.016 -0.008 -0.151 0.018 -0.100 0.100 0.0503195172 44 -0.016 -0.008 -0.151 0.026 -0.100 0.100 0.0503181839 55 -0.016 -0.008 -0.151 0.025 0.035 0.100 0.0499375319 56 -0.016 -0.008 -0.151 0.025 0.016 0.100 0.0499215845 57 -0.016 -0.008 -0.151 0.025 0.013 0.100 0.0499208641 58 -0.016 -0.008 -0.151 0.025 0.010 0.100 0.0499206197 67 -0.016 -0.008 -0.151 0.025 0.010 0.018 0.0497423918 68 -0.016 -0.008 -0.151 0.025 0.010 0.005 0.0497412825 69 -0.016 -0.008 -0.151 0.025 0.010 0.010 0.0497410172 powell nthiter 1: fret = 0.049741 79 -0.004 -0.008 -0.151 0.025 0.010 0.010 0.0497220357 80 0.008 -0.008 -0.151 0.025 0.010 0.010 0.0497177367 81 0.005 -0.008 -0.151 0.025 0.010 0.010 0.0497174576 90 0.005 -0.011 -0.151 0.025 0.010 0.010 0.0497155499 91 0.005 -0.020 -0.151 0.025 0.010 0.010 0.0497127192 101 0.005 -0.020 -0.188 0.025 0.010 0.010 0.0496951522 102 0.005 -0.020 -0.180 0.025 0.010 0.010 0.0496926816 105 0.005 -0.020 -0.179 0.025 0.010 0.010 0.0496926606 113 0.005 -0.020 -0.179 0.016 0.010 0.010 0.0496909934 114 0.005 -0.020 -0.179 0.017 0.010 0.010 0.0496909928 123 0.005 -0.020 -0.179 0.017 0.011 0.010 0.0496909256 124 0.005 -0.020 -0.179 0.017 0.012 0.010 0.0496908956 126 0.005 -0.020 -0.179 0.017 0.013 0.010 0.0496908592 136 0.005 -0.020 -0.179 0.017 0.013 -0.008 0.0496834562 powell nthiter 2: fret = 0.049683 158 0.005 -0.022 -0.179 0.017 0.013 -0.008 0.0496833792 168 0.005 -0.022 -0.180 0.017 0.013 -0.008 0.0496832387 169 0.005 -0.022 -0.182 0.017 0.013 -0.008 0.0496831627 179 0.005 -0.022 -0.182 0.016 0.013 -0.008 0.0496831389 190 0.005 -0.022 -0.182 0.016 0.012 -0.008 0.0496830638 powell nthiter 3: fret = 0.049683 219 0.005 -0.023 -0.182 0.016 0.012 -0.008 0.0496830579 260 0.005 -0.023 -0.182 0.016 0.012 -0.009 0.0496830543 powell nthiter 4: fret = 0.049683 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.992579 1 -25.0 -25.0 25.0 0.965302 2 -25.0 25.0 -25.0 0.991696 3 -25.0 25.0 25.0 1.008700 4 25.0 -25.0 -25.0 0.968560 5 25.0 -25.0 25.0 0.975473 6 25.0 25.0 -25.0 1.001452 7 25.0 25.0 25.0 1.004433 REL: 8 0.049683 7.908194 0.988524 rel = 0.0502598 Number of iterations 4 Min cost was 0.049683 Number of FunctionCalls 318 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 12.546000 sec Parameters at optimum (transmm) 0.00510 -0.02283 -0.18164 Parameters at optimum (rotdeg) 0.01585 0.01173 -0.00898 Final costs ---------------- Number of surface hits 275745 WM Intensity 469.9911 +/- 69.2450 Ctx Intensity 643.5560 +/- 97.4194 Pct Contrast 30.9062 +/- 15.8597 Cost 0.0497 RelCost 0.0509 Reg at min cost was 1.00000 0.00040 -0.00061 0.07899; 0.00061 -0.00103 1.00000 -0.04876; 0.00039 -1.00000 -0.00103 -0.09210; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to transforms/T2raw.auto.dat, type = 14 Original Reg 1.00000 0.00060 -0.00076 0.07387; 0.00076 -0.00131 1.00000 -0.02590; 0.00060 -1.00000 -0.00131 0.08956; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 0.00020 -0.00016 -0.00512; 0.00016 -0.00028 -0.00000 0.02287; 0.00020 0.00000 -0.00028 0.18166; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.179908 Computing change in rh position Surface-RMS-Diff-mm 0.186017 0.009569 0.209311 mri_segreg done MinCost: 0.049683 469.991118 643.556009 30.906193 tkregister2_cmdl --mov orig/T2raw.mgz --reg transforms/T2raw.auto.dat --noedit --ltaout transforms/T2raw.auto.lta tkregister_tcl /opt/freesurfer/freesurfer-6.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume orig/T2raw.mgz reg file transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.00000 0.00040 -0.00061 0.07899; 0.00061 -0.00103 1.00000 -0.04876; 0.00039 -1.00000 -0.00103 -0.09210; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable orig/T2raw.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 91.00000; 0.00000 0.00000 1.00000 -91.00000; 0.00000 -1.00000 0.00000 109.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.00000 0.00040 -0.00061 0.07899; 0.00061 -0.00103 1.00000 -0.04876; 0.00039 -1.00000 -0.00103 -0.09210; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = FM0001 RegMat --------------------------- 1.00000 0.00040 -0.00061 0.07899; 0.00061 -0.00103 1.00000 -0.04876; 0.00039 -1.00000 -0.00103 -0.09210; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Fri Sep 9 16:11:35 CDT 2022 Ended at Fri Sep 9 16:12:25 CDT 2022 BBR-Run-Time-Sec 50 bbregister Done To check results, run: tkregisterfv --mov orig/T2raw.mgz --reg transforms/T2raw.auto.lta --surfs cp transforms/T2raw.auto.lta transforms/T2raw.lta #=============================== mri_concatenate_lta transforms/T2raw.lta transforms/conf2rawavg.lta transforms/T2raw.rawavg.lta Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file transforms/T2raw.rawavg.lta... mri_concatenate_lta.bin successful. #=============================== mri_vol2vol --mov orig/T2raw.mgz --targ rawavg.cmdc.mgz --reg transforms/T2raw.rawavg.lta --o rawavg.T2.prenorm.mgz --interp cubic regio_read_register: loading lta Matrix from regfile: 1.00000 0.00040 -0.00061 0.07899; 0.00061 -0.00103 1.00000 -0.04878; 0.00039 -1.00000 -0.00103 -0.09211; 0.00000 0.00000 0.00000 1.00000; movvol orig/T2raw.mgz targvol rawavg.cmdc.mgz outvol rawavg.T2.prenorm.mgz regfile transforms/T2raw.rawavg.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp cubic (5) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1663671284 Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00040 -0.00061 0.07899; 0.00061 -0.00103 1.00000 -0.04878; 0.00039 -1.00000 -0.00103 -0.09211; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 -0.00061 -0.00040 -36.95078; 0.00039 -0.00103 1.00000 -18.82632; -0.00061 -1.00000 -0.00103 219.16072; 0.00000 0.00000 0.00000 1.00000; Resampling MRItoBSpline degree 3 Output registration matrix is identity mri_vol2vol done Fri Sep 9 16:12:29 CDT 2022 #=============================== mri_normalize -sigma 8 -nonmax_suppress 0 -min_dist 1 -surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.rawavg identity.nofile -surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.rawavg identity.nofile -aseg aseg.presurf.mgz rawavg.T2.prenorm.mgz rawavg.T2.norm.mgz using Gaussian smoothing of bias field, sigma=8.000 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading from rawavg.T2.prenorm.mgz... computing distance transform computing distance transform 43463 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=8.000 writing normalized volume to rawavg.T2.norm.mgz #=============================== mri_mask -keep_mask_deletion_edits rawavg.T2.norm.mgz rawavg.brain.finalsurfs.mgz rawavg.T2.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to rawavg.T2.mgz...done. mri_vol2vol --targ orig.mgz --mov rawavg.T2.mgz --reg transforms/rawavg2conf.dat --o conf.T2.mgz Matrix from regfile: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; movvol rawavg.T2.mgz targvol orig.mgz outvol conf.T2.mgz regfile transforms/rawavg2conf.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1662889161 Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Fri Sep 9 16:13:02 CDT 2022 #=============================== mris_make_surfaces -cortex 0 -noaparc -pial pial.rawavg -white NOWRITE -nowhite -orig white.preaparc.rawavg -orig_white white.rawavg -orig_pial woT2.pial.rawavg -aseg rawavg.aseg.presurf -wm rawavg.wm -filled rawavg.filled -mgz -T1 rawavg.brain.finalsurfs -T2 rawavg.T2 -nsigma_above 2 -nsigma_below 3 FM0001 lh writing pial surface to file named pial.rawavg -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... reading previously compute gray/white surface reading original vertex positions from white.preaparc.rawavg using rawavg.wm as filled name using rawavg.filled as filled name refining pial surfaces placement using T2 volume rawavg.T2 using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) not generating cortex label to subject's label/?h.cortex.label file not using aparc to prevent surfaces crossing the midline using white.rawavg starting white location... using woT2.pial.rawavg starting pial locations... using aseg volume rawavg.aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using rawavg.brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.filled.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.brain.finalsurfs.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.aseg.presurf.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.wm.mgz... 244777 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white.preaparc.rawavg... computing class statistics... border white: 277660 voxels (1.65%) border gray 299649 voxels (1.79%) WM (103.0): 102.5 +- 7.2 [70.0 --> 110.0] GM (79.0) : 78.3 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.4 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 56.7 (was 40) setting MAX_GRAY to 101.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... changing type of input wm volume to UCHAR... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=78+-6.1 mean inside = 101.1, mean outside = 84.2 reading initial white vertex positions from white.rawavg... reading white vertex positions from white.rawavg... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group reading initial pial vertex positions from woT2.pial.rawavg... repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (box.dx, box.dy, box.dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) locating cortical regions not in the range [108.56 186.11], gm=155.09+-15.51, and vertices in regions > 147.3 119164 surface locations found to contain inconsistent values (41482 in, 77682 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 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 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=100431.6, rms=0.521 001: dt: 0.0500, sse=100433.2, rms=0.521 (0.130%) 002: dt: 0.0500, sse=100432.1, rms=0.520 (0.143%) 003: dt: 0.0500, sse=100430.7, rms=0.519 (0.142%) 004: dt: 0.0500, sse=100429.3, rms=0.518 (0.141%) 005: dt: 0.0500, sse=100427.6, rms=0.518 (0.140%) 006: dt: 0.0500, sse=100425.7, rms=0.517 (0.139%) 007: dt: 0.0500, sse=100423.6, rms=0.516 (0.138%) 008: dt: 0.0500, sse=100421.5, rms=0.516 (0.137%) 009: dt: 0.0500, sse=100419.2, rms=0.515 (0.136%) 010: dt: 0.0500, sse=100416.8, rms=0.514 (0.135%) positioning took 0.8 minutes tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=99950.8, rms=0.514 011: dt: 0.0500, sse=99948.0, rms=0.513 (0.135%) 012: dt: 0.0500, sse=99945.3, rms=0.513 (0.134%) 013: dt: 0.0500, sse=99942.4, rms=0.512 (0.133%) 014: dt: 0.0500, sse=99939.4, rms=0.511 (0.132%) 015: dt: 0.0500, sse=99936.2, rms=0.511 (0.132%) 016: dt: 0.0500, sse=99932.9, rms=0.510 (0.131%) 017: dt: 0.0500, sse=99929.4, rms=0.509 (0.130%) 018: dt: 0.0500, sse=99925.9, rms=0.509 (0.129%) 019: dt: 0.0500, sse=99922.2, rms=0.508 (0.128%) 020: dt: 0.0500, sse=99918.4, rms=0.507 (0.128%) positioning took 0.8 minutes tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=99508.7, rms=0.507 021: dt: 0.0500, sse=99504.7, rms=0.507 (0.127%) 022: dt: 0.0500, sse=99500.7, rms=0.506 (0.126%) 023: dt: 0.0500, sse=99496.5, rms=0.505 (0.125%) 024: dt: 0.0500, sse=99492.4, rms=0.505 (0.124%) 025: dt: 0.0500, sse=99488.0, rms=0.504 (0.124%) 026: dt: 0.0500, sse=99483.8, rms=0.504 (0.123%) 027: dt: 0.0500, sse=99479.4, rms=0.503 (0.122%) 028: dt: 0.0500, sse=99475.0, rms=0.502 (0.121%) 029: dt: 0.0500, sse=99470.5, rms=0.502 (0.121%) 030: dt: 0.0500, sse=99466.0, rms=0.501 (0.120%) positioning took 0.8 minutes tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=99103.2, rms=0.501 031: dt: 0.5000, sse=99059.8, rms=0.495 (1.158%) 032: dt: 0.5000, sse=99018.1, rms=0.490 (1.081%) 033: dt: 0.5000, sse=98964.6, rms=0.485 (1.036%) 034: dt: 0.5000, sse=98909.2, rms=0.480 (0.977%) 035: dt: 0.5000, sse=98846.5, rms=0.476 (0.938%) 036: dt: 0.5000, sse=98788.6, rms=0.471 (0.885%) 037: dt: 0.5000, sse=98725.3, rms=0.467 (0.855%) 038: dt: 0.5000, sse=98661.8, rms=0.464 (0.824%) 039: dt: 0.5000, sse=98600.2, rms=0.460 (0.790%) 040: dt: 0.5000, sse=98539.7, rms=0.456 (0.759%) 041: dt: 0.5000, sse=98475.9, rms=0.453 (0.735%) 042: dt: 0.5000, sse=98421.5, rms=0.450 (0.698%) 043: dt: 0.5000, sse=98359.4, rms=0.447 (0.697%) 044: dt: 0.5000, sse=98305.1, rms=0.444 (0.652%) 045: dt: 0.5000, sse=98251.5, rms=0.441 (0.634%) 046: dt: 0.5000, sse=98200.8, rms=0.438 (0.601%) 047: dt: 0.5000, sse=98153.2, rms=0.436 (0.598%) 048: dt: 0.5000, sse=98106.2, rms=0.433 (0.569%) 049: dt: 0.5000, sse=98061.4, rms=0.431 (0.551%) 050: dt: 0.5000, sse=98016.9, rms=0.429 (0.530%) 051: dt: 0.5000, sse=97968.2, rms=0.426 (0.526%) 052: dt: 0.5000, sse=97925.6, rms=0.424 (0.506%) 053: dt: 0.5000, sse=97880.2, rms=0.422 (0.490%) 054: dt: 0.5000, sse=97839.9, rms=0.420 (0.467%) 055: dt: 0.5000, sse=97798.5, rms=0.418 (0.464%) 056: dt: 0.5000, sse=97760.7, rms=0.416 (0.431%) 057: dt: 0.5000, sse=97721.5, rms=0.415 (0.433%) 058: dt: 0.5000, sse=97684.8, rms=0.413 (0.413%) 059: dt: 0.5000, sse=97647.9, rms=0.411 (0.401%) 060: dt: 0.5000, sse=97616.4, rms=0.410 (0.379%) positioning took 2.6 minutes repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (box.dx, box.dy, box.dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) locating cortical regions not in the range [108.86 185.91], gm=155.09+-15.41, and vertices in regions > 147.4 115758 surface locations found to contain inconsistent values (37950 in, 77808 out) tol=1.0e-04, sigma=1.0, host=acn17, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=94323.4, rms=0.431 061: dt: 0.5000, sse=94236.9, rms=0.427 (0.920%) 062: dt: 0.5000, sse=94134.2, rms=0.422 (1.025%) 063: dt: 0.5000, sse=94034.7, rms=0.418 (0.930%) 064: dt: 0.5000, sse=93940.7, rms=0.415 (0.869%) 065: dt: 0.5000, sse=93856.2, rms=0.411 (0.819%) 066: dt: 0.5000, sse=93774.9, rms=0.408 (0.761%) 067: dt: 0.5000, sse=93700.9, rms=0.405 (0.713%) 068: dt: 0.5000, sse=93632.8, rms=0.403 (0.676%) 069: dt: 0.5000, sse=93565.5, rms=0.400 (0.643%) 070: dt: 0.5000, sse=93500.7, rms=0.398 (0.617%) 071: dt: 0.5000, sse=93443.7, rms=0.395 (0.596%) 072: dt: 0.5000, sse=93384.9, rms=0.393 (0.580%) 073: dt: 0.5000, sse=93329.4, rms=0.391 (0.554%) 074: dt: 0.5000, sse=93276.8, rms=0.389 (0.536%) 075: dt: 0.5000, sse=93227.5, rms=0.387 (0.524%) 076: dt: 0.5000, sse=93176.0, rms=0.385 (0.509%) 077: dt: 0.5000, sse=93127.7, rms=0.383 (0.495%) 078: dt: 0.5000, sse=93080.0, rms=0.381 (0.469%) 079: dt: 0.5000, sse=93035.6, rms=0.379 (0.464%) 080: dt: 0.5000, sse=92993.8, rms=0.378 (0.438%) 081: dt: 0.5000, sse=92952.6, rms=0.376 (0.435%) 082: dt: 0.5000, sse=92911.8, rms=0.374 (0.413%) 083: dt: 0.5000, sse=92874.1, rms=0.373 (0.397%) 084: dt: 0.5000, sse=92837.7, rms=0.371 (0.390%) 085: dt: 0.5000, sse=92801.8, rms=0.370 (0.374%) 086: dt: 0.5000, sse=92765.9, rms=0.369 (0.357%) 087: dt: 0.5000, sse=92735.7, rms=0.367 (0.349%) 088: dt: 0.5000, sse=92701.7, rms=0.366 (0.340%) 089: dt: 0.5000, sse=92672.1, rms=0.365 (0.324%) 090: dt: 0.5000, sse=92641.5, rms=0.364 (0.315%) positioning took 3.1 minutes repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (box.dx, box.dy, box.dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) locating cortical regions not in the range [105.06 190.11], gm=156.09+-17.01, and vertices in regions > 147.6 116094 surface locations found to contain inconsistent values (21685 in, 94409 out) tol=1.0e-04, sigma=0.5, host=acn17, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=92342.1, rms=0.383 091: dt: 0.5000, sse=92304.7, rms=0.380 (0.771%) 092: dt: 0.5000, sse=92247.1, rms=0.377 (0.844%) 093: dt: 0.5000, sse=92191.8, rms=0.374 (0.732%) 094: dt: 0.5000, sse=92140.9, rms=0.372 (0.658%) 095: dt: 0.5000, sse=92093.6, rms=0.370 (0.594%) 096: dt: 0.5000, sse=92049.6, rms=0.368 (0.540%) 097: dt: 0.5000, sse=92010.7, rms=0.366 (0.485%) 098: dt: 0.5000, sse=91976.3, rms=0.364 (0.452%) 099: dt: 0.5000, sse=91941.6, rms=0.363 (0.412%) 100: dt: 0.5000, sse=91910.0, rms=0.361 (0.395%) 101: dt: 0.5000, sse=91879.1, rms=0.360 (0.379%) 102: dt: 0.5000, sse=91849.0, rms=0.359 (0.358%) 103: dt: 0.5000, sse=91819.9, rms=0.357 (0.342%) 104: dt: 0.5000, sse=91791.6, rms=0.356 (0.332%) 105: dt: 0.5000, sse=91765.3, rms=0.355 (0.311%) 106: dt: 0.5000, sse=91740.9, rms=0.354 (0.296%) 107: dt: 0.5000, sse=91717.3, rms=0.353 (0.282%) 108: dt: 0.5000, sse=91695.1, rms=0.352 (0.269%) 109: dt: 0.5000, sse=91673.0, rms=0.351 (0.260%) 110: dt: 0.5000, sse=91653.0, rms=0.350 (0.247%) 111: dt: 0.5000, sse=91632.9, rms=0.350 (0.234%) 112: dt: 0.5000, sse=91614.3, rms=0.349 (0.226%) 113: dt: 0.5000, sse=91595.9, rms=0.348 (0.218%) 114: dt: 0.5000, sse=91580.4, rms=0.347 (0.206%) 115: dt: 0.5000, sse=91564.6, rms=0.347 (0.190%) 116: dt: 0.5000, sse=91549.0, rms=0.346 (0.185%) 117: dt: 0.5000, sse=91533.7, rms=0.345 (0.177%) 118: dt: 0.5000, sse=91518.9, rms=0.345 (0.166%) 119: dt: 0.5000, sse=91505.2, rms=0.344 (0.161%) 120: dt: 0.5000, sse=91491.6, rms=0.344 (0.148%) positioning took 3.6 minutes repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (region->dx, region->dy, region->dz) = (138, 326, 215) (box.dx, box.dy, box.dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) (region->dx, region->dy, region->dz) = (146, 334, 230) locating cortical regions not in the range [103.26 191.31], gm=156.09+-17.61, and vertices in regions > 147.3 114021 surface locations found to contain inconsistent values (19231 in, 94790 out) tol=1.0e-04, sigma=0.2, host=acn17, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 writing pial surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial.rawavg... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=92313.2, rms=0.366 121: dt: 0.5000, sse=92296.6, rms=0.364 (0.495%) 122: dt: 0.5000, sse=92257.9, rms=0.362 (0.561%) 123: dt: 0.5000, sse=92220.4, rms=0.361 (0.478%) 124: dt: 0.5000, sse=92185.8, rms=0.359 (0.421%) 125: dt: 0.5000, sse=92154.6, rms=0.358 (0.369%) 126: dt: 0.5000, sse=92126.1, rms=0.357 (0.335%) 127: dt: 0.5000, sse=92100.3, rms=0.355 (0.297%) 128: dt: 0.5000, sse=92075.4, rms=0.355 (0.279%) 129: dt: 0.5000, sse=92050.8, rms=0.354 (0.256%) 130: dt: 0.5000, sse=92029.7, rms=0.353 (0.241%) 131: dt: 0.5000, sse=92007.6, rms=0.352 (0.228%) 132: dt: 0.5000, sse=91987.2, rms=0.351 (0.211%) 133: dt: 0.5000, sse=91968.1, rms=0.350 (0.203%) 134: dt: 0.5000, sse=91950.6, rms=0.350 (0.194%) 135: dt: 0.5000, sse=91932.8, rms=0.349 (0.181%) 136: dt: 0.5000, sse=91917.5, rms=0.349 (0.171%) 137: dt: 0.5000, sse=91903.5, rms=0.348 (0.162%) 138: dt: 0.5000, sse=91889.2, rms=0.347 (0.157%) 139: dt: 0.5000, sse=91875.6, rms=0.347 (0.152%) 140: dt: 0.5000, sse=91861.9, rms=0.346 (0.145%) 141: dt: 0.5000, sse=91848.2, rms=0.346 (0.130%) 142: dt: 0.5000, sse=91836.3, rms=0.346 (0.128%) 143: dt: 0.5000, sse=91825.0, rms=0.345 (0.124%) 144: dt: 0.5000, sse=91814.9, rms=0.345 (0.110%) 145: dt: 0.5000, sse=91804.4, rms=0.344 (0.113%) 146: dt: 0.5000, sse=91795.1, rms=0.344 (0.110%) 147: dt: 0.5000, sse=91784.2, rms=0.344 (0.104%) 148: dt: 0.5000, sse=91774.4, rms=0.343 (0.098%) 149: dt: 0.5000, sse=91765.9, rms=0.343 (0.091%) 150: dt: 0.5000, sse=91757.2, rms=0.343 (0.095%) positioning took 4.1 minutes writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.area.pial vertex spacing 0.95 +- 0.42 (0.05-->6.42) (max @ vno 94078 --> 95116) face area 0.36 +- 0.29 (0.00-->7.75) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 143971 vertices processed 25000 of 143971 vertices processed 50000 of 143971 vertices processed 75000 of 143971 vertices processed 100000 of 143971 vertices processed 125000 of 143971 vertices processed 0 of 143971 vertices processed 25000 of 143971 vertices processed 50000 of 143971 vertices processed 75000 of 143971 vertices processed 100000 of 143971 vertices processed 125000 of 143971 vertices processed thickness calculation complete, 530:456 truncations. 