Mon Oct 17 15:14:33 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon1 -i /localscratch/bpinsard.32335141.0/smriprep_sub03.job/workdir/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_validate/sub-03_ses-001_T1w_template_ras_valid.nii.gz -T2 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-03 -sd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer -expert /localscratch/bpinsard.32335141.0/smriprep_sub03.job/workdir/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts subjid sub-03 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux bc11910.int.ets1.calculquebec.ca 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 unlimited coredumpsize unlimited memoryuse 33554432 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767717 maxlocks unlimited maxsignal 767717 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638244 32761604 155707508 2737068 8169132 158388288 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/10/17-15:14:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:34-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:14:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_convert /localscratch/bpinsard.32335141.0/smriprep_sub03.job/workdir/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_validate/sub-03_ses-001_T1w_template_ras_valid.nii.gz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/001.mgz mri_convert.bin /localscratch/bpinsard.32335141.0/smriprep_sub03.job/workdir/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_validate/sub-03_ses-001_T1w_template_ras_valid.nii.gz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/workdir/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_validate/sub-03_ses-001_T1w_template_ras_valid.nii.gz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999977, 0.00610838, -0.0027878) j_ras = (-0.00610857, 0.999981, -5.96363e-05) k_ras = (0.00278738, 7.66645e-05, 0.999996) writing to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Mon Oct 17 15:14:45 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_convert --no_scale 1 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz... TR=3200.00, 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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Mon Oct 17 15:14:57 UTC 2022 Found 1 runs /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/001.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/rawavg.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_convert /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/rawavg.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz --conform_min mri_convert.bin /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/rawavg.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999977, 0.00610838, -0.0027878) j_ras = (-0.00610857, 0.999981, -5.96363e-05) k_ras = (0.00278738, 7.66645e-05, 0.999996) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz... mri_add_xform_to_header -c /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/talairach.xfm /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 15:15:14 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri /opt/freesurfer/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 bc11910.int.ets1.calculquebec.ca 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 Mon Oct 17 15:15:14 UTC 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.253499 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.253499/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.253499/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.10898e-10, 0) j_ras = (0, 9.09495e-12, -1) k_ras = (7.12142e-11, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.253499/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Mon Oct 17 15:15:34 UTC 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.253499/nu0.mnc ./tmp.mri_nu_correct.mni.253499/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.253499/0/ -iterations 1000 -distance 50 [bpinsard@bc11910.int.ets1.calculquebec.ca:/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/] [2022-10-17 15:15:34] running: /opt/freesurfer/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.253499/0/ ./tmp.mri_nu_correct.mni.253499/nu0.mnc ./tmp.mri_nu_correct.mni.253499/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 Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 47 CV of field change: 0.000985206 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.253499/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.253499/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.253499/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.10898e-10, 0) j_ras = (0, 9.09495e-12, -1) k_ras = (7.12142e-11, 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... Mon Oct 17 15:17:38 UTC 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 Mon Oct 17 15:17:38 UTC 2022 Ended at Mon Oct 17 15:18:18 UTC 2022 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 17 15:18:20 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7763, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/talairach_avi.log tal_QC_AZS /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/talairach_avi.log TalAviQA: 0.97185 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Mon Oct 17 15:18:20 UTC 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux bc11910.int.ets1.calculquebec.ca 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 Mon Oct 17 15:18:20 UTC 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.257529 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.257529/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.257529/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.10898e-10, 0) j_ras = (0, 9.09495e-12, -1) k_ras = (7.12142e-11, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.257529/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Mon Oct 17 15:18:42 UTC 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.257529/nu0.mnc ./tmp.mri_nu_correct.mni.257529/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.257529/0/ [bpinsard@bc11910.int.ets1.calculquebec.ca:/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/] [2022-10-17 15:18:42] running: /opt/freesurfer/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.257529/0/ ./tmp.mri_nu_correct.mni.257529/nu0.mnc ./tmp.mri_nu_correct.mni.257529/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 Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 45 CV of field change: 0.000961271 Outputting Volume: ............................................................ Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Mon Oct 17 15:20:14 UTC 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.257529/nu1.mnc ./tmp.mri_nu_correct.mni.257529/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.257529/1/ [bpinsard@bc11910.int.ets1.calculquebec.ca:/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/] [2022-10-17 15:20:14] running: /opt/freesurfer/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.257529/1/ ./tmp.mri_nu_correct.mni.257529/nu1.mnc ./tmp.mri_nu_correct.mni.257529/nu2.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 Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 28 CV of field change: 0.00098355 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.257529/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.257529/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.257529/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.257529/ones.mgz sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard input ./tmp.mri_nu_correct.mni.257529/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.257529/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 32768000 values in range Counting number of voxels in first frame Found 32768000 voxels in final mask Count: 32768000 16777212.890625 32768000 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.257529/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.257529/sum.junk --avgwf ./tmp.mri_nu_correct.mni.257529/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.257529/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.257529/sum.junk --avgwf ./tmp.mri_nu_correct.mni.257529/input.mean.dat sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.257529/ones.mgz Loading orig.mgz Voxel Volume is 0.512 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.257529/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.257529/ones.mgz --i ./tmp.mri_nu_correct.mni.257529/nu2.mnc --sum ./tmp.mri_nu_correct.mni.257529/sum.junk --avgwf ./tmp.mri_nu_correct.mni.257529/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.257529/ones.mgz --i ./tmp.mri_nu_correct.mni.257529/nu2.mnc --sum ./tmp.mri_nu_correct.mni.257529/sum.junk --avgwf ./tmp.mri_nu_correct.mni.257529/output.mean.dat sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.257529/ones.mgz Loading ./tmp.mri_nu_correct.mni.257529/nu2.mnc Voxel Volume is 0.512 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.257529/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.257529/nu2.mnc ./tmp.mri_nu_correct.mni.257529/nu2.mnc mul 1.02682963658371030900 Saving result to './tmp.mri_nu_correct.mni.257529/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.257529/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.257529/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.257529/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.10898e-10, 0) j_ras = (0, 9.09495e-12, -1) k_ras = (7.12142e-11, 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 15 seconds. mapping ( 8, 149) to ( 3, 110) Mon Oct 17 15:23:18 UTC 2022 mri_nu_correct.mni done mri_add_xform_to_header -c /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Oct 17 15:23:19 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_normalize -g 1 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform 1.06270 0.03174 -0.01989 -1.42696; 0.02427 1.01381 0.16455 -30.04033; 0.01157 -0.09165 1.09237 -11.08775; 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 = 23 Starting OpenSpline(): npoints = 23 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 110 gm peak at 84 (84), valley at 48 (48) csf peak at 43, setting threshold to 70 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 82 (82), valley at 34 (34) csf peak at 41, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 5 minutes and 9 seconds. Started at Mon Oct 17 15:14:33 UTC 2022 Ended at Mon Oct 17 15:28:30 UTC 2022 #@#%# recon-all-run-time-hours 0.233 recon-all -s sub-03 finished without error at Mon Oct 17 15:28:30 UTC 2022 New invocation of recon-all Mon Oct 17 15:30:36 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-03 -sd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer subjid sub-03 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux bc11910.int.ets1.calculquebec.ca 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 unlimited coredumpsize unlimited memoryuse 33554432 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767717 maxlocks unlimited maxsignal 767717 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638244 32870248 155072132 2737104 8695864 158291616 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/17-15:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Mon Oct 17 15:30:37 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_em_register -rusage /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/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/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'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() 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=28.1 skull bounding box = (81, 54, 69) --> (242, 205, 277) using (135, 104, 173) as brain centroid... mean wm in atlas = 107, using box (115,85,147) --> (154, 122,198) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 4.6 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.438 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.935887 @ (-9.091, 9.091, -27.273) max log p = -3.934536 @ (4.545, 4.545, 4.545) max log p = -3.893582 @ (-2.273, 2.273, -2.273) max log p = -3.855126 @ (1.136, -3.409, -1.136) max log p = -3.855126 @ (0.000, 0.000, 0.000) max log p = -3.850092 @ (0.284, -3.125, -2.557) Found translation: (-5.4, 9.4, -28.7): log p = -3.850 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.836, old_max_log_p =-3.850 (thresh=-3.8) 0.80000 0.00000 0.00000 -5.39773; 0.00000 0.85264 0.11225 -14.94010; 0.00000 -0.10442 0.79316 -9.01386; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.828, old_max_log_p =-3.836 (thresh=-3.8) 0.80000 0.00000 0.00000 -5.39773; 0.00000 0.92340 0.00835 -5.93992; 0.00000 0.00776 0.80102 -29.28086; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.828, old_max_log_p =-3.828 (thresh=-3.8) 0.80000 0.00000 0.00000 -5.39773; 0.00000 0.92340 0.00835 -5.93992; 0.00000 0.00776 0.80102 -29.28086; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.788, old_max_log_p =-3.828 (thresh=-3.8) 0.81271 0.03215 -0.05389 -0.64575; -0.02621 0.92271 0.03282 -5.21699; 0.05291 -0.01805 0.78367 -32.13349; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.773, old_max_log_p =-3.788 (thresh=-3.8) 0.81445 -0.02755 -0.00294 -3.12604; 0.02540 0.92298 0.00698 -8.69705; -0.00124 0.01003 0.78617 -28.18784; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.772, old_max_log_p =-3.773 (thresh=-3.8) 0.82972 -0.02807 -0.00300 -6.16413; 0.02492 0.90568 0.00685 -7.60411; -0.00124 0.01003 0.78617 -26.31284; 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=-3.747, old_max_log_p =-3.772 (thresh=-3.8) 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.747, old_max_log_p =-3.747 (thresh=-3.7) 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 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 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.747 (old=-4.438) transform before final EM align: 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 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 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 2239.488165 mri_em_register stimesec 7.802051 mri_em_register ru_maxrss 757128 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1341472 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 44490 mri_em_register ru_oublock 3 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 736 mri_em_register ru_nivcsw 4222 registration took 5 minutes and 46 seconds. #-------------------------------------- #@# CA Normalize Mon Oct 17 15:36:23 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/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/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... INFO: MRImask() using MRImaskDifferentGeometry() resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.1 skull bounding box = (81, 54, 69) --> (242, 205, 277) using (135, 104, 173) as brain centroid... mean wm in atlas = 107, using box (115,85,147) --> (154, 122,198) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 4.6 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 0.83264 -0.02817 -0.00301 -5.80629; 0.02481 0.90254 0.01965 -9.61680; -0.00165 -0.00480 0.78687 -24.84099; 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 (163, 60, 66) --> (243, 191, 279) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 2 of 7254 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (86, 61, 66) --> (166, 194, 279) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 4 of 7308 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (166, 156, 94) --> (225, 202, 163) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 0 of 523 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (112, 156, 91) --> (165, 203, 165) Right_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 0 of 304 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (145, 146, 137) --> (187, 224, 178) Brain_Stem: limiting intensities to 102.0 --> 132.0 0 of 332 (0.0%) samples deleted using 15721 total control points for intensity normalization... bias field = 0.964 +- 0.088 17 of 15715 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (163, 60, 66) --> (243, 191, 279) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 7842 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (86, 61, 66) --> (166, 194, 279) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 97 of 8015 (1.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (166, 156, 94) --> (225, 202, 163) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 546 (1.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (112, 156, 91) --> (165, 203, 165) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 317 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (145, 146, 137) --> (187, 224, 178) Brain_Stem: limiting intensities to 88.0 --> 132.0 225 of 678 (33.2%) samples deleted using 17398 total control points for intensity normalization... bias field = 1.073 +- 0.069 9 of 16973 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (163, 60, 66) --> (243, 191, 279) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 7998 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (86, 61, 66) --> (166, 194, 279) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 28 of 8203 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (166, 156, 94) --> (225, 202, 163) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 315 of 588 (53.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (112, 156, 91) --> (165, 203, 165) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 118 of 352 (33.