Tue May 25 17:30:01 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 /opt/freesurfer/bin/recon-all -autorecon1 -i /work/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-02_ses-001_T1w_template.nii.gz -T2 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-02/ses-001/anat/sub-02_ses-001_T2w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-02 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -expert /work/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts subjid sub-02 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 blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 64365628 121399420 2013048 10873384 127165596 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: 2021/05/25-17:30:01-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:02-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:03-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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: 2021/05/25-17:30:04-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: blg8112.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-02 mri_convert /work/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-02_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/001.mgz mri_convert.bin /work/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-02_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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_02_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-02_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-02/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Tue May 25 17:30:10 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 mri_convert --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-02/ses-001/anat/sub-02_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-02/ses-001/anat/sub-02_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/ses-001/anat/sub-02_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-02/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Tue May 25 17:30:20 UTC 2021 Found 1 runs /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/orig/001.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig.mgz --conform_min mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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-02/mri/orig.mgz... mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/talairach.xfm /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 25 17:30:32 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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 blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Tue May 25 17:30:32 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.230850 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.230850/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.230850/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.230850/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue May 25 17:30:47 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.230850/nu0.mnc ./tmp.mri_nu_correct.mni.230850/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.230850/0/ -iterations 1000 -distance 50 [bpinsard@blg8112.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/] [2021-05-25 17:30:47] 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.230850/0/ ./tmp.mri_nu_correct.mni.230850/nu0.mnc ./tmp.mri_nu_correct.mni.230850/nu1.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 127 CV of field change: 0.000953194 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.230850/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.230850/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.230850/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 17:34:34 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 17:34:34 UTC 2021 Ended at Tue May 25 17:35:11 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 25 17:35:13 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5541, pval=0.2115 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/talairach_avi.log tal_QC_AZS /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/talairach_avi.log TalAviQA: 0.97299 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Tue May 25 17:35:13 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-02/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 blg8112.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 17:35:13 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.234948 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.234948/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.234948/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.234948/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Tue May 25 17:35:29 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.234948/nu0.mnc ./tmp.mri_nu_correct.mni.234948/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.234948/0/ [bpinsard@blg8112.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/] [2021-05-25 17:35:29] 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.234948/0/ ./tmp.mri_nu_correct.mni.234948/nu0.mnc ./tmp.mri_nu_correct.mni.234948/nu1.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 50 CV of field change: 0.00162485 Outputting Volume: ............................................................ Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Tue May 25 17:37:31 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.234948/nu1.mnc ./tmp.mri_nu_correct.mni.234948/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.234948/1/ [bpinsard@blg8112.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/] [2021-05-25 17:37:31] 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.234948/1/ ./tmp.mri_nu_correct.mni.234948/nu1.mnc ./tmp.mri_nu_correct.mni.234948/nu2.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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: 50 CV of field change: 0.00127871 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.234948/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-02/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.234948/ones.mgz sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard input ./tmp.mri_nu_correct.mni.234948/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.234948/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.234948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/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.234948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/input.mean.dat sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.234948/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.234948/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.234948/ones.mgz --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/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.234948/ones.mgz --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/output.mean.dat sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.234948/ones.mgz Loading ./tmp.mri_nu_correct.mni.234948/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.234948/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.234948/nu2.mnc ./tmp.mri_nu_correct.mni.234948/nu2.mnc mul .91770764551582458463 Saving result to './tmp.mri_nu_correct.mni.234948/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.234948/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.234948/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.234948/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 10 seconds. mapping ( 8, 165) to ( 3, 110) Tue May 25 17:40:33 UTC 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue May 25 17:40:34 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 1.04660 0.02140 -0.01041 -0.49535; -0.07061 0.94290 0.30381 -19.69897; 0.00693 -0.37570 0.95001 18.83723; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 23 Starting OpenSpline(): npoints = 23 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 84 (84), valley at 41 (41) csf peak at 43, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 40 (40) 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 59 seconds. Started at Tue May 25 17:30:01 UTC 2021 Ended at Tue May 25 17:46:33 UTC 2021 #@#%# recon-all-run-time-hours 0.276 recon-all -s sub-02 finished without error at Tue May 25 17:46:33 UTC 2021 New invocation of recon-all Tue May 25 17:46:40 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-02 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-02 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 blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 66891952 116944804 2022496 12801676 124509972 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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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: 2021/05/25-17:46:40-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: blg8112.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 17:46:41 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_em_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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=24.0 skull bounding box = (75, 71, 35) --> (240, 255, 236) using (130, 132, 136) as brain centroid... mean wm in atlas = 107, using box (110,109,111) --> (150, 154,160) to find MRI wm before smoothing, mri peak at 99 robust fit to distribution - 99 +- 5.2 after smoothing, mri peak at 99, scaling input intensities by 1.081 scaling channel 0 by 1.08081 initial log_p = -4.017 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.090193 @ (0.000, 0.000, 0.000) max log p = -4.079875 @ (-4.545, -4.545, -4.545) max log p = -4.045702 @ (2.273, -2.273, 2.273) max log p = -4.009410 @ (1.136, 1.136, -1.136) max log p = -4.003066 @ (0.568, -0.568, -0.568) max log p = -3.989744 @ (-0.284, -0.284, -0.284) Found translation: (-0.9, -6.5, -4.3): log p = -3.990 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.917, old_max_log_p =-3.990 (thresh=-4.0) 0.79316 0.02703 -0.10086 12.45615; 0.00000 0.77274 0.20706 -29.05599; 0.09659 -0.18989 0.70867 29.09710; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.906, old_max_log_p =-3.917 (thresh=-3.9) 0.85879 -0.01176 -0.01271 -8.26434; 0.01166 0.68574 0.27545 -26.70263; -0.00923 -0.31194 0.73419 61.14960; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.906, old_max_log_p =-3.906 (thresh=-3.9) 0.85879 -0.01176 -0.01271 -8.26434; 0.01166 0.68574 0.27545 -26.70263; -0.00923 -0.31194 0.73419 61.14960; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.855, old_max_log_p =-3.906 (thresh=-3.9) 0.82401 0.05378 0.00791 -13.06201; -0.07844 0.73330 0.26382 -17.14439; -0.00473 -0.28007 0.71441 58.05458; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.854, old_max_log_p =-3.855 (thresh=-3.9) 0.84162 0.03002 0.00004 -12.59375; -0.05220 0.75738 0.24494 -23.34789; -0.00716 -0.25112 0.70911 54.13228; 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=-3.835, old_max_log_p =-3.854 (thresh=-3.9) 0.83978 0.02936 0.01945 -14.16653; -0.05936 0.75337 0.26317 -23.01015; -0.02659 -0.26973 0.70099 62.36839; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.826, old_max_log_p =-3.835 (thresh=-3.8) 0.83912 0.03373 0.00797 -12.79741; -0.05929 0.75248 0.26286 -22.80739; -0.01289 -0.27016 0.70369 60.22865; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.824, old_max_log_p =-3.826 (thresh=-3.8) 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 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 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.824 (old=-4.017) transform before final EM align: 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 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 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1113.776293 mri_em_register stimesec 3.668335 mri_em_register ru_maxrss 753824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 886324 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 542 mri_em_register ru_nivcsw 392 registration took 3 minutes and 5 seconds. #-------------------------------------- #@# CA Normalize Tue May 25 17:49:46 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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=24.0 skull bounding box = (75, 71, 35) --> (240, 255, 236) using (130, 132, 136) as brain centroid... mean wm in atlas = 107, using box (110,109,111) --> (150, 154,160) to find MRI wm before smoothing, mri peak at 99 robust fit to distribution - 99 +- 5.2 after smoothing, mri peak at 99, scaling input intensities by 1.081 scaling channel 0 by 1.08081 using 246344 sample points... INFO: compute sample coordinates transform 0.83912 0.03373 0.00797 -12.79741; -0.05936 0.75336 0.26317 -23.00941; -0.01290 -0.27048 0.70451 60.14421; 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 (156, 75, 30) --> (237, 228, 247) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 1323 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (81, 72, 27) --> (161, 214, 246) Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 220 of 1344 (16.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (158, 193, 75) --> (215, 248, 146) Left_Cerebellum_White_Matter: limiting intensities to 118.0 --> 132.0 6 of 12 (50.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (103, 192, 69) --> (157, 242, 145) Right_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0 0 of 13 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (136, 170, 116) --> (178, 258, 159) Brain_Stem: limiting intensities to 108.0 --> 132.0 0 of 10 (0.0%) samples deleted using 2702 total control points for intensity normalization... bias field = 0.945 +- 0.068 5 of 2476 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (156, 75, 30) --> (237, 228, 247) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 2324 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (81, 72, 27) --> (161, 214, 246) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 2267 (0.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (158, 193, 75) --> (215, 248, 146) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 77 (13.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (103, 192, 69) --> (157, 242, 145) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 84 (29.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (136, 170, 116) --> (178, 258, 159) Brain_Stem: limiting intensities to 88.0 --> 132.0 7 of 67 (10.4%) samples deleted using 4819 total control points for intensity normalization... bias field = 1.060 +- 0.076 6 of 4714 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (156, 75, 30) --> (237, 228, 247) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 2460 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (81, 72, 27) --> (161, 214, 246) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 2434 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (158, 193, 75) --> (215, 248, 146) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 79 of 99 (79.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (103, 192, 69) --> (157, 242, 145) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 78 of 88 (88.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (136, 170, 116) --> (178, 258, 159) Brain_Stem: limiting intensities to 88.0 --> 132.0 88 of 162 (54.3%) samples deleted using 5243 total control points for intensity normalization... bias field = 1.058 +- 0.067 9 of 4914 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 31 seconds. #-------------------------------------- #@# CA Reg Tue May 25 17:52:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_ca_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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) = 0.51 (predicted orig area = 15.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.928, neg=0, invalid=762 0001: dt=507.055452, rms=0.803 (13.434%), neg=0, invalid=762 0002: dt=327.259259, rms=0.781 (2.728%), neg=0, invalid=762 0003: dt=338.624339, rms=0.766 (1.901%), neg=0, invalid=762 0004: dt=140.985507, rms=0.761 (0.735%), neg=0, invalid=762 0005: dt=1479.680000, rms=0.744 (2.244%), neg=0, invalid=762 0006: dt=295.936000, rms=0.741 (0.403%), neg=0, invalid=762 0007: dt=443.904000, rms=0.738 (0.365%), neg=0, invalid=762 0008: dt=129.472000, rms=0.737 (0.111%), neg=0, invalid=762 0009: dt=129.472000, rms=0.737 (0.074%), neg=0, invalid=762 0010: dt=129.472000, rms=0.736 (0.112%), neg=0, invalid=762 0011: dt=129.472000, rms=0.735 (0.158%), neg=0, invalid=762 0012: dt=129.472000, rms=0.733 (0.197%), neg=0, invalid=762 0013: dt=129.472000, rms=0.731 (0.221%), neg=0, invalid=762 0014: dt=129.472000, rms=0.730 (0.221%), neg=0, invalid=762 0015: dt=129.472000, rms=0.728 (0.198%), neg=0, invalid=762 0016: dt=129.472000, rms=0.727 (0.173%), neg=0, invalid=762 0017: dt=129.472000, rms=0.726 (0.153%), neg=0, invalid=762 0018: dt=129.472000, rms=0.725 (0.142%), neg=0, invalid=762 0019: dt=129.472000, rms=0.724 (0.124%), neg=0, invalid=762 0020: dt=129.472000, rms=0.723 (0.102%), neg=0, invalid=762 0021: dt=1183.744000, rms=0.723 (0.105%), neg=0, invalid=762 0022: dt=443.904000, rms=0.721 (0.194%), neg=0, invalid=762 0023: dt=27.744000, rms=0.721 (0.001%), neg=0, invalid=762 0024: dt=27.744000, rms=0.721 (0.007%), neg=0, invalid=762 0025: dt=27.744000, rms=0.721 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.722, neg=0, invalid=762 0026: dt=129.472000, rms=0.720 (0.176%), neg=0, invalid=762 0027: dt=295.936000, rms=0.720 (0.073%), neg=0, invalid=762 0028: dt=295.936000, rms=0.719 (0.111%), neg=0, invalid=762 0029: dt=295.936000, rms=0.718 (0.098%), neg=0, invalid=762 0030: dt=295.936000, rms=0.718 (0.033%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=762 0031: dt=143.539936, rms=0.719 (0.934%), neg=0, invalid=762 0032: dt=383.877979, rms=0.701 (2.477%), neg=0, invalid=762 0033: dt=64.000000, rms=0.697 (0.557%), neg=0, invalid=762 0034: dt=124.416000, rms=0.696 (0.193%), neg=0, invalid=762 0035: dt=124.416000, rms=0.693 (0.452%), neg=0, invalid=762 0036: dt=124.416000, rms=0.688 (0.641%), neg=0, invalid=762 0037: dt=124.416000, rms=0.684 (0.673%), neg=0, invalid=762 0038: dt=124.416000, rms=0.679 (0.680%), neg=0, invalid=762 0039: dt=124.416000, rms=0.674 (0.781%), neg=0, invalid=762 0040: dt=124.416000, rms=0.670 (0.629%), neg=0, invalid=762 0041: dt=124.416000, rms=0.666 (0.534%), neg=0, invalid=762 0042: dt=124.416000, rms=0.663 (0.456%), neg=0, invalid=762 0043: dt=124.416000, rms=0.661 (0.293%), neg=0, invalid=762 0044: dt=124.416000, rms=0.659 (0.285%), neg=0, invalid=762 0045: dt=124.416000, rms=0.657 (0.378%), neg=0, invalid=762 0046: dt=124.416000, rms=0.656 (0.170%), neg=0, invalid=762 0047: dt=124.416000, rms=0.655 (0.138%), neg=0, invalid=762 0048: dt=124.416000, rms=0.654 (0.134%), neg=0, invalid=762 0049: dt=124.416000, rms=0.653 (0.173%), neg=0, invalid=762 0050: dt=124.416000, rms=0.651 (0.261%), neg=0, invalid=762 0051: dt=124.416000, rms=0.650 (0.128%), neg=0, invalid=762 0052: dt=124.416000, rms=0.650 (0.049%), neg=0, invalid=762 0053: dt=124.416000, rms=0.649 (0.140%), neg=0, invalid=762 0054: dt=124.416000, rms=0.648 (0.160%), neg=0, invalid=762 0055: dt=124.416000, rms=0.648 (0.057%), neg=0, invalid=762 0056: dt=124.416000, rms=0.647 (0.051%), neg=0, invalid=762 0057: dt=62.208000, rms=0.647 (0.049%), neg=0, invalid=762 0058: dt=62.208000, rms=0.647 (0.049%), neg=0, invalid=762 0059: dt=62.208000, rms=0.646 (0.040%), neg=0, invalid=762 0060: dt=62.208000, rms=0.646 (0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.647, neg=0, invalid=762 0061: dt=103.680000, rms=0.645 (0.354%), neg=0, invalid=762 0062: dt=9.072000, rms=0.644 (0.005%), neg=0, invalid=762 0063: dt=9.072000, rms=0.644 (0.003%), neg=0, invalid=762 0064: dt=9.072000, rms=0.644 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.690, neg=0, invalid=762 0065: dt=8.000000, rms=0.689 (0.192%), neg=0, invalid=762 0066: dt=2.800000, rms=0.689 (0.008%), neg=0, invalid=762 0067: dt=2.800000, rms=0.689 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.689, neg=0, invalid=762 0068: dt=2.800000, rms=0.689 (0.095%), neg=0, invalid=762 0069: dt=1.600000, rms=0.689 (0.009%), neg=0, invalid=762 0070: dt=1.600000, rms=0.689 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.797, neg=0, invalid=762 0071: dt=6.923513, rms=0.764 (4.138%), neg=0, invalid=762 0072: dt=8.428571, rms=0.758 (0.789%), neg=0, invalid=762 0073: dt=5.846154, rms=0.757 (0.097%), neg=0, invalid=762 0074: dt=5.846154, rms=0.756 (0.123%), neg=0, invalid=762 0075: dt=5.846154, rms=0.756 (0.037%), neg=0, invalid=762 0076: dt=5.846154, rms=0.756 (-0.204%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.756, neg=0, invalid=762 0077: dt=0.000000, rms=0.756 (0.062%), neg=0, invalid=762 0078: dt=0.000000, rms=0.756 (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=0.817, neg=0, invalid=762 0079: dt=0.000000, rms=0.816 (0.053%), neg=0, invalid=762 0080: dt=0.000000, rms=0.816 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.817, neg=0, invalid=762 0081: dt=0.000000, rms=0.816 (0.053%), neg=0, invalid=762 0082: dt=0.000000, rms=0.816 (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=0.713, neg=0, invalid=762 0083: dt=0.718599, rms=0.698 (2.083%), neg=0, invalid=762 0084: dt=0.064000, rms=0.698 (0.075%), neg=0, invalid=762 0085: dt=0.064000, rms=0.698 (-0.059%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.698, neg=0, invalid=762 0086: dt=0.016000, rms=0.697 (0.079%), neg=0, invalid=762 0087: dt=0.000438, rms=0.698 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11796 (30) Left_Lateral_Ventricle (4): linear fit = 1.59 x + 0.0 (6537 voxels, overlap=0.353) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (6537 voxels, peak = 32), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.11063 (30) Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (5072 voxels, overlap=0.124) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (5072 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09669 (101) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (2686 voxels, overlap=0.787) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (2686 voxels, peak = 102), gca=102.2 gca peak = 0.20183 (93) mri peak = 0.06268 (101) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (2309 voxels, overlap=0.441) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (2309 voxels, peak = 99), gca=99.0 gca peak = 0.21683 (55) mri peak = 0.07918 (73) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2887 voxels, overlap=0.021) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2887 voxels, peak = 70), gca=69.6 gca peak = 0.30730 (58) mri peak = 0.06882 (74) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (3060 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (3060 voxels, peak = 73), gca=73.4 gca peak = 0.11430 (101) mri peak = 0.09710 (99) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (207453 voxels, overlap=0.902) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (207453 voxels, peak = 101), gca=101.0 gca peak = 0.12076 (102) mri peak = 0.09372 (100) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (211933 voxels, overlap=0.878) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (211933 voxels, peak = 102), gca=102.0 gca peak = 0.14995 (59) mri peak = 0.03731 (74) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (99505 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (99505 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.03780 (72) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (99096 voxels, overlap=0.002) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (99096 voxels, peak = 73), gca=73.4 gca peak = 0.14161 (67) mri peak = 0.09534 (79) Right_Caudate (50): linear fit = 1.16 x + 0.0 (2455 voxels, overlap=0.049) Right_Caudate (50): linear fit = 1.16 x + 0.0 (2455 voxels, peak = 78), gca=78.1 gca peak = 0.15243 (71) mri peak = 0.11331 (81) Left_Caudate (11): linear fit = 1.09 x + 0.0 (2097 voxels, overlap=0.351) Left_Caudate (11): linear fit = 1.09 x + 0.0 (2097 voxels, peak = 77), gca=77.0 gca peak = 0.13336 (57) mri peak = 0.05054 (68) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (46598 voxels, overlap=0.033) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (46598 voxels, peak = 70), gca=70.4 gca peak = 0.13252 (56) mri peak = 0.05233 (65) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (54195 voxels, overlap=0.442) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (54195 voxels, peak = 66), gca=66.4 gca peak = 0.18181 (84) mri peak = 0.07507 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (19433 voxels, overlap=0.929) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (19433 voxels, peak = 84), gca=84.0 gca peak = 0.20573 (83) mri peak = 0.08344 (80) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (19643 voxels, overlap=0.971) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (19643 voxels, peak = 81), gca=80.9 gca peak = 0.21969 (57) mri peak = 0.08207 (73) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (1396 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (1396 voxels, peak = 70), gca=69.8 gca peak = 0.39313 (56) mri peak = 0.08563 (73) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1704 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (1704 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.05836 (97) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (12736 voxels, overlap=0.628) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (12736 voxels, peak = 92), gca=92.2 gca peak = 0.11978 (83) mri peak = 0.06528 (92) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (10610 voxels, overlap=0.249) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (10610 voxels, peak = 93), gca=93.4 gca peak = 0.13399 (79) mri peak = 0.05935 (88) Left_Putamen (12): linear fit = 1.11 x + 0.0 (6559 voxels, overlap=0.504) Left_Putamen (12): linear fit = 1.11 x + 0.0 (6559 voxels, peak = 87), gca=87.3 gca peak = 0.14159 (79) mri peak = 0.06641 (88) Right_Putamen (51): linear fit = 1.14 x + 0.0 (6902 voxels, overlap=0.566) Right_Putamen (51): linear fit = 1.14 x + 0.0 (6902 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.08463 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24301 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (24301 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06981 (95) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (3557 voxels, overlap=0.433) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (3557 voxels, peak = 96), gca=95.9 gca peak = 0.12801 (89) mri peak = 0.06874 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (3453 voxels, overlap=0.540) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (3453 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.12119 (32) Third_Ventricle (14): linear fit = 1.28 x + 0.0 (158 voxels, overlap=0.622) Third_Ventricle (14): linear fit = 1.28 x + 0.0 (158 voxels, peak = 30), gca=29.6 gca peak = 0.15061 (21) mri peak = 0.13597 (27) Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (1950 voxels, overlap=0.480) Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (1950 voxels, peak = 27), gca=26.6 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 1.28 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.39 x + 0.0 Left_Pallidum too bright - rescaling by 0.994 (from 1.065) to 98.5 (was 99.0) Right_Pallidum too bright - rescaling by 0.963 (from 1.065) to 98.5 (was 102.2) 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=0.682, neg=0, invalid=762 0088: dt=152.577947, rms=0.657 (3.672%), neg=0, invalid=762 0089: dt=369.920000, rms=0.649 (1.262%), neg=0, invalid=762 0090: dt=369.920000, rms=0.645 (0.511%), neg=0, invalid=762 0091: dt=129.472000, rms=0.643 (0.383%), neg=0, invalid=762 0092: dt=517.888000, rms=0.641 (0.376%), neg=0, invalid=762 0093: dt=129.472000, rms=0.640 (0.112%), neg=0, invalid=762 0094: dt=1183.744000, rms=0.638 (0.364%), neg=0, invalid=762 0095: dt=129.472000, rms=0.636 (0.193%), neg=0, invalid=762 0096: dt=295.936000, rms=0.636 (0.056%), neg=0, invalid=762 0097: dt=129.472000, rms=0.636 (0.053%), neg=0, invalid=762 0098: dt=2071.552000, rms=0.634 (0.264%), neg=0, invalid=762 0099: dt=129.472000, rms=0.633 (0.209%), neg=0, invalid=762 0100: dt=369.920000, rms=0.632 (0.068%), neg=0, invalid=762 0101: dt=129.472000, rms=0.632 (0.038%), neg=0, invalid=762 0102: dt=129.472000, rms=0.632 (0.022%), neg=0, invalid=762 0103: dt=129.472000, rms=0.632 (0.037%), neg=0, invalid=762 0104: dt=129.472000, rms=0.631 (0.055%), neg=0, invalid=762 0105: dt=129.472000, rms=0.631 (0.070%), neg=0, invalid=762 0106: dt=129.472000, rms=0.630 (0.073%), neg=0, invalid=762 0107: dt=129.472000, rms=0.630 (0.082%), neg=0, invalid=762 0108: dt=129.472000, rms=0.629 (0.090%), neg=0, invalid=762 0109: dt=129.472000, rms=0.629 (0.094%), neg=0, invalid=762 0110: dt=129.472000, rms=0.628 (0.101%), neg=0, invalid=762 0111: dt=129.472000, rms=0.627 (0.104%), neg=0, invalid=762 0112: dt=129.472000, rms=0.627 (0.099%), neg=0, invalid=762 0113: dt=129.472000, rms=0.626 (0.096%), neg=0, invalid=762 0114: dt=129.472000, rms=0.626 (0.083%), neg=0, invalid=762 0115: dt=129.472000, rms=0.625 (0.079%), neg=0, invalid=762 0116: dt=129.472000, rms=0.625 (0.086%), neg=0, invalid=762 0117: dt=129.472000, rms=0.624 (0.095%), neg=0, invalid=762 0118: dt=129.472000, rms=0.623 (0.088%), neg=0, invalid=762 0119: dt=129.472000, rms=0.623 (0.079%), neg=0, invalid=762 0120: dt=129.472000, rms=0.623 (0.070%), neg=0, invalid=762 0121: dt=129.472000, rms=0.622 (0.062%), neg=0, invalid=762 0122: dt=129.472000, rms=0.622 (0.070%), neg=0, invalid=762 0123: dt=129.472000, rms=0.621 (0.071%), neg=0, invalid=762 0124: dt=129.472000, rms=0.621 (0.072%), neg=0, invalid=762 0125: dt=129.472000, rms=0.620 (0.076%), neg=0, invalid=762 0126: dt=129.472000, rms=0.620 (0.057%), neg=0, invalid=762 0127: dt=129.472000, rms=0.620 (0.053%), neg=0, invalid=762 0128: dt=129.472000, rms=0.619 (0.058%), neg=0, invalid=762 0129: dt=129.472000, rms=0.619 (0.052%), neg=0, invalid=762 0130: dt=129.472000, rms=0.619 (0.070%), neg=0, invalid=762 0131: dt=129.472000, rms=0.618 (0.062%), neg=0, invalid=762 0132: dt=129.472000, rms=0.618 (0.058%), neg=0, invalid=762 0133: dt=129.472000, rms=0.618 (0.048%), neg=0, invalid=762 0134: dt=129.472000, rms=0.617 (0.040%), neg=0, invalid=762 0135: dt=129.472000, rms=0.617 (0.037%), neg=0, invalid=762 0136: dt=129.472000, rms=0.617 (0.043%), neg=0, invalid=762 0137: dt=129.472000, rms=0.616 (0.051%), neg=0, invalid=762 0138: dt=129.472000, rms=0.616 (0.048%), neg=0, invalid=762 0139: dt=129.472000, rms=0.616 (0.046%), neg=0, invalid=762 0140: dt=129.472000, rms=0.616 (0.038%), neg=0, invalid=762 0141: dt=129.472000, rms=0.615 (0.035%), neg=0, invalid=762 0142: dt=129.472000, rms=0.615 (0.034%), neg=0, invalid=762 0143: dt=129.472000, rms=0.615 (0.037%), neg=0, invalid=762 0144: dt=129.472000, rms=0.615 (0.035%), neg=0, invalid=762 0145: dt=129.472000, rms=0.615 (0.037%), neg=0, invalid=762 0146: dt=129.472000, rms=0.614 (0.034%), neg=0, invalid=762 0147: dt=129.472000, rms=0.614 (0.031%), neg=0, invalid=762 0148: dt=129.472000, rms=0.614 (0.031%), neg=0, invalid=762 0149: dt=129.472000, rms=0.614 (0.027%), neg=0, invalid=762 0150: dt=129.472000, rms=0.614 (0.024%), neg=0, invalid=762 0151: dt=129.472000, rms=0.614 (0.023%), neg=0, invalid=762 0152: dt=517.888000, rms=0.613 (0.022%), neg=0, invalid=762 0153: dt=517.888000, rms=0.613 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=762 0154: dt=443.904000, rms=0.613 (0.151%), neg=0, invalid=762 0155: dt=295.936000, rms=0.612 (0.065%), neg=0, invalid=762 0156: dt=129.472000, rms=0.612 (0.007%), neg=0, invalid=762 0157: dt=129.472000, rms=0.612 (0.012%), neg=0, invalid=762 0158: dt=129.472000, rms=0.612 (0.018%), neg=0, invalid=762 0159: dt=129.472000, rms=0.612 (0.030%), neg=0, invalid=762 0160: dt=129.472000, rms=0.612 (0.029%), neg=0, invalid=762 0161: dt=129.472000, rms=0.611 (0.030%), neg=0, invalid=762 0162: dt=129.472000, rms=0.611 (0.026%), neg=0, invalid=762 0163: dt=129.472000, rms=0.611 (0.024%), neg=0, invalid=762 0164: dt=129.472000, rms=0.611 (0.020%), neg=0, invalid=762 0165: dt=2071.552000, rms=0.611 (0.076%), neg=0, invalid=762 0166: dt=73.984000, rms=0.610 (0.007%), neg=0, invalid=762 0167: dt=73.984000, rms=0.610 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.612, neg=0, invalid=762 0168: dt=145.152000, rms=0.608 (0.576%), neg=0, invalid=762 0169: dt=414.720000, rms=0.600 (1.345%), neg=0, invalid=762 0170: dt=66.308802, rms=0.597 (0.510%), neg=0, invalid=762 0171: dt=248.832000, rms=0.595 (0.331%), neg=0, invalid=762 0172: dt=91.151515, rms=0.593 (0.354%), neg=0, invalid=762 0173: dt=103.680000, rms=0.592 (0.197%), neg=0, invalid=762 0174: dt=92.342857, rms=0.591 (0.177%), neg=0, invalid=762 0175: dt=103.680000, rms=0.590 (0.154%), neg=0, invalid=762 0176: dt=103.680000, rms=0.589 (0.170%), neg=0, invalid=762 0177: dt=82.944000, rms=0.588 (0.129%), neg=0, invalid=762 0178: dt=103.680000, rms=0.587 (0.144%), neg=0, invalid=762 0179: dt=82.944000, rms=0.587 (0.115%), neg=0, invalid=762 0180: dt=124.416000, rms=0.586 (0.148%), neg=0, invalid=762 0181: dt=62.208000, rms=0.585 (0.101%), neg=0, invalid=762 0182: dt=248.832000, rms=0.584 (0.207%), neg=0, invalid=762 0183: dt=36.288000, rms=0.583 (0.118%), neg=0, invalid=762 0184: dt=331.776000, rms=0.582 (0.163%), neg=0, invalid=762 0185: dt=36.288000, rms=0.581 (0.175%), neg=0, invalid=762 0186: dt=145.152000, rms=0.581 (0.101%), neg=0, invalid=762 0187: dt=36.288000, rms=0.580 (0.066%), neg=0, invalid=762 0188: dt=414.720000, rms=0.579 (0.184%), neg=0, invalid=762 0189: dt=36.288000, rms=0.578 (0.155%), neg=0, invalid=762 0190: dt=145.152000, rms=0.578 (0.089%), neg=0, invalid=762 0191: dt=36.288000, rms=0.578 (0.053%), neg=0, invalid=762 0192: dt=414.720000, rms=0.577 (0.138%), neg=0, invalid=762 0193: dt=36.288000, rms=0.576 (0.137%), neg=0, invalid=762 0194: dt=124.416000, rms=0.576 (0.066%), neg=0, invalid=762 0195: dt=82.944000, rms=0.575 (0.052%), neg=0, invalid=762 0196: dt=103.680000, rms=0.575 (0.069%), neg=0, invalid=762 0197: dt=36.288000, rms=0.575 (0.031%), neg=0, invalid=762 0198: dt=36.288000, rms=0.575 (0.018%), neg=0, invalid=762 0199: dt=36.288000, rms=0.574 (0.035%), neg=0, invalid=762 0200: dt=36.288000, rms=0.574 (0.050%), neg=0, invalid=762 0201: dt=36.288000, rms=0.574 (0.068%), neg=0, invalid=762 0202: dt=36.288000, rms=0.573 (0.077%), neg=0, invalid=762 0203: dt=36.288000, rms=0.573 (0.090%), neg=0, invalid=762 0204: dt=36.288000, rms=0.572 (0.087%), neg=0, invalid=762 0205: dt=36.288000, rms=0.572 (0.096%), neg=0, invalid=762 0206: dt=36.288000, rms=0.571 (0.099%), neg=0, invalid=762 0207: dt=36.288000, rms=0.571 (0.102%), neg=0, invalid=762 0208: dt=36.288000, rms=0.570 (0.100%), neg=0, invalid=762 0209: dt=36.288000, rms=0.570 (0.095%), neg=0, invalid=762 0210: dt=36.288000, rms=0.569 (0.089%), neg=0, invalid=762 0211: dt=36.288000, rms=0.569 (0.086%), neg=0, invalid=762 0212: dt=36.288000, rms=0.568 (0.089%), neg=0, invalid=762 0213: dt=36.288000, rms=0.568 (0.085%), neg=0, invalid=762 0214: dt=36.288000, rms=0.567 (0.084%), neg=0, invalid=762 0215: dt=36.288000, rms=0.567 (0.086%), neg=0, invalid=762 0216: dt=36.288000, rms=0.566 (0.083%), neg=0, invalid=762 0217: dt=36.288000, rms=0.566 (0.078%), neg=0, invalid=762 0218: dt=36.288000, rms=0.565 (0.078%), neg=0, invalid=762 0219: dt=36.288000, rms=0.565 (0.074%), neg=0, invalid=762 0220: dt=36.288000, rms=0.564 (0.068%), neg=0, invalid=762 0221: dt=36.288000, rms=0.564 (0.064%), neg=0, invalid=762 0222: dt=36.288000, rms=0.564 (0.062%), neg=0, invalid=762 0223: dt=36.288000, rms=0.563 (0.064%), neg=0, invalid=762 0224: dt=36.288000, rms=0.563 (0.060%), neg=0, invalid=762 0225: dt=36.288000, rms=0.563 (0.059%), neg=0, invalid=762 0226: dt=36.288000, rms=0.562 (0.062%), neg=0, invalid=762 0227: dt=36.288000, rms=0.562 (0.061%), neg=0, invalid=762 0228: dt=36.288000, rms=0.562 (0.051%), neg=0, invalid=762 0229: dt=36.288000, rms=0.561 (0.056%), neg=0, invalid=762 0230: dt=36.288000, rms=0.561 (0.060%), neg=0, invalid=762 0231: dt=36.288000, rms=0.561 (0.059%), neg=0, invalid=762 0232: dt=36.288000, rms=0.560 (0.049%), neg=0, invalid=762 0233: dt=36.288000, rms=0.560 (0.050%), neg=0, invalid=762 0234: dt=36.288000, rms=0.560 (0.048%), neg=0, invalid=762 0235: dt=36.288000, rms=0.560 (0.038%), neg=0, invalid=762 0236: dt=36.288000, rms=0.559 (0.036%), neg=0, invalid=762 0237: dt=36.288000, rms=0.559 (0.044%), neg=0, invalid=762 0238: dt=36.288000, rms=0.559 (0.047%), neg=0, invalid=762 0239: dt=36.288000, rms=0.559 (0.048%), neg=0, invalid=762 0240: dt=36.288000, rms=0.558 (0.045%), neg=0, invalid=762 0241: dt=36.288000, rms=0.558 (0.042%), neg=0, invalid=762 0242: dt=36.288000, rms=0.558 (0.033%), neg=0, invalid=762 0243: dt=36.288000, rms=0.558 (0.035%), neg=0, invalid=762 0244: dt=36.288000, rms=0.558 (0.032%), neg=0, invalid=762 0245: dt=36.288000, rms=0.557 (0.037%), neg=0, invalid=762 0246: dt=36.288000, rms=0.557 (0.043%), neg=0, invalid=762 0247: dt=36.288000, rms=0.557 (0.033%), neg=0, invalid=762 0248: dt=36.288000, rms=0.557 (0.035%), neg=0, invalid=762 0249: dt=36.288000, rms=0.557 (0.030%), neg=0, invalid=762 0250: dt=36.288000, rms=0.556 (0.027%), neg=0, invalid=762 0251: dt=36.288000, rms=0.556 (0.028%), neg=0, invalid=762 0252: dt=36.288000, rms=0.556 (0.031%), neg=0, invalid=762 0253: dt=36.288000, rms=0.556 (0.032%), neg=0, invalid=762 0254: dt=36.288000, rms=0.556 (0.030%), neg=0, invalid=762 0255: dt=36.288000, rms=0.556 (0.026%), neg=0, invalid=762 0256: dt=36.288000, rms=0.556 (0.029%), neg=0, invalid=762 0257: dt=36.288000, rms=0.555 (0.029%), neg=0, invalid=762 0258: dt=36.288000, rms=0.555 (0.028%), neg=0, invalid=762 0259: dt=36.288000, rms=0.555 (0.027%), neg=0, invalid=762 0260: dt=36.288000, rms=0.555 (0.031%), neg=0, invalid=762 0261: dt=36.288000, rms=0.555 (0.024%), neg=0, invalid=762 0262: dt=36.288000, rms=0.555 (0.029%), neg=0, invalid=762 0263: dt=36.288000, rms=0.554 (0.027%), neg=0, invalid=762 0264: dt=36.288000, rms=0.554 (0.024%), neg=0, invalid=762 0265: dt=36.288000, rms=0.554 (0.024%), neg=0, invalid=762 0266: dt=103.680000, rms=0.554 (0.004%), neg=0, invalid=762 0267: dt=103.680000, rms=0.554 (0.005%), neg=0, invalid=762 0268: dt=103.680000, rms=0.554 (0.017%), neg=0, invalid=762 0269: dt=103.680000, rms=0.554 (0.015%), neg=0, invalid=762 0270: dt=103.680000, rms=0.554 (0.019%), neg=0, invalid=762 0271: dt=103.680000, rms=0.554 (0.023%), neg=0, invalid=762 0272: dt=103.680000, rms=0.554 (0.029%), neg=0, invalid=762 0273: dt=103.680000, rms=0.553 (0.029%), neg=0, invalid=762 0274: dt=103.680000, rms=0.553 (0.034%), neg=0, invalid=762 0275: dt=103.680000, rms=0.553 (0.009%), neg=0, invalid=762 0276: dt=103.680000, rms=0.553 (0.015%), neg=0, invalid=762 0277: dt=103.680000, rms=0.553 (0.011%), neg=0, invalid=762 0278: dt=82.944000, rms=0.553 (0.007%), neg=0, invalid=762 0279: dt=82.944000, rms=0.553 (0.007%), neg=0, invalid=762 0280: dt=82.944000, rms=0.553 (0.002%), neg=0, invalid=762 0281: dt=2.592000, rms=0.553 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0282: dt=145.152000, rms=0.551 (0.324%), neg=0, invalid=762 0283: dt=36.288000, rms=0.551 (0.036%), neg=0, invalid=762 0284: dt=36.288000, rms=0.551 (0.021%), neg=0, invalid=762 0285: dt=36.288000, rms=0.551 (0.038%), neg=0, invalid=762 0286: dt=36.288000, rms=0.551 (0.043%), neg=0, invalid=762 0287: dt=36.288000, rms=0.550 (0.057%), neg=0, invalid=762 0288: dt=36.288000, rms=0.550 (0.054%), neg=0, invalid=762 0289: dt=36.288000, rms=0.550 (0.045%), neg=0, invalid=762 0290: dt=36.288000, rms=0.550 (0.040%), neg=0, invalid=762 0291: dt=36.288000, rms=0.549 (0.038%), neg=0, invalid=762 0292: dt=36.288000, rms=0.549 (0.036%), neg=0, invalid=762 0293: dt=36.288000, rms=0.549 (0.030%), neg=0, invalid=762 0294: dt=36.288000, rms=0.549 (0.029%), neg=0, invalid=762 0295: dt=36.288000, rms=0.549 (0.028%), neg=0, invalid=762 0296: dt=36.288000, rms=0.549 (0.024%), neg=0, invalid=762 0297: dt=36.288000, rms=0.548 (0.025%), neg=0, invalid=762 0298: dt=36.288000, rms=0.548 (0.021%), neg=0, invalid=762 0299: dt=36.288000, rms=0.548 (0.018%), neg=0, invalid=762 0300: dt=124.416000, rms=0.548 (0.020%), neg=0, invalid=762 0301: dt=82.944000, rms=0.548 (0.022%), neg=0, invalid=762 0302: dt=248.832000, rms=0.548 (0.030%), neg=0, invalid=762 0303: dt=36.288000, rms=0.548 (0.011%), neg=0, invalid=762 0304: dt=36.288000, rms=0.548 (0.009%), neg=0, invalid=762 0305: dt=36.288000, rms=0.548 (0.006%), neg=0, invalid=762 0306: dt=36.288000, rms=0.548 (0.012%), neg=0, invalid=762 0307: dt=36.288000, rms=0.547 (0.018%), neg=0, invalid=762 0308: dt=36.288000, rms=0.547 (0.020%), neg=0, invalid=762 0309: dt=36.288000, rms=0.547 (0.021%), neg=0, invalid=762 0310: dt=36.288000, rms=0.547 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 0311: dt=25.600000, rms=0.557 (0.168%), neg=0, invalid=762 0312: dt=81.142857, rms=0.554 (0.412%), neg=0, invalid=762 0313: dt=84.945455, rms=0.552 (0.388%), neg=0, invalid=762 0314: dt=31.713262, rms=0.549 (0.628%), neg=0, invalid=762 0315: dt=19.200000, rms=0.548 (0.087%), neg=0, invalid=762 0316: dt=409.600000, rms=0.542 (1.112%), neg=0, invalid=762 0317: dt=37.021898, rms=0.540 (0.502%), neg=0, invalid=762 0318: dt=32.000000, rms=0.538 (0.257%), neg=0, invalid=762 0319: dt=32.000000, rms=0.538 (0.098%), neg=0, invalid=762 0320: dt=44.800000, rms=0.537 (0.147%), neg=0, invalid=762 0321: dt=25.600000, rms=0.537 (0.058%), neg=0, invalid=762 0322: dt=102.400000, rms=0.536 (0.164%), neg=0, invalid=762 0323: dt=11.200000, rms=0.535 (0.079%), neg=0, invalid=762 0324: dt=32.000000, rms=0.535 (0.046%), neg=0, invalid=762 0325: dt=32.000000, rms=0.535 (0.070%), neg=0, invalid=762 0326: dt=32.000000, rms=0.534 (0.100%), neg=0, invalid=762 0327: dt=32.000000, rms=0.533 (0.131%), neg=0, invalid=762 0328: dt=32.000000, rms=0.533 (0.146%), neg=0, invalid=762 0329: dt=32.000000, rms=0.532 (0.197%), neg=0, invalid=762 0330: dt=32.000000, rms=0.531 (0.177%), neg=0, invalid=762 0331: dt=32.000000, rms=0.530 (0.192%), neg=0, invalid=762 0332: dt=32.000000, rms=0.529 (0.179%), neg=0, invalid=762 0333: dt=32.000000, rms=0.528 (0.188%), neg=0, invalid=762 0334: dt=32.000000, rms=0.527 (0.171%), neg=0, invalid=762 0335: dt=32.000000, rms=0.526 (0.144%), neg=0, invalid=762 0336: dt=32.000000, rms=0.525 (0.119%), neg=0, invalid=762 0337: dt=32.000000, rms=0.525 (0.123%), neg=0, invalid=762 0338: dt=32.000000, rms=0.524 (0.135%), neg=0, invalid=762 0339: dt=32.000000, rms=0.523 (0.108%), neg=0, invalid=762 0340: dt=32.000000, rms=0.523 (0.084%), neg=0, invalid=762 0341: dt=32.000000, rms=0.523 (0.084%), neg=0, invalid=762 0342: dt=32.000000, rms=0.522 (0.089%), neg=0, invalid=762 0343: dt=32.000000, rms=0.522 (0.076%), neg=0, invalid=762 0344: dt=32.000000, rms=0.521 (0.052%), neg=0, invalid=762 0345: dt=32.000000, rms=0.521 (0.053%), neg=0, invalid=762 0346: dt=32.000000, rms=0.521 (0.054%), neg=0, invalid=762 0347: dt=32.000000, rms=0.521 (0.064%), neg=0, invalid=762 0348: dt=32.000000, rms=0.520 (0.050%), neg=0, invalid=762 0349: dt=32.000000, rms=0.520 (0.020%), neg=0, invalid=762 0350: dt=32.000000, rms=0.520 (0.051%), neg=0, invalid=762 0351: dt=32.000000, rms=0.520 (0.042%), neg=0, invalid=762 0352: dt=32.000000, rms=0.520 (0.021%), neg=0, invalid=762 0353: dt=32.000000, rms=0.519 (0.045%), neg=0, invalid=762 0354: dt=32.000000, rms=0.519 (0.054%), neg=0, invalid=762 0355: dt=32.000000, rms=0.519 (0.016%), neg=0, invalid=762 0356: dt=32.000000, rms=0.519 (0.032%), neg=0, invalid=762 0357: dt=32.000000, rms=0.519 (0.023%), neg=0, invalid=762 0358: dt=32.000000, rms=0.519 (0.017%), neg=0, invalid=762 0359: dt=38.400000, rms=0.518 (0.061%), neg=0, invalid=762 0360: dt=11.200000, rms=0.518 (-0.003%), neg=0, invalid=762 0361: dt=11.200000, rms=0.518 (0.004%), neg=0, invalid=762 0362: dt=11.200000, rms=0.518 (0.003%), neg=0, invalid=762 0363: dt=11.200000, rms=0.518 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=762 0364: dt=44.800000, rms=0.516 (0.409%), neg=0, invalid=762 0365: dt=19.200000, rms=0.516 (0.021%), neg=0, invalid=762 0366: dt=19.200000, rms=0.516 (0.025%), neg=0, invalid=762 0367: dt=19.200000, rms=0.516 (0.033%), neg=0, invalid=762 0368: dt=19.200000, rms=0.516 (0.019%), neg=0, invalid=762 0369: dt=19.200000, rms=0.516 (-0.008%), neg=0, invalid=762 0370: dt=44.800000, rms=0.516 (0.018%), neg=0, invalid=762 0371: dt=25.600000, rms=0.516 (0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.541, neg=0, invalid=762 0372: dt=0.000000, rms=0.540 (0.044%), neg=0, invalid=762 0373: dt=0.000000, rms=0.540 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=762 0374: dt=0.000000, rms=0.540 (0.044%), neg=0, invalid=762 0375: dt=0.000000, rms=0.540 (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=0.590, neg=0, invalid=762 0376: dt=2.219828, rms=0.580 (1.684%), neg=0, invalid=762 0377: dt=1.024000, rms=0.579 (0.141%), neg=0, invalid=762 0378: dt=0.448000, rms=0.579 (0.011%), neg=0, invalid=762 0379: dt=0.448000, rms=0.579 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0380: dt=1.280000, rms=0.578 (0.168%), neg=0, invalid=762 0381: dt=0.448000, rms=0.578 (0.022%), neg=0, invalid=762 0382: dt=0.448000, rms=0.578 (0.003%), neg=0, invalid=762 0383: dt=0.448000, rms=0.578 (-0.019%), 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=0.543, neg=0, invalid=762 0384: dt=1.280000, rms=0.506 (6.745%), neg=0, invalid=762 0385: dt=0.000000, rms=0.506 (0.008%), neg=0, invalid=762 0386: dt=0.050000, rms=0.506 (-0.209%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=762 0387: dt=0.000000, rms=0.506 (0.064%), neg=0, invalid=762 0388: dt=0.000000, rms=0.506 (0.000%), neg=0, invalid=762 0389: dt=0.050000, rms=0.506 (-0.140%), 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 0390: dt=23.120000, rms=0.498 (0.070%), neg=0, invalid=762 0391: dt=8.092000, rms=0.498 (0.002%), neg=0, invalid=762 0392: dt=8.092000, rms=0.498 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0393: dt=295.936000, rms=0.498 (0.165%), neg=0, invalid=762 0394: dt=129.472000, rms=0.497 (0.032%), neg=0, invalid=762 0395: dt=129.472000, rms=0.497 (0.020%), neg=0, invalid=762 0396: dt=129.472000, rms=0.497 (0.028%), neg=0, invalid=762 0397: dt=129.472000, rms=0.497 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0398: dt=129.472000, rms=0.497 (0.027%), neg=0, invalid=762 0399: dt=129.472000, rms=0.497 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 0400: dt=77.913043, rms=0.496 (0.259%), neg=0, invalid=762 0401: dt=145.152000, rms=0.495 (0.268%), neg=0, invalid=762 0402: dt=36.288000, rms=0.494 (0.081%), neg=0, invalid=762 0403: dt=36.288000, rms=0.494 (0.059%), neg=0, invalid=762 0404: dt=36.288000, rms=0.493 (0.082%), neg=0, invalid=762 0405: dt=36.288000, rms=0.493 (0.094%), neg=0, invalid=762 0406: dt=36.288000, rms=0.493 (0.089%), neg=0, invalid=762 0407: dt=36.288000, rms=0.492 (0.070%), neg=0, invalid=762 0408: dt=145.152000, rms=0.492 (0.063%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=762 0409: dt=103.680000, rms=0.490 (0.414%), neg=0, invalid=762 0410: dt=36.288000, rms=0.490 (0.119%), neg=0, invalid=762 0411: dt=36.288000, rms=0.489 (0.055%), neg=0, invalid=762 0412: dt=36.288000, rms=0.489 (0.065%), neg=0, invalid=762 0413: dt=36.288000, rms=0.489 (0.100%), neg=0, invalid=762 0414: dt=36.288000, rms=0.488 (0.099%), neg=0, invalid=762 0415: dt=36.288000, rms=0.488 (0.079%), neg=0, invalid=762 0416: dt=36.288000, rms=0.488 (0.014%), 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 = 5 after 0 iterations, nbhd size=0, neg = 0 0417: dt=61.572414, rms=0.485 (0.822%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0418: dt=69.041096, rms=0.480 (0.918%), neg=0, invalid=762 0419: dt=11.200000, rms=0.479 (0.262%), neg=0, invalid=762 0420: dt=19.200000, rms=0.478 (0.111%), neg=0, invalid=762 0421: dt=19.200000, rms=0.478 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0422: dt=19.200000, rms=0.477 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0423: dt=19.200000, rms=0.476 (0.231%), neg=0, invalid=762 0424: dt=19.200000, rms=0.475 (0.272%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0425: dt=19.200000, rms=0.473 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0426: dt=19.200000, rms=0.472 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0427: dt=19.200000, rms=0.471 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0428: dt=19.200000, rms=0.470 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0429: dt=19.200000, rms=0.470 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0430: dt=19.200000, rms=0.469 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0431: dt=19.200000, rms=0.468 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0432: dt=19.200000, rms=0.468 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0433: dt=19.200000, rms=0.467 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0434: dt=19.200000, rms=0.467 (0.107%), neg=0, invalid=762 0435: dt=38.400000, rms=0.467 (0.028%), neg=0, invalid=762 0436: dt=38.400000, rms=0.466 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0437: dt=38.400000, rms=0.466 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0438: dt=38.400000, rms=0.466 (0.003%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0439: dt=38.400000, rms=0.466 (0.020%), neg=0, invalid=762 0440: dt=38.400000, rms=0.466 (0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0441: dt=62.730159, rms=0.463 (0.759%), neg=0, invalid=762 0442: dt=19.200000, rms=0.462 (0.152%), neg=0, invalid=762 0443: dt=19.200000, rms=0.462 (0.079%), neg=0, invalid=762 0444: dt=19.200000, rms=0.462 (0.062%), neg=0, invalid=762 0445: dt=19.200000, rms=0.461 (0.074%), neg=0, invalid=762 0446: dt=19.200000, rms=0.461 (0.080%), neg=0, invalid=762 0447: dt=19.200000, rms=0.461 (0.057%), neg=0, invalid=762 0448: dt=25.600000, rms=0.460 (0.041%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0449: dt=0.000000, rms=0.468 (0.064%), neg=0, invalid=762 0450: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0451: dt=2.304000, rms=0.468 (0.093%), neg=0, invalid=762 0452: dt=1.008000, rms=0.468 (0.006%), neg=0, invalid=762 0453: dt=1.008000, rms=0.468 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0454: dt=0.384000, rms=0.483 (0.085%), neg=0, invalid=762 0455: dt=0.064000, rms=0.483 (0.003%), neg=0, invalid=762 0456: dt=0.064000, rms=0.483 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0457: dt=0.448000, rms=0.483 (0.122%), neg=0, invalid=762 0458: dt=0.384000, rms=0.482 (0.018%), neg=0, invalid=762 0459: dt=0.384000, rms=0.482 (-0.009%), 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=0.464, neg=0, invalid=762 iter 0, gcam->neg = 478 after 13 iterations, nbhd size=1, neg = 0 0460: dt=2.296615, rms=0.435 (6.248%), neg=0, invalid=762 0461: dt=0.112000, rms=0.434 (0.131%), neg=0, invalid=762 0462: dt=0.112000, rms=0.434 (-0.078%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0463: dt=0.064000, rms=0.434 (0.116%), neg=0, invalid=762 0464: dt=0.001500, rms=0.434 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0465: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0466: dt=18.496000, rms=0.418 (0.000%), neg=0, invalid=762 0467: dt=1.734000, rms=0.418 (0.000%), neg=0, invalid=762 0468: dt=1.734000, rms=0.418 (-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=0.418, neg=0, invalid=762 0469: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0470: dt=36.288000, rms=0.418 (0.014%), neg=0, invalid=762 0471: dt=36.288000, rms=0.418 (0.007%), neg=0, invalid=762 0472: dt=36.288000, rms=0.418 (0.006%), neg=0, invalid=762 0473: dt=36.288000, rms=0.418 (0.005%), neg=0, invalid=762 0474: dt=36.288000, rms=0.418 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0475: dt=11.200000, rms=0.418 (0.062%), neg=0, invalid=762 0476: dt=9.600000, rms=0.418 (0.015%), neg=0, invalid=762 0477: dt=9.600000, rms=0.418 (0.001%), neg=0, invalid=762 0478: dt=9.600000, rms=0.418 (-0.040%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0479: dt=44.800000, rms=0.417 (0.366%), neg=0, invalid=762 0480: dt=32.000000, rms=0.416 (0.131%), neg=0, invalid=762 0481: dt=32.000000, rms=0.416 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0482: dt=32.000000, rms=0.415 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0483: dt=32.000000, rms=0.415 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0484: dt=32.000000, rms=0.414 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0485: dt=32.000000, rms=0.413 (0.124%), neg=0, invalid=762 0486: dt=32.000000, rms=0.413 (0.093%), neg=0, invalid=762 0487: dt=32.000000, rms=0.413 (0.037%), neg=0, invalid=762 0488: dt=32.000000, rms=0.413 (0.026%), neg=0, invalid=762 0489: dt=32.000000, rms=0.413 (0.034%), neg=0, invalid=762 0490: dt=32.000000, rms=0.413 (0.042%), neg=0, invalid=762 0491: dt=32.000000, rms=0.412 (0.041%), neg=0, invalid=762 0492: dt=32.000000, rms=0.412 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=32.000000, rms=0.412 (0.037%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0494: dt=0.864000, rms=0.416 (0.002%), neg=0, invalid=762 0495: dt=0.054000, rms=0.416 (0.000%), neg=0, invalid=762 0496: dt=0.054000, rms=0.416 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0497: dt=4.032000, rms=0.416 (0.038%), neg=0, invalid=762 0498: dt=6.918919, rms=0.416 (0.030%), neg=0, invalid=762 0499: dt=6.918919, rms=0.415 (0.023%), neg=0, invalid=762 0500: dt=6.918919, rms=0.415 (0.011%), neg=0, invalid=762 0501: dt=6.918919, rms=0.415 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0502: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0503: dt=0.000000, rms=0.422 (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=0.411, neg=0, invalid=762 iter 0, gcam->neg = 308 after 13 iterations, nbhd size=1, neg = 0 0504: dt=1.536000, rms=0.401 (2.539%), neg=0, invalid=762 0505: dt=0.016000, rms=0.401 (0.002%), neg=0, invalid=762 0506: dt=0.016000, rms=0.401 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0507: dt=0.096000, rms=0.400 (0.052%), neg=0, invalid=762 0508: dt=0.028000, rms=0.400 (0.004%), neg=0, invalid=762 0509: dt=0.028000, rms=0.400 (-0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 41 minutes and 12 seconds. mri_ca_register utimesec 7265.373188 mri_ca_register stimesec 26.572543 mri_ca_register ru_maxrss 1630172 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 27137392 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63048 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 18352 mri_ca_register ru_nivcsw 7103 FSRUNTIME@ mri_ca_register 1.6868 hours 8 threads #-------------------------------------- #@# SubCort Seg Tue May 25 19:33:29 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 blg8112.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-02/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 15.79 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.11241 (28) Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (9682 voxels, overlap=0.219) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (9682 voxels, peak = 31), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.10948 (30) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (7050 voxels, overlap=0.147) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (7050 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.10995 (101) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (2145 voxels, overlap=0.558) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (2145 voxels, peak = 100), gca=100.2 gca peak = 0.16930 (96) mri peak = 0.09784 (103) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (2082 voxels, overlap=0.508) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (2082 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.07657 (73) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (3502 voxels, overlap=0.025) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (3502 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.07376 (74) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (3134 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (3134 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.10157 (99) Right_Cerebral_White_Matter (41): linear fit = 0.99 x + 0.0 (162945 voxels, overlap=0.789) Right_Cerebral_White_Matter (41): linear fit = 0.99 x + 0.0 (162945 voxels, peak = 101), gca=101.5 gca peak = 0.07714 (104) mri peak = 0.09516 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (156655 voxels, overlap=0.776) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (156655 voxels, peak = 103), gca=103.5 gca peak = 0.09712 (58) mri peak = 0.04196 (76) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (104161 voxels, overlap=0.003) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (104161 voxels, peak = 75), gca=75.1 gca peak = 0.11620 (58) mri peak = 0.04342 (72) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (97373 voxels, overlap=0.033) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (97373 voxels, peak = 73), gca=73.4 gca peak = 0.30970 (66) mri peak = 0.11011 (80) Right_Caudate (50): linear fit = 1.17 x + 0.0 (2698 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.17 x + 0.0 (2698 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.11088 (81) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2591 voxels, overlap=0.429) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2591 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.05907 (68) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (54020 voxels, overlap=0.220) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (54020 voxels, peak = 69), gca=68.6 gca peak = 0.14777 (55) mri peak = 0.05658 (65) Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (60306 voxels, overlap=0.439) Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (60306 voxels, peak = 65), gca=64.6 gca peak = 0.16765 (84) mri peak = 0.10880 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (14086 voxels, overlap=0.903) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (14086 voxels, peak = 84), gca=84.0 gca peak = 0.18739 (84) mri peak = 0.11134 (81) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (14018 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (14018 voxels, peak = 83), gca=82.7 gca peak = 0.29869 (57) mri peak = 0.09390 (73) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (1493 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (1493 voxels, peak = 72), gca=72.1 gca peak = 0.33601 (57) mri peak = 0.09465 (73) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (1699 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (1699 voxels, peak = 72), gca=72.1 gca peak = 0.11131 (90) mri peak = 0.06780 (93) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (9570 voxels, overlap=0.619) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (9570 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.07073 (93) Right_Thalamus_Proper (49): linear fit = 1.13 x + 0.0 (9376 voxels, overlap=0.309) Right_Thalamus_Proper (49): linear fit = 1.13 x + 0.0 (9376 voxels, peak = 94), gca=94.2 gca peak = 0.08324 (81) mri peak = 0.07383 (88) Left_Putamen (12): linear fit = 1.12 x + 0.0 (4104 voxels, overlap=0.569) Left_Putamen (12): linear fit = 1.12 x + 0.0 (4104 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.07651 (88) Right_Putamen (51): linear fit = 1.09 x + 0.0 (5006 voxels, overlap=0.633) Right_Putamen (51): linear fit = 1.09 x + 0.0 (5006 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.08480 (81) Brain_Stem (16): linear fit = 1.10 x + 0.0 (31276 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (31276 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.06885 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (4159 voxels, overlap=0.393) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (4159 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.06962 (95) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (4162 voxels, overlap=0.475) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (4162 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.11806 (32) Third_Ventricle (14): linear fit = 1.18 x + 0.0 (288 voxels, overlap=0.570) Third_Ventricle (14): linear fit = 1.18 x + 0.0 (288 voxels, peak = 28), gca=28.4 gca peak = 0.19357 (14) mri peak = 0.12327 (27) Fourth_Ventricle (15): linear fit = 1.68 x + 0.0 (1217 voxels, overlap=0.227) Fourth_Ventricle (15): linear fit = 1.68 x + 0.0 (1217 voxels, peak = 24), gca=23.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak 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 1.28 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 1.39 x + 0.0 Left_Pallidum too bright - rescaling by 0.963 (from 1.075) to 99.4 (was 103.2) Right_Pallidum too bright - rescaling by 0.992 (from 1.055) to 99.4 (was 100.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12545 (31) mri peak = 0.11241 (28) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (9682 voxels, overlap=0.789) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (9682 voxels, peak = 31), gca=31.5 gca peak = 0.13981 (19) mri peak = 0.10948 (30) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (7050 voxels, overlap=0.398) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (7050 voxels, peak = 27), gca=26.5 gca peak = 0.28555 (100) mri peak = 0.10995 (101) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (2145 voxels, overlap=1.009) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (2145 voxels, peak = 102), gca=101.5 gca peak = 0.16813 (100) mri peak = 0.09784 (103) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (2082 voxels, overlap=0.915) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (2082 voxels, peak = 104), gca=103.5 gca peak = 0.24404 (71) mri peak = 0.07657 (73) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (3502 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (3502 voxels, peak = 71), gca=71.0 gca peak = 0.26717 (73) mri peak = 0.07376 (74) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (3134 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (3134 voxels, peak = 71), gca=71.2 gca peak = 0.07820 (101) mri peak = 0.10157 (99) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (162945 voxels, overlap=0.763) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (162945 voxels, peak = 100), gca=100.5 gca peak = 0.08054 (104) mri peak = 0.09516 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (156655 voxels, overlap=0.767) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (156655 voxels, peak = 103), gca=103.5 gca peak = 0.07494 (75) mri peak = 0.04196 (76) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (104161 voxels, overlap=0.939) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (104161 voxels, peak = 75), gca=75.0 gca peak = 0.09320 (73) mri peak = 0.04342 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (97373 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (97373 voxels, peak = 72), gca=71.9 gca peak = 0.23087 (78) mri peak = 0.11011 (80) Right_Caudate (50): linear fit = 1.01 x + 0.0 (2698 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.01 x + 0.0 (2698 voxels, peak = 79), gca=79.2 gca peak = 0.16641 (87) mri peak = 0.11088 (81) Left_Caudate (11): linear fit = 0.99 x + 0.0 (2591 voxels, overlap=0.999) Left_Caudate (11): linear fit = 0.99 x + 0.0 (2591 voxels, peak = 86), gca=85.7 gca peak = 0.11735 (68) mri peak = 0.05907 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (54020 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (54020 voxels, peak = 67), gca=67.0 gca peak = 0.12881 (64) mri peak = 0.05658 (65) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (60306 voxels, overlap=0.995) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (60306 voxels, peak = 64), gca=64.0 gca peak = 0.16745 (84) mri peak = 0.10880 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (14086 voxels, overlap=0.906) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (14086 voxels, peak = 84), gca=84.0 gca peak = 0.16902 (83) mri peak = 0.11134 (81) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (14018 voxels, overlap=0.940) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (14018 voxels, peak = 83), gca=83.0 gca peak = 0.26550 (72) mri peak = 0.09390 (73) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (1493 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (1493 voxels, peak = 72), gca=72.0 gca peak = 0.31741 (72) mri peak = 0.09465 (73) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (1699 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (1699 voxels, peak = 74), gca=73.8 gca peak = 0.10086 (96) mri peak = 0.06780 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (9570 voxels, overlap=0.940) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (9570 voxels, peak = 96), gca=96.5 gca peak = 0.09427 (92) mri peak = 0.07073 (93) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (9376 voxels, overlap=0.935) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (9376 voxels, peak = 92), gca=92.5 gca peak = 0.08274 (92) mri peak = 0.07383 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (4104 voxels, overlap=0.940) Left_Putamen (12): linear fit = 1.00 x + 0.0 (4104 voxels, peak = 92), gca=91.5 gca peak = 0.08953 (85) mri peak = 0.07651 (88) Right_Putamen (51): linear fit = 1.01 x + 0.0 (5006 voxels, overlap=0.938) Right_Putamen (51): linear fit = 1.01 x + 0.0 (5006 voxels, peak = 86), gca=86.3 gca peak = 0.07632 (86) mri peak = 0.08480 (81) Brain_Stem (16): linear fit = 1.01 x + 0.0 (31276 voxels, overlap=0.762) Brain_Stem (16): linear fit = 1.01 x + 0.0 (31276 voxels, peak = 87), gca=87.3 gca peak = 0.12970 (92) mri peak = 0.06885 (95) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (4159 voxels, overlap=0.811) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (4159 voxels, peak = 93), gca=93.4 gca peak = 0.15786 (92) mri peak = 0.06962 (95) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (4162 voxels, overlap=0.878) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (4162 voxels, peak = 94), gca=94.3 gca peak = 0.13197 (30) mri peak = 0.11806 (32) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (288 voxels, overlap=0.855) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (288 voxels, peak = 31), gca=31.3 gca peak = 0.14735 (21) mri peak = 0.12327 (27) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (1217 voxels, overlap=0.749) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (1217 voxels, peak = 25), gca=24.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.36646 (102) gca peak CSF = 0.17474 (51) gca peak Left_Accumbens_area = 0.61348 (70) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.29845 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (43) gca peak WM_hypointensities = 0.08583 (76) gca peak non_WM_hypointensities = 0.08491 (54) gca peak Optic_Chiasm = 0.70834 (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 1.16 x + 0.0 Left_Putamen too bright - rescaling by 1.003 (from 0.995) to 91.8 (was 91.5) Left_Pallidum too bright - rescaling by 0.956 (from 1.035) to 98.9 (was 103.5) Right_Pallidum too bright - rescaling by 0.975 (from 1.015) to 98.9 (was 101.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 158960 voxels changed in iteration 0 of unlikely voxel relabeling 944 voxels changed in iteration 1 of unlikely voxel relabeling 21 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 160616 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 742 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 147793 changed. image ll: -2.189, PF=0.500 pass 2: 38846 changed. image ll: -2.188, PF=0.500 pass 3: 12831 changed. pass 4: 5297 changed. pass 5: 2648 changed. 156110 voxels changed in iteration 0 of unlikely voxel relabeling 803 voxels changed in iteration 1 of unlikely voxel relabeling 23 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 16130 voxels changed in iteration 0 of unlikely voxel relabeling 322 voxels changed in iteration 1 of unlikely voxel relabeling 17 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 15172 voxels changed in iteration 0 of unlikely voxel relabeling 182 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 15129 voxels changed in iteration 0 of unlikely voxel relabeling 66 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 5017.653656 mri_ca_label stimesec 15.598653 mri_ca_label ru_maxrss 3167388 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 17556176 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 5648 mri_ca_label ru_oublock 848 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 739 mri_ca_label ru_nivcsw 4854 auto-labeling took 82 minutes and 42 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/cc_up.lta sub-02 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-02/mri/transforms/cc_up.lta reading aseg from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/aseg.auto_noCCseg.mgz reading norm from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/norm.mgz 48248 voxels in left wm, 112958 in right wm, xrange [151, 163] searching rotation angles z=[-8 6], y=[-9 5] searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 global minimum found at slice 158.0, rotations (-1.78, -0.67) final transformation (x=158.0, yr=-1.777, zr=-0.674): 0.99945 0.01176 -0.03101 -28.28452; -0.01176 0.99993 0.00036 -11.17127; 0.03101 0.00000 0.99952 17.15096; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 141 106 eigenvectors: 0.00009 0.00065 1.00000; -0.21183 -0.97731 0.00065; 0.97731 -0.21183 0.00005; writing aseg with callosum to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/aseg.auto.mgz... corpus callosum segmentation took 1.3 minutes #-------------------------------------- #@# Merge ASeg Tue May 25 20:57:28 UTC 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue May 25 20:57:31 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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... 454 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 79 (79), valley at 48 (48) csf peak at 30, setting threshold to 62 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 4 minutes and 39 seconds. #-------------------------------------------- #@# Mask BFS Tue May 25 21:02:14 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 3289640 voxels in mask (pct= 10.04) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue May 25 21:02:19 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): 102.8 +- 6.5 [79.0 --> 125.0] GM (78.0) : 76.7 +- 10.9 [30.0 --> 95.0] setting bottom of white matter range to 87.5 setting top of gray matter range to 98.4 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, 4602 filled 70 bright non-wm voxels segmented. 9661 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 0.64 minutes reading wm segmentation from wm.seg.mgz... 143 voxels added to wm to prevent paths from MTL structures to cortex 9736 additional wm voxels added 0 additional wm voxels added SEG EDIT: 125323 voxels turned on, 94874 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 57 found - 57 modified | TOTAL: 57 pass 2 (xy+): 0 found - 57 modified | TOTAL: 57 pass 1 (xy-): 70 found - 70 modified | TOTAL: 127 pass 2 (xy-): 0 found - 70 modified | TOTAL: 127 pass 1 (yz+): 61 found - 61 modified | TOTAL: 188 pass 2 (yz+): 0 found - 61 modified | TOTAL: 188 pass 1 (yz-): 59 found - 59 modified | TOTAL: 247 pass 2 (yz-): 0 found - 59 modified | TOTAL: 247 pass 1 (xz+): 47 found - 47 modified | TOTAL: 294 pass 2 (xz+): 0 found - 47 modified | TOTAL: 294 pass 1 (xz-): 50 found - 50 modified | TOTAL: 344 pass 2 (xz-): 0 found - 50 modified | TOTAL: 344 Iteration Number : 1 pass 1 (+++): 35 found - 35 modified | TOTAL: 35 pass 2 (+++): 0 found - 35 modified | TOTAL: 35 pass 1 (+++): 36 found - 36 modified | TOTAL: 71 pass 2 (+++): 0 found - 36 modified | TOTAL: 71 pass 1 (+++): 43 found - 43 modified | TOTAL: 114 pass 2 (+++): 0 found - 43 modified | TOTAL: 114 pass 1 (+++): 42 found - 42 modified | TOTAL: 156 pass 2 (+++): 0 found - 42 modified | TOTAL: 156 Iteration Number : 1 pass 1 (++): 180 found - 180 modified | TOTAL: 180 pass 2 (++): 0 found - 180 modified | TOTAL: 180 pass 1 (+-): 135 found - 135 modified | TOTAL: 315 pass 2 (+-): 0 found - 135 modified | TOTAL: 315 pass 1 (--): 159 found - 159 modified | TOTAL: 474 pass 2 (--): 0 found - 159 modified | TOTAL: 474 pass 1 (-+): 142 found - 142 modified | TOTAL: 616 pass 2 (-+): 0 found - 142 modified | TOTAL: 616 Iteration Number : 2 pass 1 (xy+): 20 found - 20 modified | TOTAL: 20 pass 2 (xy+): 0 found - 20 modified | TOTAL: 20 pass 1 (xy-): 22 found - 22 modified | TOTAL: 42 pass 2 (xy-): 0 found - 22 modified | TOTAL: 42 pass 1 (yz+): 17 found - 17 modified | TOTAL: 59 pass 2 (yz+): 0 found - 17 modified | TOTAL: 59 pass 1 (yz-): 11 found - 11 modified | TOTAL: 70 pass 2 (yz-): 0 found - 11 modified | TOTAL: 70 pass 1 (xz+): 22 found - 22 modified | TOTAL: 92 pass 2 (xz+): 0 found - 22 modified | TOTAL: 92 pass 1 (xz-): 17 found - 17 modified | TOTAL: 109 pass 2 (xz-): 0 found - 17 modified | TOTAL: 109 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 8 found - 8 modified | TOTAL: 12 pass 2 (+++): 0 found - 8 modified | TOTAL: 12 pass 1 (+++): 6 found - 6 modified | TOTAL: 18 pass 2 (+++): 0 found - 6 modified | TOTAL: 18 Iteration Number : 2 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 11 found - 11 modified | TOTAL: 18 pass 2 (+-): 0 found - 11 modified | TOTAL: 18 pass 1 (--): 5 found - 5 modified | TOTAL: 23 pass 2 (--): 0 found - 5 modified | TOTAL: 23 pass 1 (-+): 14 found - 14 modified | TOTAL: 37 pass 2 (-+): 0 found - 14 modified | TOTAL: 37 Iteration Number : 3 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 Iteration Number : 5 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 : 5 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 : 5 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 = 1293 (out of 1274556: 0.101447) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue May 25 21:05:25 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 1.04890 0.04216 0.00996 -15.99678; -0.07420 0.94170 0.32896 -28.76181; -0.01613 -0.33810 0.88064 75.18027; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04890 0.04216 0.00996 -15.99678; -0.07420 0.94170 0.32896 -28.76181; -0.01613 -0.33810 0.88064 75.18027; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (546, 2188) area[0] = 4384 (min = 546, max = 2188), aspect = 1.17 (min = 0.10, max = 0.75) need search nearby using seed (156, 140, 118), TAL = (3.2, -33.6, 16.0) talairach voxel to voxel transform 0.95056 -0.04093 0.00454 13.68755; 0.06068 0.93372 -0.34947 54.09926; 0.04071 0.35773 1.00145 -64.34935; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (156, 140, 118) --> (3.2, -33.6, 16.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (3.20, -33.60, 16.00) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(21.20, -33.60, 16.00) SRC: (135.39, 151.68, 109.34) search lh wm seed point around talairach space (-14.80, -33.60, 16.00), SRC: (178.17, 154.41, 111.17) 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 17:46:39 UTC 2021 Ended at Tue May 25 21:06:19 UTC 2021 #@#%# recon-all-run-time-hours 3.328 recon-all -s sub-02 finished without error at Tue May 25 21:06:19 UTC 2021 New invocation of recon-all Tue May 25 23:07:46 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 /opt/freesurfer/bin/recon-all -parallel -subjid sub-02 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -T2pial -cortribbon subjid sub-02 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 blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 70547888 116269220 2023108 9821324 120891920 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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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: 2021/05/25-23:07:46-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: blg8112.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 23:07:48 UTC 2021 bbregister --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.lta --init-coreg --T2 tmp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021 Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat.log Tue May 25 23:07:48 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-02/scripts /opt/freesurfer/bin/bbregister --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg8112.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-02/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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-02/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-02/mri/transforms/tmp.bbregister.64021/template.nii... mri_coreg --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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-02/scripts cmdline mri_coreg --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg8112.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-02/mri/transforms/tmp.bbregister.64021/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.7992 -0.0326 -0.7944 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 = 4095.0000 mov gstd 1.9140 1.9140 1.9140 Smoothing mov refsat = 117.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0341397340 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.79917; 0.00000 1.00000 0.00000 -0.03257; 0.00000 0.00000 1.00000 -0.79439; 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 -0.79917 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0322699 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0341397524 #@# 4 188 -0.79917 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0341398 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.034140 #@# 4 190 0.20083 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0342592 #@# 4 194 -0.18114 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0342776 #@# 4 195 -0.07101 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0342813 #@# 4 207 -0.09176 0.10432 -0.79439 0.00000 0.00000 0.00000 -1.0342847 #@# 4 213 -0.09176 0.08432 0.20561 0.00000 0.00000 0.00000 -1.0343511 #@# 4 217 -0.09176 0.08432 -0.17635 0.00000 0.00000 0.00000 -1.0343649 #@# 4 218 -0.09176 0.08432 -0.15842 0.00000 0.00000 0.00000 -1.0343655 #@# 4 219 -0.09176 0.08432 -0.08027 0.00000 0.00000 0.00000 -1.0343664 #@# 4 228 -0.09176 0.08432 -0.10660 -0.61803 0.00000 0.00000 -1.0344540 #@# 4 230 -0.09176 0.08432 -0.10660 -0.76948 0.00000 0.00000 -1.0344571 #@# 4 239 -0.09176 0.08432 -0.10660 -0.75948 0.11692 0.00000 -1.0344592 #@# 4 248 -0.09176 0.08432 -0.10660 -0.75948 0.11692 0.15584 -1.0344644 powell nthiter 1: fret = -1.034464 #@# 4 266 -0.03912 0.08432 -0.10660 -0.75948 0.11692 0.18732 -1.0344650 #@# 4 268 -0.05912 0.08432 -0.10660 -0.75948 0.11692 0.18732 -1.0344652 #@# 4 277 -0.05912 0.06874 -0.10660 -0.75948 0.11692 0.18732 -1.0344653 #@# 4 293 -0.05912 0.06874 -0.12143 -0.76948 0.11692 0.18732 -1.0344654 #@# 4 315 -0.05912 0.06874 -0.12143 -0.76948 0.07866 0.17646 -1.0344656 Powell done niters total = 1 OptTimeSec 8.7 sec OptTimeMin 0.14 min nEvals 315 Final parameters -0.05911822 0.06873842 -0.12143438 -0.76948369 0.07866431 0.17646255 Final cost -1.034465547068095 --------------------------------- mri_coreg utimesec 185.353647 mri_coreg stimesec 1.802833 mri_coreg ru_maxrss 890756 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 1290565 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 11440 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 590 mri_coreg ru_nivcsw 236 Final RefRAS-to-MovRAS 0.99999 0.00308 0.00137 -0.05912; -0.00306 0.99991 -0.01343 0.06874; -0.00141 0.01343 0.99991 -0.12143; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99999 -0.00137 0.00308 263.72699; 0.00306 0.01343 0.99990 -12.26554; 0.00141 -0.99991 0.01343 317.88937; 0.00000 0.00000 0.00000 1.00000; Final parameters -0.0591 0.0687 -0.1214 -0.7695 0.0787 0.1765 nhits = 307862 out of 32768000, Percent Overlap: 60.1 mri_coreg RunTimeSec 72.7 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/mri_coreg.lta --s sub-02 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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-02/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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 blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat subject sub-02 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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 1622325550 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 -0.00308 -0.00137 -0.00080; -0.00141 0.01343 0.99991 0.22266; 0.00306 -0.99990 0.01343 -0.28619; 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 0.953097 1 -25.0 -25.0 25.0 0.968256 2 -25.0 25.0 -25.0 0.908299 3 -25.0 25.0 25.0 0.979697 4 25.0 -25.0 -25.0 0.966936 5 25.0 -25.0 25.0 0.936912 6 25.0 25.0 -25.0 0.952659 7 25.0 25.0 25.0 0.948138 REL: 8 0.052933 7.613993 0.951749 rel = 0.0556165 Initial costs ---------------- Number of surface hits 4368 WM Intensity 777.3781 +/- 267.5105 Ctx Intensity 1080.1838 +/- 319.8988 Pct Contrast 33.6743 +/- 16.9473 Cost 0.0529 RelCost 0.0556 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9693 0.9693 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9455 0.9455 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9194 0.9194 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8535 0.8535 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8168 0.8168 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.7874 0.7874 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.7607 0.7607 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.7544 0.7544 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7071 0.7071 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.6410 0.6410 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.6339 0.6339 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5894 0.5894 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5659 0.5659 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0529 0.0529 0.0 Brute Force -------------------------- Min cost was 0.052933 Number of iterations 729 Search time 1.771000 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 = 0.052933 7 -0.065 0.000 0.000 0.000 0.000 0.000 0.0525446552 8 -0.078 0.000 0.000 0.000 0.000 0.000 0.0523925015 11 -0.105 0.000 0.000 0.000 0.000 0.000 0.0521963731 13 -0.104 0.000 0.000 0.000 0.000 0.000 0.0521962243 21 -0.104 -0.285 0.000 0.000 0.000 0.000 0.0458121304 22 -0.104 -0.278 0.000 0.000 0.000 0.000 0.0457553509 24 -0.104 -0.266 0.000 0.000 0.000 0.000 0.0457181712 25 -0.104 -0.267 0.000 0.000 0.000 0.000 0.0457134393 26 -0.104 -0.270 0.000 0.000 0.000 0.000 0.0457132475 29 -0.104 -0.269 0.000 0.000 0.000 0.000 0.0457104934 30 -0.104 -0.268 0.000 0.000 0.000 0.000 0.0457087239 37 -0.104 -0.268 0.100 0.000 0.000 0.000 0.0444169918 38 -0.104 -0.268 0.121 0.000 0.000 0.000 0.0443391510 40 -0.104 -0.268 0.116 0.000 0.000 0.000 0.0443297114 49 -0.104 -0.268 0.116 -0.067 0.000 0.000 0.0432371990 50 -0.104 -0.268 0.116 -0.129 0.000 0.000 0.0425212141 55 -0.104 -0.268 0.116 -0.112 0.000 0.000 0.0425178610 57 -0.104 -0.268 0.116 -0.120 0.000 0.000 0.0425078528 68 -0.104 -0.268 0.116 -0.120 0.029 0.000 0.0424617503 73 -0.104 -0.268 0.116 -0.120 0.034 0.000 0.0424577097 74 -0.104 -0.268 0.116 -0.120 0.035 0.000 0.0424571851 82 -0.104 -0.268 0.116 -0.120 0.035 -0.271 0.0392052412 83 -0.104 -0.268 0.116 -0.120 0.035 -0.274 0.0392032131 84 -0.104 -0.268 0.116 -0.120 0.035 -0.283 0.0391991065 powell nthiter 1: fret = 0.039199 95 -0.112 -0.268 0.116 -0.120 0.035 -0.283 0.0391774819 96 -0.124 -0.268 0.116 -0.120 0.035 -0.283 0.0391403399 112 -0.124 -0.372 0.116 -0.120 0.035 -0.283 0.0385429913 113 -0.124 -0.344 0.116 -0.120 0.035 -0.283 0.0383825381 114 -0.124 -0.339 0.116 -0.120 0.035 -0.283 0.0383404573 116 -0.124 -0.328 0.116 -0.120 0.035 -0.283 0.0383114908 128 -0.124 -0.328 0.117 -0.120 0.035 -0.283 0.0383112462 139 -0.124 -0.328 0.117 -0.115 0.035 -0.283 0.0383072575 140 -0.124 -0.328 0.117 -0.116 0.035 -0.283 0.0383064351 148 -0.124 -0.328 0.117 -0.116 -0.048 -0.283 0.0382531252 149 -0.124 -0.328 0.117 -0.116 -0.009 -0.283 0.0382252645 151 -0.124 -0.328 0.117 -0.116 0.008 -0.283 0.0381571504 154 -0.124 -0.328 0.117 -0.116 0.010 -0.283 0.0381552496 156 -0.124 -0.328 0.117 -0.116 0.011 -0.283 0.0381549855 157 -0.124 -0.328 0.117 -0.116 0.012 -0.283 0.0381549291 164 -0.124 -0.328 0.117 -0.116 0.012 -0.279 0.0381233859 165 -0.124 -0.328 0.117 -0.116 0.012 -0.226 0.0378770850 168 -0.124 -0.328 0.117 -0.116 0.012 -0.237 0.0378727158 170 -0.124 -0.328 0.117 -0.116 0.012 -0.232 0.0378651193 powell nthiter 2: fret = 0.037865 180 -0.114 -0.328 0.117 -0.116 0.012 -0.232 0.0377580310 182 -0.097 -0.328 0.117 -0.116 0.012 -0.232 0.0377317931 183 -0.103 -0.328 0.117 -0.116 0.012 -0.232 0.0377157824 193 -0.103 -0.342 0.117 -0.116 0.012 -0.232 0.0376064268 194 -0.103 -0.348 0.117 -0.116 0.012 -0.232 0.0376035954 195 -0.103 -0.346 0.117 -0.116 0.012 -0.232 0.0376022107 205 -0.103 -0.346 0.103 -0.116 0.012 -0.232 0.0375969613 206 -0.103 -0.346 0.104 -0.116 0.012 -0.232 0.0375939236 207 -0.103 -0.346 0.109 -0.116 0.012 -0.232 0.0375858994 209 -0.103 -0.346 0.110 -0.116 0.012 -0.232 0.0375858763 216 -0.103 -0.346 0.110 -0.130 0.012 -0.232 0.0375467164 218 -0.103 -0.346 0.110 -0.126 0.012 -0.232 0.0375388016 219 -0.103 -0.346 0.110 -0.125 0.012 -0.232 0.0375384540 227 -0.103 -0.346 0.110 -0.125 -0.059 -0.232 0.0373402329 228 -0.103 -0.346 0.110 -0.125 -0.036 -0.232 0.0373200986 229 -0.103 -0.346 0.110 -0.125 -0.042 -0.232 0.0373124528 232 -0.103 -0.346 0.110 -0.125 -0.043 -0.232 0.0373123932 243 -0.103 -0.346 0.110 -0.125 -0.043 -0.230 0.0373108215 powell nthiter 3: fret = 0.037311 253 -0.079 -0.346 0.110 -0.125 -0.043 -0.230 0.0370367568 255 -0.062 -0.346 0.110 -0.125 -0.043 -0.230 0.0370277824 256 -0.069 -0.346 0.110 -0.125 -0.043 -0.230 0.0370197858 258 -0.067 -0.346 0.110 -0.125 -0.043 -0.230 0.0370179783 268 -0.067 -0.351 0.110 -0.125 -0.043 -0.230 0.0370099115 277 -0.067 -0.351 0.078 -0.125 -0.043 -0.230 0.0369066611 279 -0.067 -0.351 0.083 -0.125 -0.043 -0.230 0.0369048066 281 -0.067 -0.351 0.081 -0.125 -0.043 -0.230 0.0369042755 301 -0.067 -0.351 0.081 -0.125 -0.052 -0.230 0.0368984212 303 -0.067 -0.351 0.081 -0.125 -0.048 -0.230 0.0368904049 314 -0.067 -0.351 0.081 -0.125 -0.048 -0.228 0.0368894383 315 -0.067 -0.351 0.081 -0.125 -0.048 -0.227 0.0368890987 powell nthiter 4: fret = 0.036889 326 -0.073 -0.351 0.081 -0.125 -0.048 -0.227 0.0368643196 337 -0.073 -0.354 0.081 -0.125 -0.048 -0.227 0.0368615726 339 -0.073 -0.353 0.081 -0.125 -0.048 -0.227 0.0368615186 348 -0.073 -0.353 0.087 -0.125 -0.048 -0.227 0.0368587364 349 -0.073 -0.353 0.086 -0.125 -0.048 -0.227 0.0368581383 350 -0.073 -0.353 0.085 -0.125 -0.048 -0.227 0.0368579792 371 -0.073 -0.353 0.085 -0.125 -0.046 -0.227 0.0368556940 383 -0.073 -0.353 0.085 -0.125 -0.046 -0.226 0.0368535307 384 -0.073 -0.353 0.085 -0.125 -0.046 -0.223 0.0368521671 387 -0.080 -0.355 0.089 -0.125 -0.044 -0.219 0.0368422289 394 -0.080 -0.355 0.089 -0.125 -0.044 -0.219 0.0368422129 395 -0.080 -0.355 0.089 -0.125 -0.044 -0.219 0.0368421549 powell nthiter 5: fret = 0.036842 429 -0.080 -0.355 0.090 -0.125 -0.044 -0.219 0.0368419548 440 -0.080 -0.355 0.090 -0.124 -0.044 -0.219 0.0368406774 451 -0.080 -0.355 0.090 -0.124 -0.041 -0.219 0.0368395169 453 -0.080 -0.355 0.090 -0.124 -0.042 -0.219 0.0368388407 463 -0.080 -0.355 0.090 -0.124 -0.042 -0.219 0.0368388264 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.944049 1 -25.0 -25.0 25.0 0.967834 2 -25.0 25.0 -25.0 0.924407 3 -25.0 25.0 25.0 0.982311 4 25.0 -25.0 -25.0 0.965107 5 25.0 -25.0 25.0 0.938819 6 25.0 25.0 -25.0 0.946237 7 25.0 25.0 25.0 0.939212 REL: 8 0.036839 7.607973 0.950997 rel = 0.0387371 Number of iterations 5 Min cost was 0.036839 Number of FunctionCalls 469 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.958000 sec Parameters at optimum (transmm) -0.07989 -0.35528 0.08970 Parameters at optimum (rotdeg) -0.12379 -0.04217 -0.21922 Final costs ---------------- Number of surface hits 4368 WM Intensity 773.2077 +/- 264.4077 Ctx Intensity 1077.6959 +/- 319.8867 Pct Contrast 33.9525 +/- 16.3422 Cost 0.0368 RelCost 0.0556 Reg at min cost was -0.99999 -0.00230 0.00244 -0.07963; 0.00242 0.01127 0.99993 -0.13323; 0.00233 -0.99993 0.01127 -0.19697; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat, type = 14 Original Reg -0.99999 -0.00308 -0.00137 -0.00080; -0.00141 0.01343 0.99991 0.22266; 0.00306 -0.99990 0.01343 -0.28619; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00078 -0.00382 0.07883; -0.00383 0.00215 -0.00002 0.35589; 0.00073 0.00003 0.00216 -0.08922; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.436140 Computing change in rh position Surface-RMS-Diff-mm 0.340431 0.134726 0.617613 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/transforms/tmp.bbregister.64021/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-02/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/transforms/tmp.bbregister.64021/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat subject sub-02 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 1622196159 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 -0.00230 0.00244 -0.07963; 0.00242 0.01127 0.99993 -0.13323; 0.00233 -0.99993 0.01127 -0.19697; 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 0.959044 1 -25.0 -25.0 25.0 0.970090 2 -25.0 25.0 -25.0 0.957144 3 -25.0 25.0 25.0 0.969944 4 25.0 -25.0 -25.0 0.947720 5 25.0 -25.0 25.0 0.953069 6 25.0 25.0 -25.0 0.955544 7 25.0 25.0 25.0 0.951301 REL: 8 0.040606 7.663855 0.957982 rel = 0.0423869 Initial costs ---------------- Number of surface hits 438318 WM Intensity 771.6843 +/- 261.4513 Ctx Intensity 1078.8109 +/- 320.8907 Pct Contrast 34.1664 +/- 16.0298 Cost 0.0406 RelCost 0.0424 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0437 0.0437 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0431 0.0431 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0419 0.0419 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0419 0.0419 0.0 27 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.0412 0.0412 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0401 0.0401 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.0398 0.0398 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0397 0.0397 0.0 61 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.0389 0.0389 0.0 273 0.0000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0386 0.0386 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0380 0.0380 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0376 0.0376 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0368 0.0368 0.0 688 0.1000 0.1000 0.0000 0.0000 0.0000 0.0000 0.0368 0.0368 0.0 Brute Force -------------------------- Min cost was 0.036753 Number of iterations 729 Search time 1.409000 sec Parameters at best (transmm, rotdeg) 0.100 0.100 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0.1 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 = 0.041079 7 0.024 0.100 0.000 0.000 0.000 0.000 0.0408025151 8 0.040 0.100 0.000 0.000 0.000 0.000 0.0407884339 9 0.038 0.100 0.000 0.000 0.000 0.000 0.0407879402 17 0.038 0.025 0.000 0.000 0.000 0.000 0.0404870908 18 0.038 0.039 0.000 0.000 0.000 0.000 0.0404825500 19 0.038 0.035 0.000 0.000 0.000 0.000 0.0404802387 28 0.038 0.035 0.073 0.000 0.000 0.000 0.0401575746 30 0.038 0.035 0.071 0.000 0.000 0.000 0.0401572399 39 0.038 0.035 0.071 0.012 0.000 0.000 0.0401533131 40 0.038 0.035 0.071 0.008 0.000 0.000 0.0401508921 49 0.038 0.035 0.071 0.008 -0.042 0.000 0.0401048792 50 0.038 0.035 0.071 0.008 -0.027 0.000 0.0400721727 52 0.038 0.035 0.071 0.008 -0.028 0.000 0.0400720370 60 0.038 0.035 0.071 0.008 -0.028 0.117 0.0396891137 61 0.038 0.035 0.071 0.008 -0.028 0.101 0.0396783160 powell nthiter 1: fret = 0.039678 71 0.046 0.035 0.071 0.008 -0.028 0.101 0.0396496596 72 0.063 0.035 0.071 0.008 -0.028 0.101 0.0396234920 74 0.062 0.035 0.071 0.008 -0.028 0.101 0.0396233592 83 0.062 0.027 0.071 0.008 -0.028 0.101 0.0396111638 85 0.062 0.024 0.071 0.008 -0.028 0.101 0.0396102267 94 0.062 0.024 0.070 0.008 -0.028 0.101 0.0396084919 95 0.062 0.024 0.060 0.008 -0.028 0.101 0.0396035483 97 0.062 0.024 0.062 0.008 -0.028 0.101 0.0396028219 107 0.062 0.024 0.062 -0.003 -0.028 0.101 0.0396008474 109 0.062 0.024 0.062 0.002 -0.028 0.101 0.0395975537 119 0.062 0.024 0.062 0.002 -0.040 0.101 0.0395938808 120 0.062 0.024 0.062 0.002 -0.038 0.101 0.0395932821 130 0.062 0.024 0.062 0.002 -0.038 0.108 0.0395887292 131 0.062 0.024 0.062 0.002 -0.038 0.110 0.0395884261 powell nthiter 2: fret = 0.039588 142 0.064 0.024 0.062 0.002 -0.038 0.110 0.0395883531 150 0.064 0.023 0.062 0.002 -0.038 0.110 0.0395880203 169 0.064 0.023 0.062 0.000 -0.038 0.110 0.0395877015 179 0.064 0.023 0.062 0.000 -0.039 0.110 0.0395874328 189 0.064 0.023 0.062 0.000 -0.039 0.111 0.0395874282 191 0.066 0.022 0.062 -0.001 -0.040 0.112 0.0395874258 powell nthiter 3: fret = 0.039587 209 0.064 0.019 0.062 0.000 -0.039 0.111 0.0395873308 212 0.064 0.021 0.062 0.000 -0.039 0.111 0.0395870569 231 0.064 0.021 0.062 -0.001 -0.039 0.111 0.0395867113 253 0.064 0.019 0.062 -0.002 -0.039 0.111 0.0395863723 258 0.064 0.017 0.062 -0.003 -0.039 0.111 0.0395863009 259 0.064 0.017 0.062 -0.003 -0.039 0.111 0.0395862264 powell nthiter 4: fret = 0.039586 289 0.064 0.017 0.062 -0.003 -0.039 0.112 0.0395861462 298 0.064 0.017 0.064 -0.003 -0.039 0.112 0.0395857627 309 0.064 0.017 0.064 -0.004 -0.039 0.112 0.0395857473 322 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856746 326 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856523 327 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856357 329 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856311 330 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856291 powell nthiter 5: fret = 0.039586 362 0.064 0.015 0.065 -0.005 -0.039 0.112 0.0395856016 388 0.064 0.014 0.065 -0.005 -0.039 0.112 0.0395855548 389 0.064 0.014 0.065 -0.006 -0.039 0.112 0.0395855150 395 0.064 0.014 0.065 -0.006 -0.039 0.112 0.0395855148 powell nthiter 6: fret = 0.039586 410 0.065 0.014 0.065 -0.006 -0.039 0.112 0.0395854902 420 0.065 0.014 0.065 -0.006 -0.039 0.113 0.0395853489 powell nthiter 7: fret = 0.039585 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.959254 1 -25.0 -25.0 25.0 0.969806 2 -25.0 25.0 -25.0 0.957942 3 -25.0 25.0 25.0 0.971125 4 25.0 -25.0 -25.0 0.947928 5 25.0 -25.0 25.0 0.953762 6 25.0 25.0 -25.0 0.956370 7 25.0 25.0 25.0 0.951489 REL: 8 0.039585 7.667676 0.958460 rel = 0.041301 Number of iterations 7 Min cost was 0.039585 Number of FunctionCalls 534 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 62.869000 sec Parameters at optimum (transmm) 0.06545 0.01405 0.06516 Parameters at optimum (rotdeg) -0.00561 -0.03856 0.11317 Final costs ---------------- Number of surface hits 438318 WM Intensity 771.9051 +/- 262.0067 Ctx Intensity 1079.0478 +/- 320.9891 Pct Contrast 34.1771 +/- 16.0155 Cost 0.0396 RelCost 0.0424 Reg at min cost was -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 -0.00230 0.00244 -0.07963; 0.00242 0.01127 0.99993 -0.13323; 0.00233 -0.99993 0.01127 -0.19697; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00065 0.00198 -0.06585; 0.00197 0.00010 -0.00000 -0.01387; 0.00067 0.00000 0.00010 -0.06512; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.125091 Computing change in rh position Surface-RMS-Diff-mm 0.107070 0.033584 0.206688 mri_segreg done MinCost: 0.039585 771.905145 1079.047757 34.177113 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 -------- -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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 -------- -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-02 RegMat --------------------------- -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 23:07:48 UTC 2021 Ended at Tue May 25 23:10:33 UTC 2021 BBR-Run-Time-Sec 165 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.lta --surfs cp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.lta mri_convert -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/T2.prenorm.mgz mri_convert.bin -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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-02/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig.mgz... INFO: Applying transformation from file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.00000 -0.00165 0.00044 0.03469; 0.00165 0.99994 0.01117 0.05932; -0.00046 -0.01117 0.99994 0.40359; 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-02/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-02/mri/aseg.presurf.mgz -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.white identity.nofile -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.white identity.nofile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/T2.prenorm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/T2.prenorm.mgz... computing distance transform computing distance transform 119199 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-02/mri/T2.norm.mgz mri_mask /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/T2.norm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brainmask.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/T2.mgz DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/T2.mgz...done. /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 rh Waiting for PID 65695 of (65695 65701) to complete... Waiting for PID 65701 of (65695 65701) 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-02 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-02/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/wm.mgz... 51007 bright wm thresholded. 116 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.orig... computing class statistics... border white: 510838 voxels (1.56%) border gray 492141 voxels (1.50%) WM (103.0): 102.6 +- 6.3 [70.0 --> 110.0] GM (83.0) : 81.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.5 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.0 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.4 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=78+-7.0 mean inside = 100.6, mean outside = 83.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) 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 106 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 66 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 60 points - only 0.00% unknown deleting segment 14 with 34 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) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (box.dx, box.dy, box.dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) locating cortical regions not in the range [56.00 219.80], gm=173.00+-23.40, and vertices in regions > 161.3 195872 surface locations found to contain inconsistent values (78679 in, 117193 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg81, 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=157905.2, rms=0.347 001: dt: 0.0500, sse=157911.7, rms=0.347 (0.171%) 002: dt: 0.0500, sse=157913.6, rms=0.346 (0.193%) 003: dt: 0.0500, sse=157915.8, rms=0.346 (0.187%) 004: dt: 0.0500, sse=157917.8, rms=0.345 (0.186%) 005: dt: 0.0500, sse=157919.7, rms=0.344 (0.185%) 006: dt: 0.0500, sse=157921.2, rms=0.344 (0.184%) 007: dt: 0.0500, sse=157922.5, rms=0.343 (0.182%) 008: dt: 0.0500, sse=157923.9, rms=0.342 (0.181%) 009: dt: 0.0500, sse=157924.4, rms=0.342 (0.180%) 010: dt: 0.0500, sse=157925.1, rms=0.341 (0.179%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg81, 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=157425.8, rms=0.341 011: dt: 0.0500, sse=157426.0, rms=0.341 (0.178%) 012: dt: 0.0500, sse=157426.5, rms=0.340 (0.176%) 013: dt: 0.0500, sse=157426.5, rms=0.339 (0.175%) 014: dt: 0.0500, sse=157426.6, rms=0.339 (0.174%) 015: dt: 0.0500, sse=157426.3, rms=0.338 (0.173%) 016: dt: 0.0500, sse=157425.9, rms=0.338 (0.172%) 017: dt: 0.0500, sse=157425.4, rms=0.337 (0.171%) 018: dt: 0.0500, sse=157424.7, rms=0.336 (0.170%) 019: dt: 0.0500, sse=157423.8, rms=0.336 (0.169%) 020: dt: 0.0500, sse=157422.8, rms=0.335 (0.168%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg81, 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=156992.8, rms=0.335 021: dt: 0.0500, sse=156991.6, rms=0.335 (0.167%) 022: dt: 0.0500, sse=156990.5, rms=0.334 (0.166%) 023: dt: 0.0500, sse=156989.0, rms=0.334 (0.165%) 024: dt: 0.0500, sse=156987.5, rms=0.333 (0.164%) 025: dt: 0.0500, sse=156985.8, rms=0.333 (0.163%) 026: dt: 0.0500, sse=156983.9, rms=0.332 (0.162%) 027: dt: 0.0500, sse=156982.1, rms=0.331 (0.161%) 028: dt: 0.0500, sse=156979.9, rms=0.331 (0.160%) 029: dt: 0.0500, sse=156977.6, rms=0.330 (0.159%) 030: dt: 0.0500, sse=156975.3, rms=0.330 (0.158%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg81, 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=156600.9, rms=0.330 031: dt: 0.5000, sse=156571.3, rms=0.325 (1.540%) 032: dt: 0.5000, sse=156542.1, rms=0.320 (1.453%) 033: dt: 0.5000, sse=156498.7, rms=0.316 (1.373%) 034: dt: 0.5000, sse=156452.5, rms=0.312 (1.275%) 035: dt: 0.5000, sse=156403.4, rms=0.308 (1.221%) 036: dt: 0.5000, sse=156360.0, rms=0.304 (1.154%) 037: dt: 0.5000, sse=156312.0, rms=0.301 (1.095%) 038: dt: 0.5000, sse=156268.4, rms=0.298 (1.042%) 039: dt: 0.5000, sse=156220.2, rms=0.295 (0.992%) 040: dt: 0.5000, sse=156178.7, rms=0.292 (0.948%) 041: dt: 0.5000, sse=156131.1, rms=0.289 (0.896%) 042: dt: 0.5000, sse=156093.3, rms=0.287 (0.861%) 043: dt: 0.5000, sse=156052.5, rms=0.285 (0.823%) 044: dt: 0.5000, sse=156017.2, rms=0.282 (0.788%) 045: dt: 0.5000, sse=155977.0, rms=0.280 (0.751%) 046: dt: 0.5000, sse=155941.5, rms=0.278 (0.722%) 047: dt: 0.5000, sse=155902.6, rms=0.276 (0.696%) 048: dt: 0.5000, sse=155864.0, rms=0.274 (0.670%) 049: dt: 0.5000, sse=155830.9, rms=0.273 (0.642%) 050: dt: 0.5000, sse=155800.2, rms=0.271 (0.612%) 051: dt: 0.5000, sse=155773.4, rms=0.269 (0.567%) 052: dt: 0.5000, sse=155742.9, rms=0.268 (0.549%) 053: dt: 0.5000, sse=155714.2, rms=0.267 (0.532%) 054: dt: 0.5000, sse=155688.2, rms=0.265 (0.504%) 055: dt: 0.5000, sse=155663.0, rms=0.264 (0.497%) 056: dt: 0.5000, sse=155637.7, rms=0.263 (0.471%) 057: dt: 0.5000, sse=155614.5, rms=0.261 (0.445%) 058: dt: 0.5000, sse=155595.6, rms=0.260 (0.424%) 059: dt: 0.5000, sse=155571.3, rms=0.259 (0.404%) 060: dt: 0.5000, sse=155553.7, rms=0.258 (0.378%) positioning took 4.7 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (box.dx, box.dy, box.dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) locating cortical regions not in the range [53.50 220.80], gm=173.00+-23.90, and vertices in regions > 161.0 183637 surface locations found to contain inconsistent values (52357 in, 131280 out) tol=1.0e-04, sigma=1.0, host=blg81, 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=151896.2, rms=0.259 061: dt: 0.5000, sse=151858.2, rms=0.256 (1.147%) 062: dt: 0.5000, sse=151781.9, rms=0.253 (1.435%) 063: dt: 0.5000, sse=151718.9, rms=0.250 (1.198%) 064: dt: 0.5000, sse=151656.1, rms=0.247 (1.108%) 065: dt: 0.5000, sse=151598.8, rms=0.244 (0.999%) 066: dt: 0.5000, sse=151541.6, rms=0.242 (0.917%) 067: dt: 0.5000, sse=151500.2, rms=0.240 (0.832%) 068: dt: 0.5000, sse=151461.2, rms=0.238 (0.780%) 069: dt: 0.5000, sse=151426.8, rms=0.237 (0.720%) 070: dt: 0.5000, sse=151391.1, rms=0.235 (0.677%) 071: dt: 0.5000, sse=151364.7, rms=0.234 (0.631%) 072: dt: 0.5000, sse=151334.3, rms=0.232 (0.608%) 073: dt: 0.5000, sse=151308.5, rms=0.231 (0.574%) 074: dt: 0.5000, sse=151284.6, rms=0.230 (0.535%) 075: dt: 0.5000, sse=151261.8, rms=0.228 (0.521%) 076: dt: 0.5000, sse=151242.0, rms=0.227 (0.503%) 077: dt: 0.5000, sse=151220.8, rms=0.226 (0.487%) 078: dt: 0.5000, sse=151202.2, rms=0.225 (0.457%) 079: dt: 0.5000, sse=151179.0, rms=0.224 (0.439%) 080: dt: 0.5000, sse=151164.8, rms=0.223 (0.430%) 081: dt: 0.5000, sse=151143.9, rms=0.222 (0.412%) 082: dt: 0.5000, sse=151125.1, rms=0.221 (0.397%) 083: dt: 0.5000, sse=151107.4, rms=0.220 (0.379%) 084: dt: 0.5000, sse=151090.9, rms=0.220 (0.367%) 085: dt: 0.5000, sse=151075.6, rms=0.219 (0.348%) 086: dt: 0.5000, sse=151062.8, rms=0.218 (0.331%) 087: dt: 0.5000, sse=151046.9, rms=0.217 (0.316%) 088: dt: 0.5000, sse=151031.2, rms=0.217 (0.308%) 089: dt: 0.5000, sse=151018.8, rms=0.216 (0.295%) 090: dt: 0.5000, sse=151004.6, rms=0.216 (0.286%) positioning took 5.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (box.dx, box.dy, box.dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) locating cortical regions not in the range [51.00 221.80], gm=173.00+-24.40, and vertices in regions > 160.8 179854 surface locations found to contain inconsistent values (39443 in, 140411 out) tol=1.0e-04, sigma=0.5, host=blg81, 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=151463.4, rms=0.227 091: dt: 0.5000, sse=151451.6, rms=0.225 (0.878%) 092: dt: 0.5000, sse=151404.2, rms=0.222 (1.108%) 093: dt: 0.5000, sse=151360.9, rms=0.220 (0.895%) 094: dt: 0.5000, sse=151321.2, rms=0.218 (0.799%) 095: dt: 0.5000, sse=151286.0, rms=0.217 (0.707%) 096: dt: 0.5000, sse=151257.3, rms=0.215 (0.631%) 097: dt: 0.5000, sse=151231.8, rms=0.214 (0.569%) 098: dt: 0.5000, sse=151210.8, rms=0.213 (0.517%) 099: dt: 0.5000, sse=151186.7, rms=0.212 (0.469%) 100: dt: 0.5000, sse=151171.1, rms=0.211 (0.436%) 101: dt: 0.5000, sse=151154.5, rms=0.210 (0.410%) 102: dt: 0.5000, sse=151139.1, rms=0.209 (0.383%) 103: dt: 0.5000, sse=151126.5, rms=0.209 (0.365%) 104: dt: 0.5000, sse=151113.1, rms=0.208 (0.351%) 105: dt: 0.5000, sse=151098.0, rms=0.207 (0.328%) 106: dt: 0.5000, sse=151089.6, rms=0.207 (0.320%) 107: dt: 0.5000, sse=151079.6, rms=0.206 (0.305%) 108: dt: 0.5000, sse=151070.0, rms=0.205 (0.287%) 109: dt: 0.5000, sse=151059.9, rms=0.205 (0.277%) 110: dt: 0.5000, sse=151052.5, rms=0.204 (0.272%) 111: dt: 0.5000, sse=151044.0, rms=0.204 (0.253%) 112: dt: 0.5000, sse=151034.3, rms=0.203 (0.243%) 113: dt: 0.5000, sse=151027.1, rms=0.203 (0.238%) 114: dt: 0.5000, sse=151020.8, rms=0.202 (0.229%) 115: dt: 0.5000, sse=151010.7, rms=0.202 (0.221%) 116: dt: 0.5000, sse=151004.8, rms=0.201 (0.213%) 117: dt: 0.5000, sse=150999.2, rms=0.201 (0.201%) 118: dt: 0.5000, sse=150991.2, rms=0.201 (0.191%) 119: dt: 0.5000, sse=150985.5, rms=0.200 (0.191%) 120: dt: 0.5000, sse=150977.7, rms=0.200 (0.185%) positioning took 5.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (region->dx, region->dy, region->dz) = (172, 407, 293) (box.dx, box.dy, box.dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) (region->dx, region->dy, region->dz) = (183, 418, 313) locating cortical regions not in the range [50.50 222.00], gm=173.00+-24.50, and vertices in regions > 160.7 177347 surface locations found to contain inconsistent values (40187 in, 137160 out) tol=1.0e-04, sigma=0.2, host=blg81, 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-02/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=152215.0, rms=0.213 121: dt: 0.5000, sse=152207.2, rms=0.212 (0.688%) 122: dt: 0.5000, sse=152158.1, rms=0.210 (0.857%) 123: dt: 0.5000, sse=152117.7, rms=0.209 (0.682%) 124: dt: 0.5000, sse=152079.4, rms=0.207 (0.598%) 125: dt: 0.5000, sse=152049.1, rms=0.206 (0.513%) 126: dt: 0.5000, sse=152021.1, rms=0.205 (0.463%) 127: dt: 0.5000, sse=151994.8, rms=0.204 (0.411%) 128: dt: 0.5000, sse=151973.1, rms=0.204 (0.376%) 129: dt: 0.5000, sse=151953.7, rms=0.203 (0.337%) 130: dt: 0.5000, sse=151936.7, rms=0.202 (0.313%) 131: dt: 0.5000, sse=151923.6, rms=0.202 (0.292%) 132: dt: 0.5000, sse=151913.0, rms=0.201 (0.271%) 133: dt: 0.5000, sse=151900.9, rms=0.201 (0.254%) 134: dt: 0.5000, sse=151889.6, rms=0.200 (0.242%) 135: dt: 0.5000, sse=151879.5, rms=0.200 (0.224%) 136: dt: 0.5000, sse=151870.8, rms=0.199 (0.216%) 137: dt: 0.5000, sse=151862.4, rms=0.199 (0.207%) 138: dt: 0.5000, sse=151854.7, rms=0.199 (0.204%) 139: dt: 0.5000, sse=151847.0, rms=0.198 (0.190%) 140: dt: 0.5000, sse=151840.0, rms=0.198 (0.183%) 141: dt: 0.5000, sse=151831.7, rms=0.197 (0.175%) 142: dt: 0.5000, sse=151824.8, rms=0.197 (0.168%) 143: dt: 0.5000, sse=151818.0, rms=0.197 (0.154%) 144: dt: 0.5000, sse=151813.3, rms=0.197 (0.155%) 145: dt: 0.5000, sse=151806.2, rms=0.196 (0.150%) 146: dt: 0.5000, sse=151799.4, rms=0.196 (0.139%) 147: dt: 0.5000, sse=151794.0, rms=0.196 (0.132%) 148: dt: 0.5000, sse=151787.3, rms=0.195 (0.133%) 149: dt: 0.5000, sse=151782.4, rms=0.195 (0.123%) 150: dt: 0.5000, sse=151777.6, rms=0.195 (0.117%) positioning took 6.2 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.area.pial vertex spacing 0.79 +- 0.35 (0.04-->6.64) (max @ vno 170079 --> 170080) face area 0.24 +- 0.20 (0.00-->7.44) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 232333 vertices processed 25000 of 232333 vertices processed 50000 of 232333 vertices processed 75000 of 232333 vertices processed 100000 of 232333 vertices processed 125000 of 232333 vertices processed 150000 of 232333 vertices processed 175000 of 232333 vertices processed 200000 of 232333 vertices processed 225000 of 232333 vertices processed 0 of 232333 vertices processed 25000 of 232333 vertices processed 50000 of 232333 vertices processed 75000 of 232333 vertices processed 100000 of 232333 vertices processed 125000 of 232333 vertices processed 150000 of 232333 vertices processed 175000 of 232333 vertices processed 200000 of 232333 vertices processed 225000 of 232333 vertices processed thickness calculation complete, 272:848 truncations. 44854 vertices at 0 distance 138253 vertices at 1 distance 139876 vertices at 2 distance 73231 vertices at 3 distance 29593 vertices at 4 distance 10470 vertices at 5 distance 3544 vertices at 6 distance 1222 vertices at 7 distance 491 vertices at 8 distance 217 vertices at 9 distance 104 vertices at 10 distance 52 vertices at 11 distance 36 vertices at 12 distance 35 vertices at 13 distance 16 vertices at 14 distance 12 vertices at 15 distance 18 vertices at 16 distance 16 vertices at 17 distance 8 vertices at 18 distance 8 vertices at 19 distance 10 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.thickness positioning took 48.4 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-02 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-02/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/wm.mgz... 51007 bright wm thresholded. 116 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.orig... computing class statistics... border white: 510838 voxels (1.56%) border gray 492141 voxels (1.50%) WM (103.0): 102.6 +- 6.3 [70.0 --> 110.0] GM (83.0) : 81.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.5 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 58.0 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.4 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=79+-7.0 mean inside = 100.6, mean outside = 83.8 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 60 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 116 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 29 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 124 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 11 with 27 points - only 0.00% unknown deleting segment 12 with 16 points - only 0.00% unknown deleting segment 13 with 75 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown deleting segment 16 with 25 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown deleting segment 18 with 19 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 19 with 4 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) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (box.dx, box.dy, box.dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) locating cortical regions not in the range [65.00 216.20], gm=173.00+-21.60, and vertices in regions > 162.2 198304 surface locations found to contain inconsistent values (102389 in, 95915 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg81, 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=158491.4, rms=0.386 001: dt: 0.0500, sse=158492.0, rms=0.385 (0.163%) 002: dt: 0.0500, sse=158486.9, rms=0.385 (0.180%) 003: dt: 0.0500, sse=158481.6, rms=0.384 (0.175%) 004: dt: 0.0500, sse=158476.6, rms=0.383 (0.175%) 005: dt: 0.0500, sse=158471.1, rms=0.383 (0.174%) 006: dt: 0.0500, sse=158465.7, rms=0.382 (0.173%) 007: dt: 0.0500, sse=158460.1, rms=0.381 (0.172%) 008: dt: 0.0500, sse=158454.4, rms=0.381 (0.171%) 009: dt: 0.0500, sse=158448.7, rms=0.380 (0.170%) 010: dt: 0.0500, sse=158442.8, rms=0.379 (0.169%) positioning took 1.3 minutes tol=1.0e-04, sigma=2.0, host=blg81, 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=157946.3, rms=0.379 011: dt: 0.0500, sse=157940.2, rms=0.379 (0.168%) 012: dt: 0.0500, sse=157933.8, rms=0.378 (0.167%) 013: dt: 0.0500, sse=157927.6, rms=0.377 (0.166%) 014: dt: 0.0500, sse=157921.1, rms=0.377 (0.165%) 015: dt: 0.0500, sse=157914.4, rms=0.376 (0.165%) 016: dt: 0.0500, sse=157906.9, rms=0.376 (0.164%) 017: dt: 0.0500, sse=157900.0, rms=0.375 (0.163%) 018: dt: 0.0500, sse=157892.8, rms=0.374 (0.162%) 019: dt: 0.0500, sse=157885.7, rms=0.374 (0.161%) 020: dt: 0.0500, sse=157878.3, rms=0.373 (0.161%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg81, 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=157448.9, rms=0.373 021: dt: 0.0500, sse=157441.1, rms=0.373 (0.160%) 022: dt: 0.0500, sse=157433.5, rms=0.372 (0.159%) 023: dt: 0.0500, sse=157425.6, rms=0.371 (0.158%) 024: dt: 0.0500, sse=157416.7, rms=0.371 (0.158%) 025: dt: 0.0500, sse=157408.4, rms=0.370 (0.157%) 026: dt: 0.0500, sse=157401.2, rms=0.370 (0.156%) 027: dt: 0.0500, sse=157393.2, rms=0.369 (0.155%) 028: dt: 0.0500, sse=157384.9, rms=0.368 (0.154%) 029: dt: 0.0500, sse=157376.5, rms=0.368 (0.154%) 030: dt: 0.0500, sse=157368.1, rms=0.367 (0.153%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg81, 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=156990.3, rms=0.367 031: dt: 0.5000, sse=156903.0, rms=0.362 (1.485%) 032: dt: 0.5000, sse=156815.1, rms=0.357 (1.411%) 033: dt: 0.5000, sse=156721.3, rms=0.352 (1.354%) 034: dt: 0.5000, sse=156617.9, rms=0.347 (1.319%) 035: dt: 0.5000, sse=156514.2, rms=0.343 (1.250%) 036: dt: 0.5000, sse=156413.7, rms=0.339 (1.205%) 037: dt: 0.5000, sse=156317.9, rms=0.335 (1.154%) 038: dt: 0.5000, sse=156220.5, rms=0.331 (1.118%) 039: dt: 0.5000, sse=156131.2, rms=0.328 (1.077%) 040: dt: 0.5000, sse=156040.7, rms=0.324 (1.041%) 041: dt: 0.5000, sse=155953.1, rms=0.321 (1.009%) 042: dt: 0.5000, sse=155864.1, rms=0.318 (0.975%) 043: dt: 0.5000, sse=155780.6, rms=0.315 (0.949%) 044: dt: 0.5000, sse=155701.0, rms=0.312 (0.911%) 045: dt: 0.5000, sse=155622.8, rms=0.309 (0.881%) 046: dt: 0.5000, sse=155543.6, rms=0.307 (0.861%) 047: dt: 0.5000, sse=155471.8, rms=0.304 (0.823%) 048: dt: 0.5000, sse=155400.1, rms=0.302 (0.807%) 049: dt: 0.5000, sse=155334.3, rms=0.299 (0.775%) 050: dt: 0.5000, sse=155265.7, rms=0.297 (0.758%) 051: dt: 0.5000, sse=155207.4, rms=0.295 (0.719%) 052: dt: 0.5000, sse=155144.6, rms=0.293 (0.708%) 053: dt: 0.5000, sse=155088.1, rms=0.291 (0.674%) 054: dt: 0.5000, sse=155030.3, rms=0.289 (0.669%) 055: dt: 0.5000, sse=154977.3, rms=0.287 (0.643%) 056: dt: 0.5000, sse=154923.6, rms=0.285 (0.631%) 057: dt: 0.5000, sse=154870.7, rms=0.283 (0.609%) 058: dt: 0.5000, sse=154824.2, rms=0.282 (0.586%) 059: dt: 0.5000, sse=154773.6, rms=0.280 (0.568%) 060: dt: 0.5000, sse=154727.5, rms=0.279 (0.542%) positioning took 4.4 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (box.dx, box.dy, box.dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) locating cortical regions not in the range [58.00 220.40], gm=174.00+-23.20, and vertices in regions > 162.4 189973 surface locations found to contain inconsistent values (52257 in, 137716 out) tol=1.0e-04, sigma=1.0, host=blg81, 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=150523.7, rms=0.268 061: dt: 0.5000, sse=150489.1, rms=0.264 (1.172%) 062: dt: 0.5000, sse=150409.8, rms=0.261 (1.435%) 063: dt: 0.5000, sse=150337.1, rms=0.257 (1.233%) 064: dt: 0.5000, sse=150272.2, rms=0.255 (1.145%) 065: dt: 0.5000, sse=150215.5, rms=0.252 (1.029%) 066: dt: 0.5000, sse=150160.8, rms=0.249 (0.969%) 067: dt: 0.5000, sse=150114.3, rms=0.247 (0.878%) 068: dt: 0.5000, sse=150071.3, rms=0.245 (0.826%) 069: dt: 0.5000, sse=150036.8, rms=0.243 (0.752%) 070: dt: 0.5000, sse=149998.3, rms=0.242 (0.728%) 071: dt: 0.5000, sse=149970.4, rms=0.240 (0.664%) 072: dt: 0.5000, sse=149936.1, rms=0.238 (0.655%) 073: dt: 0.5000, sse=149908.7, rms=0.237 (0.622%) 074: dt: 0.5000, sse=149884.2, rms=0.235 (0.607%) 075: dt: 0.5000, sse=149863.0, rms=0.234 (0.579%) 076: dt: 0.5000, sse=149835.8, rms=0.233 (0.565%) 077: dt: 0.5000, sse=149810.0, rms=0.232 (0.542%) 078: dt: 0.5000, sse=149783.4, rms=0.230 (0.525%) 079: dt: 0.5000, sse=149759.1, rms=0.229 (0.502%) 080: dt: 0.5000, sse=149734.6, rms=0.228 (0.489%) 081: dt: 0.5000, sse=149715.1, rms=0.227 (0.474%) 082: dt: 0.5000, sse=149695.5, rms=0.226 (0.458%) 083: dt: 0.5000, sse=149671.9, rms=0.225 (0.441%) 084: dt: 0.5000, sse=149649.9, rms=0.224 (0.426%) 085: dt: 0.5000, sse=149631.0, rms=0.223 (0.415%) 086: dt: 0.5000, sse=149610.9, rms=0.222 (0.405%) 087: dt: 0.5000, sse=149587.1, rms=0.221 (0.386%) 088: dt: 0.5000, sse=149570.9, rms=0.220 (0.365%) 089: dt: 0.5000, sse=149555.5, rms=0.220 (0.364%) 090: dt: 0.5000, sse=149539.1, rms=0.219 (0.351%) positioning took 4.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (box.dx, box.dy, box.dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) locating cortical regions not in the range [58.50 221.60], gm=175.00+-23.30, and vertices in regions > 163.3 184723 surface locations found to contain inconsistent values (39891 in, 144832 out) tol=1.0e-04, sigma=0.5, host=blg81, 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=149804.5, rms=0.229 091: dt: 0.5000, sse=149788.6, rms=0.227 (0.891%) 092: dt: 0.5000, sse=149749.9, rms=0.225 (1.151%) 093: dt: 0.5000, sse=149707.1, rms=0.222 (0.924%) 094: dt: 0.5000, sse=149664.7, rms=0.221 (0.832%) 095: dt: 0.5000, sse=149625.7, rms=0.219 (0.743%) 096: dt: 0.5000, sse=149594.9, rms=0.217 (0.668%) 097: dt: 0.5000, sse=149566.9, rms=0.216 (0.603%) 098: dt: 0.5000, sse=149543.8, rms=0.215 (0.557%) 099: dt: 0.5000, sse=149522.3, rms=0.214 (0.510%) 100: dt: 0.5000, sse=149498.6, rms=0.213 (0.481%) 101: dt: 0.5000, sse=149475.4, rms=0.212 (0.446%) 102: dt: 0.5000, sse=149457.9, rms=0.211 (0.429%) 103: dt: 0.5000, sse=149442.3, rms=0.210 (0.407%) 104: dt: 0.5000, sse=149423.7, rms=0.209 (0.393%) 105: dt: 0.5000, sse=149408.7, rms=0.209 (0.373%) 106: dt: 0.5000, sse=149394.9, rms=0.208 (0.359%) 107: dt: 0.5000, sse=149380.6, rms=0.207 (0.344%) 108: dt: 0.5000, sse=149364.1, rms=0.206 (0.333%) 109: dt: 0.5000, sse=149350.5, rms=0.206 (0.325%) 110: dt: 0.5000, sse=149337.1, rms=0.205 (0.311%) 111: dt: 0.5000, sse=149326.3, rms=0.204 (0.297%) 112: dt: 0.5000, sse=149312.8, rms=0.204 (0.284%) 113: dt: 0.5000, sse=149300.1, rms=0.203 (0.280%) 114: dt: 0.5000, sse=149287.0, rms=0.203 (0.270%) 115: dt: 0.5000, sse=149277.2, rms=0.202 (0.258%) 116: dt: 0.5000, sse=149263.5, rms=0.202 (0.251%) 117: dt: 0.5000, sse=149253.9, rms=0.201 (0.239%) 118: dt: 0.5000, sse=149245.5, rms=0.201 (0.235%) 119: dt: 0.5000, sse=149239.7, rms=0.200 (0.225%) 120: dt: 0.5000, sse=149227.8, rms=0.200 (0.216%) positioning took 5.3 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (region->dx, region->dy, region->dz) = (166, 404, 281) (box.dx, box.dy, box.dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) (region->dx, region->dy, region->dz) = (176, 414, 300) locating cortical regions not in the range [58.50 220.20], gm=174.00+-23.10, and vertices in regions > 162.4 177388 surface locations found to contain inconsistent values (50605 in, 126783 out) tol=1.0e-04, sigma=0.2, host=blg81, 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-02/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=150428.4, rms=0.216 121: dt: 0.5000, sse=150408.0, rms=0.214 (0.734%) 122: dt: 0.5000, sse=150352.9, rms=0.212 (0.914%) 123: dt: 0.5000, sse=150304.8, rms=0.211 (0.739%) 124: dt: 0.5000, sse=150263.9, rms=0.209 (0.655%) 125: dt: 0.5000, sse=150227.4, rms=0.208 (0.587%) 126: dt: 0.5000, sse=150189.5, rms=0.207 (0.528%) 127: dt: 0.5000, sse=150156.5, rms=0.206 (0.479%) 128: dt: 0.5000, sse=150129.9, rms=0.205 (0.442%) 129: dt: 0.5000, sse=150102.2, rms=0.204 (0.407%) 130: dt: 0.5000, sse=150071.8, rms=0.204 (0.381%) 131: dt: 0.5000, sse=150053.1, rms=0.203 (0.357%) 132: dt: 0.5000, sse=150033.8, rms=0.202 (0.338%) 133: dt: 0.5000, sse=150015.6, rms=0.202 (0.322%) 134: dt: 0.5000, sse=149992.9, rms=0.201 (0.310%) 135: dt: 0.5000, sse=149976.0, rms=0.200 (0.291%) 136: dt: 0.5000, sse=149960.9, rms=0.200 (0.272%) 137: dt: 0.5000, sse=149943.3, rms=0.199 (0.266%) 138: dt: 0.5000, sse=149929.5, rms=0.199 (0.258%) 139: dt: 0.5000, sse=149918.0, rms=0.198 (0.246%) 140: dt: 0.5000, sse=149905.5, rms=0.198 (0.236%) 141: dt: 0.5000, sse=149891.6, rms=0.197 (0.228%) 142: dt: 0.5000, sse=149883.3, rms=0.197 (0.219%) 143: dt: 0.5000, sse=149873.7, rms=0.197 (0.211%) 144: dt: 0.5000, sse=149861.6, rms=0.196 (0.207%) 145: dt: 0.5000, sse=149850.3, rms=0.196 (0.195%) 146: dt: 0.5000, sse=149835.9, rms=0.195 (0.186%) 147: dt: 0.5000, sse=149827.3, rms=0.195 (0.184%) 148: dt: 0.5000, sse=149819.7, rms=0.195 (0.175%) 149: dt: 0.5000, sse=149810.7, rms=0.194 (0.164%) 150: dt: 0.5000, sse=149805.1, rms=0.194 (0.158%) positioning took 5.6 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.area.pial vertex spacing 0.78 +- 0.35 (0.03-->7.96) (max @ vno 183652 --> 232724) face area 0.24 +- 0.20 (0.00-->7.28) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 232806 vertices processed 25000 of 232806 vertices processed 50000 of 232806 vertices processed 75000 of 232806 vertices processed 100000 of 232806 vertices processed 125000 of 232806 vertices processed 150000 of 232806 vertices processed 175000 of 232806 vertices processed 200000 of 232806 vertices processed 225000 of 232806 vertices processed 0 of 232806 vertices processed 25000 of 232806 vertices processed 50000 of 232806 vertices processed 75000 of 232806 vertices processed 100000 of 232806 vertices processed 125000 of 232806 vertices processed 150000 of 232806 vertices processed 175000 of 232806 vertices processed 200000 of 232806 vertices processed 225000 of 232806 vertices processed thickness calculation complete, 281:1223 truncations. 43877 vertices at 0 distance 135435 vertices at 1 distance 140209 vertices at 2 distance 75783 vertices at 3 distance 30055 vertices at 4 distance 10519 vertices at 5 distance 3487 vertices at 6 distance 1137 vertices at 7 distance 392 vertices at 8 distance 150 vertices at 9 distance 65 vertices at 10 distance 75 vertices at 11 distance 47 vertices at 12 distance 42 vertices at 13 distance 24 vertices at 14 distance 14 vertices at 15 distance 12 vertices at 16 distance 10 vertices at 17 distance 15 vertices at 18 distance 10 vertices at 19 distance 8 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.thickness positioning took 46.0 minutes PIDs (65695 65701) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Wed May 26 00:00:20 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf vertexvol --s sub-02 --lh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/label/lh.cortex.label Total face volume 265959 Total vertex volume 263521 (mask=0) #@# sub-02 lh 263521 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed May 26 00:00:25 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf vertexvol --s sub-02 --rh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/label/rh.cortex.label Total face volume 260492 Total vertex volume 258635 (mask=0) #@# sub-02 rh 258635 vertexvol Done #-------------------------------------------- #@# Surf Volume lh Wed May 26 00:00:30 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/label/lh.cortex.label Total face volume 265959 Total vertex volume 263521 (mask=0) #@# sub-02 lh 263521 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed May 26 00:00:34 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/label/rh.cortex.label Total face volume 260492 Total vertex volume 258635 (mask=0) #@# sub-02 rh 258635 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Wed May 26 00:00:39 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02 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 = 244 writing volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/ribbon.mgz mris_volmask took 16.18 minutes writing ribbon files Started at Tue May 25 23:07:45 UTC 2021 Ended at Wed May 26 00:16:50 UTC 2021 #@#%# recon-all-run-time-hours 1.151 recon-all -s sub-02 finished without error at Wed May 26 00:16:51 UTC 2021 New invocation of recon-all Wed May 26 00:26:36 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 /opt/freesurfer/bin/recon-all -autorecon3 -openmp 8 -subjid sub-02 -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-02 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 blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 70926356 117018880 2014756 8693196 120514836 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:26:37-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: blg8112.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Relabel Hypointensities Wed May 26 00:26:37 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 4704 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2941 voxels changed to hypointensity... 7369 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed May 26 00:27:10 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 mri_aparc2aseg --s sub-02 --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-02 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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-02/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 15.79 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 31 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 84 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 31 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 71 rescaling Left_Amygdala from 56 --> 72 rescaling CSF from 32 --> 59 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 100 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 64 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 86 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 --> 93 rescaling Fifth_Ventricle from 40 --> 50 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1016011 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 172 changed. pass 2: 3 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Wed May 26 00:34:31 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 mri_aparc2aseg --s sub-02 --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-02 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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-02/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 15.79 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 31 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 84 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 31 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 71 rescaling Left_Amygdala from 56 --> 72 rescaling CSF from 32 --> 59 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 100 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 64 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 86 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 --> 93 rescaling Fifth_Ventricle from 40 --> 50 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1015578 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 172 changed. pass 2: 3 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed May 26 00:41:45 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 mri_aparc2aseg --s sub-02 --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-02 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-02/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/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-02/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 15.79 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 31 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 84 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 31 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 71 rescaling Left_Amygdala from 56 --> 72 rescaling CSF from 32 --> 59 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 100 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 64 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 86 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 --> 93 rescaling Fifth_Ventricle from 40 --> 50 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 nctx = 1015578 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 172 changed. pass 2: 3 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Wed May 26 00:48:56 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Wed May 26 00:48:56 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-02/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 blg8112.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-02/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 blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 32768000 0.000000 mri_binarize done Started at Wed May 26 00:48:56 UTC 2021 Ended at Wed May 26 00:49:02 UTC 2021 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed May 26 00:49:02 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 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-02 $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-02 sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1840909 mm^3 (det: 1.058230 ) Computing euler number orig.nofix lheno = -118, rheno = -134 orig.nofix lhholes = 60, rhholes = 68 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 259016.730 511385.000 diff=-252368.3 pctdiff=-97.433 rhCtxGM: 256125.607 502936.000 diff=-246810.4 pctdiff=-96.363 lhCtxWM: 227970.968 515199.500 diff=-287228.5 pctdiff=-125.993 rhCtxWM: 226703.819 509995.500 diff=-283291.7 pctdiff=-124.961 SubCortGMVol 119686.000 SupraTentVol 1120650.124 (2208268.000) diff=-1087617.876 pctdiff=-97.052 SupraTentVolNotVent 1071644.124 (2159262.000) diff=-1087617.876 pctdiff=-101.491 BrainSegVol 2524979.000 (2518415.000) diff=6564.000 pctdiff=0.260 BrainSegVolNotVent 2467319.000 (1397378.124) diff=1069940.876 pctdiff=43.365 BrainSegVolNotVent 2467319.000 CerebellumVol 307815.000 VentChorVol 49006.000 3rd4th5thCSF 8654.000 CSFVol 2090.000, OptChiasmVol 242.000 MaskVol 3327007.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Wed May 26 00:49:58 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02 mri_aparc2aseg --s sub-02 --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-02 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-02/mri/aparc+aseg.mgz Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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-02/mri/ribbon.mgz Loading filled from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 13290 vertices from left hemi Ripped 13417 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-02/mri/aseg.mgz Loading Ctx Seg File /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 = 2035391 Used brute-force search on 603 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1647.078247 1 k 0.512000 2 k 1.024000 3 k 4.095999 4 k 0.512000 5 k 0.512000 6 k 23.551989 7 k 0.512000 Fixing Parahip RH WM Found 4 clusters 0 k 1.024000 1 k 0.512000 2 k 20.479994 3 k 1870.805908 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-02 --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-02 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1840909 mm^3 (det: 1.058230 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 259016.730 511385.000 diff=-252368.3 pctdiff=-97.433 rhCtxGM: 256125.607 502936.000 diff=-246810.4 pctdiff=-96.363 lhCtxWM: 227970.968 515199.500 diff=-287228.5 pctdiff=-125.993 rhCtxWM: 226703.819 509995.500 diff=-283291.7 pctdiff=-124.961 SubCortGMVol 119686.000 SupraTentVol 1120650.124 (2208268.000) diff=-1087617.876 pctdiff=-97.052 SupraTentVolNotVent 1071644.124 (2159262.000) diff=-1087617.876 pctdiff=-101.491 BrainSegVol 2524979.000 (2518415.000) diff=6564.000 pctdiff=0.260 BrainSegVolNotVent 2467319.000 (1397378.124) diff=1069940.876 pctdiff=43.365 BrainSegVolNotVent 2467319.000 CerebellumVol 307815.000 VentChorVol 49006.000 3rd4th5thCSF 8654.000 CSFVol 2090.000, OptChiasmVol 242.000 MaskVol 3327007.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done Started at Wed May 26 00:26:36 UTC 2021 Ended at Wed May 26 01:00:10 UTC 2021 #@#%# recon-all-run-time-hours 0.559 recon-all -s sub-02 finished without error at Wed May 26 01:00:10 UTC 2021