32525 vertices at 0 distance 98152 vertices at 1 distance 88233 vertices at 2 distance 37993 vertices at 3 distance 13341 vertices at 4 distance 4485 vertices at 5 distance 1584 vertices at 6 distance 549 vertices at 7 distance 216 vertices at 8 distance 93 vertices at 9 distance 61 vertices at 10 distance 45 vertices at 11 distance 51 vertices at 12 distance 39 vertices at 13 distance 18 vertices at 14 distance 13 vertices at 15 distance 5 vertices at 16 distance 8 vertices at 17 distance 11 vertices at 18 distance 3 vertices at 19 distance 3 vertices at 20 distance writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.thickness positioning took 25.8 minutes #=============================== mri_surf2surf --s FM0001 --hemi lh --sval-xyz pial.rawavg --surfreg pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval pial.rawavg.conf Reading header for orig.mgz Source registration surface changed to pial.rawavg Target registration surface changed to pial.rawavg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi lh --sval-xyz pial.rawavg --surfreg pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval pial.rawavg.conf sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = pial.rawavg.conf trgtype = srcsurfreg = pial.rawavg trgsurfreg = pial.rawavg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial.rawavg Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial.rawavg Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri Fri Sep 9 16:38:56 CDT 2022 #=============================== mris_make_surfaces -cortex 0 -noaparc -pial pial.rawavg -white NOWRITE -nowhite -orig white.preaparc.rawavg -orig_white white.rawavg -orig_pial woT2.pial.rawavg -aseg rawavg.aseg.presurf -wm rawavg.wm -filled rawavg.filled -mgz -T1 rawavg.brain.finalsurfs -T2 rawavg.T2 -nsigma_above 2 -nsigma_below 3 FM0001 rh writing pial surface to file named pial.rawavg -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... reading previously compute gray/white surface reading original vertex positions from white.preaparc.rawavg using rawavg.wm as filled name using rawavg.filled as filled name refining pial surfaces placement using T2 volume rawavg.T2 using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) not generating cortex label to subject's label/?h.cortex.label file not using aparc to prevent surfaces crossing the midline using white.rawavg starting white location... using woT2.pial.rawavg starting pial locations... using aseg volume rawavg.aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using rawavg.brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.filled.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.brain.finalsurfs.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.aseg.presurf.mgz... reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.wm.mgz... 244777 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white.preaparc.rawavg... computing class statistics... border white: 277660 voxels (1.65%) border gray 299649 voxels (1.79%) WM (103.0): 102.5 +- 7.2 [70.0 --> 110.0] GM (79.0) : 78.3 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.4 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 56.7 (was 40) setting MAX_GRAY to 101.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... changing type of input wm volume to UCHAR... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=78+-7.0 mean inside = 101.1, mean outside = 84.7 reading initial white vertex positions from white.rawavg... reading white vertex positions from white.rawavg... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group reading initial pial vertex positions from woT2.pial.rawavg... repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (box.dx, box.dy, box.dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) locating cortical regions not in the range [111.17 187.71], gm=157.09+-15.31, and vertices in regions > 149.4 119889 surface locations found to contain inconsistent values (40041 in, 79848 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 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 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=100550.7, rms=0.512 001: dt: 0.0500, sse=100553.1, rms=0.512 (0.131%) 002: dt: 0.0500, sse=100552.5, rms=0.511 (0.145%) 003: dt: 0.0500, sse=100551.6, rms=0.510 (0.143%) 004: dt: 0.0500, sse=100550.5, rms=0.510 (0.142%) 005: dt: 0.0500, sse=100549.6, rms=0.509 (0.141%) 006: dt: 0.0500, sse=100548.3, rms=0.508 (0.140%) 007: dt: 0.0500, sse=100546.9, rms=0.507 (0.139%) 008: dt: 0.0500, sse=100545.3, rms=0.507 (0.139%) 009: dt: 0.0500, sse=100543.5, rms=0.506 (0.138%) 010: dt: 0.0500, sse=100541.9, rms=0.505 (0.137%) positioning took 0.8 minutes tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=100075.4, rms=0.505 011: dt: 0.0500, sse=100072.8, rms=0.505 (0.136%) 012: dt: 0.0500, sse=100070.7, rms=0.504 (0.135%) 013: dt: 0.0500, sse=100068.2, rms=0.503 (0.134%) 014: dt: 0.0500, sse=100065.2, rms=0.503 (0.134%) 015: dt: 0.0500, sse=100062.7, rms=0.502 (0.133%) 016: dt: 0.0500, sse=100060.0, rms=0.501 (0.132%) 017: dt: 0.0500, sse=100057.0, rms=0.501 (0.131%) 018: dt: 0.0500, sse=100053.6, rms=0.500 (0.130%) 019: dt: 0.0500, sse=100050.6, rms=0.499 (0.129%) 020: dt: 0.0500, sse=100047.3, rms=0.499 (0.129%) positioning took 0.9 minutes tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=99636.6, rms=0.499 021: dt: 0.0500, sse=99633.1, rms=0.498 (0.128%) 022: dt: 0.0500, sse=99629.3, rms=0.497 (0.127%) 023: dt: 0.0500, sse=99625.6, rms=0.497 (0.126%) 024: dt: 0.0500, sse=99621.9, rms=0.496 (0.126%) 025: dt: 0.0500, sse=99618.0, rms=0.496 (0.125%) 026: dt: 0.0500, sse=99613.5, rms=0.495 (0.124%) 027: dt: 0.0500, sse=99609.7, rms=0.494 (0.123%) 028: dt: 0.0500, sse=99605.9, rms=0.494 (0.122%) 029: dt: 0.0500, sse=99601.9, rms=0.493 (0.121%) 030: dt: 0.0500, sse=99597.5, rms=0.493 (0.121%) positioning took 0.9 minutes tol=1.0e-04, sigma=2.0, host=acn17, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=99234.4, rms=0.493 031: dt: 0.5000, sse=99191.2, rms=0.487 (1.179%) 032: dt: 0.5000, sse=99139.8, rms=0.481 (1.110%) 033: dt: 0.5000, sse=99085.7, rms=0.476 (1.041%) 034: dt: 0.5000, sse=99026.3, rms=0.472 (0.985%) 035: dt: 0.5000, sse=98964.8, rms=0.467 (0.935%) 036: dt: 0.5000, sse=98905.4, rms=0.463 (0.891%) 037: dt: 0.5000, sse=98842.4, rms=0.459 (0.849%) 038: dt: 0.5000, sse=98780.5, rms=0.455 (0.811%) 039: dt: 0.5000, sse=98719.9, rms=0.452 (0.783%) 040: dt: 0.5000, sse=98659.1, rms=0.448 (0.745%) 041: dt: 0.5000, sse=98601.3, rms=0.445 (0.722%) 042: dt: 0.5000, sse=98543.8, rms=0.442 (0.690%) 043: dt: 0.5000, sse=98489.1, rms=0.439 (0.666%) 044: dt: 0.5000, sse=98433.7, rms=0.436 (0.643%) 045: dt: 0.5000, sse=98380.4, rms=0.434 (0.620%) 046: dt: 0.5000, sse=98329.0, rms=0.431 (0.597%) 047: dt: 0.5000, sse=98279.0, rms=0.429 (0.579%) 048: dt: 0.5000, sse=98230.3, rms=0.426 (0.553%) 049: dt: 0.5000, sse=98183.9, rms=0.424 (0.539%) 050: dt: 0.5000, sse=98138.3, rms=0.422 (0.523%) 051: dt: 0.5000, sse=98097.2, rms=0.420 (0.496%) 052: dt: 0.5000, sse=98055.6, rms=0.418 (0.482%) 053: dt: 0.5000, sse=98018.9, rms=0.416 (0.466%) 054: dt: 0.5000, sse=97978.3, rms=0.414 (0.455%) 055: dt: 0.5000, sse=97941.5, rms=0.412 (0.434%) 056: dt: 0.5000, sse=97904.9, rms=0.410 (0.421%) 057: dt: 0.5000, sse=97869.3, rms=0.409 (0.404%) 058: dt: 0.5000, sse=97836.8, rms=0.407 (0.393%) 059: dt: 0.5000, sse=97805.4, rms=0.405 (0.372%) 060: dt: 0.5000, sse=97776.4, rms=0.404 (0.360%) positioning took 2.8 minutes repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (box.dx, box.dy, box.dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) locating cortical regions not in the range [108.46 189.51], gm=157.09+-16.21, and vertices in regions > 149.0 117453 surface locations found to contain inconsistent values (30723 in, 86730 out) tol=1.0e-04, sigma=1.0, host=acn17, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=94393.7, rms=0.418 061: dt: 0.5000, sse=94322.4, rms=0.415 (0.924%) 062: dt: 0.5000, sse=94231.4, rms=0.410 (1.020%) 063: dt: 0.5000, sse=94149.0, rms=0.407 (0.906%) 064: dt: 0.5000, sse=94070.7, rms=0.403 (0.832%) 065: dt: 0.5000, sse=94000.2, rms=0.400 (0.772%) 066: dt: 0.5000, sse=93934.6, rms=0.397 (0.716%) 067: dt: 0.5000, sse=93877.7, rms=0.395 (0.659%) 068: dt: 0.5000, sse=93822.4, rms=0.392 (0.618%) 069: dt: 0.5000, sse=93772.7, rms=0.390 (0.586%) 070: dt: 0.5000, sse=93722.8, rms=0.388 (0.553%) 071: dt: 0.5000, sse=93675.5, rms=0.386 (0.537%) 072: dt: 0.5000, sse=93631.5, rms=0.384 (0.516%) 073: dt: 0.5000, sse=93588.7, rms=0.382 (0.496%) 074: dt: 0.5000, sse=93546.8, rms=0.380 (0.482%) 075: dt: 0.5000, sse=93508.2, rms=0.378 (0.460%) 076: dt: 0.5000, sse=93468.7, rms=0.377 (0.447%) 077: dt: 0.5000, sse=93431.8, rms=0.375 (0.426%) 078: dt: 0.5000, sse=93394.4, rms=0.373 (0.412%) 079: dt: 0.5000, sse=93360.6, rms=0.372 (0.396%) 080: dt: 