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (145, 146, 137) --> (187, 224, 178) Brain_Stem: limiting intensities to 88.0 --> 132.0 542 of 745 (72.8%) samples deleted using 17886 total control points for intensity normalization... bias field = 1.072 +- 0.054 29 of 16708 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 3 minutes and 24 seconds. #-------------------------------------- #@# CA Reg Mon Oct 17 15:39:47 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_ca_register -rusage /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/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'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.59 (predicted orig area = 13.5) 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=0.948, neg=0, invalid=762 0001: dt=348.197334, rms=0.832 (12.237%), neg=0, invalid=762 0002: dt=229.122366, rms=0.801 (3.767%), neg=0, invalid=762 0003: dt=443.904000, rms=0.782 (2.308%), neg=0, invalid=762 0004: dt=146.076336, rms=0.777 (0.738%), neg=0, invalid=762 0005: dt=1183.744000, rms=0.767 (1.247%), neg=0, invalid=762 0006: dt=295.936000, rms=0.764 (0.408%), neg=0, invalid=762 0007: dt=129.472000, rms=0.763 (0.149%), neg=0, invalid=762 0008: dt=129.472000, rms=0.762 (0.075%), neg=0, invalid=762 0009: dt=129.472000, rms=0.761 (0.118%), neg=0, invalid=762 0010: dt=129.472000, rms=0.760 (0.139%), neg=0, invalid=762 0011: dt=129.472000, rms=0.759 (0.179%), neg=0, invalid=762 0012: dt=129.472000, rms=0.757 (0.233%), neg=0, invalid=762 0013: dt=129.472000, rms=0.755 (0.236%), neg=0, invalid=762 0014: dt=129.472000, rms=0.754 (0.172%), neg=0, invalid=762 0015: dt=129.472000, rms=0.752 (0.177%), neg=0, invalid=762 0016: dt=129.472000, rms=0.751 (0.155%), neg=0, invalid=762 0017: dt=129.472000, rms=0.750 (0.134%), neg=0, invalid=762 0018: dt=129.472000, rms=0.750 (0.103%), neg=0, invalid=762 0019: dt=129.472000, rms=0.749 (0.120%), neg=0, invalid=762 0020: dt=129.472000, rms=0.748 (0.114%), neg=0, invalid=762 0021: dt=887.808000, rms=0.746 (0.237%), neg=0, invalid=762 0022: dt=73.984000, rms=0.746 (0.024%), neg=0, invalid=762 0023: dt=73.984000, rms=0.746 (0.008%), neg=0, invalid=762 0024: dt=73.984000, rms=0.746 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.746, neg=0, invalid=762 0025: dt=369.920000, rms=0.743 (0.398%), neg=0, invalid=762 0026: dt=517.888000, rms=0.742 (0.157%), neg=0, invalid=762 0027: dt=517.888000, rms=0.741 (0.123%), neg=0, invalid=762 0028: dt=517.888000, rms=0.739 (0.259%), neg=0, invalid=762 0029: dt=517.888000, rms=0.738 (0.172%), neg=0, invalid=762 0030: dt=517.888000, rms=0.736 (0.229%), neg=0, invalid=762 0031: dt=517.888000, rms=0.735 (0.221%), neg=0, invalid=762 0032: dt=517.888000, rms=0.734 (0.149%), neg=0, invalid=762 0033: dt=517.888000, rms=0.732 (0.153%), neg=0, invalid=762 0034: dt=517.888000, rms=0.730 (0.270%), neg=0, invalid=762 0035: dt=517.888000, rms=0.730 (0.063%), neg=0, invalid=762 0036: dt=517.888000, rms=0.728 (0.311%), neg=0, invalid=762 0037: dt=517.888000, rms=0.726 (0.226%), neg=0, invalid=762 0038: dt=517.888000, rms=0.725 (0.077%), neg=0, invalid=762 0039: dt=517.888000, rms=0.723 (0.287%), neg=0, invalid=762 0040: dt=517.888000, rms=0.723 (-0.096%), neg=0, invalid=762 0041: dt=73.984000, rms=0.723 (0.025%), neg=0, invalid=762 0042: dt=4.624000, rms=0.723 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.732, neg=0, invalid=762 0043: dt=36.288000, rms=0.730 (0.238%), neg=0, invalid=762 0044: dt=118.229008, rms=0.728 (0.262%), neg=0, invalid=762 0045: dt=497.664000, rms=0.712 (2.228%), neg=0, invalid=762 0046: dt=52.363636, rms=0.710 (0.353%), neg=0, invalid=762 0047: dt=124.416000, rms=0.708 (0.213%), neg=0, invalid=762 0048: dt=124.416000, rms=0.704 (0.527%), neg=0, invalid=762 0049: dt=124.416000, rms=0.700 (0.610%), neg=0, invalid=762 0050: dt=124.416000, rms=0.696 (0.537%), neg=0, invalid=762 0051: dt=124.416000, rms=0.691 (0.686%), neg=0, invalid=762 0052: dt=124.416000, rms=0.685 (0.916%), neg=0, invalid=762 0053: dt=124.416000, rms=0.681 (0.653%), neg=0, invalid=762 0054: dt=124.416000, rms=0.678 (0.387%), neg=0, invalid=762 0055: dt=124.416000, rms=0.674 (0.636%), neg=0, invalid=762 0056: dt=124.416000, rms=0.671 (0.448%), neg=0, invalid=762 0057: dt=124.416000, rms=0.668 (0.415%), neg=0, invalid=762 0058: dt=124.416000, rms=0.667 (0.134%), neg=0, invalid=762 0059: dt=124.416000, rms=0.665 (0.357%), neg=0, invalid=762 0060: dt=124.416000, rms=0.665 (-0.011%), neg=0, invalid=762 0061: dt=20.736000, rms=0.664 (0.025%), neg=0, invalid=762 0062: dt=25.920000, rms=0.664 (0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0063: dt=85.052632, rms=0.662 (0.427%), neg=0, invalid=762 0064: dt=15.552000, rms=0.662 (0.017%), neg=0, invalid=762 0065: dt=15.552000, rms=0.662 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.712, neg=0, invalid=762 0066: dt=11.200000, rms=0.708 (0.453%), neg=0, invalid=762 0067: dt=11.200000, rms=0.707 (0.133%), neg=0, invalid=762 0068: dt=11.200000, rms=0.707 (0.063%), neg=0, invalid=762 0069: dt=11.200000, rms=0.707 (-0.088%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.708, neg=0, invalid=762 0070: dt=6.400000, rms=0.707 (0.100%), neg=0, invalid=762 0071: dt=1.600000, rms=0.707 (0.008%), neg=0, invalid=762 0072: dt=1.600000, rms=0.707 (-0.018%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.792, neg=0, invalid=762 0073: dt=6.968037, rms=0.771 (2.599%), neg=0, invalid=762 0074: dt=10.112360, rms=0.765 (0.817%), neg=0, invalid=762 0075: dt=1.728000, rms=0.765 (0.006%), neg=0, invalid=762 0076: dt=1.728000, rms=0.765 (0.013%), neg=0, invalid=762 0077: dt=1.728000, rms=0.765 (0.012%), neg=0, invalid=762 0078: dt=1.728000, rms=0.765 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0079: dt=0.000000, rms=0.765 (0.063%), neg=0, invalid=762 0080: dt=0.000000, rms=0.765 (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=0.820, neg=0, invalid=762 0081: dt=0.000000, rms=0.820 (0.055%), neg=0, invalid=762 0082: dt=0.000000, rms=0.820 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.820, neg=0, invalid=762 0083: dt=0.000000, rms=0.820 (0.055%), neg=0, invalid=762 0084: dt=0.000000, rms=0.820 (0.000%), neg=0, invalid=762 0085: dt=0.100000, rms=0.820 (-0.015%), 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=0.726, neg=0, invalid=762 0086: dt=0.742788, rms=0.710 (2.214%), neg=0, invalid=762 0087: dt=0.064000, rms=0.709 (0.074%), neg=0, invalid=762 0088: dt=0.064000, rms=0.709 (-0.056%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.710, neg=0, invalid=762 0089: dt=0.016000, rms=0.709 (0.076%), neg=0, invalid=762 0090: dt=0.000023, rms=0.709 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.20489 (27) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (4659 voxels, overlap=0.316) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (4659 voxels, peak = 30), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.20307 (27) Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (3138 voxels, overlap=0.158) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3138 voxels, peak = 26), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.04979 (82) Right_Pallidum (52): linear fit = 0.87 x + 0.0 (2166 voxels, overlap=0.129) Right_Pallidum (52): linear fit = 0.87 x + 0.0 (2166 voxels, peak = 83), gca=83.0 gca peak = 0.20183 (93) mri peak = 0.06024 (84) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (2004 voxels, overlap=0.227) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (2004 voxels, peak = 84), gca=84.2 gca peak = 0.21683 (55) mri peak = 0.07496 (72) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2988 voxels, overlap=0.014) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2988 voxels, peak = 70), gca=69.6 gca peak = 0.30730 (58) mri peak = 0.10230 (71) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2811 voxels, overlap=0.009) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2811 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.09623 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (187748 voxels, overlap=0.855) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (187748 voxels, peak = 101), gca=101.0 gca peak = 0.12076 (102) mri peak = 0.10608 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (196527 voxels, overlap=0.876) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (196527 voxels, peak = 102), gca=102.0 gca peak = 0.14995 (59) mri peak = 0.03432 (78) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (102816 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (102816 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.03748 (76) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (114139 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (114139 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.10612 (81) Right_Caudate (50): linear fit = 1.20 x + 0.0 (2474 voxels, overlap=0.011) Right_Caudate (50): linear fit = 1.20 x + 0.0 (2474 voxels, peak = 80), gca=80.1 gca peak = 0.15243 (71) mri peak = 0.08748 (81) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2900 voxels, overlap=0.147) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2900 voxels, peak = 80), gca=79.9 gca peak = 0.13336 (57) mri peak = 0.04607 (71) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (48467 voxels, overlap=0.442) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (48467 voxels, peak = 70), gca=70.4 gca peak = 0.13252 (56) mri peak = 0.04870 (71) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (57227 voxels, overlap=0.014) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (57227 voxels, peak = 73), gca=72.5 gca peak = 0.18181 (84) mri peak = 0.07560 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (24547 voxels, overlap=0.421) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (24547 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.08594 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (20277 voxels, overlap=0.325) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (20277 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.08856 (72) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (1252 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (1252 voxels, peak = 73), gca=72.7 gca peak = 0.39313 (56) mri peak = 0.08356 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1524 voxels, overlap=0.042) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1524 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.07160 (101) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (12833 voxels, overlap=0.062) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (12833 voxels, peak = 102), gca=101.6 gca peak = 0.11978 (83) mri peak = 0.06886 (101) Right_Thalamus_Proper (49): linear fit = 1.22 x + 0.0 (10069 voxels, overlap=0.016) Right_Thalamus_Proper (49): linear fit = 1.22 x + 0.0 (10069 voxels, peak = 101), gca=100.8 gca peak = 0.13399 (79) mri peak = 0.06477 (90) Left_Putamen (12): linear fit = 1.12 x + 0.0 (6325 voxels, overlap=0.161) Left_Putamen (12): linear fit = 1.12 x + 0.0 (6325 voxels, peak = 89), gca=88.9 gca peak = 0.14159 (79) mri peak = 0.05637 (87) Right_Putamen (51): linear fit = 1.12 x + 0.0 (6154 voxels, overlap=0.338) Right_Putamen (51): linear fit = 1.12 x + 0.0 (6154 voxels, peak = 89), gca=88.9 gca peak = 0.10025 (80) mri peak = 0.08017 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (26922 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (26922 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.10014 (96) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (3115 voxels, overlap=0.076) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (3115 voxels, peak = 95), gca=95.0 gca peak = 0.12801 (89) mri peak = 0.07487 (96) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (3538 voxels, overlap=0.167) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (3538 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.16465 (26) Fourth_Ventricle (15): linear fit = 1.58 x + 0.0 (1473 voxels, overlap=0.293) Fourth_Ventricle (15): linear fit = 1.58 x + 0.0 (1473 voxels, peak = 33), gca=33.1 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 Fourth_Ventricle = 0.15061 (21) 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 1.29 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.50 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=0.675, neg=0, invalid=762 0091: dt=136.685714, rms=0.649 (3.810%), neg=0, invalid=762 0092: dt=295.936000, rms=0.643 (0.943%), neg=0, invalid=762 0093: dt=295.936000, rms=0.639 (0.578%), neg=0, invalid=762 0094: dt=129.472000, rms=0.638 (0.190%), neg=0, invalid=762 0095: dt=1183.744000, rms=0.635 (0.532%), neg=0, invalid=762 0096: dt=110.976000, rms=0.634 (0.161%), neg=0, invalid=762 0097: dt=1479.680000, rms=0.632 (0.352%), neg=0, invalid=762 0098: dt=129.472000, rms=0.630 (0.244%), neg=0, invalid=762 0099: dt=129.472000, rms=0.630 (0.019%), neg=0, invalid=762 0100: dt=129.472000, rms=0.630 (0.026%), neg=0, invalid=762 0101: dt=129.472000, rms=0.629 (0.043%), neg=0, invalid=762 0102: dt=129.472000, rms=0.629 (0.053%), neg=0, invalid=762 0103: dt=129.472000, rms=0.629 (0.070%), neg=0, invalid=762 0104: dt=129.472000, rms=0.628 (0.088%), neg=0, invalid=762 0105: dt=129.472000, rms=0.628 (0.101%), neg=0, invalid=762 0106: dt=129.472000, rms=0.627 (0.111%), neg=0, invalid=762 0107: dt=129.472000, rms=0.626 (0.118%), neg=0, invalid=762 0108: dt=129.472000, rms=0.625 (0.114%), neg=0, invalid=762 0109: dt=129.472000, rms=0.625 (0.092%), neg=0, invalid=762 0110: dt=129.472000, rms=0.624 (0.105%), neg=0, invalid=762 0111: dt=129.472000, rms=0.623 (0.107%), neg=0, invalid=762 0112: dt=129.472000, rms=0.623 (0.091%), neg=0, invalid=762 0113: dt=129.472000, rms=0.622 (0.083%), neg=0, invalid=762 0114: dt=129.472000, rms=0.622 (0.058%), neg=0, invalid=762 0115: dt=129.472000, rms=0.622 (0.061%), neg=0, invalid=762 0116: dt=129.472000, rms=0.621 (0.065%), neg=0, invalid=762 0117: dt=129.472000, rms=0.621 (0.073%), neg=0, invalid=762 0118: dt=129.472000, rms=0.620 (0.072%), neg=0, invalid=762 0119: dt=129.472000, rms=0.620 (0.067%), neg=0, invalid=762 0120: dt=129.472000, rms=0.619 (0.078%), neg=0, invalid=762 0121: dt=129.472000, rms=0.619 (0.067%), neg=0, invalid=762 0122: dt=129.472000, rms=0.619 (0.067%), neg=0, invalid=762 0123: dt=129.472000, rms=0.618 (0.056%), neg=0, invalid=762 0124: dt=129.472000, rms=0.618 (0.044%), neg=0, invalid=762 0125: dt=129.472000, rms=0.618 (0.040%), neg=0, invalid=762 0126: dt=129.472000, rms=0.618 (0.033%), neg=0, invalid=762 0127: dt=129.472000, rms=0.617 (0.039%), neg=0, invalid=762 0128: dt=129.472000, rms=0.617 (0.069%), neg=0, invalid=762 0129: dt=129.472000, rms=0.616 (0.063%), neg=0, invalid=762 0130: dt=129.472000, rms=0.616 (0.041%), neg=0, invalid=762 0131: dt=129.472000, rms=0.616 (0.026%), neg=0, invalid=762 0132: dt=129.472000, rms=0.616 (0.027%), neg=0, invalid=762 0133: dt=129.472000, rms=0.616 (0.037%), neg=0, invalid=762 0134: dt=129.472000, rms=0.615 (0.037%), neg=0, invalid=762 0135: dt=129.472000, rms=0.615 (0.036%), neg=0, invalid=762 0136: dt=129.472000, rms=0.615 (0.033%), neg=0, invalid=762 0137: dt=129.472000, rms=0.615 (0.024%), neg=0, invalid=762 0138: dt=129.472000, rms=0.615 (0.037%), neg=0, invalid=762 0139: dt=129.472000, rms=0.614 (0.051%), neg=0, invalid=762 0140: dt=129.472000, rms=0.614 (0.046%), neg=0, invalid=762 0141: dt=129.472000, rms=0.614 (0.033%), neg=0, invalid=762 0142: dt=129.472000, rms=0.614 (0.017%), neg=0, invalid=762 0143: dt=129.472000, rms=0.614 (0.012%), neg=0, invalid=762 0144: dt=1479.680000, rms=0.613 (0.070%), neg=0, invalid=762 0145: dt=32.368000, rms=0.613 (-0.004%), neg=0, invalid=762 0146: dt=32.368000, rms=0.613 (0.006%), neg=0, invalid=762 0147: dt=32.368000, rms=0.613 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0148: dt=129.472000, rms=0.613 (0.123%), neg=0, invalid=762 0149: dt=517.888000, rms=0.612 (0.159%), neg=0, invalid=762 0150: dt=295.936000, rms=0.611 (0.043%), neg=0, invalid=762 0151: dt=295.936000, rms=0.611 (0.005%), neg=0, invalid=762 0152: dt=295.936000, rms=0.611 (0.068%), neg=0, invalid=762 0153: dt=295.936000, rms=0.610 (0.068%), neg=0, invalid=762 0154: dt=295.936000, rms=0.610 (0.049%), neg=0, invalid=762 0155: dt=295.936000, rms=0.610 (-0.001%), neg=0, invalid=762 0156: dt=0.031609, rms=0.610 (0.000%), neg=0, invalid=762 0157: dt=0.000000, rms=0.610 (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=0.611, neg=0, invalid=762 0158: dt=124.416000, rms=0.609 (0.323%), neg=0, invalid=762 0159: dt=331.776000, rms=0.602 (1.288%), neg=0, invalid=762 0160: dt=62.117647, rms=0.599 (0.421%), neg=0, invalid=762 0161: dt=580.608000, rms=0.595 (0.762%), neg=0, invalid=762 0162: dt=72.237624, rms=0.590 (0.811%), neg=0, invalid=762 0163: dt=82.944000, rms=0.589 (0.156%), neg=0, invalid=762 0164: dt=124.416000, rms=0.588 (0.182%), neg=0, invalid=762 0165: dt=62.208000, rms=0.587 (0.139%), neg=0, invalid=762 0166: dt=248.832000, rms=0.586 (0.229%), neg=0, invalid=762 0167: dt=36.288000, rms=0.585 (0.170%), neg=0, invalid=762 0168: dt=145.152000, rms=0.584 (0.165%), neg=0, invalid=762 0169: dt=82.944000, rms=0.583 (0.108%), neg=0, invalid=762 0170: dt=103.680000, rms=0.582 (0.124%), neg=0, invalid=762 0171: dt=82.944000, rms=0.582 (0.090%), neg=0, invalid=762 0172: dt=103.680000, rms=0.581 (0.117%), neg=0, invalid=762 0173: dt=62.208000, rms=0.581 (0.085%), neg=0, invalid=762 0174: dt=145.152000, rms=0.580 (0.122%), neg=0, invalid=762 0175: dt=82.944000, rms=0.579 (0.093%), neg=0, invalid=762 0176: dt=103.680000, rms=0.579 (0.089%), neg=0, invalid=762 0177: dt=62.208000, rms=0.578 (0.072%), neg=0, invalid=762 0178: dt=145.152000, rms=0.578 (0.135%), neg=0, invalid=762 0179: dt=62.208000, rms=0.577 (0.059%), neg=0, invalid=762 0180: dt=145.152000, rms=0.577 (0.116%), neg=0, invalid=762 0181: dt=82.944000, rms=0.576 (0.068%), neg=0, invalid=762 0182: dt=103.680000, rms=0.576 (0.077%), neg=0, invalid=762 0183: dt=82.944000, rms=0.575 (0.079%), neg=0, invalid=762 0184: dt=82.944000, rms=0.575 (0.055%), neg=0, invalid=762 0185: dt=103.680000, rms=0.575 (0.072%), neg=0, invalid=762 0186: dt=36.288000, rms=0.574 (0.051%), neg=0, invalid=762 0187: dt=580.608000, rms=0.573 (0.156%), neg=0, invalid=762 0188: dt=36.288000, rms=0.572 (0.206%), neg=0, invalid=762 0189: dt=145.152000, rms=0.572 (0.102%), neg=0, invalid=762 0190: dt=36.288000, rms=0.571 (0.034%), neg=0, invalid=762 0191: dt=36.288000, rms=0.571 (0.024%), neg=0, invalid=762 0192: dt=36.288000, rms=0.571 (0.027%), neg=0, invalid=762 0193: dt=36.288000, rms=0.571 (0.045%), neg=0, invalid=762 0194: dt=36.288000, rms=0.570 (0.071%), neg=0, invalid=762 0195: dt=36.288000, rms=0.570 (0.088%), neg=0, invalid=762 0196: dt=36.288000, rms=0.569 (0.084%), neg=0, invalid=762 0197: dt=36.288000, rms=0.569 (0.086%), neg=0, invalid=762 0198: dt=36.288000, rms=0.569 (0.083%), neg=0, invalid=762 0199: dt=36.288000, rms=0.568 (0.086%), neg=0, invalid=762 0200: dt=36.288000, rms=0.567 (0.113%), neg=0, invalid=762 0201: dt=36.288000, rms=0.567 (0.113%), neg=0, invalid=762 0202: dt=36.288000, rms=0.566 (0.103%), neg=0, invalid=762 0203: dt=36.288000, rms=0.566 (0.096%), neg=0, invalid=762 0204: dt=36.288000, rms=0.565 (0.090%), neg=0, invalid=762 0205: dt=36.288000, rms=0.565 (0.086%), neg=0, invalid=762 0206: dt=36.288000, rms=0.564 (0.087%), neg=0, invalid=762 0207: dt=36.288000, rms=0.564 (0.095%), neg=0, invalid=762 0208: dt=36.288000, rms=0.563 (0.101%), neg=0, invalid=762 0209: dt=36.288000, rms=0.563 (0.092%), neg=0, invalid=762 0210: dt=36.288000, rms=0.562 (0.084%), neg=0, invalid=762 0211: dt=36.288000, rms=0.562 (0.076%), neg=0, invalid=762 0212: dt=36.288000, rms=0.561 (0.072%), neg=0, invalid=762 0213: dt=36.288000, rms=0.561 (0.077%), neg=0, invalid=762 0214: dt=36.288000, rms=0.560 (0.075%), neg=0, invalid=762 0215: dt=36.288000, rms=0.560 (0.076%), neg=0, invalid=762 0216: dt=36.288000, rms=0.560 (0.069%), neg=0, invalid=762 0217: dt=36.288000, rms=0.559 (0.061%), neg=0, invalid=762 0218: dt=36.288000, rms=0.559 (0.058%), neg=0, invalid=762 0219: dt=36.288000, rms=0.559 (0.052%), neg=0, invalid=762 0220: dt=36.288000, rms=0.558 (0.053%), neg=0, invalid=762 0221: dt=36.288000, rms=0.558 (0.060%), neg=0, invalid=762 0222: dt=36.288000, rms=0.558 (0.058%), neg=0, invalid=762 0223: dt=36.288000, rms=0.557 (0.057%), neg=0, invalid=762 0224: dt=36.288000, rms=0.557 (0.046%), neg=0, invalid=762 0225: dt=36.288000, rms=0.557 (0.042%), neg=0, invalid=762 0226: dt=36.288000, rms=0.557 (0.045%), neg=0, invalid=762 0227: dt=36.288000, rms=0.556 (0.044%), neg=0, invalid=762 0228: dt=36.288000, rms=0.556 (0.047%), neg=0, invalid=762 0229: dt=36.288000, rms=0.556 (0.050%), neg=0, invalid=762 0230: dt=36.288000, rms=0.556 (0.043%), neg=0, invalid=762 0231: dt=36.288000, rms=0.555 (0.038%), neg=0, invalid=762 0232: dt=36.288000, rms=0.555 (0.027%), neg=0, invalid=762 0233: dt=36.288000, rms=0.555 (0.028%), neg=0, invalid=762 0234: dt=36.288000, rms=0.555 (0.030%), neg=0, invalid=762 0235: dt=36.288000, rms=0.555 (0.042%), neg=0, invalid=762 0236: dt=36.288000, rms=0.554 (0.043%), neg=0, invalid=762 0237: dt=36.288000, rms=0.554 (0.040%), neg=0, invalid=762 0238: dt=36.288000, rms=0.554 (0.029%), neg=0, invalid=762 0239: dt=36.288000, rms=0.554 (0.026%), neg=0, invalid=762 0240: dt=36.288000, rms=0.554 (0.024%), neg=0, invalid=762 0241: dt=36.288000, rms=0.554 (0.029%), neg=0, invalid=762 0242: dt=36.288000, rms=0.553 (0.035%), neg=0, invalid=762 0243: dt=36.288000, rms=0.553 (0.036%), neg=0, invalid=762 0244: dt=36.288000, rms=0.553 (0.034%), neg=0, invalid=762 0245: dt=36.288000, rms=0.553 (0.024%), neg=0, invalid=762 0246: dt=36.288000, rms=0.553 (0.016%), neg=0, invalid=762 0247: dt=103.680000, rms=0.553 (0.013%), neg=0, invalid=762 0248: dt=103.680000, rms=0.553 (0.000%), neg=0, invalid=762 0249: dt=103.680000, rms=0.553 (0.021%), neg=0, invalid=762 0250: dt=103.680000, rms=0.552 (0.020%), neg=0, invalid=762 0251: dt=103.680000, rms=0.552 (0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0252: dt=145.152000, rms=0.550 (0.436%), neg=0, invalid=762 0253: dt=36.288000, rms=0.550 (0.048%), neg=0, invalid=762 0254: dt=36.288000, rms=0.550 (0.023%), neg=0, invalid=762 0255: dt=36.288000, rms=0.550 (0.018%), neg=0, invalid=762 0256: dt=36.288000, rms=0.550 (0.030%), neg=0, invalid=762 0257: dt=36.288000, rms=0.549 (0.049%), neg=0, invalid=762 0258: dt=36.288000, rms=0.549 (0.064%), neg=0, invalid=762 0259: dt=36.288000, rms=0.549 (0.052%), neg=0, invalid=762 0260: dt=36.288000, rms=0.548 (0.036%), neg=0, invalid=762 0261: dt=36.288000, rms=0.548 (0.018%), neg=0, invalid=762 0262: dt=36.288000, rms=0.548 (0.017%), neg=0, invalid=762 0263: dt=145.152000, rms=0.548 (0.028%), neg=0, invalid=762 0264: dt=36.288000, rms=0.548 (0.008%), neg=0, invalid=762 0265: dt=36.288000, rms=0.548 (0.004%), neg=0, invalid=762 0266: dt=36.288000, rms=0.548 (0.010%), neg=0, invalid=762 0267: dt=36.288000, rms=0.548 (0.011%), neg=0, invalid=762 0268: dt=36.288000, rms=0.548 (0.015%), neg=0, invalid=762 0269: dt=36.288000, rms=0.548 (0.015%), neg=0, invalid=762 0270: dt=36.288000, rms=0.548 (0.019%), neg=0, invalid=762 0271: dt=36.288000, rms=0.548 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 0272: dt=23.006536, rms=0.557 (0.151%), neg=0, invalid=762 0273: dt=102.400000, rms=0.554 (0.596%), neg=0, invalid=762 0274: dt=121.623329, rms=0.548 (1.091%), neg=0, invalid=762 0275: dt=26.816600, rms=0.544 (0.670%), neg=0, invalid=762 0276: dt=11.200000, rms=0.544 (0.020%), neg=0, invalid=762 0277: dt=11.200000, rms=0.544 (0.026%), neg=0, invalid=762 0278: dt=11.200000, rms=0.543 (0.054%), neg=0, invalid=762 0279: dt=11.200000, rms=0.543 (0.086%), neg=0, invalid=762 0280: dt=11.200000, rms=0.542 (0.145%), neg=0, invalid=762 0281: dt=11.200000, rms=0.541 (0.202%), neg=0, invalid=762 0282: dt=11.200000, rms=0.540 (0.243%), neg=0, invalid=762 0283: dt=11.200000, rms=0.538 (0.274%), neg=0, invalid=762 0284: dt=11.200000, rms=0.537 (0.287%), neg=0, invalid=762 0285: dt=11.200000, rms=0.535 (0.270%), neg=0, invalid=762 0286: dt=11.200000, rms=0.534 (0.237%), neg=0, invalid=762 0287: dt=11.200000, rms=0.533 (0.211%), neg=0, invalid=762 0288: dt=11.200000, rms=0.533 (0.010%), neg=0, invalid=762 0289: dt=11.200000, rms=0.533 (0.018%), neg=0, invalid=762 0290: dt=11.200000, rms=0.533 (0.026%), neg=0, invalid=762 0291: dt=11.200000, rms=0.532 (0.044%), neg=0, invalid=762 0292: dt=11.200000, rms=0.532 (0.026%), neg=0, invalid=762 0293: dt=11.200000, rms=0.532 (0.048%), neg=0, invalid=762 0294: dt=5.600000, rms=0.532 (0.010%), neg=0, invalid=762 0295: dt=2.800000, rms=0.532 (0.005%), neg=0, invalid=762 0296: dt=0.700000, rms=0.532 (0.000%), neg=0, invalid=762 0297: dt=0.350000, rms=0.532 (0.001%), neg=0, invalid=762 0298: dt=0.021875, rms=0.532 (0.000%), neg=0, invalid=762 0299: dt=0.010937, rms=0.532 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0300: dt=64.290909, rms=0.529 (0.555%), neg=0, invalid=762 0301: dt=11.200000, rms=0.529 (0.082%), neg=0, invalid=762 0302: dt=11.200000, rms=0.529 (0.017%), neg=0, invalid=762 0303: dt=11.200000, rms=0.529 (0.008%), neg=0, invalid=762 0304: dt=11.200000, rms=0.529 (0.009%), neg=0, invalid=762 0305: dt=11.200000, rms=0.529 (0.006%), neg=0, invalid=762 0306: dt=11.200000, rms=0.529 (0.018%), neg=0, invalid=762 0307: dt=11.200000, rms=0.528 (0.043%), neg=0, invalid=762 0308: dt=11.200000, rms=0.528 (0.048%), neg=0, invalid=762 0309: dt=11.200000, rms=0.528 (0.053%), neg=0, invalid=762 0310: dt=11.200000, rms=0.528 (0.046%), neg=0, invalid=762 0311: dt=11.200000, rms=0.527 (0.037%), neg=0, invalid=762 0312: dt=11.200000, rms=0.527 (0.034%), neg=0, invalid=762 0313: dt=11.200000, rms=0.527 (0.038%), neg=0, invalid=762 0314: dt=11.200000, rms=0.527 (0.055%), neg=0, invalid=762 0315: dt=11.200000, rms=0.526 (0.061%), neg=0, invalid=762 0316: dt=11.200000, rms=0.526 (0.073%), neg=0, invalid=762 0317: dt=11.200000, rms=0.525 (0.094%), neg=0, invalid=762 0318: dt=11.200000, rms=0.525 (0.097%), neg=0, invalid=762 0319: dt=11.200000, rms=0.524 (0.100%), neg=0, invalid=762 0320: dt=11.200000, rms=0.524 (0.093%), neg=0, invalid=762 0321: dt=11.200000, rms=0.523 (0.090%), neg=0, invalid=762 0322: dt=11.200000, rms=0.523 (0.087%), neg=0, invalid=762 0323: dt=11.200000, rms=0.523 (0.083%), neg=0, invalid=762 0324: dt=11.200000, rms=0.522 (0.081%), neg=0, invalid=762 0325: dt=11.200000, rms=0.522 (0.073%), neg=0, invalid=762 0326: dt=11.200000, rms=0.521 (0.074%), neg=0, invalid=762 0327: dt=11.200000, rms=0.521 (0.065%), neg=0, invalid=762 0328: dt=11.200000, rms=0.521 (0.063%), neg=0, invalid=762 0329: dt=11.200000, rms=0.520 (0.062%), neg=0, invalid=762 0330: dt=11.200000, rms=0.520 (0.007%), neg=0, invalid=762 0331: dt=11.200000, rms=0.520 (0.009%), neg=0, invalid=762 0332: dt=2.800000, rms=0.520 (-0.002%), neg=0, invalid=762 0333: dt=2.800000, rms=0.520 (0.001%), neg=0, invalid=762 0334: dt=2.400000, rms=0.520 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0335: dt=0.000000, rms=0.538 (0.041%), neg=0, invalid=762 0336: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0337: dt=0.000000, rms=0.538 (0.041%), neg=0, invalid=762 0338: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.575, neg=0, invalid=762 0339: dt=1.792000, rms=0.570 (0.888%), neg=0, invalid=762 0340: dt=0.448000, rms=0.570 (0.036%), neg=0, invalid=762 0341: dt=0.448000, rms=0.570 (0.002%), neg=0, invalid=762 0342: dt=0.448000, rms=0.570 (-0.077%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=762 0343: dt=0.768000, rms=0.570 (0.084%), neg=0, invalid=762 0344: dt=0.256000, rms=0.570 (0.006%), neg=0, invalid=762 0345: dt=0.256000, rms=0.570 (-0.002%), 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=0.533, neg=0, invalid=762 0346: dt=1.280000, rms=0.499 (6.349%), neg=0, invalid=762 0347: dt=0.000000, rms=0.499 (0.012%), neg=0, invalid=762 0348: dt=0.050000, rms=0.499 (-0.191%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=762 0349: dt=0.000000, rms=0.499 (0.061%), neg=0, invalid=762 0350: dt=0.000000, rms=0.499 (0.000%), neg=0, invalid=762 0351: dt=0.050000, rms=0.499 (-0.130%), 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=0.491, neg=0, invalid=762 0352: dt=0.000000, rms=0.491 (0.063%), neg=0, invalid=762 0353: dt=0.000000, rms=0.491 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0354: dt=129.472000, rms=0.490 (0.127%), neg=0, invalid=762 0355: dt=32.368000, rms=0.490 (0.001%), neg=0, invalid=762 0356: dt=32.368000, rms=0.490 (0.000%), neg=0, invalid=762 0357: dt=32.368000, rms=0.490 (0.001%), neg=0, invalid=762 0358: dt=32.368000, rms=0.490 (0.005%), neg=0, invalid=762 0359: dt=32.368000, rms=0.490 (0.003%), neg=0, invalid=762 0360: dt=32.368000, rms=0.490 (0.008%), neg=0, invalid=762 0361: dt=32.368000, rms=0.490 (0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0362: dt=25.920000, rms=0.490 (0.098%), neg=0, invalid=762 0363: dt=31.104000, rms=0.490 (0.026%), neg=0, invalid=762 0364: dt=31.104000, rms=0.490 (0.035%), neg=0, invalid=762 0365: dt=31.104000, rms=0.490 (0.029%), neg=0, invalid=762 0366: dt=31.104000, rms=0.490 (0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0367: dt=124.049383, rms=0.486 (0.778%), neg=0, invalid=762 0368: dt=36.288000, rms=0.486 (0.102%), neg=0, invalid=762 0369: dt=36.288000, rms=0.486 (0.031%), neg=0, invalid=762 0370: dt=36.288000, rms=0.485 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0371: dt=36.288000, rms=0.485 (0.071%), neg=0, invalid=762 0372: dt=36.288000, rms=0.485 (0.109%), neg=0, invalid=762 0373: dt=36.288000, rms=0.484 (0.126%), neg=0, invalid=762 0374: dt=36.288000, rms=0.483 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0375: dt=36.288000, rms=0.483 (0.079%), neg=0, invalid=762 0376: dt=62.208000, rms=0.483 (0.019%), neg=0, invalid=762 0377: dt=62.208000, rms=0.483 (0.026%), neg=0, invalid=762 0378: dt=62.208000, rms=0.483 (0.042%), neg=0, invalid=762 0379: dt=62.208000, rms=0.482 (0.062%), neg=0, invalid=762 0380: dt=62.208000, rms=0.482 (0.068%), neg=0, invalid=762 0381: dt=62.208000, rms=0.482 (0.081%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0382: dt=62.208000, rms=0.481 (0.063%), neg=0, invalid=762 0383: dt=62.208000, rms=0.481 (0.087%), neg=0, invalid=762 0384: dt=62.208000, rms=0.480 (0.076%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0385: dt=11.200000, rms=0.481 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0386: dt=32.000000, rms=0.480 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0387: dt=102.400000, rms=0.477 (0.666%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0388: dt=25.600000, rms=0.476 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=25.600000, rms=0.475 (0.301%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0390: dt=25.600000, rms=0.473 (0.291%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0391: dt=25.600000, rms=0.472 (0.226%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 2 iterations, nbhd size=0, neg = 0 0392: dt=25.600000, rms=0.471 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 10 iterations, nbhd size=1, neg = 0 0393: dt=25.600000, rms=0.470 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 12 iterations, nbhd size=1, neg = 0 0394: dt=25.600000, rms=0.469 (0.212%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 3 iterations, nbhd size=0, neg = 0 0395: dt=25.600000, rms=0.469 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 0396: dt=25.600000, rms=0.468 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 4 iterations, nbhd size=0, neg = 0 0397: dt=25.600000, rms=0.468 (0.073%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0398: dt=38.400000, rms=0.467 (0.117%), neg=0, invalid=762 0399: dt=11.200000, rms=0.467 (0.019%), neg=0, invalid=762 0400: dt=11.200000, rms=0.467 (0.021%), neg=0, invalid=762 0401: dt=11.200000, rms=0.467 (0.002%), neg=0, invalid=762 0402: dt=11.200000, rms=0.467 (0.014%), neg=0, invalid=762 0403: dt=11.200000, rms=0.467 (0.036%), neg=0, invalid=762 0404: dt=11.200000, rms=0.467 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0405: dt=11.200000, rms=0.466 (0.029%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0406: dt=60.666667, rms=0.463 (0.809%), neg=0, invalid=762 0407: dt=11.200000, rms=0.462 (0.110%), neg=0, invalid=762 0408: dt=11.200000, rms=0.462 (0.050%), neg=0, invalid=762 0409: dt=11.200000, rms=0.462 (0.022%), neg=0, invalid=762 0410: dt=11.200000, rms=0.462 (0.002%), neg=0, invalid=762 0411: dt=44.800000, rms=0.461 (0.147%), neg=0, invalid=762 0412: dt=11.200000, rms=0.461 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0413: dt=2.500000, rms=0.469 (0.097%), neg=0, invalid=762 0414: dt=0.864000, rms=0.469 (0.007%), neg=0, invalid=762 0415: dt=0.864000, rms=0.469 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0416: dt=7.663866, rms=0.468 (0.225%), neg=0, invalid=762 0417: dt=8.380952, rms=0.468 (0.075%), neg=0, invalid=762 0418: dt=8.380952, rms=0.468 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0419: dt=8.380952, rms=0.467 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0420: dt=8.380952, rms=0.467 (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=0.474, neg=0, invalid=762 0421: dt=0.000050, rms=0.474 (0.052%), neg=0, invalid=762 0422: dt=0.000000, rms=0.474 (0.000%), neg=0, invalid=762 0423: dt=0.100000, rms=0.474 (-0.064%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0424: dt=0.000000, rms=0.474 (0.052%), neg=0, invalid=762 0425: dt=0.000000, rms=0.474 (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=0.463, neg=0, invalid=762 iter 0, gcam->neg = 548 after 14 iterations, nbhd size=1, neg = 0 0426: dt=2.101313, rms=0.440 (5.078%), neg=0, invalid=762 0427: dt=0.080000, rms=0.440 (0.060%), neg=0, invalid=762 0428: dt=0.080000, rms=0.440 (-0.043%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 0429: dt=0.064000, rms=0.439 (0.096%), neg=0, invalid=762 0430: dt=0.000000, rms=0.439 (0.003%), neg=0, invalid=762 0431: dt=0.050000, rms=0.439 (-0.017%), 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=0.426, neg=0, invalid=762 0432: dt=0.000000, rms=0.426 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0433: dt=55.488000, rms=0.426 (0.006%), neg=0, invalid=762 0434: dt=0.005645, rms=0.426 (0.000%), neg=0, invalid=762 0435: dt=0.005645, rms=0.426 (-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=0.426, neg=0, invalid=762 0436: dt=0.000000, rms=0.426 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0437: dt=36.288000, rms=0.426 (0.025%), neg=0, invalid=762 0438: dt=103.680000, rms=0.425 (0.026%), neg=0, invalid=762 0439: dt=331.776000, rms=0.425 (0.101%), neg=0, invalid=762 0440: dt=36.288000, rms=0.425 (0.011%), neg=0, invalid=762 0441: dt=36.288000, rms=0.425 (0.006%), neg=0, invalid=762 0442: dt=36.288000, rms=0.425 (0.009%), neg=0, invalid=762 0443: dt=36.288000, rms=0.425 (0.016%), neg=0, invalid=762 0444: dt=36.288000, rms=0.425 (0.027%), neg=0, invalid=762 0445: dt=36.288000, rms=0.425 (0.034%), neg=0, invalid=762 0446: dt=36.288000, rms=0.425 (0.031%), neg=0, invalid=762 0447: dt=36.288000, rms=0.424 (0.024%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 0448: dt=8.000000, rms=0.425 (0.028%), neg=0, invalid=762 0449: dt=6.400000, rms=0.425 (0.008%), neg=0, invalid=762 0450: dt=6.400000, rms=0.425 (0.005%), neg=0, invalid=762 0451: dt=6.400000, rms=0.425 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 0452: dt=69.135802, rms=0.423 (0.557%), neg=0, invalid=762 0453: dt=11.200000, rms=0.422 (0.193%), neg=0, invalid=762 0454: dt=11.200000, rms=0.421 (0.060%), neg=0, invalid=762 0455: dt=11.200000, rms=0.421 (0.046%), neg=0, invalid=762 0456: dt=11.200000, rms=0.421 (0.033%), neg=0, invalid=762 0457: dt=44.800000, rms=0.420 (0.185%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0458: dt=19.200000, rms=0.420 (0.051%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.423, neg=0, invalid=762 0459: dt=5.692308, rms=0.423 (0.072%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0460: dt=4.032000, rms=0.423 (0.003%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0461: dt=4.032000, rms=0.423 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0462: dt=4.032000, rms=0.423 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0463: dt=4.032000, rms=0.423 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0464: dt=14.987342, rms=0.421 (0.494%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0465: dt=11.929825, rms=0.420 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0466: dt=11.929825, rms=0.420 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0467: dt=11.929825, rms=0.419 