Tue May 25 17:29:56 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon1 -i /work/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-03_ses-001_T1w_template.nii.gz -T2 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-03 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -expert /work/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts subjid sub-03 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 23895308 161068748 1955680 11674376 168515228 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: 2021/05/25-17:29:56-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:29:56-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:57-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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) /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 mri_convert /work/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-03_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/001.mgz mri_convert.bin /work/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-03_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /work/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-03_ses-001_T1w_template.nii.gz... TR=2400.00, 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Tue May 25 17:30:05 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 mri_convert --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-03/ses-001/anat/sub-03_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Tue May 25 17:30:15 UTC 2021 Found 1 runs /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/001.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz --conform_min mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz... mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/talairach.xfm /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 25 17:30:29 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Tue May 25 17:30:29 UTC 2021 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.72790 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.72790/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.72790/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, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.72790/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Tue May 25 17:30:45 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.72790/nu0.mnc ./tmp.mri_nu_correct.mni.72790/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.72790/0/ -iterations 1000 -distance 50 [bpinsard@blg5611.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/] [2021-05-25 17:30:45] 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.72790/0/ ./tmp.mri_nu_correct.mni.72790/nu0.mnc ./tmp.mri_nu_correct.mni.72790/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 Number of iterations: 43 CV of field change: 0.000977737 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.72790/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.72790/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.72790/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue May 25 17:33:03 UTC 2021 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 Tue May 25 17:33:03 UTC 2021 Ended at Tue May 25 17:33:41 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 25 17:33:43 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7791, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/talairach_avi.log tal_QC_AZS /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/talairach_avi.log TalAviQA: 0.97185 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Tue May 25 17:33:44 UTC 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Tue May 25 17:33:44 UTC 2021 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.74807 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.74807/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.74807/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, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.74807/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue May 25 17:33:59 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.74807/nu0.mnc ./tmp.mri_nu_correct.mni.74807/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.74807/0/ [bpinsard@blg5611.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/] [2021-05-25 17:33:59] 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.74807/0/ ./tmp.mri_nu_correct.mni.74807/nu0.mnc ./tmp.mri_nu_correct.mni.74807/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 Number of iterations: 38 CV of field change: 0.000991292 Outputting Volume: ............................................................ Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Tue May 25 17:35:49 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.74807/nu1.mnc ./tmp.mri_nu_correct.mni.74807/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.74807/1/ [bpinsard@blg5611.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/] [2021-05-25 17:35:49] 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.74807/1/ ./tmp.mri_nu_correct.mni.74807/nu1.mnc ./tmp.mri_nu_correct.mni.74807/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 Number of iterations: 19 CV of field change: 0.000981641 Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.74807/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.74807/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.74807/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.74807/ones.mgz sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard input ./tmp.mri_nu_correct.mni.74807/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.74807/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.74807/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.74807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.74807/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.74807/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.74807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.74807/input.mean.dat sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.74807/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.74807/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.74807/ones.mgz --i ./tmp.mri_nu_correct.mni.74807/nu2.mnc --sum ./tmp.mri_nu_correct.mni.74807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.74807/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.74807/ones.mgz --i ./tmp.mri_nu_correct.mni.74807/nu2.mnc --sum ./tmp.mri_nu_correct.mni.74807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.74807/output.mean.dat sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.74807/ones.mgz Loading ./tmp.mri_nu_correct.mni.74807/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.74807/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.74807/nu2.mnc ./tmp.mri_nu_correct.mni.74807/nu2.mnc mul 1.02478485500726956614 Saving result to './tmp.mri_nu_correct.mni.74807/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.74807/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.74807/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.74807/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 11 seconds. mapping ( 5, 155) to ( 3, 110) Tue May 25 17:38:27 UTC 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue May 25 17:38:28 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 1.06234 0.03637 -0.01361 -0.60483; 0.01742 1.01100 0.19183 -29.80986; 0.00951 -0.12065 1.08597 2.19537; 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 87 (87), valley at 58 (58) csf peak at 44, setting threshold to 72 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 21 (21) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 52 seconds. Started at Tue May 25 17:29:55 UTC 2021 Ended at Tue May 25 17:42:21 UTC 2021 #@#%# recon-all-run-time-hours 0.207 recon-all -s sub-03 finished without error at Tue May 25 17:42:21 UTC 2021 New invocation of recon-all Tue May 25 17:44:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-03 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-03 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 26901172 155819212 1966792 13918048 165450224 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: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:08-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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 Tue May 25 17:44:08 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri mri_em_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 = (79, 51, 46) --> (239, 206, 254) using (132, 103, 150) as brain centroid... mean wm in atlas = 107, using box (112,84,124) --> (151, 122,175) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 102 +- 4.4 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 initial log_p = -4.344 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.005520 @ (-9.091, 9.091, -9.091) max log p = -3.948731 @ (4.545, 13.636, 4.545) max log p = -3.912721 @ (2.273, -6.818, -2.273) max log p = -3.865084 @ (-1.136, -1.136, -1.136) max log p = -3.862203 @ (0.568, -0.568, -0.568) max log p = -3.840291 @ (-1.420, 1.420, 0.284) Found translation: (-4.3, 15.6, -8.2): log p = -3.840 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.840, old_max_log_p =-3.840 (thresh=-3.8) 0.80000 0.00000 0.00000 -4.26137; 0.00000 0.80000 0.00000 15.62500; 0.00000 0.00000 0.80000 -8.23864; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.788, old_max_log_p =-3.840 (thresh=-3.8) 0.82783 -0.01997 -0.05649 3.45122; 0.02932 0.83420 0.13483 -15.94882; 0.05052 -0.13102 0.78761 3.57649; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.761, old_max_log_p =-3.788 (thresh=-3.8) 0.81285 -0.04897 -0.00594 0.37825; 0.05043 0.87354 0.05803 -11.14983; -0.00112 -0.04922 0.81396 -5.74886; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.761, old_max_log_p =-3.761 (thresh=-3.8) 0.81285 -0.04897 -0.00594 0.37825; 0.05043 0.87354 0.05803 -11.14983; -0.00112 -0.04922 0.81396 -5.74886; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.740, old_max_log_p =-3.761 (thresh=-3.8) 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.740, old_max_log_p =-3.740 (thresh=-3.7) 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 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 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.740 (old=-4.344) transform before final EM align: 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 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 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1010.788282 mri_em_register stimesec 3.076780 mri_em_register ru_maxrss 753840 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 886438 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 26212 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 654 mri_em_register ru_nivcsw 309 registration took 3 minutes and 3 seconds. #-------------------------------------- #@# CA Normalize Tue May 25 17:47:11 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 = (79, 51, 46) --> (239, 206, 254) using (132, 103, 150) as brain centroid... mean wm in atlas = 107, using box (112,84,124) --> (151, 122,175) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 102 +- 4.4 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 using 246344 sample points... INFO: compute sample coordinates transform 0.81370 -0.04936 0.00742 -1.19379; 0.05032 0.87263 0.03129 -7.11884; -0.01274 -0.01976 0.81350 -7.05428; 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, 52, 47) --> (245, 187, 253) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 1247 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (83, 55, 46) --> (164, 192, 253) Right_Cerebral_White_Matter: limiting intensities to 104.0 --> 132.0 359 of 1223 (29.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (167, 153, 75) --> (228, 199, 141) Left_Cerebellum_White_Matter: limiting intensities to 110.0 --> 132.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (113, 153, 72) --> (166, 202, 143) Right_Cerebellum_White_Matter: limiting intensities to 110.0 --> 132.0 0 of 18 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (145, 142, 117) --> (188, 223, 156) Brain_Stem: limiting intensities to 104.0 --> 132.0 0 of 38 (0.0%) samples deleted using 2537 total control points for intensity normalization... bias field = 0.953 +- 0.073 14 of 2178 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (163, 52, 47) --> (245, 187, 253) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 1783 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (83, 55, 46) --> (164, 192, 253) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 56 of 1891 (3.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (167, 153, 75) --> (228, 199, 141) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 71 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (113, 153, 72) --> (166, 202, 143) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 58 (1.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (145, 142, 117) --> (188, 223, 156) Brain_Stem: limiting intensities to 88.0 --> 132.0 22 of 106 (20.8%) samples deleted using 3909 total control points for intensity normalization... bias field = 1.060 +- 0.074 6 of 3806 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (163, 52, 47) --> (245, 187, 253) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 1831 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (83, 55, 46) --> (164, 192, 253) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 1878 (0.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (167, 153, 75) --> (228, 199, 141) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 79 of 135 (58.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (113, 153, 72) --> (166, 202, 143) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 51 of 90 (56.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (145, 142, 117) --> (188, 223, 156) Brain_Stem: limiting intensities to 88.0 --> 132.0 90 of 173 (52.0%) samples deleted using 4107 total control points for intensity normalization... bias field = 1.057 +- 0.063 10 of 3833 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 28 seconds. #-------------------------------------- #@# CA Reg Tue May 25 17:49:39 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri mri_ca_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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) = 0.58 (predicted orig area = 13.8) 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=0.997, neg=0, invalid=762 0001: dt=394.793203, rms=0.862 (13.475%), neg=0, invalid=762 0002: dt=281.760413, rms=0.829 (3.914%), neg=0, invalid=762 0003: dt=295.936000, rms=0.813 (1.929%), neg=0, invalid=762 0004: dt=174.769231, rms=0.806 (0.837%), neg=0, invalid=762 0005: dt=887.808000, rms=0.794 (1.473%), neg=0, invalid=762 0006: dt=129.472000, rms=0.791 (0.321%), neg=0, invalid=762 0007: dt=517.888000, rms=0.789 (0.265%), neg=0, invalid=762 0008: dt=517.888000, rms=0.787 (0.273%), neg=0, invalid=762 0009: dt=129.472000, rms=0.786 (0.196%), neg=0, invalid=762 0010: dt=129.472000, rms=0.785 (0.076%), neg=0, invalid=762 0011: dt=129.472000, rms=0.784 (0.104%), neg=0, invalid=762 0012: dt=129.472000, rms=0.783 (0.134%), neg=0, invalid=762 0013: dt=129.472000, rms=0.782 (0.153%), neg=0, invalid=762 0014: dt=129.472000, rms=0.780 (0.193%), neg=0, invalid=762 0015: dt=129.472000, rms=0.779 (0.216%), neg=0, invalid=762 0016: dt=129.472000, rms=0.777 (0.208%), neg=0, invalid=762 0017: dt=129.472000, rms=0.776 (0.183%), neg=0, invalid=762 0018: dt=129.472000, rms=0.775 (0.146%), neg=0, invalid=762 0019: dt=129.472000, rms=0.773 (0.138%), neg=0, invalid=762 0020: dt=129.472000, rms=0.773 (0.113%), neg=0, invalid=762 0021: dt=129.472000, rms=0.772 (0.087%), neg=0, invalid=762 0022: dt=517.888000, rms=0.772 (0.043%), neg=0, invalid=762 0023: dt=517.888000, rms=0.770 (0.187%), neg=0, invalid=762 0024: dt=517.888000, rms=0.770 (-0.247%), neg=0, invalid=762 0025: dt=27.744000, rms=0.770 (0.004%), neg=0, invalid=762 0026: dt=8.092000, rms=0.770 (0.011%), neg=0, invalid=762 0027: dt=23.120000, rms=0.770 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.770, neg=0, invalid=762 0028: dt=295.936000, rms=0.768 (0.359%), neg=0, invalid=762 0029: dt=1479.680000, rms=0.765 (0.399%), neg=0, invalid=762 0030: dt=129.472000, rms=0.764 (0.111%), neg=0, invalid=762 0031: dt=129.472000, rms=0.764 (0.031%), neg=0, invalid=762 0032: dt=129.472000, rms=0.763 (0.024%), neg=0, invalid=762 0033: dt=129.472000, rms=0.763 (0.023%), neg=0, invalid=762 0034: dt=517.888000, rms=0.762 (0.124%), neg=0, invalid=762 0035: dt=129.472000, rms=0.762 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.769, neg=0, invalid=762 0036: dt=94.802993, rms=0.765 (0.571%), neg=0, invalid=762 0037: dt=580.608000, rms=0.741 (3.091%), neg=0, invalid=762 0038: dt=36.288000, rms=0.739 (0.317%), neg=0, invalid=762 0039: dt=111.746032, rms=0.737 (0.320%), neg=0, invalid=762 0040: dt=331.776000, rms=0.728 (1.168%), neg=0, invalid=762 0041: dt=36.288000, rms=0.727 (0.180%), neg=0, invalid=762 0042: dt=36.288000, rms=0.727 (0.001%), neg=0, invalid=762 0043: dt=36.288000, rms=0.727 (-0.109%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.727, neg=0, invalid=762 0044: dt=140.871508, rms=0.723 (0.548%), neg=0, invalid=762 0045: dt=103.680000, rms=0.722 (0.139%), neg=0, invalid=762 0046: dt=103.680000, rms=0.721 (0.108%), neg=0, invalid=762 0047: dt=103.680000, rms=0.720 (0.193%), neg=0, invalid=762 0048: dt=103.680000, rms=0.718 (0.247%), neg=0, invalid=762 0049: dt=103.680000, rms=0.716 (0.251%), neg=0, invalid=762 0050: dt=103.680000, rms=0.715 (0.246%), neg=0, invalid=762 0051: dt=103.680000, rms=0.712 (0.303%), neg=0, invalid=762 0052: dt=103.680000, rms=0.710 (0.332%), neg=0, invalid=762 0053: dt=103.680000, rms=0.708 (0.335%), neg=0, invalid=762 0054: dt=103.680000, rms=0.706 (0.296%), neg=0, invalid=762 0055: dt=103.680000, rms=0.704 (0.287%), neg=0, invalid=762 0056: dt=103.680000, rms=0.701 (0.341%), neg=0, invalid=762 0057: dt=103.680000, rms=0.699 (0.287%), neg=0, invalid=762 0058: dt=103.680000, rms=0.698 (0.219%), neg=0, invalid=762 0059: dt=103.680000, rms=0.696 (0.204%), neg=0, invalid=762 0060: dt=103.680000, rms=0.694 (0.264%), neg=0, invalid=762 0061: dt=103.680000, rms=0.693 (0.227%), neg=0, invalid=762 0062: dt=103.680000, rms=0.692 (0.160%), neg=0, invalid=762 0063: dt=103.680000, rms=0.691 (0.147%), neg=0, invalid=762 0064: dt=103.680000, rms=0.689 (0.171%), neg=0, invalid=762 0065: dt=103.680000, rms=0.689 (0.131%), neg=0, invalid=762 0066: dt=103.680000, rms=0.688 (0.116%), neg=0, invalid=762 0067: dt=103.680000, rms=0.687 (0.099%), neg=0, invalid=762 0068: dt=124.416000, rms=0.687 (0.061%), neg=0, invalid=762 0069: dt=124.416000, rms=0.687 (-0.069%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0070: dt=0.000000, rms=0.722 (0.061%), neg=0, invalid=762 0071: dt=0.000000, rms=0.722 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0072: dt=0.000000, rms=0.722 (0.061%), neg=0, invalid=762 0073: dt=0.000000, rms=0.722 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.828, neg=0, invalid=762 0074: dt=6.352657, rms=0.796 (3.921%), neg=0, invalid=762 0075: dt=6.836364, rms=0.791 (0.602%), neg=0, invalid=762 0076: dt=2.304000, rms=0.791 (0.018%), neg=0, invalid=762 0077: dt=2.304000, rms=0.791 (0.006%), neg=0, invalid=762 0078: dt=2.304000, rms=0.791 (-0.047%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.791, neg=0, invalid=762 0079: dt=0.000000, rms=0.791 (0.057%), neg=0, invalid=762 0080: dt=0.000000, rms=0.791 (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=0.865, neg=0, invalid=762 0081: dt=0.192000, rms=0.865 (0.060%), neg=0, invalid=762 0082: dt=0.192000, rms=0.865 (0.010%), neg=0, invalid=762 0083: dt=0.192000, rms=0.865 (0.007%), neg=0, invalid=762 0084: dt=0.192000, rms=0.865 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.865, neg=0, invalid=762 0085: dt=0.448000, rms=0.864 (0.098%), neg=0, invalid=762 0086: dt=1.024000, rms=0.863 (0.088%), neg=0, invalid=762 0087: dt=1.024000, rms=0.862 (0.206%), neg=0, invalid=762 0088: dt=1.024000, rms=0.860 (0.169%), neg=0, invalid=762 0089: dt=1.024000, rms=0.860 (-0.038%), neg=0, invalid=762 0090: dt=1.792000, rms=0.859 (0.160%), neg=0, invalid=762 0091: dt=3.081794, rms=0.857 (0.250%), neg=0, invalid=762 0092: dt=0.000000, rms=0.857 (0.001%), neg=0, invalid=762 0093: dt=0.100000, rms=0.857 (-0.002%), 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=0.791, neg=0, invalid=762 0094: dt=0.829837, rms=0.772 (2.282%), neg=0, invalid=762 0095: dt=0.080000, rms=0.772 (0.114%), neg=0, invalid=762 0096: dt=0.080000, rms=0.772 (-0.059%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.772, neg=0, invalid=762 0097: dt=0.028000, rms=0.772 (0.070%), neg=0, invalid=762 0098: dt=0.005000, rms=0.772 (0.002%), neg=0, invalid=762 0099: dt=0.005000, rms=0.772 (0.000%), neg=0, invalid=762 0100: dt=0.005000, rms=0.772 (-0.003%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.17561 (28) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (4676 voxels, overlap=0.338) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (4676 voxels, peak = 30), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.14405 (28) Right_Lateral_Ventricle (43): linear fit = 1.71 x + 0.0 (2572 voxels, overlap=0.218) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2572 voxels, peak = 27), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.04104 (80) Right_Pallidum (52): linear fit = 0.87 x + 0.0 (2019 voxels, overlap=0.228) Right_Pallidum (52): linear fit = 0.87 x + 0.0 (2019 voxels, peak = 83), gca=83.0 gca peak = 0.20183 (93) mri peak = 0.07033 (86) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (1823 voxels, overlap=0.102) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (1823 voxels, peak = 84), gca=84.2 gca peak = 0.21683 (55) mri peak = 0.05729 (73) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (2461 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (2461 voxels, peak = 72), gca=72.3 gca peak = 0.30730 (58) mri peak = 0.09054 (71) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2493 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2493 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.08394 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (177255 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (177255 voxels, peak = 103), gca=102.5 gca peak = 0.12076 (102) mri peak = 0.09043 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (176905 voxels, overlap=0.876) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (176905 voxels, peak = 102), gca=102.0 gca peak = 0.14995 (59) mri peak = 0.03616 (84) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (78849 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (78849 voxels, peak = 83), gca=83.5 gca peak = 0.15082 (58) mri peak = 0.04006 (78) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (91227 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (91227 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.08323 (76) Right_Caudate (50): linear fit = 1.15 x + 0.0 (2323 voxels, overlap=0.054) Right_Caudate (50): linear fit = 1.15 x + 0.0 (2323 voxels, peak = 77), gca=77.4 gca peak = 0.15243 (71) mri peak = 0.07949 (82) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2884 voxels, overlap=0.350) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2884 voxels, peak = 79), gca=79.2 gca peak = 0.13336 (57) mri peak = 0.04692 (68) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (38302 voxels, overlap=0.186) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (38302 voxels, peak = 70), gca=70.4 gca peak = 0.13252 (56) mri peak = 0.04186 (71) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (49494 voxels, overlap=0.005) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (49494 voxels, peak = 73), gca=73.1 gca peak = 0.18181 (84) mri peak = 0.05258 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (21634 voxels, overlap=0.655) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (21634 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.05270 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (18000 voxels, overlap=0.747) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (18000 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.08342 (73) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (1117 voxels, overlap=0.052) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (1117 voxels, peak = 72), gca=72.1 gca peak = 0.39313 (56) mri peak = 0.05500 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1336 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1336 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.07873 (100) Left_Thalamus_Proper (10): linear fit = 1.16 x + 0.0 (12952 voxels, overlap=0.031) Left_Thalamus_Proper (10): linear fit = 1.16 x + 0.0 (12952 voxels, peak = 99), gca=99.0 gca peak = 0.11978 (83) mri peak = 0.06025 (100) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (9611 voxels, overlap=0.104) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (9611 voxels, peak = 98), gca=97.5 gca peak = 0.13399 (79) mri peak = 0.04985 (88) Left_Putamen (12): linear fit = 1.12 x + 0.0 (5955 voxels, overlap=0.391) Left_Putamen (12): linear fit = 1.12 x + 0.0 (5955 voxels, peak = 88), gca=88.1 gca peak = 0.14159 (79) mri peak = 0.05678 (89) Right_Putamen (51): linear fit = 1.10 x + 0.0 (5696 voxels, overlap=0.338) Right_Putamen (51): linear fit = 1.10 x + 0.0 (5696 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.07982 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24411 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24411 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07793 (93) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (2693 voxels, overlap=0.300) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (2693 voxels, peak = 96), gca=95.9 gca peak = 0.12801 (89) mri peak = 0.06706 (98) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (3247 voxels, overlap=0.165) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (3247 voxels, peak = 102), gca=101.9 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.12335 (28) Fourth_Ventricle (15): linear fit = 1.71 x + 0.0 (1255 voxels, overlap=0.280) Fourth_Ventricle (15): linear fit = 1.71 x + 0.0 (1255 voxels, peak = 36), gca=35.8 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 1.31 x + 0.0 estimating mean wm scale to be 1.01 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=0.729, neg=0, invalid=762 0101: dt=161.401051, rms=0.699 (4.128%), neg=0, invalid=762 0102: dt=369.920000, rms=0.689 (1.393%), neg=0, invalid=762 0103: dt=221.952000, rms=0.684 (0.702%), neg=0, invalid=762 0104: dt=129.472000, rms=0.683 (0.201%), neg=0, invalid=762 0105: dt=1183.744000, rms=0.678 (0.766%), neg=0, invalid=762 0106: dt=129.472000, rms=0.677 (0.111%), neg=0, invalid=762 0107: dt=1183.744000, rms=0.675 (0.243%), neg=0, invalid=762 0108: dt=369.920000, rms=0.673 (0.301%), neg=0, invalid=762 0109: dt=110.976000, rms=0.673 (0.032%), neg=0, invalid=762 0110: dt=110.976000, rms=0.673 (0.024%), neg=0, invalid=762 0111: dt=110.976000, rms=0.673 (0.040%), neg=0, invalid=762 0112: dt=110.976000, rms=0.672 (0.057%), neg=0, invalid=762 0113: dt=110.976000, rms=0.672 (0.089%), neg=0, invalid=762 0114: dt=110.976000, rms=0.671 (0.106%), neg=0, invalid=762 0115: dt=110.976000, rms=0.670 (0.113%), neg=0, invalid=762 0116: dt=110.976000, rms=0.669 (0.104%), neg=0, invalid=762 0117: dt=110.976000, rms=0.669 (0.099%), neg=0, invalid=762 0118: dt=110.976000, rms=0.668 (0.100%), neg=0, invalid=762 0119: dt=110.976000, rms=0.667 (0.099%), neg=0, invalid=762 0120: dt=110.976000, rms=0.667 (0.097%), neg=0, invalid=762 0121: dt=110.976000, rms=0.666 (0.100%), neg=0, invalid=762 0122: dt=110.976000, rms=0.665 (0.109%), neg=0, invalid=762 0123: dt=110.976000, rms=0.665 (0.097%), neg=0, invalid=762 0124: dt=110.976000, rms=0.664 (0.083%), neg=0, invalid=762 0125: dt=110.976000, rms=0.664 (0.083%), neg=0, invalid=762 0126: dt=110.976000, rms=0.663 (0.076%), neg=0, invalid=762 0127: dt=110.976000, rms=0.663 (0.082%), neg=0, invalid=762 0128: dt=110.976000, rms=0.662 (0.087%), neg=0, invalid=762 0129: dt=110.976000, rms=0.661 (0.084%), neg=0, invalid=762 0130: dt=110.976000, rms=0.661 (0.069%), neg=0, invalid=762 0131: dt=110.976000, rms=0.661 (0.068%), neg=0, invalid=762 0132: dt=110.976000, rms=0.660 (0.060%), neg=0, invalid=762 0133: dt=110.976000, rms=0.660 (0.063%), neg=0, invalid=762 0134: dt=110.976000, rms=0.659 (0.068%), neg=0, invalid=762 0135: dt=110.976000, rms=0.659 (0.071%), neg=0, invalid=762 0136: dt=110.976000, rms=0.658 (0.065%), neg=0, invalid=762 0137: dt=110.976000, rms=0.658 (0.062%), neg=0, invalid=762 0138: dt=110.976000, rms=0.658 (0.038%), neg=0, invalid=762 0139: dt=110.976000, rms=0.657 (0.040%), neg=0, invalid=762 0140: dt=110.976000, rms=0.657 (0.047%), neg=0, invalid=762 0141: dt=110.976000, rms=0.657 (0.050%), neg=0, invalid=762 0142: dt=110.976000, rms=0.656 (0.052%), neg=0, invalid=762 0143: dt=110.976000, rms=0.656 (0.055%), neg=0, invalid=762 0144: dt=110.976000, rms=0.656 (0.048%), neg=0, invalid=762 0145: dt=110.976000, rms=0.655 (0.049%), neg=0, invalid=762 0146: dt=110.976000, rms=0.655 (0.035%), neg=0, invalid=762 0147: dt=110.976000, rms=0.655 (0.035%), neg=0, invalid=762 0148: dt=110.976000, rms=0.655 (0.043%), neg=0, invalid=762 0149: dt=110.976000, rms=0.654 (0.047%), neg=0, invalid=762 0150: dt=110.976000, rms=0.654 (0.046%), neg=0, invalid=762 0151: dt=110.976000, rms=0.654 (0.051%), neg=0, invalid=762 0152: dt=110.976000, rms=0.654 (0.036%), neg=0, invalid=762 0153: dt=110.976000, rms=0.653 (0.030%), neg=0, invalid=762 0154: dt=110.976000, rms=0.653 (0.028%), neg=0, invalid=762 0155: dt=110.976000, rms=0.653 (0.023%), neg=0, invalid=762 0156: dt=110.976000, rms=0.653 (0.037%), neg=0, invalid=762 0157: dt=110.976000, rms=0.653 (0.035%), neg=0, invalid=762 0158: dt=110.976000, rms=0.652 (0.039%), neg=0, invalid=762 0159: dt=110.976000, rms=0.652 (0.028%), neg=0, invalid=762 0160: dt=110.976000, rms=0.652 (0.022%), neg=0, invalid=762 0161: dt=110.976000, rms=0.652 (0.023%), neg=0, invalid=762 0162: dt=110.976000, rms=0.652 (0.026%), neg=0, invalid=762 0163: dt=110.976000, rms=0.651 (0.031%), neg=0, invalid=762 0164: dt=110.976000, rms=0.651 (0.036%), neg=0, invalid=762 0165: dt=110.976000, rms=0.651 (0.028%), neg=0, invalid=762 0166: dt=110.976000, rms=0.651 (0.020%), neg=0, invalid=762 0167: dt=110.976000, rms=0.651 (0.018%), neg=0, invalid=762 0168: dt=369.920000, rms=0.651 (0.010%), neg=0, invalid=762 0169: dt=369.920000, rms=0.651 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0170: dt=295.936000, rms=0.650 (0.101%), neg=0, invalid=762 0171: dt=295.936000, rms=0.650 (0.086%), neg=0, invalid=762 0172: dt=129.472000, rms=0.650 (0.025%), neg=0, invalid=762 0173: dt=129.472000, rms=0.649 (0.022%), neg=0, invalid=762 0174: dt=129.472000, rms=0.649 (0.027%), neg=0, invalid=762 0175: dt=129.472000, rms=0.649 (0.038%), neg=0, invalid=762 0176: dt=129.472000, rms=0.649 (0.045%), neg=0, invalid=762 0177: dt=129.472000, rms=0.648 (0.055%), neg=0, invalid=762 0178: dt=129.472000, rms=0.648 (0.048%), neg=0, invalid=762 0179: dt=129.472000, rms=0.648 (0.047%), neg=0, invalid=762 0180: dt=129.472000, rms=0.647 (0.038%), neg=0, invalid=762 0181: dt=129.472000, rms=0.647 (0.034%), neg=0, invalid=762 0182: dt=129.472000, rms=0.647 (0.031%), neg=0, invalid=762 0183: dt=129.472000, rms=0.647 (0.030%), neg=0, invalid=762 0184: dt=129.472000, rms=0.647 (0.034%), neg=0, invalid=762 0185: dt=129.472000, rms=0.646 (0.034%), neg=0, invalid=762 0186: dt=129.472000, rms=0.646 (0.023%), neg=0, invalid=762 0187: dt=129.472000, rms=0.646 (0.026%), neg=0, invalid=762 0188: dt=129.472000, rms=0.646 (0.023%), neg=0, invalid=762 0189: dt=129.472000, rms=0.646 (0.023%), neg=0, invalid=762 0190: dt=443.904000, rms=0.646 (0.020%), neg=0, invalid=762 0191: dt=443.904000, rms=0.646 (-0.039%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.647, neg=0, invalid=762 0192: dt=145.152000, rms=0.644 (0.574%), neg=0, invalid=762 0193: dt=145.152000, rms=0.640 (0.568%), neg=0, invalid=762 0194: dt=162.728682, rms=0.637 (0.501%), neg=0, invalid=762 0195: dt=92.911197, rms=0.635 (0.350%), neg=0, invalid=762 0196: dt=145.152000, rms=0.632 (0.426%), neg=0, invalid=762 0197: dt=94.881119, rms=0.631 (0.211%), neg=0, invalid=762 0198: dt=145.152000, rms=0.628 (0.370%), neg=0, invalid=762 0199: dt=86.325581, rms=0.627 (0.175%), neg=0, invalid=762 0200: dt=145.152000, rms=0.625 (0.334%), neg=0, invalid=762 0201: dt=62.208000, rms=0.624 (0.121%), neg=0, invalid=762 0202: dt=1327.104000, rms=0.616 (1.329%), neg=0, invalid=762 0203: dt=75.377778, rms=0.613 (0.466%), neg=0, invalid=762 0204: dt=96.888889, rms=0.612 (0.242%), neg=0, invalid=762 0205: dt=36.288000, rms=0.611 (0.059%), neg=0, invalid=762 0206: dt=414.720000, rms=0.610 (0.208%), neg=0, invalid=762 0207: dt=62.208000, rms=0.609 (0.240%), neg=0, invalid=762 0208: dt=145.152000, rms=0.608 (0.062%), neg=0, invalid=762 0209: dt=82.944000, rms=0.608 (0.095%), neg=0, invalid=762 0210: dt=82.944000, rms=0.607 (0.052%), neg=0, invalid=762 0211: dt=124.416000, rms=0.607 (0.098%), neg=0, invalid=762 0212: dt=36.288000, rms=0.606 (0.040%), neg=0, invalid=762 0213: dt=36.288000, rms=0.606 (0.025%), neg=0, invalid=762 0214: dt=36.288000, rms=0.606 (0.043%), neg=0, invalid=762 0215: dt=36.288000, rms=0.606 (0.057%), neg=0, invalid=762 0216: dt=36.288000, rms=0.605 (0.083%), neg=0, invalid=762 0217: dt=36.288000, rms=0.605 (0.094%), neg=0, invalid=762 0218: dt=36.288000, rms=0.604 (0.103%), neg=0, invalid=762 0219: dt=36.288000, rms=0.603 (0.115%), neg=0, invalid=762 0220: dt=36.288000, rms=0.603 (0.119%), neg=0, invalid=762 0221: dt=36.288000, rms=0.602 (0.128%), neg=0, invalid=762 0222: dt=36.288000, rms=0.601 (0.132%), neg=0, invalid=762 0223: dt=36.288000, rms=0.600 (0.131%), neg=0, invalid=762 0224: dt=36.288000, rms=0.599 (0.129%), neg=0, invalid=762 0225: dt=36.288000, rms=0.599 (0.125%), neg=0, invalid=762 0226: dt=36.288000, rms=0.598 (0.121%), neg=0, invalid=762 0227: dt=36.288000, rms=0.597 (0.117%), neg=0, invalid=762 0228: dt=36.288000, rms=0.597 (0.120%), neg=0, invalid=762 0229: dt=36.288000, rms=0.596 (0.121%), neg=0, invalid=762 0230: dt=36.288000, rms=0.595 (0.123%), neg=0, invalid=762 0231: dt=36.288000, rms=0.594 (0.122%), neg=0, invalid=762 0232: dt=36.288000, rms=0.594 (0.115%), neg=0, invalid=762 0233: dt=36.288000, rms=0.593 (0.111%), neg=0, invalid=762 0234: dt=36.288000, rms=0.592 (0.111%), neg=0, invalid=762 0235: dt=36.288000, rms=0.592 (0.102%), neg=0, invalid=762 0236: dt=36.288000, rms=0.591 (0.108%), neg=0, invalid=762 0237: dt=36.288000, rms=0.591 (0.102%), neg=0, invalid=762 0238: dt=36.288000, rms=0.590 (0.099%), neg=0, invalid=762 0239: dt=36.288000, rms=0.589 (0.083%), neg=0, invalid=762 0240: dt=36.288000, rms=0.589 (0.080%), neg=0, invalid=762 0241: dt=36.288000, rms=0.589 (0.008%), neg=0, invalid=762 0242: dt=36.288000, rms=0.589 (0.013%), neg=0, invalid=762 0243: dt=36.288000, rms=0.589 (0.017%), neg=0, invalid=762 0244: dt=36.288000, rms=0.589 (0.025%), neg=0, invalid=762 0245: dt=36.288000, rms=0.588 (0.030%), neg=0, invalid=762 0246: dt=36.288000, rms=0.588 (0.030%), neg=0, invalid=762 0247: dt=36.288000, rms=0.588 (0.032%), neg=0, invalid=762 0248: dt=36.288000, rms=0.588 (0.033%), neg=0, invalid=762 0249: dt=36.288000, rms=0.588 (0.035%), neg=0, invalid=762 0250: dt=36.288000, rms=0.587 (0.039%), neg=0, invalid=762 0251: dt=36.288000, rms=0.587 (0.043%), neg=0, invalid=762 0252: dt=36.288000, rms=0.587 (0.043%), neg=0, invalid=762 0253: dt=36.288000, rms=0.587 (0.047%), neg=0, invalid=762 0254: dt=36.288000, rms=0.586 (0.042%), neg=0, invalid=762 0255: dt=36.288000, rms=0.586 (0.046%), neg=0, invalid=762 0256: dt=36.288000, rms=0.586 (0.052%), neg=0, invalid=762 0257: dt=36.288000, rms=0.586 (0.051%), neg=0, invalid=762 0258: dt=36.288000, rms=0.585 (0.049%), neg=0, invalid=762 0259: dt=36.288000, rms=0.585 (0.045%), neg=0, invalid=762 0260: dt=36.288000, rms=0.585 (0.047%), neg=0, invalid=762 0261: dt=36.288000, rms=0.584 (0.047%), neg=0, invalid=762 0262: dt=36.288000, rms=0.584 (0.045%), neg=0, invalid=762 0263: dt=36.288000, rms=0.584 (0.047%), neg=0, invalid=762 0264: dt=36.288000, rms=0.584 (0.046%), neg=0, invalid=762 0265: dt=36.288000, rms=0.583 (0.046%), neg=0, invalid=762 0266: dt=36.288000, rms=0.583 (0.046%), neg=0, invalid=762 0267: dt=36.288000, rms=0.583 (0.052%), neg=0, invalid=762 0268: dt=36.288000, rms=0.583 (0.048%), neg=0, invalid=762 0269: dt=36.288000, rms=0.582 (0.043%), neg=0, invalid=762 0270: dt=36.288000, rms=0.582 (0.042%), neg=0, invalid=762 0271: dt=36.288000, rms=0.582 (0.041%), neg=0, invalid=762 0272: dt=36.288000, rms=0.582 (0.042%), neg=0, invalid=762 0273: dt=36.288000, rms=0.581 (0.038%), neg=0, invalid=762 0274: dt=36.288000, rms=0.581 (0.038%), neg=0, invalid=762 0275: dt=36.288000, rms=0.581 (0.033%), neg=0, invalid=762 0276: dt=36.288000, rms=0.581 (0.036%), neg=0, invalid=762 0277: dt=36.288000, rms=0.581 (0.030%), neg=0, invalid=762 0278: dt=36.288000, rms=0.580 (0.033%), neg=0, invalid=762 0279: dt=36.288000, rms=0.580 (0.034%), neg=0, invalid=762 0280: dt=36.288000, rms=0.580 (0.039%), neg=0, invalid=762 0281: dt=36.288000, rms=0.580 (0.039%), neg=0, invalid=762 0282: dt=36.288000, rms=0.580 (0.032%), neg=0, invalid=762 0283: dt=36.288000, rms=0.579 (0.029%), neg=0, invalid=762 0284: dt=36.288000, rms=0.579 (0.027%), neg=0, invalid=762 0285: dt=36.288000, rms=0.579 (0.024%), neg=0, invalid=762 0286: dt=36.288000, rms=0.579 (0.031%), neg=0, invalid=762 0287: dt=36.288000, rms=0.579 (0.033%), neg=0, invalid=762 0288: dt=36.288000, rms=0.579 (0.030%), neg=0, invalid=762 0289: dt=36.288000, rms=0.578 (0.026%), neg=0, invalid=762 0290: dt=36.288000, rms=0.578 (0.020%), neg=0, invalid=762 0291: dt=36.288000, rms=0.578 (0.020%), neg=0, invalid=762 0292: dt=62.208000, rms=0.578 (0.001%), neg=0, invalid=762 0293: dt=62.208000, rms=0.578 (0.007%), neg=0, invalid=762 0294: dt=62.208000, rms=0.578 (0.012%), neg=0, invalid=762 0295: dt=62.208000, rms=0.578 (0.006%), neg=0, invalid=762 0296: dt=62.208000, rms=0.578 (0.007%), neg=0, invalid=762 0297: dt=62.208000, rms=0.578 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=762 0298: dt=145.152000, rms=0.576 (0.415%), neg=0, invalid=762 0299: dt=36.288000, rms=0.576 (0.043%), neg=0, invalid=762 0300: dt=36.288000, rms=0.575 (0.020%), neg=0, invalid=762 0301: dt=36.288000, rms=0.575 (0.025%), neg=0, invalid=762 0302: dt=36.288000, rms=0.575 (0.042%), neg=0, invalid=762 0303: dt=36.288000, rms=0.575 (0.057%), neg=0, invalid=762 0304: dt=36.288000, rms=0.574 (0.064%), neg=0, invalid=762 0305: dt=36.288000, rms=0.574 (0.054%), neg=0, invalid=762 0306: dt=36.288000, rms=0.574 (0.037%), neg=0, invalid=762 0307: dt=36.288000, rms=0.574 (0.030%), neg=0, invalid=762 0308: dt=36.288000, rms=0.573 (0.027%), neg=0, invalid=762 0309: dt=36.288000, rms=0.573 (0.030%), neg=0, invalid=762 0310: dt=36.288000, rms=0.573 (0.034%), neg=0, invalid=762 0311: dt=36.288000, rms=0.573 (0.029%), neg=0, invalid=762 0312: dt=36.288000, rms=0.573 (0.024%), neg=0, invalid=762 0313: dt=36.288000, rms=0.573 (0.022%), neg=0, invalid=762 0314: dt=124.416000, rms=0.573 (0.011%), neg=0, invalid=762 0315: dt=124.416000, rms=0.572 (0.039%), neg=0, invalid=762 0316: dt=124.416000, rms=0.572 (0.028%), neg=0, invalid=762 0317: dt=124.416000, rms=0.572 (0.019%), neg=0, invalid=762 0318: dt=124.416000, rms=0.572 (0.051%), neg=0, invalid=762 0319: dt=124.416000, rms=0.572 (0.034%), neg=0, invalid=762 0320: dt=124.416000, rms=0.571 (0.030%), neg=0, invalid=762 0321: dt=124.416000, rms=0.571 (0.069%), neg=0, invalid=762 0322: dt=124.416000, rms=0.571 (0.050%), neg=0, invalid=762 0323: dt=124.416000, rms=0.571 (0.041%), neg=0, invalid=762 0324: dt=124.416000, rms=0.570 (0.062%), neg=0, invalid=762 0325: dt=124.416000, rms=0.570 (0.050%), neg=0, invalid=762 0326: dt=124.416000, rms=0.570 (0.023%), neg=0, invalid=762 0327: dt=124.416000, rms=0.570 (0.019%), neg=0, invalid=762 0328: dt=82.944000, rms=0.570 (0.023%), neg=0, invalid=762 0329: dt=103.680000, rms=0.569 (0.012%), neg=0, invalid=762 0330: dt=103.680000, rms=0.569 (0.009%), neg=0, invalid=762 0331: dt=103.680000, rms=0.569 (0.012%), neg=0, invalid=762 0332: dt=103.680000, rms=0.569 (0.021%), neg=0, invalid=762 0333: dt=103.680000, rms=0.569 (0.011%), neg=0, invalid=762 0334: dt=103.680000, rms=0.569 (0.027%), neg=0, invalid=762 0335: dt=103.680000, rms=0.569 (0.020%), neg=0, invalid=762 0336: dt=103.680000, rms=0.569 (0.017%), neg=0, invalid=762 0337: dt=82.944000, rms=0.569 (0.015%), neg=0, invalid=762 0338: dt=82.944000, rms=0.569 (0.002%), neg=0, invalid=762 0339: dt=82.944000, rms=0.569 (0.003%), neg=0, invalid=762 0340: dt=82.944000, rms=0.569 (0.015%), neg=0, invalid=762 0341: dt=82.944000, rms=0.569 (0.007%), neg=0, invalid=762 0342: dt=82.944000, rms=0.569 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.581, neg=0, invalid=762 0343: dt=11.200000, rms=0.581 (0.092%), neg=0, invalid=762 0344: dt=11.200000, rms=0.580 (0.045%), neg=0, invalid=762 0345: dt=11.200000, rms=0.580 (0.049%), neg=0, invalid=762 0346: dt=11.200000, rms=0.580 (0.056%), neg=0, invalid=762 0347: dt=11.200000, rms=0.579 (0.046%), neg=0, invalid=762 0348: dt=11.200000, rms=0.579 (0.060%), neg=0, invalid=762 0349: dt=11.200000, rms=0.578 (0.121%), neg=0, invalid=762 0350: dt=11.200000, rms=0.577 (0.206%), neg=0, invalid=762 0351: dt=11.200000, rms=0.576 (0.282%), neg=0, invalid=762 0352: dt=11.200000, rms=0.574 (0.339%), neg=0, invalid=762 0353: dt=11.200000, rms=0.571 (0.378%), neg=0, invalid=762 0354: dt=11.200000, rms=0.569 (0.375%), neg=0, invalid=762 0355: dt=11.200000, rms=0.569 (0.091%), neg=0, invalid=762 0356: dt=11.200000, rms=0.568 (0.158%), neg=0, invalid=762 0357: dt=11.200000, rms=0.567 (0.199%), neg=0, invalid=762 0358: dt=11.200000, rms=0.565 (0.224%), neg=0, invalid=762 0359: dt=11.200000, rms=0.565 (0.061%), neg=0, invalid=762 0360: dt=11.200000, rms=0.565 (0.047%), neg=0, invalid=762 0361: dt=2.800000, rms=0.565 (0.016%), neg=0, invalid=762 0362: dt=1.400000, rms=0.565 (0.006%), neg=0, invalid=762 0363: dt=0.700000, rms=0.565 (0.003%), neg=0, invalid=762 0364: dt=0.087500, rms=0.565 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=762 0365: dt=70.285714, rms=0.561 (0.627%), neg=0, invalid=762 0366: dt=11.200000, rms=0.561 (0.115%), neg=0, invalid=762 0367: dt=11.200000, rms=0.561 (0.037%), neg=0, invalid=762 0368: dt=11.200000, rms=0.560 (0.019%), neg=0, invalid=762 0369: dt=11.200000, rms=0.560 (0.020%), neg=0, invalid=762 0370: dt=11.200000, rms=0.560 (0.027%), neg=0, invalid=762 0371: dt=11.200000, rms=0.560 (0.051%), neg=0, invalid=762 0372: dt=11.200000, rms=0.560 (0.074%), neg=0, invalid=762 0373: dt=11.200000, rms=0.559 (0.091%), neg=0, invalid=762 0374: dt=11.200000, rms=0.559 (0.089%), neg=0, invalid=762 0375: dt=11.200000, rms=0.558 (0.081%), neg=0, invalid=762 0376: dt=11.200000, rms=0.558 (0.080%), neg=0, invalid=762 0377: dt=11.200000, rms=0.557 (0.072%), neg=0, invalid=762 0378: dt=11.200000, rms=0.557 (0.070%), neg=0, invalid=762 0379: dt=11.200000, rms=0.556 (0.081%), neg=0, invalid=762 0380: dt=11.200000, rms=0.556 (0.095%), neg=0, invalid=762 0381: dt=11.200000, rms=0.555 (0.106%), neg=0, invalid=762 0382: dt=11.200000, rms=0.555 (0.124%), neg=0, invalid=762 0383: dt=11.200000, rms=0.554 (0.135%), neg=0, invalid=762 0384: dt=11.200000, rms=0.553 (0.134%), neg=0, invalid=762 0385: dt=11.200000, rms=0.552 (0.130%), neg=0, invalid=762 0386: dt=11.200000, rms=0.552 (0.127%), neg=0, invalid=762 0387: dt=11.200000, rms=0.551 (0.120%), neg=0, invalid=762 0388: dt=11.200000, rms=0.550 (0.105%), neg=0, invalid=762 0389: dt=11.200000, rms=0.550 (0.102%), neg=0, invalid=762 0390: dt=11.200000, rms=0.549 (0.106%), neg=0, invalid=762 0391: dt=11.200000, rms=0.549 (0.097%), neg=0, invalid=762 0392: dt=11.200000, rms=0.548 (0.094%), neg=0, invalid=762 0393: dt=11.200000, rms=0.548 (0.087%), neg=0, invalid=762 0394: dt=11.200000, rms=0.547 (0.081%), neg=0, invalid=762 0395: dt=11.200000, rms=0.547 (0.074%), neg=0, invalid=762 0396: dt=11.200000, rms=0.547 (0.062%), neg=0, invalid=762 0397: dt=11.200000, rms=0.546 (0.053%), neg=0, invalid=762 0398: dt=11.200000, rms=0.546 (0.055%), neg=0, invalid=762 0399: dt=11.200000, rms=0.546 (0.052%), neg=0, invalid=762 0400: dt=11.200000, rms=0.545 (0.052%), neg=0, invalid=762 0401: dt=11.200000, rms=0.545 (0.047%), neg=0, invalid=762 0402: dt=11.200000, rms=0.545 (0.045%), neg=0, invalid=762 0403: dt=11.200000, rms=0.545 (0.036%), neg=0, invalid=762 0404: dt=11.200000, rms=0.545 (0.035%), neg=0, invalid=762 0405: dt=11.200000, rms=0.544 (0.029%), neg=0, invalid=762 0406: dt=11.200000, rms=0.544 (0.030%), neg=0, invalid=762 0407: dt=11.200000, rms=0.544 (0.036%), neg=0, invalid=762 0408: dt=11.200000, rms=0.544 (0.032%), neg=0, invalid=762 0409: dt=11.200000, rms=0.544 (0.032%), neg=0, invalid=762 0410: dt=11.200000, rms=0.543 (0.032%), neg=0, invalid=762 0411: dt=11.200000, rms=0.543 (0.032%), neg=0, invalid=762 0412: dt=11.200000, rms=0.543 (0.035%), neg=0, invalid=762 0413: dt=11.200000, rms=0.543 (0.035%), neg=0, invalid=762 0414: dt=11.200000, rms=0.543 (0.029%), neg=0, invalid=762 0415: dt=11.200000, rms=0.543 (0.029%), neg=0, invalid=762 0416: dt=11.200000, rms=0.542 (0.032%), neg=0, invalid=762 0417: dt=11.200000, rms=0.542 (0.030%), neg=0, invalid=762 0418: dt=11.200000, rms=0.542 (0.032%), neg=0, invalid=762 0419: dt=11.200000, rms=0.542 (0.028%), neg=0, invalid=762 0420: dt=11.200000, rms=0.542 (0.022%), neg=0, invalid=762 0421: dt=11.200000, rms=0.542 (0.023%), neg=0, invalid=762 0422: dt=11.200000, rms=0.542 (0.025%), neg=0, invalid=762 0423: dt=11.200000, rms=0.541 (0.024%), neg=0, invalid=762 0424: dt=44.800000, rms=0.541 (0.010%), neg=0, invalid=762 0425: dt=44.800000, rms=0.541 (-0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0426: dt=0.000000, rms=0.563 (0.043%), neg=0, invalid=762 0427: dt=0.000000, rms=0.563 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0428: dt=0.000000, rms=0.563 (0.043%), neg=0, invalid=762 0429: dt=0.000000, rms=0.563 (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=0.607, neg=0, invalid=762 0430: dt=1.536000, rms=0.603 (0.613%), neg=0, invalid=762 0431: dt=0.192000, rms=0.603 (0.009%), neg=0, invalid=762 0432: dt=0.192000, rms=0.603 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=762 0433: dt=0.448000, rms=0.603 (0.096%), neg=0, invalid=762 0434: dt=0.384000, rms=0.603 (0.015%), neg=0, invalid=762 0435: dt=0.384000, rms=0.603 (-0.006%), 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=0.552, neg=0, invalid=762 0436: dt=0.448000, rms=0.537 (2.730%), neg=0, invalid=762 0437: dt=0.448000, rms=0.534 (0.608%), neg=0, invalid=762 0438: dt=0.448000, rms=0.532 (0.336%), neg=0, invalid=762 0439: dt=0.448000, rms=0.531 (0.209%), neg=0, invalid=762 0440: dt=0.583333, rms=0.530 (0.194%), neg=0, invalid=762 0441: dt=0.448000, rms=0.529 (0.103%), neg=0, invalid=762 0442: dt=0.448000, rms=0.529 (0.082%), neg=0, invalid=762 0443: dt=0.448000, rms=0.529 (0.067%), neg=0, invalid=762 0444: dt=0.448000, rms=0.528 (0.055%), neg=0, invalid=762 0445: dt=0.448000, rms=0.528 (0.046%), neg=0, invalid=762 0446: dt=0.448000, rms=0.528 (0.044%), neg=0, invalid=762 0447: dt=0.448000, rms=0.527 (0.068%), neg=0, invalid=762 0448: dt=0.448000, rms=0.527 (0.087%), neg=0, invalid=762 0449: dt=0.448000, rms=0.526 (0.090%), neg=0, invalid=762 0450: dt=0.448000, rms=0.526 (0.004%), neg=0, invalid=762 0451: dt=0.448000, rms=0.526 (0.009%), neg=0, invalid=762 0452: dt=0.448000, rms=0.526 (0.009%), neg=0, invalid=762 0453: dt=0.448000, rms=0.526 (0.009%), neg=0, invalid=762 0454: dt=0.448000, rms=0.526 (0.017%), neg=0, invalid=762 0455: dt=0.448000, rms=0.526 (0.005%), neg=0, invalid=762 0456: dt=0.448000, rms=0.526 (0.002%), neg=0, invalid=762 0457: dt=0.448000, rms=0.526 (0.005%), neg=0, invalid=762 0458: dt=0.448000, rms=0.526 (0.005%), neg=0, invalid=762 0459: dt=0.448000, rms=0.526 (0.011%), neg=0, invalid=762 0460: dt=0.448000, rms=0.526 (0.013%), neg=0, invalid=762 0461: dt=0.448000, rms=0.526 (0.009%), neg=0, invalid=762 0462: dt=0.448000, rms=0.526 (0.013%), neg=0, invalid=762 0463: dt=0.448000, rms=0.526 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=762 0464: dt=0.448000, rms=0.522 (0.888%), neg=0, invalid=762 0465: dt=0.448000, rms=0.521 (0.117%), neg=0, invalid=762 0466: dt=0.448000, rms=0.521 (0.042%), neg=0, invalid=762 0467: dt=0.448000, rms=0.521 (0.012%), neg=0, invalid=762 0468: dt=0.448000, rms=0.521 (0.012%), neg=0, invalid=762 0469: dt=0.448000, rms=0.521 (0.001%), neg=0, invalid=762 0470: dt=0.000000, rms=0.521 (-0.000%), 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=0.518, neg=0, invalid=762 0471: dt=0.000000, rms=0.518 (0.062%), neg=0, invalid=762 0472: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 0473: dt=73.984000, rms=0.518 (0.067%), neg=0, invalid=762 0474: dt=221.952000, rms=0.518 (0.019%), neg=0, invalid=762 0475: dt=221.952000, rms=0.518 (0.004%), neg=0, invalid=762 0476: dt=221.952000, rms=0.518 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0477: dt=25.920000, rms=0.518 (0.098%), neg=0, invalid=762 0478: dt=20.736000, rms=0.518 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0479: dt=20.736000, rms=0.518 (0.009%), neg=0, invalid=762 0480: dt=20.736000, rms=0.518 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 0481: dt=124.416000, rms=0.515 (0.493%), neg=0, invalid=762 0482: dt=36.288000, rms=0.515 (0.110%), neg=0, invalid=762 0483: dt=36.288000, rms=0.515 (0.035%), neg=0, invalid=762 0484: dt=36.288000, rms=0.514 (0.059%), neg=0, invalid=762 0485: dt=36.288000, rms=0.514 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0486: dt=36.288000, rms=0.513 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0487: dt=36.288000, rms=0.513 (0.117%), neg=0, invalid=762 0488: dt=36.288000, rms=0.512 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0489: dt=36.288000, rms=0.512 (0.082%), neg=0, invalid=762 0490: dt=103.680000, rms=0.512 (0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.512, neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0491: dt=25.600000, rms=0.511 (0.336%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 4 iterations, nbhd size=0, neg = 0 0492: dt=79.466667, rms=0.509 (0.394%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0493: dt=25.600000, rms=0.508 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0494: dt=25.600000, rms=0.507 (0.225%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0495: dt=25.600000, rms=0.505 (0.234%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0496: dt=25.600000, rms=0.504 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 4 iterations, nbhd size=0, neg = 0 0497: dt=25.600000, rms=0.504 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 5 iterations, nbhd size=0, neg = 0 0498: dt=25.600000, rms=0.503 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0499: dt=25.600000, rms=0.502 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 5 iterations, nbhd size=0, neg = 0 0500: dt=25.600000, rms=0.502 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 12 iterations, nbhd size=1, neg = 0 0501: dt=25.600000, rms=0.502 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0502: dt=38.400000, rms=0.501 (0.094%), neg=0, invalid=762 0503: dt=11.200000, rms=0.501 (0.046%), neg=0, invalid=762 0504: dt=11.200000, rms=0.501 (0.021%), neg=0, invalid=762 0505: dt=11.200000, rms=0.501 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0506: dt=11.200000, rms=0.501 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0507: dt=11.200000, rms=0.500 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0508: dt=11.200000, rms=0.500 (0.046%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0509: dt=11.200000, rms=0.500 (0.039%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0510: dt=61.391304, rms=0.495 (0.969%), neg=0, invalid=762 0511: dt=11.200000, rms=0.495 (0.174%), neg=0, invalid=762 0512: dt=11.200000, rms=0.494 (0.057%), neg=0, invalid=762 0513: dt=11.200000, rms=0.494 (0.044%), neg=0, invalid=762 0514: dt=11.200000, rms=0.494 (0.028%), neg=0, invalid=762 0515: dt=44.800000, rms=0.493 (0.202%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0516: dt=11.200000, rms=0.493 (0.034%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 0517: dt=3.456000, rms=0.499 (0.113%), neg=0, invalid=762 0518: dt=2.117647, rms=0.499 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0519: dt=2.117647, rms=0.499 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0520: dt=2.117647, rms=0.499 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0521: dt=12.231405, rms=0.497 (0.467%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0522: dt=23.733333, rms=0.495 (0.388%), neg=0, invalid=762 0523: dt=19.578947, rms=0.494 (0.334%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0524: dt=10.632911, rms=0.493 (0.232%), neg=0, invalid=762 0525: dt=10.632911, rms=0.492 (0.138%), neg=0, invalid=762 0526: dt=10.632911, rms=0.491 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0527: dt=10.632911, rms=0.490 (0.269%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 13 iterations, nbhd size=1, neg = 0 0528: dt=10.632911, rms=0.489 (0.220%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=0, neg = 0 0529: dt=10.632911, rms=0.487 (0.253%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0530: dt=10.632911, rms=0.486 (0.229%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0531: dt=10.632911, rms=0.485 (0.206%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 5 iterations, nbhd size=0, neg = 0 0532: dt=10.632911, rms=0.485 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0533: dt=10.632911, rms=0.484 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 5 iterations, nbhd size=0, neg = 0 0534: dt=10.632911, rms=0.484 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0535: dt=8.827586, rms=0.483 (0.017%), neg=0, invalid=762 0536: dt=8.827586, rms=0.483 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0537: dt=8.827586, rms=0.483 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0538: dt=0.000000, rms=0.489 (0.068%), neg=0, invalid=762 0539: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0540: dt=0.000000, rms=0.489 (0.068%), neg=0, invalid=762 0541: dt=0.000000, rms=0.489 (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=0.480, neg=0, invalid=762 iter 0, gcam->neg = 412 after 13 iterations, nbhd size=1, neg = 0 0542: dt=2.090863, rms=0.450 (6.155%), neg=0, invalid=762 0543: dt=0.080000, rms=0.450 (0.054%), neg=0, invalid=762 0544: dt=0.080000, rms=0.450 (-0.053%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0545: dt=0.064000, rms=0.450 (0.126%), neg=0, invalid=762 0546: dt=0.004000, rms=0.450 (0.003%), neg=0, invalid=762 0547: dt=0.004000, rms=0.450 (0.000%), neg=0, invalid=762 0548: dt=0.004000, rms=0.450 (-0.001%), 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=0.435, neg=0, invalid=762 0549: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 0550: dt=2.023000, rms=0.435 (0.000%), neg=0, invalid=762 0551: dt=0.433500, rms=0.435 (0.000%), neg=0, invalid=762 0552: dt=0.433500, rms=0.435 (0.000%), neg=0, invalid=762 0553: dt=0.433500, rms=0.435 (-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=0.435, neg=0, invalid=762 0554: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 0555: dt=15.552000, rms=0.435 (0.010%), neg=0, invalid=762 0556: dt=9.072000, rms=0.435 (0.002%), neg=0, invalid=762 0557: dt=9.072000, rms=0.435 (0.000%), neg=0, invalid=762 0558: dt=9.072000, rms=0.435 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0559: dt=6.400000, rms=0.436 (0.033%), neg=0, invalid=762 0560: dt=2.400000, rms=0.436 (0.003%), neg=0, invalid=762 0561: dt=2.400000, rms=0.436 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0562: dt=44.800000, rms=0.434 (0.362%), neg=0, invalid=762 0563: dt=32.000000, rms=0.433 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0564: dt=32.000000, rms=0.433 (0.119%), neg=0, invalid=762 0565: dt=32.000000, rms=0.432 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 0566: dt=32.000000, rms=0.432 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 0567: dt=32.000000, rms=0.431 (0.100%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0568: dt=32.000000, rms=0.431 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 17 iterations, nbhd size=1, neg = 0 0569: dt=32.000000, rms=0.431 (-0.027%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 10 iterations, nbhd size=1, neg = 0 0570: dt=25.600000, rms=0.431 (-0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0571: dt=2.640000, rms=0.434 (0.038%), neg=0, invalid=762 0572: dt=0.576000, rms=0.434 (0.001%), neg=0, invalid=762 0573: dt=0.576000, rms=0.434 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0574: dt=13.824000, rms=0.433 (0.303%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=1, neg = 0 0575: dt=25.931034, rms=0.432 (0.219%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 4 iterations, nbhd size=0, neg = 0 0576: dt=25.931034, rms=0.432 (-0.162%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0577: dt=0.000078, rms=0.438 (0.000%), neg=0, invalid=762 0578: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0579: dt=0.000000, rms=0.438 (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=0.428, neg=0, invalid=762 iter 0, gcam->neg = 203 after 14 iterations, nbhd size=1, neg = 0 0580: dt=1.325451, rms=0.419 (2.046%), neg=0, invalid=762 0581: dt=0.000023, rms=0.419 (0.000%), neg=0, invalid=762 0582: dt=0.000023, rms=0.419 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0583: dt=0.112000, rms=0.419 (0.072%), neg=0, invalid=762 0584: dt=0.080000, rms=0.419 (0.019%), neg=0, invalid=762 0585: dt=0.080000, rms=0.419 (0.007%), neg=0, invalid=762 0586: dt=0.080000, rms=0.419 (-0.040%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 39 minutes and 18 seconds. mri_ca_register utimesec 7383.499490 mri_ca_register stimesec 13.621452 mri_ca_register ru_maxrss 1633772 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 9418569 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62872 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 18146 mri_ca_register ru_nivcsw 3503 FSRUNTIME@ mri_ca_register 1.6549 hours 8 threads #-------------------------------------- #@# SubCort Seg Tue May 25 19:28:57 UTC 2021 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 blg5611.int.ets1.calculquebec.ca machine x86_64 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 13.79 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 = 0.13953 (28) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (1711 voxels, overlap=0.188) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (1711 voxels, peak = 30), gca=29.5 gca peak = 0.17677 (13) mri peak = 0.11962 (28) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (1368 voxels, overlap=0.191) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1368 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.06473 (102) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (1920 voxels, overlap=1.025) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (1920 voxels, peak = 101), gca=101.2 gca peak = 0.16930 (96) mri peak = 0.08212 (102) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (1810 voxels, overlap=0.754) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (1810 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.07284 (74) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2856 voxels, overlap=0.025) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2856 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.09137 (71) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (2680 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (2680 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.08340 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (122992 voxels, overlap=0.815) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (122992 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.08963 (102) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (115386 voxels, overlap=0.776) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (115386 voxels, peak = 102), gca=102.4 gca peak = 0.09712 (58) mri peak = 0.03718 (78) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (111469 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (111469 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.04027 (78) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (97129 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (97129 voxels, peak = 78), gca=78.0 gca peak = 0.30970 (66) mri peak = 0.10441 (78) Right_Caudate (50): linear fit = 1.15 x + 0.0 (2575 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.15 x + 0.0 (2575 voxels, peak = 76), gca=76.2 gca peak = 0.15280 (69) mri peak = 0.12381 (83) Left_Caudate (11): linear fit = 1.10 x + 0.0 (2307 voxels, overlap=0.428) Left_Caudate (11): linear fit = 1.10 x + 0.0 (2307 voxels, peak = 76), gca=75.6 gca peak = 0.13902 (56) mri peak = 0.05684 (68) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (54051 voxels, overlap=0.132) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (54051 voxels, peak = 69), gca=68.6 gca peak = 0.14777 (55) mri peak = 0.05424 (70) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (56027 voxels, overlap=0.040) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (56027 voxels, peak = 70), gca=69.6 gca peak = 0.16765 (84) mri peak = 0.10732 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (14330 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (14330 voxels, peak = 87), gca=86.9 gca peak = 0.18739 (84) mri peak = 0.12437 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (12905 voxels, overlap=0.466) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (12905 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.10184 (73) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (1414 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (1414 voxels, peak = 72), gca=72.1 gca peak = 0.33601 (57) mri peak = 0.09664 (77) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (1401 voxels, overlap=0.053) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (1401 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.06843 (100) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (10592 voxels, overlap=0.479) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (10592 voxels, peak = 99), gca=99.5 gca peak = 0.11793 (83) mri peak = 0.06538 (95) Right_Thalamus_Proper (49): linear fit = 1.16 x + 0.0 (9866 voxels, overlap=0.099) Right_Thalamus_Proper (49): linear fit = 1.16 x + 0.0 (9866 voxels, peak = 97), gca=96.7 gca peak = 0.08324 (81) mri peak = 0.08821 (88) Left_Putamen (12): linear fit = 1.11 x + 0.0 (3775 voxels, overlap=0.427) Left_Putamen (12): linear fit = 1.11 x + 0.0 (3775 voxels, peak = 90), gca=89.5 gca peak = 0.10360 (77) mri peak = 0.07945 (85) Right_Putamen (51): linear fit = 1.09 x + 0.0 (3614 voxels, overlap=0.549) Right_Putamen (51): linear fit = 1.09 x + 0.0 (3614 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.07007 (86) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24709 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24709 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.07214 (100) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (3251 voxels, overlap=0.086) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (3251 voxels, peak = 102), gca=101.9 gca peak = 0.14500 (87) mri peak = 0.08271 (100) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (3487 voxels, overlap=0.181) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (3487 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.17241 (28) gca peak = 0.19357 (14) mri peak = 0.15878 (27) Fourth_Ventricle (15): linear fit = 1.83 x + 0.0 (353 voxels, overlap=0.173) Fourth_Ventricle (15): linear fit = 1.83 x + 0.0 (353 voxels, peak = 26), gca=25.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak 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 1.49 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 0.982 (from 1.065) to 99.4 (was 101.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15664 (27) mri peak = 0.13953 (28) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1711 voxels, overlap=0.786) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1711 voxels, peak = 27), gca=26.6 gca peak = 0.13981 (19) mri peak = 0.11962 (28) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (1368 voxels, overlap=0.460) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (1368 voxels, peak = 25), gca=24.6 gca peak = 0.27189 (100) mri peak = 0.06473 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1920 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1920 voxels, peak = 100), gca=100.5 gca peak = 0.17492 (100) mri peak = 0.08212 (102) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1810 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1810 voxels, peak = 102), gca=102.5 gca peak = 0.24467 (71) mri peak = 0.07284 (74) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (2856 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (2856 voxels, peak = 73), gca=73.5 gca peak = 0.27649 (69) mri peak = 0.09137 (71) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (2680 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (2680 voxels, peak = 70), gca=70.0 gca peak = 0.07811 (102) mri peak = 0.08340 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (122992 voxels, overlap=0.801) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (122992 voxels, peak = 101), gca=101.5 gca peak = 0.07921 (103) mri peak = 0.08963 (102) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (115386 voxels, overlap=0.770) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (115386 voxels, peak = 102), gca=102.5 gca peak = 0.07326 (78) mri peak = 0.03718 (78) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (111469 voxels, overlap=0.956) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (111469 voxels, peak = 82), gca=81.5 gca peak = 0.08777 (78) mri peak = 0.04027 (78) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (97129 voxels, overlap=0.959) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (97129 voxels, peak = 76), gca=76.1 gca peak = 0.25022 (77) mri peak = 0.10441 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2575 voxels, overlap=1.004) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2575 voxels, peak = 77), gca=77.0 gca peak = 0.12831 (75) mri peak = 0.12381 (83) Left_Caudate (11): linear fit = 1.00 x + 0.0 (2307 voxels, overlap=0.962) Left_Caudate (11): linear fit = 1.00 x + 0.0 (2307 voxels, peak = 75), gca=75.0 gca peak = 0.11797 (68) mri peak = 0.05684 (68) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (54051 voxels, overlap=0.989) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (54051 voxels, peak = 68), gca=68.0 gca peak = 0.12186 (69) mri peak = 0.05424 (70) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (56027 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (56027 voxels, peak = 69), gca=69.0 gca peak = 0.15881 (87) mri peak = 0.10732 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (14330 voxels, overlap=0.902) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (14330 voxels, peak = 87), gca=87.0 gca peak = 0.15254 (90) mri peak = 0.12437 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (12905 voxels, overlap=0.868) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (12905 voxels, peak = 90), gca=89.6 gca peak = 0.27743 (72) mri peak = 0.10184 (73) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (1414 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (1414 voxels, peak = 73), gca=73.1 gca peak = 0.33040 (74) mri peak = 0.09664 (77) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (1401 voxels, overlap=1.008) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (1401 voxels, peak = 76), gca=75.8 gca peak = 0.09230 (99) mri peak = 0.06843 (100) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (10592 voxels, overlap=0.913) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (10592 voxels, peak = 100), gca=100.5 gca peak = 0.10535 (94) mri peak = 0.06538 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (9866 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (9866 voxels, peak = 94), gca=94.5 gca peak = 0.08025 (83) mri peak = 0.08821 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3775 voxels, overlap=0.845) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3775 voxels, peak = 83), gca=82.6 gca peak = 0.08953 (85) mri peak = 0.07945 (85) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3614 voxels, overlap=0.885) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3614 voxels, peak = 85), gca=84.6 gca peak = 0.07725 (86) mri peak = 0.07007 (86) Brain_Stem (16): linear fit = 1.01 x + 0.0 (24709 voxels, overlap=0.805) Brain_Stem (16): linear fit = 1.01 x + 0.0 (24709 voxels, peak = 87), gca=87.3 gca peak = 0.11748 (102) mri peak = 0.07214 (100) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (3251 voxels, overlap=0.826) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (3251 voxels, peak = 102), gca=102.0 gca peak = 0.15511 (97) mri peak = 0.08271 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (3487 voxels, overlap=0.914) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (3487 voxels, peak = 97), gca=96.5 gca peak = 0.12356 (31) mri peak = 0.17241 (28) gca peak = 0.15108 (22) mri peak = 0.15878 (27) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (353 voxels, overlap=0.612) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (353 voxels, peak = 27), gca=26.7 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 = 0.12356 (31) gca peak CSF = 0.16908 (54) gca peak Left_Accumbens_area = 0.45609 (68) gca peak Left_undetermined = 0.96707 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11818 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.32652 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (46) gca peak WM_hypointensities = 0.08015 (76) gca peak non_WM_hypointensities = 0.08491 (54) gca peak Optic_Chiasm = 0.61303 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.16 x + 0.0 Left_Pallidum too bright - rescaling by 0.965 (from 1.025) to 98.9 (was 102.5) Right_Pallidum too bright - rescaling by 0.984 (from 1.005) to 98.9 (was 100.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 183996 voxels changed in iteration 0 of unlikely voxel relabeling 944 voxels changed in iteration 1 of unlikely voxel relabeling 21 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 228118 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 701 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 153587 changed. image ll: -2.120, PF=0.500 pass 2: 43445 changed. image ll: -2.119, PF=0.500 pass 3: 14214 changed. pass 4: 5690 changed. pass 5: 2775 changed. 209026 voxels changed in iteration 0 of unlikely voxel relabeling 1843 voxels changed in iteration 1 of unlikely voxel relabeling 194 voxels changed in iteration 2 of unlikely voxel relabeling 64 voxels changed in iteration 3 of unlikely voxel relabeling 6 voxels changed in iteration 4 of unlikely voxel relabeling 17709 voxels changed in iteration 0 of unlikely voxel relabeling 303 voxels changed in iteration 1 of unlikely voxel relabeling 70 voxels changed in iteration 2 of unlikely voxel relabeling 13 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 15281 voxels changed in iteration 0 of unlikely voxel relabeling 226 voxels changed in iteration 1 of unlikely voxel relabeling 155 voxels changed in iteration 2 of unlikely voxel relabeling 30 voxels changed in iteration 3 of unlikely voxel relabeling 24 voxels changed in iteration 4 of unlikely voxel relabeling 13327 voxels changed in iteration 0 of unlikely voxel relabeling 70 voxels changed in iteration 1 of unlikely voxel relabeling 15 voxels changed in iteration 2 of unlikely voxel relabeling 15 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4895.404952 mri_ca_label stimesec 5.147949 mri_ca_label ru_maxrss 3178112 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 6024352 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 4840 mri_ca_label ru_oublock 800 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 812 mri_ca_label ru_nivcsw 1370 auto-labeling took 80 minutes and 21 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/cc_up.lta reading aseg from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aseg.auto_noCCseg.mgz reading norm from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/norm.mgz 41097 voxels in left wm, 50948 in right wm, xrange [158, 165] 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 161.0, rotations (-0.43, 0.11) final transformation (x=161.0, yr=-0.431, zr=0.113): 0.99997 -0.00198 -0.00752 -31.77959; 0.00198 1.00000 -0.00001 18.68358; 0.00752 0.00000 0.99997 -6.20657; 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 127 109 133 eigenvectors: -0.00017 -0.00038 1.00000; 0.02350 -0.99972 -0.00038; 0.99972 0.02350 0.00018; writing aseg with callosum to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Tue May 25 20:49:56 UTC 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue May 25 20:49:56 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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... 1078 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 81 (81), valley at 36 (36) csf peak at 41, setting threshold to 67 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 36 (36) 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 4 minutes and 38 seconds. #-------------------------------------------- #@# Mask BFS Tue May 25 20:54:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2858129 voxels in mask (pct= 8.72) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue May 25 20:54:43 UTC 2021 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.5 +- 6.3 [79.0 --> 125.0] GM (79.0) : 77.9 +- 10.1 [30.0 --> 95.0] setting bottom of white matter range to 88.0 setting top of gray matter range to 98.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... thickening thin strands.... 20 segments, 7395 filled 810 bright non-wm voxels segmented. 7528 diagonally connected voxels added... white matter segmentation took 2.1 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 0.61 minutes reading wm segmentation from wm.seg.mgz... 248 voxels added to wm to prevent paths from MTL structures to cortex 9204 additional wm voxels added 0 additional wm voxels added SEG EDIT: 76880 voxels turned on, 79201 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 59 found - 59 modified | TOTAL: 59 pass 2 (xy+): 0 found - 59 modified | TOTAL: 59 pass 1 (xy-): 64 found - 64 modified | TOTAL: 123 pass 2 (xy-): 0 found - 64 modified | TOTAL: 123 pass 1 (yz+): 66 found - 66 modified | TOTAL: 189 pass 2 (yz+): 0 found - 66 modified | TOTAL: 189 pass 1 (yz-): 73 found - 73 modified | TOTAL: 262 pass 2 (yz-): 0 found - 73 modified | TOTAL: 262 pass 1 (xz+): 59 found - 59 modified | TOTAL: 321 pass 2 (xz+): 0 found - 59 modified | TOTAL: 321 pass 1 (xz-): 70 found - 70 modified | TOTAL: 391 pass 2 (xz-): 0 found - 70 modified | TOTAL: 391 Iteration Number : 1 pass 1 (+++): 21 found - 21 modified | TOTAL: 21 pass 2 (+++): 0 found - 21 modified | TOTAL: 21 pass 1 (+++): 25 found - 25 modified | TOTAL: 46 pass 2 (+++): 0 found - 25 modified | TOTAL: 46 pass 1 (+++): 45 found - 45 modified | TOTAL: 91 pass 2 (+++): 0 found - 45 modified | TOTAL: 91 pass 1 (+++): 52 found - 52 modified | TOTAL: 143 pass 2 (+++): 0 found - 52 modified | TOTAL: 143 Iteration Number : 1 pass 1 (++): 159 found - 159 modified | TOTAL: 159 pass 2 (++): 0 found - 159 modified | TOTAL: 159 pass 1 (+-): 171 found - 171 modified | TOTAL: 330 pass 2 (+-): 0 found - 171 modified | TOTAL: 330 pass 1 (--): 173 found - 173 modified | TOTAL: 503 pass 2 (--): 0 found - 173 modified | TOTAL: 503 pass 1 (-+): 168 found - 168 modified | TOTAL: 671 pass 2 (-+): 0 found - 168 modified | TOTAL: 671 Iteration Number : 2 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 18 found - 18 modified | TOTAL: 29 pass 2 (xy-): 0 found - 18 modified | TOTAL: 29 pass 1 (yz+): 19 found - 19 modified | TOTAL: 48 pass 2 (yz+): 0 found - 19 modified | TOTAL: 48 pass 1 (yz-): 8 found - 8 modified | TOTAL: 56 pass 2 (yz-): 0 found - 8 modified | TOTAL: 56 pass 1 (xz+): 8 found - 8 modified | TOTAL: 64 pass 2 (xz+): 0 found - 8 modified | TOTAL: 64 pass 1 (xz-): 6 found - 6 modified | TOTAL: 70 pass 2 (xz-): 0 found - 6 modified | TOTAL: 70 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 3 found - 3 modified | TOTAL: 11 pass 2 (+++): 0 found - 3 modified | TOTAL: 11 Iteration Number : 2 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 7 found - 7 modified | TOTAL: 14 pass 2 (+-): 0 found - 7 modified | TOTAL: 14 pass 1 (--): 7 found - 7 modified | TOTAL: 21 pass 2 (--): 0 found - 7 modified | TOTAL: 21 pass 1 (-+): 5 found - 5 modified | TOTAL: 26 pass 2 (-+): 0 found - 5 modified | TOTAL: 26 Iteration Number : 3 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 3 found - 3 modified | TOTAL: 8 pass 2 (yz+): 0 found - 3 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 3 found - 3 modified | TOTAL: 4 pass 2 (-+): 0 found - 3 modified | TOTAL: 4 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 = 1325 (out of 1112540: 0.119097) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue May 25 20:57:31 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 1.01713 -0.06170 0.00927 -1.49223; 0.06290 1.09079 0.03912 -8.89856; -0.01593 -0.02470 1.01688 -8.81789; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01713 -0.06170 0.00927 -1.49223; 0.06290 1.09079 0.03912 -8.89856; -0.01593 -0.02470 1.01688 -8.81789; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (546, 2188) area[0] = 1464 (min = 546, max = 2188), aspect = 0.43 (min = 0.10, max = 0.75) no need to search using seed (155, 142, 114), TAL = (4.0, -36.8, 14.4) talairach voxel to voxel transform 0.97958 0.05516 -0.01105 1.85516; -0.05698 0.91276 -0.03459 7.73215; 0.01396 0.02304 0.98239 8.88841; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (155, 142, 114) --> (4.0, -36.8, 14.4) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (4.00, -36.80, 14.40) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -36.80, 14.40) SRC: (138.22, 125.85, 126.00) search lh wm seed point around talairach space (-14.00, -36.80, 14.40), SRC: (182.30, 123.29, 126.63) 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 Tue May 25 17:44:07 UTC 2021 Ended at Tue May 25 20:58:25 UTC 2021 #@#%# recon-all-run-time-hours 3.238 recon-all -s sub-03 finished without error at Tue May 25 20:58:27 UTC 2021 New invocation of recon-all Tue May 25 22:50:06 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -parallel -subjid sub-03 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -T2pial -cortribbon subjid sub-03 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 32173064 157731664 1969492 6733704 160092048 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: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:50:06-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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 May 25 22:50:07 UTC 2021 bbregister --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --init-coreg --T2 tmp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200 Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.log Tue May 25 22:50:07 UTC 2021 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts /opt/freesurfer/bin/bbregister --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii... mri_coreg --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts cmdline mri_coreg --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg5611.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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 -0.8024 0.0165 -0.7773 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 = 117.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0419778918 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.80240; 0.00000 1.00000 0.00000 0.01649; 0.00000 0.00000 1.00000 -0.77727; 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 -0.80240 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0367672 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0428291559 #@# 4 188 -0.80240 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0428292 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.042829 #@# 4 190 0.19760 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0430363 #@# 4 195 0.04042 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0430466 #@# 4 204 0.05042 -0.09851 1.22273 2.00000 0.00000 0.00000 -1.0430495 #@# 4 208 0.05042 -0.07327 1.22273 2.00000 0.00000 0.00000 -1.0430497 #@# 4 211 0.05042 -0.07327 2.22273 2.00000 0.00000 0.00000 -1.0431803 #@# 4 216 0.05042 -0.07327 2.03645 2.00000 0.00000 0.00000 -1.0431883 #@# 4 226 0.05042 -0.07327 2.01645 1.38197 0.00000 0.00000 -1.0432138 #@# 4 228 0.05042 -0.07327 2.01645 1.48188 0.00000 0.00000 -1.0432152 #@# 4 230 0.05042 -0.07327 2.01645 1.46475 0.00000 0.00000 -1.0432153 #@# 4 240 0.05042 -0.07327 2.01645 1.45475 -0.22627 0.00000 -1.0432191 #@# 4 242 0.05042 -0.07327 2.01645 1.45475 -0.20187 0.00000 -1.0432194 #@# 4 244 0.05042 -0.07327 2.01645 1.45475 -0.16678 0.00000 -1.0432198 #@# 4 246 0.05042 -0.07327 2.01645 1.45475 -0.15073 0.00000 -1.0432199 #@# 4 254 0.05042 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432259 powell nthiter 1: fret = -1.043226 #@# 4 264 0.12409 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432301 #@# 4 265 0.14303 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432304 #@# 4 266 0.15670 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432305 #@# 4 267 0.16670 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432307 #@# 4 285 0.16670 -0.08327 1.84817 1.45475 -0.15073 -0.16685 -1.0432358 #@# 4 287 0.16670 -0.08327 1.86831 1.45475 -0.15073 -0.16685 -1.0432359 #@# 4 299 0.16670 -0.08327 1.87831 1.44475 -0.15073 -0.16685 -1.0432360 #@# 4 307 0.16670 -0.08327 1.87831 1.44475 -0.23715 -0.16685 -1.0432370 Powell done niters total = 1 OptTimeSec 7.8 sec OptTimeMin 0.13 min nEvals 325 Final parameters 0.16670455 -0.08326772 1.87831187 1.44474971 -0.26079917 -0.16684802 Final cost -1.043236928798848 --------------------------------- mri_coreg utimesec 175.245643 mri_coreg stimesec 1.004721 mri_coreg ru_maxrss 890760 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 881872 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10600 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 514 mri_coreg ru_nivcsw 123 Final RefRAS-to-MovRAS 0.99999 -0.00291 -0.00455 0.16670; 0.00303 0.99968 0.02521 -0.08327; 0.00448 -0.02523 0.99967 1.87831; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99999 0.00455 -0.00291 263.98157; -0.00303 -0.02521 0.99968 -6.18447; -0.00448 -0.99967 -0.02523 326.35886; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.1667 -0.0833 1.8783 1.4447 -0.2608 -0.1668 nhits = 306594 out of 32768000, Percent Overlap: 59.9 mri_coreg RunTimeSec 66.8 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/mri_coreg.lta --s sub-03 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat subject sub-03 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 1622708522 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 0.00291 0.00455 -0.19703; 0.00448 -0.02523 0.99967 1.32716; -0.00303 -0.99968 -0.02521 0.60342; 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 0.979306 1 -25.0 -25.0 25.0 0.981441 2 -25.0 25.0 -25.0 0.992603 3 -25.0 25.0 25.0 0.992560 4 25.0 -25.0 -25.0 0.989204 5 25.0 -25.0 25.0 0.993794 6 25.0 25.0 -25.0 0.974398 7 25.0 25.0 25.0 0.979559 REL: 8 0.396413 7.882866 0.985358 rel = 0.402304 Initial costs ---------------- Number of surface hits 4755 WM Intensity 840.0646 +/- 288.3324 Ctx Intensity 1066.8640 +/- 387.3010 Pct Contrast 22.8496 +/- 28.4583 Cost 0.3964 RelCost 0.4023 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9001 0.9001 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8426 0.8426 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8082 0.8082 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7301 0.7301 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7262 0.7262 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6884 0.6884 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5419 0.5419 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3964 0.3964 0.0 Brute Force -------------------------- Min cost was 0.396413 Number of iterations 729 Search time 1.472000 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 = 0.396413 7 0.112 0.000 0.000 0.000 0.000 0.000 0.3930577383 8 0.163 0.000 0.000 0.000 0.000 0.000 0.3920264926 11 0.167 0.000 0.000 0.000 0.000 0.000 0.3920233930 13 0.169 0.000 0.000 0.000 0.000 0.000 0.3920233158 17 0.169 -1.618 0.000 0.000 0.000 0.000 0.1601101220 22 0.169 -1.811 0.000 0.000 0.000 0.000 0.1558531787 23 0.169 -1.822 0.000 0.000 0.000 0.000 0.1556547163 25 0.169 -1.844 0.000 0.000 0.000 0.000 0.1553324032 26 0.169 -1.874 0.000 0.000 0.000 0.000 0.1552697331 27 0.169 -1.863 0.000 0.000 0.000 0.000 0.1551825568 29 0.169 -1.864 0.000 0.000 0.000 0.000 0.1551803398 31 0.169 -1.865 0.000 0.000 0.000 0.000 0.1551794268 38 0.169 -1.866 0.382 0.000 0.000 0.000 0.1479714814 41 0.169 -1.866 0.367 0.000 0.000 0.000 0.1479484631 43 0.169 -1.866 0.370 0.000 0.000 0.000 0.1479484068 45 0.169 -1.866 0.369 0.000 0.000 0.000 0.1479480919 51 0.169 -1.866 0.369 0.382 0.000 0.000 0.1116183901 53 0.169 -1.866 0.369 0.476 0.000 0.000 0.1080326605 54 0.169 -1.866 0.369 0.485 0.000 0.000 0.1078138735 56 0.169 -1.866 0.369 0.492 0.000 0.000 0.1077435819 58 0.169 -1.866 0.369 0.493 0.000 0.000 0.1077422030 66 0.169 -1.866 0.369 0.493 0.076 0.000 0.1072058127 67 0.169 -1.866 0.369 0.493 0.070 0.000 0.1069867449 68 0.169 -1.866 0.369 0.493 0.044 0.000 0.1066752923 70 0.169 -1.866 0.369 0.493 0.046 0.000 0.1066676570 71 0.169 -1.866 0.369 0.493 0.049 0.000 0.1066643663 72 0.169 -1.866 0.369 0.493 0.050 0.000 0.1066640724 80 0.169 -1.866 0.369 0.493 0.050 0.048 0.1066061256 81 0.169 -1.866 0.369 0.493 0.050 0.030 0.1064096070 82 0.169 -1.866 0.369 0.493 0.050 0.026 0.1064028864 powell nthiter 1: fret = 0.106403 97 0.168 -1.866 0.369 0.493 0.050 0.026 0.1064025809 104 0.168 -1.484 0.369 0.493 0.050 0.026 0.1003347697 105 0.168 -1.621 0.369 0.493 0.050 0.026 0.0973056971 106 0.168 -1.624 0.369 0.493 0.050 0.026 0.0972303721 108 0.168 -1.657 0.369 0.493 0.050 0.026 0.0967635732 110 0.168 -1.654 0.369 0.493 0.050 0.026 0.0967603705 111 0.168 -1.655 0.369 0.493 0.050 0.026 0.0967595658 117 0.168 -1.655 -0.249 0.493 0.050 0.026 0.0734131214 119 0.168 -1.655 -0.093 0.493 0.050 0.026 0.0721645220 120 0.168 -1.655 -0.131 0.493 0.050 0.026 0.0718052953 121 0.168 -1.655 -0.144 0.493 0.050 0.026 0.0717905267 122 0.168 -1.655 -0.141 0.493 0.050 0.026 0.0717875881 123 0.168 -1.655 -0.140 0.493 0.050 0.026 0.0717874212 130 0.168 -1.655 -0.140 0.875 0.050 0.026 0.0596714167 131 0.168 -1.655 -0.140 0.782 0.050 0.026 0.0566453415 133 0.168 -1.655 -0.140 0.783 0.050 0.026 0.0566401971 134 0.168 -1.655 -0.140 0.793 0.050 0.026 0.0566304972 136 0.168 -1.655 -0.140 0.790 0.050 0.026 0.0566291636 145 0.168 -1.655 -0.140 0.790 0.079 0.026 0.0565296132 147 0.168 -1.655 -0.140 0.790 0.071 0.026 0.0565175458 149 0.168 -1.655 -0.140 0.790 0.072 0.026 0.0565174303 150 0.168 -1.655 -0.140 0.790 0.073 0.026 0.0565171462 161 0.168 -1.655 -0.140 0.790 0.073 -0.008 0.0563738367 162 0.168 -1.655 -0.140 0.790 0.073 -0.002 0.0563686869 165 0.167 -1.443 -0.648 1.087 0.097 -0.029 0.0478954639 171 0.167 -1.524 -0.454 0.973 0.088 -0.018 0.0472596858 172 0.167 -1.490 -0.535 1.020 0.092 -0.023 0.0463633257 173 0.167 -1.489 -0.538 1.022 0.092 -0.023 0.0463623996 174 0.167 -1.489 -0.538 1.022 0.092 -0.023 0.0463621310 powell nthiter 2: fret = 0.046362 184 0.164 -1.489 -0.538 1.022 0.092 -0.023 0.0463600522 193 0.164 -1.472 -0.538 1.022 0.092 -0.023 0.0462104221 195 0.164 -1.465 -0.538 1.022 0.092 -0.023 0.0461946064 196 0.164 -1.463 -0.538 1.022 0.092 -0.023 0.0461928143 198 0.164 -1.462 -0.538 1.022 0.092 -0.023 0.0461924605 206 0.164 -1.462 -0.538 1.022 0.092 -0.006 0.0460765121 207 0.164 -1.462 -0.538 1.022 0.092 0.003 0.0460566329 216 0.164 -1.462 -0.538 1.006 0.092 0.003 0.0458808249 228 0.164 -1.462 -0.538 1.006 0.084 0.003 0.0458393624 231 0.164 -1.462 -0.538 1.006 0.083 0.003 0.0458382152 239 0.164 -1.471 -0.515 0.993 0.082 0.004 0.0457659097 powell nthiter 3: fret = 0.045766 250 0.194 -1.471 -0.515 0.993 0.082 0.004 0.0456728705 252 0.202 -1.471 -0.515 0.993 0.082 0.004 0.0456662120 255 0.205 -1.471 -0.515 0.993 0.082 0.004 0.0456642592 256 0.206 -1.471 -0.515 0.993 0.082 0.004 0.0456641116 264 0.206 -1.479 -0.515 0.993 0.082 0.004 0.0456542489 265 0.206 -1.480 -0.515 0.993 0.082 0.004 0.0456527153 268 0.206 -1.481 -0.515 0.993 0.082 0.004 0.0456519694 269 0.206 -1.482 -0.515 0.993 0.082 0.004 0.0456517448 278 0.206 -1.482 -0.515 0.993 0.082 0.065 0.0456064477 279 0.206 -1.482 -0.515 0.993 0.082 0.039 0.0455048146 281 0.206 -1.482 -0.515 0.993 0.082 0.040 0.0455045873 289 0.206 -1.482 -0.515 0.988 0.082 0.040 0.0454737298 291 0.206 -1.482 -0.515 0.986 0.082 0.040 0.0454703284 301 0.206 -1.482 -0.515 0.986 0.079 0.040 0.0454546592 302 0.206 -1.482 -0.515 0.986 0.071 0.040 0.0454306154 312 0.206 -1.483 -0.512 0.984 0.071 0.041 0.0454232534 313 0.206 -1.485 -0.508 0.982 0.071 0.041 0.0454204394 314 0.206 -1.485 -0.508 0.982 0.071 0.041 0.0454203982 316 0.248 -1.498 -0.501 0.970 0.060 0.077 0.0451029446 321 0.274 -1.507 -0.497 0.963 0.054 0.100 0.0451020181 323 0.261 -1.502 -0.499 0.967 0.057 0.089 0.0450562335 324 0.261 -1.502 -0.499 0.967 0.057 0.089 0.0450561682 325 0.263 -1.503 -0.498 0.966 0.057 0.090 0.0450550930 328 0.263 -1.503 -0.498 0.966 0.057 0.090 0.0450550765 powell nthiter 4: fret = 0.045055 339 0.268 -1.503 -0.498 0.966 0.057 0.090 0.0450263589 340 0.271 -1.503 -0.498 0.966 0.057 0.090 0.0450218788 341 0.272 -1.503 -0.498 0.966 0.057 0.090 0.0450218371 350 0.272 -1.501 -0.498 0.966 0.057 0.090 0.0450170305 351 0.272 -1.499 -0.498 0.966 0.057 0.090 0.0450163073 359 0.272 -1.498 -0.502 0.968 0.057 0.090 0.0449977224 361 0.272 -1.495 -0.510 0.973 0.057 0.090 0.0449766504 362 0.272 -1.494 -0.512 0.974 0.057 0.089 0.0449750568 363 0.272 -1.493 -0.512 0.974 0.057 0.089 0.0449750034 371 0.272 -1.493 -0.512 0.981 0.057 0.089 0.0449230137 373 0.272 -1.493 -0.512 0.987 0.057 0.089 0.0449158766 374 0.272 -1.493 -0.512 0.985 0.057 0.089 0.0449134807 383 0.272 -1.493 -0.512 0.985 0.048 0.089 0.0448510925 384 0.272 -1.493 -0.512 0.985 0.045 0.089 0.0448481324 385 0.272 -1.493 -0.512 0.985 0.046 0.089 0.0448481215 393 0.275 -1.494 -0.512 0.984 0.045 0.092 0.0448417447 394 0.276 -1.495 -0.512 0.984 0.045 0.093 0.0448412038 powell nthiter 5: fret = 0.044841 408 0.281 -1.495 -0.512 0.984 0.045 0.093 0.0448186314 409 0.283 -1.495 -0.512 0.984 0.045 0.093 0.0448170728 417 0.283 -1.490 -0.512 0.984 0.045 0.093 0.0448155718 418 0.283 -1.491 -0.512 0.984 0.045 0.093 0.0448145505 419 0.283 -1.492 -0.512 0.984 0.045 0.093 0.0448144399 439 0.283 -1.492 -0.512 0.987 0.045 0.093 0.0448106172 440 0.283 -1.492 -0.512 0.986 0.045 0.093 0.0448100533 450 0.283 -1.492 -0.512 0.986 0.041 0.093 0.0448058138 451 0.283 -1.492 -0.512 0.986 0.042 0.093 0.0448052961 459 0.280 -1.491 -0.512 0.987 0.042 0.091 0.0448026591 460 0.281 -1.491 -0.512 0.987 0.042 0.091 0.0448025552 462 0.281 -1.492 -0.512 0.987 0.042 0.091 0.0448024219 463 0.281 -1.492 -0.512 0.987 0.042 0.091 0.0448023373 466 0.285 -1.488 -0.513 0.990 0.040 0.089 0.0447883681 473 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447877032 475 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447876488 478 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447875525 powell nthiter 6: fret = 0.044788 492 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447875291 501 0.287 -1.488 -0.513 0.991 0.039 0.088 0.0447870773 510 0.287 -1.489 -0.510 0.990 0.039 0.088 0.0447854610 521 0.287 -1.490 -0.510 0.988 0.039 0.088 0.0447839666 531 0.287 -1.490 -0.510 0.988 0.036 0.088 0.0447832694 533 0.287 -1.490 -0.510 0.988 0.037 0.088 0.0447823878 534 0.287 -1.490 -0.510 0.988 0.038 0.088 0.0447823080 541 0.288 -1.489 -0.510 0.988 0.037 0.088 0.0447818328 543 0.288 -1.489 -0.510 0.988 0.037 0.088 0.0447818133 547 0.288 -1.489 -0.510 0.988 0.037 0.088 0.0447816339 powell nthiter 7: fret = 0.044782 559 0.285 -1.488 -0.510 0.989 0.038 0.086 0.0447787611 560 0.285 -1.488 -0.510 0.989 0.038 0.085 0.0447786930 564 0.285 -1.488 -0.510 0.989 0.038 0.085 0.0447785458 573 0.285 -1.489 -0.510 0.989 0.038 0.085 0.0447785132 592 0.285 -1.489 -0.510 0.988 0.038 0.085 0.0447780016 604 0.285 -1.489 -0.510 0.988 0.037 0.085 0.0447778706 610 0.287 -1.488 -0.510 0.989 0.036 0.085 0.0447777238 611 0.286 -1.488 -0.510 0.989 0.036 0.085 0.0447774031 612 0.286 -1.488 -0.510 0.989 0.036 0.085 0.0447773339 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.983942 1 -25.0 -25.0 25.0 0.972793 2 -25.0 25.0 -25.0 0.973125 3 -25.0 25.0 25.0 0.988273 4 25.0 -25.0 -25.0 0.962400 5 25.0 -25.0 25.0 0.990656 6 25.0 25.0 -25.0 0.973856 7 25.0 25.0 25.0 0.967412 REL: 8 0.044777 7.812458 0.976557 rel = 0.0458522 Number of iterations 7 Min cost was 0.044777 Number of FunctionCalls 619 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.212000 sec Parameters at optimum (transmm) 0.28570 -1.48848 -0.51028 Parameters at optimum (rotdeg) 0.98867 0.03642 0.08492 Final costs ---------------- Number of surface hits 4755 WM Intensity 778.9781 +/- 235.5277 Ctx Intensity 1047.3860 +/- 260.1751 Pct Contrast 30.5612 +/- 15.3889 Cost 0.0448 RelCost 0.4023 Reg at min cost was -0.99999 0.00229 0.00306 0.08712; 0.00305 -0.00797 0.99996 -0.17222; -0.00231 -0.99997 -0.00796 0.11608; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat, type = 14 Original Reg -0.99999 0.00291 0.00455 -0.19703; 0.00448 -0.02523 0.99967 1.32716; -0.00303 -0.99968 -0.02521 0.60342; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 0.00062 0.00149 -0.28415; 0.00143 -0.01726 -0.00029 1.49938; -0.00071 0.00029 -0.01725 0.48735; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.764248 Computing change in rh position Surface-RMS-Diff-mm 1.830926 0.684858 3.153883 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat subject sub-03 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 1622258830 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 0.00229 0.00306 0.08712; 0.00305 -0.00797 0.99996 -0.17222; -0.00231 -0.99997 -0.00796 0.11608; 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 0.998525 1 -25.0 -25.0 25.0 0.972817 2 -25.0 25.0 -25.0 0.977586 3 -25.0 25.0 25.0 0.990926 4 25.0 -25.0 -25.0 0.966947 5 25.0 -25.0 25.0 0.981464 6 25.0 25.0 -25.0 0.972770 7 25.0 25.0 25.0 0.974843 REL: 8 0.049489 7.835879 0.979485 rel = 0.0505257 Initial costs ---------------- Number of surface hits 476337 WM Intensity 784.7650 +/- 240.5626 Ctx Intensity 1051.3769 +/- 265.5817 Pct Contrast 30.2423 +/- 15.5869 Cost 0.0495 RelCost 0.0505 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0537 0.0537 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0531 0.0531 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0519 0.0519 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0516 0.0516 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0511 0.0511 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0502 0.0502 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0498 0.0498 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0493 0.0493 0.0 16 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0489 0.0489 0.0 35 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.0486 0.0486 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0479 0.0479 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0463 0.0463 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0463 0.0463 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0448 0.0448 0.0 Brute Force -------------------------- Min cost was 0.044777 Number of iterations 729 Search time 1.438000 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 = 0.049489 7 -0.047 0.000 0.000 0.000 0.000 0.000 0.0491758049 8 -0.055 0.000 0.000 0.000 0.000 0.000 0.0491650411 9 -0.057 0.000 0.000 0.000 0.000 0.000 0.0491639107 10 -0.059 0.000 0.000 0.000 0.000 0.000 0.0491637759 12 -0.058 0.000 0.000 0.000 0.000 0.000 0.0491637182 19 -0.058 -0.029 0.000 0.000 0.000 0.000 0.0488499981 20 -0.058 -0.058 0.000 0.000 0.000 0.000 0.0487730192 21 -0.058 -0.053 0.000 0.000 0.000 0.000 0.0487676084 22 -0.058 -0.052 0.000 0.000 0.000 0.000 0.0487674785 30 -0.058 -0.052 0.048 0.000 0.000 0.000 0.0485622085 31 -0.058 -0.052 0.044 0.000 0.000 0.000 0.0485581165 32 -0.058 -0.052 0.041 0.000 0.000 0.000 0.0485570579 42 -0.058 -0.052 0.041 0.001 0.000 0.000 0.0485567418 51 -0.058 -0.052 0.041 0.001 0.012 0.000 0.0485429525 52 -0.058 -0.052 0.041 0.001 0.011 0.000 0.0485424795 61 -0.058 -0.052 0.041 0.001 0.011 -0.010 0.0485303588 powell nthiter 1: fret = 0.048530 71 -0.059 -0.052 0.041 0.001 0.011 -0.010 0.0485281644 72 -0.069 -0.052 0.041 0.001 0.011 -0.010 0.0485178220 84 -0.069 -0.051 0.041 0.001 0.011 -0.010 0.0485175067 102 -0.069 -0.051 0.041 0.003 0.011 -0.010 0.0485169935 110 -0.069 -0.051 0.041 0.003 0.014 -0.010 0.0485150776 111 -0.069 -0.051 0.041 0.003 0.015 -0.010 0.0485147533 120 -0.069 -0.051 0.041 0.003 0.015 -0.016 0.0485111203 121 -0.069 -0.051 0.041 0.003 0.015 -0.015 0.0485110919 123 -0.080 -0.049 0.041 0.005 0.019 -0.020 0.0485022990 130 -0.083 -0.049 0.041 0.006 0.021 -0.021 0.0485016419 powell nthiter 2: fret = 0.048502 165 -0.083 -0.049 0.039 0.006 0.021 -0.021 0.0485012546 184 -0.083 -0.049 0.039 0.006 0.022 -0.021 0.0485011084 185 -0.083 -0.049 0.039 0.006 0.023 -0.021 0.0485010274 194 -0.085 -0.049 0.039 0.006 0.023 -0.022 0.0485009881 195 -0.085 -0.049 0.039 0.006 0.023 -0.022 0.0485008647 198 -0.085 -0.049 0.039 0.006 0.023 -0.022 0.0485008603 powell nthiter 3: fret = 0.048501 222 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008454 261 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008401 263 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008388 powell nthiter 4: fret = 0.048501 322 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008330 326 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008267 327 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008239 powell nthiter 5: fret = 0.048501 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.998287 1 -25.0 -25.0 25.0 0.972938 2 -25.0 25.0 -25.0 0.978167 3 -25.0 25.0 25.0 0.990750 4 25.0 -25.0 -25.0 0.967053 5 25.0 -25.0 25.0 0.981527 6 25.0 25.0 -25.0 0.972196 7 25.0 25.0 25.0 0.975655 REL: 8 0.048501 7.836574 0.979572 rel = 0.0495123 Number of iterations 5 Min cost was 0.048501 Number of FunctionCalls 407 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 45.330000 sec Parameters at optimum (transmm) -0.08480 -0.04975 0.03909 Parameters at optimum (rotdeg) 0.00592 0.02326 -0.02199 Final costs ---------------- Number of surface hits 476337 WM Intensity 784.5522 +/- 240.8351 Ctx Intensity 1051.0080 +/- 266.0569 Pct Contrast 30.2354 +/- 15.5644 Cost 0.0485 RelCost 0.0505 Reg at min cost was -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 0.00229 0.00306 0.08712; 0.00305 -0.00797 0.99996 -0.17222; -0.00231 -0.99997 -0.00796 0.11608; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 0.00041 -0.00038 0.08482; -0.00038 -0.00010 0.00000 0.04979; -0.00041 0.00000 -0.00010 -0.03904; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.098146 Computing change in rh position Surface-RMS-Diff-mm 0.096985 0.010817 0.124480 mri_segreg done MinCost: 0.048501 784.552237 1051.008000 30.235351 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 -------- -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 -------- -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-03 RegMat --------------------------- -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 22:50:07 UTC 2021 Ended at Tue May 25 22:52:27 UTC 2021 BBR-Run-Time-Sec 140 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --surfs cp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta mri_convert -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz mri_convert.bin -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz... INFO: Applying transformation from file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99999 0.00191 0.00343 0.03290; -0.00188 0.99997 -0.00787 -0.01630; -0.00345 0.00786 0.99996 0.03498; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz... mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aseg.presurf.mgz -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white identity.nofile -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white identity.nofile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.prenorm.mgz... computing distance transform computing distance transform 86475 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.norm.mgz mri_mask /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.norm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brainmask.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.mgz DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/T2.mgz...done. /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 130087 of (130087 130093) to complete... Waiting for PID 130093 of (130087 130093) 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... 48538 bright wm thresholded. 856 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.orig... computing class statistics... border white: 523483 voxels (1.60%) border gray 522637 voxels (1.59%) WM (103.0): 103.0 +- 6.3 [70.0 --> 110.0] GM (83.0) : 82.3 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.3 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-2.6, GM=78+-7.8 mean inside = 101.4, mean outside = 84.2 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) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 46 points - only 0.00% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 138 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown deleting segment 9 with 78 points - only 0.00% unknown deleting segment 10 with 23 points - only 0.00% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 17 points - only 0.00% unknown deleting segment 18 with 11 points - only 0.00% unknown deleting segment 19 with 42 points - only 0.00% unknown deleting segment 20 with 54 points - only 0.00% unknown deleting segment 21 with 7 points - only 0.00% unknown deleting segment 22 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown deleting segment 24 with 44 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) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (box.dx, box.dy, box.dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) locating cortical regions not in the range [63.00 211.40], gm=169.00+-21.20, and vertices in regions > 158.4 202594 surface locations found to contain inconsistent values (49480 in, 153114 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg56, 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=168825.4, rms=0.358 001: dt: 0.0500, sse=168849.7, rms=0.357 (0.151%) 002: dt: 0.0500, sse=168868.8, rms=0.356 (0.171%) 003: dt: 0.0500, sse=168887.4, rms=0.356 (0.167%) 004: dt: 0.0500, sse=168906.0, rms=0.355 (0.165%) 005: dt: 0.0500, sse=168924.6, rms=0.355 (0.163%) 006: dt: 0.0500, sse=168942.9, rms=0.354 (0.162%) 007: dt: 0.0500, sse=168960.9, rms=0.353 (0.161%) 008: dt: 0.0500, sse=168977.9, rms=0.353 (0.159%) 009: dt: 0.0500, sse=168995.3, rms=0.352 (0.157%) 010: dt: 0.0500, sse=169012.1, rms=0.352 (0.156%) positioning took 1.6 minutes tol=1.0e-04, sigma=2.0, host=blg56, 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=168341.3, rms=0.352 011: dt: 0.0500, sse=168357.2, rms=0.351 (0.155%) 012: dt: 0.0500, sse=168373.4, rms=0.351 (0.153%) 013: dt: 0.0500, sse=168388.7, rms=0.350 (0.151%) 014: dt: 0.0500, sse=168404.2, rms=0.350 (0.150%) 015: dt: 0.0500, sse=168418.3, rms=0.349 (0.149%) 016: dt: 0.0500, sse=168433.0, rms=0.349 (0.148%) 017: dt: 0.0500, sse=168446.7, rms=0.348 (0.146%) 018: dt: 0.0500, sse=168460.8, rms=0.348 (0.145%) 019: dt: 0.0500, sse=168473.8, rms=0.347 (0.143%) 020: dt: 0.0500, sse=168487.0, rms=0.347 (0.142%) positioning took 1.7 minutes tol=1.0e-04, sigma=2.0, host=blg56, 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=167913.7, rms=0.347 021: dt: 0.0500, sse=167926.7, rms=0.346 (0.141%) 022: dt: 0.0500, sse=167940.2, rms=0.346 (0.139%) 023: dt: 0.0500, sse=167952.5, rms=0.345 (0.138%) 024: dt: 0.0500, sse=167964.6, rms=0.345 (0.138%) 025: dt: 0.0500, sse=167976.5, rms=0.344 (0.136%) 026: dt: 0.0500, sse=167988.5, rms=0.344 (0.134%) 027: dt: 0.0500, sse=167999.9, rms=0.343 (0.134%) 028: dt: 0.0500, sse=168011.3, rms=0.343 (0.133%) 029: dt: 0.0500, sse=168022.0, rms=0.342 (0.131%) 030: dt: 0.0500, sse=168033.5, rms=0.342 (0.130%) positioning took 1.7 minutes tol=1.0e-04, sigma=2.0, host=blg56, 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 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=167536.3, rms=0.342 031: dt: 0.5000, sse=167641.6, rms=0.338 (1.235%) 032: dt: 0.5000, sse=167739.9, rms=0.334 (1.145%) 033: dt: 0.5000, sse=167796.6, rms=0.330 (1.061%) 034: dt: 0.5000, sse=167855.5, rms=0.327 (0.969%) 035: dt: 0.5000, sse=167897.4, rms=0.324 (0.889%) 036: dt: 0.5000, sse=167939.2, rms=0.322 (0.841%) 037: dt: 0.5000, sse=167964.6, rms=0.319 (0.759%) 038: dt: 0.5000, sse=168006.3, rms=0.317 (0.717%) 039: dt: 0.5000, sse=168026.1, rms=0.315 (0.670%) 040: dt: 0.5000, sse=168049.0, rms=0.313 (0.625%) 041: dt: 0.5000, sse=168065.2, rms=0.311 (0.593%) 042: dt: 0.5000, sse=168086.8, rms=0.309 (0.542%) 043: dt: 0.5000, sse=168098.4, rms=0.307 (0.537%) 044: dt: 0.5000, sse=168110.3, rms=0.306 (0.509%) 045: dt: 0.5000, sse=168122.9, rms=0.305 (0.458%) 046: dt: 0.5000, sse=168137.7, rms=0.303 (0.448%) 047: dt: 0.5000, sse=168140.7, rms=0.302 (0.410%) 048: dt: 0.5000, sse=168147.1, rms=0.301 (0.413%) 049: dt: 0.5000, sse=168156.5, rms=0.300 (0.374%) 050: dt: 0.5000, sse=168156.2, rms=0.298 (0.365%) 051: dt: 0.5000, sse=168171.3, rms=0.297 (0.322%) 052: dt: 0.5000, sse=168172.4, rms=0.297 (0.319%) 053: dt: 0.5000, sse=168186.6, rms=0.296 (0.288%) 054: dt: 0.5000, sse=168184.6, rms=0.295 (0.302%) 055: dt: 0.5000, sse=168198.1, rms=0.294 (0.251%) 056: dt: 0.5000, sse=168199.8, rms=0.293 (0.266%) 057: dt: 0.5000, sse=168216.6, rms=0.293 (0.228%) 058: dt: 0.5000, sse=168231.7, rms=0.292 (0.204%) 059: dt: 0.5000, sse=168237.0, rms=0.291 (0.208%) 060: dt: 0.5000, sse=168233.2, rms=0.291 (0.219%) positioning took 5.4 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (box.dx, box.dy, box.dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) locating cortical regions not in the range [56.00 215.60], gm=170.00+-22.80, and vertices in regions > 158.6 199085 surface locations found to contain inconsistent values (26502 in, 172583 out) tol=1.0e-04, sigma=1.0, host=blg56, 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 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=164159.3, rms=0.304 061: dt: 0.5000, sse=164155.2, rms=0.301 (1.063%) 062: dt: 0.5000, sse=164110.4, rms=0.297 (1.221%) 063: dt: 0.5000, sse=164064.6, rms=0.294 (1.031%) 064: dt: 0.5000, sse=164034.6, rms=0.291 (0.910%) 065: dt: 0.5000, sse=164006.0, rms=0.289 (0.801%) 066: dt: 0.5000, sse=163985.8, rms=0.287 (0.722%) 067: dt: 0.5000, sse=163967.9, rms=0.285 (0.637%) 068: dt: 0.5000, sse=163958.8, rms=0.283 (0.578%) 069: dt: 0.5000, sse=163948.9, rms=0.282 (0.514%) 070: dt: 0.5000, sse=163945.7, rms=0.281 (0.471%) 071: dt: 0.5000, sse=163944.1, rms=0.279 (0.434%) 072: dt: 0.5000, sse=163946.0, rms=0.278 (0.405%) 073: dt: 0.5000, sse=163942.6, rms=0.277 (0.384%) 074: dt: 0.5000, sse=163941.6, rms=0.276 (0.374%) 075: dt: 0.5000, sse=163940.2, rms=0.275 (0.353%) 076: dt: 0.5000, sse=163938.2, rms=0.274 (0.339%) 077: dt: 0.5000, sse=163932.9, rms=0.273 (0.325%) 078: dt: 0.5000, sse=163926.0, rms=0.273 (0.308%) 079: dt: 0.5000, sse=163924.7, rms=0.272 (0.284%) 080: dt: 0.5000, sse=163918.8, rms=0.271 (0.288%) 081: dt: 0.5000, sse=163914.2, rms=0.270 (0.266%) 082: dt: 0.5000, sse=163907.0, rms=0.270 (0.263%) 083: dt: 0.5000, sse=163905.0, rms=0.269 (0.238%) 084: dt: 0.5000, sse=163901.9, rms=0.268 (0.231%) 085: dt: 0.5000, sse=163895.7, rms=0.268 (0.222%) 086: dt: 0.5000, sse=163890.5, rms=0.267 (0.215%) 087: dt: 0.5000, sse=163888.1, rms=0.267 (0.203%) 088: dt: 0.5000, sse=163884.8, rms=0.266 (0.192%) 089: dt: 0.5000, sse=163876.5, rms=0.266 (0.189%) 090: dt: 0.5000, sse=163870.4, rms=0.265 (0.181%) positioning took 6.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (box.dx, box.dy, box.dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) locating cortical regions not in the range [54.50 216.20], gm=170.00+-23.10, and vertices in regions > 158.4 194511 surface locations found to contain inconsistent values (28198 in, 166313 out) tol=1.0e-04, sigma=0.5, host=blg56, 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 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=164725.1, rms=0.285 091: dt: 0.5000, sse=164724.1, rms=0.283 (0.766%) 092: dt: 0.5000, sse=164676.7, rms=0.281 (0.890%) 093: dt: 0.5000, sse=164635.0, rms=0.279 (0.734%) 094: dt: 0.5000, sse=164592.8, rms=0.277 (0.641%) 095: dt: 0.5000, sse=164559.1, rms=0.275 (0.558%) 096: dt: 0.5000, sse=164532.1, rms=0.274 (0.491%) 097: dt: 0.5000, sse=164508.4, rms=0.273 (0.432%) 098: dt: 0.5000, sse=164491.6, rms=0.272 (0.388%) 099: dt: 0.5000, sse=164475.7, rms=0.271 (0.348%) 100: dt: 0.5000, sse=164461.2, rms=0.270 (0.320%) 101: dt: 0.5000, sse=164449.3, rms=0.269 (0.298%) 102: dt: 0.5000, sse=164439.3, rms=0.268 (0.277%) 103: dt: 0.5000, sse=164427.3, rms=0.268 (0.264%) 104: dt: 0.5000, sse=164422.3, rms=0.267 (0.250%) 105: dt: 0.5000, sse=164407.6, rms=0.266 (0.235%) 106: dt: 0.5000, sse=164396.6, rms=0.266 (0.226%) 107: dt: 0.5000, sse=164384.6, rms=0.265 (0.217%) 108: dt: 0.5000, sse=164373.9, rms=0.265 (0.207%) 109: dt: 0.5000, sse=164365.5, rms=0.264 (0.197%) 110: dt: 0.5000, sse=164353.8, rms=0.264 (0.190%) 111: dt: 0.5000, sse=164346.4, rms=0.263 (0.180%) 112: dt: 0.5000, sse=164338.6, rms=0.263 (0.174%) 113: dt: 0.5000, sse=164331.4, rms=0.262 (0.167%) 114: dt: 0.5000, sse=164323.9, rms=0.262 (0.161%) 115: dt: 0.5000, sse=164318.8, rms=0.261 (0.153%) 116: dt: 0.5000, sse=164312.8, rms=0.261 (0.149%) 117: dt: 0.5000, sse=164304.1, rms=0.261 (0.142%) 118: dt: 0.5000, sse=164297.8, rms=0.260 (0.136%) 119: dt: 0.5000, sse=164287.8, rms=0.260 (0.128%) 120: dt: 0.5000, sse=164283.5, rms=0.260 (0.126%) positioning took 7.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (region->dx, region->dy, region->dz) = (161, 418, 271) (box.dx, box.dy, box.dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) (region->dx, region->dy, region->dz) = (168, 428, 284) locating cortical regions not in the range [53.50 216.60], gm=170.00+-23.30, and vertices in regions > 158.3 191934 surface locations found to contain inconsistent values (30800 in, 161134 out) tol=1.0e-04, sigma=0.2, host=blg56, 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 writing pial surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=166092.0, rms=0.278 121: dt: 0.5000, sse=166101.1, rms=0.277 (0.574%) 122: dt: 0.5000, sse=166054.1, rms=0.275 (0.655%) 123: dt: 0.5000, sse=166014.5, rms=0.273 (0.531%) 124: dt: 0.5000, sse=165976.7, rms=0.272 (0.456%) 125: dt: 0.5000, sse=165947.6, rms=0.271 (0.398%) 126: dt: 0.5000, sse=165916.5, rms=0.270 (0.348%) 127: dt: 0.5000, sse=165893.0, rms=0.269 (0.306%) 128: dt: 0.5000, sse=165873.3, rms=0.268 (0.274%) 129: dt: 0.5000, sse=165855.0, rms=0.268 (0.247%) 130: dt: 0.5000, sse=165839.9, rms=0.267 (0.227%) 131: dt: 0.5000, sse=165826.0, rms=0.267 (0.212%) 132: dt: 0.5000, sse=165814.2, rms=0.266 (0.196%) 133: dt: 0.5000, sse=165801.6, rms=0.266 (0.187%) 134: dt: 0.5000, sse=165787.2, rms=0.265 (0.177%) 135: dt: 0.5000, sse=165778.3, rms=0.265 (0.167%) 136: dt: 0.5000, sse=165767.8, rms=0.264 (0.159%) 137: dt: 0.5000, sse=165759.0, rms=0.264 (0.153%) 138: dt: 0.5000, sse=165751.8, rms=0.263 (0.142%) 139: dt: 0.5000, sse=165742.5, rms=0.263 (0.135%) 140: dt: 0.5000, sse=165735.1, rms=0.263 (0.129%) 141: dt: 0.5000, sse=165727.9, rms=0.262 (0.124%) 142: dt: 0.5000, sse=165720.6, rms=0.262 (0.119%) 143: dt: 0.5000, sse=165714.9, rms=0.262 (0.114%) 144: dt: 0.5000, sse=165708.7, rms=0.262 (0.107%) 145: dt: 0.5000, sse=165703.7, rms=0.261 (0.105%) 146: dt: 0.5000, sse=165697.4, rms=0.261 (0.101%) 147: dt: 0.5000, sse=165692.0, rms=0.261 (0.097%) 148: dt: 0.5000, sse=165685.7, rms=0.261 (0.091%) 149: dt: 0.5000, sse=165680.8, rms=0.260 (0.089%) 150: dt: 0.5000, sse=165676.1, rms=0.260 (0.085%) positioning took 8.5 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.area.pial vertex spacing 0.79 +- 0.36 (0.02-->7.84) (max @ vno 149485 --> 244951) face area 0.25 +- 0.21 (0.00-->9.99) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 245295 vertices processed 25000 of 245295 vertices processed 50000 of 245295 vertices processed 75000 of 245295 vertices processed 100000 of 245295 vertices processed 125000 of 245295 vertices processed 150000 of 245295 vertices processed 175000 of 245295 vertices processed 200000 of 245295 vertices processed 225000 of 245295 vertices processed 0 of 245295 vertices processed 25000 of 245295 vertices processed 50000 of 245295 vertices processed 75000 of 245295 vertices processed 100000 of 245295 vertices processed 125000 of 245295 vertices processed 150000 of 245295 vertices processed 175000 of 245295 vertices processed 200000 of 245295 vertices processed 225000 of 245295 vertices processed thickness calculation complete, 307:699 truncations. 44926 vertices at 0 distance 138619 vertices at 1 distance 150776 vertices at 2 distance 85153 vertices at 3 distance 34291 vertices at 4 distance 11887 vertices at 5 distance 3989 vertices at 6 distance 1359 vertices at 7 distance 485 vertices at 8 distance 226 vertices at 9 distance 130 vertices at 10 distance 80 vertices at 11 distance 73 vertices at 12 distance 68 vertices at 13 distance 53 vertices at 14 distance 42 vertices at 15 distance 38 vertices at 16 distance 38 vertices at 17 distance 33 vertices at 18 distance 27 vertices at 19 distance 31 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.thickness positioning took 57.5 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... 48538 bright wm thresholded. 856 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.orig... computing class statistics... border white: 523483 voxels (1.60%) border gray 522637 voxels (1.59%) WM (103.0): 103.0 +- 6.3 [70.0 --> 110.0] GM (83.0) : 82.3 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.3 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-2.6, GM=78+-7.8 mean inside = 101.0, mean outside = 83.6 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) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 45 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 32 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown deleting segment 6 with 41 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 9 with 146 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 245 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown deleting segment 13 with 241 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown deleting segment 15 with 31 points - only 0.00% unknown deleting segment 16 with 39 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown deleting segment 18 with 247 points - only 2.43% unknown deleting segment 19 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown deleting segment 21 with 136 points - only 0.00% unknown deleting segment 22 with 13 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) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (box.dx, box.dy, box.dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) locating cortical regions not in the range [48.50 220.00], gm=171.00+-24.50, and vertices in regions > 158.7 208686 surface locations found to contain inconsistent values (34696 in, 173990 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg56, 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=169850.5, rms=0.338 001: dt: 0.0500, sse=169869.7, rms=0.337 (0.159%) 002: dt: 0.0500, sse=169884.7, rms=0.336 (0.179%) 003: dt: 0.0500, sse=169899.4, rms=0.336 (0.174%) 004: dt: 0.0500, sse=169913.8, rms=0.335 (0.172%) 005: dt: 0.0500, sse=169927.7, rms=0.335 (0.170%) 006: dt: 0.0500, sse=169941.2, rms=0.334 (0.169%) 007: dt: 0.0500, sse=169954.7, rms=0.334 (0.167%) 008: dt: 0.0500, sse=169968.0, rms=0.333 (0.166%) 009: dt: 0.0500, sse=169980.8, rms=0.332 (0.164%) 010: dt: 0.0500, sse=169993.5, rms=0.332 (0.163%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg56, 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=169430.7, rms=0.332 011: dt: 0.0500, sse=169442.4, rms=0.331 (0.161%) 012: dt: 0.0500, sse=169454.5, rms=0.331 (0.160%) 013: dt: 0.0500, sse=169466.3, rms=0.330 (0.158%) 014: dt: 0.0500, sse=169477.8, rms=0.330 (0.157%) 015: dt: 0.0500, sse=169489.2, rms=0.329 (0.156%) 016: dt: 0.0500, sse=169500.3, rms=0.329 (0.154%) 017: dt: 0.0500, sse=169511.3, rms=0.328 (0.152%) 018: dt: 0.0500, sse=169521.7, rms=0.328 (0.151%) 019: dt: 0.0500, sse=169532.4, rms=0.327 (0.150%) 020: dt: 0.0500, sse=169542.7, rms=0.327 (0.149%) positioning took 1.6 minutes tol=1.0e-04, sigma=2.0, host=blg56, 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=169062.3, rms=0.327 021: dt: 0.0500, sse=169072.4, rms=0.326 (0.147%) 022: dt: 0.0500, sse=169082.5, rms=0.326 (0.146%) 023: dt: 0.0500, sse=169091.6, rms=0.325 (0.145%) 024: dt: 0.0500, sse=169101.1, rms=0.325 (0.143%) 025: dt: 0.0500, sse=169110.7, rms=0.324 (0.142%) 026: dt: 0.0500, sse=169120.0, rms=0.324 (0.141%) 027: dt: 0.0500, sse=169129.0, rms=0.324 (0.139%) 028: dt: 0.0500, sse=169138.0, rms=0.323 (0.138%) 029: dt: 0.0500, sse=169147.0, rms=0.323 (0.137%) 030: dt: 0.0500, sse=169155.6, rms=0.322 (0.136%) positioning took 1.7 minutes tol=1.0e-04, sigma=2.0, host=blg56, 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 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=168738.0, rms=0.322 031: dt: 0.5000, sse=168819.4, rms=0.318 (1.307%) 032: dt: 0.5000, sse=168897.5, rms=0.314 (1.192%) 033: dt: 0.5000, sse=168953.0, rms=0.311 (1.094%) 034: dt: 0.5000, sse=169005.6, rms=0.308 (1.002%) 035: dt: 0.5000, sse=169047.8, rms=0.305 (0.914%) 036: dt: 0.5000, sse=169093.4, rms=0.302 (0.837%) 037: dt: 0.5000, sse=169127.8, rms=0.300 (0.771%) 038: dt: 0.5000, sse=169166.8, rms=0.298 (0.715%) 039: dt: 0.5000, sse=169198.2, rms=0.296 (0.665%) 040: dt: 0.5000, sse=169232.8, rms=0.294 (0.615%) 041: dt: 0.5000, sse=169266.9, rms=0.292 (0.569%) 042: dt: 0.5000, sse=169296.7, rms=0.291 (0.536%) 043: dt: 0.5000, sse=169322.6, rms=0.289 (0.508%) 044: dt: 0.5000, sse=169351.2, rms=0.288 (0.470%) 045: dt: 0.5000, sse=169372.3, rms=0.287 (0.444%) 046: dt: 0.5000, sse=169399.3, rms=0.286 (0.409%) 047: dt: 0.5000, sse=169416.3, rms=0.284 (0.391%) 048: dt: 0.5000, sse=169439.8, rms=0.283 (0.370%) 049: dt: 0.5000, sse=169459.5, rms=0.282 (0.339%) 050: dt: 0.5000, sse=169478.7, rms=0.281 (0.333%) 051: dt: 0.5000, sse=169497.7, rms=0.281 (0.302%) 052: dt: 0.5000, sse=169519.8, rms=0.280 (0.290%) 053: dt: 0.5000, sse=169532.7, rms=0.279 (0.274%) 054: dt: 0.5000, sse=169553.1, rms=0.278 (0.259%) 055: dt: 0.5000, sse=169567.3, rms=0.278 (0.239%) 056: dt: 0.5000, sse=169586.0, rms=0.277 (0.226%) 057: dt: 0.5000, sse=169601.2, rms=0.276 (0.221%) 058: dt: 0.5000, sse=169618.6, rms=0.276 (0.193%) 059: dt: 0.5000, sse=169630.4, rms=0.275 (0.183%) 060: dt: 0.5000, sse=169644.7, rms=0.275 (0.179%) positioning took 5.5 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (box.dx, box.dy, box.dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) locating cortical regions not in the range [48.50 220.00], gm=171.00+-24.50, and vertices in regions > 158.7 200043 surface locations found to contain inconsistent values (30845 in, 169198 out) tol=1.0e-04, sigma=1.0, host=blg56, 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 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=166364.1, rms=0.288 061: dt: 0.5000, sse=166338.1, rms=0.285 (1.164%) 062: dt: 0.5000, sse=166290.1, rms=0.281 (1.306%) 063: dt: 0.5000, sse=166243.4, rms=0.278 (1.098%) 064: dt: 0.5000, sse=166205.8, rms=0.275 (0.977%) 065: dt: 0.5000, sse=166175.4, rms=0.273 (0.862%) 066: dt: 0.5000, sse=166150.2, rms=0.271 (0.773%) 067: dt: 0.5000, sse=166133.4, rms=0.269 (0.680%) 068: dt: 0.5000, sse=166118.5, rms=0.267 (0.617%) 069: dt: 0.5000, sse=166112.1, rms=0.266 (0.555%) 070: dt: 0.5000, sse=166107.0, rms=0.265 (0.506%) 071: dt: 0.5000, sse=166105.2, rms=0.263 (0.468%) 072: dt: 0.5000, sse=166101.5, rms=0.262 (0.438%) 073: dt: 0.5000, sse=166101.1, rms=0.261 (0.416%) 074: dt: 0.5000, sse=166098.1, rms=0.260 (0.397%) 075: dt: 0.5000, sse=166095.3, rms=0.259 (0.381%) 076: dt: 0.5000, sse=166092.3, rms=0.258 (0.366%) 077: dt: 0.5000, sse=166087.6, rms=0.257 (0.346%) 078: dt: 0.5000, sse=166084.6, rms=0.256 (0.336%) 079: dt: 0.5000, sse=166080.3, rms=0.255 (0.321%) 080: dt: 0.5000, sse=166074.4, rms=0.255 (0.307%) 081: dt: 0.5000, sse=166069.1, rms=0.254 (0.293%) 082: dt: 0.5000, sse=166062.4, rms=0.253 (0.281%) 083: dt: 0.5000, sse=166055.1, rms=0.253 (0.262%) 084: dt: 0.5000, sse=166050.7, rms=0.252 (0.256%) 085: dt: 0.5000, sse=166043.5, rms=0.251 (0.251%) 086: dt: 0.5000, sse=166040.0, rms=0.251 (0.230%) 087: dt: 0.5000, sse=166033.7, rms=0.250 (0.226%) 088: dt: 0.5000, sse=166028.4, rms=0.250 (0.209%) 089: dt: 0.5000, sse=166023.8, rms=0.249 (0.203%) 090: dt: 0.5000, sse=166019.8, rms=0.249 (0.198%) positioning took 6.9 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (box.dx, box.dy, box.dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) locating cortical regions not in the range [42.50 222.40], gm=171.00+-25.70, and vertices in regions > 158.1 200113 surface locations found to contain inconsistent values (22234 in, 177879 out) tol=1.0e-04, sigma=0.5, host=blg56, 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 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=167249.8, rms=0.276 091: dt: 0.5000, sse=167251.7, rms=0.274 (0.919%) 092: dt: 0.5000, sse=167215.2, rms=0.271 (1.010%) 093: dt: 0.5000, sse=167182.9, rms=0.269 (0.836%) 094: dt: 0.5000, sse=167156.3, rms=0.267 (0.724%) 095: dt: 0.5000, sse=167133.2, rms=0.265 (0.628%) 096: dt: 0.5000, sse=167115.1, rms=0.264 (0.547%) 097: dt: 0.5000, sse=167100.6, rms=0.262 (0.474%) 098: dt: 0.5000, sse=167089.7, rms=0.261 (0.423%) 099: dt: 0.5000, sse=167082.0, rms=0.260 (0.379%) 100: dt: 0.5000, sse=167074.7, rms=0.259 (0.345%) 101: dt: 0.5000, sse=167070.3, rms=0.258 (0.321%) 102: dt: 0.5000, sse=167066.2, rms=0.258 (0.300%) 103: dt: 0.5000, sse=167062.3, rms=0.257 (0.283%) 104: dt: 0.5000, sse=167058.5, rms=0.256 (0.269%) 105: dt: 0.5000, sse=167055.1, rms=0.256 (0.255%) 106: dt: 0.5000, sse=167051.1, rms=0.255 (0.238%) 107: dt: 0.5000, sse=167047.9, rms=0.254 (0.230%) 108: dt: 0.5000, sse=167043.4, rms=0.254 (0.219%) 109: dt: 0.5000, sse=167039.0, rms=0.253 (0.209%) 110: dt: 0.5000, sse=167033.9, rms=0.253 (0.200%) 111: dt: 0.5000, sse=167029.3, rms=0.252 (0.192%) 112: dt: 0.5000, sse=167023.9, rms=0.252 (0.184%) 113: dt: 0.5000, sse=167019.5, rms=0.251 (0.173%) 114: dt: 0.5000, sse=167013.7, rms=0.251 (0.164%) 115: dt: 0.5000, sse=167009.1, rms=0.251 (0.160%) 116: dt: 0.5000, sse=167003.7, rms=0.250 (0.151%) 117: dt: 0.5000, sse=166998.4, rms=0.250 (0.145%) 118: dt: 0.5000, sse=166993.5, rms=0.250 (0.138%) 119: dt: 0.5000, sse=166989.1, rms=0.249 (0.130%) 120: dt: 0.5000, sse=166985.2, rms=0.249 (0.127%) positioning took 7.9 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (region->dx, region->dy, region->dz) = (167, 420, 268) (box.dx, box.dy, box.dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) (region->dx, region->dy, region->dz) = (176, 431, 281) locating cortical regions not in the range [44.50 221.60], gm=171.00+-25.30, and vertices in regions > 158.3 195748 surface locations found to contain inconsistent values (32959 in, 162789 out) tol=1.0e-04, sigma=0.2, host=blg56, 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 writing pial surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=168868.8, rms=0.267 121: dt: 0.5000, sse=168860.8, rms=0.265 (0.672%) 122: dt: 0.5000, sse=168817.5, rms=0.264 (0.723%) 123: dt: 0.5000, sse=168778.9, rms=0.262 (0.586%) 124: dt: 0.5000, sse=168746.3, rms=0.261 (0.502%) 125: dt: 0.5000, sse=168715.4, rms=0.260 (0.431%) 126: dt: 0.5000, sse=168690.2, rms=0.259 (0.377%) 127: dt: 0.5000, sse=168668.7, rms=0.258 (0.328%) 128: dt: 0.5000, sse=168649.8, rms=0.257 (0.291%) 129: dt: 0.5000, sse=168636.1, rms=0.256 (0.266%) 130: dt: 0.5000, sse=168620.8, rms=0.256 (0.242%) 131: dt: 0.5000, sse=168609.9, rms=0.255 (0.224%) 132: dt: 0.5000, sse=168601.7, rms=0.255 (0.211%) 133: dt: 0.5000, sse=168585.9, rms=0.254 (0.196%) 134: dt: 0.5000, sse=168579.6, rms=0.254 (0.187%) 135: dt: 0.5000, sse=168570.2, rms=0.253 (0.177%) 136: dt: 0.5000, sse=168561.2, rms=0.253 (0.168%) 137: dt: 0.5000, sse=168552.9, rms=0.252 (0.159%) 138: dt: 0.5000, sse=168544.8, rms=0.252 (0.150%) 139: dt: 0.5000, sse=168537.0, rms=0.252 (0.141%) 140: dt: 0.5000, sse=168530.2, rms=0.251 (0.137%) 141: dt: 0.5000, sse=168523.1, rms=0.251 (0.128%) 142: dt: 0.5000, sse=168517.3, rms=0.251 (0.125%) 143: dt: 0.5000, sse=168511.3, rms=0.250 (0.118%) 144: dt: 0.5000, sse=168504.4, rms=0.250 (0.114%) 145: dt: 0.5000, sse=168498.4, rms=0.250 (0.108%) 146: dt: 0.5000, sse=168492.6, rms=0.250 (0.102%) 147: dt: 0.5000, sse=168487.5, rms=0.249 (0.099%) 148: dt: 0.5000, sse=168482.1, rms=0.249 (0.095%) 149: dt: 0.5000, sse=168476.5, rms=0.249 (0.089%) 150: dt: 0.5000, sse=168471.3, rms=0.249 (0.086%) positioning took 8.7 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.area.pial vertex spacing 0.79 +- 0.36 (0.03-->7.21) (max @ vno 169536 --> 169507) face area 0.24 +- 0.20 (0.00-->7.07) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 253649 vertices processed 25000 of 253649 vertices processed 50000 of 253649 vertices processed 75000 of 253649 vertices processed 100000 of 253649 vertices processed 125000 of 253649 vertices processed 150000 of 253649 vertices processed 175000 of 253649 vertices processed 200000 of 253649 vertices processed 225000 of 253649 vertices processed 250000 of 253649 vertices processed 0 of 253649 vertices processed 25000 of 253649 vertices processed 50000 of 253649 vertices processed 75000 of 253649 vertices processed 100000 of 253649 vertices processed 125000 of 253649 vertices processed 150000 of 253649 vertices processed 175000 of 253649 vertices processed 200000 of 253649 vertices processed 225000 of 253649 vertices processed 250000 of 253649 vertices processed thickness calculation complete, 180:533 truncations. 50774 vertices at 0 distance 152800 vertices at 1 distance 151499 vertices at 2 distance 81205 vertices at 3 distance 33108 vertices at 4 distance 11905 vertices at 5 distance 4055 vertices at 6 distance 1310 vertices at 7 distance 422 vertices at 8 distance 146 vertices at 9 distance 94 vertices at 10 distance 82 vertices at 11 distance 40 vertices at 12 distance 35 vertices at 13 distance 44 vertices at 14 distance 36 vertices at 15 distance 38 vertices at 16 distance 43 vertices at 17 distance 31 vertices at 18 distance 21 vertices at 19 distance 22 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.thickness positioning took 58.3 minutes PIDs (130087 130093) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Tue May 25 23:52:02 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf vertexvol --s sub-03 --lh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Total face volume 282888 Total vertex volume 280012 (mask=0) #@# sub-03 lh 280012 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue May 25 23:52:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf vertexvol --s sub-03 --rh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Total face volume 287397 Total vertex volume 284830 (mask=0) #@# sub-03 rh 284830 vertexvol Done #-------------------------------------------- #@# Surf Volume lh Tue May 25 23:52:11 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Total face volume 282888 Total vertex volume 280012 (mask=0) #@# sub-03 lh 280012 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue May 25 23:52:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Total face volume 287397 Total vertex volume 284830 (mask=0) #@# sub-03 rh 284830 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue May 25 23:52:20 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 = 701 writing volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/ribbon.mgz mris_volmask took 16.81 minutes writing ribbon files Started at Tue May 25 22:50:05 UTC 2021 Ended at Wed May 26 00:09:09 UTC 2021 #@#%# recon-all-run-time-hours 1.318 recon-all -s sub-03 finished without error at Wed May 26 00:09:09 UTC 2021 New invocation of recon-all Wed May 26 00:19:17 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon3 -openmp 8 -subjid sub-03 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels subjid sub-03 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 32440008 157578624 1957264 6619800 159840152 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: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:17-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:19:18-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.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 Wed May 26 00:19:18 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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... 8253 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 5260 voxels changed to hypointensity... 13098 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed May 26 00:19:49 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subject sub-03 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 13.79 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 --> 82 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 68 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 36 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 63 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 76 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 69 rescaling Right_Thalamus_Proper from 85 --> 94 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 76 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 54 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 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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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subject sub-03 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 13.79 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 --> 82 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 68 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 36 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 63 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 76 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 69 rescaling Right_Thalamus_Proper from 85 --> 94 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 76 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 54 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 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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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subject sub-03 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 13.79 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 --> 82 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 68 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 36 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 63 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 76 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 69 rescaling Right_Thalamus_Proper from 85 --> 94 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 76 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 54 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 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/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.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 Wed May 26 00:43:57 UTC 2021 Ended at Wed May 26 00:44:03 UTC 2021 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed May 26 00:44:03 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1636395 mm^3 (det: 1.190486 ) Computing euler number orig.nofix lheno = -124, rheno = -82 orig.nofix lhholes = 63, rhholes = 42 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 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 Wed May 26 00:44:54 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aparc+aseg.mgz Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/ribbon.mgz Loading filled from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 11185 vertices from left hemi Ripped 11464 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/aseg.mgz Loading Ctx Seg File /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/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 = 2001003 Used brute-force search on 2 voxels Fixing Parahip LH WM Found 16 clusters 0 k 0.512000 1 k 0.512000 2 k 0.512000 3 k 1.536000 4 k 1642.982178 5 k 0.512000 6 k 0.512000 7 k 49.152008 8 k 0.512000 9 k 0.512000 10 k 0.512000 11 k 0.512000 12 k 1.024000 13 k 3.583999 14 k 0.512000 15 k 0.512000 Fixing Parahip RH WM Found 13 clusters 0 k 1570.283569 1 k 0.512000 2 k 1.024000 3 k 1.536000 4 k 1.536000 5 k 0.512000 6 k 44.031998 7 k 1.024000 8 k 0.512000 9 k 1.536000 10 k 0.512000 11 k 0.512000 12 k 0.512000 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 blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1636395 mm^3 (det: 1.190486 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 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 Wed May 26 00:19:17 UTC 2021 Ended at Wed May 26 00:54:42 UTC 2021 #@#%# recon-all-run-time-hours 0.590 recon-all -s sub-03 finished without error at Wed May 26 00:54:43 UTC 2021