0.5000, sse=93325.5, rms=0.370 (0.383%) 081: dt: 0.5000, sse=93293.4, rms=0.369 (0.368%) 082: dt: 0.5000, sse=93262.6, rms=0.368 (0.357%) 083: dt: 0.5000, sse=93233.8, rms=0.367 (0.340%) 084: dt: 0.5000, sse=93203.8, rms=0.365 (0.329%) 085: dt: 0.5000, sse=93176.4, rms=0.364 (0.315%) 086: dt: 0.5000, sse=93150.8, rms=0.363 (0.304%) 087: dt: 0.5000, sse=93125.6, rms=0.362 (0.293%) 088: dt: 0.5000, sse=93100.0, rms=0.361 (0.281%) 089: dt: 0.5000, sse=93077.5, rms=0.360 (0.254%) 090: dt: 0.5000, sse=93053.1, rms=0.359 (0.256%) positioning took 3.5 minutes repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (box.dx, box.dy, box.dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) locating cortical regions not in the range [95.26 198.32], gm=157.09+-20.61, and vertices in regions > 146.8 117426 surface locations found to contain inconsistent values (10892 in, 106534 out) tol=1.0e-04, sigma=0.5, host=acn17, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=93432.1, rms=0.398 091: dt: 0.5000, sse=93395.1, rms=0.394 (0.911%) 092: dt: 0.5000, sse=93341.7, rms=0.390 (0.931%) 093: dt: 0.5000, sse=93293.6, rms=0.387 (0.821%) 094: dt: 0.5000, sse=93249.2, rms=0.384 (0.736%) 095: dt: 0.5000, sse=93208.3, rms=0.382 (0.663%) 096: dt: 0.5000, sse=93172.7, rms=0.379 (0.595%) 097: dt: 0.5000, sse=93143.3, rms=0.377 (0.534%) 098: dt: 0.5000, sse=93112.7, rms=0.375 (0.493%) 099: dt: 0.5000, sse=93084.5, rms=0.374 (0.467%) 100: dt: 0.5000, sse=93056.9, rms=0.372 (0.447%) 101: dt: 0.5000, sse=93030.4, rms=0.371 (0.422%) 102: dt: 0.5000, sse=93004.5, rms=0.369 (0.406%) 103: dt: 0.5000, sse=92979.3, rms=0.368 (0.389%) 104: dt: 0.5000, sse=92952.2, rms=0.366 (0.371%) 105: dt: 0.5000, sse=92928.6, rms=0.365 (0.345%) 106: dt: 0.5000, sse=92905.0, rms=0.364 (0.335%) 107: dt: 0.5000, sse=92883.3, rms=0.363 (0.315%) 108: dt: 0.5000, sse=92862.9, rms=0.361 (0.301%) 109: dt: 0.5000, sse=92843.6, rms=0.360 (0.284%) 110: dt: 0.5000, sse=92822.6, rms=0.359 (0.268%) 111: dt: 0.5000, sse=92805.6, rms=0.359 (0.251%) 112: dt: 0.5000, sse=92789.4, rms=0.358 (0.245%) 113: dt: 0.5000, sse=92772.8, rms=0.357 (0.228%) 114: dt: 0.5000, sse=92756.9, rms=0.356 (0.222%) 115: dt: 0.5000, sse=92743.5, rms=0.355 (0.215%) 116: dt: 0.5000, sse=92727.2, rms=0.355 (0.194%) 117: dt: 0.5000, sse=92714.9, rms=0.354 (0.191%) 118: dt: 0.5000, sse=92701.6, rms=0.353 (0.180%) 119: dt: 0.5000, sse=92689.1, rms=0.353 (0.172%) 120: dt: 0.5000, sse=92676.3, rms=0.352 (0.165%) positioning took 4.1 minutes repositioning pial surface locations using rawavg.T2.mgz (box.dx, box.dy, box.dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (region->dx, region->dy, region->dz) = (135, 326, 226) (box.dx, box.dy, box.dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) (region->dx, region->dy, region->dz) = (142, 334, 242) locating cortical regions not in the range [94.96 198.52], gm=157.09+-20.71, and vertices in regions > 146.7 114684 surface locations found to contain inconsistent values (14051 in, 100633 out) tol=1.0e-04, sigma=0.2, host=acn17, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 writing pial surface to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial.rawavg... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=93757.7, rms=0.377 121: dt: 0.5000, sse=93744.7, rms=0.375 (0.521%) 122: dt: 0.5000, sse=93707.4, rms=0.373 (0.561%) 123: dt: 0.5000, sse=93676.6, rms=0.371 (0.471%) 124: dt: 0.5000, sse=93649.0, rms=0.369 (0.416%) 125: dt: 0.5000, sse=93622.2, rms=0.368 (0.367%) 126: dt: 0.5000, sse=93598.8, rms=0.367 (0.318%) 127: dt: 0.5000, sse=93576.6, rms=0.366 (0.289%) 128: dt: 0.5000, sse=93562.1, rms=0.365 (0.264%) 129: dt: 0.5000, sse=93538.8, rms=0.364 (0.251%) 130: dt: 0.5000, sse=93521.0, rms=0.363 (0.227%) 131: dt: 0.5000, sse=93502.1, rms=0.362 (0.222%) 132: dt: 0.5000, sse=93484.6, rms=0.361 (0.210%) 133: dt: 0.5000, sse=93468.2, rms=0.361 (0.203%) 134: dt: 0.5000, sse=93452.0, rms=0.360 (0.192%) 135: dt: 0.5000, sse=93435.4, rms=0.359 (0.181%) 136: dt: 0.5000, sse=93424.3, rms=0.359 (0.161%) 137: dt: 0.5000, sse=93410.4, rms=0.358 (0.162%) 138: dt: 0.5000, sse=93396.6, rms=0.358 (0.159%) 139: dt: 0.5000, sse=93381.8, rms=0.357 (0.147%) 140: dt: 0.5000, sse=93373.2, rms=0.357 (0.141%) 141: dt: 0.5000, sse=93359.4, rms=0.356 (0.135%) 142: dt: 0.5000, sse=93347.6, rms=0.356 (0.128%) 143: dt: 0.5000, sse=93336.4, rms=0.355 (0.124%) 144: dt: 0.5000, sse=93326.8, rms=0.355 (0.118%) 145: dt: 0.5000, sse=93316.4, rms=0.354 (0.109%) 146: dt: 0.5000, sse=93305.5, rms=0.354 (0.099%) 147: dt: 0.5000, sse=93294.7, rms=0.354 (0.102%) 148: dt: 0.5000, sse=93287.7, rms=0.353 (0.090%) 149: dt: 0.5000, sse=93278.7, rms=0.353 (0.087%) 150: dt: 0.5000, sse=93270.2, rms=0.353 (0.091%) positioning took 4.6 minutes writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.area.pial vertex spacing 0.95 +- 0.42 (0.04-->8.94) (max @ vno 94455 --> 94456) face area 0.36 +- 0.29 (0.00-->6.86) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146402 vertices processed 25000 of 146402 vertices processed 50000 of 146402 vertices processed 75000 of 146402 vertices processed 100000 of 146402 vertices processed 125000 of 146402 vertices processed 0 of 146402 vertices processed 25000 of 146402 vertices processed 50000 of 146402 vertices processed 75000 of 146402 vertices processed 100000 of 146402 vertices processed 125000 of 146402 vertices processed thickness calculation complete, 806:773 truncations. 31945 vertices at 0 distance 97031 vertices at 1 distance 88898 vertices at 2 distance 40722 vertices at 3 distance 15033 vertices at 4 distance 5532 vertices at 5 distance 1910 vertices at 6 distance 619 vertices at 7 distance 238 vertices at 8 distance 64 vertices at 9 distance 37 vertices at 10 distance 21 vertices at 11 distance 22 vertices at 12 distance 30 vertices at 13 distance 19 vertices at 14 distance 11 vertices at 15 distance 14 vertices at 16 distance 7 vertices at 17 distance 5 vertices at 18 distance 9 vertices at 19 distance 23 vertices at 20 distance writing curvature file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.thickness positioning took 28.2 minutes #=============================== mri_surf2surf --s FM0001 --hemi rh --sval-xyz pial.rawavg --surfreg pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval pial.rawavg.conf Reading header for orig.mgz Source registration surface changed to pial.rawavg Target registration surface changed to pial.rawavg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_surf2surf --s FM0001 --hemi rh --sval-xyz pial.rawavg --surfreg pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz --tval pial.rawavg.conf sysname Linux hostname acn179 machine x86_64 user moana004 srcsubject = FM0001 srcval = (null) srctype = trgsubject = FM0001 trgval = pial.rawavg.conf trgtype = srcsurfreg = pial.rawavg trgsurfreg = pial.rawavg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial.rawavg Loading source data Reading surface file /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial.rawavg Applying linear registration transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: trgsubject = srcsubject Saving target data /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri Fri Sep 9 17:07:09 CDT 2022 Started at Fri Sep 9 15:52:57 CDT 2022 Ended at Fri Sep 9 17:07:09 CDT 2022 Conf2hires-Run-Time-Sec 4452 Conf2hires-Run-Time-Min 89.04 Conf2hires-Run-Time-Hours 1.24 conf2hires Done #-------------------------------------------- #@# Surf Volume lh Fri Sep 9 17:07:09 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume FM0001 lh /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.volume masking with /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label Total face volume 250068 Total vertex volume 246628 (mask=0) #@# FM0001 lh 246628 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fri Sep 9 17:07:12 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 FM0001 rh /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.volume masking with /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label Total face volume 259021 Total vertex volume 255126 (mask=0) #@# FM0001 rh 255126 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fri Sep 9 17:07:15 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon FM0001 SUBJECTS_DIR is /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 265 writing volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/ribbon.mgz mris_volmask took 5.70 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fri Sep 9 17:12:58 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FM0001 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FM0001 lh pial #----------------------------------------- #@# Parcellation Stats rh Fri Sep 9 17:12:58 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 FM0001 rh white 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 FM0001 rh pial Waiting for PID 973443 of (973443 973446 973449 973452) to complete... Waiting for PID 973446 of (973443 973446 973449 973452) to complete... Waiting for PID 973449 of (973443 973446 973449 973452) to complete... Waiting for PID 973452 of (973443 973446 973449 973452) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FM0001 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 250068 Total vertex volume 246628 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1534 1023 2754 2.864 0.454 0.109 0.029 12 2.2 bankssts 1034 672 1999 2.658 0.757 0.132 0.026 16 1.1 caudalanteriorcingulate 3677 2328 6704 2.643 0.537 0.120 0.035 39 5.0 caudalmiddlefrontal 