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0468: dt=11.929825, rms=0.419 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0469: dt=11.929825, rms=0.419 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 11 iterations, nbhd size=1, neg = 0 0470: dt=11.929825, rms=0.418 (0.078%), neg=0, invalid=762 0471: dt=13.824000, rms=0.418 (0.026%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0472: dt=0.000000, rms=0.424 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0473: dt=0.000000, rms=0.424 (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=0.414, neg=0, invalid=762 iter 0, gcam->neg = 333 after 11 iterations, nbhd size=1, neg = 0 0474: dt=1.536000, rms=0.403 (2.652%), neg=0, invalid=762 0475: dt=0.000023, rms=0.403 (0.000%), neg=0, invalid=762 0476: dt=0.000023, rms=0.403 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=762 0477: dt=0.080000, rms=0.403 (0.033%), neg=0, invalid=762 0478: dt=0.016000, rms=0.403 (0.001%), neg=0, invalid=762 0479: dt=0.016000, rms=0.403 (-0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 6 minutes and 53 seconds. mri_ca_register utimesec 9593.569503 mri_ca_register stimesec 42.887405 mri_ca_register ru_maxrss 1624504 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 23852934 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 10674 mri_ca_register ru_oublock 62288 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 96583 mri_ca_register ru_nivcsw 9399 FSRUNTIME@ mri_ca_register 2.1147 hours 8 threads #-------------------------------------- #@# SubCort Seg Mon Oct 17 17:46:40 UTC 2022 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer cd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/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/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 13.51 Atlas used for the 3D morph was /opt/freesurfer/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 = 0.19857 (27) Left_Lateral_Ventricle (4): linear fit = 1.42 x + 0.0 (1817 voxels, overlap=0.186) Left_Lateral_Ventricle (4): linear fit = 1.42 x + 0.0 (1817 voxels, peak = 28), gca=28.5 gca peak = 0.17677 (13) mri peak = 0.17241 (27) Right_Lateral_Ventricle (43): linear fit = 1.88 x + 0.0 (1571 voxels, overlap=0.173) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1571 voxels, peak = 25), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.06431 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (1752 voxels, overlap=0.744) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (1752 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.06839 (101) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (1618 voxels, overlap=0.714) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (1618 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.10611 (72) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2678 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2678 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.11954 (71) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (2957 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (2957 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.09976 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (125368 voxels, overlap=0.789) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (125368 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.10117 (99) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (125899 voxels, overlap=0.735) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (125899 voxels, peak = 102), gca=102.4 gca peak = 0.09712 (58) mri peak = 0.03697 (78) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (120804 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (120804 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.03888 (76) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (114009 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (114009 voxels, peak = 77), gca=76.9 gca peak = 0.30970 (66) mri peak = 0.14268 (81) Right_Caudate (50): linear fit = 1.21 x + 0.0 (2367 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.21 x + 0.0 (2367 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.15757 (81) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2225 voxels, overlap=0.210) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2225 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.05776 (68) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (64212 voxels, overlap=0.220) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (64212 voxels, peak = 69), gca=68.6 gca peak = 0.14777 (55) mri peak = 0.05717 (71) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (64730 voxels, overlap=0.086) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (64730 voxels, peak = 70), gca=69.6 gca peak = 0.16765 (84) mri peak = 0.13945 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (15113 voxels, overlap=0.636) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (15113 voxels, peak = 87), gca=86.9 gca peak = 0.18739 (84) mri peak = 0.14967 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (14031 voxels, overlap=0.326) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (14031 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.13339 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (1475 voxels, overlap=0.044) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (1475 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.12989 (75) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (1351 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (1351 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.06566 (97) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (11529 voxels, overlap=0.284) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (11529 voxels, peak = 102), gca=102.2 gca peak = 0.11793 (83) mri peak = 0.06766 (100) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (10832 voxels, overlap=0.061) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (10832 voxels, peak = 98), gca=97.5 gca peak = 0.08324 (81) mri peak = 0.09943 (90) Left_Putamen (12): linear fit = 1.12 x + 0.0 (3435 voxels, overlap=0.292) Left_Putamen (12): linear fit = 1.12 x + 0.0 (3435 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.08277 (88) Right_Putamen (51): linear fit = 1.12 x + 0.0 (3421 voxels, overlap=0.549) Right_Putamen (51): linear fit = 1.12 x + 0.0 (3421 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.06710 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24227 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24227 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.07484 (98) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (3251 voxels, overlap=0.014) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (3251 voxels, peak = 102), gca=101.9 gca peak = 0.14500 (87) mri peak = 0.07210 (98) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (3527 voxels, overlap=0.088) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (3527 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.19952 (28) gca peak = 0.19357 (14) mri peak = 0.20549 (26) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (374 voxels, overlap=0.177) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (374 voxels, peak = 25), gca=24.7 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 Fourth_Ventricle = 0.19357 (14) 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 1.29 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 1.46 x + 0.0 Left_Pallidum too bright - rescaling by 0.963 (from 1.075) to 99.4 (was 103.2) Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 99.4 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15429 (26) mri peak = 0.19857 (27) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1817 voxels, overlap=0.732) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1817 voxels, peak = 25), gca=24.6 gca peak = 0.13981 (19) mri peak = 0.17241 (27) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (1571 voxels, overlap=0.361) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (1571 voxels, peak = 25), gca=24.6 gca peak = 0.27196 (100) mri peak = 0.06431 (103) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (1752 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (1752 voxels, peak = 102), gca=102.5 gca peak = 0.17749 (100) mri peak = 0.06839 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1618 voxels, overlap=0.754) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1618 voxels, peak = 104), gca=104.5 gca peak = 0.24466 (71) mri peak = 0.10611 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (2678 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (2678 voxels, peak = 71), gca=71.0 gca peak = 0.27388 (69) mri peak = 0.11954 (71) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (2957 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (2957 voxels, peak = 69), gca=69.0 gca peak = 0.07791 (102) mri peak = 0.09976 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (125368 voxels, overlap=0.786) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (125368 voxels, peak = 101), gca=101.5 gca peak = 0.07952 (103) mri peak = 0.10117 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (125899 voxels, overlap=0.726) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (125899 voxels, peak = 102), gca=102.5 gca peak = 0.07323 (78) mri peak = 0.03697 (78) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (120804 voxels, overlap=0.958) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (120804 voxels, peak = 77), gca=76.8 gca peak = 0.09033 (77) mri peak = 0.03888 (76) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (114009 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (114009 voxels, peak = 75), gca=75.1 gca peak = 0.22214 (80) mri peak = 0.14268 (81) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2367 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2367 voxels, peak = 80), gca=80.0 gca peak = 0.16641 (87) mri peak = 0.15757 (81) Left_Caudate (11): linear fit = 1.01 x + 0.0 (2225 voxels, overlap=0.810) Left_Caudate (11): linear fit = 1.01 x + 0.0 (2225 voxels, peak = 88), gca=88.3 gca peak = 0.11797 (68) mri peak = 0.05776 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (64212 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (64212 voxels, peak = 67), gca=67.0 gca peak = 0.12177 (69) mri peak = 0.05717 (71) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (64730 voxels, overlap=0.978) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (64730 voxels, peak = 68), gca=68.0 gca peak = 0.15881 (87) mri peak = 0.13945 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (15113 voxels, overlap=0.854) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (15113 voxels, peak = 87), gca=87.0 gca peak = 0.15254 (90) mri peak = 0.14967 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (14031 voxels, overlap=0.806) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (14031 voxels, peak = 90), gca=90.0 gca peak = 0.28754 (75) mri peak = 0.13339 (75) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (1475 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (1475 voxels, peak = 74), gca=73.9 gca peak = 0.33040 (74) mri peak = 0.12989 (75) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1351 voxels, overlap=0.997) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1351 voxels, peak = 74), gca=74.0 gca peak = 0.11232 (100) mri peak = 0.06566 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (11529 voxels, overlap=0.928) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (11529 voxels, peak = 100), gca=100.5 gca peak = 0.09359 (95) mri peak = 0.06766 (100) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (10832 voxels, overlap=0.946) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (10832 voxels, peak = 96), gca=96.4 gca peak = 0.08060 (90) mri peak = 0.09943 (90) Left_Putamen (12): linear fit = 0.99 x + 0.0 (3435 voxels, overlap=0.756) Left_Putamen (12): linear fit = 0.99 x + 0.0 (3435 voxels, peak = 89), gca=88.7 gca peak = 0.08153 (84) mri peak = 0.08277 (88) Right_Putamen (51): linear fit = 0.99 x + 0.0 (3421 voxels, overlap=0.879) Right_Putamen (51): linear fit = 0.99 x + 0.0 (3421 voxels, peak = 83), gca=82.7 gca peak = 0.07725 (86) mri peak = 0.06710 (87) Brain_Stem (16): linear fit = 1.01 x + 0.0 (24227 voxels, overlap=0.766) Brain_Stem (16): linear fit = 1.01 x + 0.0 (24227 voxels, peak = 87), gca=87.3 gca peak = 0.11748 (102) mri peak = 0.07484 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (3251 voxels, overlap=0.802) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (3251 voxels, peak = 103), gca=102.5 gca peak = 0.15351 (97) mri peak = 0.07210 (98) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (3527 voxels, overlap=0.891) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (3527 voxels, peak = 97), gca=97.5 gca peak = 0.12657 (37) mri peak = 0.19952 (28) gca peak = 0.14735 (22) mri peak = 0.20549 (26) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (374 voxels, overlap=0.540) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (374 voxels, peak = 25), gca=24.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (101) gca peak Third_Ventricle = 0.12657 (37) gca peak CSF = 0.17072 (53) gca peak Left_Accumbens_area = 0.59238 (70) gca peak Left_undetermined = 0.96707 (33) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12606 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.38123 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (45) gca peak WM_hypointensities = 0.07988 (76) gca peak non_WM_hypointensities = 0.08497 (43) gca peak Optic_Chiasm = 0.61303 (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 1.12 x + 0.0 Left_Pallidum too bright - rescaling by 0.947 (from 1.045) to 98.9 (was 104.5) Right_Pallidum too bright - rescaling by 0.965 (from 1.025) to 98.9 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 148781 voxels changed in iteration 0 of unlikely voxel relabeling 913 voxels changed in iteration 1 of unlikely voxel relabeling 41 voxels changed in iteration 2 of unlikely voxel relabeling 65 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 182149 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 617 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 123268 changed. image ll: -2.101, PF=0.500 pass 2: 42216 changed. image ll: -2.100, PF=0.500 pass 3: 13559 changed. pass 4: 5399 changed. pass 5: 2531 changed. 181821 voxels changed in iteration 0 of unlikely voxel relabeling 1462 voxels changed in iteration 1 of unlikely voxel relabeling 96 voxels changed in iteration 2 of unlikely voxel relabeling 37 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 16850 voxels changed in iteration 0 of unlikely voxel relabeling 218 voxels changed in iteration 1 of unlikely voxel relabeling 65 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 14971 voxels changed in iteration 0 of unlikely voxel relabeling 198 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 13239 voxels changed in iteration 0 of unlikely voxel relabeling 43 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 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 6907.050722 mri_ca_label stimesec 10.929302 mri_ca_label ru_maxrss 3196528 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 7508236 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 66904 mri_ca_label ru_oublock 762 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 909 mri_ca_label ru_nivcsw 3181 auto-labeling took 113 minutes and 33 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/cc_up.lta sub-03 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/cc_up.lta reading aseg from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.auto_noCCseg.mgz reading norm from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/norm.mgz 45361 voxels in left wm, 44654 in right wm, xrange [160, 167] searching rotation angles z=[-6 8], y=[-7 7] 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 global minimum found at slice 163.0, rotations (-0.36, 0.12) final transformation (x=163.0, yr=-0.362, zr=0.117): 0.99998 -0.00204 -0.00632 -33.79659; 0.00204 1.00000 -0.00001 13.66890; 0.00632 -0.00000 0.99998 -26.02684; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 114 153 eigenvectors: -0.00065 0.00317 0.99999; 0.04880 -0.99880 0.00320; 0.99881 0.04880 0.00049; writing aseg with callosum to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.auto.mgz... corpus callosum segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Mon Oct 17 19:41:13 UTC 2022 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Oct 17 19:41:13 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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... INFO: MRImask() using MRImaskDifferentGeometry() Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 747 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 110 gm peak at 82 (82), valley at 30 (30) csf peak at 42, setting threshold to 68 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 81 (81), valley at 29 (29) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 7 minutes and 26 seconds. #-------------------------------------------- #@# Mask BFS Mon Oct 17 19:48:45 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2852692 voxels in mask (pct= 8.71) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Oct 17 19:48:52 UTC 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 (103.0): 102.5 +- 6.1 [79.0 --> 125.0] GM (80.0) : 79.0 +- 9.7 [30.0 --> 95.0] setting bottom of white matter range to 88.6 setting top of gray matter range to 98.3 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... thickening thin strands.... 20 segments, 5512 filled 80 bright non-wm voxels segmented. 