Tue May 25 17:30:34 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon1 -i /work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-05_ses-001_T1w_template.nii.gz -T2 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-05/ses-001/anat/sub-05_ses-001_T2w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-05 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -expert /work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts subjid sub-05 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 blg4313.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: 196638428 104003048 77685384 2007328 14949996 87509204 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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:35-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: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-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: blg4313.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: 2021/05/25-17:30:37-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: blg4313.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: 2021/05/25-17:30:37-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: blg4313.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: 2021/05/25-17:30:37-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: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/25-17:30:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: blg4313.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-05 mri_convert /work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-05_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/001.mgz mri_convert.bin /work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-05_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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_05_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-05_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-05/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Tue May 25 17:30:45 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 mri_convert --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-05/ses-001/anat/sub-05_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-05/ses-001/anat/sub-05_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/ses-001/anat/sub-05_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-05/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Tue May 25 17:30:56 UTC 2021 Found 1 runs /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/orig/001.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz --conform_min mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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-05/mri/orig.mgz... mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/talairach.xfm /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 25 17:31:08 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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 blg4313.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 17:31:09 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.41289 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.41289/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.41289/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.41289/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Tue May 25 17:31:25 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.41289/nu0.mnc ./tmp.mri_nu_correct.mni.41289/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.41289/0/ -iterations 1000 -distance 50 [bpinsard@blg4313.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/] [2021-05-25 17:31:26] 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.41289/0/ ./tmp.mri_nu_correct.mni.41289/nu0.mnc ./tmp.mri_nu_correct.mni.41289/nu1.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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field change: 0.000941045 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.41289/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.41289/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.41289/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 17:34:53 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 17:34:53 UTC 2021 Ended at Tue May 25 17:35:34 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 25 17:35:36 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6756, pval=0.4932 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/talairach_avi.log tal_QC_AZS /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/talairach_avi.log TalAviQA: 0.97108 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Tue May 25 17:35:36 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-05/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 blg4313.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 17:35:36 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.46975 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.46975/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.46975/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.46975/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Tue May 25 17:35:55 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.46975/nu0.mnc ./tmp.mri_nu_correct.mni.46975/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.46975/0/ [bpinsard@blg4313.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/] [2021-05-25 17:35:55] 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.46975/0/ ./tmp.mri_nu_correct.mni.46975/nu0.mnc ./tmp.mri_nu_correct.mni.46975/nu1.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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............................................................ Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Tue May 25 17:38:32 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.46975/nu1.mnc ./tmp.mri_nu_correct.mni.46975/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.46975/1/ [bpinsard@blg4313.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/] [2021-05-25 17:38:32] 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.46975/1/ ./tmp.mri_nu_correct.mni.46975/nu1.mnc ./tmp.mri_nu_correct.mni.46975/nu2.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 26 CV of field change: 0.000954431 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.46975/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.46975/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-05/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.46975/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.46975/ones.mgz sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard input ./tmp.mri_nu_correct.mni.46975/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.46975/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.46975/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.46975/sum.junk --avgwf ./tmp.mri_nu_correct.mni.46975/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.46975/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.46975/sum.junk --avgwf ./tmp.mri_nu_correct.mni.46975/input.mean.dat sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.46975/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.46975/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.46975/ones.mgz --i ./tmp.mri_nu_correct.mni.46975/nu2.mnc --sum ./tmp.mri_nu_correct.mni.46975/sum.junk --avgwf ./tmp.mri_nu_correct.mni.46975/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.46975/ones.mgz --i ./tmp.mri_nu_correct.mni.46975/nu2.mnc --sum ./tmp.mri_nu_correct.mni.46975/sum.junk --avgwf ./tmp.mri_nu_correct.mni.46975/output.mean.dat sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.46975/ones.mgz Loading ./tmp.mri_nu_correct.mni.46975/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.46975/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.46975/nu2.mnc ./tmp.mri_nu_correct.mni.46975/nu2.mnc mul 1.00797006259038073055 Saving result to './tmp.mri_nu_correct.mni.46975/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.46975/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.46975/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.46975/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 12 seconds. mapping ( 8, 149) to ( 3, 110) Tue May 25 17:41:46 UTC 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue May 25 17:41:47 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 1.08497 0.01162 0.03957 2.60555; -0.06387 0.98116 0.31117 -31.70048; -0.04034 -0.24925 1.02534 -6.38844; 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 = 22 Starting OpenSpline(): npoints = 22 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 84 (84), valley at 41 (41) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 16 (16) 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 5 minutes and 45 seconds. Started at Tue May 25 17:30:31 UTC 2021 Ended at Tue May 25 17:47:33 UTC 2021 #@#%# recon-all-run-time-hours 0.284 recon-all -s sub-05 finished without error at Tue May 25 17:47:33 UTC 2021 New invocation of recon-all Tue May 25 17:47:39 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-05 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-05 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 blg4313.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: 196638428 106509756 72815088 2007340 17313584 84826488 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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:39-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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: 2021/05/25-17:47:40-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: blg4313.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 17:47:40 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri mri_em_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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=25.0 skull bounding box = (84, 64, 46) --> (240, 231, 246) using (136, 120, 146) as brain centroid... mean wm in atlas = 107, using box (117,99,121) --> (155, 140,170) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 5.1 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 initial log_p = -4.086 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.091068 @ (-9.091, 9.091, -9.091) max log p = -3.992266 @ (4.545, -4.545, 4.545) max log p = -3.992266 @ (0.000, 0.000, 0.000) max log p = -3.978668 @ (1.136, 1.136, -1.136) max log p = -3.962191 @ (-1.705, 1.705, 0.568) max log p = -3.951763 @ (0.852, -0.852, -0.852) Found translation: (-4.3, 6.5, -6.0): log p = -3.952 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.843, old_max_log_p =-3.952 (thresh=-3.9) 0.85264 0.10843 0.02905 -31.90862; -0.11225 0.82359 0.22068 -12.92698; 0.00000 -0.20706 0.77274 28.27134; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.843, old_max_log_p =-3.843 (thresh=-3.8) 0.85264 0.10843 0.02905 -31.90862; -0.11225 0.82359 0.22068 -12.92698; 0.00000 -0.20706 0.77274 28.27134; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.759, old_max_log_p =-3.843 (thresh=-3.8) 0.87553 0.00884 -0.02483 -14.94744; 0.00200 0.81597 0.21337 -27.13385; 0.02772 -0.20163 0.77375 23.71881; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.748, old_max_log_p =-3.759 (thresh=-3.8) 0.87553 0.00884 -0.02483 -14.94744; 0.00109 0.82213 0.18794 -23.48692; 0.02829 -0.17810 0.79495 17.72658; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.748, old_max_log_p =-3.748 (thresh=-3.7) 0.87553 0.00884 -0.02483 -14.94744; 0.00109 0.82213 0.18794 -23.48692; 0.02829 -0.17810 0.79495 17.72658; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.714, old_max_log_p =-3.748 (thresh=-3.7) 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.714, old_max_log_p =-3.714 (thresh=-3.7) 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 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 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.714 (old=-4.086) transform before final EM align: 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 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 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.1 tol 0.000000 final transform: 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1487.580844 mri_em_register stimesec 4.942182 mri_em_register ru_maxrss 753856 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1347078 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 717 mri_em_register ru_nivcsw 2071 registration took 3 minutes and 59 seconds. #-------------------------------------- #@# CA Normalize Tue May 25 17:51:39 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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=25.0 skull bounding box = (84, 64, 46) --> (240, 231, 246) using (136, 120, 146) as brain centroid... mean wm in atlas = 107, using box (117,99,121) --> (155, 140,170) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 5.1 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 using 246344 sample points... INFO: compute sample coordinates transform 0.87442 0.02217 -0.02131 -17.13951; -0.01209 0.81486 0.22095 -25.84338; 0.02844 -0.21230 0.78936 23.56488; 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 (160, 65, 44) --> (239, 205, 245) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 1340 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (89, 64, 43) --> (167, 198, 246) Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 130 of 1101 (11.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (163, 175, 80) --> (218, 227, 146) Left_Cerebellum_White_Matter: limiting intensities to 110.0 --> 132.0 0 of 21 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (111, 175, 78) --> (162, 223, 148) Right_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0 0 of 29 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (144, 157, 124) --> (183, 241, 161) Brain_Stem: limiting intensities to 106.0 --> 132.0 0 of 8 (0.0%) samples deleted using 2499 total control points for intensity normalization... bias field = 0.943 +- 0.071 5 of 2369 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (160, 65, 44) --> (239, 205, 245) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 2151 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (89, 64, 43) --> (167, 198, 246) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 22 of 1866 (1.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (163, 175, 80) --> (218, 227, 146) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 74 (1.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (111, 175, 78) --> (162, 223, 148) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 80 (10.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (144, 157, 124) --> (183, 241, 161) Brain_Stem: limiting intensities to 88.0 --> 132.0 33 of 92 (35.9%) samples deleted using 4263 total control points for intensity normalization... bias field = 1.057 +- 0.073 5 of 4163 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (160, 65, 44) --> (239, 205, 245) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 2164 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (89, 64, 43) --> (167, 198, 246) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 1969 (0.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (163, 175, 80) --> (218, 227, 146) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 94 of 137 (68.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (111, 175, 78) --> (162, 223, 148) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 76 of 101 (75.