2650 1705 3110 1.858 0.440 0.154 0.039 42 4.4 cuneus 653 418 2259 3.879 0.821 0.114 0.034 8 0.9 entorhinal 5366 3539 11489 2.977 0.599 0.129 0.033 75 7.1 fusiform 6439 4126 11609 2.683 0.471 0.126 0.031 87 8.4 inferiorparietal 5126 3328 9990 2.799 0.806 0.132 0.044 78 9.3 inferiortemporal 1504 949 2279 2.207 0.861 0.127 0.036 29 1.6 isthmuscingulate 9118 5499 12839 2.219 0.545 0.137 0.043 128 15.6 lateraloccipital 4461 2990 8623 2.735 0.561 0.143 0.037 80 6.7 lateralorbitofrontal 4267 2815 5800 2.038 0.635 0.146 0.039 63 6.9 lingual 3049 2061 5516 2.590 0.779 0.130 0.037 52 4.3 medialorbitofrontal 5243 3420 11836 2.912 0.668 0.138 0.044 91 9.5 middletemporal 1127 685 2272 2.934 0.651 0.085 0.016 7 0.6 parahippocampal 2635 1468 4204 2.640 0.471 0.099 0.023 21 2.5 paracentral 2434 1660 4351 2.522 0.445 0.120 0.029 28 2.9 parsopercularis 987 673 2550 3.035 0.614 0.156 0.040 17 1.8 parsorbitalis 2241 1487 4547 2.685 0.399 0.127 0.033 28 2.9 parstriangularis 1986 1477 2115 1.719 0.470 0.161 0.036 27 3.2 pericalcarine 7124 4584 11027 2.203 0.640 0.120 0.029 85 8.3 postcentral 1882 1221 3145 2.430 0.705 0.132 0.029 28 2.1 posteriorcingulate 8945 5703 15747 2.613 0.539 0.121 0.033 87 12.5 precentral 6033 3940 10209 2.545 0.510 0.129 0.028 80 6.4 precuneus 1380 898 2807 2.807 0.800 0.130 0.041 32 2.4 rostralanteriorcingulate 9122 6141 17203 2.576 0.484 0.141 0.039 159 14.0 rostralmiddlefrontal 10796 7066 20982 2.724 0.469 0.126 0.032 134 14.0 superiorfrontal 8125 5339 12641 2.285 0.421 0.125 0.028 97 9.1 superiorparietal 5545 3637 11287 2.802 0.610 0.117 0.031 61 6.5 superiortemporal 6815 4488 12769 2.750 0.499 0.126 0.030 88 8.1 supramarginal 359 236 809 2.864 0.375 0.150 0.041 6 0.6 frontalpole 635 431 2544 3.938 0.581 0.127 0.027 9 0.8 temporalpole 866 472 1329 2.528 0.545 0.115 0.040 9 1.4 transversetemporal 3612 2388 7254 3.169 0.802 0.119 0.036 38 5.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FM0001 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 250068 Total vertex volume 246628 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1534 875 2754 2.864 0.454 0.094 0.030 35 1.1 bankssts 1034 799 1999 2.658 0.757 0.130 0.035 90 1.0 caudalanteriorcingulate 3677 2652 6704 2.643 0.537 0.107 0.023 46 3.4 caudalmiddlefrontal 2650 1818 3110 1.858 0.440 0.114 0.027 29 2.7 cuneus 653 767 2259 3.879 0.821 0.146 0.020 3 0.7 entorhinal 5366 4016 11489 2.977 0.599 0.107 0.020 45 4.9 fusiform 6439 4556 11609 2.683 0.471 0.110 0.023 118 6.5 inferiorparietal 5126 3749 9990 2.799 0.806 0.107 0.026 51 5.5 inferiortemporal 1504 1097 2279 2.207 0.861 0.113 0.027 63 1.6 isthmuscingulate 9118 6054 12839 2.219 0.545 0.102 0.023 76 8.8 lateraloccipital 4461 3189 8623 2.735 0.561 0.112 0.026 53 4.8 lateralorbitofrontal 4267 2925 5800 2.038 0.635 0.103 0.023 35 4.0 lingual 3049 2205 5516 2.590 0.779 0.106 0.027 32 3.8 medialorbitofrontal 5243 4485 11836 2.912 0.668 0.119 0.022 57 4.9 middletemporal 1127 873 2272 2.934 0.651 0.092 0.018 4 0.9 parahippocampal 2635 1714 4204 2.640 0.471 0.100 0.022 21 2.5 paracentral 2434 1781 4351 2.522 0.445 0.112 0.025 25 2.4 parsopercularis 987 947 2550 3.035 0.614 0.138 0.022 10 1.0 parsorbitalis 2241 1806 4547 2.685 0.399 0.111 0.022 17 2.0 parstriangularis 1986 1099 2115 1.719 0.470 0.081 0.023 21 1.5 pericalcarine 7124 5367 11027 2.203 0.640 0.113 0.022 57 6.4 postcentral 1882 1314 3145 2.430 0.705 0.108 0.025 33 1.7 posteriorcingulate 8945 6137 15747 2.613 0.539 0.095 0.024 160 8.1 precentral 6033 4022 10209 2.545 0.510 0.108 0.023 63 5.7 precuneus 1380 1115 2807 2.807 0.800 0.121 0.029 24 1.5 rostralanteriorcingulate 9122 6935 17203 2.576 0.484 0.124 0.028 118 11.2 rostralmiddlefrontal 10796 8180 20982 2.724 0.469 0.116 0.024 101 10.6 superiorfrontal 8125 5729 12641 2.285 0.421 0.108 0.022 73 7.6 superiorparietal 5545 4179 11287 2.802 0.610 0.106 0.022 55 5.2 superiortemporal 6815 4809 12769 2.750 0.499 0.106 0.023 82 6.6 supramarginal 359 318 809 2.864 0.375 0.139 0.026 2 0.5 frontalpole 635 818 2544 3.938 0.581 0.155 0.020 4 0.6 temporalpole 866 588 1329 2.528 0.545 0.097 0.021 8 0.7 transversetemporal 3612 2034 7254 3.169 0.802 0.089 0.027 40 3.4 insula 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 FM0001 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 259021 Total vertex volume 255126 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1077 748 2016 2.936 0.380 0.106 0.021 6 0.9 bankssts 1060 663 2008 2.816 0.735 0.132 0.023 17 0.9 caudalanteriorcingulate 3403 2274 6524 2.632 0.471 0.123 0.030 37 4.2 caudalmiddlefrontal 3332 2059 4156 1.965 0.496 0.147 0.037 51 5.1 cuneus 671 465 2548 3.851 0.982 0.123 0.038 8 1.1 entorhinal 4115 2721 8699 2.917 0.660 0.137 0.037 60 6.4 fusiform 7648 4954 13182 2.595 0.436 0.133 0.035 114 10.3 inferiorparietal 5663 3594 11467 2.825 0.826 0.136 0.051 102 12.5 inferiortemporal 1309 789 2399 2.620 0.921 0.118 0.037 20 1.4 isthmuscingulate 8300 4906 12492 2.400 0.629 0.135 0.041 116 14.0 lateraloccipital 4739 2958 7845 2.547 0.696 0.135 0.049 89 9.5 lateralorbitofrontal 5778 3722 7818 2.078 0.783 0.147 0.044 92 10.5 lingual 2786 1947 6016 2.748 0.641 0.115 0.022 39 2.7 medialorbitofrontal 5648 3700 12915 3.006 0.637 0.125 0.032 76 7.4 middletemporal 945 604 2093 3.185 0.779 0.121 0.030 13 1.0 parahippocampal 2722 1628 4529 2.624 0.459 0.111 0.031 28 3.1 paracentral 2397 1574 4413 2.679 0.459 0.126 0.032 28 2.9 parsopercularis 1475 948 3351 2.963 0.601 0.139 0.033 20 1.9 parsorbitalis 2839 1869 5722 2.892 0.502 0.136 0.036 38 4.2 parstriangularis 3096 2080 2656 1.528 0.428 0.153 0.041 43 5.3 pericalcarine 6167 3851 8945 2.172 0.642 0.111 0.030 69 7.4 postcentral 1820 1205 3255 2.537 0.824 0.127 0.021 27 1.5 posteriorcingulate 8208 5275 14571 2.630 0.545 0.118 0.032 73 10.8 precentral 6209 4087 10584 2.609 0.477 0.129 0.032 84 7.7 precuneus 991 660 2321 3.074 0.514 0.135 0.039 22 1.3 rostralanteriorcingulate 9759 6420 18544 2.662 0.477 0.137 0.036 150 14.7 rostralmiddlefrontal 9685 6490 21123 2.940 0.493 0.128 0.034 118 13.0 superiorfrontal 8831 5524 14136 2.361 0.449 0.121 0.028 110 9.5 superiorparietal 5892 3740 12716 3.067 0.649 0.114 0.030 65 7.0 superiortemporal 6548 4292 12618 2.703 0.524 0.128 0.031 89 7.7 supramarginal 463 313 1289 2.989 0.421 0.166 0.054 17 0.9 frontalpole 670 448 2870 4.222 0.549 0.137 0.045 14 0.9 temporalpole 650 323 1027 2.638 0.390 0.110 0.031 7 0.7 transversetemporal 4118 2682 8264 3.169 0.858 0.127 0.142 152 39.1 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 FM0001 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 259021 Total vertex volume 255126 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1077 605 2016 2.936 0.380 0.076 0.022 7 0.9 bankssts 1060 756 2008 2.816 0.735 0.110 0.022 37 0.7 caudalanteriorcingulate 3403 2628 6524 2.632 0.471 0.109 0.022 34 3.1 caudalmiddlefrontal 3332 2240 4156 1.965 0.496 0.103 0.022 31 3.3 cuneus 671 812 2548 3.851 0.982 0.128 0.018 3 0.5 entorhinal 4115 3003 8699 2.917 0.660 0.105 0.023 43 3.8 fusiform 7648 5070 13182 2.595 0.436 0.098 0.028 262 6.2 inferiorparietal 5663 4250 11467 2.825 0.826 0.111 0.025 59 6.3 inferiortemporal 1309 915 2399 2.620 0.921 0.099 0.030 28 1.3 isthmuscingulate 8300 5325 12492 2.400 0.629 0.092 0.020 92 6.8 lateraloccipital 4739 3031 7845 2.547 0.696 0.102 0.063 146 18.5 lateralorbitofrontal 5778 3910 7818 2.078 0.783 0.101 0.022 62 5.5 lingual 2786 2340 6016 2.748 0.641 0.110 0.018 26 2.2 medialorbitofrontal 5648 4691 12915 3.006 0.637 0.111 0.020 80 5.3 middletemporal 945 680 2093 3.185 0.779 0.093 0.018 7 0.6 parahippocampal 2722 1779 4529 2.624 0.459 0.098 0.021 30 2.4 paracentral 2397 1722 4413 2.679 0.459 0.101 0.019 20 1.9 parsopercularis 1475 1258 3351 2.963 0.601 0.116 0.021 15 1.2 parsorbitalis 2839 2065 5722 2.892 0.502 0.103 0.023 31 2.5 parstriangularis 3096 1652 2656 1.528 0.428 0.084 0.020 56 2.3 pericalcarine 6167 4462 8945 2.172 0.642 0.094 0.017 40 4.3 postcentral 1820 1313 3255 2.537 0.824 0.106 0.026 21 1.5 posteriorcingulate 8208 5683 14571 2.630 0.545 0.089 0.018 117 6.0 precentral 6209 4002 10584 2.609 0.477 0.106 0.024 73 6.2 precuneus 991 844 2321 3.074 0.514 0.122 0.021 7 0.9 rostralanteriorcingulate 9759 7340 18544 2.662 0.477 0.120 0.025 133 11.2 rostralmiddlefrontal 9685 7643 21123 2.940 0.493 0.112 0.024 89 9.1 superiorfrontal 8831 6291 14136 2.361 0.449 0.106 0.020 86 7.7 superiorparietal 5892 4432 12716 3.067 0.649 0.103 0.020 47 4.9 superiortemporal 6548 4849 12618 2.703 0.524 0.106 0.022 86 5.9 supramarginal 463 537 1289 2.989 0.421 0.148 0.020 3 0.4 frontalpole 670 801 2870 4.222 0.549 0.147 0.025 4 0.8 temporalpole 650 431 1027 2.638 0.390 0.093 0.018 3 0.5 transversetemporal 4118 2278 8264 3.169 0.858 0.136 0.725 3426 230.0 insula PIDs (973443 973446 973449 973452) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Fri Sep 9 17:13:22 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 lh ../surf/lh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Fri Sep 9 17:13:22 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 rh ../surf/rh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 973545 of (973545 973549) to complete... Waiting for PID 973549 of (973545 973549) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 lh ../surf/lh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/freesurfer-6.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 3 labels changed using aseg relabeling using gibbs priors... 000: 9629 changed, 143971 examined... 001: 2265 changed, 37341 examined... 002: 691 changed, 11766 examined... 