3189 diagonally connected voxels added... white matter segmentation took 3.1 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 0.84 minutes reading wm segmentation from wm.seg.mgz... 142 voxels added to wm to prevent paths from MTL structures to cortex 8689 additional wm voxels added 0 additional wm voxels added SEG EDIT: 70230 voxels turned on, 76785 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 93 new 93 115,126,128 old 93 new 93 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 37 found - 37 modified | TOTAL: 37 pass 2 (xy+): 0 found - 37 modified | TOTAL: 37 pass 1 (xy-): 44 found - 44 modified | TOTAL: 81 pass 2 (xy-): 0 found - 44 modified | TOTAL: 81 pass 1 (yz+): 56 found - 56 modified | TOTAL: 137 pass 2 (yz+): 0 found - 56 modified | TOTAL: 137 pass 1 (yz-): 53 found - 53 modified | TOTAL: 190 pass 2 (yz-): 0 found - 53 modified | TOTAL: 190 pass 1 (xz+): 31 found - 31 modified | TOTAL: 221 pass 2 (xz+): 0 found - 31 modified | TOTAL: 221 pass 1 (xz-): 41 found - 41 modified | TOTAL: 262 pass 2 (xz-): 0 found - 41 modified | TOTAL: 262 Iteration Number : 1 pass 1 (+++): 16 found - 16 modified | TOTAL: 16 pass 2 (+++): 0 found - 16 modified | TOTAL: 16 pass 1 (+++): 6 found - 6 modified | TOTAL: 22 pass 2 (+++): 0 found - 6 modified | TOTAL: 22 pass 1 (+++): 12 found - 12 modified | TOTAL: 34 pass 2 (+++): 0 found - 12 modified | TOTAL: 34 pass 1 (+++): 18 found - 18 modified | TOTAL: 52 pass 2 (+++): 0 found - 18 modified | TOTAL: 52 Iteration Number : 1 pass 1 (++): 62 found - 62 modified | TOTAL: 62 pass 2 (++): 0 found - 62 modified | TOTAL: 62 pass 1 (+-): 74 found - 74 modified | TOTAL: 136 pass 2 (+-): 0 found - 74 modified | TOTAL: 136 pass 1 (--): 60 found - 60 modified | TOTAL: 196 pass 2 (--): 0 found - 60 modified | TOTAL: 196 pass 1 (-+): 68 found - 68 modified | TOTAL: 264 pass 2 (-+): 0 found - 68 modified | TOTAL: 264 Iteration Number : 2 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 4 found - 4 modified | TOTAL: 12 pass 2 (xy-): 0 found - 4 modified | TOTAL: 12 pass 1 (yz+): 2 found - 2 modified | TOTAL: 14 pass 2 (yz+): 0 found - 2 modified | TOTAL: 14 pass 1 (yz-): 7 found - 7 modified | TOTAL: 21 pass 2 (yz-): 0 found - 7 modified | TOTAL: 21 pass 1 (xz+): 5 found - 5 modified | TOTAL: 26 pass 2 (xz+): 0 found - 5 modified | TOTAL: 26 pass 1 (xz-): 0 found - 0 modified | TOTAL: 26 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 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 3 found - 3 modified | TOTAL: 5 pass 2 (--): 0 found - 3 modified | TOTAL: 5 pass 1 (-+): 1 found - 1 modified | TOTAL: 6 pass 2 (-+): 0 found - 1 modified | TOTAL: 6 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 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 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 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 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 4 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 : 4 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 : 4 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 = 614 (out of 1120745: 0.054785) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Oct 17 19:52:56 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 1.04080 -0.03521 -0.00376 -7.25793; 0.03101 1.12817 0.02456 -12.02107; -0.00207 -0.00600 0.98359 -31.05128; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04080 -0.03521 -0.00376 -7.25793; 0.03101 1.12817 0.02456 -12.02107; -0.00207 -0.00600 0.98359 -31.05128; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (546, 2188) area[0] = 1441 (min = 546, max = 2188), aspect = 0.47 (min = 0.10, max = 0.75) no need to search using seed (156, 142, 183), TAL = (3.2, 18.4, 14.4) talairach voxel to voxel transform 0.95991 0.02997 0.00292 7.41797; -0.02643 0.88545 -0.02221 9.76259; 0.00185 0.00546 1.01655 31.64444; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (156, 142, 183) --> (3.2, 18.4, 14.4) done. writing output to filled.mgz... filling took 1.3 minutes talairach cc position changed to (3.20, 18.40, 14.40) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(21.20, 18.40, 14.40) SRC: (140.36, 127.90, 218.70) search lh wm seed point around talairach space (-14.80, 18.40, 14.40), SRC: (183.55, 126.71, 218.78) 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 ... Started at Mon Oct 17 15:30:36 UTC 2022 Ended at Mon Oct 17 19:54:18 UTC 2022 #@#%# recon-all-run-time-hours 4.395 recon-all -s sub-03 finished without error at Mon Oct 17 19:54:18 UTC 2022 New invocation of recon-all Tue Oct 18 00:17:32 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -parallel -subjid sub-03 -sd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer -T2pial -cortribbon subjid sub-03 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux bc11910.int.ets1.calculquebec.ca 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 unlimited coredumpsize unlimited memoryuse 33554432 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767717 maxlocks unlimited maxsignal 767717 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638244 52606632 79124312 2720992 64907300 134538216 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-00:17:33-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Oct 18 00:17:33 UTC 2022 bbregister --s sub-03 --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --lta /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --init-coreg --T2 tmp /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966 Log file is /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.log Tue Oct 18 00:17:33 UTC 2022 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer cd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/scripts /opt/freesurfer/bin/bbregister --s sub-03 --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --lta /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux bc11910.int.ets1.calculquebec.ca 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 mri_convert /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii mri_convert.bin /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz... TR=3200.00, 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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii... mri_coreg --s sub-03 --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --regdat /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.init.dat --reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/mri_coreg.lta --nthreads 4 --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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/scripts cmdline mri_coreg --s sub-03 --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --regdat /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.init.dat --reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard 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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii Reading in ref /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -3.3883 20.1945 -15.5022 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 4 movsat = 3432.0000 mov gstd 1.9140 1.9140 1.9140 Smoothing mov refsat = 114.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0303121134 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -3.38825; 0.00000 1.00000 0.00000 20.19454; 0.00000 0.00000 1.00000 -15.50219; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -1.00000 0.00000 0.00000 262.99997; 0.00000 0.00000 1.00000 -9.99998; 0.00000 -1.00000 0.00000 318.99994; 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 -1.38825 2.19454 -9.50219 0.00000 0.00000 0.00000 -1.0368477 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0433776379 #@# 4 188 -1.38825 2.19454 -9.50219 0.00000 0.00000 0.00000 -1.0433776 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.043378 #@# 4 194 -1.00629 2.19454 -9.50219 0.00000 0.00000 0.00000 -1.0434244 #@# 4 196 -1.04923 2.19454 -9.50219 0.00000 0.00000 0.00000 -1.0434248 #@# 4 203 -1.03865 1.57651 -9.50219 0.00000 0.00000 0.00000 -1.0434480 #@# 4 205 -1.03865 1.78458 -9.50219 0.00000 0.00000 0.00000 -1.0434575 #@# 4 216 -1.03865 1.81458 -10.12022 0.00000 0.00000 0.00000 -1.0435603 #@# 4 218 -1.03865 1.81458 -10.18130 0.00000 0.00000 0.00000 -1.0435613 #@# 4 219 -1.03865 1.81458 -10.19130 0.00000 0.00000 0.00000 -1.0435615 #@# 4 240 -1.03865 1.81458 -10.20805 0.03984 -0.61803 0.00000 -1.0435718 #@# 4 242 -1.03865 1.81458 -10.20805 0.03984 -0.37337 0.00000 -1.0435799 #@# 4 243 -1.03865 1.81458 -10.20805 0.03984 -0.36337 0.00000 -1.0435802 #@# 4 251 -1.03865 1.81458 -10.20805 0.03984 -0.36337 -0.61803 -1.0435895 #@# 4 253 -1.03865 1.81458 -10.20805 0.03984 -0.36337 -0.35692 -1.0436018 powell nthiter 1: fret = -1.043602 #@# 4 264 -0.89919 1.81458 -10.20805 0.03984 -0.36337 -0.35692 -1.0436144 #@# 4 274 -0.88517 1.78586 -10.20805 0.03984 -0.36337 -0.35692 -1.0436145 #@# 4 283 -0.88517 1.79586 -10.22881 0.03984 -0.36337 -0.35692 -1.0436146 #@# 4 306 -0.88517 1.79586 -10.22881 0.01063 -0.41686 -0.35692 -1.0436149 #@# 4 320 -0.88517 1.79586 -10.22881 0.01063 -0.44832 -0.38962 -1.0436151 Powell done niters total = 1 OptTimeSec 9.6 sec OptTimeMin 0.16 min nEvals 322 Final parameters -0.88516814 1.79585552 -10.22881031 0.01062789 -0.44831696 -0.38962057 Final cost -1.043615122079999 --------------------------------- mri_coreg utimesec 239.942068 mri_coreg stimesec 2.093193 mri_coreg ru_maxrss 817336 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 1274099 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 166476 mri_coreg ru_oublock 4 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 334 mri_coreg ru_nivcsw 338 Final RefRAS-to-MovRAS 0.99995 -0.00680 -0.00782 -0.88517; 0.00680 0.99998 0.00019 1.79586; 0.00782 -0.00024 0.99997 -10.22881; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99995 0.00782 -0.00680 265.99564; -0.00680 -0.00019 0.99998 -31.84742; -0.00782 -0.99997 -0.00024 326.91159; 0.00000 0.00000 0.00000 1.00000; Final parameters -0.8852 1.7959 -10.2288 0.0106 -0.4483 -0.3896 nhits = 290870 out of 32768000, Percent Overlap: 56.8 mri_coreg RunTimeSec 93.6 sec To check run: tkregisterfv --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --targ /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/brainmask.mgz --reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/mri_coreg.lta --s sub-03 --surfs mri_coreg done mri_segreg --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --init-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.init.dat --out-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer cd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/scripts mri_segreg --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --init-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.init.dat --out-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii regfile /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.init.dat subject sub-03 dof 6 outregfile /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 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 1666085418 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99995 0.00680 0.00782 -1.73454; 0.00782 -0.00024 0.99997 4.50133; -0.00680 -0.99998 -0.00019 18.37526; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.998298 1 -25.0 -25.0 25.0 0.983439 2 -25.0 25.0 -25.0 0.996758 3 -25.0 25.0 25.0 0.991746 4 25.0 -25.0 -25.0 0.971435 5 25.0 -25.0 25.0 0.968026 6 25.0 25.0 -25.0 0.976409 7 25.0 25.0 25.0 0.993897 REL: 8 0.441819 7.880007 0.985001 rel = 0.448547 Initial costs ---------------- Number of surface hits 4562 WM Intensity 846.7877 +/- 287.2157 Ctx Intensity 1059.1023 +/- 383.7819 Pct Contrast 21.3287 +/- 28.6837 Cost 0.4418 RelCost 0.4485 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9050 0.9050 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9039 0.9039 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.8939 0.8939 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8287 0.8287 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.7604 0.7604 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7155 0.7155 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6890 0.6890 0.0 265 0.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.6878 0.6878 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5053 0.5053 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4418 0.4418 0.0 Brute Force -------------------------- Min cost was 0.441819 Number of iterations 729 Search time 2.104000 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 = 0.441819 6 0.382 0.000 0.000 0.000 0.000 0.000 0.4387242993 7 0.303 0.000 0.000 0.000 0.000 0.000 0.4374961009 8 0.243 0.000 0.000 0.000 0.000 0.000 0.4365435566 10 0.234 0.000 0.000 0.000 0.000 0.000 0.4365114822 11 0.228 0.000 0.000 0.000 0.000 0.000 0.4365089969 12 0.230 0.000 0.000 0.000 0.000 0.000 0.4365044857 17 0.230 -1.618 0.000 0.000 0.000 0.000 0.1371022016 22 0.230 -1.946 0.000 0.000 0.000 0.000 0.1251072799 23 0.230 -1.956 0.000 0.000 0.000 0.000 0.1249964563 24 0.230 -2.026 0.000 0.000 0.000 0.000 0.1237293432 27 0.230 -2.045 0.000 0.000 0.000 0.000 0.1236967030 28 0.230 -2.042 0.000 0.000 0.000 0.000 0.1236735269 29 0.230 -2.037 0.000 0.000 0.000 0.000 0.1236622501 37 0.230 -2.037 0.382 0.000 0.000 0.000 0.1134096642 38 0.230 -2.037 0.381 0.000 0.000 0.000 0.1133978709 40 0.230 -2.037 0.364 0.000 0.000 0.000 0.1133705746 41 0.230 -2.037 0.370 0.000 0.000 0.000 0.1133627641 42 0.230 -2.037 0.369 0.000 0.000 0.000 0.1133621407 49 0.230 -2.037 0.369 0.382 0.000 0.000 0.0878218062 55 0.230 -2.037 0.369 0.387 0.000 0.000 0.0878125621 65 0.230 -2.037 0.369 0.387 -0.054 0.000 0.0872572010 66 0.230 -2.037 0.369 0.387 -0.084 0.000 0.0867315971 68 0.230 -2.037 0.369 0.387 -0.162 0.000 0.0860841977 71 0.230 -2.037 0.369 0.387 -0.155 0.000 0.0860615661 80 0.230 -2.037 0.369 0.387 -0.155 0.098 0.0849569537 81 0.230 -2.037 0.369 0.387 -0.155 0.107 0.0849220331 82 0.230 -2.037 0.369 0.387 -0.155 0.136 0.0848647020 83 0.230 -2.037 0.369 0.387 -0.155 0.137 0.0848646331 84 0.230 -2.037 0.369 0.387 -0.155 0.138 0.0848639021 powell nthiter 1: fret = 0.084864 102 0.229 -2.037 0.369 0.387 -0.155 0.138 0.0848633588 109 0.229 -1.655 0.369 0.387 -0.155 0.138 0.0745836617 110 0.229 -1.751 0.369 0.387 -0.155 0.138 0.0721287513 111 0.229 -1.773 0.369 0.387 -0.155 0.138 0.0719703989 113 0.229 -1.767 0.369 0.387 -0.155 0.138 0.0719445792 114 0.229 -1.766 0.369 0.387 -0.155 0.138 0.0719440456 120 0.229 -1.766 -0.249 0.387 -0.155 0.138 0.0684981365 122 0.229 -1.766 0.033 0.387 -0.155 0.138 0.0594234567 123 0.229 -1.766 0.035 0.387 -0.155 0.138 0.0593974677 125 0.229 -1.766 0.062 0.387 -0.155 0.138 0.0591233932 126 0.229 -1.766 0.079 0.387 -0.155 0.138 0.0591058009 127 0.229 -1.766 0.073 0.387 -0.155 0.138 0.0590936573 128 0.229 -1.766 0.072 0.387 -0.155 0.138 0.0590933183 135 0.229 -1.766 0.072 0.769 -0.155 0.138 0.0532581409 136 0.229 -1.766 0.072 0.622 -0.155 0.138 0.0491172604 137 0.229 -1.766 0.072 0.620 -0.155 0.138 0.0491090181 139 0.229 -1.766 0.072 0.616 -0.155 0.138 0.0490996256 140 0.229 -1.766 0.072 0.615 -0.155 0.138 0.0490984595 148 0.229 -1.766 0.072 0.615 -0.044 0.138 0.0483751776 149 0.229 -1.766 0.072 0.615 -0.063 0.138 0.0480791578 150 0.229 -1.766 0.072 0.615 -0.086 0.138 0.0479776985 151 0.229 -1.766 0.072 0.615 -0.083 0.138 0.0479734273 152 0.229 -1.766 0.072 0.615 -0.082 0.138 0.0479732464 161 0.229 -1.766 0.072 0.615 -0.082 0.137 0.0479686942 162 0.229 -1.766 0.072 0.615 -0.082 0.126 0.0479483837 164 0.229 -1.766 0.072 0.615 -0.082 0.127 0.0479481505 166 0.228 -1.496 -0.225 0.842 -0.009 0.117 0.0421125383 powell nthiter 2: fret = 0.047948 205 0.101 -1.705 -0.156 0.615 -0.082 0.127 0.0412759175 206 0.101 -1.705 -0.132 0.615 -0.082 0.127 0.0409308735 208 0.101 -1.705 -0.120 0.615 -0.082 0.127 0.0408619606 209 0.101 -1.705 -0.117 0.615 -0.082 0.127 0.0408603512 218 0.101 -1.705 -0.117 0.741 -0.082 0.127 0.0393837003 221 0.101 -1.705 -0.117 0.736 -0.082 0.127 0.0393827202 222 0.101 -1.705 -0.117 0.738 -0.082 0.127 0.0393822263 232 0.101 -1.705 -0.117 0.738 -0.134 0.127 0.0390672588 233 0.101 -1.705 -0.117 0.738 -0.136 0.127 0.0390647778 236 0.101 -1.705 -0.117 0.738 -0.137 0.127 0.0390640371 237 0.101 -1.705 -0.117 0.738 -0.138 0.127 0.0390640318 244 0.101 -1.705 -0.117 0.738 -0.138 -0.012 0.0390200024 245 0.101 -1.705 -0.117 0.738 -0.138 0.056 0.0386270333 246 0.101 -1.705 -0.117 0.738 -0.138 0.057 0.0386241393 247 0.101 -1.705 -0.117 0.738 -0.138 0.089 0.0385978969 249 0.101 -1.705 -0.117 0.738 -0.138 0.079 0.0385655628 250 0.101 -1.705 -0.117 0.738 -0.138 0.075 0.0385615033 powell nthiter 3: fret = 0.038562 262 0.093 -1.705 -0.117 0.738 -0.138 0.075 0.0385093469 263 0.085 -1.705 -0.117 0.738 -0.138 0.075 0.0384805466 265 0.082 -1.705 -0.117 0.738 -0.138 0.075 0.0384791236 266 0.083 -1.705 -0.117 0.738 -0.138 0.075 0.0384789550 275 0.083 -1.767 -0.117 0.738 -0.138 0.075 0.0384413463 276 0.083 -1.737 -0.117 0.738 -0.138 0.075 0.0381579103 278 0.083 -1.740 -0.117 0.738 -0.138 0.075 0.0381509107 281 0.083 -1.742 -0.117 0.738 -0.138 0.075 0.0381496406 289 0.083 -1.742 -0.272 0.738 -0.138 0.075 0.0378590674 290 0.083 -1.742 -0.205 0.738 -0.138 0.075 0.0374595678 291 0.083 -1.742 -0.206 0.738 -0.138 0.075 0.0374580703 292 0.083 -1.742 -0.212 0.738 -0.138 0.075 0.0374564636 293 0.083 -1.742 -0.235 0.738 -0.138 0.075 0.0374514633 295 0.083 -1.742 -0.227 0.738 -0.138 0.075 0.0374461867 296 0.083 -1.742 -0.226 0.738 -0.138 0.075 0.0374453340 297 0.083 -1.742 -0.220 0.738 -0.138 0.075 0.0374409463 312 0.083 -1.742 -0.220 0.736 -0.138 0.075 0.0374376732 321 0.083 -1.742 -0.220 0.736 -0.060 0.075 0.0371004566 324 0.083 -1.742 -0.220 0.736 -0.062 0.075 0.0370983118 325 0.083 -1.742 -0.220 0.736 -0.064 0.075 0.0370967771 334 0.083 -1.742 -0.220 0.736 -0.064 0.001 0.0361545204 336 0.083 -1.742 -0.220 0.736 -0.064 0.002 0.0361542265 337 0.083 -1.742 -0.220 0.736 -0.064 0.003 0.0361541636 powell nthiter 4: fret = 0.036154 351 0.080 -1.742 -0.220 0.736 -0.064 0.003 0.0361511963 352 0.079 -1.742 -0.220 0.736 -0.064 0.003 0.0361507294 362 0.079 -1.751 -0.220 0.736 -0.064 0.003 0.0360878783 364 0.079 -1.755 -0.220 0.736 -0.064 0.003 0.0360825647 373 0.079 -1.755 -0.248 0.736 -0.064 0.003 0.0359269991 374 0.079 -1.755 -0.261 0.736 -0.064 0.003 0.0358785116 378 0.079 -1.755 -0.259 0.736 -0.064 0.003 0.0358779804 386 0.079 -1.755 -0.259 0.810 -0.064 0.003 0.0356588027 387 0.079 -1.755 -0.259 0.782 -0.064 0.003 0.0354831417 388 0.079 -1.755 -0.259 0.780 -0.064 0.003 0.0354628070 390 0.079 -1.755 -0.259 0.774 -0.064 0.003 0.0354357778 402 0.079 -1.755 -0.259 0.774 -0.078 0.003 0.0353582692 403 0.079 -1.755 -0.259 0.774 -0.080 0.003 0.0353580393 411 0.079 -1.755 -0.259 0.774 -0.080 -0.001 0.0353093328 413 0.079 -1.755 -0.259 0.774 -0.080 -0.032 0.0352175646 414 0.079 -1.755 -0.259 0.774 -0.080 -0.023 0.0351928586 powell nthiter 5: fret = 0.035193 427 0.069 -1.755 -0.259 0.774 -0.080 -0.023 0.0351764722 428 0.071 -1.755 -0.259 0.774 -0.080 -0.023 0.0351724952 429 0.073 -1.755 -0.259 0.774 -0.080 -0.023 0.0351716461 440 0.073 -1.754 -0.259 0.774 -0.080 -0.023 0.0351703170 441 0.073 -1.753 -0.259 0.774 -0.080 -0.023 0.0351692253 450 0.073 -1.753 -0.284 0.774 -0.080 -0.023 0.0350612332 451 0.073 -1.753 -0.291 0.774 -0.080 -0.023 0.0349938668 454 0.073 -1.753 -0.324 0.774 -0.080 -0.023 0.0349927029 455 0.073 -1.753 -0.308 0.774 -0.080 -0.023 0.0348907878 457 0.073 -1.753 -0.309 0.774 -0.080 -0.023 0.0348897029 472 0.073 -1.753 -0.309 0.783 -0.080 -0.023 0.0348682856 473 0.073 -1.753 -0.309 0.780 -0.080 -0.023 0.0348649712 484 0.073 -1.753 -0.309 0.780 -0.095 -0.023 0.0348545826 485 0.073 -1.753 -0.309 0.780 -0.092 -0.023 0.0348473860 486 0.073 -1.753 -0.309 0.780 -0.089 -0.023 0.0348452848 487 0.073 -1.753 -0.309 0.780 -0.090 -0.023 0.0348451460 497 0.073 -1.753 -0.309 0.780 -0.090 -0.044 0.0347726860 498 0.073 -1.753 -0.309 0.780 -0.090 -0.045 0.0347717026 500 0.073 -1.753 -0.309 0.780 -0.090 -0.046 0.0347716798 501 0.073 -1.753 -0.309 0.780 -0.090 -0.047 0.0347716134 powell nthiter 6: fret = 0.034772 512 0.056 -1.753 -0.309 0.780 -0.090 -0.047 0.0347602900 513 0.062 -1.753 -0.309 0.780 -0.090 -0.047 0.0347531730 524 0.062 -1.729 -0.309 0.780 -0.090 -0.047 0.0346294933 526 0.062 -1.732 -0.309 0.780 -0.090 -0.047 0.0346230967 527 0.062 -1.733 -0.309 0.780 -0.090 -0.047 0.0346225498 537 0.062 -1.733 -0.315 0.780 -0.090 -0.047 0.0346104169 538 0.062 -1.733 -0.314 0.780 -0.090 -0.047 0.0346099717 549 0.062 -1.733 -0.314 0.782 -0.090 -0.047 0.0346063991 550 0.062 -1.733 -0.314 0.783 -0.090 -0.047 0.0346062735 561 0.062 -1.733 -0.314 0.783 -0.093 -0.047 0.0346051261 572 0.062 -1.733 -0.314 0.783 -0.093 -0.056 0.0345988171 576 0.051 -1.714 -0.319 0.786 -0.095 -0.065 0.0345926756 582 0.055 -1.721 -0.317 0.785 -0.094 -0.062 0.0345739642 584 0.055 -1.721 -0.317 0.785 -0.094 -0.062 0.0345739186 587 0.055 -1.721 -0.317 0.785 -0.094 -0.062 0.0345737974 powell nthiter 7: fret = 0.034574 601 0.053 -1.721 -0.317 0.785 -0.094 -0.062 0.0345727928 612 0.053 -1.721 -0.317 0.785 -0.094 -0.063 0.0345685500 613 0.053 -1.721 -0.317 0.785 -0.094 -0.068 0.0345612741 626 0.053 -1.721 -0.318 0.785 -0.094 -0.068 0.0345611273 636 0.053 -1.721 -0.318 0.783 -0.094 -0.068 0.0345606033 638 0.053 -1.721 -0.318 0.784 -0.094 -0.068 0.0345598562 648 0.053 -1.721 -0.318 0.784 -0.093 -0.068 0.0345593428 656 0.054 -1.723 -0.318 0.783 -0.093 -0.068 0.0345569052 658 0.054 -1.723 -0.318 0.783 -0.093 -0.067 0.0345567883 660 0.054 -1.724 -0.318 0.783 -0.093 -0.067 0.0345565459 powell nthiter 8: fret = 0.034557 678 0.051 -1.724 -0.318 0.783 -0.093 -0.067 0.0345544615 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 1.001792 1 -25.0 -25.0 25.0 0.973533 2 -25.0 25.0 -25.0 0.984127 3 -25.0 25.0 25.0 1.020127 4 25.0 -25.0 -25.0 0.973650 5 25.0 -25.0 25.0 0.967169 6 25.0 25.0 -25.0 0.972806 7 25.0 25.0 25.0 0.976284 REL: 8 0.034554 7.869488 0.983686 rel = 0.0351275 Number of iterations 8 Min cost was 0.034554 Number of FunctionCalls 737 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.037000 sec Parameters at optimum (transmm) 0.05121 -1.72354 -0.31766 Parameters at optimum (rotdeg) 0.78325 -0.09257 -0.06716 Final costs ---------------- Number of surface hits 4562 WM Intensity 773.9952 +/- 235.1026 Ctx Intensity 1052.7264 +/- 271.1265 Pct Contrast 31.5442 +/- 15.2769 Cost 0.0346 RelCost 0.4485 Reg at min cost was -0.99992 0.00843 0.00897 -1.70812; 0.00909 0.01342 0.99987 2.52825; -0.00831 -0.99987 0.01350 18.11458; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat, type = 14 Original Reg -0.99995 0.00680 0.00782 -1.73454; 0.00782 -0.00024 0.99997 4.50133; -0.00680 -0.99998 -0.00019 18.37526; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00002 -0.00163 -0.00115 -0.02642; -0.00126 -0.01366 0.00010 1.97308; 0.00151 -0.00010 -0.01368 0.26068; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.985087 Computing change in rh position Surface-RMS-Diff-mm 1.970562 0.544658 2.995994 mri_segreg done mri_segreg --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --init-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat --out-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.curopt.dat --gm-proj-frac 0.5 --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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer cd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/scripts mri_segreg --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii --init-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat --out-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/template.nii regfile /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.136966/bbr.pass1.dat subject sub-03 dof 6 outregfile /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 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 1666202877 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99992 0.00843 0.00897 -1.70812; 0.00909 0.01342 0.99987 2.52825; -0.00831 -0.99987 0.01350 18.11458; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.999007 1 -25.0 -25.0 25.0 0.971153 2 -25.0 25.0 -25.0 0.976815 3 -25.0 25.0 25.0 0.998037 4 25.0 -25.0 -25.0 0.963582 5 25.0 -25.0 25.0 0.979981 6 25.0 25.0 -25.0 0.975957 7 25.0 25.0 25.0 0.975333 REL: 8 0.037836 7.839864 0.979983 rel = 0.0386086 Initial costs ---------------- Number of surface hits 455732 WM Intensity 773.9948 +/- 232.2607 Ctx Intensity 1050.8976 +/- 268.2923 Pct Contrast 31.3454 +/- 15.1020 Cost 0.0378 RelCost 0.0386 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0482 0.0482 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0477 0.0477 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0461 0.0461 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0456 0.0456 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0437 0.0437 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0429 0.0429 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0405 0.0405 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0402 0.0402 0.0 16 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0399 0.0399 0.0 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.0393 0.0393 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.0383 0.0383 0.0 25 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.0000 0.0383 0.0383 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0380 0.0380 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0372 0.0372 0.0 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.0370 0.0370 0.0 102 -0.1000 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.0366 0.0366 0.0 103 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.0365 0.0365 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0361 0.0361 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0360 0.0360 0.0 187 -0.1000 0.1000 -0.1000 0.1000 0.1000 0.0000 0.0358 0.0358 0.0 286 0.0000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0357 0.0357 0.0 295 0.0000 -0.1000 0.0000 0.1000 0.1000 0.0000 0.0350 0.0350 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0346 0.0346 0.0 Brute Force -------------------------- Min cost was 0.034554 Number of iterations 729 Search time 2.018000 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 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.037836 7 0.072 0.000 0.000 0.000 0.000 0.000 0.0376054562 8 0.054 0.000 0.000 0.000 0.000 0.000 0.0375722180 17 0.054 0.057 0.000 0.000 0.000 0.000 0.0373948049 18 0.054 0.041 0.000 0.000 0.000 0.000 0.0373699998 19 0.054 0.042 0.000 0.000 0.000 0.000 0.0373695743 20 0.054 0.043 0.000 0.000 0.000 0.000 0.0373694571 28 0.054 0.043 0.066 0.000 0.000 0.000 0.0370148813 30 0.054 0.043 0.067 0.000 0.000 0.000 0.0370148277 38 0.054 0.043 0.067 0.070 0.000 0.000 0.0362159554 40 0.054 0.043 0.067 0.071 0.000 0.000 0.0362156634 49 0.054 0.043 0.067 0.071 0.041 0.000 0.0361314767 50 0.054 0.043 0.067 0.071 0.031 0.000 0.0361260154 51 0.054 0.043 0.067 0.071 0.033 0.000 0.0361256772 59 0.054 0.043 0.067 0.071 0.033 0.060 0.0357452914 60 0.054 0.043 0.067 0.071 0.033 0.064 0.0357434625 61 0.054 0.043 0.067 0.071 0.033 0.065 0.0357434595 powell nthiter 1: fret = 0.035743 70 0.097 0.043 0.067 0.071 0.033 0.065 0.0356486444 71 0.087 0.043 0.067 0.071 0.033 0.065 0.0356436246 72 0.089 0.043 0.067 0.071 0.033 0.065 0.0356433671 82 0.089 0.040 0.067 0.071 0.033 0.065 0.0356420780 91 0.089 0.040 0.009 0.071 0.033 0.065 0.0353773552 92 0.089 0.040 0.016 0.071 0.033 0.065 0.0353763065 93 0.089 0.040 0.013 0.071 0.033 0.065 0.0353754725 102 0.089 0.040 0.013 0.091 0.033 0.065 0.0352539395 103 0.089 0.040 0.013 0.098 0.033 0.065 0.0352406178 104 0.089 0.040 0.013 0.101 0.033 0.065 0.0352392651 108 0.089 0.040 0.013 0.102 0.033 0.065 0.0352390685 117 0.089 0.040 0.013 0.102 0.034 0.065 0.0352390501 125 0.089 0.040 0.013 0.102 0.034 0.072 0.0352176105 126 0.089 0.040 0.013 0.102 0.034 0.083 0.0352025008 127 0.089 0.040 0.013 0.102 0.034 0.085 0.0352024980 powell nthiter 2: fret = 0.035202 136 0.107 0.040 0.013 0.102 0.034 0.085 0.0351863077 137 0.103 0.040 0.013 0.102 0.034 0.085 0.0351831214 138 0.102 0.040 0.013 0.102 0.034 0.085 0.0351831018 156 0.102 0.040 -0.013 0.102 0.034 0.085 0.0351304376 158 0.102 0.040 -0.012 0.102 0.034 0.085 0.0351301182 166 0.102 0.040 -0.012 0.103 0.034 0.085 0.0351273894 167 0.102 0.040 -0.012 0.110 0.034 0.085 0.0351171174 169 0.102 0.040 -0.012 0.111 0.034 0.085 0.0351166741 186 0.102 0.040 -0.012 0.111 0.034 0.090 0.0351138344 187 0.102 0.040 -0.012 0.111 0.034 0.089 0.0351137711 powell nthiter 3: fret = 0.035114 197 0.103 0.040 -0.012 0.111 0.034 0.089 0.0351133941 198 0.104 0.040 -0.012 0.111 0.034 0.089 0.0351133768 208 0.104 0.041 -0.012 0.111 0.034 0.089 0.0351133490 216 0.104 0.041 -0.019 0.111 0.034 0.089 0.0351123787 217 0.104 0.041 -0.016 0.111 0.034 0.089 0.0351117036 227 0.104 0.041 -0.016 0.112 0.034 0.089 0.0351114030 228 0.104 0.041 -0.016 0.113 0.034 0.089 0.0351112984 237 0.104 0.041 -0.016 0.113 0.035 0.089 0.0351112346 246 0.104 0.041 -0.016 0.113 0.035 0.091 0.0351110122 248 0.104 0.041 -0.016 0.113 0.035 0.090 0.0351109798 powell nthiter 4: fret = 0.035111 276 0.104 0.041 -0.017 0.113 0.035 0.090 0.0351109127 powell nthiter 5: fret = 0.035111 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.999976 1 -25.0 -25.0 25.0 0.970828 2 -25.0 25.0 -25.0 0.977314 3 -25.0 25.0 25.0 0.996839 4 25.0 -25.0 -25.0 0.963863 5 25.0 -25.0 25.0 0.979585 6 25.0 25.0 -25.0 0.975510 7 25.0 25.0 25.0 0.976323 REL: 8 0.035111 7.840238 0.980030 rel = 0.0358264 Number of iterations 5 Min cost was 0.035111 Number of FunctionCalls 359 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 47.729000 sec Parameters at optimum (transmm) 0.10397 0.04097 -0.01725 Parameters at optimum (rotdeg) 0.11336 0.03467 0.09028 Final costs ---------------- Number of surface hits 455732 WM Intensity 773.8652 +/- 231.7893 Ctx Intensity 1050.7416 +/- 267.3896 Pct Contrast 31.3524 +/- 15.0596 Cost 0.0351 RelCost 0.0386 Reg at min cost was -0.99994 0.00780 0.00741 -1.59711; 0.00753 0.01541 0.99985 2.53069; -0.00769 -0.99985 0.01547 18.10333; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99992 0.00843 0.00897 -1.70812; 0.00909 0.01342 0.99987 2.52825; -0.00831 -0.99987 0.01350 18.11458; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00002 0.00063 0.00157 -0.11101; 0.00156 -0.00199 0.00002 -0.00244; -0.00062 -0.00002 -0.00197 0.01125; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.135910 Computing change in rh position Surface-RMS-Diff-mm 0.137773 0.034867 0.236160 mri_segreg done MinCost: 0.035111 773.865180 1050.741552 31.352367 tkregister2_cmdl --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --noedit --ltaout /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta tkregister_tcl /opt/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz reg file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/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 -------- -0.99994 0.00780 0.00741 -1.59711; 0.00753 0.01541 0.99985 2.53069; -0.00769 -0.99985 0.01547 18.10333; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. 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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz Tmov: -------------------- -0.80000 0.00000 0.00000 83.20000; 0.00000 0.00000 0.80000 -128.00000; 0.00000 -0.80000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.99994 0.00780 0.00741 -1.59711; 0.00753 0.01541 0.99985 2.53069; -0.00769 -0.99985 0.01547 18.10333; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-03 RegMat --------------------------- -0.99994 0.00780 0.00741 -1.59711; 0.00753 0.01541 0.99985 2.53069; -0.00769 -0.99985 0.01547 18.10333; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Oct 18 00:17:33 UTC 2022 Ended at Tue Oct 18 00:20:28 UTC 2022 BBR-Run-Time-Sec 175 bbregister Done To check results, run: tkregisterfv --mov /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --reg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --surfs cp /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta mri_convert -odt float -at /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta -rl /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz mri_convert.bin -odt float -at /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta -rl /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz... TR=3200.00, 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) INFO: Reading transformation from file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/orig.mgz... INFO: Applying transformation from file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99994 0.00769 0.00753 1.09595; -0.00780 0.99985 0.01541 -1.80430; -0.00741 -0.01547 0.99985 12.23920; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz... mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.presurf.mgz -surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.white identity.nofile -surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.white identity.nofile /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.norm.mgz using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz... computing distance transform computing distance transform 87122 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 writing normalized volume to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.norm.mgz mri_mask /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.norm.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/brainmask.mgz /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.mgz DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/T2.mgz...done. /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/scripts cp -v /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.woT2.pial '/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial' -> '/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-03 lh /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/scripts cp -v /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.woT2.pial '/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial' -> '/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-03 rh Waiting for PID 140641 of (140641 140644) to complete... Waiting for PID 140644 of (140641 140644) to complete... mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-03 lh reading previously compute gray/white surface refining pial surfaces placement using T2 volume ../mri/T2 using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 5.00 sigmas below the mean (default=2) using white starting white location... using woT2.pial starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/filled.mgz... reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/wm.mgz... 31305 bright wm thresholded. 103 bright non-wm voxels segmented. reading original surface position from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.orig... computing class statistics... border white: 483206 voxels (1.47%) border gray 497210 voxels (1.52%) WM (103.0): 102.5 +- 6.1 [70.0 --> 110.0] GM (84.0) : 83.1 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.9 (was 70) setting MAX_BORDER_WHITE to 114.1 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 59.8 (was 40) setting MAX_GRAY to 101.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.6 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=108+-2.6, GM=78+-7.0 mean inside = 100.9, mean outside = 85.0 reading initial white vertex positions from white... 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 white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 70 points - only 0.00% unknown deleting segment 1 with 15 points - only 0.00% unknown deleting segment 2 with 24 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 124 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 7 points - only 0.00% unknown deleting segment 18 with 30 points - only 0.00% unknown deleting segment 19 with 19 points - only 0.00% unknown deleting segment 21 with 20 points - only 0.00% unknown deleting segment 22 with 9 points - only 0.00% unknown deleting segment 23 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 24 with 3 points - only 0.00% unknown deleting segment 25 with 5 points - only 0.00% unknown deleting segment 26 with 10 points - only 0.00% unknorepositioning cortical surface to gray/csf boundary. wn deleting segment 27 with 25 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 28 with 3 points - only 0.00% unknown deleting segment 29 with 20 points - only 0.00% unknown reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (box.dx, box.dy, box.dz) = (169, smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) locating cortical regions not in the range [69.50 210.20], gm=170.00+-20.10, and vertices in regions > 159.9 198954 surface locations found to contain inconsistent values (35826 in, 163128 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.156, l_nspring=0.063, 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=163035.1, rms=0.366 001: dt: 0.0500, sse=163044.7, rms=0.366 (0.155%) 002: dt: 0.0500, sse=163050.2, rms=0.365 (0.174%) 003: dt: 0.0500, sse=163055.7, rms=0.365 (0.170%) 004: dt: 0.0500, sse=163060.5, rms=0.364 (0.168%) 005: dt: 0.0500, sse=163065.4, rms=0.363 (0.166%) 006: dt: 0.0500, sse=163070.1, rms=0.363 (0.165%) 007: dt: 0.0500, sse=163074.7, rms=0.362 (0.164%) 008: dt: 0.0500, sse=163079.0, rms=0.362 (0.163%) 009: dt: 0.0500, sse=163083.2, rms=0.361 (0.161%) 010: dt: 0.0500, sse=163087.2, rms=0.360 (0.160%) positioning took 2.1 minutes tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=162637.4, rms=0.360 011: dt: 0.0500, sse=162641.2, rms=0.360 (0.159%) 012: dt: 0.0500, sse=162645.0, rms=0.359 (0.158%) 013: dt: 0.0500, sse=162648.6, rms=0.359 (0.157%) 014: dt: 0.0500, sse=162652.1, rms=0.358 (0.156%) 015: dt: 0.0500, sse=162655.6, rms=0.358 (0.155%) 016: dt: 0.0500, sse=162658.9, rms=0.357 (0.154%) 017: dt: 0.0500, sse=162662.1, rms=0.357 (0.152%) 018: dt: 0.0500, sse=162665.2, rms=0.356 (0.151%) 019: dt: 0.0500, sse=162668.1, rms=0.355 (0.150%) 020: dt: 0.0500, sse=162671.0, rms=0.355 (0.149%) positioning took 2.2 minutes tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=162285.5, rms=0.355 021: dt: 0.0500, sse=162288.1, rms=0.354 (0.148%) 022: dt: 0.0500, sse=162290.7, rms=0.354 (0.147%) 023: dt: 0.0500, sse=162293.1, rms=0.353 (0.146%) 024: dt: 0.0500, sse=162295.4, rms=0.353 (0.145%) 025: dt: 0.0500, sse=162297.7, rms=0.352 (0.144%) 026: dt: 0.0500, sse=162299.8, rms=0.352 (0.143%) 027: dt: 0.0500, sse=162301.8, rms=0.351 (0.142%) 028: dt: 0.0500, sse=162303.7, rms=0.351 (0.141%) 029: dt: 0.0500, sse=162305.7, rms=0.350 (0.140%) 030: dt: 0.0500, sse=162307.6, rms=0.350 (0.139%) positioning took 2.2 minutes tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=161972.5, rms=0.350 031: dt: 0.5000, sse=161988.9, rms=0.345 (1.353%) 032: dt: 0.5000, sse=162003.3, rms=0.341 (1.259%) 033: dt: 0.5000, sse=162011.5, rms=0.337 (1.171%) 034: dt: 0.5000, sse=162012.0, rms=0.333 (1.087%) 035: dt: 0.5000, sse=162017.0, rms=0.330 (1.011%) 036: dt: 0.5000, sse=162018.9, rms=0.327 (0.944%) 037: dt: 0.5000, sse=162020.5, rms=0.324 (0.882%) 038: dt: 0.5000, sse=162022.8, rms=0.321 (0.836%) 039: dt: 0.5000, sse=162025.5, rms=0.319 (0.789%) 040: dt: 0.5000, sse=162027.2, rms=0.316 (0.754%) 041: dt: 0.5000, sse=162026.0, rms=0.314 (0.715%) 042: dt: 0.5000, sse=162028.9, rms=0.312 (0.676%) 043: dt: 0.5000, sse=162030.5, rms=0.310 (0.644%) 044: dt: 0.5000, sse=162032.6, rms=0.308 (0.613%) 045: dt: 0.5000, sse=162035.2, rms=0.306 (0.582%) 046: dt: 0.5000, sse=162037.8, rms=0.304 (0.558%) 047: dt: 0.5000, sse=162040.9, rms=0.303 (0.533%) 048: dt: 0.5000, sse=162041.4, rms=0.301 (0.505%) 049: dt: 0.5000, sse=162040.9, rms=0.300 (0.483%) 050: dt: 0.5000, sse=162045.8, rms=0.298 (0.464%) 051: dt: 0.5000, sse=162047.2, rms=0.297 (0.437%) 052: dt: 0.5000, sse=162051.2, rms=0.296 (0.423%) 053: dt: 0.5000, sse=162051.6, rms=0.295 (0.401%) 054: dt: 0.5000, sse=162056.1, rms=0.293 (0.383%) 055: dt: 0.5000, sse=162058.4, rms=0.292 (0.363%) 056: dt: 0.5000, sse=162064.0, rms=0.291 (0.346%) 057: dt: 0.5000, sse=162066.1, rms=0.290 (0.328%) 058: dt: 0.5000, sse=162070.3, rms=0.290 (0.318%) 059: dt: 0.5000, sse=162075.2, rms=0.289 (0.299%) 060: dt: 0.5000, sse=162080.6, rms=0.288 (0.280%) positioning took 7.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (box.dx, box.dy, box.dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) locating cortical regions not in the range [61.00 213.60], gm=170.00+-21.80, and vertices in regions > 159.1 19536smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 0 surface locations found to contain inconsistent values (21915 in, 173445 out) tol=1.0e-04, sigma=1.0, host=bc119, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=159518.8, rms=0.307 061: dt: 0.5000, sse=159493.1, rms=0.303 (1.216%) 062: dt: 0.5000, sse=159438.3, rms=0.299 (1.348%) 063: dt: 0.5000, sse=159389.5, rms=0.296 (1.165%) 064: dt: 0.5000, sse=159351.4, rms=0.293 (1.051%) 065: dt: 0.5000, sse=159318.6, rms=0.290 (0.942%) 066: dt: 0.5000, sse=159292.8, rms=0.287 (0.851%) 067: dt: 0.5000, sse=159274.1, rms=0.285 (0.761%) 068: dt: 0.5000, sse=159260.2, rms=0.283 (0.693%) 069: dt: 0.5000, sse=159252.0, rms=0.281 (0.630%) 070: dt: 0.5000, sse=159247.4, rms=0.280 (0.587%) 071: dt: 0.5000, sse=159244.8, rms=0.278 (0.544%) 072: dt: 0.5000, sse=159243.0, rms=0.277 (0.520%) 073: dt: 0.5000, sse=159240.9, rms=0.275 (0.495%) 074: dt: 0.5000, sse=159237.0, rms=0.274 (0.479%) 075: dt: 0.5000, sse=159235.2, rms=0.273 (0.456%) 076: dt: 0.5000, sse=159233.0, rms=0.272 (0.445%) 077: dt: 0.5000, sse=159229.1, rms=0.270 (0.423%) 078: dt: 0.5000, sse=159224.9, rms=0.269 (0.409%) 079: dt: 0.5000, sse=159218.8, rms=0.268 (0.391%) 080: dt: 0.5000, sse=159212.5, rms=0.267 (0.377%) 081: dt: 0.5000, sse=159205.8, rms=0.266 (0.359%) 082: dt: 0.5000, sse=159200.0, rms=0.265 (0.343%) 083: dt: 0.5000, sse=159194.2, rms=0.265 (0.328%) 084: dt: 0.5000, sse=159189.2, rms=0.264 (0.319%) 085: dt: 0.5000, sse=159182.8, rms=0.263 (0.301%) 086: dt: 0.5000, sse=159177.4, rms=0.262 (0.286%) 087: dt: 0.5000, sse=159171.1, rms=0.261 (0.273%) 088: dt: 0.5000, sse=159164.4, rms=0.261 (0.263%) 089: dt: 0.5000, sse=159156.5, rms=0.260 (0.249%) 090: dt: 0.5000, sse=159152.3, rms=0.259 (0.238%) positioning took 8.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (box.dx, box.dy, box.dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) locating cortical regions not in the range [56.00 214.20], gm=169.00+-22.60, and vertices in regions > 157.7 19113smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 0 surface locations found to contain inconsistent values (24363 in, 166767 out) tol=1.0e-04, sigma=0.5, host=bc119, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=160414.0, rms=0.283 091: dt: 0.5000, sse=160414.0, rms=0.281 (0.900%) 092: dt: 0.5000, sse=160377.0, rms=0.278 (1.004%) 093: dt: 0.5000, sse=160342.5, rms=0.276 (0.830%) 094: dt: 0.5000, sse=160314.7, rms=0.274 (0.730%) 095: dt: 0.5000, sse=160290.5, rms=0.272 (0.638%) 096: dt: 0.5000, sse=160272.8, rms=0.270 (0.567%) 097: dt: 0.5000, sse=160256.4, rms=0.269 (0.497%) 098: dt: 0.5000, sse=160244.0, rms=0.268 (0.445%) 099: dt: 0.5000, sse=160233.7, rms=0.267 (0.401%) 100: dt: 0.5000, sse=160225.6, rms=0.266 (0.371%) 101: dt: 0.5000, sse=160218.3, rms=0.265 (0.345%) 102: dt: 0.5000, sse=160212.3, rms=0.264 (0.327%) 103: dt: 0.5000, sse=160204.9, rms=0.263 (0.307%) 104: dt: 0.5000, sse=160199.5, rms=0.262 (0.294%) 105: dt: 0.5000, sse=160192.5, rms=0.262 (0.280%) 106: dt: 0.5000, sse=160186.7, rms=0.261 (0.267%) 107: dt: 0.5000, sse=160180.0, rms=0.260 (0.255%) 108: dt: 0.5000, sse=160172.9, rms=0.260 (0.246%) 109: dt: 0.5000, sse=160163.5, rms=0.259 (0.230%) 110: dt: 0.5000, sse=160157.8, rms=0.259 (0.224%) 111: dt: 0.5000, sse=160149.6, rms=0.258 (0.211%) 112: dt: 0.5000, sse=160142.5, rms=0.257 (0.202%) 113: dt: 0.5000, sse=160135.2, rms=0.257 (0.193%) 114: dt: 0.5000, sse=160128.8, rms=0.257 (0.185%) 115: dt: 0.5000, sse=160121.3, rms=0.256 (0.175%) 116: dt: 0.5000, sse=160116.5, rms=0.256 (0.169%) 117: dt: 0.5000, sse=160110.4, rms=0.255 (0.162%) 118: dt: 0.5000, sse=160104.3, rms=0.255 (0.155%) 119: dt: 0.5000, sse=160098.1, rms=0.254 (0.146%) 120: dt: 0.5000, sse=160093.2, rms=0.254 (0.145%) positioning took 10.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (region->dx, region->dy, region->dz) = (160, 418, 272) (box.dx, box.dy, box.dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) (region->dx, region->dy, region->dz) = (169, 428, 285) locating cortical regions not in the range [54.00 215.00], gm=169.00+-23.00, and vertices in regions > 157.5 1890smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 96 surface locations found to contain inconsistent values (26100 in, 162996 out) tol=1.0e-04, sigma=0.2, host=bc119, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=162047.4, rms=0.275 121: dt: 0.5000, sse=162057.1, rms=0.274 (0.679%) 122: dt: 0.5000, sse=162022.8, rms=0.272 (0.747%) 123: dt: 0.5000, sse=161991.3, rms=0.270 (0.609%) 124: dt: 0.5000, sse=161964.1, rms=0.268 (0.524%) 125: dt: 0.5000, sse=161938.0, rms=0.267 (0.450%) 126: dt: 0.5000, sse=161919.0, rms=0.266 (0.393%) 127: dt: 0.5000, sse=161901.4, rms=0.265 (0.340%) 128: dt: 0.5000, sse=161888.5, rms=0.264 (0.305%) 129: dt: 0.5000, sse=161875.5, rms=0.264 (0.272%) 130: dt: 0.5000, sse=161866.2, rms=0.263 (0.253%) 131: dt: 0.5000, sse=161854.4, rms=0.262 (0.234%) 132: dt: 0.5000, sse=161844.6, rms=0.262 (0.220%) 133: dt: 0.5000, sse=161834.8, rms=0.261 (0.205%) 134: dt: 0.5000, sse=161827.9, rms=0.261 (0.196%) 135: dt: 0.5000, sse=161819.8, rms=0.260 (0.184%) 136: dt: 0.5000, sse=161812.9, rms=0.260 (0.175%) 137: dt: 0.5000, sse=161804.7, rms=0.259 (0.165%) 138: dt: 0.5000, sse=161797.7, rms=0.259 (0.159%) 139: dt: 0.5000, sse=161790.9, rms=0.259 (0.149%) 140: dt: 0.5000, sse=161784.8, rms=0.258 (0.144%) 141: dt: 0.5000, sse=161777.9, rms=0.258 (0.135%) 142: dt: 0.5000, sse=161771.5, rms=0.258 (0.130%) 143: dt: 0.5000, sse=161766.8, rms=0.257 (0.121%) 144: dt: 0.5000, sse=161762.9, rms=0.257 (0.118%) 145: dt: 0.5000, sse=161758.0, rms=0.257 (0.111%) 146: dt: 0.5000, sse=161754.5, rms=0.256 (0.107%) 147: dt: 0.5000, sse=161749.4, rms=0.256 (0.102%) 148: dt: 0.5000, sse=161745.7, rms=0.256 (0.098%) 149: dt: 0.5000, sse=161740.3, rms=0.256 (0.093%) 150: dt: 0.5000, sse=161737.2, rms=0.255 (0.0writing pial surface to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial... writing smoothed curvature to lh.curv.pial 89%) positioning took 11.5 minutes writing curvature file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.area.pial vertex spacing 0.80 +- 0.35 (0.03-->9.39) (max @ vno 89596 --> 97481) face area 0.25 +- 0.21 (0.00-->16.36) measuring cortical thickness... 0 of 236764 vertices processed 25000 of 236764 vertices processed 50000 of 236764 vertices processed 75000 of 236764 vertices processed 100000 of 236764 vertices processed 125000 of 236764 vertices processed 150000 of 236764 vertices processed 175000 of 236764 vertices processed 200000 of 236764 vertices processed 225000 of 236764 vertices processed 0 of 236764 vertices processed 25000 of 236764 vertices processed 50000 of 236764 vertices processed 75000 of 236764 vertices processed 100000 of 236764 vertices processed 125000 of 236764 vertices processed 150000 of 236764 vertices processed 175000 of 236764 vertices processed 200000 of 236764 vertices processed 225000 of 236764 vertices processed thickness calculation complete, 308:734 truncations. 47868 vertices at 0 distance 139557 vertices at 1 distance 141794 vertices at 2 distance 77856 vertices at 3 distance 31969 vertices at 4 distance 10718 vertices at 5 distance 3435 vertices at 6 distance 1097 vertices at 7 distance 453 vertices at 8 distance 188 vertwriting cortical thickness estimate to 'thickness' file. ices at 9 distance 99 vertices at 10 distance 89 vertices at 11 distance 51 vertices at 12 distance 39 vertices at 13 distance 46 vertices at 14 distance 34 vertices at 15 distance 43 vertices at 16 distance 45 vertices at 17 distance 24 vertices at 18 distance 32 vertices at 19 distance 15 vertices at 20 distance writing curvature file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.thickness positioning took 77.5 minutes mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-03 rh reading previously compute gray/white surface refining pial surfaces placement using T2 volume ../mri/T2 using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 5.00 sigmas below the mean (default=2) using white starting white location... using woT2.pial starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/filled.mgz... reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/wm.mgz... 31305 bright wm thresholded. 103 bright non-wm voxels segmented. reading original surface position from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.orig... computing class statistics... border white: 483206 voxels (1.47%) border gray 497210 voxels (1.52%) WM (103.0): 102.5 +- 6.1 [70.0 --> 110.0] GM (84.0) : 83.1 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.9 (was 70) setting MAX_BORDER_WHITE to 114.1 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 59.8 (was 40) setting MAX_GRAY to 101.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.6 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=108+-2.6, GM=78+-7.8 mean inside = 100.6, mean outside = 84.3 reading initial white vertex positions from white... 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 white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 48 points - only 0.00% unknown deleting segment 1 with 24 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 46 points - only 0.00% unknown deleting segment 6 with 132 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown deleting segment 8 with 136 points - only 0.00% unknown deleting segment 11 with 109 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 118 points - only 0.00% unknown deleting segment 14 with 27 points - only 0.00% unknown deleting segment 15 with 104 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group drepositioning cortical surface to gray/csf boundary. eleting segment 17 with 4 points - only 0.00% unknown deleting segment 18 with 27 points - only 0.00% unknown deleting segment 19 with 123 points - only 0.00% unknown deleting segment 20 with 14 points - only 0.00% unknown reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (box.dx, box.dy, box.dsmoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... z) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) locating cortical regions not in the range [52.00 215.80], gm=169.00+-23.40, and vertices in regions > 157.3 202316 surface locations found to contain inconsistent values (27561 in, 174755 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.156, l_nspring=0.063, 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=165352.6, rms=0.357 001: dt: 0.0500, sse=165358.2, rms=0.356 (0.160%) 002: dt: 0.0500, sse=165360.4, rms=0.356 (0.177%) 003: dt: 0.0500, sse=165362.5, rms=0.355 (0.173%) 004: dt: 0.0500, sse=165364.9, rms=0.354 (0.172%) 005: dt: 0.0500, sse=165366.9, rms=0.354 (0.170%) 006: dt: 0.0500, sse=165368.8, rms=0.353 (0.169%) 007: dt: 0.0500, sse=165370.8, rms=0.353 (0.168%) 008: dt: 0.0500, sse=165372.4, rms=0.352 (0.166%) 009: dt: 0.0500, sse=165374.0, rms=0.352 (0.165%) 010: dt: 0.0500, sse=165375.5, rms=0.351 (0.164%) positioning took 2.1 minutes tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=164990.9, rms=0.351 011: dt: 0.0500, sse=164992.4, rms=0.350 (0.163%) 012: dt: 0.0500, sse=164993.7, rms=0.350 (0.162%) 013: dt: 0.0500, sse=164995.0, rms=0.349 (0.161%) 014: dt: 0.0500, sse=164996.2, rms=0.349 (0.159%) 015: dt: 0.0500, sse=164997.2, rms=0.348 (0.158%) 016: dt: 0.0500, sse=164998.3, rms=0.348 (0.157%) 017: dt: 0.0500, sse=164999.2, rms=0.347 (0.156%) 018: dt: 0.0500, sse=165000.2, rms=0.347 (0.155%) 019: dt: 0.0500, sse=165001.0, rms=0.346 (0.154%) 020: dt: 0.0500, sse=165001.8, rms=0.345 (0.152%) positioning took 2.2 minutes tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=164669.6, rms=0.345 021: dt: 0.0500, sse=164670.1, rms=0.345 (0.151%) 022: dt: 0.0500, sse=164670.7, rms=0.344 (0.150%) 023: dt: 0.0500, sse=164671.2, rms=0.344 (0.149%) 024: dt: 0.0500, sse=164671.8, rms=0.343 (0.148%) 025: dt: 0.0500, sse=164672.2, rms=0.343 (0.147%) 026: dt: 0.0500, sse=164672.6, rms=0.342 (0.146%) 027: dt: 0.0500, sse=164672.9, rms=0.342 (0.145%) 028: dt: 0.0500, sse=164673.3, rms=0.341 (0.144%) 029: dt: 0.0500, sse=164673.4, rms=0.341 (0.143%) 030: dt: 0.0500, sse=164673.8, rms=0.340 (0.142%) positioning took 2.2 minutes tol=1.0e-04, sigma=2.0, host=bc119, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=164383.6, rms=0.340 031: dt: 0.5000, sse=164388.3, rms=0.336 (1.374%) 032: dt: 0.5000, sse=164396.9, rms=0.331 (1.275%) 033: dt: 0.5000, sse=164398.7, rms=0.328 (1.189%) 034: dt: 0.5000, sse=164400.9, rms=0.324 (1.095%) 035: dt: 0.5000, sse=164403.4, rms=0.321 (1.024%) 036: dt: 0.5000, sse=164408.2, rms=0.318 (0.960%) 037: dt: 0.5000, sse=164411.1, rms=0.315 (0.907%) 038: dt: 0.5000, sse=164418.9, rms=0.312 (0.852%) 039: dt: 0.5000, sse=164424.7, rms=0.309 (0.800%) 040: dt: 0.5000, sse=164437.4, rms=0.307 (0.751%) 041: dt: 0.5000, sse=164445.8, rms=0.305 (0.718%) 042: dt: 0.5000, sse=164454.4, rms=0.303 (0.687%) 043: dt: 0.5000, sse=164459.5, rms=0.301 (0.650%) 044: dt: 0.5000, sse=164466.4, rms=0.299 (0.629%) 045: dt: 0.5000, sse=164473.3, rms=0.297 (0.583%) 046: dt: 0.5000, sse=164477.4, rms=0.296 (0.576%) 047: dt: 0.5000, sse=164484.5, rms=0.294 (0.541%) 048: dt: 0.5000, sse=164492.2, rms=0.292 (0.509%) 049: dt: 0.5000, sse=164499.2, rms=0.291 (0.498%) 050: dt: 0.5000, sse=164506.4, rms=0.290 (0.466%) 051: dt: 0.5000, sse=164515.2, rms=0.288 (0.438%) 052: dt: 0.5000, sse=164523.2, rms=0.287 (0.418%) 053: dt: 0.5000, sse=164531.5, rms=0.286 (0.399%) 054: dt: 0.5000, sse=164537.8, rms=0.285 (0.387%) 055: dt: 0.5000, sse=164550.4, rms=0.284 (0.349%) 056: dt: 0.5000, sse=164556.3, rms=0.283 (0.351%) 057: dt: 0.5000, sse=164568.1, rms=0.282 (0.326%) 058: dt: 0.5000, sse=164577.9, rms=0.281 (0.308%) 059: dt: 0.5000, sse=164586.8, rms=0.280 (0.296%) 060: dt: 0.5000, sse=164597.7, rms=0.280 (0.278%) positioning took 7.4 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (box.dx, box.dy, box.dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) locating cortical regions not in the range [54.00 216.40], gm=170.00+-23.20, and vertices in regions > 158.4 19569smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 7 surface locations found to contain inconsistent values (25795 in, 169902 out) tol=1.0e-04, sigma=1.0, host=bc119, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=162388.3, rms=0.297 061: dt: 0.5000, sse=162365.0, rms=0.293 (1.259%) 062: dt: 0.5000, sse=162309.2, rms=0.289 (1.400%) 063: dt: 0.5000, sse=162261.3, rms=0.286 (1.209%) 064: dt: 0.5000, sse=162219.1, rms=0.283 (1.092%) 065: dt: 0.5000, sse=162185.8, rms=0.280 (0.985%) 066: dt: 0.5000, sse=162157.3, rms=0.277 (0.889%) 067: dt: 0.5000, sse=162136.7, rms=0.275 (0.803%) 068: dt: 0.5000, sse=162120.3, rms=0.273 (0.734%) 069: dt: 0.5000, sse=162109.4, rms=0.271 (0.669%) 070: dt: 0.5000, sse=162101.2, rms=0.270 (0.625%) 071: dt: 0.5000, sse=162093.2, rms=0.268 (0.581%) 072: dt: 0.5000, sse=162089.6, rms=0.266 (0.559%) 073: dt: 0.5000, sse=162083.7, rms=0.265 (0.533%) 074: dt: 0.5000, sse=162076.9, rms=0.264 (0.516%) 075: dt: 0.5000, sse=162070.9, rms=0.262 (0.494%) 076: dt: 0.5000, sse=162066.1, rms=0.261 (0.480%) 077: dt: 0.5000, sse=162059.1, rms=0.260 (0.464%) 078: dt: 0.5000, sse=162052.4, rms=0.259 (0.447%) 079: dt: 0.5000, sse=162043.5, rms=0.258 (0.430%) 080: dt: 0.5000, sse=162034.8, rms=0.257 (0.416%) 081: dt: 0.5000, sse=162026.3, rms=0.256 (0.397%) 082: dt: 0.5000, sse=162017.0, rms=0.255 (0.383%) 083: dt: 0.5000, sse=162009.3, rms=0.254 (0.364%) 084: dt: 0.5000, sse=161999.9, rms=0.253 (0.351%) 085: dt: 0.5000, sse=161992.4, rms=0.252 (0.334%) 086: dt: 0.5000, sse=161984.2, rms=0.251 (0.325%) 087: dt: 0.5000, sse=161975.6, rms=0.250 (0.305%) 088: dt: 0.5000, sse=161967.8, rms=0.250 (0.294%) 089: dt: 0.5000, sse=161962.0, rms=0.249 (0.279%) 090: dt: 0.5000, sse=161955.4, rms=0.248 (0.271%) positioning took 8.9 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (box.dx, box.dy, box.dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) locating cortical regions not in the range [51.00 216.20], gm=169.00+-23.60, and vertices in regions > 157.2 19077smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 1 surface locations found to contain inconsistent values (29460 in, 161311 out) tol=1.0e-04, sigma=0.5, host=bc119, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=163206.8, rms=0.271 091: dt: 0.5000, sse=163203.0, rms=0.269 (0.978%) 092: dt: 0.5000, sse=163163.3, rms=0.266 (1.082%) 093: dt: 0.5000, sse=163128.8, rms=0.263 (0.897%) 094: dt: 0.5000, sse=163101.4, rms=0.261 (0.787%) 095: dt: 0.5000, sse=163076.2, rms=0.259 (0.692%) 096: dt: 0.5000, sse=163056.6, rms=0.258 (0.616%) 097: dt: 0.5000, sse=163041.8, rms=0.256 (0.542%) 098: dt: 0.5000, sse=163027.0, rms=0.255 (0.491%) 099: dt: 0.5000, sse=163016.3, rms=0.254 (0.446%) 100: dt: 0.5000, sse=163006.5, rms=0.253 (0.417%) 101: dt: 0.5000, sse=162998.4, rms=0.252 (0.387%) 102: dt: 0.5000, sse=162988.3, rms=0.251 (0.371%) 103: dt: 0.5000, sse=162978.7, rms=0.250 (0.349%) 104: dt: 0.5000, sse=162968.2, rms=0.249 (0.340%) 105: dt: 0.5000, sse=162960.1, rms=0.248 (0.322%) 106: dt: 0.5000, sse=162951.1, rms=0.248 (0.313%) 107: dt: 0.5000, sse=162942.3, rms=0.247 (0.296%) 108: dt: 0.5000, sse=162934.2, rms=0.246 (0.285%) 109: dt: 0.5000, sse=162924.5, rms=0.246 (0.271%) 110: dt: 0.5000, sse=162914.1, rms=0.245 (0.261%) 111: dt: 0.5000, sse=162903.5, rms=0.244 (0.250%) 112: dt: 0.5000, sse=162893.8, rms=0.244 (0.240%) 113: dt: 0.5000, sse=162885.6, rms=0.243 (0.227%) 114: dt: 0.5000, sse=162876.5, rms=0.243 (0.222%) 115: dt: 0.5000, sse=162867.7, rms=0.242 (0.209%) 116: dt: 0.5000, sse=162857.5, rms=0.242 (0.204%) 117: dt: 0.5000, sse=162848.8, rms=0.241 (0.192%) 118: dt: 0.5000, sse=162841.0, rms=0.241 (0.185%) 119: dt: 0.5000, sse=162831.8, rms=0.240 (0.178%) 120: dt: 0.5000, sse=162825.8, rms=0.240 (0.173%) positioning took 10.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (region->dx, region->dy, region->dz) = (163, 421, 269) (box.dx, box.dy, box.dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) (region->dx, region->dy, region->dz) = (176, 432, 283) locating cortical regions not in the range [49.50 215.40], gm=168.00+-23.70, and vertices in regions > 156.1 1871smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 04 surface locations found to contain inconsistent values (37681 in, 149423 out) tol=1.0e-04, sigma=0.2, host=bc119, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.156, l_nspring=0.063, l_location=0.250, l_curv=0.100 mom=0.00, dt=0.50 000: dt: 0.0000, sse=164701.0, rms=0.260 121: dt: 0.5000, sse=164691.8, rms=0.258 (0.765%) 122: dt: 0.5000, sse=164645.3, rms=0.255 (0.842%) 123: dt: 0.5000, sse=164607.0, rms=0.254 (0.682%) 124: dt: 0.5000, sse=164571.3, rms=0.252 (0.595%) 125: dt: 0.5000, sse=164540.3, rms=0.251 (0.514%) 126: dt: 0.5000, sse=164512.9, rms=0.250 (0.456%) 127: dt: 0.5000, sse=164488.5, rms=0.249 (0.399%) 128: dt: 0.5000, sse=164466.5, rms=0.248 (0.365%) 129: dt: 0.5000, sse=164447.5, rms=0.247 (0.326%) 130: dt: 0.5000, sse=164429.6, rms=0.246 (0.308%) 131: dt: 0.5000, sse=164413.6, rms=0.246 (0.285%) 132: dt: 0.5000, sse=164398.1, rms=0.245 (0.273%) 133: dt: 0.5000, sse=164383.2, rms=0.244 (0.256%) 134: dt: 0.5000, sse=164369.3, rms=0.244 (0.245%) 135: dt: 0.5000, sse=164356.7, rms=0.243 (0.233%) 136: dt: 0.5000, sse=164343.7, rms=0.242 (0.223%) 137: dt: 0.5000, sse=164331.5, rms=0.242 (0.210%) 138: dt: 0.5000, sse=164319.8, rms=0.241 (0.202%) 139: dt: 0.5000, sse=164309.4, rms=0.241 (0.193%) 140: dt: 0.5000, sse=164298.7, rms=0.241 (0.185%) 141: dt: 0.5000, sse=164289.2, rms=0.240 (0.175%) 142: dt: 0.5000, sse=164278.2, rms=0.240 (0.168%) 143: dt: 0.5000, sse=164268.7, rms=0.239 (0.158%) 144: dt: 0.5000, sse=164258.5, rms=0.239 (0.154%) 145: dt: 0.5000, sse=164251.2, rms=0.239 (0.149%) 146: dt: 0.5000, sse=164242.0, rms=0.238 (0.142%) 147: dt: 0.5000, sse=164235.2, rms=0.238 (0.138%) 148: dt: 0.5000, sse=164226.7, rms=0.238 (0.133%) 149: dt: 0.5000, sse=164219.5, rms=0.237 (0.124%) 150: dt: 0.5000, sse=164212.7, rms=0.237 (0.1writing pial surface to /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial... writing smoothed curvature to rh.curv.pial 21%) positioning took 11.2 minutes writing curvature file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.area.pial vertex spacing 0.80 +- 0.35 (0.03-->6.95) (max @ vno 164978 --> 163727) face area 0.25 +- 0.20 (0.00-->7.06) measuring cortical thickness... 0 of 242369 vertices processed 25000 of 242369 vertices processed 50000 of 242369 vertices processed 75000 of 242369 vertices processed 100000 of 242369 vertices processed 125000 of 242369 vertices processed 150000 of 242369 vertices processed 175000 of 242369 vertices processed 200000 of 242369 vertices processed 225000 of 242369 vertices processed 0 of 242369 vertices processed 25000 of 242369 vertices processed 50000 of 242369 vertices processed 75000 of 242369 vertices processed 100000 of 242369 vertices processed 125000 of 242369 vertices processed 150000 of 242369 vertices processed 175000 of 242369 vertices processed 200000 of 242369 vertices processed 225000 of 242369 vertices processed thickness calculation complete, 221:720 truncations. 55902 vertices at 0 distance 154069 vertices at 1 distance 142172 vertices at 2 distance 71434 vertices at 3 distance 27872 vertices at 4 distance 9496 vertices at 5 distance 2968 vertices at 6 distance 938 vertices at 7 distance 303 vertices at 8 distance 141 verticwriting cortical thickness estimate to 'thickness' file. es at 9 distance 68 vertices at 10 distance 46 vertices at 11 distance 24 vertices at 12 distance 32 vertices at 13 distance 18 vertices at 14 distance 30 vertices at 15 distance 24 vertices at 16 distance 32 vertices at 17 distance 34 vertices at 18 distance 27 vertices at 19 distance 24 vertices at 20 distance writing curvature file /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.thickness positioning took 76.7 minutes PIDs (140641 140644) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Tue Oct 18 01:39:54 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf vertexvol --s sub-03 --lh --th3 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-03 lh /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.volume masking with /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/label/lh.cortex.label Total face volume 278579 Total vertex volume 275334 (mask=0) #@# sub-03 lh 275334 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Oct 18 01:40:00 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf vertexvol --s sub-03 --rh --th3 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-03 rh /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.volume masking with /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/label/rh.cortex.label Total face volume 279433 Total vertex volume 276238 (mask=0) #@# sub-03 rh 276238 vertexvol Done #-------------------------------------------- #@# Surf Volume lh Tue Oct 18 01:40:06 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-03 lh /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.volume masking with /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/label/lh.cortex.label Total face volume 278579 Total vertex volume 275334 (mask=0) #@# sub-03 lh 275334 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Oct 18 01:40:11 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-03 rh /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.volume masking with /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/label/rh.cortex.label Total face volume 279433 Total vertex volume 276238 (mask=0) #@# sub-03 rh 276238 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue Oct 18 01:40:17 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 sub-03 SUBJECTS_DIR is /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer 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 = 461 writing volume /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/ribbon.mgz mris_volmask took 26.48 minutes writing ribbon files Started at Tue Oct 18 00:17:32 UTC 2022 Ended at Tue Oct 18 02:06:46 UTC 2022 #@#%# recon-all-run-time-hours 1.821 recon-all -s sub-03 finished without error at Tue Oct 18 02:06:46 UTC 2022 New invocation of recon-all Tue Oct 18 02:32:47 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon3 -openmp 8 -subjid sub-03 -sd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels subjid sub-03 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux bc11910.int.ets1.calculquebec.ca 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 unlimited coredumpsize unlimited memoryuse 33554432 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767717 maxlocks unlimited maxsignal 767717 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638244 117602964 32150172 2721156 46885108 70511180 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca 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: 2022/10/18-02:32:47-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: bc11910.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Relabel Hypointensities Tue Oct 18 02:32:47 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 5360 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 5622 voxels changed to hypointensity... 10716 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Tue Oct 18 02:33:30 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer subject sub-03 outvol /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 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 13.51 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 88 rescaling Left_Putamen from 80 --> 89 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 42 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 59 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 68 rescaling Right_Thalamus_Proper from 85 --> 96 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 78 rescaling Right_VentralDC from 86 --> 103 rescaling Fifth_Ventricle from 40 --> 50 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 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 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/localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Tue Oct 18 02:45:36 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer subject sub-03 outvol /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 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 13.51 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 88 rescaling Left_Putamen from 80 --> 89 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 42 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 59 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 68 rescaling Right_Thalamus_Proper from 85 --> 96 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 78 rescaling Right_VentralDC from 86 --> 103 rescaling Fifth_Ventricle from 40 --> 50 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 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 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AParc-to-ASeg DKTatlas Tue Oct 18 02:57:59 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer subject sub-03 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 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 13.51 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 88 rescaling Left_Putamen from 80 --> 89 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 42 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 59 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 68 rescaling Right_Thalamus_Proper from 85 --> 96 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 78 rescaling Right_VentralDC from 86 --> 103 rescaling Fifth_Ventricle from 40 --> 50 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 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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apas2aseg --i aparc+aseg.mgz --o aseg.mgz Tue Oct 18 03:10:17 UTC 2022 setenv SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer cd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux bc11910.int.ets1.calculquebec.ca 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 mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 32768000 0.000000 mri_binarize done Started at Tue Oct 18 03:10:17 UTC 2022 Ended at Tue Oct 18 03:10:27 UTC 2022 Apas2aseg-Run-Time-Sec 10 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Tue Oct 18 03:10:27 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-03 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-03 sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1633735 mm^3 (det: 1.192424 ) Computing euler number orig.nofix lheno = -32, rheno = -50 orig.nofix lhholes = 17, rhholes = 26 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 268851.991 533501.000 diff=-264649.0 pctdiff=-98.437 rhCtxGM: 270203.299 535028.000 diff=-264824.7 pctdiff=-98.009 lhCtxWM: 205642.924 452844.500 diff=-247201.6 pctdiff=-120.209 rhCtxWM: 212668.691 467128.500 diff=-254459.8 pctdiff=-119.651 SubCortGMVol 111237.000 SupraTentVol 1081119.906 (2117412.000) diff=-1036292.094 pctdiff=-95.854 SupraTentVolNotVent 1063464.906 (2099757.000) diff=-1036292.094 pctdiff=-97.445 BrainSegVol 2406497.000 (2402803.000) diff=3694.000 pctdiff=0.154 BrainSegVolNotVent 2383498.000 (1352228.906) diff=1031269.094 pctdiff=43.267 BrainSegVolNotVent 2383498.000 CerebellumVol 283607.000 VentChorVol 17655.000 3rd4th5thCSF 5344.000 CSFVol 1650.000, OptChiasmVol 134.000 MaskVol 2858806.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Tue Oct 18 03:11:45 UTC 2022 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03 mri_aparc2aseg --s sub-03 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer subject sub-03 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aparc+aseg.mgz Reading lh white surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/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 /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/ribbon.mgz Loading filled from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 11542 vertices from left hemi Ripped 11916 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aseg.mgz Loading Ctx Seg File /localscratch/bpinsard.32335141.0/smriprep_sub03.job/sourcedata/freesurfer/sub-03/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1989221 Used brute-force search on 6 voxels Fixing Parahip LH WM Found 13 clusters 0 k 1.024000 1 k 0.512000 2 k 0.512000 3 k 1684.451294 4 k 0.512000 5 k 1.024000 6 k 0.512000 7 k 0.512000 8 k 30.719976 9 k 15.872001 10 k 0.512000 11 k 1.024000 12 k 0.512000 Fixing Parahip RH WM Found 12 clusters 0 k 1593.833740 1 k 0.512000 2 k 1.024000 3 k 2.048000 4 k 0.512000 5 k 1.024000 6 k 0.512000 7 k 1.536000 8 k 49.152008 9 k 0.512000 10 k 0.512000 11 k 3.071999 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-03 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-03 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname bc11910.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1633735 mm^3 (det: 1.192424 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 268851.991 533501.000 diff=-264649.0 pctdiff=-98.437 rhCtxGM: 270203.299 535028.000 diff=-264824.7 pctdiff=-98.009 lhCtxWM: 205642.924 452844.500 diff=-247201.6 pctdiff=-120.209 rhCtxWM: 212668.691 467128.500 diff=-254459.8 pctdiff=-119.651 SubCortGMVol 111237.000 SupraTentVol 1081119.906 (2117412.000) diff=-1036292.094 pctdiff=-95.854 SupraTentVolNotVent 1063464.906 (2099757.000) diff=-1036292.094 pctdiff=-97.445 BrainSegVol 2406497.000 (2402803.000) diff=3694.000 pctdiff=0.154 BrainSegVolNotVent 2383498.000 (1352228.906) diff=1031269.094 pctdiff=43.267 BrainSegVolNotVent 2383498.000 CerebellumVol 283607.000 VentChorVol 17655.000 3rd4th5thCSF 5344.000 CSFVol 1650.000, OptChiasmVol 134.000 MaskVol 2858806.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done Started at Tue Oct 18 02:32:47 UTC 2022 Ended at Tue Oct 18 03:27:43 UTC 2022 #@#%# recon-all-run-time-hours 0.916 recon-all -s sub-03 finished without error at Tue Oct 18 03:27:43 UTC 2022