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (144, 157, 124) --> (183, 241, 161) Brain_Stem: limiting intensities to 88.0 --> 132.0 158 of 211 (74.9%) samples deleted using 4582 total control points for intensity normalization... bias field = 1.056 +- 0.060 5 of 4177 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 40 seconds. #-------------------------------------- #@# CA Reg Tue May 25 17:54:19 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri mri_ca_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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) = 0.60 (predicted orig area = 13.2) 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=0.889, neg=0, invalid=762 0001: dt=265.363233, rms=0.790 (11.155%), neg=0, invalid=762 0002: dt=221.952000, rms=0.767 (2.886%), neg=0, invalid=762 0003: dt=295.936000, rms=0.756 (1.473%), neg=0, invalid=762 0004: dt=145.548387, rms=0.751 (0.690%), neg=0, invalid=762 0005: dt=517.888000, rms=0.744 (0.806%), neg=0, invalid=762 0006: dt=129.472000, rms=0.743 (0.192%), neg=0, invalid=762 0007: dt=129.472000, rms=0.742 (0.126%), neg=0, invalid=762 0008: dt=129.472000, rms=0.740 (0.220%), neg=0, invalid=762 0009: dt=129.472000, rms=0.738 (0.278%), neg=0, invalid=762 0010: dt=129.472000, rms=0.736 (0.329%), neg=0, invalid=762 0011: dt=129.472000, rms=0.734 (0.320%), neg=0, invalid=762 0012: dt=129.472000, rms=0.732 (0.284%), neg=0, invalid=762 0013: dt=129.472000, rms=0.730 (0.239%), neg=0, invalid=762 0014: dt=129.472000, rms=0.728 (0.216%), neg=0, invalid=762 0015: dt=129.472000, rms=0.727 (0.196%), neg=0, invalid=762 0016: dt=129.472000, rms=0.725 (0.199%), neg=0, invalid=762 0017: dt=129.472000, rms=0.724 (0.175%), neg=0, invalid=762 0018: dt=129.472000, rms=0.723 (0.143%), neg=0, invalid=762 0019: dt=129.472000, rms=0.722 (0.095%), neg=0, invalid=762 0020: dt=129.472000, rms=0.722 (0.065%), neg=0, invalid=762 0021: dt=1183.744000, rms=0.720 (0.203%), neg=0, invalid=762 0022: dt=92.480000, rms=0.720 (0.039%), neg=0, invalid=762 0023: dt=92.480000, rms=0.720 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.721, neg=0, invalid=762 0024: dt=295.936000, rms=0.718 (0.357%), neg=0, invalid=762 0025: dt=517.888000, rms=0.716 (0.237%), neg=0, invalid=762 0026: dt=517.888000, rms=0.716 (-0.052%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.722, neg=0, invalid=762 0027: dt=121.504478, rms=0.717 (0.741%), neg=0, invalid=762 0028: dt=414.720000, rms=0.697 (2.799%), neg=0, invalid=762 0029: dt=49.504274, rms=0.693 (0.590%), neg=0, invalid=762 0030: dt=36.288000, rms=0.692 (0.037%), neg=0, invalid=762 0031: dt=36.288000, rms=0.692 (0.057%), neg=0, invalid=762 0032: dt=36.288000, rms=0.691 (0.100%), neg=0, invalid=762 0033: dt=36.288000, rms=0.690 (0.174%), neg=0, invalid=762 0034: dt=36.288000, rms=0.688 (0.307%), neg=0, invalid=762 0035: dt=36.288000, rms=0.685 (0.445%), neg=0, invalid=762 0036: dt=36.288000, rms=0.681 (0.512%), neg=0, invalid=762 0037: dt=36.288000, rms=0.678 (0.497%), neg=0, invalid=762 0038: dt=36.288000, rms=0.675 (0.445%), neg=0, invalid=762 0039: dt=36.288000, rms=0.673 (0.329%), neg=0, invalid=762 0040: dt=36.288000, rms=0.671 (0.246%), neg=0, invalid=762 0041: dt=36.288000, rms=0.670 (0.224%), neg=0, invalid=762 0042: dt=36.288000, rms=0.668 (0.266%), neg=0, invalid=762 0043: dt=36.288000, rms=0.666 (0.310%), neg=0, invalid=762 0044: dt=36.288000, rms=0.664 (0.304%), neg=0, invalid=762 0045: dt=36.288000, rms=0.662 (0.262%), neg=0, invalid=762 0046: dt=36.288000, rms=0.661 (0.196%), neg=0, invalid=762 0047: dt=36.288000, rms=0.660 (0.149%), neg=0, invalid=762 0048: dt=36.288000, rms=0.659 (0.130%), neg=0, invalid=762 0049: dt=36.288000, rms=0.658 (0.127%), neg=0, invalid=762 0050: dt=36.288000, rms=0.657 (0.153%), neg=0, invalid=762 0051: dt=36.288000, rms=0.656 (0.150%), neg=0, invalid=762 0052: dt=36.288000, rms=0.655 (0.147%), neg=0, invalid=762 0053: dt=36.288000, rms=0.654 (0.128%), neg=0, invalid=762 0054: dt=36.288000, rms=0.653 (0.105%), neg=0, invalid=762 0055: dt=36.288000, rms=0.653 (0.084%), neg=0, invalid=762 0056: dt=103.680000, rms=0.653 (0.019%), neg=0, invalid=762 0057: dt=103.680000, rms=0.653 (0.018%), neg=0, invalid=762 0058: dt=103.680000, rms=0.652 (0.050%), neg=0, invalid=762 0059: dt=103.680000, rms=0.652 (0.075%), neg=0, invalid=762 0060: dt=103.680000, rms=0.652 (0.002%), neg=0, invalid=762 0061: dt=103.680000, rms=0.652 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0062: dt=115.439252, rms=0.649 (0.554%), neg=0, invalid=762 0063: dt=31.104000, rms=0.649 (0.029%), neg=0, invalid=762 0064: dt=31.104000, rms=0.649 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0065: dt=11.200000, rms=0.681 (0.327%), neg=0, invalid=762 0066: dt=8.000000, rms=0.681 (0.053%), neg=0, invalid=762 0067: dt=8.000000, rms=0.681 (0.025%), neg=0, invalid=762 0068: dt=8.000000, rms=0.681 (-0.058%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.682, neg=0, invalid=762 0069: dt=11.200000, rms=0.680 (0.163%), neg=0, invalid=762 0070: dt=2.800000, rms=0.680 (0.005%), neg=0, invalid=762 0071: dt=2.800000, rms=0.680 (0.005%), neg=0, invalid=762 0072: dt=2.800000, rms=0.680 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.741, neg=0, invalid=762 0073: dt=6.251572, rms=0.729 (1.682%), neg=0, invalid=762 0074: dt=6.857143, rms=0.726 (0.331%), neg=0, invalid=762 0075: dt=4.032000, rms=0.726 (0.036%), neg=0, invalid=762 0076: dt=4.032000, rms=0.726 (0.021%), neg=0, invalid=762 0077: dt=4.032000, rms=0.726 (-0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.726, neg=0, invalid=762 0078: dt=0.000000, rms=0.726 (0.080%), neg=0, invalid=762 0079: dt=0.000000, rms=0.726 (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=0.771, neg=0, invalid=762 0080: dt=0.000000, rms=0.771 (0.071%), neg=0, invalid=762 0081: dt=0.000000, rms=0.771 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.771, neg=0, invalid=762 0082: dt=0.000000, rms=0.771 (0.071%), neg=0, invalid=762 0083: dt=0.000000, rms=0.771 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0084: dt=0.742718, rms=0.679 (2.288%), neg=0, invalid=762 0085: dt=0.064000, rms=0.678 (0.074%), neg=0, invalid=762 0086: dt=0.064000, rms=0.678 (-0.061%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0087: dt=0.016000, rms=0.678 (0.095%), neg=0, invalid=762 0088: dt=0.000000, rms=0.678 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11567 (26) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (3850 voxels, overlap=0.538) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (3850 voxels, peak = 28), gca=27.5 gca peak = 0.15565 (16) mri peak = 0.12635 (26) Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (2442 voxels, overlap=0.268) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2442 voxels, peak = 26), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06378 (97) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1661 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1661 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.06074 (97) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1851 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1851 voxels, peak = 95), gca=95.3 gca peak = 0.21683 (55) mri peak = 0.06541 (71) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2234 voxels, overlap=0.023) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2234 voxels, peak = 70), gca=69.6 gca peak = 0.30730 (58) mri peak = 0.07718 (72) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2383 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2383 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.08939 (100) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (167670 voxels, overlap=0.857) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (167670 voxels, peak = 103), gca=102.5 gca peak = 0.12076 (102) mri peak = 0.09695 (100) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (169884 voxels, overlap=0.878) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (169884 voxels, peak = 102), gca=102.0 gca peak = 0.14995 (59) mri peak = 0.04056 (75) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (80680 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (80680 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.04163 (76) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (86735 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (86735 voxels, peak = 77), gca=76.9 gca peak = 0.14161 (67) mri peak = 0.09636 (79) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1950 voxels, overlap=0.012) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1950 voxels, peak = 80), gca=80.1 gca peak = 0.15243 (71) mri peak = 0.11329 (80) Left_Caudate (11): linear fit = 1.11 x + 0.0 (2772 voxels, overlap=0.348) Left_Caudate (11): linear fit = 1.11 x + 0.0 (2772 voxels, peak = 78), gca=78.5 gca peak = 0.13336 (57) mri peak = 0.05647 (71) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (41441 voxels, overlap=0.010) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (41441 voxels, peak = 74), gca=73.8 gca peak = 0.13252 (56) mri peak = 0.04575 (71) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (48766 voxels, overlap=0.005) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (48766 voxels, peak = 71), gca=70.8 gca peak = 0.18181 (84) mri peak = 0.08392 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (20093 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (20093 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.07405 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (16690 voxels, overlap=0.871) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (16690 voxels, peak = 84), gca=84.2 gca peak = 0.21969 (57) mri peak = 0.08957 (71) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (1154 voxels, overlap=0.044) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (1154 voxels, peak = 70), gca=69.8 gca peak = 0.39313 (56) mri peak = 0.08123 (72) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (1272 voxels, overlap=0.054) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (1272 voxels, peak = 71), gca=71.4 gca peak = 0.14181 (85) mri peak = 0.07253 (95) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (11975 voxels, overlap=0.415) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (11975 voxels, peak = 94), gca=93.9 gca peak = 0.11978 (83) mri peak = 0.07040 (93) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (9669 voxels, overlap=0.362) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (9669 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.06293 (86) Left_Putamen (12): linear fit = 1.11 x + 0.0 (5578 voxels, overlap=0.491) Left_Putamen (12): linear fit = 1.11 x + 0.0 (5578 voxels, peak = 87), gca=87.3 gca peak = 0.14159 (79) mri peak = 0.06143 (86) Right_Putamen (51): linear fit = 1.10 x + 0.0 (5520 voxels, overlap=0.454) Right_Putamen (51): linear fit = 1.10 x + 0.0 (5520 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.08651 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (23158 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (23158 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07672 (96) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (2491 voxels, overlap=0.462) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (2491 voxels, peak = 97), gca=96.8 gca peak = 0.12801 (89) mri peak = 0.07706 (93) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (2997 voxels, overlap=0.539) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (2997 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 0.13336 (28) Third_Ventricle (14): linear fit = 1.07 x + 0.0 (89 voxels, overlap=0.989) Third_Ventricle (14): linear fit = 1.07 x + 0.0 (89 voxels, peak = 24), gca=24.5 gca peak = 0.15061 (21) mri peak = 0.11422 (24) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (1105 voxels, overlap=0.496) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (1105 voxels, peak = 27), gca=27.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak 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 1.27 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 Right_Pallidum too bright - rescaling by 0.998 (from 1.035) to 99.2 (was 99.4) 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=0.665, neg=0, invalid=762 0089: dt=112.165926, rms=0.647 (2.614%), neg=0, invalid=762 0090: dt=129.472000, rms=0.645 (0.333%), neg=0, invalid=762 0091: dt=295.936000, rms=0.643 (0.369%), neg=0, invalid=762 0092: dt=887.808000, rms=0.636 (0.957%), neg=0, invalid=762 0093: dt=73.984000, rms=0.636 (0.056%), neg=0, invalid=762 0094: dt=73.984000, rms=0.636 (0.011%), neg=0, invalid=762 0095: dt=73.984000, rms=0.636 (0.015%), neg=0, invalid=762 0096: dt=73.984000, rms=0.636 (0.024%), neg=0, invalid=762 0097: dt=73.984000, rms=0.636 (0.045%), neg=0, invalid=762 0098: dt=73.984000, rms=0.635 (0.087%), neg=0, invalid=762 0099: dt=73.984000, rms=0.634 (0.134%), neg=0, invalid=762 0100: dt=73.984000, rms=0.633 (0.173%), neg=0, invalid=762 0101: dt=73.984000, rms=0.632 (0.170%), neg=0, invalid=762 0102: dt=73.984000, rms=0.631 (0.153%), neg=0, invalid=762 0103: dt=73.984000, rms=0.630 (0.120%), neg=0, invalid=762 0104: dt=73.984000, rms=0.630 (0.086%), neg=0, invalid=762 0105: dt=73.984000, rms=0.629 (0.063%), neg=0, invalid=762 0106: dt=73.984000, rms=0.629 (0.055%), neg=0, invalid=762 0107: dt=73.984000, rms=0.629 (0.060%), neg=0, invalid=762 0108: dt=73.984000, rms=0.628 (0.073%), neg=0, invalid=762 0109: dt=73.984000, rms=0.628 (0.091%), neg=0, invalid=762 0110: dt=73.984000, rms=0.627 (0.100%), neg=0, invalid=762 0111: dt=73.984000, rms=0.626 (0.094%), neg=0, invalid=762 0112: dt=73.984000, rms=0.626 (0.085%), neg=0, invalid=762 0113: dt=73.984000, rms=0.625 (0.071%), neg=0, invalid=762 0114: dt=73.984000, rms=0.625 (0.061%), neg=0, invalid=762 0115: dt=73.984000, rms=0.625 (0.052%), neg=0, invalid=762 0116: dt=73.984000, rms=0.624 (0.050%), neg=0, invalid=762 0117: dt=73.984000, rms=0.624 (0.053%), neg=0, invalid=762 0118: dt=73.984000, rms=0.624 (0.063%), neg=0, invalid=762 0119: dt=73.984000, rms=0.623 (0.065%), neg=0, invalid=762 0120: dt=73.984000, rms=0.623 (0.064%), neg=0, invalid=762 0121: dt=73.984000, rms=0.622 (0.065%), neg=0, invalid=762 0122: dt=73.984000, rms=0.622 (0.059%), neg=0, invalid=762 0123: dt=73.984000, rms=0.622 (0.060%), neg=0, invalid=762 0124: dt=73.984000, rms=0.621 (0.053%), neg=0, invalid=762 0125: dt=73.984000, rms=0.621 (0.049%), neg=0, invalid=762 0126: dt=73.984000, rms=0.621 (0.047%), neg=0, invalid=762 0127: dt=73.984000, rms=0.620 (0.042%), neg=0, invalid=762 0128: dt=73.984000, rms=0.620 (0.042%), neg=0, invalid=762 0129: dt=73.984000, rms=0.620 (0.043%), neg=0, invalid=762 0130: dt=73.984000, rms=0.620 (0.046%), neg=0, invalid=762 0131: dt=73.984000, rms=0.619 (0.044%), neg=0, invalid=762 0132: dt=73.984000, rms=0.619 (0.043%), neg=0, invalid=762 0133: dt=73.984000, rms=0.619 (0.043%), neg=0, invalid=762 0134: dt=73.984000, rms=0.619 (0.037%), neg=0, invalid=762 0135: dt=73.984000, rms=0.618 (0.032%), neg=0, invalid=762 0136: dt=73.984000, rms=0.618 (0.028%), neg=0, invalid=762 0137: dt=73.984000, rms=0.618 (0.026%), neg=0, invalid=762 0138: dt=73.984000, rms=0.618 (0.030%), neg=0, invalid=762 0139: dt=73.984000, rms=0.618 (0.025%), neg=0, invalid=762 0140: dt=73.984000, rms=0.618 (0.025%), neg=0, invalid=762 0141: dt=73.984000, rms=0.617 (0.024%), neg=0, invalid=762 0142: dt=73.984000, rms=0.617 (0.027%), neg=0, invalid=762 0143: dt=73.984000, rms=0.617 (0.025%), neg=0, invalid=762 0144: dt=73.984000, rms=0.617 (0.023%), neg=0, invalid=762 0145: dt=1183.744000, rms=0.617 (0.019%), neg=0, invalid=762 0146: dt=1183.744000, rms=0.617 (-0.539%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=762 0147: dt=517.888000, rms=0.614 (0.471%), neg=0, invalid=762 0148: dt=32.368000, rms=0.614 (0.004%), neg=0, invalid=762 0149: dt=32.368000, rms=0.614 (0.001%), neg=0, invalid=762 0150: dt=32.368000, rms=0.614 (-0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.615, neg=0, invalid=762 0151: dt=103.680000, rms=0.613 (0.366%), neg=0, invalid=762 0152: dt=497.664000, rms=0.601 (1.937%), neg=0, invalid=762 0153: dt=59.885714, rms=0.598 (0.591%), neg=0, invalid=762 0154: dt=497.664000, rms=0.593 (0.679%), neg=0, invalid=762 0155: dt=103.680000, rms=0.589 (0.727%), neg=0, invalid=762 0156: dt=82.944000, rms=0.588 (0.138%), neg=0, invalid=762 0157: dt=248.832000, rms=0.587 (0.212%), neg=0, invalid=762 0158: dt=87.466667, rms=0.585 (0.297%), neg=0, invalid=762 0159: dt=124.416000, rms=0.585 (0.125%), neg=0, invalid=762 0160: dt=145.152000, rms=0.583 (0.234%), neg=0, invalid=762 0161: dt=62.208000, rms=0.583 (0.095%), neg=0, invalid=762 0162: dt=580.608000, rms=0.580 (0.509%), neg=0, invalid=762 0163: dt=36.288000, rms=0.579 (0.195%), neg=0, invalid=762 0164: dt=103.680000, rms=0.578 (0.116%), neg=0, invalid=762 0165: dt=124.416000, rms=0.577 (0.128%), neg=0, invalid=762 0166: dt=82.944000, rms=0.577 (0.090%), neg=0, invalid=762 0167: dt=124.416000, rms=0.576 (0.098%), neg=0, invalid=762 0168: dt=82.944000, rms=0.576 (0.089%), neg=0, invalid=762 0169: dt=145.152000, rms=0.575 (0.112%), neg=0, invalid=762 0170: dt=82.944000, rms=0.575 (0.075%), neg=0, invalid=762 0171: dt=145.152000, rms=0.574 (0.118%), neg=0, invalid=762 0172: dt=82.944000, rms=0.574 (0.055%), neg=0, invalid=762 0173: dt=145.152000, rms=0.573 (0.098%), neg=0, invalid=762 0174: dt=62.208000, rms=0.573 (0.061%), neg=0, invalid=762 0175: dt=497.664000, rms=0.571 (0.199%), neg=0, invalid=762 0176: dt=36.288000, rms=0.571 (0.134%), neg=0, invalid=762 0177: dt=82.944000, rms=0.570 (0.039%), neg=0, invalid=762 0178: dt=82.944000, rms=0.570 (0.070%), neg=0, invalid=762 0179: dt=82.944000, rms=0.570 (0.076%), neg=0, invalid=762 0180: dt=82.944000, rms=0.569 (0.125%), neg=0, invalid=762 0181: dt=82.944000, rms=0.568 (0.128%), neg=0, invalid=762 0182: dt=82.944000, rms=0.567 (0.179%), neg=0, invalid=762 0183: dt=82.944000, rms=0.566 (0.161%), neg=0, invalid=762 0184: dt=82.944000, rms=0.565 (0.181%), neg=0, invalid=762 0185: dt=82.944000, rms=0.564 (0.186%), neg=0, invalid=762 0186: dt=82.944000, rms=0.563 (0.199%), neg=0, invalid=762 0187: dt=82.944000, rms=0.562 (0.184%), neg=0, invalid=762 0188: dt=82.944000, rms=0.561 (0.171%), neg=0, invalid=762 0189: dt=82.944000, rms=0.560 (0.175%), neg=0, invalid=762 0190: dt=82.944000, rms=0.559 (0.170%), neg=0, invalid=762 0191: dt=82.944000, rms=0.558 (0.157%), neg=0, invalid=762 0192: dt=82.944000, rms=0.557 (0.142%), neg=0, invalid=762 0193: dt=82.944000, rms=0.557 (0.123%), neg=0, invalid=762 0194: dt=82.944000, rms=0.556 (0.117%), neg=0, invalid=762 0195: dt=82.944000, rms=0.555 (0.131%), neg=0, invalid=762 0196: dt=82.944000, rms=0.555 (0.010%), neg=0, invalid=762 0197: dt=82.944000, rms=0.555 (0.014%), neg=0, invalid=762 0198: dt=82.944000, rms=0.555 (0.038%), neg=0, invalid=762 0199: dt=82.944000, rms=0.555 (0.035%), neg=0, invalid=762 0200: dt=82.944000, rms=0.555 (0.020%), neg=0, invalid=762 0201: dt=82.944000, rms=0.555 (0.034%), neg=0, invalid=762 0202: dt=82.944000, rms=0.554 (0.075%), neg=0, invalid=762 0203: dt=82.944000, rms=0.554 (0.055%), neg=0, invalid=762 0204: dt=82.944000, rms=0.554 (0.054%), neg=0, invalid=762 0205: dt=82.944000, rms=0.553 (0.062%), neg=0, invalid=762 0206: dt=82.944000, rms=0.553 (0.055%), neg=0, invalid=762 0207: dt=82.944000, rms=0.553 (0.047%), neg=0, invalid=762 0208: dt=82.944000, rms=0.552 (0.055%), neg=0, invalid=762 0209: dt=82.944000, rms=0.552 (0.061%), neg=0, invalid=762 0210: dt=82.944000, rms=0.552 (0.074%), neg=0, invalid=762 0211: dt=82.944000, rms=0.551 (0.058%), neg=0, invalid=762 0212: dt=82.944000, rms=0.551 (0.055%), neg=0, invalid=762 0213: dt=82.944000, rms=0.551 (0.013%), neg=0, invalid=762 0214: dt=82.944000, rms=0.551 (0.016%), neg=0, invalid=762 0215: dt=82.944000, rms=0.551 (0.017%), neg=0, invalid=762 0216: dt=5.184000, rms=0.551 (0.001%), neg=0, invalid=762 0217: dt=2.268000, rms=0.551 (0.001%), neg=0, invalid=762 0218: dt=0.567000, rms=0.551 (0.002%), neg=0, invalid=762 0219: dt=0.035437, rms=0.551 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.551, neg=0, invalid=762 0220: dt=145.152000, rms=0.549 (0.407%), neg=0, invalid=762 0221: dt=62.208000, rms=0.549 (0.043%), neg=0, invalid=762 0222: dt=62.208000, rms=0.548 (0.038%), neg=0, invalid=762 0223: dt=62.208000, rms=0.548 (0.056%), neg=0, invalid=762 0224: dt=62.208000, rms=0.548 (0.072%), neg=0, invalid=762 0225: dt=62.208000, rms=0.547 (0.059%), neg=0, invalid=762 0226: dt=62.208000, rms=0.547 (0.038%), neg=0, invalid=762 0227: dt=62.208000, rms=0.547 (0.054%), neg=0, invalid=762 0228: dt=62.208000, rms=0.547 (0.044%), neg=0, invalid=762 0229: dt=62.208000, rms=0.546 (0.037%), neg=0, invalid=762 0230: dt=62.208000, rms=0.546 (0.035%), neg=0, invalid=762 0231: dt=62.208000, rms=0.546 (0.039%), neg=0, invalid=762 0232: dt=15.552000, rms=0.546 (0.003%), neg=0, invalid=762 0233: dt=3.888000, rms=0.546 (0.002%), neg=0, invalid=762 0234: dt=0.567000, rms=0.546 (-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=0.556, neg=0, invalid=762 0235: dt=38.400000, rms=0.554 (0.344%), neg=0, invalid=762 0236: dt=135.833102, rms=0.547 (1.108%), neg=0, invalid=762 0237: dt=25.600000, rms=0.546 (0.346%), neg=0, invalid=762 0238: dt=153.600000, rms=0.539 (1.239%), neg=0, invalid=762 0239: dt=19.320755, rms=0.537 (0.279%), neg=0, invalid=762 0240: dt=44.800000, rms=0.536 (0.202%), neg=0, invalid=762 0241: dt=153.600000, rms=0.534 (0.408%), neg=0, invalid=762 0242: dt=24.552727, rms=0.533 (0.254%), neg=0, invalid=762 0243: dt=128.000000, rms=0.530 (0.475%), neg=0, invalid=762 0244: dt=11.200000, rms=0.530 (0.068%), neg=0, invalid=762 0245: dt=25.600000, rms=0.529 (0.061%), neg=0, invalid=762 0246: dt=153.600000, rms=0.528 (0.273%), neg=0, invalid=762 0247: dt=25.600000, rms=0.527 (0.109%), neg=0, invalid=762 0248: dt=102.400000, rms=0.526 (0.284%), neg=0, invalid=762 0249: dt=11.200000, rms=0.526 (0.041%), neg=0, invalid=762 0250: dt=11.200000, rms=0.526 (0.025%), neg=0, invalid=762 0251: dt=11.200000, rms=0.525 (0.020%), neg=0, invalid=762 0252: dt=11.200000, rms=0.525 (0.017%), neg=0, invalid=762 0253: dt=44.800000, rms=0.525 (0.153%), neg=0, invalid=762 0254: dt=11.200000, rms=0.525 (0.014%), neg=0, invalid=762 0255: dt=11.200000, rms=0.524 (0.013%), neg=0, invalid=762 0256: dt=11.200000, rms=0.524 (0.015%), neg=0, invalid=762 0257: dt=11.200000, rms=0.524 (0.037%), neg=0, invalid=762 0258: dt=11.200000, rms=0.524 (0.055%), neg=0, invalid=762 0259: dt=11.200000, rms=0.523 (0.081%), neg=0, invalid=762 0260: dt=11.200000, rms=0.523 (0.094%), neg=0, invalid=762 0261: dt=11.200000, rms=0.522 (0.095%), neg=0, invalid=762 0262: dt=11.200000, rms=0.522 (0.095%), neg=0, invalid=762 0263: dt=11.200000, rms=0.522 (0.087%), neg=0, invalid=762 0264: dt=11.200000, rms=0.521 (0.079%), neg=0, invalid=762 0265: dt=11.200000, rms=0.521 (0.084%), neg=0, invalid=762 0266: dt=11.200000, rms=0.520 (0.090%), neg=0, invalid=762 0267: dt=11.200000, rms=0.520 (0.099%), neg=0, invalid=762 0268: dt=11.200000, rms=0.519 (0.103%), neg=0, invalid=762 0269: dt=11.200000, rms=0.519 (0.094%), neg=0, invalid=762 0270: dt=11.200000, rms=0.518 (0.090%), neg=0, invalid=762 0271: dt=11.200000, rms=0.518 (0.074%), neg=0, invalid=762 0272: dt=11.200000, rms=0.517 (0.073%), neg=0, invalid=762 0273: dt=11.200000, rms=0.517 (0.073%), neg=0, invalid=762 0274: dt=11.200000, rms=0.517 (0.073%), neg=0, invalid=762 0275: dt=11.200000, rms=0.516 (0.082%), neg=0, invalid=762 0276: dt=11.200000, rms=0.516 (0.072%), neg=0, invalid=762 0277: dt=11.200000, rms=0.516 (0.066%), neg=0, invalid=762 0278: dt=11.200000, rms=0.515 (0.058%), neg=0, invalid=762 0279: dt=11.200000, rms=0.515 (0.052%), neg=0, invalid=762 0280: dt=11.200000, rms=0.515 (0.043%), neg=0, invalid=762 0281: dt=11.200000, rms=0.515 (0.050%), neg=0, invalid=762 0282: dt=11.200000, rms=0.514 (0.052%), neg=0, invalid=762 0283: dt=11.200000, rms=0.514 (0.056%), neg=0, invalid=762 0284: dt=11.200000, rms=0.514 (0.050%), neg=0, invalid=762 0285: dt=11.200000, rms=0.513 (0.047%), neg=0, invalid=762 0286: dt=11.200000, rms=0.513 (0.034%), neg=0, invalid=762 0287: dt=11.200000, rms=0.513 (0.035%), neg=0, invalid=762 0288: dt=11.200000, rms=0.513 (0.032%), neg=0, invalid=762 0289: dt=11.200000, rms=0.513 (0.029%), neg=0, invalid=762 0290: dt=11.200000, rms=0.513 (0.037%), neg=0, invalid=762 0291: dt=11.200000, rms=0.512 (0.041%), neg=0, invalid=762 0292: dt=11.200000, rms=0.512 (0.035%), neg=0, invalid=762 0293: dt=11.200000, rms=0.512 (0.033%), neg=0, invalid=762 0294: dt=11.200000, rms=0.512 (0.026%), neg=0, invalid=762 0295: dt=11.200000, rms=0.512 (0.027%), neg=0, invalid=762 0296: dt=11.200000, rms=0.512 (0.023%), neg=0, invalid=762 0297: dt=11.200000, rms=0.511 (0.035%), neg=0, invalid=762 0298: dt=11.200000, rms=0.511 (0.028%), neg=0, invalid=762 0299: dt=11.200000, rms=0.511 (0.025%), neg=0, invalid=762 0300: dt=11.200000, rms=0.511 (0.025%), neg=0, invalid=762 0301: dt=11.200000, rms=0.511 (0.028%), neg=0, invalid=762 0302: dt=11.200000, rms=0.511 (0.020%), neg=0, invalid=762 0303: dt=11.200000, rms=0.511 (0.019%), neg=0, invalid=762 0304: dt=38.400000, rms=0.511 (0.017%), neg=0, invalid=762 0305: dt=38.400000, rms=0.511 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0306: dt=44.800000, rms=0.509 (0.428%), neg=0, invalid=762 0307: dt=25.600000, rms=0.509 (0.017%), neg=0, invalid=762 0308: dt=25.600000, rms=0.508 (0.040%), neg=0, invalid=762 0309: dt=25.600000, rms=0.508 (0.013%), neg=0, invalid=762 0310: dt=25.600000, rms=0.508 (-0.017%), neg=0, invalid=762 0311: dt=8.000000, rms=0.508 (0.000%), neg=0, invalid=762 0312: dt=0.001172, rms=0.508 (0.001%), neg=0, invalid=762 0313: dt=0.000000, rms=0.508 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0314: dt=0.000000, rms=0.532 (0.054%), neg=0, invalid=762 0315: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=762 0316: dt=0.150000, rms=0.532 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0317: dt=0.000000, rms=0.532 (0.054%), neg=0, invalid=762 0318: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=762 0319: dt=0.150000, rms=0.532 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0320: dt=2.000000, rms=0.571 (1.405%), neg=0, invalid=762 0321: dt=1.024000, rms=0.571 (0.095%), neg=0, invalid=762 0322: dt=0.112000, rms=0.571 (0.002%), neg=0, invalid=762 0323: dt=0.112000, rms=0.571 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.571, neg=0, invalid=762 0324: dt=1.024000, rms=0.570 (0.143%), neg=0, invalid=762 0325: dt=0.448000, rms=0.570 (0.015%), neg=0, invalid=762 0326: dt=0.448000, rms=0.570 (0.001%), neg=0, invalid=762 0327: dt=0.448000, rms=0.570 (-0.031%), 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=0.532, neg=0, invalid=762 0328: dt=0.448000, rms=0.517 (2.861%), neg=0, invalid=762 0329: dt=0.448000, rms=0.514 (0.679%), neg=0, invalid=762 0330: dt=0.448000, rms=0.512 (0.380%), neg=0, invalid=762 0331: dt=0.448000, rms=0.510 (0.241%), neg=0, invalid=762 0332: dt=0.448000, rms=0.509 (0.174%), neg=0, invalid=762 0333: dt=0.448000, rms=0.509 (0.135%), neg=0, invalid=762 0334: dt=0.448000, rms=0.508 (0.104%), neg=0, invalid=762 0335: dt=0.448000, rms=0.508 (0.083%), neg=0, invalid=762 0336: dt=0.448000, rms=0.507 (0.071%), neg=0, invalid=762 0337: dt=0.448000, rms=0.507 (0.060%), neg=0, invalid=762 0338: dt=0.448000, rms=0.507 (0.049%), neg=0, invalid=762 0339: dt=0.448000, rms=0.507 (0.044%), neg=0, invalid=762 0340: dt=0.448000, rms=0.506 (0.073%), neg=0, invalid=762 0341: dt=0.448000, rms=0.506 (0.098%), neg=0, invalid=762 0342: dt=0.448000, rms=0.505 (0.102%), neg=0, invalid=762 0343: dt=0.448000, rms=0.505 (0.084%), neg=0, invalid=762 0344: dt=0.448000, rms=0.505 (0.070%), neg=0, invalid=762 0345: dt=0.448000, rms=0.504 (0.056%), neg=0, invalid=762 0346: dt=0.448000, rms=0.504 (0.029%), neg=0, invalid=762 0347: dt=0.448000, rms=0.504 (-0.012%), neg=0, invalid=762 0348: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0349: dt=0.448000, rms=0.501 (0.689%), neg=0, invalid=762 0350: dt=0.448000, rms=0.501 (0.047%), neg=0, invalid=762 0351: dt=0.448000, rms=0.501 (-0.001%), 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=0.498, neg=0, invalid=762 0352: dt=0.000000, rms=0.498 (0.074%), neg=0, invalid=762 0353: dt=0.000000, rms=0.498 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0354: dt=369.920000, rms=0.497 (0.259%), neg=0, invalid=762 0355: dt=23.120000, rms=0.497 (0.004%), neg=0, invalid=762 0356: dt=23.120000, rms=0.497 (0.001%), neg=0, invalid=762 0357: dt=23.120000, rms=0.497 (-0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0358: dt=20.736000, rms=0.497 (0.096%), neg=0, invalid=762 0359: dt=25.920000, rms=0.497 (0.012%), neg=0, invalid=762 0360: dt=25.920000, rms=0.497 (0.023%), neg=0, invalid=762 0361: dt=25.920000, rms=0.497 (0.025%), neg=0, invalid=762 0362: dt=25.920000, rms=0.497 (0.024%), neg=0, invalid=762 0363: dt=25.920000, rms=0.496 (0.042%), neg=0, invalid=762 0364: dt=25.920000, rms=0.496 (0.067%), neg=0, invalid=762 0365: dt=25.920000, rms=0.496 (0.086%), neg=0, invalid=762 0366: dt=25.920000, rms=0.495 (0.084%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.496, neg=0, invalid=762 0367: dt=145.152000, rms=0.492 (0.812%), neg=0, invalid=762 0368: dt=36.288000, rms=0.491 (0.057%), neg=0, invalid=762 0369: dt=36.288000, rms=0.491 (0.038%), neg=0, invalid=762 0370: dt=36.288000, rms=0.491 (0.058%), neg=0, invalid=762 0371: dt=36.288000, rms=0.490 (0.083%), neg=0, invalid=762 0372: dt=36.288000, rms=0.490 (0.096%), neg=0, invalid=762 0373: dt=36.288000, rms=0.489 (0.107%), neg=0, invalid=762 0374: dt=36.288000, rms=0.489 (0.099%), neg=0, invalid=762 0375: dt=36.288000, rms=0.489 (0.080%), neg=0, invalid=762 0376: dt=62.208000, rms=0.488 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0377: dt=44.800000, rms=0.486 (0.573%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0378: dt=108.838323, rms=0.481 (1.113%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0379: dt=22.304950, rms=0.480 (0.241%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0380: dt=22.304950, rms=0.479 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0381: dt=22.304950, rms=0.478 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0382: dt=22.304950, rms=0.477 (0.259%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0383: dt=22.304950, rms=0.475 (0.397%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0384: dt=22.304950, rms=0.474 (0.270%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0385: dt=22.304950, rms=0.473 (0.288%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0386: dt=22.304950, rms=0.471 (0.269%), neg=0, invalid=762 0387: dt=22.304950, rms=0.471 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0388: dt=22.304950, rms=0.470 (0.160%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0389: dt=22.304950, rms=0.469 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0390: dt=22.304950, rms=0.469 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0391: dt=22.304950, rms=0.468 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0392: dt=22.304950, rms=0.467 (0.127%), neg=0, invalid=762 0393: dt=22.304950, rms=0.467 (0.112%), neg=0, invalid=762 0394: dt=22.304950, rms=0.466 (0.110%), neg=0, invalid=762 0395: dt=19.200000, rms=0.466 (0.017%), neg=0, invalid=762 0396: dt=19.200000, rms=0.466 (0.017%), neg=0, invalid=762 0397: dt=19.200000, rms=0.466 (0.005%), neg=0, invalid=762 0398: dt=19.200000, rms=0.466 (0.013%), neg=0, invalid=762 0399: dt=19.200000, rms=0.466 (0.023%), neg=0, invalid=762 0400: dt=19.200000, rms=0.466 (0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0401: dt=89.791045, rms=0.463 (0.716%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0402: dt=11.200000, rms=0.462 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0403: dt=11.200000, rms=0.462 (0.053%), neg=0, invalid=762 0404: dt=11.200000, rms=0.462 (-0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0405: dt=2.880000, rms=0.471 (0.126%), neg=0, invalid=762 0406: dt=1.008000, rms=0.471 (0.010%), neg=0, invalid=762 0407: dt=1.008000, rms=0.471 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0408: dt=4.727273, rms=0.470 (0.158%), neg=0, invalid=762 0409: dt=2.880000, rms=0.470 (0.022%), neg=0, invalid=762 0410: dt=2.880000, rms=0.470 (0.006%), neg=0, invalid=762 0411: dt=2.880000, rms=0.470 (-0.039%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.481, neg=0, invalid=762 0412: dt=0.448000, rms=0.481 (0.091%), neg=0, invalid=762 0413: dt=0.096000, rms=0.481 (0.001%), neg=0, invalid=762 0414: dt=0.096000, rms=0.481 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.481, neg=0, invalid=762 0415: dt=1.024000, rms=0.481 (0.166%), neg=0, invalid=762 0416: dt=0.448000, rms=0.481 (0.015%), neg=0, invalid=762 0417: dt=0.448000, rms=0.481 (0.002%), neg=0, invalid=762 0418: dt=0.448000, rms=0.481 (-0.026%), 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=0.469, neg=0, invalid=762 iter 0, gcam->neg = 440 after 14 iterations, nbhd size=1, neg = 0 0419: dt=2.460733, rms=0.433 (7.641%), neg=0, invalid=762 0420: dt=0.112000, rms=0.432 (0.190%), neg=0, invalid=762 0421: dt=0.112000, rms=0.432 (-0.026%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0422: dt=0.080000, rms=0.432 (0.160%), neg=0, invalid=762 0423: dt=0.006000, rms=0.432 (0.000%), neg=0, invalid=762 0424: dt=0.006000, rms=0.432 (-0.000%), 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=0.414, neg=0, invalid=762 0425: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0426: dt=55.488000, rms=0.414 (0.006%), neg=0, invalid=762 0427: dt=32.368000, rms=0.414 (0.001%), neg=0, invalid=762 0428: dt=32.368000, rms=0.414 (0.000%), neg=0, invalid=762 0429: dt=32.368000, rms=0.414 (-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=0.414, neg=0, invalid=762 0430: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0431: dt=82.944000, rms=0.414 (0.036%), neg=0, invalid=762 0432: dt=145.152000, rms=0.413 (0.060%), neg=0, invalid=762 0433: dt=36.288000, rms=0.413 (0.004%), neg=0, invalid=762 0434: dt=36.288000, rms=0.413 (0.007%), neg=0, invalid=762 0435: dt=36.288000, rms=0.413 (0.012%), neg=0, invalid=762 0436: dt=36.288000, rms=0.413 (0.016%), neg=0, invalid=762 0437: dt=36.288000, rms=0.413 (0.019%), neg=0, invalid=762 0438: dt=36.288000, rms=0.413 (0.018%), neg=0, invalid=762 0439: dt=36.288000, rms=0.413 (0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0440: dt=11.200000, rms=0.414 (0.061%), neg=0, invalid=762 0441: dt=11.200000, rms=0.414 (0.031%), neg=0, invalid=762 0442: dt=11.200000, rms=0.413 (0.020%), neg=0, invalid=762 0443: dt=11.200000, rms=0.413 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0444: dt=88.150943, rms=0.411 (0.555%), neg=0, invalid=762 0445: dt=25.600000, rms=0.410 (0.271%), neg=0, invalid=762 0446: dt=44.800000, rms=0.410 (0.090%), neg=0, invalid=762 0447: dt=44.800000, rms=0.409 (0.095%), neg=0, invalid=762 0448: dt=44.800000, rms=0.409 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0449: dt=44.800000, rms=0.408 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0450: dt=44.800000, rms=0.407 (0.184%), neg=0, invalid=762 0451: dt=44.800000, rms=0.406 (0.156%), neg=0, invalid=762 0452: dt=44.800000, rms=0.406 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0453: dt=44.800000, rms=0.405 (0.124%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0454: dt=44.800000, rms=0.405 (0.092%), neg=0, invalid=762 0455: dt=19.200000, rms=0.405 (0.018%), neg=0, invalid=762 0456: dt=19.200000, rms=0.405 (0.004%), neg=0, invalid=762 0457: dt=19.200000, rms=0.405 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0458: dt=19.200000, rms=0.405 (0.001%), neg=0, invalid=762 0459: dt=19.200000, rms=0.405 (0.006%), neg=0, invalid=762 0460: dt=19.200000, rms=0.405 (0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0461: dt=0.000844, rms=0.410 (0.000%), neg=0, invalid=762 0462: dt=0.000000, rms=0.410 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0463: dt=2.880000, rms=0.410 (0.015%), neg=0, invalid=762 0464: dt=0.864000, rms=0.410 (0.001%), neg=0, invalid=762 0465: dt=0.864000, rms=0.410 (-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=0.419, neg=0, invalid=762 0466: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762 0467: dt=0.100000, rms=0.419 (-0.026%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0468: dt=0.000000, rms=0.419 (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=0.403, neg=0, invalid=762 iter 0, gcam->neg = 287 after 15 iterations, nbhd size=1, neg = 0 0469: dt=1.415964, rms=0.394 (2.358%), neg=0, invalid=762 0470: dt=0.000023, rms=0.394 (0.000%), neg=0, invalid=762 0471: dt=0.000023, rms=0.394 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 0472: dt=0.080000, rms=0.394 (0.033%), neg=0, invalid=762 0473: dt=0.024000, rms=0.394 (0.003%), neg=0, invalid=762 0474: dt=0.024000, rms=0.394 (-0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 42 minutes and 13 seconds. mri_ca_register utimesec 7574.752263 mri_ca_register stimesec 71.579468 mri_ca_register ru_maxrss 1614540 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 50238370 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62928 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 145658 mri_ca_register ru_nivcsw 6633 FSRUNTIME@ mri_ca_register 1.7036 hours 8 threads #-------------------------------------- #@# SubCort Seg Tue May 25 19:36:33 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 blg4313.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-05/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 13.24 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 = 0.11894 (27) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (4012 voxels, overlap=0.554) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (4012 voxels, peak = 26), gca=26.1 gca peak = 0.17677 (13) mri peak = 0.14248 (27) Right_Lateral_Ventricle (43): linear fit = 1.88 x + 0.0 (3397 voxels, overlap=0.249) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3397 voxels, peak = 25), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.09860 (98) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (1885 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (1885 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.08375 (99) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1779 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1779 voxels, peak = 98), gca=98.4 gca peak = 0.24553 (55) mri peak = 0.09152 (72) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2392 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2392 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.09566 (72) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (2167 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (2167 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.09082 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (99217 voxels, overlap=0.774) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (99217 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.09327 (100) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (104222 voxels, overlap=0.735) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (104222 voxels, peak = 102), gca=102.4 gca peak = 0.09712 (58) mri peak = 0.04445 (75) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (102011 voxels, overlap=0.008) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (102011 voxels, peak = 75), gca=75.1 gca peak = 0.11620 (58) mri peak = 0.04468 (76) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (97788 voxels, overlap=0.008) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (97788 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.09712 (81) Right_Caudate (50): linear fit = 1.21 x + 0.0 (2533 voxels, overlap=0.021) Right_Caudate (50): linear fit = 1.21 x + 0.0 (2533 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.11447 (80) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2608 voxels, overlap=0.428) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2608 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.06408 (71) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (55568 voxels, overlap=0.036) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (55568 voxels, peak = 71), gca=70.8 gca peak = 0.14777 (55) mri peak = 0.05574 (71) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (57369 voxels, overlap=0.040) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (57369 voxels, peak = 70), gca=69.6 gca peak = 0.16765 (84) mri peak = 0.11881 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (13387 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (13387 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.11178 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (15539 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (15539 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.10015 (71) Left_Amygdala (18): linear fit = 1.24 x + 0.0 (1314 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.24 x + 0.0 (1314 voxels, peak = 70), gca=70.4 gca peak = 0.33601 (57) mri peak = 0.09422 (72) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1400 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1400 voxels, peak = 74), gca=73.8 gca peak = 0.11131 (90) mri peak = 0.07738 (92) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (10882 voxels, overlap=0.528) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (10882 voxels, peak = 96), gca=95.9 gca peak = 0.11793 (83) mri peak = 0.08500 (92) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (10054 voxels, overlap=0.309) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (10054 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.07152 (86) Left_Putamen (12): linear fit = 1.11 x + 0.0 (4528 voxels, overlap=0.501) Left_Putamen (12): linear fit = 1.11 x + 0.0 (4528 voxels, peak = 90), gca=89.5 gca peak = 0.10360 (77) mri peak = 0.07496 (88) Right_Putamen (51): linear fit = 1.12 x + 0.0 (5336 voxels, overlap=0.447) Right_Putamen (51): linear fit = 1.12 x + 0.0 (5336 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.08054 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (28302 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (28302 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.07857 (98) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (3558 voxels, overlap=0.325) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (3558 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.07379 (98) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (3781 voxels, overlap=0.475) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (3781 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.11976 (28) Third_Ventricle (14): linear fit = 1.14 x + 0.0 (80 voxels, overlap=0.785) Third_Ventricle (14): linear fit = 1.14 x + 0.0 (80 voxels, peak = 27), gca=27.5 gca peak = 0.19357 (14) mri peak = 0.12813 (26) Fourth_Ventricle (15): linear fit = 1.66 x + 0.0 (1127 voxels, overlap=0.210) Fourth_Ventricle (15): linear fit = 1.66 x + 0.0 (1127 voxels, peak = 23), gca=23.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) 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 1.27 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 1.32 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15817 (24) mri peak = 0.11894 (27) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (4012 voxels, overlap=0.842) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (4012 voxels, peak = 25), gca=25.3 gca peak = 0.14041 (19) mri peak = 0.14248 (27) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (3397 voxels, overlap=0.444) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (3397 voxels, peak = 25), gca=24.6 gca peak = 0.28342 (100) mri peak = 0.09860 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1885 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1885 voxels, peak = 100), gca=100.5 gca peak = 0.17801 (97) mri peak = 0.08375 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1779 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1779 voxels, peak = 97), gca=97.5 gca peak = 0.24040 (71) mri peak = 0.09152 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (2392 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (2392 voxels, peak = 71), gca=71.0 gca peak = 0.29629 (69) mri peak = 0.09566 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (2167 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (2167 voxels, peak = 69), gca=69.0 gca peak = 0.07847 (102) mri peak = 0.09082 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (99217 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (99217 voxels, peak = 101), gca=101.5 gca peak = 0.07918 (103) mri peak = 0.09327 (100) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (104222 voxels, overlap=0.726) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (104222 voxels, peak = 102), gca=102.5 gca peak = 0.07493 (75) mri peak = 0.04445 (75) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (102011 voxels, overlap=0.955) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (102011 voxels, peak = 74), gca=73.9 gca peak = 0.09080 (75) mri peak = 0.04468 (76) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (97788 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (97788 voxels, peak = 74), gca=73.9 gca peak = 0.22214 (80) mri peak = 0.09712 (81) Right_Caudate (50): linear fit = 0.99 x + 0.0 (2533 voxels, overlap=1.003) Right_Caudate (50): linear fit = 0.99 x + 0.0 (2533 voxels, peak = 79), gca=78.8 gca peak = 0.16641 (87) mri peak = 0.11447 (80) Left_Caudate (11): linear fit = 0.99 x + 0.0 (2608 voxels, overlap=0.832) Left_Caudate (11): linear fit = 0.99 x + 0.0 (2608 voxels, peak = 86), gca=85.7 gca peak = 0.11327 (70) mri peak = 0.06408 (71) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (55568 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (55568 voxels, peak = 70), gca=70.0 gca peak = 0.12251 (69) mri peak = 0.05574 (71) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (57369 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (57369 voxels, peak = 69), gca=69.0 gca peak = 0.15744 (86) mri peak = 0.11881 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (13387 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (13387 voxels, peak = 86), gca=86.0 gca peak = 0.18296 (87) mri peak = 0.11178 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (15539 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (15539 voxels, peak = 87), gca=87.0 gca peak = 0.28232 (70) mri peak = 0.10015 (71) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (1314 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (1314 voxels, peak = 70), gca=70.0 gca peak = 0.27167 (74) mri peak = 0.09422 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1400 voxels, overlap=1.001) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1400 voxels, peak = 74), gca=74.0 gca peak = 0.11208 (94) mri peak = 0.07738 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (10882 voxels, overlap=0.837) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (10882 voxels, peak = 94), gca=93.5 gca peak = 0.10776 (90) mri peak = 0.08500 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (10054 voxels, overlap=0.902) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (10054 voxels, peak = 90), gca=90.4 gca peak = 0.08025 (83) mri peak = 0.07152 (86) Left_Putamen (12): linear fit = 1.00 x + 0.0 (4528 voxels, overlap=0.902) Left_Putamen (12): linear fit = 1.00 x + 0.0 (4528 voxels, peak = 83), gca=82.6 gca peak = 0.08153 (84) mri peak = 0.07496 (88) Right_Putamen (51): linear fit = 0.99 x + 0.0 (5336 voxels, overlap=0.954) Right_Putamen (51): linear fit = 0.99 x + 0.0 (5336 voxels, peak = 83), gca=82.7 gca peak = 0.07757 (86) mri peak = 0.08054 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (28302 voxels, overlap=0.766) Brain_Stem (16): linear fit = 1.00 x + 0.0 (28302 voxels, peak = 86), gca=86.0 gca peak = 0.09930 (100) mri peak = 0.07857 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (3558 voxels, overlap=0.828) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (3558 voxels, peak = 100), gca=100.5 gca peak = 0.15043 (96) mri peak = 0.07379 (98) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (3781 voxels, overlap=0.923) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (3781 voxels, peak = 97), gca=97.4 gca peak = 0.13229 (29) mri peak = 0.11976 (28) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (80 voxels, overlap=0.988) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (80 voxels, peak = 29), gca=29.4 gca peak = 0.16541 (21) mri peak = 0.12813 (26) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (1127 voxels, overlap=0.572) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (1127 voxels, peak = 27), gca=27.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (101) gca peak CSF = 0.23763 (48) gca peak Left_Accumbens_area = 0.61344 (70) gca peak Left_undetermined = 0.96707 (30) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.29900 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14509 (37) gca peak Fifth_Ventricle = 0.75707 (41) gca peak WM_hypointensities = 0.08549 (76) gca peak non_WM_hypointensities = 0.08497 (43) gca peak Optic_Chiasm = 0.70804 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.17 x + 0.0 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 132694 voxels changed in iteration 0 of unlikely voxel relabeling 569 voxels changed in iteration 1 of unlikely voxel relabeling 14 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 158360 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 826 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 126515 changed. image ll: -2.087, PF=0.500 pass 2: 32038 changed. image ll: -2.086, PF=0.500 pass 3: 10335 changed. pass 4: 4069 changed. 139859 voxels changed in iteration 0 of unlikely voxel relabeling 935 voxels changed in iteration 1 of unlikely voxel relabeling 73 voxels changed in iteration 2 of unlikely voxel relabeling 8 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 12713 voxels changed in iteration 0 of unlikely voxel relabeling 182 voxels changed in iteration 1 of unlikely voxel relabeling 36 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 10713 voxels changed in iteration 0 of unlikely voxel relabeling 72 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 3 voxels changed in iteration 4 of unlikely voxel relabeling 10659 voxels changed in iteration 0 of unlikely voxel relabeling 43 voxels changed in iteration 1 of unlikely voxel relabeling 3 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 MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 5148.297083 mri_ca_label stimesec 31.744688 mri_ca_label ru_maxrss 3120576 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 29597907 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 4752 mri_ca_label ru_oublock 776 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 654 mri_ca_label ru_nivcsw 5121 auto-labeling took 84 minutes and 53 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/cc_up.lta sub-05 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-05/mri/transforms/cc_up.lta reading aseg from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/aseg.auto_noCCseg.mgz reading norm from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/norm.mgz 58630 voxels in left wm, 159120 in right wm, xrange [153, 169] searching rotation angles z=[-10 4], y=[-8 6] searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 global minimum found at slice 163.3, rotations (-1.30, -2.78) final transformation (x=163.3, yr=-1.301, zr=-2.779): 0.99857 0.04849 -0.02269 -38.58487; -0.04848 0.99882 0.00110 8.93777; 0.02271 -0.00000 0.99974 8.32127; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 127 116 eigenvectors: -0.00083 -0.00013 1.00000; -0.08023 -0.99678 -0.00020; 0.99678 -0.08023 0.00082; writing aseg with callosum to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/aseg.auto.mgz... corpus callosum segmentation took 2.0 minutes #-------------------------------------- #@# Merge ASeg Tue May 25 21:03:26 UTC 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue May 25 21:03:27 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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... 708 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 80 (80), valley at 47 (47) csf peak at 30, setting threshold to 63 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 80 (80), valley at 46 (46) csf peak at 30, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 5 minutes and 6 seconds. #-------------------------------------------- #@# Mask BFS Tue May 25 21:08:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2795750 voxels in mask (pct= 8.53) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue May 25 21:08:47 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 (103.0): 102.9 +- 6.4 [79.0 --> 125.0] GM (78.0) : 76.9 +- 10.7 [30.0 --> 95.0] setting bottom of white matter range to 87.5 setting top of gray matter range to 98.2 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, 5469 filled 1 bright non-wm voxels segmented. 7776 diagonally connected voxels added... white matter segmentation took 2.3 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 0.67 minutes reading wm segmentation from wm.seg.mgz... 335 voxels added to wm to prevent paths from MTL structures to cortex 7589 additional wm voxels added 0 additional wm voxels added SEG EDIT: 89000 voxels turned on, 88072 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 103 new 103 115,126,128 old 103 new 103 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 49 found - 49 modified | TOTAL: 49 pass 2 (xy+): 0 found - 49 modified | TOTAL: 49 pass 1 (xy-): 33 found - 33 modified | TOTAL: 82 pass 2 (xy-): 0 found - 33 modified | TOTAL: 82 pass 1 (yz+): 52 found - 52 modified | TOTAL: 134 pass 2 (yz+): 0 found - 52 modified | TOTAL: 134 pass 1 (yz-): 37 found - 37 modified | TOTAL: 171 pass 2 (yz-): 0 found - 37 modified | TOTAL: 171 pass 1 (xz+): 47 found - 47 modified | TOTAL: 218 pass 2 (xz+): 0 found - 47 modified | TOTAL: 218 pass 1 (xz-): 39 found - 39 modified | TOTAL: 257 pass 2 (xz-): 0 found - 39 modified | TOTAL: 257 Iteration Number : 1 pass 1 (+++): 22 found - 22 modified | TOTAL: 22 pass 2 (+++): 0 found - 22 modified | TOTAL: 22 pass 1 (+++): 32 found - 32 modified | TOTAL: 54 pass 2 (+++): 0 found - 32 modified | TOTAL: 54 pass 1 (+++): 17 found - 17 modified | TOTAL: 71 pass 2 (+++): 0 found - 17 modified | TOTAL: 71 pass 1 (+++): 38 found - 38 modified | TOTAL: 109 pass 2 (+++): 0 found - 38 modified | TOTAL: 109 Iteration Number : 1 pass 1 (++): 198 found - 198 modified | TOTAL: 198 pass 2 (++): 0 found - 198 modified | TOTAL: 198 pass 1 (+-): 180 found - 180 modified | TOTAL: 378 pass 2 (+-): 0 found - 180 modified | TOTAL: 378 pass 1 (--): 162 found - 162 modified | TOTAL: 540 pass 2 (--): 0 found - 162 modified | TOTAL: 540 pass 1 (-+): 192 found - 192 modified | TOTAL: 732 pass 2 (-+): 0 found - 192 modified | TOTAL: 732 Iteration Number : 2 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 9 found - 9 modified | TOTAL: 21 pass 2 (xy-): 0 found - 9 modified | TOTAL: 21 pass 1 (yz+): 13 found - 13 modified | TOTAL: 34 pass 2 (yz+): 0 found - 13 modified | TOTAL: 34 pass 1 (yz-): 14 found - 14 modified | TOTAL: 48 pass 2 (yz-): 0 found - 14 modified | TOTAL: 48 pass 1 (xz+): 11 found - 11 modified | TOTAL: 59 pass 2 (xz+): 0 found - 11 modified | TOTAL: 59 pass 1 (xz-): 8 found - 8 modified | TOTAL: 67 pass 2 (xz-): 0 found - 8 modified | TOTAL: 67 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 6 found - 6 modified | TOTAL: 9 pass 2 (+-): 0 found - 6 modified | TOTAL: 9 pass 1 (--): 4 found - 4 modified | TOTAL: 13 pass 2 (--): 0 found - 4 modified | TOTAL: 13 pass 1 (-+): 9 found - 9 modified | TOTAL: 22 pass 2 (-+): 0 found - 9 modified | TOTAL: 22 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1198 (out of 1023876: 0.117006) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue May 25 21:11:50 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 1.09302 0.02771 -0.02663 -21.42439; -0.01512 1.01857 0.27618 -32.30424; 0.03555 -0.26537 0.98670 29.45610; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.09302 0.02771 -0.02663 -21.42439; -0.01512 1.01857 0.27618 -32.30424; 0.03555 -0.26537 0.98670 29.45610; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (546, 2188) area[0] = 2085 (min = 546, max = 2188), aspect = 0.43 (min = 0.10, max = 0.75) no need to search using seed (158, 142, 113), TAL = (1.6, -37.6, 14.4) talairach voxel to voxel transform 0.91370 -0.01718 0.02947 18.15259; 0.02096 0.91464 -0.25545 37.52046; -0.02728 0.24661 0.94371 -20.41592; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (158, 142, 113) --> (1.6, -37.6, 14.4) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (1.60, -37.60, 14.40) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(19.60, -37.60, 14.40) SRC: (142.85, 141.37, 117.55) search lh wm seed point around talairach space (-16.40, -37.60, 14.40), SRC: (183.97, 142.32, 116.32) 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 17:47:39 UTC 2021 Ended at Tue May 25 21:12:47 UTC 2021 #@#%# recon-all-run-time-hours 3.419 recon-all -s sub-05 finished without error at Tue May 25 21:12:48 UTC 2021 New invocation of recon-all Tue May 25 23:29:20 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -parallel -subjid sub-05 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -T2pial -cortribbon subjid sub-05 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 blg4313.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: 196638428 115606856 71526444 2007844 9505128 75905212 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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:20-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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: 2021/05/25-23:29:21-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: blg4313.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 23:29:21 UTC 2021 bbregister --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.lta --init-coreg --T2 tmp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641 Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.dat.log Tue May 25 23:29:21 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-05/scripts /opt/freesurfer/bin/bbregister --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg4313.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-05/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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-05/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-05/mri/transforms/tmp.bbregister.208641/template.nii... mri_coreg --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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-05/scripts cmdline mri_coreg --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg4313.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-05/mri/transforms/tmp.bbregister.208641/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.8178 0.0283 -0.7568 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 = 3906.0000 mov gstd 1.9140 1.9140 1.9140 Smoothing mov refsat = 116.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0327892828 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.81781; 0.00000 1.00000 0.00000 0.02825; 0.00000 0.00000 1.00000 -0.75679; 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 -9.99997; 0.00000 -1.00000 0.00000 318.99997; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 1.18219 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0304538 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0336357355 #@# 4 188 1.18219 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0336357 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.033636 #@# 4 193 0.56416 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0337844 #@# 4 195 0.38827 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0337927 #@# 4 203 0.37827 0.41022 1.24321 0.00000 0.00000 0.00000 -1.0338249 #@# 4 212 0.37827 0.42184 1.32620 0.00000 0.00000 0.00000 -1.0338255 #@# 4 222 0.37827 0.42184 1.29598 0.38197 0.00000 0.00000 -1.0338274 #@# 4 223 0.37827 0.42184 1.29598 0.20435 0.00000 0.00000 -1.0338329 #@# 4 227 0.37827 0.42184 1.29598 0.21435 1.00000 0.00000 -1.0338402 #@# 4 231 0.37827 0.42184 1.29598 0.21435 0.61803 0.00000 -1.0338731 #@# 4 232 0.37827 0.42184 1.29598 0.21435 0.48420 0.00000 -1.0338740 #@# 4 233 0.37827 0.42184 1.29598 0.21435 0.52786 0.00000 -1.0338743 #@# 4 241 0.37827 0.42184 1.29598 0.21435 0.51786 0.38197 -1.0338981 #@# 4 243 0.37827 0.42184 1.29598 0.21435 0.51786 0.36047 -1.0338982 powell nthiter 1: fret = -1.033898 #@# 4 256 0.11696 0.42184 1.29598 0.21435 0.51786 0.34047 -1.0339202 #@# 4 257 0.10696 0.42184 1.29598 0.21435 0.51786 0.34047 -1.0339203 #@# 4 269 0.07950 0.28033 1.29598 0.21435 0.51786 0.34047 -1.0339247 #@# 4 289 0.07950 0.27033 1.24753 0.24972 0.51786 0.34047 -1.0339248 #@# 4 298 0.07950 0.27033 1.24753 0.23972 0.67566 0.34047 -1.0339293 #@# 4 299 0.07950 0.27033 1.24753 0.23972 0.68566 0.34047 -1.0339295 #@# 4 309 0.07950 0.27033 1.24753 0.23972 0.68566 0.43813 -1.0339314 Powell done niters total = 1 OptTimeSec 9.9 sec OptTimeMin 0.16 min nEvals 311 Final parameters 0.07950100 0.27032870 1.24753082 0.23971693 0.68565995 0.44813165 Final cost -1.033931332303622 --------------------------------- mri_coreg utimesec 202.812725 mri_coreg stimesec 2.950362 mri_coreg ru_maxrss 890724 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 1893387 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10464 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 3550 mri_coreg ru_nivcsw 247 Final RefRAS-to-MovRAS 0.99990 0.00782 0.01197 0.07950; -0.00787 0.99996 0.00418 0.27033; -0.01193 -0.00428 0.99992 1.24753; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99990 -0.01197 0.00782 265.00970; 0.00787 -0.00418 0.99996 -10.28118; 0.01193 -0.99992 -0.00428 320.13733; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.0795 0.2703 1.2475 0.2397 0.6857 0.4481 nhits = 307114 out of 32768000, Percent Overlap: 60.0 mri_coreg RunTimeSec 79.0 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/mri_coreg.lta --s sub-05 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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-05/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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 blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat subject sub-05 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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 1622905986 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99990 -0.00782 -0.01197 -0.29019; -0.01193 -0.00428 0.99992 1.10014; 0.00787 -0.99996 -0.00418 -0.24197; 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 0.979810 1 -25.0 -25.0 25.0 0.971489 2 -25.0 25.0 -25.0 0.974906 3 -25.0 25.0 25.0 0.989773 4 25.0 -25.0 -25.0 0.996222 5 25.0 -25.0 25.0 0.968273 6 25.0 25.0 -25.0 0.978305 7 25.0 25.0 25.0 0.952391 REL: 8 0.204462 7.811169 0.976396 rel = 0.209405 Initial costs ---------------- Number of surface hits 4154 WM Intensity 804.3198 +/- 261.9725 Ctx Intensity 1060.0917 +/- 287.0919 Pct Contrast 28.6009 +/- 20.7152 Cost 0.2045 RelCost 0.2094 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.8983 0.8983 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8744 0.8744 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8623 0.8623 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8035 0.8035 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.7685 0.7685 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7649 0.7649 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6865 0.6865 0.0 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.6776 0.6776 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6374 0.6374 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2045 0.2045 0.0 Brute Force -------------------------- Min cost was 0.204462 Number of iterations 729 Search time 1.733000 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 = 0.204462 7 0.070 0.000 0.000 0.000 0.000 0.000 0.2030432312 9 0.093 0.000 0.000 0.000 0.000 0.000 0.2029453398 14 0.093 -1.618 0.000 0.000 0.000 0.000 0.1237897981 15 0.093 -1.131 0.000 0.000 0.000 0.000 0.0785780639 19 0.093 -1.016 0.000 0.000 0.000 0.000 0.0778297511 20 0.093 -1.052 0.000 0.000 0.000 0.000 0.0774849666 22 0.093 -1.050 0.000 0.000 0.000 0.000 0.0774829968 30 0.093 -1.050 0.382 0.000 0.000 0.000 0.0692065931 32 0.093 -1.050 0.343 0.000 0.000 0.000 0.0685013939 33 0.093 -1.050 0.335 0.000 0.000 0.000 0.0684782603 35 0.093 -1.050 0.336 0.000 0.000 0.000 0.0684779139 44 0.093 -1.050 0.336 -0.087 0.000 0.000 0.0671949200 46 0.093 -1.050 0.336 -0.069 0.000 0.000 0.0671457955 48 0.093 -1.050 0.336 -0.075 0.000 0.000 0.0671231014 49 0.093 -1.050 0.336 -0.076 0.000 0.000 0.0671215799 59 0.093 -1.050 0.336 -0.076 -0.006 0.000 0.0670725015 60 0.093 -1.050 0.336 -0.076 -0.011 0.000 0.0670588724 61 0.093 -1.050 0.336 -0.076 -0.010 0.000 0.0670580788 68 0.093 -1.050 0.336 -0.076 -0.010 0.382 0.0666619473 69 0.093 -1.050 0.336 -0.076 -0.010 0.197 0.0638280827 70 0.093 -1.050 0.336 -0.076 -0.010 0.198 0.0638235674 71 0.093 -1.050 0.336 -0.076 -0.010 0.218 0.0637764123 powell nthiter 1: fret = 0.063776 83 0.077 -1.050 0.336 -0.076 -0.010 0.218 0.0637530128 85 0.076 -1.050 0.336 -0.076 -0.010 0.218 0.0637510580 86 0.069 -1.050 0.336 -0.076 -0.010 0.218 0.0637487471 87 0.072 -1.050 0.336 -0.076 -0.010 0.218 0.0637476606 96 0.072 -1.004 0.336 -0.076 -0.010 0.218 0.0628888753 97 0.072 -0.967 0.336 -0.076 -0.010 0.218 0.0625044274 99 0.072 -0.915 0.336 -0.076 -0.010 0.218 0.0619493948 100 0.072 -0.912 0.336 -0.076 -0.010 0.218 0.0619416089 101 0.072 -0.904 0.336 -0.076 -0.010 0.218 0.0619256881 102 0.072 -0.885 0.336 -0.076 -0.010 0.218 0.0618848541 106 0.072 -0.887 0.336 -0.076 -0.010 0.218 0.0618815691 107 0.072 -0.886 0.336 -0.076 -0.010 0.218 0.0618813146 116 0.072 -0.886 0.350 -0.076 -0.010 0.218 0.0618542970 117 0.072 -0.886 0.345 -0.076 -0.010 0.218 0.0618406756 129 0.072 -0.886 0.345 -0.098 -0.010 0.218 0.0617655684 130 0.072 -0.886 0.345 -0.089 -0.010 0.218 0.0616817337 131 0.072 -0.886 0.345 -0.088 -0.010 0.218 0.0616783351 139 0.072 -0.886 0.345 -0.088 -0.045 0.218 0.0613349510 143 0.072 -0.886 0.345 -0.088 -0.041 0.218 0.0613244028 144 0.072 -0.886 0.345 -0.088 -0.040 0.218 0.0613243449 153 0.072 -0.886 0.345 -0.088 -0.040 0.213 0.0612879915 154 0.072 -0.886 0.345 -0.088 -0.040 0.202 0.0612539251 156 0.072 -0.886 0.345 -0.088 -0.040 0.200 0.0612515921 157 0.072 -0.886 0.345 -0.088 -0.040 0.198 0.0612511252 powell nthiter 2: fret = 0.061251 167 0.055 -0.886 0.345 -0.088 -0.040 0.198 0.0612298832 168 0.058 -0.886 0.345 -0.088 -0.040 0.198 0.0612163924 169 0.061 -0.886 0.345 -0.088 -0.040 0.198 0.0612132866 170 0.060 -0.886 0.345 -0.088 -0.040 0.198 0.0612131807 181 0.060 -0.902 0.345 -0.088 -0.040 0.198 0.0610612784 183 0.060 -0.901 0.345 -0.088 -0.040 0.198 0.0610601144 194 0.060 -0.901 0.344 -0.088 -0.040 0.198 0.0610597969 205 0.060 -0.901 0.344 -0.093 -0.040 0.198 0.0610433686 206 0.060 -0.901 0.344 -0.092 -0.040 0.198 0.0610412179 217 0.060 -0.901 0.344 -0.092 -0.044 0.198 0.0610357137 228 0.060 -0.901 0.344 -0.092 -0.044 0.197 0.0610354613 229 0.060 -0.901 0.344 -0.092 -0.044 0.196 0.0610350274 240 0.056 -0.906 0.343 -0.093 -0.045 0.195 0.0610229520 241 0.057 -0.905 0.344 -0.093 -0.045 0.195 0.0610216617 242 0.057 -0.905 0.344 -0.093 -0.045 0.195 0.0610216579 246 0.057 -0.905 0.344 -0.093 -0.045 0.195 0.0610214450 powell nthiter 3: fret = 0.061021 259 0.064 -0.905 0.344 -0.093 -0.045 0.195 0.0610117669 284 0.064 -0.905 0.354 -0.093 -0.045 0.195 0.0610098214 285 0.064 -0.905 0.349 -0.093 -0.045 0.195 0.0609983799 298 0.064 -0.905 0.349 -0.094 -0.045 0.195 0.0609905437 299 0.064 -0.905 0.349 -0.096 -0.045 0.195 0.0609868289 302 0.064 -0.905 0.349 -0.095 -0.045 0.195 0.0609867667 318 0.060 -0.910 0.348 -0.097 -0.046 0.194 0.0609643720 319 0.060 -0.910 0.348 -0.097 -0.046 0.194 0.0609641621 323 0.060 -0.910 0.348 -0.097 -0.046 0.194 0.0609640012 327 0.059 -0.920 0.353 -0.102 -0.049 0.193 0.0609258366 334 0.059 -0.920 0.353 -0.102 -0.049 0.193 0.0609255390 powell nthiter 4: fret = 0.060926 350 0.072 -0.920 0.353 -0.102 -0.049 0.193 0.0609141647 351 0.067 -0.920 0.353 -0.102 -0.049 0.193 0.0608920924 362 0.067 -0.920 0.353 -0.102 -0.049 0.206 0.0608730552 363 0.067 -0.920 0.353 -0.102 -0.049 0.203 0.0608728138 385 0.067 -0.920 0.353 -0.109 -0.049 0.203 0.0608024754 388 0.067 -0.920 0.353 -0.110 -0.049 0.203 0.0608022920 400 0.066 -0.929 0.358 -0.115 -0.051 0.202 0.0607092185 405 0.066 -0.930 0.358 -0.115 -0.051 0.202 0.0607081078 407 0.066 -0.930 0.358 -0.115 -0.051 0.202 0.0607079567 411 0.066 -0.930 0.358 -0.115 -0.051 0.202 0.0607079416 powell nthiter 5: fret = 0.060708 425 0.073 -0.930 0.358 -0.115 -0.051 0.202 0.0606695212 436 0.073 -0.930 0.358 -0.115 -0.051 0.220 0.0606081040 458 0.073 -0.930 0.358 -0.117 -0.051 0.220 0.0605866617 459 0.073 -0.930 0.358 -0.121 -0.051 0.220 0.0605702535 468 0.073 -0.930 0.358 -0.121 -0.044 0.220 0.0605615077 470 0.073 -0.930 0.358 -0.121 -0.046 0.220 0.0605599116 472 0.073 -0.930 0.358 -0.121 -0.045 0.220 0.0605597192 478 0.073 -0.934 0.360 -0.123 -0.046 0.219 0.0605307234 480 0.073 -0.935 0.360 -0.123 -0.046 0.219 0.0605300248 485 0.080 -0.939 0.362 -0.131 -0.041 0.236 0.0605247559 powell nthiter 6: fret = 0.060530 495 0.077 -0.935 0.360 -0.123 -0.046 0.219 0.0605178744 506 0.077 -0.935 0.360 -0.123 -0.046 0.228 0.0605032485 507 0.077 -0.935 0.360 -0.123 -0.046 0.227 0.0605032399 517 0.077 -0.935 0.362 -0.123 -0.046 0.227 0.0605018950 529 0.077 -0.935 0.362 -0.125 -0.046 0.227 0.0605007754 539 0.077 -0.935 0.362 -0.125 -0.044 0.227 0.0605001244 547 0.077 -0.936 0.362 -0.125 -0.045 0.226 0.0604973576 548 0.077 -0.936 0.362 -0.125 -0.045 0.226 0.0604971982 powell nthiter 7: fret = 0.060497 565 0.080 -0.936 0.362 -0.125 -0.045 0.226 0.0604961614 567 0.079 -0.936 0.362 -0.125 -0.045 0.226 0.0604946788 577 0.079 -0.936 0.362 -0.125 -0.045 0.229 0.0604937707 617 0.079 -0.937 0.363 -0.126 -0.045 0.229 0.0604926921 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.971056 1 -25.0 -25.0 25.0 0.982991 2 -25.0 25.0 -25.0 0.961614 3 -25.0 25.0 25.0 0.977821 4 25.0 -25.0 -25.0 0.962561 5 25.0 -25.0 25.0 0.970800 6 25.0 25.0 -25.0 0.973439 7 25.0 25.0 25.0 0.971351 REL: 8 0.060493 7.771635 0.971454 rel = 0.0622702 Number of iterations 7 Min cost was 0.060493 Number of FunctionCalls 624 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.362000 sec Parameters at optimum (transmm) 0.07921 -0.93683 0.36267 Parameters at optimum (rotdeg) -0.12576 -0.04490 0.22919 Final costs ---------------- Number of surface hits 4154 WM Intensity 788.7582 +/- 253.1406 Ctx Intensity 1052.4076 +/- 260.2808 Pct Contrast 30.3521 +/- 16.6186 Cost 0.0605 RelCost 0.2094 Reg at min cost was -0.99985 -0.00701 -0.01596 -0.21518; -0.01592 -0.00650 0.99985 0.16161; 0.00711 -0.99995 -0.00639 0.11805; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat, type = 14 Original Reg -0.99990 -0.00782 -0.01197 -0.29019; -0.01193 -0.00428 0.99992 1.10014; 0.00787 -0.99996 -0.00418 -0.24197; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00005 -0.00081 0.00399 -0.07501; 0.00398 0.00222 0.00007 0.93853; 0.00076 -0.00001 0.00220 -0.36003; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.848310 Computing change in rh position Surface-RMS-Diff-mm 0.943407 0.133758 1.234396 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/tmp.bbregister.208641/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-05/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/tmp.bbregister.208641/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat subject sub-05 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 1622269029 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99985 -0.00701 -0.01596 -0.21518; -0.01592 -0.00650 0.99985 0.16161; 0.00711 -0.99995 -0.00639 0.11805; 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 0.980598 1 -25.0 -25.0 25.0 0.970003 2 -25.0 25.0 -25.0 0.969964 3 -25.0 25.0 25.0 0.983508 4 25.0 -25.0 -25.0 0.975738 5 25.0 -25.0 25.0 0.964835 6 25.0 25.0 -25.0 0.956883 7 25.0 25.0 25.0 0.968609 REL: 8 0.063363 7.770139 0.971267 rel = 0.0652377 Initial costs ---------------- Number of surface hits 413992 WM Intensity 790.9959 +/- 248.9912 Ctx Intensity 1058.1995 +/- 259.2725 Pct Contrast 30.4992 +/- 16.5520 Cost 0.0634 RelCost 0.0652 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0677 0.0677 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0668 0.0668 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0661 0.0661 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0655 0.0655 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0649 0.0649 0.0 28 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0645 0.0645 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0635 0.0635 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0630 0.0630 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.0629 0.0629 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0625 0.0625 0.0 57 -0.1000 -0.1000 0.1000 -0.1000 0.0000 -0.1000 0.0620 0.0620 0.0 58 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.0000 0.0617 0.0617 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0605 0.0605 0.0 Brute Force -------------------------- Min cost was 0.060493 Number of iterations 729 Search time 1.559000 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 = 0.063363 7 0.071 0.000 0.000 0.000 0.000 0.000 0.0627813036 8 0.072 0.000 0.000 0.000 0.000 0.000 0.0627801144 9 0.076 0.000 0.000 0.000 0.000 0.000 0.0627792329 11 0.075 0.000 0.000 0.000 0.000 0.000 0.0627788591 19 0.075 -0.082 0.000 0.000 0.000 0.000 0.0618798065 21 0.075 -0.083 0.000 0.000 0.000 0.000 0.0618795719 29 0.075 -0.083 -0.051 0.000 0.000 0.000 0.0613067904 30 0.075 -0.083 -0.081 0.000 0.000 0.000 0.0612588987 31 0.075 -0.083 -0.073 0.000 0.000 0.000 0.0612517577 40 0.075 -0.083 -0.073 0.046 0.000 0.000 0.0610758919 41 0.075 -0.083 -0.073 0.036 0.000 0.000 0.0610604251 42 0.075 -0.083 -0.073 0.035 0.000 0.000 0.0610601190 43 0.075 -0.083 -0.073 0.034 0.000 0.000 0.0610599000 45 0.075 -0.083 -0.073 0.032 0.000 0.000 0.0610598094 47 0.075 -0.083 -0.073 0.033 0.000 0.000 0.0610597286 54 0.075 -0.083 -0.073 0.033 0.007 0.000 0.0610216826 55 0.075 -0.083 -0.073 0.033 0.024 0.000 0.0609860914 57 0.075 -0.083 -0.073 0.033 0.025 0.000 0.0609860310 67 0.075 -0.083 -0.073 0.033 0.025 -0.008 0.0609797022 powell nthiter 1: fret = 0.060980 77 0.052 -0.083 -0.073 0.033 0.025 -0.008 0.0609568392 78 0.059 -0.083 -0.073 0.033 0.025 -0.008 0.0609496678 87 0.059 -0.077 -0.073 0.033 0.025 -0.008 0.0609414509 88 0.059 -0.075 -0.073 0.033 0.025 -0.008 0.0609412470 90 0.059 -0.076 -0.073 0.033 0.025 -0.008 0.0609410561 98 0.059 -0.076 -0.087 0.033 0.025 -0.008 0.0609240535 100 0.059 -0.076 -0.084 0.033 0.025 -0.008 0.0609236715 109 0.059 -0.076 -0.084 0.053 0.025 -0.008 0.0609182126 110 0.059 -0.076 -0.084 0.044 0.025 -0.008 0.0609113082 111 0.059 -0.076 -0.084 0.045 0.025 -0.008 0.0609112167 120 0.059 -0.076 -0.084 0.045 0.027 -0.008 0.0609112036 122 0.059 -0.076 -0.084 0.045 0.026 -0.008 0.0609109404 130 0.059 -0.076 -0.084 0.045 0.026 -0.015 0.0609068690 powell nthiter 2: fret = 0.060907 141 0.058 -0.076 -0.084 0.045 0.026 -0.015 0.0609063509 142 0.057 -0.076 -0.084 0.045 0.026 -0.015 0.0609063197 150 0.057 -0.073 -0.084 0.045 0.026 -0.015 0.0609030532 151 0.057 -0.069 -0.084 0.045 0.026 -0.015 0.0609015478 152 0.057 -0.070 -0.084 0.045 0.026 -0.015 0.0609014579 161 0.057 -0.070 -0.090 0.045 0.026 -0.015 0.0608991052 162 0.057 -0.070 -0.089 0.045 0.026 -0.015 0.0608990997 171 0.057 -0.070 -0.089 0.049 0.026 -0.015 0.0608976685 172 0.057 -0.070 -0.089 0.048 0.026 -0.015 0.0608975890 182 0.057 -0.070 -0.089 0.048 0.025 -0.015 0.0608974968 191 0.057 -0.070 -0.089 0.048 0.025 -0.016 0.0608974937 powell nthiter 3: fret = 0.060897 201 0.059 -0.070 -0.089 0.048 0.025 -0.016 0.0608974840 210 0.059 -0.068 -0.089 0.048 0.025 -0.016 0.0608971472 219 0.059 -0.068 -0.091 0.048 0.025 -0.016 0.0608969831 221 0.059 -0.068 -0.090 0.048 0.025 -0.016 0.0608969290 229 0.059 -0.068 -0.090 0.050 0.025 -0.016 0.0608966372 248 0.059 -0.068 -0.090 0.050 0.025 -0.015 0.0608966328 powell nthiter 4: fret = 0.060897 259 0.058 -0.068 -0.090 0.050 0.025 -0.015 0.0608965953 305 0.058 -0.068 -0.090 0.050 0.025 -0.016 0.0608965645 powell nthiter 5: fret = 0.060897 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.979760 1 -25.0 -25.0 25.0 0.969871 2 -25.0 25.0 -25.0 0.969018 3 -25.0 25.0 25.0 0.983653 4 25.0 -25.0 -25.0 0.975831 5 25.0 -25.0 25.0 0.964628 6 25.0 25.0 -25.0 0.957090 7 25.0 25.0 25.0 0.968355 REL: 8 0.060897 7.768205 0.971026 rel = 0.0627136 Number of iterations 5 Min cost was 0.060897 Number of FunctionCalls 362 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 52.484000 sec Parameters at optimum (transmm) 0.05759 -0.06841 -0.09004 Parameters at optimum (rotdeg) 0.05048 0.02524 -0.01640 Final costs ---------------- Number of surface hits 413992 WM Intensity 790.0398 +/- 248.4195 Ctx Intensity 1056.9888 +/- 258.5034 Pct Contrast 30.5068 +/- 16.4886 Cost 0.0609 RelCost 0.0652 Reg at min cost was -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99985 -0.00701 -0.01596 -0.21518; -0.01592 -0.00650 0.99985 0.16161; 0.00711 -0.99995 -0.00639 0.11805; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 0.00044 -0.00028 -0.05769; -0.00028 -0.00088 -0.00001 0.06845; -0.00043 0.00000 -0.00089 0.08980; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.152952 Computing change in rh position Surface-RMS-Diff-mm 0.139752 0.035932 0.216314 mri_segreg done MinCost: 0.060897 790.039762 1056.988755 30.506751 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 -------- -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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 -------- -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-05 RegMat --------------------------- -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 23:29:21 UTC 2021 Ended at Tue May 25 23:32:08 UTC 2021 BBR-Run-Time-Sec 167 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.lta --surfs cp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.lta mri_convert -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/T2.prenorm.mgz mri_convert.bin -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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-05/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz... INFO: Applying transformation from file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99985 -0.00754 -0.01564 0.04865; 0.00745 0.99996 -0.00562 0.00171; 0.01568 0.00550 0.99986 -0.27238; 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-05/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-05/mri/aseg.presurf.mgz -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.white identity.nofile -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white identity.nofile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/T2.prenorm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/T2.prenorm.mgz... computing distance transform computing distance transform 101254 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-05/mri/T2.norm.mgz mri_mask /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/T2.norm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brainmask.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/T2.mgz DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/T2.mgz...done. /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 rh Waiting for PID 210788 of (210788 210794) to complete... Waiting for PID 210794 of (210788 210794) 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-05 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-05/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... 43249 bright wm thresholded. 3 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.orig... computing class statistics... border white: 444408 voxels (1.36%) border gray 456912 voxels (1.39%) WM (103.0): 102.4 +- 6.3 [70.0 --> 110.0] GM (83.0) : 81.8 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.0 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.0 (was 40) setting MAX_GRAY to 101.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.0 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=108+-3.5, GM=78+-7.0 mean inside = 100.5, mean outside = 83.4 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 109 points - only 0.00% unknown deleting segment 1 with 48 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 24 points - only 0.00% unknown deleting segment 8 with 62 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown deleting segment 10 with 21 points - only 0.00% unknown reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (box.dx, box.dy, box.dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) locating cortical regions not in the range [72.00 212.00], gm=172.00+-20.00, and vertices in regions > 162.0 181816 surface locations found to contain inconsistent values (63011 in, 118805 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg43, 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=157791.0, rms=0.387 001: dt: 0.0500, sse=157801.2, rms=0.386 (0.138%) 002: dt: 0.0500, sse=157807.5, rms=0.385 (0.157%) 003: dt: 0.0500, sse=157813.6, rms=0.385 (0.154%) 004: dt: 0.0500, sse=157819.5, rms=0.384 (0.152%) 005: dt: 0.0500, sse=157825.3, rms=0.384 (0.151%) 006: dt: 0.0500, sse=157831.1, rms=0.383 (0.150%) 007: dt: 0.0500, sse=157836.1, rms=0.383 (0.149%) 008: dt: 0.0500, sse=157840.8, rms=0.382 (0.148%) 009: dt: 0.0500, sse=157845.3, rms=0.381 (0.146%) 010: dt: 0.0500, sse=157849.5, rms=0.381 (0.145%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg43, 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=157325.3, rms=0.381 011: dt: 0.0500, sse=157329.2, rms=0.380 (0.144%) 012: dt: 0.0500, sse=157332.7, rms=0.380 (0.143%) 013: dt: 0.0500, sse=157336.2, rms=0.379 (0.142%) 014: dt: 0.0500, sse=157339.4, rms=0.379 (0.141%) 015: dt: 0.0500, sse=157342.8, rms=0.378 (0.140%) 016: dt: 0.0500, sse=157345.8, rms=0.378 (0.139%) 017: dt: 0.0500, sse=157347.8, rms=0.377 (0.138%) 018: dt: 0.0500, sse=157350.1, rms=0.377 (0.137%) 019: dt: 0.0500, sse=157352.0, rms=0.376 (0.135%) 020: dt: 0.0500, sse=157354.0, rms=0.376 (0.134%) positioning took 1.6 minutes tol=1.0e-04, sigma=2.0, host=blg43, 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=156901.8, rms=0.376 021: dt: 0.0500, sse=156903.2, rms=0.375 (0.134%) 022: dt: 0.0500, sse=156904.8, rms=0.375 (0.133%) 023: dt: 0.0500, sse=156906.3, rms=0.374 (0.132%) 024: dt: 0.0500, sse=156907.6, rms=0.374 (0.131%) 025: dt: 0.0500, sse=156908.9, rms=0.373 (0.130%) 026: dt: 0.0500, sse=156909.8, rms=0.373 (0.129%) 027: dt: 0.0500, sse=156910.5, rms=0.372 (0.128%) 028: dt: 0.0500, sse=156911.1, rms=0.372 (0.127%) 029: dt: 0.0500, sse=156912.2, rms=0.371 (0.126%) 030: dt: 0.0500, sse=156912.6, rms=0.371 (0.125%) positioning took 1.6 minutes tol=1.0e-04, sigma=2.0, host=blg43, 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=156518.3, rms=0.371 031: dt: 0.5000, sse=156518.2, rms=0.366 (1.206%) 032: dt: 0.5000, sse=156520.4, rms=0.362 (1.117%) 033: dt: 0.5000, sse=156505.5, rms=0.358 (1.045%) 034: dt: 0.5000, sse=156490.2, rms=0.355 (0.971%) 035: dt: 0.5000, sse=156468.0, rms=0.352 (0.913%) 036: dt: 0.5000, sse=156447.1, rms=0.349 (0.854%) 037: dt: 0.5000, sse=156423.3, rms=0.346 (0.809%) 038: dt: 0.5000, sse=156391.5, rms=0.343 (0.765%) 039: dt: 0.5000, sse=156368.0, rms=0.341 (0.728%) 040: dt: 0.5000, sse=156342.1, rms=0.338 (0.688%) 041: dt: 0.5000, sse=156306.9, rms=0.336 (0.662%) 042: dt: 0.5000, sse=156285.3, rms=0.334 (0.620%) 043: dt: 0.5000, sse=156260.6, rms=0.332 (0.600%) 044: dt: 0.5000, sse=156232.8, rms=0.330 (0.570%) 045: dt: 0.5000, sse=156203.0, rms=0.328 (0.541%) 046: dt: 0.5000, sse=156182.6, rms=0.327 (0.527%) 047: dt: 0.5000, sse=156153.2, rms=0.325 (0.486%) 048: dt: 0.5000, sse=156132.3, rms=0.324 (0.472%) 049: dt: 0.5000, sse=156111.8, rms=0.322 (0.459%) 050: dt: 0.5000, sse=156087.8, rms=0.321 (0.429%) 051: dt: 0.5000, sse=156068.3, rms=0.319 (0.412%) 052: dt: 0.5000, sse=156047.4, rms=0.318 (0.399%) 053: dt: 0.5000, sse=156023.2, rms=0.317 (0.380%) 054: dt: 0.5000, sse=156009.1, rms=0.316 (0.357%) 055: dt: 0.5000, sse=155989.4, rms=0.315 (0.355%) 056: dt: 0.5000, sse=155968.9, rms=0.314 (0.328%) 057: dt: 0.5000, sse=155953.3, rms=0.313 (0.310%) 058: dt: 0.5000, sse=155941.0, rms=0.312 (0.306%) 059: dt: 0.5000, sse=155921.5, rms=0.311 (0.289%) 060: dt: 0.5000, sse=155907.8, rms=0.310 (0.272%) positioning took 5.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (box.dx, box.dy, box.dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) locating cortical regions not in the range [73.50 211.40], gm=172.00+-19.70, and vertices in regions > 162.1 170984 surface locations found to contain inconsistent values (52745 in, 118239 out) tol=1.0e-04, sigma=1.0, host=blg43, 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=152302.1, rms=0.322 061: dt: 0.5000, sse=152256.1, rms=0.320 (0.924%) 062: dt: 0.5000, sse=152172.5, rms=0.316 (1.095%) 063: dt: 0.5000, sse=152097.6, rms=0.313 (0.939%) 064: dt: 0.5000, sse=152026.8, rms=0.310 (0.856%) 065: dt: 0.5000, sse=151959.4, rms=0.308 (0.785%) 066: dt: 0.5000, sse=151898.2, rms=0.306 (0.721%) 067: dt: 0.5000, sse=151833.8, rms=0.304 (0.660%) 068: dt: 0.5000, sse=151793.6, rms=0.302 (0.609%) 069: dt: 0.5000, sse=151744.2, rms=0.300 (0.567%) 070: dt: 0.5000, sse=151705.4, rms=0.299 (0.535%) 071: dt: 0.5000, sse=151671.9, rms=0.297 (0.502%) 072: dt: 0.5000, sse=151637.0, rms=0.296 (0.480%) 073: dt: 0.5000, sse=151602.0, rms=0.294 (0.460%) 074: dt: 0.5000, sse=151570.8, rms=0.293 (0.443%) 075: dt: 0.5000, sse=151541.0, rms=0.292 (0.424%) 076: dt: 0.5000, sse=151516.2, rms=0.291 (0.408%) 077: dt: 0.5000, sse=151483.3, rms=0.289 (0.395%) 078: dt: 0.5000, sse=151456.2, rms=0.288 (0.383%) 079: dt: 0.5000, sse=151432.1, rms=0.287 (0.372%) 080: dt: 0.5000, sse=151407.7, rms=0.286 (0.358%) 081: dt: 0.5000, sse=151381.3, rms=0.285 (0.350%) 082: dt: 0.5000, sse=151364.4, rms=0.284 (0.337%) 083: dt: 0.5000, sse=151334.4, rms=0.283 (0.326%) 084: dt: 0.5000, sse=151314.8, rms=0.282 (0.316%) 085: dt: 0.5000, sse=151286.2, rms=0.282 (0.303%) 086: dt: 0.5000, sse=151270.4, rms=0.281 (0.293%) 087: dt: 0.5000, sse=151252.6, rms=0.280 (0.286%) 088: dt: 0.5000, sse=151225.2, rms=0.279 (0.276%) 089: dt: 0.5000, sse=151204.8, rms=0.278 (0.271%) 090: dt: 0.5000, sse=151192.0, rms=0.278 (0.262%) positioning took 6.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (box.dx, box.dy, box.dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) locating cortical regions not in the range [72.00 212.00], gm=172.00+-20.00, and vertices in regions > 162.0 166627 surface locations found to contain inconsistent values (40599 in, 126028 out) tol=1.0e-04, sigma=0.5, host=blg43, 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=151619.8, rms=0.292 091: dt: 0.5000, sse=151600.0, rms=0.289 (0.687%) 092: dt: 0.5000, sse=151542.9, rms=0.287 (0.830%) 093: dt: 0.5000, sse=151489.8, rms=0.285 (0.686%) 094: dt: 0.5000, sse=151444.5, rms=0.283 (0.619%) 095: dt: 0.5000, sse=151401.0, rms=0.282 (0.555%) 096: dt: 0.5000, sse=151359.8, rms=0.280 (0.507%) 097: dt: 0.5000, sse=151332.0, rms=0.279 (0.457%) 098: dt: 0.5000, sse=151298.7, rms=0.278 (0.421%) 099: dt: 0.5000, sse=151268.8, rms=0.277 (0.389%) 100: dt: 0.5000, sse=151247.4, rms=0.276 (0.371%) 101: dt: 0.5000, sse=151221.2, rms=0.275 (0.349%) 102: dt: 0.5000, sse=151198.1, rms=0.274 (0.333%) 103: dt: 0.5000, sse=151179.5, rms=0.273 (0.319%) 104: dt: 0.5000, sse=151161.8, rms=0.272 (0.302%) 105: dt: 0.5000, sse=151138.1, rms=0.271 (0.297%) 106: dt: 0.5000, sse=151126.3, rms=0.271 (0.280%) 107: dt: 0.5000, sse=151104.3, rms=0.270 (0.275%) 108: dt: 0.5000, sse=151085.0, rms=0.269 (0.263%) 109: dt: 0.5000, sse=151070.5, rms=0.269 (0.252%) 110: dt: 0.5000, sse=151051.9, rms=0.268 (0.250%) 111: dt: 0.5000, sse=151034.1, rms=0.267 (0.242%) 112: dt: 0.5000, sse=151022.9, rms=0.267 (0.234%) 113: dt: 0.5000, sse=151004.3, rms=0.266 (0.224%) 114: dt: 0.5000, sse=150986.1, rms=0.265 (0.222%) 115: dt: 0.5000, sse=150974.2, rms=0.265 (0.214%) 116: dt: 0.5000, sse=150957.8, rms=0.264 (0.205%) 117: dt: 0.5000, sse=150940.3, rms=0.264 (0.203%) 118: dt: 0.5000, sse=150934.3, rms=0.263 (0.188%) 119: dt: 0.5000, sse=150918.3, rms=0.263 (0.193%) 120: dt: 0.5000, sse=150907.7, rms=0.262 (0.176%) positioning took 7.0 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (region->dx, region->dy, region->dz) = (163, 402, 271) (box.dx, box.dy, box.dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) (region->dx, region->dy, region->dz) = (180, 413, 287) locating cortical regions not in the range [71.00 213.80], gm=173.00+-20.40, and vertices in regions > 162.8 169653 surface locations found to contain inconsistent values (31454 in, 138199 out) tol=1.0e-04, sigma=0.2, host=blg43, 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-05/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=152174.4, rms=0.274 121: dt: 0.5000, sse=152185.2, rms=0.273 (0.568%) 122: dt: 0.5000, sse=152141.9, rms=0.271 (0.677%) 123: dt: 0.5000, sse=152102.0, rms=0.269 (0.550%) 124: dt: 0.5000, sse=152068.5, rms=0.268 (0.486%) 125: dt: 0.5000, sse=152035.8, rms=0.267 (0.428%) 126: dt: 0.5000, sse=152005.8, rms=0.266 (0.382%) 127: dt: 0.5000, sse=151982.8, rms=0.265 (0.338%) 128: dt: 0.5000, sse=151961.8, rms=0.264 (0.309%) 129: dt: 0.5000, sse=151941.2, rms=0.263 (0.281%) 130: dt: 0.5000, sse=151923.7, rms=0.263 (0.261%) 131: dt: 0.5000, sse=151911.0, rms=0.262 (0.243%) 132: dt: 0.5000, sse=151895.7, rms=0.261 (0.230%) 133: dt: 0.5000, sse=151885.7, rms=0.261 (0.218%) 134: dt: 0.5000, sse=151872.2, rms=0.260 (0.210%) 135: dt: 0.5000, sse=151863.3, rms=0.260 (0.197%) 136: dt: 0.5000, sse=151850.9, rms=0.259 (0.193%) 137: dt: 0.5000, sse=151840.2, rms=0.259 (0.180%) 138: dt: 0.5000, sse=151831.0, rms=0.258 (0.176%) 139: dt: 0.5000, sse=151823.0, rms=0.258 (0.168%) 140: dt: 0.5000, sse=151813.0, rms=0.257 (0.164%) 141: dt: 0.5000, sse=151804.5, rms=0.257 (0.156%) 142: dt: 0.5000, sse=151795.8, rms=0.257 (0.152%) 143: dt: 0.5000, sse=151787.9, rms=0.256 (0.146%) 144: dt: 0.5000, sse=151778.9, rms=0.256 (0.142%) 145: dt: 0.5000, sse=151773.6, rms=0.256 (0.134%) 146: dt: 0.5000, sse=151765.1, rms=0.255 (0.133%) 147: dt: 0.5000, sse=151757.0, rms=0.255 (0.125%) 148: dt: 0.5000, sse=151748.8, rms=0.255 (0.123%) 149: dt: 0.5000, sse=151742.9, rms=0.254 (0.119%) 150: dt: 0.5000, sse=151734.6, rms=0.254 (0.114%) positioning took 7.5 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.area.pial vertex spacing 0.80 +- 0.37 (0.03-->6.72) (max @ vno 161103 --> 161104) face area 0.25 +- 0.21 (0.00-->5.27) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 219913 vertices processed 25000 of 219913 vertices processed 50000 of 219913 vertices processed 75000 of 219913 vertices processed 100000 of 219913 vertices processed 125000 of 219913 vertices processed 150000 of 219913 vertices processed 175000 of 219913 vertices processed 200000 of 219913 vertices processed 0 of 219913 vertices processed 25000 of 219913 vertices processed 50000 of 219913 vertices processed 75000 of 219913 vertices processed 100000 of 219913 vertices processed 125000 of 219913 vertices processed 150000 of 219913 vertices processed 175000 of 219913 vertices processed 200000 of 219913 vertices processed thickness calculation complete, 277:1152 truncations. 37797 vertices at 0 distance 118980 vertices at 1 distance 131467 vertices at 2 distance 77451 vertices at 3 distance 33158 vertices at 4 distance 12326 vertices at 5 distance 4583 vertices at 6 distance 1616 vertices at 7 distance 570 vertices at 8 distance 235 vertices at 9 distance 142 vertices at 10 distance 110 vertices at 11 distance 63 vertices at 12 distance 55 vertices at 13 distance 47 vertices at 14 distance 55 vertices at 15 distance 25 vertices at 16 distance 17 vertices at 17 distance 20 vertices at 18 distance 24 vertices at 19 distance 27 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.thickness positioning took 56.9 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-05 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-05/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... 43249 bright wm thresholded. 3 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.orig... computing class statistics... border white: 444408 voxels (1.36%) border gray 456912 voxels (1.39%) WM (103.0): 102.4 +- 6.3 [70.0 --> 110.0] GM (83.0) : 81.8 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.0 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 57.0 (was 40) setting MAX_GRAY to 101.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.0 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=108+-3.5, GM=77+-8.7 mean inside = 100.5, mean outside = 83.5 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 11 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 4 with 38 points - only 0.00% unknown deleting segment 5 with 32 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 14 points - only 0.00% unknown deleting segment 9 with 6 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) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (box.dx, box.dy, box.dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) locating cortical regions not in the range [71.50 212.20], gm=172.00+-20.10, and vertices in regions > 161.9 177859 surface locations found to contain inconsistent values (59119 in, 118740 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg43, 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=157918.5, rms=0.383 001: dt: 0.0500, sse=157933.6, rms=0.383 (0.144%) 002: dt: 0.0500, sse=157944.6, rms=0.382 (0.163%) 003: dt: 0.0500, sse=157955.2, rms=0.381 (0.159%) 004: dt: 0.0500, sse=157965.4, rms=0.381 (0.158%) 005: dt: 0.0500, sse=157974.7, rms=0.380 (0.156%) 006: dt: 0.0500, sse=157984.0, rms=0.380 (0.155%) 007: dt: 0.0500, sse=157993.1, rms=0.379 (0.153%) 008: dt: 0.0500, sse=158001.8, rms=0.378 (0.152%) 009: dt: 0.0500, sse=158010.1, rms=0.378 (0.151%) 010: dt: 0.0500, sse=158018.3, rms=0.377 (0.150%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg43, 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=157426.9, rms=0.377 011: dt: 0.0500, sse=157434.2, rms=0.377 (0.149%) 012: dt: 0.0500, sse=157441.0, rms=0.376 (0.148%) 013: dt: 0.0500, sse=157448.3, rms=0.376 (0.146%) 014: dt: 0.0500, sse=157454.5, rms=0.375 (0.146%) 015: dt: 0.0500, sse=157461.2, rms=0.375 (0.145%) 016: dt: 0.0500, sse=157467.7, rms=0.374 (0.144%) 017: dt: 0.0500, sse=157473.9, rms=0.373 (0.143%) 018: dt: 0.0500, sse=157479.9, rms=0.373 (0.141%) 019: dt: 0.0500, sse=157485.9, rms=0.372 (0.140%) 020: dt: 0.0500, sse=157491.7, rms=0.372 (0.139%) positioning took 1.6 minutes tol=1.0e-04, sigma=2.0, host=blg43, 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=156980.8, rms=0.372 021: dt: 0.0500, sse=156986.1, rms=0.371 (0.139%) 022: dt: 0.0500, sse=156990.9, rms=0.371 (0.138%) 023: dt: 0.0500, sse=156995.7, rms=0.370 (0.137%) 024: dt: 0.0500, sse=157000.2, rms=0.370 (0.136%) 025: dt: 0.0500, sse=157004.4, rms=0.369 (0.135%) 026: dt: 0.0500, sse=157008.6, rms=0.369 (0.134%) 027: dt: 0.0500, sse=157013.1, rms=0.368 (0.132%) 028: dt: 0.0500, sse=157017.0, rms=0.368 (0.132%) 029: dt: 0.0500, sse=157020.9, rms=0.367 (0.131%) 030: dt: 0.0500, sse=157024.5, rms=0.367 (0.129%) positioning took 1.6 minutes tol=1.0e-04, sigma=2.0, host=blg43, 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=156576.1, rms=0.367 031: dt: 0.5000, sse=156606.8, rms=0.362 (1.261%) 032: dt: 0.5000, sse=156629.6, rms=0.358 (1.182%) 033: dt: 0.5000, sse=156640.9, rms=0.354 (1.092%) 034: dt: 0.5000, sse=156638.7, rms=0.350 (1.018%) 035: dt: 0.5000, sse=156633.8, rms=0.347 (0.944%) 036: dt: 0.5000, sse=156619.2, rms=0.344 (0.893%) 037: dt: 0.5000, sse=156609.5, rms=0.341 (0.831%) 038: dt: 0.5000, sse=156597.8, rms=0.339 (0.790%) 039: dt: 0.5000, sse=156583.9, rms=0.336 (0.741%) 040: dt: 0.5000, sse=156560.6, rms=0.334 (0.724%) 041: dt: 0.5000, sse=156547.0, rms=0.331 (0.646%) 042: dt: 0.5000, sse=156521.2, rms=0.329 (0.654%) 043: dt: 0.5000, sse=156501.7, rms=0.327 (0.592%) 044: dt: 0.5000, sse=156486.0, rms=0.325 (0.578%) 045: dt: 0.5000, sse=156463.3, rms=0.324 (0.553%) 046: dt: 0.5000, sse=156441.8, rms=0.322 (0.550%) 047: dt: 0.5000, sse=156418.1, rms=0.320 (0.508%) 048: dt: 0.5000, sse=156407.7, rms=0.319 (0.475%) 049: dt: 0.5000, sse=156381.7, rms=0.317 (0.464%) 050: dt: 0.5000, sse=156368.2, rms=0.316 (0.459%) 051: dt: 0.5000, sse=156346.5, rms=0.314 (0.421%) 052: dt: 0.5000, sse=156326.6, rms=0.313 (0.420%) 053: dt: 0.5000, sse=156319.6, rms=0.312 (0.364%) 054: dt: 0.5000, sse=156304.5, rms=0.311 (0.371%) 055: dt: 0.5000, sse=156286.6, rms=0.310 (0.343%) 056: dt: 0.5000, sse=156270.6, rms=0.309 (0.358%) 057: dt: 0.5000, sse=156255.8, rms=0.308 (0.316%) 058: dt: 0.5000, sse=156247.4, rms=0.307 (0.313%) 059: dt: 0.5000, sse=156235.7, rms=0.306 (0.284%) 060: dt: 0.5000, sse=156219.6, rms=0.305 (0.298%) positioning took 5.2 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (box.dx, box.dy, box.dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) locating cortical regions not in the range [78.50 209.40], gm=172.00+-18.70, and vertices in regions > 162.6 167609 surface locations found to contain inconsistent values (61812 in, 105797 out) tol=1.0e-04, sigma=1.0, host=blg43, 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=152460.0, rms=0.326 061: dt: 0.5000, sse=152406.3, rms=0.323 (0.993%) 062: dt: 0.5000, sse=152302.0, rms=0.319 (1.176%) 063: dt: 0.5000, sse=152210.1, rms=0.316 (1.020%) 064: dt: 0.5000, sse=152123.5, rms=0.313 (0.949%) 065: dt: 0.5000, sse=152047.2, rms=0.310 (0.863%) 066: dt: 0.5000, sse=151966.8, rms=0.307 (0.803%) 067: dt: 0.5000, sse=151900.4, rms=0.305 (0.744%) 068: dt: 0.5000, sse=151840.4, rms=0.303 (0.692%) 069: dt: 0.5000, sse=151785.7, rms=0.301 (0.647%) 070: dt: 0.5000, sse=151727.3, rms=0.299 (0.613%) 071: dt: 0.5000, sse=151689.1, rms=0.297 (0.575%) 072: dt: 0.5000, sse=151639.4, rms=0.296 (0.545%) 073: dt: 0.5000, sse=151597.2, rms=0.294 (0.525%) 074: dt: 0.5000, sse=151553.1, rms=0.293 (0.535%) 075: dt: 0.5000, sse=151513.7, rms=0.291 (0.497%) 076: dt: 0.5000, sse=151471.1, rms=0.290 (0.482%) 077: dt: 0.5000, sse=151426.6, rms=0.288 (0.483%) 078: dt: 0.5000, sse=151393.1, rms=0.287 (0.465%) 079: dt: 0.5000, sse=151362.5, rms=0.286 (0.440%) 080: dt: 0.5000, sse=151315.7, rms=0.285 (0.446%) 081: dt: 0.5000, sse=151287.5, rms=0.283 (0.413%) 082: dt: 0.5000, sse=151253.2, rms=0.282 (0.407%) 083: dt: 0.5000, sse=151221.2, rms=0.281 (0.391%) 084: dt: 0.5000, sse=151190.3, rms=0.280 (0.383%) 085: dt: 0.5000, sse=151167.3, rms=0.279 (0.364%) 086: dt: 0.5000, sse=151130.2, rms=0.278 (0.371%) 087: dt: 0.5000, sse=151109.6, rms=0.277 (0.344%) 088: dt: 0.5000, sse=151073.5, rms=0.276 (0.348%) 089: dt: 0.5000, sse=151055.3, rms=0.275 (0.323%) 090: dt: 0.5000, sse=151014.0, rms=0.274 (0.317%) positioning took 6.1 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (box.dx, box.dy, box.dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) locating cortical regions not in the range [72.00 212.00], gm=172.00+-20.00, and vertices in regions > 162.0 168255 surface locations found to contain inconsistent values (33909 in, 134346 out) tol=1.0e-04, sigma=0.5, host=blg43, 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=150923.1, rms=0.279 091: dt: 0.5000, sse=150913.1, rms=0.277 (0.748%) 092: dt: 0.5000, sse=150859.2, rms=0.275 (0.908%) 093: dt: 0.5000, sse=150810.2, rms=0.273 (0.753%) 094: dt: 0.5000, sse=150765.6, rms=0.271 (0.675%) 095: dt: 0.5000, sse=150727.2, rms=0.269 (0.608%) 096: dt: 0.5000, sse=150692.2, rms=0.268 (0.544%) 097: dt: 0.5000, sse=150662.3, rms=0.266 (0.492%) 098: dt: 0.5000, sse=150634.2, rms=0.265 (0.453%) 099: dt: 0.5000, sse=150607.1, rms=0.264 (0.418%) 100: dt: 0.5000, sse=150583.3, rms=0.263 (0.394%) 101: dt: 0.5000, sse=150562.9, rms=0.262 (0.368%) 102: dt: 0.5000, sse=150543.0, rms=0.261 (0.350%) 103: dt: 0.5000, sse=150525.3, rms=0.260 (0.335%) 104: dt: 0.5000, sse=150504.0, rms=0.260 (0.318%) 105: dt: 0.5000, sse=150493.7, rms=0.259 (0.304%) 106: dt: 0.5000, sse=150474.6, rms=0.258 (0.300%) 107: dt: 0.5000, sse=150458.2, rms=0.257 (0.285%) 108: dt: 0.5000, sse=150439.7, rms=0.257 (0.279%) 109: dt: 0.5000, sse=150426.5, rms=0.256 (0.263%) 110: dt: 0.5000, sse=150409.9, rms=0.255 (0.253%) 111: dt: 0.5000, sse=150396.4, rms=0.255 (0.245%) 112: dt: 0.5000, sse=150384.7, rms=0.254 (0.241%) 113: dt: 0.5000, sse=150369.6, rms=0.253 (0.236%) 114: dt: 0.5000, sse=150358.0, rms=0.253 (0.223%) 115: dt: 0.5000, sse=150343.1, rms=0.252 (0.220%) 116: dt: 0.5000, sse=150333.0, rms=0.252 (0.204%) 117: dt: 0.5000, sse=150317.3, rms=0.251 (0.206%) 118: dt: 0.5000, sse=150305.8, rms=0.251 (0.201%) 119: dt: 0.5000, sse=150295.7, rms=0.250 (0.185%) 120: dt: 0.5000, sse=150284.4, rms=0.250 (0.181%) positioning took 6.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (region->dx, region->dy, region->dz) = (164, 406, 262) (box.dx, box.dy, box.dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) (region->dx, region->dy, region->dz) = (172, 419, 276) locating cortical regions not in the range [72.50 211.80], gm=172.00+-19.90, and vertices in regions > 162.0 164763 surface locations found to contain inconsistent values (38729 in, 126034 out) tol=1.0e-04, sigma=0.2, host=blg43, 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-05/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=151408.2, rms=0.263 121: dt: 0.5000, sse=151394.0, rms=0.261 (0.558%) 122: dt: 0.5000, sse=151339.1, rms=0.260 (0.682%) 123: dt: 0.5000, sse=151290.8, rms=0.258 (0.560%) 124: dt: 0.5000, sse=151252.9, rms=0.257 (0.497%) 125: dt: 0.5000, sse=151214.1, rms=0.256 (0.440%) 126: dt: 0.5000, sse=151178.8, rms=0.255 (0.400%) 127: dt: 0.5000, sse=151148.1, rms=0.254 (0.358%) 128: dt: 0.5000, sse=151121.7, rms=0.253 (0.333%) 129: dt: 0.5000, sse=151097.6, rms=0.252 (0.305%) 130: dt: 0.5000, sse=151075.8, rms=0.252 (0.290%) 131: dt: 0.5000, sse=151054.0, rms=0.251 (0.269%) 132: dt: 0.5000, sse=151034.3, rms=0.250 (0.258%) 133: dt: 0.5000, sse=151015.6, rms=0.250 (0.242%) 134: dt: 0.5000, sse=150999.8, rms=0.249 (0.235%) 135: dt: 0.5000, sse=150979.8, rms=0.248 (0.222%) 136: dt: 0.5000, sse=150968.6, rms=0.248 (0.212%) 137: dt: 0.5000, sse=150955.8, rms=0.247 (0.205%) 138: dt: 0.5000, sse=150944.3, rms=0.247 (0.200%) 139: dt: 0.5000, sse=150930.7, rms=0.246 (0.190%) 140: dt: 0.5000, sse=150920.1, rms=0.246 (0.184%) 141: dt: 0.5000, sse=150907.1, rms=0.246 (0.173%) 142: dt: 0.5000, sse=150896.5, rms=0.245 (0.171%) 143: dt: 0.5000, sse=150883.0, rms=0.245 (0.163%) 144: dt: 0.5000, sse=150872.6, rms=0.244 (0.158%) 145: dt: 0.5000, sse=150863.4, rms=0.244 (0.153%) 146: dt: 0.5000, sse=150854.9, rms=0.244 (0.150%) 147: dt: 0.5000, sse=150843.8, rms=0.243 (0.141%) 148: dt: 0.5000, sse=150838.6, rms=0.243 (0.139%) 149: dt: 0.5000, sse=150828.6, rms=0.243 (0.131%) 150: dt: 0.5000, sse=150819.7, rms=0.242 (0.130%) positioning took 7.3 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.area.pial vertex spacing 0.80 +- 0.37 (0.03-->7.10) (max @ vno 167206 --> 165877) face area 0.25 +- 0.21 (0.00-->5.40) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 218501 vertices processed 25000 of 218501 vertices processed 50000 of 218501 vertices processed 75000 of 218501 vertices processed 100000 of 218501 vertices processed 125000 of 218501 vertices processed 150000 of 218501 vertices processed 175000 of 218501 vertices processed 200000 of 218501 vertices processed 0 of 218501 vertices processed 25000 of 218501 vertices processed 50000 of 218501 vertices processed 75000 of 218501 vertices processed 100000 of 218501 vertices processed 125000 of 218501 vertices processed 150000 of 218501 vertices processed 175000 of 218501 vertices processed 200000 of 218501 vertices processed thickness calculation complete, 300:1011 truncations. 36408 vertices at 0 distance 114153 vertices at 1 distance 128814 vertices at 2 distance 80421 vertices at 3 distance 35567 vertices at 4 distance 13033 vertices at 5 distance 4637 vertices at 6 distance 1660 vertices at 7 distance 609 vertices at 8 distance 284 vertices at 9 distance 172 vertices at 10 distance 111 vertices at 11 distance 59 vertices at 12 distance 68 vertices at 13 distance 53 vertices at 14 distance 35 vertices at 15 distance 24 vertices at 16 distance 21 vertices at 17 distance 18 vertices at 18 distance 15 vertices at 19 distance 14 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.thickness positioning took 53.4 minutes PIDs (210788 210794) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Wed May 26 00:30:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf vertexvol --s sub-05 --lh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Total face volume 263179 Total vertex volume 260936 (mask=0) #@# sub-05 lh 260936 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed May 26 00:30:43 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf vertexvol --s sub-05 --rh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/rh.cortex.label Total face volume 259885 Total vertex volume 258192 (mask=0) #@# sub-05 rh 258192 vertexvol Done #-------------------------------------------- #@# Surf Volume lh Wed May 26 00:30:48 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Total face volume 263179 Total vertex volume 260936 (mask=0) #@# sub-05 lh 260936 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed May 26 00:30:53 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/rh.cortex.label Total face volume 259885 Total vertex volume 258192 (mask=0) #@# sub-05 rh 258192 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Wed May 26 00:30:58 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05 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 = 365 writing volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/ribbon.mgz mris_volmask took 23.90 minutes writing ribbon files Started at Tue May 25 23:29:19 UTC 2021 Ended at Wed May 26 00:54:52 UTC 2021 #@#%# recon-all-run-time-hours 1.426 recon-all -s sub-05 finished without error at Wed May 26 00:54:53 UTC 2021 New invocation of recon-all Wed May 26 01:06:14 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon3 -openmp 8 -subjid sub-05 -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-05 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 blg4313.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: 196638428 118911060 68406396 2008964 9320972 72563620 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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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: 2021/05/26-01:06:14-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: blg4313.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 01:06:15 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2894 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2365 voxels changed to hypointensity... 5254 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed May 26 01:06:53 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --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-05 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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-05/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 13.24 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 --> 74 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 70 rescaling CSF from 32 --> 56 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 69 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 48 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1007809 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 150 changed. pass 2: 5 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Wed May 26 01:16:30 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subject sub-05 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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-05/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 13.24 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 --> 74 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 70 rescaling CSF from 32 --> 56 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 69 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 48 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1007880 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 150 changed. pass 2: 5 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed May 26 01:25:42 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subject sub-05 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-05/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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-05/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 13.24 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 --> 74 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 70 rescaling CSF from 32 --> 56 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 25 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 69 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 48 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1007880 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 150 changed. pass 2: 5 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Wed May 26 01:35:09 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Wed May 26 01:35:09 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-05/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 blg4313.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-05/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 blg4313.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 01:35:09 UTC 2021 Ended at Wed May 26 01:35:17 UTC 2021 Apas2aseg-Run-Time-Sec 8 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed May 26 01:35:17 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 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-05 $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-05 sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1653081 mm^3 (det: 1.178470 ) Computing euler number orig.nofix lheno = -186, rheno = -96 orig.nofix lhholes = 94, rhholes = 49 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 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 01:36:33 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --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-05 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-05/mri/aparc+aseg.mgz Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/ribbon.mgz Loading filled from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 12669 vertices from left hemi Ripped 11795 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-05/mri/aseg.mgz Loading Ctx Seg File /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 = 1818692 Used brute-force search on 110 voxels Fixing Parahip LH WM Found 16 clusters 0 k 3.071999 1 k 1.024000 2 k 0.512000 3 k 1.536000 4 k 0.512000 5 k 1.536000 6 k 1235.971924 7 k 0.512000 8 k 2.559999 9 k 0.512000 10 k 0.512000 11 k 0.512000 12 k 39.423988 13 k 0.512000 14 k 0.512000 15 k 0.512000 Fixing Parahip RH WM Found 13 clusters 0 k 0.512000 1 k 0.512000 2 k 0.512000 3 k 0.512000 4 k 0.512000 5 k 0.512000 6 k 1397.751953 7 k 1.024000 8 k 1.024000 9 k 13.312000 10 k 0.512000 11 k 0.512000 12 k 1.024000 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-05 --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-05 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1653081 mm^3 (det: 1.178470 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 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 01:06:14 UTC 2021 Ended at Wed May 26 01:50:01 UTC 2021 #@#%# recon-all-run-time-hours 0.730 recon-all -s sub-05 finished without error at Wed May 26 01:50:01 UTC 2021