003: 308 changed, 3871 examined... 004: 131 changed, 1684 examined... 005: 56 changed, 750 examined... 006: 25 changed, 325 examined... 007: 15 changed, 143 examined... 008: 8 changed, 72 examined... 009: 1 changed, 44 examined... 010: 0 changed, 5 examined... 0 labels changed using aseg 000: 265 total segments, 183 labels (2737 vertices) changed 001: 99 total segments, 17 labels (64 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1414 vertices marked for relabeling... 1414 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 rh ../surf/rh.sphere.reg /opt/freesurfer/freesurfer-6.0/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/freesurfer-6.0/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... 1 labels changed using aseg relabeling using gibbs priors... 000: 9541 changed, 146402 examined... 001: 2197 changed, 37118 examined... 002: 667 changed, 11623 examined... 003: 294 changed, 3749 examined... 004: 121 changed, 1766 examined... 005: 57 changed, 735 examined... 006: 31 changed, 318 examined... 007: 20 changed, 174 examined... 008: 10 changed, 100 examined... 009: 4 changed, 47 examined... 010: 2 changed, 23 examined... 011: 0 changed, 12 examined... 7 labels changed using aseg 000: 297 total segments, 214 labels (2846 vertices) changed 001: 94 total segments, 12 labels (82 vertices) changed 002: 83 total segments, 1 labels (5 vertices) changed 003: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 44 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1322 vertices marked for relabeling... 1322 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 13 seconds. PIDs (973545 973549) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Sep 9 17:13:36 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab FM0001 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Fri Sep 9 17:13:36 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 FM0001 rh white Waiting for PID 973615 of (973615 973618) to complete... Waiting for PID 973618 of (973615 973618) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab FM0001 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 250068 Total vertex volume 246628 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1186 831 2304 2.643 0.449 0.143 0.037 19 1.7 G&S_frontomargin 2452 1482 4229 2.516 0.466 0.125 0.039 35 3.5 G&S_occipital_inf 2020 1065 3211 2.516 0.488 0.114 0.031 24 2.6 G&S_paracentral 1966 1287 3674 2.649 0.490 0.132 0.033 27 2.5 G&S_subcentral 776 515 1489 2.588 0.366 0.153 0.041 15 1.3 G&S_transv_frontopol 2363 1624 4598 2.828 0.552 0.122 0.027 28 2.3 G&S_cingul-Ant 1251 873 2410 2.802 0.497 0.114 0.024 10 1.2 G&S_cingul-Mid-Ant 1555 1034 2604 2.621 0.396 0.121 0.029 16 1.7 G&S_cingul-Mid-Post 644 420 1534 2.961 0.564 0.157 0.037 12 0.9 G_cingul-Post-dorsal 292 181 551 2.503 1.021 0.125 0.032 4 0.2 G_cingul-Post-ventral 2398 1553 2817 1.735 0.467 0.165 0.046 43 4.5 G_cuneus 1511 1012 3412 2.618 0.546 0.136 0.036 25 2.3 G_front_inf-Opercular 422 259 1099 2.966 0.422 0.165 0.051 10 0.8 G_front_inf-Orbital 1350 892 3233 2.763 0.382 0.146 0.042 25 2.1 G_front_inf-Triangul 4987 3190 10453 2.678 0.545 0.142 0.044 93 8.7 G_front_middle 7436 4688 16251 2.856 0.453 0.138 0.038 116 11.5 G_front_sup 809 508 1635 3.405 0.752 0.130 0.051 12 1.5 G_Ins_lg&S_cent_ins 595 399 2077 3.621 0.730 0.138 0.041 10 0.9 G_insular_short 2472 1394 4209 2.398 0.528 0.143 0.050 49 4.8 G_occipital_middle 1483 949 2086 2.074 0.460 0.144 0.034 24 2.1 G_occipital_sup 2277 1460 5770 3.177 0.584 0.146 0.038 44 3.4 G_oc-temp_lat-fusifor 3182 2035 4020 1.853 0.619 0.156 0.046 55 6.2 G_oc-temp_med-Lingual 1441 858 3773 3.282 0.874 0.093 0.023 12 1.2 G_oc-temp_med-Parahip 2725 1812 6666 2.903 0.675 0.158 0.047 68 5.4 G_orbital 2604 1635 5389 2.689 0.517 0.137 0.032 46 3.5 G_pariet_inf-Angular 3291 2154 7447 2.917 0.508 0.139 0.037 58 4.8 G_pariet_inf-Supramar 3177 2044 5177 2.270 0.474 0.128 0.029 46 3.7 G_parietal_sup 2791 1690 4726 2.238 0.671 0.129 0.035 44 3.8 G_postcentral 3292 1999 7157 2.812 0.572 0.124 0.039 37 5.2 G_precentral 2894 1863 5997 2.607 0.490 0.140 0.034 54 3.8 G_precuneus 1095 714 2286 2.467 0.859 0.154 0.046 30 1.9 G_rectus 811 507 1346 2.742 1.060 0.150 0.085 25 2.9 G_subcallosal 638 344 1114 2.604 0.598 0.121 0.048 9 1.1 G_temp_sup-G_T_transv 2001 1296 5235 3.100 0.552 0.137 0.042 34 2.9 G_temp_sup-Lateral 631 428 1599 3.282 0.762 0.069 0.016 2 0.4 G_temp_sup-Plan_polar 961 641 1840 2.755 0.395 0.100 0.021 5 0.9 G_temp_sup-Plan_tempo 2625 1615 5622 2.768 0.940 0.148 0.063 56 6.6 G_temporal_inf 3254 2045 8164 2.973 0.715 0.147 0.051 68 7.1 G_temporal_middle 393 264 629 2.539 0.320 0.100 0.019 2 0.3 Lat_Fis-ant-Horizont 437 290 573 2.624 0.392 0.109 0.026 2 0.4 Lat_Fis-ant-Vertical 1319 831 1663 2.626 0.445 0.118 0.028 11 1.6 Lat_Fis-post 2576 1482 2913 1.841 0.534 0.149 0.053 40 5.9 Pole_occipital 1701 1145 5579 3.490 0.802 0.142 0.041 31 3.0 Pole_temporal 2352 1717 2859 2.048 0.561 0.151 0.033 30 3.2 S_calcarine 3416 2366 4158 2.058 0.577 0.112 0.026 24 4.2 S_central 1194 794 1647 2.299 0.448 0.096 0.014 6 0.7 S_cingul-Marginalis 596 390 931 2.878 0.517 0.100 0.025 3 0.6 S_circular_insula_ant 1431 1003 2193 2.692 0.953 0.102 0.022 7 1.6 S_circular_insula_inf 1850 1228 2687 2.774 0.438 0.100 0.019 8 1.6 S_circular_insula_sup 1044 680 1821 3.074 0.680 0.115 0.032 10 1.2 S_collat_transv_ant 520 357 754 2.407 0.485 0.118 0.022 4 0.4 S_collat_transv_post 2036 1407 3226 2.461 0.318 0.100 0.019 12 1.7 S_front_inf 2201 1501 3959 2.560 0.476 0.141 0.036 33 3.2 S_front_middle 2903 1921 4276 2.337 0.446 0.102 0.024 24 2.7 S_front_sup 439 297 740 2.785 0.561 0.123 0.028 4 0.5 S_interm_prim-Jensen 2647 1774 3997 2.355 0.354 0.113 0.025 24 2.6 S_intrapariet&P_trans 1332 868 1693 2.360 0.283 0.119 0.026 10 1.5 S_oc_middle&Lunatus 1496 1002 2058 2.394 0.402 0.119 0.025 12 1.5 S_oc_sup&transversal 714 495 921 2.353 0.322 0.131 0.032 7 0.9 S_occipital_ant 1129 757 1701 2.682 0.323 0.096 0.016 6 0.8 S_oc-temp_lat 2251 1556 3750 2.658 0.477 0.121 0.026 18 2.4 S_oc-temp_med&Lingual 572 412 1022 2.673 0.556 0.145 0.039 7 0.8 S_orbital_lateral 717 504 989 2.510 0.510 0.116 0.018 5 0.5 S_orbital_med-olfact 1646 1133 2938 2.672 0.495 0.138 0.033 22 2.1 S_orbital-H_Shaped 2715 1793 3775 2.441 0.447 0.117 0.022 24 2.3 S_parieto_occipital 1478 858 1114 1.707 0.681 0.124 0.027 33 1.2 S_pericallosal 3155 2118 4313 2.299 0.355 0.111 0.023 26 3.0 S_postcentral 1872 1252 2729 2.466 0.365 0.111 0.026 14 1.9 S_precentral-inf-part 1697 1107 2449 2.497 0.386 0.115 0.025 13 1.8 S_precentral-sup-part 736 511 1161 2.634 0.603 0.110 0.017 6 0.5 S_suborbital 984 649 1386 2.503 0.381 0.116 0.024 7 0.9 S_subparietal 1569 1108 2600 2.789 0.538 0.115 0.022 12 1.4 S_temporal_inf 5582 3728 9706 2.841 0.437 0.114 0.027 49 6.6 S_temporal_sup 407 266 515 2.332 0.552 0.130 0.029 4 0.5 S_temporal_transverse 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 FM0001 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 259021 Total vertex volume 255126 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 995 654 2041 2.851 0.453 0.148 0.039 24 1.5 G&S_frontomargin 1201 716 2278 2.831 0.640 0.134 0.044 18 2.4 G&S_occipital_inf 1482 934 2725 2.467 0.563 0.125 0.033 18 2.0 G&S_paracentral 2129 1320 3686 2.774 0.534 0.130 0.041 28 3.5 G&S_subcentral 1332 898 2863 2.722 0.409 0.158 0.047 27 2.5 G&S_transv_frontopol 3326 2240 6951 3.027 0.444 0.128 0.029 50 3.7 G&S_cingul-Ant 1457 977 2949 2.993 0.445 0.113 0.020 13 1.2 G&S_cingul-Mid-Ant 1421 943 2614 2.734 0.470 0.117 0.024 13 1.2 G&S_cingul-Mid-Post 555 355 1553 3.313 0.473 0.154 0.034 10 0.7 G_cingul-Post-dorsal 385 214 805 2.868 0.863 0.113 0.055 7 0.7 G_cingul-Post-ventral 3082 1884 3710 1.887 0.533 0.152 0.041 52 5.3 G_cuneus 1693 1083 3932 2.859 0.518 0.129 0.039 25 2.4 G_front_inf-Opercular 401 244 936 3.093 0.428 0.132 0.031 6 0.4 G_front_inf-Orbital 1385 884 3208 2.941 0.501 0.147 0.045 25 2.6 G_front_inf-Triangul 4542 2958 10526 2.757 0.517 0.149 0.045 85 8.5 G_front_middle 6285 4001 15369 3.064 0.478 0.136 0.041 100 10.2 G_front_sup 617 415 1537 3.580 0.940 0.143 0.050 10 1.0 G_Ins_lg&S_cent_ins 931 585 2509 3.309 1.057 0.159 0.061 17 2.3 G_insular_short 2716 1548 5618 2.800 0.552 0.141 0.047 59 4.5 G_occipital_middle 2052 1111 3025 2.275 0.543 0.135 0.036 33 3.0 G_occipital_sup 1743 1074 4158 2.919 0.757 0.149 0.050 36 3.6 G_oc-temp_lat-fusifor 3787 2395 5377 2.056 0.872 0.159 0.051 74 7.5 G_oc-temp_med-Lingual 1341 850 4059 3.477 0.944 0.121 0.038 17 1.9 G_oc-temp_med-Parahip 3410 2057 6862 2.622 0.811 0.149 0.064 87 9.0 G_orbital 3301 2096 7166 2.714 0.492 0.143 0.040 67 5.2 G_pariet_inf-Angular 3109 2053 6675 2.826 0.528 0.140 0.037 47 4.4 G_pariet_inf-Supramar 2556 1639 4936 2.372 0.459 0.133 0.032 43 3.1 G_parietal_sup 2115 1247 3238 2.062 0.561 0.118 0.034 31 2.9 G_postcentral 3079 1832 6582 2.767 0.563 0.116 0.036 31 4.2 G_precentral 2568 1640 5192 2.628 0.533 0.135 0.035 49 3.4 G_precuneus 955 643 2516 2.688 0.783 0.128 0.033 20 1.4 G_rectus 583 350 894 2.820 1.025 0.107 0.754 108 33.4 G_subcallosal 583 274 1032 2.667 0.397 0.116 0.033 8 0.7 G_temp_sup-G_T_transv 1979 1204 5575 3.474 0.587 0.134 0.047 34 3.6 G_temp_sup-Lateral 678 454 1676 3.264 0.718 0.070 0.014 2 0.4 G_temp_sup-Plan_polar 1013 666 2058 2.881 0.477 0.111 0.026 10 1.0 G_temp_sup-Plan_tempo 3344 2038 7394 2.754 0.942 0.149 0.067 81 9.8 G_temporal_inf 3350 2152 8753 3.087 0.697 0.136 0.040 60 5.5 G_temporal_middle 392 266 767 3.108 0.390 0.108 0.021 2 0.3 Lat_Fis-ant-Horizont 407 272 539 2.643 0.408 0.127 0.033 3 0.5 Lat_Fis-ant-Vertical 1642 1067 2302 2.771 0.509 0.113 0.025 12 1.6 Lat_Fis-post 4294 2506 4903 1.928 0.632 0.145 0.046 63 8.6 Pole_occipital 1838 1290 6702 3.763 0.713 0.157 0.044 35 3.2 Pole_temporal 2934 2018 3057 1.851 0.593 0.136 0.035 32 4.4 S_calcarine 2865 1972 3274 2.011 0.578 0.115 0.028 19 3.5 S_central 1551 1029 2265 2.437 0.341 0.103 0.018 11 1.1 S_cingul-Marginalis 704 484 1121 2.917 0.401 0.113 0.023 4 0.7 S_circular_insula_ant 1302 859 1853 2.710 0.679 0.088 0.015 6 0.8 S_circular_insula_inf 1435 970 2364 3.034 0.461 0.104 0.022 7 1.4 S_circular_insula_sup 1183 786 1977 2.924 0.444 0.105 0.022 8 1.1 S_collat_transv_ant 671 459 753 2.141 0.432 0.140 0.034 7 1.0 S_collat_transv_post 2510 1674 4004 2.513 0.383 0.118 0.026 22 2.8 S_front_inf 2380 1609 4216 2.581 0.454 0.122 0.029 28 2.7 S_front_middle 2616 1796 3886 2.459 0.336 0.104 0.020 17 2.2 S_front_sup 424 290 607 2.250 0.306 0.100 0.017 3 0.2 S_interm_prim-Jensen 3563 2356 5320 2.415 0.413 0.114 0.024 33 3.4 S_intrapariet&P_trans 1250 835 1645 2.442 0.367 0.124 0.026 10 1.4 S_oc_middle&Lunatus 1358 892 1772 2.368 0.379 0.121 0.028 12 1.3 S_oc_sup&transversal 489 323 855 2.564 0.358 0.086 0.013 2 0.3 S_occipital_ant 982 691 1553 2.705 0.382 0.115 0.022 7 0.8 S_oc-temp_lat 1820 1231 2924 2.801 0.595 0.109 0.022 13 1.5 S_oc-temp_med&Lingual 592 411 1040 2.738 0.653 0.144 0.032 7 0.8 S_orbital_lateral 742 512 1000 2.315 0.416 0.113 0.018 6 0.5 S_orbital_med-olfact 1824 1182 3065 2.766 0.534 0.124 0.026 20 2.1 S_orbital-H_Shaped 3291 2165 4695 2.455 0.466 0.126 0.030 33 4.1 S_parieto_occipital 1303 788 1246 1.950 0.877 0.129 0.023 26 1.0 S_pericallosal 2535 1659 3255 2.175 0.377 0.095 0.018 17 1.8 S_postcentral 2159 1452 3035 2.507 0.362 0.108 0.020 14 1.8 S_precentral-inf-part 1259 845 1873 2.449 0.347 0.108 0.022 8 1.1 S_precentral-sup-part 392 296 535 2.469 0.441 0.121 0.014 3 0.3 S_suborbital 902 639 1583 2.699 0.410 0.132 0.026 9 0.8 S_subparietal 1582 1047 2347 2.824 0.482 0.124 0.027 14 1.7 S_temporal_inf 5985 3978 9332 2.712 0.420 0.111 0.023 46 5.6 S_temporal_sup 323 217 483 2.920 0.420 0.144 0.031 3 0.4 S_temporal_transverse PIDs (973615 973618) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Fri Sep 9 17:14:01 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 lh ../surf/lh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Fri Sep 9 17:14:01 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 rh ../surf/rh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 973791 of (973791 973794) to complete... Waiting for PID 973794 of (973791 973794) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 lh ../surf/lh.sphere.reg /opt/freesurfer/freesurfer-6.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/freesurfer-6.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1000 labels changed using aseg relabeling using gibbs priors... 000: 2032 changed, 143971 examined... 001: 460 changed, 9439 examined... 002: 99 changed, 2632 examined... 003: 48 changed, 579 examined... 004: 21 changed, 290 examined... 005: 13 changed, 116 examined... 006: 7 changed, 83 examined... 007: 6 changed, 46 examined... 008: 3 changed, 32 examined... 009: 2 changed, 20 examined... 010: 2 changed, 12 examined... 011: 2 changed, 17 examined... 012: 1 changed, 15 examined... 013: 0 changed, 6 examined... 151 labels changed using aseg 000: 56 total segments, 23 labels (102 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 11 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 996 vertices marked for relabeling... 996 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 FM0001 rh ../surf/rh.sphere.reg /opt/freesurfer/freesurfer-6.0/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/freesurfer-6.0/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... 1214 labels changed using aseg relabeling using gibbs priors... 000: 2171 changed, 146402 examined... 001: 533 changed, 10004 examined... 002: 152 changed, 2954 examined... 003: 68 changed, 931 examined... 004: 36 changed, 406 examined... 005: 24 changed, 203 examined... 006: 7 changed, 118 examined... 007: 5 changed, 44 examined... 008: 3 changed, 34 examined... 009: 0 changed, 20 examined... 178 labels changed using aseg 000: 53 total segments, 20 labels (132 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 901 vertices marked for relabeling... 901 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. PIDs (973791 973794) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Sep 9 17:14:11 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab FM0001 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Fri Sep 9 17:14:11 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 FM0001 rh white Waiting for PID 973857 of (973857 973860) to complete... Waiting for PID 973860 of (973857 973860) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab FM0001 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 250068 Total vertex volume 246628 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1671 1081 3037 2.731 0.687 0.129 0.028 23 1.9 caudalanteriorcingulate 3947 2491 7185 2.640 0.537 0.122 0.035 45 5.4 caudalmiddlefrontal 3684 2388 4559 1.954 0.448 0.144 0.036 53 5.5 cuneus 637 403 2107 3.728 0.849 0.110 0.032 7 0.7 entorhinal 4997 3301 10300 2.934 0.572 0.128 0.031 66 6.1 fusiform 6600 4230 11661 2.673 0.467 0.126 0.031 89 8.3 inferiorparietal 5086 3289 10148 2.836 0.842 0.136 0.046 81 9.8 inferiortemporal 1458 916 2214 2.213 0.857 0.128 0.037 29 1.6 isthmuscingulate 9018 5419 12794 2.222 0.543 0.136 0.042 127 15.2 lateraloccipital 5088 3406 9821 2.763 0.567 0.149 0.043 102 8.5 lateralorbitofrontal 4438 2925 5988 2.034 0.625 0.147 0.040 65 7.4 lingual 2499 1666 4784 2.619 0.817 0.130 0.039 45 3.9 medialorbitofrontal 6809 4484 14958 2.887 0.639 0.132 0.040 104 11.4 middletemporal 1177 713 2346 2.924 0.663 0.087 0.016 8 0.7 parahippocampal 3010 1707 4948 2.642 0.459 0.102 0.024 25 2.9 paracentral 2314 1560 4111 2.534 0.442 0.119 0.029 27 2.8 parsopercularis 1071 703 2313 2.820 0.563 0.132 0.033 13 1.4 parsorbitalis 2659 1789 5377 2.656 0.402 0.131 0.034 36 3.4 parstriangularis 1964 1439 2070 1.722 0.468 0.158 0.036 27 3.1 pericalcarine 7840 5091 12192 2.221 0.627 0.121 0.029 92 9.1 postcentral 2008 1313 3338 2.470 0.693 0.132 0.030 28 2.2 posteriorcingulate 8869 5649 15628 2.617 0.540 0.120 0.033 86 12.3 precentral 5884 3849 10128 2.540 0.520 0.131 0.029 81 6.5 precuneus 1933 1259 3584 2.745 0.739 0.130 0.036 39 2.8 rostralanteriorcingulate 6610 4492 13142 2.603 0.533 0.141 0.040 115 10.6 rostralmiddlefrontal 11670 7680 22438 2.679 0.466 0.129 0.033 149 15.6 superiorfrontal 6435 4229 10037 2.305 0.433 0.124 0.028 77 7.2 superiorparietal 7268 4784 15854 2.941 0.676 0.117 0.031 80 9.2 superiortemporal 6302 4142 11889 2.749 0.512 0.127 0.031 83 7.7 supramarginal 863 468 1307 2.525 0.543 0.114 0.040 9 1.4 transversetemporal 2956 1994 6371 3.217 0.831 0.112 0.030 27 3.6 insula 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 FM0001 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/wm.mgz... reading input surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white... reading input pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial... reading input white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 259021 Total vertex volume 255126 (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) = 1324724 mm^3 (det: 1.470574 ) lhCtxGM: 245675.534 245769.000 diff= -93.5 pctdiff=-0.038 rhCtxGM: 254417.761 254210.000 diff= 207.8 pctdiff= 0.082 lhCtxWM: 238743.259 239277.000 diff= -533.7 pctdiff=-0.224 rhCtxWM: 240464.368 240348.000 diff= 116.4 pctdiff= 0.048 SubCortGMVol 54196.000 SupraTentVol 1046866.922 (1044789.000) diff=2077.922 pctdiff=0.198 SupraTentVolNotVent 1035908.922 (1033831.000) diff=2077.922 pctdiff=0.201 BrainSegVol 1176637.000 (1173919.000) diff=2718.000 pctdiff=0.231 BrainSegVolNotVent 1162120.000 (1161662.922) diff=457.078 pctdiff=0.039 BrainSegVolNotVent 1162120.000 CerebellumVol 128135.000 VentChorVol 10958.000 3rd4th5thCSF 3559.000 CSFVol 841.000, OptChiasmVol 154.000 MaskVol 1547673.000 1171 737 2280 2.853 0.727 0.135 0.023 20 1.0 caudalanteriorcingulate 3541 2360 6679 2.623 0.464 0.125 0.032 39 4.5 caudalmiddlefrontal 4056 2501 5199 2.069 0.509 0.141 0.037 58 6.1 cuneus 604 412 2322 3.947 0.872 0.131 0.041 7 1.2 entorhinal 3710 2429 7445 2.868 0.622 0.132 0.037 53 5.5 fusiform 7735 4980 13480 2.603 0.431 0.132 0.035 118 10.3 inferiorparietal 6051 3882 12515 2.825 0.840 0.136 0.051 106 13.7 inferiortemporal 1288 770 2305 2.567 0.923 0.116 0.037 19 1.4 isthmuscingulate 8369 4954 12466 2.376 0.638 0.137 0.041 120 14.1 lateraloccipital 5538 3464 9486 2.571 0.714 0.144 0.053 119 12.1 lateralorbitofrontal 5645 3647 7658 2.084 0.772 0.147 0.044 90 10.2 lingual 2286 1573 4759 2.641 0.744 0.121 0.211 137 35.4 medialorbitofrontal 6498 4295 14583 3.006 0.607 0.126 0.030 85 8.1 middletemporal 1053 666 2311 3.167 0.792 0.117 0.030 13 1.1 parahippocampal 2752 1654 4691 2.640 0.478 0.109 0.030 28 3.1 paracentral 2736 1799 4933 2.659 0.468 0.125 0.033 31 3.3 parsopercularis 1175 749 2381 2.818 0.498 0.118 0.028 12 1.3 parsorbitalis 2846 1875 5959 2.933 0.514 0.138 0.037 40 4.3 parstriangularis 3109 2083 2631 1.507 0.434 0.155 0.042 44 5.5 pericalcarine 6876 4305 9695 2.181 0.613 0.115 0.030 78 8.4 postcentral 2015 1319 3574 2.561 0.799 0.130 0.023 30 1.8 posteriorcingulate 7968 5106 14287 2.645 0.549 0.118 0.032 71 10.4 precentral 6444 4220 11192 2.588 0.479 0.129 0.032 90 7.8 precuneus 1359 899 3020 3.046 0.563 0.125 0.033 25 1.6 rostralanteriorcingulate 7159 4708 14123 2.678 0.489 0.136 0.036 109 10.5 rostralmiddlefrontal 12516 8434 26465 2.884 0.491 0.129 0.033 158 16.7 superiorfrontal 7162 4481 11711 2.386 0.467 0.118 0.027 87 7.6 superiorparietal 7305 4691 17109 3.169 0.716 0.115 0.031 84 8.5 superiortemporal 6219 4103 12024 2.703 0.537 0.126 0.031 82 7.3 supramarginal 679 335 1073 2.636 0.386 0.111 0.032 8 0.8 transversetemporal 3115 2072 6769 3.354 0.745 0.122 0.033 31 4.1 insula PIDs (973857 973860) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Fri Sep 9 17:14:33 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts pctsurfcon --s FM0001 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Fri Sep 9 17:14:33 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts pctsurfcon --s FM0001 --rh-only Waiting for PID 973967 of (973967 973970) to complete... Waiting for PID 973970 of (973967 973970) to complete... pctsurfcon --s FM0001 --lh-only Log file is /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts/pctsurfcon.log Fri Sep 9 17:14:33 CDT 2022 setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts /opt/freesurfer/freesurfer-6.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/freesurfer-6.0 mri_vol2surf --mov /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973967/lh.wm.mgh --regheader FM0001 --cortex srcvol = /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label Reading surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 77013 Masking with /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label Writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973967/lh.wm.mgh Dim: 143971 1 1 mri_vol2surf --mov /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973967/lh.gm.mgh --projfrac 0.3 --regheader FM0001 --cortex srcvol = /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label Reading surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white Done reading source surface Reading thickness /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 92344 Masking with /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.cortex.label Writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973967/lh.gm.mgh Dim: 143971 1 1 mri_concat /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973967/lh.wm.mgh /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973967/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.w-g.pct.mgh mri_segstats --in /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.w-g.pct.mgh --annot FM0001 lh aparc --sum /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.w-g.pct.mgh --annot FM0001 lh aparc --sum /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/stats/lh.w-g.pct.stats --snr sysname Linux hostname acn179 machine x86_64 user moana004 UseRobust 0 Constructing seg from annotation Reading annotation /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.w-g.pct.mgh Vertex Area is 0.65031 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 pctsurfcon --s FM0001 --rh-only Log file is /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts/pctsurfcon.log Fri Sep 9 17:14:33 CDT 2022 setenv SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w cd /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/scripts /opt/freesurfer/freesurfer-6.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/freesurfer-6.0 mri_vol2surf --mov /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973970/rh.wm.mgh --regheader FM0001 --cortex srcvol = /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label Reading surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 = 78049 Masking with /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label Writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973970/rh.wm.mgh Dim: 146402 1 1 mri_vol2surf --mov /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973970/rh.gm.mgh --projfrac 0.3 --regheader FM0001 --cortex srcvol = /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label Reading surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white Done reading source surface Reading thickness /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 = 93274 Masking with /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.cortex.label Writing to /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973970/rh.gm.mgh Dim: 146402 1 1 mri_concat /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973970/rh.wm.mgh /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/tmp.pctsurfcon.973970/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.w-g.pct.mgh mri_segstats --in /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.w-g.pct.mgh --annot FM0001 rh aparc --sum /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.w-g.pct.mgh --annot FM0001 rh aparc --sum /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/stats/rh.w-g.pct.stats --snr sysname Linux hostname acn179 machine x86_64 user moana004 UseRobust 0 Constructing seg from annotation Reading annotation /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.w-g.pct.mgh Vertex Area is 0.645257 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 PIDs (973967 973970) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Fri Sep 9 17:14:38 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1892 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2289 voxels changed to hypointensity... 3933 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fri Sep 9 17:14:51 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 mri_aparc2aseg --s FM0001 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Fri Sep 9 17:14:51 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 mri_aparc2aseg --s FM0001 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fri Sep 9 17:14:51 CDT 2022 /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001 mri_aparc2aseg --s FM0001 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Waiting for PID 974207 of (974207 974210 974213) to complete... /opt/freesurfer/freesurfer-6.0/bin/reconbatchjobs: line 81: 974210 Killed exec $JOB >> $LOG 2>&1 Waiting for PID 974210 of (974207 974210 974213) to complete... Waiting for PID 974213 of (974207 974210 974213) to complete... mri_aparc2aseg --s FM0001 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w subject FM0001 outvol /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white Reading lh pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial Loading lh annotations from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white Reading rh pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial Loading rh annotations from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/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) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.36 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 19 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 64 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 89 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 91 rescaling Left_Pallidum from 98 --> 102 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 41 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 67 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 78 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 65 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 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/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w subject FM0001 outvol /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white Reading lh pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial Loading lh annotations from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white Reading rh pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial Loading rh annotations from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; mri_aparc2aseg --s FM0001 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w subject FM0001 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.white Reading lh pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/lh.pial Loading lh annotations from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/lh.aparc.DKTatlas.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) Reading rh white surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.white Reading rh pial surface /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/surf/rh.pial Loading rh annotations from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/label/rh.aparc.DKTatlas.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) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/moanae/shared/project_FM_Gracely_qunex01/sessions/FM0001/hcp/FM0001/T1w/FM0001/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.36 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 19 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 64 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 89 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 91 rescaling Left_Pallidum from 98 --> 102 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 41 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 67 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 78 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 65 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 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Linux acn179 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FM0001 exited with ERRORS at Fri Sep 9 17:17:39 CDT 2022 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting