Tue May 25 17:29:57 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 /opt/freesurfer/bin/recon-all -autorecon1 -i /work/fmriprep_wf/single_subject_06_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-06_ses-001_T1w_template.nii.gz -T2 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-06/ses-001/anat/sub-06_ses-001_T2w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-06 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -expert /work/fmriprep_wf/single_subject_06_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts subjid sub-06 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 blg6114.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 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 92230188 65750272 2230776 38657800 97731832 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:57-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:57-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:58-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:58-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:29:59-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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: 2021/05/25-17:30:00-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: blg6114.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-06 mri_convert /work/fmriprep_wf/single_subject_06_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-06_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/001.mgz mri_convert.bin /work/fmriprep_wf/single_subject_06_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-06_ses-001_T1w_template.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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_06_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-06_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-06/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Tue May 25 17:30:06 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 mri_convert --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-06/ses-001/anat/sub-06_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/raw/sub-06/ses-001/anat/sub-06_ses-001_T2w.nii.gz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/ses-001/anat/sub-06_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-06/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Tue May 25 17:30:16 UTC 2021 Found 1 runs /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/orig/001.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz --conform_min mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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-06/mri/orig.mgz... mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach.xfm /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 25 17:30:31 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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 blg6114.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 17:30:31 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.204121 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.204121/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.204121/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.204121/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue May 25 17:30:47 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.204121/nu0.mnc ./tmp.mri_nu_correct.mni.204121/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.204121/0/ -iterations 1000 -distance 50 [bpinsard@blg6114.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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.204121/0/ ./tmp.mri_nu_correct.mni.204121/nu0.mnc ./tmp.mri_nu_correct.mni.204121/nu1.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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: 60 CV of field change: 0.000980513 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.204121/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.204121/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.204121/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue May 25 17:33:26 UTC 2021 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue May 25 17:33:26 UTC 2021 Ended at Tue May 25 17:34:07 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 25 17:34:09 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7627, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach_avi.log tal_QC_AZS /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach_avi.log TalAviQA: 0.97222 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Tue May 25 17:34:09 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-06/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 blg6114.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 17:34:10 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.206402 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.206402/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.206402/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.206402/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue May 25 17:34:27 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.206402/nu0.mnc ./tmp.mri_nu_correct.mni.206402/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.206402/0/ [bpinsard@blg6114.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/] [2021-05-25 17:34:27] 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.206402/0/ ./tmp.mri_nu_correct.mni.206402/nu0.mnc ./tmp.mri_nu_correct.mni.206402/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 Number of iterations: 39 CV of field change: 0.000974223 Outputting Volume: ............................................................ Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Tue May 25 17:36:26 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.206402/nu1.mnc ./tmp.mri_nu_correct.mni.206402/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.206402/1/ [bpinsard@blg6114.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/] [2021-05-25 17:36:26] 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.206402/1/ ./tmp.mri_nu_correct.mni.206402/nu1.mnc ./tmp.mri_nu_correct.mni.206402/nu2.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 19 CV of field change: 0.00097888 Outputting Volume: ............................................................ Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.206402/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.206402/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-06/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.206402/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.206402/ones.mgz sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard input ./tmp.mri_nu_correct.mni.206402/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.206402/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.206402/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.206402/sum.junk --avgwf ./tmp.mri_nu_correct.mni.206402/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.206402/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.206402/sum.junk --avgwf ./tmp.mri_nu_correct.mni.206402/input.mean.dat sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.206402/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.206402/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.206402/ones.mgz --i ./tmp.mri_nu_correct.mni.206402/nu2.mnc --sum ./tmp.mri_nu_correct.mni.206402/sum.junk --avgwf ./tmp.mri_nu_correct.mni.206402/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.206402/ones.mgz --i ./tmp.mri_nu_correct.mni.206402/nu2.mnc --sum ./tmp.mri_nu_correct.mni.206402/sum.junk --avgwf ./tmp.mri_nu_correct.mni.206402/output.mean.dat sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.206402/ones.mgz Loading ./tmp.mri_nu_correct.mni.206402/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.206402/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.206402/nu2.mnc ./tmp.mri_nu_correct.mni.206402/nu2.mnc mul .10089318072973430395 Saving result to './tmp.mri_nu_correct.mni.206402/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.206402/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.206402/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.206402/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 12 seconds. mapping ( 7, 144) to ( 3, 110) Tue May 25 17:38:57 UTC 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue May 25 17:38:58 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 1.07884 -0.03146 0.00068 1.11574; 0.01991 1.07984 0.05204 -30.51630; -0.01518 -0.07526 1.11654 -7.64620; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 22 Starting OpenSpline(): npoints = 22 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 80 (80), valley at 37 (37) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 77 (77), valley at 37 (37) csf peak at 26, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 44 seconds. Started at Tue May 25 17:29:56 UTC 2021 Ended at Tue May 25 17:42:43 UTC 2021 #@#%# recon-all-run-time-hours 0.213 recon-all -s sub-06 finished without error at Tue May 25 17:42:43 UTC 2021 New invocation of recon-all Tue May 25 17:44:49 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-06 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-06 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 blg6114.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 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 96196196 59022712 2230804 41419352 93530296 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:49-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:49-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:49-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:49-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:49-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:49-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-17:44:50-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue May 25 17:44:50 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri mri_em_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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=23.0 skull bounding box = (78, 47, 47) --> (241, 189, 239) using (132, 94, 143) as brain centroid... mean wm in atlas = 107, using box (112,77,119) --> (152, 111,166) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 101 +- 4.8 after smoothing, mri peak at 101, scaling input intensities by 1.059 scaling channel 0 by 1.05941 initial log_p = -4.368 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.131614 @ (-9.091, 9.091, -9.091) max log p = -4.022693 @ (4.545, 4.545, 4.545) max log p = -3.994226 @ (2.273, 2.273, 2.273) max log p = -3.974379 @ (3.409, -3.409, -5.682) max log p = -3.963969 @ (-0.568, -0.568, -1.705) max log p = -3.950841 @ (0.284, 0.284, 0.284) Found translation: (0.9, 12.2, -9.4): log p = -3.951 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.940, old_max_log_p =-3.951 (thresh=-3.9) 0.86000 0.00000 0.00000 -11.00175; 0.00000 0.80000 0.00000 12.21591; 0.00000 0.00000 0.80000 -9.37500; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.940, old_max_log_p =-3.940 (thresh=-3.9) 0.86000 0.00000 0.00000 -11.00175; 0.00000 0.80000 0.00000 12.21591; 0.00000 0.00000 0.80000 -9.37500; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.871, old_max_log_p =-3.940 (thresh=-3.9) 0.89129 -0.02789 0.02537 -18.88511; 0.02973 0.81276 0.05418 0.25138; -0.02919 -0.05426 0.82778 2.66533; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.864, old_max_log_p =-3.871 (thresh=-3.9) 0.87176 -0.05596 0.04875 -14.43685; 0.05785 0.80912 0.08290 -7.90013; -0.06041 -0.08136 0.83975 9.40275; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.845, old_max_log_p =-3.864 (thresh=-3.9) 0.85675 -0.02900 0.05136 -16.27840; 0.02780 0.82256 0.11072 -7.12232; -0.06227 -0.10779 0.83658 14.62157; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.833, old_max_log_p =-3.845 (thresh=-3.8) 0.87320 -0.00224 0.05689 -22.94178; -0.00234 0.83446 0.13883 -7.97052; -0.06315 -0.13465 0.83251 17.93715; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.825, old_max_log_p =-3.833 (thresh=-3.8) 0.85638 -0.02912 0.05221 -14.50076; 0.02883 0.85361 0.11545 -11.12984; -0.06319 -0.10727 0.83661 14.71804; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.806, old_max_log_p =-3.825 (thresh=-3.8) 0.84024 0.02602 0.06029 -21.44111; -0.02987 0.86566 0.14164 -7.93690; -0.06410 -0.13514 0.83239 18.16469; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.806, old_max_log_p =-3.806 (thresh=-3.8) 0.84024 0.02602 0.06029 -21.44111; -0.02987 0.86566 0.14164 -7.93690; -0.06410 -0.13514 0.83239 18.16469; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.799, old_max_log_p =-3.806 (thresh=-3.8) 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 10 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.799, old_max_log_p =-3.799 (thresh=-3.8) 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 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 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.799 (old=-4.368) transform before final EM align: 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 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 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 015: -log(p) = 4.3 tol 0.000000 final transform: 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1618.083882 mri_em_register stimesec 4.874542 mri_em_register ru_maxrss 753816 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 972593 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 595 mri_em_register ru_nivcsw 829 registration took 4 minutes and 20 seconds. #-------------------------------------- #@# CA Normalize Tue May 25 17:49:10 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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=23.0 skull bounding box = (78, 47, 47) --> (241, 189, 239) using (132, 94, 143) as brain centroid... mean wm in atlas = 107, using box (112,77,119) --> (152, 111,166) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 101 +- 4.8 after smoothing, mri peak at 101, scaling input intensities by 1.059 scaling channel 0 by 1.05941 using 246344 sample points... INFO: compute sample coordinates transform 0.84024 0.02602 0.06029 -21.44111; -0.02997 0.86871 0.14214 -8.49115; -0.06417 -0.13530 0.83336 18.03096; 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 (159, 54, 48) --> (241, 186, 245) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 1146 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (85, 55, 44) --> (165, 185, 243) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 1065 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (164, 157, 81) --> (221, 207, 144) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (109, 157, 74) --> (163, 203, 142) Right_Cerebellum_White_Matter: limiting intensities to 122.0 --> 132.0 8 of 9 (88.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (140, 143, 121) --> (182, 223, 157) Brain_Stem: limiting intensities to 121.0 --> 132.0 16 of 17 (94.1%) samples deleted using 2248 total control points for intensity normalization... bias field = 0.949 +- 0.058 5 of 2224 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (159, 54, 48) --> (241, 186, 245) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 1980 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (85, 55, 44) --> (165, 185, 243) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 1820 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (164, 157, 81) --> (221, 207, 144) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 38 (2.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (109, 157, 74) --> (163, 203, 142) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 33 (6.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (140, 143, 121) --> (182, 223, 157) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 51 (2.0%) samples deleted using 3922 total control points for intensity normalization... bias field = 1.054 +- 0.068 16 of 3879 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (159, 54, 48) --> (241, 186, 245) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 2056 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (85, 55, 44) --> (165, 185, 243) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 115.0 6 of 1885 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (164, 157, 81) --> (221, 207, 144) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 26 of 50 (52.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (109, 157, 74) --> (163, 203, 142) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 47 (44.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (140, 143, 121) --> (182, 223, 157) Brain_Stem: limiting intensities to 88.0 --> 132.0 55 of 125 (44.0%) samples deleted using 4163 total control points for intensity normalization... bias field = 1.057 +- 0.063 21 of 3986 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 34 seconds. #-------------------------------------- #@# CA Reg Tue May 25 17:51:44 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri mri_ca_register -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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) = 0.63 (predicted orig area = 12.7) 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=1.017, neg=0, invalid=762 0001: dt=384.033169, rms=0.901 (11.401%), neg=0, invalid=762 0002: dt=332.787213, rms=0.851 (5.578%), neg=0, invalid=762 0003: dt=235.773344, rms=0.824 (3.171%), neg=0, invalid=762 0004: dt=369.920000, rms=0.810 (1.648%), neg=0, invalid=762 0005: dt=181.417323, rms=0.802 (1.077%), neg=0, invalid=762 0006: dt=887.808000, rms=0.789 (1.539%), neg=0, invalid=762 0007: dt=153.230769, rms=0.784 (0.653%), neg=0, invalid=762 0008: dt=1775.616000, rms=0.775 (1.117%), neg=0, invalid=762 0009: dt=221.952000, rms=0.772 (0.386%), neg=0, invalid=762 0010: dt=517.888000, rms=0.769 (0.449%), neg=0, invalid=762 0011: dt=129.472000, rms=0.769 (0.049%), neg=0, invalid=762 0012: dt=129.472000, rms=0.768 (0.028%), neg=0, invalid=762 0013: dt=129.472000, rms=0.768 (0.067%), neg=0, invalid=762 0014: dt=129.472000, rms=0.767 (0.126%), neg=0, invalid=762 0015: dt=129.472000, rms=0.766 (0.161%), neg=0, invalid=762 0016: dt=129.472000, rms=0.764 (0.172%), neg=0, invalid=762 0017: dt=129.472000, rms=0.763 (0.188%), neg=0, invalid=762 0018: dt=129.472000, rms=0.761 (0.201%), neg=0, invalid=762 0019: dt=129.472000, rms=0.760 (0.207%), neg=0, invalid=762 0020: dt=129.472000, rms=0.758 (0.178%), neg=0, invalid=762 0021: dt=129.472000, rms=0.757 (0.188%), neg=0, invalid=762 0022: dt=129.472000, rms=0.756 (0.145%), neg=0, invalid=762 0023: dt=129.472000, rms=0.755 (0.136%), neg=0, invalid=762 0024: dt=129.472000, rms=0.754 (0.134%), neg=0, invalid=762 0025: dt=129.472000, rms=0.753 (0.094%), neg=0, invalid=762 0026: dt=129.472000, rms=0.752 (0.098%), neg=0, invalid=762 0027: dt=129.472000, rms=0.751 (0.134%), neg=0, invalid=762 0028: dt=129.472000, rms=0.750 (0.162%), neg=0, invalid=762 0029: dt=129.472000, rms=0.749 (0.178%), neg=0, invalid=762 0030: dt=129.472000, rms=0.748 (0.137%), neg=0, invalid=762 0031: dt=129.472000, rms=0.747 (0.090%), neg=0, invalid=762 0032: dt=129.472000, rms=0.747 (0.085%), neg=0, invalid=762 0033: dt=1775.616000, rms=0.744 (0.276%), neg=0, invalid=762 0034: dt=73.984000, rms=0.744 (0.045%), neg=0, invalid=762 0035: dt=73.984000, rms=0.744 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.745, neg=0, invalid=762 0036: dt=129.472000, rms=0.743 (0.288%), neg=0, invalid=762 0037: dt=295.936000, rms=0.742 (0.104%), neg=0, invalid=762 0038: dt=295.936000, rms=0.742 (0.036%), neg=0, invalid=762 0039: dt=295.936000, rms=0.741 (0.089%), neg=0, invalid=762 0040: dt=295.936000, rms=0.740 (0.134%), neg=0, invalid=762 0041: dt=295.936000, rms=0.739 (0.079%), neg=0, invalid=762 0042: dt=295.936000, rms=0.739 (0.091%), neg=0, invalid=762 0043: dt=295.936000, rms=0.738 (0.093%), neg=0, invalid=762 0044: dt=295.936000, rms=0.737 (0.125%), neg=0, invalid=762 0045: dt=295.936000, rms=0.736 (0.135%), neg=0, invalid=762 0046: dt=295.936000, rms=0.736 (0.075%), neg=0, invalid=762 0047: dt=295.936000, rms=0.735 (0.111%), neg=0, invalid=762 0048: dt=295.936000, rms=0.734 (0.130%), neg=0, invalid=762 0049: dt=295.936000, rms=0.733 (0.093%), neg=0, invalid=762 0050: dt=295.936000, rms=0.733 (0.033%), neg=0, invalid=762 0051: dt=517.888000, rms=0.732 (0.131%), neg=0, invalid=762 0052: dt=0.000000, rms=0.732 (0.004%), neg=0, invalid=762 0053: dt=0.850000, rms=0.732 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.743, neg=0, invalid=762 0054: dt=62.298569, rms=0.740 (0.428%), neg=0, invalid=762 0055: dt=331.776000, rms=0.731 (1.194%), neg=0, invalid=762 0056: dt=188.568765, rms=0.717 (1.847%), neg=0, invalid=762 0057: dt=36.288000, rms=0.715 (0.268%), neg=0, invalid=762 0058: dt=36.288000, rms=0.715 (0.083%), neg=0, invalid=762 0059: dt=36.288000, rms=0.714 (0.062%), neg=0, invalid=762 0060: dt=36.288000, rms=0.714 (0.116%), neg=0, invalid=762 0061: dt=36.288000, rms=0.712 (0.186%), neg=0, invalid=762 0062: dt=36.288000, rms=0.710 (0.319%), neg=0, invalid=762 0063: dt=36.288000, rms=0.707 (0.452%), neg=0, invalid=762 0064: dt=36.288000, rms=0.703 (0.538%), neg=0, invalid=762 0065: dt=36.288000, rms=0.699 (0.524%), neg=0, invalid=762 0066: dt=36.288000, rms=0.696 (0.458%), neg=0, invalid=762 0067: dt=36.288000, rms=0.694 (0.355%), neg=0, invalid=762 0068: dt=36.288000, rms=0.692 (0.254%), neg=0, invalid=762 0069: dt=36.288000, rms=0.691 (0.186%), neg=0, invalid=762 0070: dt=36.288000, rms=0.689 (0.207%), neg=0, invalid=762 0071: dt=36.288000, rms=0.687 (0.267%), neg=0, invalid=762 0072: dt=36.288000, rms=0.685 (0.292%), neg=0, invalid=762 0073: dt=36.288000, rms=0.683 (0.269%), neg=0, invalid=762 0074: dt=36.288000, rms=0.682 (0.194%), neg=0, invalid=762 0075: dt=36.288000, rms=0.681 (0.134%), neg=0, invalid=762 0076: dt=36.288000, rms=0.680 (0.150%), neg=0, invalid=762 0077: dt=36.288000, rms=0.679 (0.189%), neg=0, invalid=762 0078: dt=36.288000, rms=0.678 (0.172%), neg=0, invalid=762 0079: dt=36.288000, rms=0.677 (0.102%), neg=0, invalid=762 0080: dt=36.288000, rms=0.677 (0.062%), neg=0, invalid=762 0081: dt=103.680000, rms=0.676 (0.054%), neg=0, invalid=762 0082: dt=103.680000, rms=0.676 (-0.053%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.677, neg=0, invalid=762 0083: dt=36.288000, rms=0.675 (0.320%), neg=0, invalid=762 0084: dt=36.288000, rms=0.675 (0.016%), neg=0, invalid=762 0085: dt=36.288000, rms=0.675 (0.009%), neg=0, invalid=762 0086: dt=36.288000, rms=0.675 (0.001%), neg=0, invalid=762 0087: dt=36.288000, rms=0.675 (-0.040%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.725, neg=0, invalid=762 0088: dt=9.600000, rms=0.722 (0.292%), neg=0, invalid=762 0089: dt=9.600000, rms=0.722 (0.075%), neg=0, invalid=762 0090: dt=9.600000, rms=0.722 (0.039%), neg=0, invalid=762 0091: dt=9.600000, rms=0.722 (-0.071%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.722, neg=0, invalid=762 0092: dt=0.500000, rms=0.722 (0.087%), neg=0, invalid=762 0093: dt=0.001953, rms=0.722 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.828, neg=0, invalid=762 0094: dt=7.342577, rms=0.804 (2.822%), neg=0, invalid=762 0095: dt=11.044983, rms=0.796 (1.087%), neg=0, invalid=762 0096: dt=4.032000, rms=0.795 (0.057%), neg=0, invalid=762 0097: dt=4.032000, rms=0.794 (0.101%), neg=0, invalid=762 0098: dt=4.032000, rms=0.794 (0.115%), neg=0, invalid=762 0099: dt=4.032000, rms=0.793 (0.063%), neg=0, invalid=762 0100: dt=4.032000, rms=0.793 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.793, neg=0, invalid=762 0101: dt=0.000000, rms=0.793 (0.065%), neg=0, invalid=762 0102: dt=0.000000, rms=0.793 (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=0.858, neg=0, invalid=762 0103: dt=0.000000, rms=0.858 (0.055%), neg=0, invalid=762 0104: dt=0.000000, rms=0.858 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.858, neg=0, invalid=762 0105: dt=0.000000, rms=0.858 (0.055%), neg=0, invalid=762 0106: dt=0.000000, rms=0.858 (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=0.747, neg=0, invalid=762 0107: dt=0.826615, rms=0.729 (2.379%), neg=0, invalid=762 0108: dt=0.080000, rms=0.728 (0.117%), neg=0, invalid=762 0109: dt=0.080000, rms=0.728 (-0.063%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.729, neg=0, invalid=762 0110: dt=0.028000, rms=0.728 (0.090%), neg=0, invalid=762 0111: dt=0.000438, rms=0.728 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.13367 (26) Left_Lateral_Ventricle (4): linear fit = 1.43 x + 0.0 (4450 voxels, overlap=0.438) Left_Lateral_Ventricle (4): linear fit = 1.43 x + 0.0 (4450 voxels, peak = 29), gca=28.7 gca peak = 0.15565 (16) mri peak = 0.13727 (25) Right_Lateral_Ventricle (43): linear fit = 1.59 x + 0.0 (3119 voxels, overlap=0.215) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3119 voxels, peak = 25), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.04854 (99) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1969 voxels, overlap=0.807) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1969 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.08524 (86) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (1754 voxels, overlap=0.100) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (1754 voxels, peak = 83), gca=83.2 gca peak = 0.21683 (55) mri peak = 0.07457 (76) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (2016 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (2016 voxels, peak = 73), gca=73.4 gca peak = 0.30730 (58) mri peak = 0.06892 (75) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2057 voxels, overlap=0.015) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (2057 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.09604 (98) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (148201 voxels, overlap=0.900) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (148201 voxels, peak = 101), gca=101.0 gca peak = 0.12076 (102) mri peak = 0.08862 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (149418 voxels, overlap=0.912) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (149418 voxels, peak = 102), gca=102.0 gca peak = 0.14995 (59) mri peak = 0.04266 (72) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (59963 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (59963 voxels, peak = 76), gca=76.4 gca peak = 0.15082 (58) mri peak = 0.04464 (72) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (72219 voxels, overlap=0.002) Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (72219 voxels, peak = 73), gca=73.4 gca peak = 0.14161 (67) mri peak = 0.17612 (100) Right_Caudate (50): linear fit = 1.49 x + 0.0 (1628 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.49 x + 0.0 (1628 voxels, peak = 99), gca=99.5 gca peak = 0.15243 (71) mri peak = 0.10206 (80) Left_Caudate (11): linear fit = 1.11 x + 0.0 (2064 voxels, overlap=0.462) Left_Caudate (11): linear fit = 1.11 x + 0.0 (2064 voxels, peak = 78), gca=78.5 gca peak = 0.13336 (57) mri peak = 0.03531 (90) Left_Cerebellum_Cortex (8): linear fit = 1.55 x + 0.0 (26247 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.55 x + 0.0 (26247 voxels, peak = 89), gca=88.6 gca peak = 0.13252 (56) mri peak = 0.04172 (90) Right_Cerebellum_Cortex (47): linear fit = 1.59 x + 0.0 (34441 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.59 x + 0.0 (34441 voxels, peak = 89), gca=88.8 gca peak = 0.18181 (84) mri peak = 0.06708 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9025 voxels, overlap=0.633) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9025 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.04987 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (9811 voxels, overlap=0.699) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (9811 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.09602 (73) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (659 voxels, overlap=0.040) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (659 voxels, peak = 68), gca=68.1 gca peak = 0.39313 (56) mri peak = 0.06867 (69) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (993 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (993 voxels, peak = 67), gca=67.5 gca peak = 0.14181 (85) mri peak = 0.07836 (103) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (11066 voxels, overlap=0.031) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (11066 voxels, peak = 102), gca=101.6 gca peak = 0.11978 (83) mri peak = 0.05891 (95) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (8470 voxels, overlap=0.104) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (8470 voxels, peak = 98), gca=97.5 gca peak = 0.13399 (79) mri peak = 0.05308 (87) Left_Putamen (12): linear fit = 1.14 x + 0.0 (5131 voxels, overlap=0.299) Left_Putamen (12): linear fit = 1.14 x + 0.0 (5131 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.06808 (87) Right_Putamen (51): linear fit = 1.10 x + 0.0 (5213 voxels, overlap=0.453) Right_Putamen (51): linear fit = 1.10 x + 0.0 (5213 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.06504 (88) Brain_Stem (16): linear fit = 1.14 x + 0.0 (12359 voxels, overlap=0.304) Brain_Stem (16): linear fit = 1.14 x + 0.0 (12359 voxels, peak = 92), gca=91.6 gca peak = 0.13281 (86) mri peak = 0.06517 (96) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1838 voxels, overlap=0.189) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1838 voxels, peak = 97), gca=96.8 gca peak = 0.12801 (89) mri peak = 0.06362 (101) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2110 voxels, overlap=0.293) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2110 voxels, peak = 101), gca=101.0 gca peak = 0.20494 (23) mri peak = 0.04243 (30) Third_Ventricle (14): linear fit = 1.58 x + 0.0 (207 voxels, overlap=0.186) Third_Ventricle (14): linear fit = 1.58 x + 0.0 (207 voxels, peak = 36), gca=36.2 gca peak = 0.15061 (21) mri peak = 0.19361 (32) Fourth_Ventricle (15): linear fit = 1.96 x + 0.0 (1595 voxels, overlap=0.029) Fourth_Ventricle (15): linear fit = 1.96 x + 0.0 (1595 voxels, peak = 41), gca=41.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Cerebellum_Cortex = 0.13336 (57) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Cerebellum_Cortex = 0.13252 (56) 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 1.25 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.47 x + 0.0 setting left cbm cortex = 1.25 x + 0.00 setting right cbm cortex = 1.25 x + 0.00 Right_Pallidum too bright - rescaling by 0.991 (from 1.035) to 98.5 (was 99.4) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.697, neg=0, invalid=762 0112: dt=146.461538, rms=0.672 (3.575%), neg=0, invalid=762 0113: dt=369.920000, rms=0.662 (1.486%), neg=0, invalid=762 0114: dt=295.936000, rms=0.656 (0.886%), neg=0, invalid=762 0115: dt=129.472000, rms=0.654 (0.298%), neg=0, invalid=762 0116: dt=1479.680000, rms=0.646 (1.228%), neg=0, invalid=762 0117: dt=110.976000, rms=0.646 (0.105%), neg=0, invalid=762 0118: dt=517.888000, rms=0.644 (0.178%), neg=0, invalid=762 0119: dt=443.904000, rms=0.642 (0.359%), neg=0, invalid=762 0120: dt=73.984000, rms=0.642 (0.047%), neg=0, invalid=762 0121: dt=73.984000, rms=0.642 (0.006%), neg=0, invalid=762 0122: dt=73.984000, rms=0.642 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.642, neg=0, invalid=762 0123: dt=295.936000, rms=0.640 (0.241%), neg=0, invalid=762 0124: dt=517.888000, rms=0.638 (0.325%), neg=0, invalid=762 0125: dt=73.984000, rms=0.638 (0.023%), neg=0, invalid=762 0126: dt=73.984000, rms=0.638 (0.003%), neg=0, invalid=762 0127: dt=73.984000, rms=0.638 (0.001%), neg=0, invalid=762 0128: dt=73.984000, rms=0.638 (0.000%), neg=0, invalid=762 0129: dt=517.888000, rms=0.637 (0.228%), neg=0, invalid=762 0130: dt=55.488000, rms=0.637 (0.011%), neg=0, invalid=762 0131: dt=55.488000, rms=0.637 (0.004%), neg=0, invalid=762 0132: dt=55.488000, rms=0.637 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=762 0133: dt=214.626263, rms=0.624 (2.021%), neg=0, invalid=762 0134: dt=178.895238, rms=0.612 (1.957%), neg=0, invalid=762 0135: dt=87.111111, rms=0.609 (0.481%), neg=0, invalid=762 0136: dt=134.127660, rms=0.606 (0.534%), neg=0, invalid=762 0137: dt=69.614035, rms=0.603 (0.410%), neg=0, invalid=762 0138: dt=145.152000, rms=0.601 (0.381%), neg=0, invalid=762 0139: dt=36.288000, rms=0.600 (0.232%), neg=0, invalid=762 0140: dt=248.832000, rms=0.597 (0.483%), neg=0, invalid=762 0141: dt=64.000000, rms=0.595 (0.262%), neg=0, invalid=762 0142: dt=77.735160, rms=0.594 (0.187%), neg=0, invalid=762 0143: dt=82.944000, rms=0.593 (0.150%), neg=0, invalid=762 0144: dt=90.557823, rms=0.592 (0.171%), neg=0, invalid=762 0145: dt=36.288000, rms=0.592 (0.099%), neg=0, invalid=762 0146: dt=36.288000, rms=0.591 (0.058%), neg=0, invalid=762 0147: dt=6.480000, rms=0.591 (0.011%), neg=0, invalid=762 0148: dt=0.101250, rms=0.591 (0.000%), neg=0, invalid=762 0149: dt=0.025312, rms=0.591 (0.000%), neg=0, invalid=762 0150: dt=0.012656, rms=0.591 (0.000%), neg=0, invalid=762 0151: dt=0.002215, rms=0.591 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 0152: dt=0.007594, rms=0.591 (0.034%), neg=0, invalid=762 0153: dt=0.000000, rms=0.591 (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=0.595, neg=0, invalid=762 0154: dt=0.000000, rms=0.595 (0.033%), neg=0, invalid=762 0155: dt=0.000000, rms=0.595 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.595, neg=0, invalid=762 0156: dt=96.395062, rms=0.574 (3.516%), neg=0, invalid=762 0157: dt=38.400000, rms=0.565 (1.541%), neg=0, invalid=762 0158: dt=43.968504, rms=0.562 (0.619%), neg=0, invalid=762 0159: dt=36.636580, rms=0.558 (0.678%), neg=0, invalid=762 0160: dt=25.600000, rms=0.556 (0.366%), neg=0, invalid=762 0161: dt=88.648649, rms=0.553 (0.579%), neg=0, invalid=762 0162: dt=24.129032, rms=0.550 (0.549%), neg=0, invalid=762 0163: dt=44.800000, rms=0.548 (0.380%), neg=0, invalid=762 0164: dt=11.200000, rms=0.547 (0.167%), neg=0, invalid=762 0165: dt=44.800000, rms=0.546 (0.204%), neg=0, invalid=762 0166: dt=38.400000, rms=0.544 (0.279%), neg=0, invalid=762 0167: dt=19.200000, rms=0.543 (0.127%), neg=0, invalid=762 0168: dt=179.200000, rms=0.540 (0.672%), neg=0, invalid=762 0169: dt=11.200000, rms=0.539 (0.229%), neg=0, invalid=762 0170: dt=25.600000, rms=0.538 (0.066%), neg=0, invalid=762 0171: dt=44.800000, rms=0.537 (0.154%), neg=0, invalid=762 0172: dt=11.200000, rms=0.537 (0.041%), neg=0, invalid=762 0173: dt=11.200000, rms=0.537 (0.030%), neg=0, invalid=762 0174: dt=11.200000, rms=0.537 (0.052%), neg=0, invalid=762 0175: dt=11.200000, rms=0.536 (0.078%), neg=0, invalid=762 0176: dt=11.200000, rms=0.536 (0.105%), neg=0, invalid=762 0177: dt=11.200000, rms=0.535 (0.127%), neg=0, invalid=762 0178: dt=11.200000, rms=0.534 (0.136%), neg=0, invalid=762 0179: dt=11.200000, rms=0.534 (0.142%), neg=0, invalid=762 0180: dt=11.200000, rms=0.533 (0.143%), neg=0, invalid=762 0181: dt=11.200000, rms=0.532 (0.145%), neg=0, invalid=762 0182: dt=11.200000, rms=0.531 (0.145%), neg=0, invalid=762 0183: dt=11.200000, rms=0.530 (0.151%), neg=0, invalid=762 0184: dt=11.200000, rms=0.530 (0.149%), neg=0, invalid=762 0185: dt=11.200000, rms=0.529 (0.140%), neg=0, invalid=762 0186: dt=11.200000, rms=0.528 (0.135%), neg=0, invalid=762 0187: dt=11.200000, rms=0.528 (0.126%), neg=0, invalid=762 0188: dt=11.200000, rms=0.527 (0.115%), neg=0, invalid=762 0189: dt=11.200000, rms=0.526 (0.112%), neg=0, invalid=762 0190: dt=11.200000, rms=0.526 (0.111%), neg=0, invalid=762 0191: dt=11.200000, rms=0.525 (0.101%), neg=0, invalid=762 0192: dt=11.200000, rms=0.525 (0.092%), neg=0, invalid=762 0193: dt=11.200000, rms=0.524 (0.088%), neg=0, invalid=762 0194: dt=11.200000, rms=0.524 (0.084%), neg=0, invalid=762 0195: dt=11.200000, rms=0.523 (0.073%), neg=0, invalid=762 0196: dt=11.200000, rms=0.523 (0.072%), neg=0, invalid=762 0197: dt=11.200000, rms=0.523 (0.070%), neg=0, invalid=762 0198: dt=11.200000, rms=0.522 (0.060%), neg=0, invalid=762 0199: dt=11.200000, rms=0.522 (0.061%), neg=0, invalid=762 0200: dt=11.200000, rms=0.522 (0.052%), neg=0, invalid=762 0201: dt=11.200000, rms=0.522 (0.048%), neg=0, invalid=762 0202: dt=11.200000, rms=0.521 (0.041%), neg=0, invalid=762 0203: dt=11.200000, rms=0.521 (0.043%), neg=0, invalid=762 0204: dt=11.200000, rms=0.521 (0.047%), neg=0, invalid=762 0205: dt=11.200000, rms=0.521 (0.044%), neg=0, invalid=762 0206: dt=11.200000, rms=0.520 (0.044%), neg=0, invalid=762 0207: dt=11.200000, rms=0.520 (0.039%), neg=0, invalid=762 0208: dt=11.200000, rms=0.520 (0.036%), neg=0, invalid=762 0209: dt=11.200000, rms=0.520 (0.032%), neg=0, invalid=762 0210: dt=11.200000, rms=0.520 (0.032%), neg=0, invalid=762 0211: dt=11.200000, rms=0.520 (0.032%), neg=0, invalid=762 0212: dt=11.200000, rms=0.519 (0.031%), neg=0, invalid=762 0213: dt=11.200000, rms=0.519 (0.034%), neg=0, invalid=762 0214: dt=11.200000, rms=0.519 (0.031%), neg=0, invalid=762 0215: dt=11.200000, rms=0.519 (0.030%), neg=0, invalid=762 0216: dt=11.200000, rms=0.519 (0.032%), neg=0, invalid=762 0217: dt=11.200000, rms=0.519 (0.033%), neg=0, invalid=762 0218: dt=11.200000, rms=0.518 (0.030%), neg=0, invalid=762 0219: dt=11.200000, rms=0.518 (0.025%), neg=0, invalid=762 0220: dt=11.200000, rms=0.518 (0.029%), neg=0, invalid=762 0221: dt=11.200000, rms=0.518 (0.027%), neg=0, invalid=762 0222: dt=11.200000, rms=0.518 (0.026%), neg=0, invalid=762 0223: dt=11.200000, rms=0.518 (0.026%), neg=0, invalid=762 0224: dt=11.200000, rms=0.518 (0.022%), neg=0, invalid=762 0225: dt=11.200000, rms=0.517 (0.024%), neg=0, invalid=762 0226: dt=11.200000, rms=0.517 (0.021%), neg=0, invalid=762 0227: dt=44.800000, rms=0.517 (0.004%), neg=0, invalid=762 0228: dt=44.800000, rms=0.517 (0.004%), neg=0, invalid=762 0229: dt=44.800000, rms=0.517 (0.013%), neg=0, invalid=762 0230: dt=44.800000, rms=0.517 (0.012%), neg=0, invalid=762 0231: dt=44.800000, rms=0.517 (0.016%), neg=0, invalid=762 0232: dt=44.800000, rms=0.517 (0.046%), neg=0, invalid=762 0233: dt=44.800000, rms=0.517 (0.025%), neg=0, invalid=762 0234: dt=44.800000, rms=0.517 (0.034%), neg=0, invalid=762 0235: dt=44.800000, rms=0.516 (0.028%), neg=0, invalid=762 0236: dt=44.800000, rms=0.516 (0.049%), neg=0, invalid=762 0237: dt=44.800000, rms=0.516 (0.027%), neg=0, invalid=762 0238: dt=44.800000, rms=0.516 (0.037%), neg=0, invalid=762 0239: dt=44.800000, rms=0.516 (0.036%), neg=0, invalid=762 0240: dt=44.800000, rms=0.515 (0.035%), neg=0, invalid=762 0241: dt=44.800000, rms=0.515 (0.056%), neg=0, invalid=762 0242: dt=44.800000, rms=0.515 (0.020%), neg=0, invalid=762 0243: dt=44.800000, rms=0.515 (0.049%), neg=0, invalid=762 0244: dt=44.800000, rms=0.515 (-0.034%), neg=0, invalid=762 0245: dt=25.600000, rms=0.515 (0.005%), neg=0, invalid=762 0246: dt=2.800000, rms=0.515 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0247: dt=0.000000, rms=0.534 (0.048%), neg=0, invalid=762 0248: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0249: dt=0.000000, rms=0.534 (0.048%), neg=0, invalid=762 0250: dt=0.000000, rms=0.534 (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=0.574, neg=0, invalid=762 0251: dt=1.280000, rms=0.571 (0.493%), neg=0, invalid=762 0252: dt=0.112000, rms=0.571 (0.003%), neg=0, invalid=762 0253: dt=0.112000, rms=0.571 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.571, neg=0, invalid=762 0254: dt=0.448000, rms=0.570 (0.087%), neg=0, invalid=762 0255: dt=0.112000, rms=0.570 (0.004%), neg=0, invalid=762 0256: dt=0.112000, rms=0.570 (0.002%), neg=0, invalid=762 0257: dt=0.112000, rms=0.570 (-0.007%), 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=0.523, neg=0, invalid=762 0258: dt=0.448000, rms=0.509 (2.772%), neg=0, invalid=762 0259: dt=0.384000, rms=0.507 (0.421%), neg=0, invalid=762 0260: dt=0.448000, rms=0.505 (0.331%), neg=0, invalid=762 0261: dt=0.448000, rms=0.504 (0.180%), neg=0, invalid=762 0262: dt=0.448000, rms=0.503 (0.143%), neg=0, invalid=762 0263: dt=0.448000, rms=0.503 (0.089%), neg=0, invalid=762 0264: dt=0.448000, rms=0.502 (0.083%), neg=0, invalid=762 0265: dt=0.448000, rms=0.502 (0.050%), neg=0, invalid=762 0266: dt=0.448000, rms=0.502 (0.057%), neg=0, invalid=762 0267: dt=0.448000, rms=0.502 (0.030%), neg=0, invalid=762 0268: dt=0.448000, rms=0.501 (0.043%), neg=0, invalid=762 0269: dt=0.448000, rms=0.501 (0.058%), neg=0, invalid=762 0270: dt=0.224000, rms=0.501 (0.012%), neg=0, invalid=762 0271: dt=0.224000, rms=0.501 (0.029%), neg=0, invalid=762 0272: dt=0.224000, rms=0.501 (0.036%), neg=0, invalid=762 0273: dt=0.224000, rms=0.501 (0.005%), neg=0, invalid=762 0274: dt=0.224000, rms=0.501 (0.011%), neg=0, invalid=762 0275: dt=0.224000, rms=0.501 (0.017%), neg=0, invalid=762 0276: dt=0.224000, rms=0.501 (0.024%), neg=0, invalid=762 0277: dt=0.224000, rms=0.500 (0.029%), neg=0, invalid=762 0278: dt=0.224000, rms=0.500 (0.020%), neg=0, invalid=762 0279: dt=0.224000, rms=0.500 (0.017%), neg=0, invalid=762 0280: dt=0.256000, rms=0.500 (0.006%), neg=0, invalid=762 0281: dt=0.256000, rms=0.500 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 0282: dt=0.320000, rms=0.497 (0.635%), neg=0, invalid=762 0283: dt=0.448000, rms=0.496 (0.294%), neg=0, invalid=762 0284: dt=0.448000, rms=0.496 (0.035%), neg=0, invalid=762 0285: dt=0.448000, rms=0.496 (0.018%), neg=0, invalid=762 0286: dt=0.448000, rms=0.496 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.494, neg=0, invalid=762 0287: dt=0.000000, rms=0.493 (0.062%), neg=0, invalid=762 0288: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.494, neg=0, invalid=762 0289: dt=23.120000, rms=0.493 (0.062%), neg=0, invalid=762 0290: dt=32.368000, rms=0.493 (0.001%), neg=0, invalid=762 0291: dt=32.368000, rms=0.493 (0.003%), neg=0, invalid=762 0292: dt=32.368000, rms=0.493 (0.004%), neg=0, invalid=762 0293: dt=32.368000, rms=0.493 (0.006%), neg=0, invalid=762 0294: dt=32.368000, rms=0.493 (0.004%), neg=0, invalid=762 0295: dt=32.368000, rms=0.493 (0.008%), neg=0, invalid=762 0296: dt=32.368000, rms=0.493 (0.009%), neg=0, invalid=762 0297: dt=32.368000, rms=0.493 (0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0298: dt=17.454545, rms=0.493 (0.091%), neg=0, invalid=762 0299: dt=9.072000, rms=0.493 (0.002%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0300: dt=9.072000, rms=0.493 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0301: dt=124.416000, rms=0.492 (0.331%), neg=0, invalid=762 0302: dt=36.288000, rms=0.491 (0.105%), neg=0, invalid=762 0303: dt=36.288000, rms=0.491 (0.037%), neg=0, invalid=762 0304: dt=36.288000, rms=0.491 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0305: dt=36.288000, rms=0.490 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0306: dt=36.288000, rms=0.490 (0.083%), neg=0, invalid=762 0307: dt=36.288000, rms=0.489 (0.083%), neg=0, invalid=762 0308: dt=36.288000, rms=0.489 (0.073%), neg=0, invalid=762 0309: dt=36.288000, rms=0.489 (0.069%), neg=0, invalid=762 0310: dt=124.416000, rms=0.489 (0.032%), 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 = 9 after 2 iterations, nbhd size=0, neg = 0 0311: dt=11.200000, rms=0.488 (0.179%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 3 iterations, nbhd size=0, neg = 0 0312: dt=25.600000, rms=0.488 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 4 iterations, nbhd size=0, neg = 0 0313: dt=25.600000, rms=0.487 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 3 iterations, nbhd size=0, neg = 0 0314: dt=25.600000, rms=0.486 (0.160%), neg=0, invalid=762 iter 0, gcam->neg = 41 after 7 iterations, nbhd size=0, neg = 0 0315: dt=25.600000, rms=0.486 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 60 after 7 iterations, nbhd size=0, neg = 0 0316: dt=25.600000, rms=0.486 (-0.054%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 6 iterations, nbhd size=0, neg = 0 0317: dt=102.400000, rms=0.485 (0.284%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0318: dt=19.200000, rms=0.484 (0.070%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0319: dt=19.200000, rms=0.484 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0320: dt=19.200000, rms=0.484 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0321: dt=19.200000, rms=0.484 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 5 iterations, nbhd size=0, neg = 0 0322: dt=19.200000, rms=0.483 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 6 iterations, nbhd size=0, neg = 0 0323: dt=19.200000, rms=0.483 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 4 iterations, nbhd size=0, neg = 0 0324: dt=19.200000, rms=0.482 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0325: dt=44.800000, rms=0.482 (0.087%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0326: dt=44.800000, rms=0.478 (0.822%), neg=0, invalid=762 0327: dt=24.177778, rms=0.477 (0.250%), neg=0, invalid=762 0328: dt=38.400000, rms=0.476 (0.202%), neg=0, invalid=762 0329: dt=38.400000, rms=0.476 (0.051%), neg=0, invalid=762 0330: dt=38.400000, rms=0.474 (0.304%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0331: dt=38.400000, rms=0.474 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0332: dt=38.400000, rms=0.474 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0333: dt=38.400000, rms=0.473 (0.094%), neg=0, invalid=762 0334: dt=38.400000, rms=0.472 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0335: dt=38.400000, rms=0.472 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 4 iterations, nbhd size=0, neg = 0 0336: dt=38.400000, rms=0.471 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0337: dt=38.400000, rms=0.470 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0338: dt=38.400000, rms=0.470 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0339: dt=38.400000, rms=0.469 (0.106%), neg=0, invalid=762 0340: dt=19.200000, rms=0.469 (0.102%), neg=0, invalid=762 0341: dt=19.200000, rms=0.469 (0.020%), neg=0, invalid=762 0342: dt=19.200000, rms=0.469 (0.022%), neg=0, invalid=762 0343: dt=19.200000, rms=0.469 (0.034%), neg=0, invalid=762 0344: dt=19.200000, rms=0.468 (0.025%), neg=0, invalid=762 0345: dt=19.200000, rms=0.468 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 0346: dt=0.576000, rms=0.473 (0.070%), neg=0, invalid=762 0347: dt=0.144000, rms=0.473 (0.000%), neg=0, invalid=762 0348: dt=0.144000, rms=0.473 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 0349: dt=1.008000, rms=0.473 (0.073%), neg=0, invalid=762 0350: dt=1.008000, rms=0.473 (0.003%), neg=0, invalid=762 0351: dt=1.008000, rms=0.473 (0.001%), neg=0, invalid=762 0352: dt=1.008000, rms=0.473 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0353: dt=1.280000, rms=0.481 (0.215%), neg=0, invalid=762 0354: dt=0.320000, rms=0.481 (0.005%), neg=0, invalid=762 0355: dt=0.320000, rms=0.481 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.481, neg=0, invalid=762 0356: dt=1.792000, rms=0.480 (0.268%), neg=0, invalid=762 0357: dt=1.792000, rms=0.479 (0.067%), neg=0, invalid=762 0358: dt=1.792000, rms=0.479 (0.032%), neg=0, invalid=762 0359: dt=1.792000, rms=0.479 (-0.036%), 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=0.474, neg=0, invalid=762 iter 0, gcam->neg = 1069 after 12 iterations, nbhd size=1, neg = 0 0360: dt=2.127237, rms=0.441 (6.966%), neg=0, invalid=762 0361: dt=0.028000, rms=0.441 (0.019%), neg=0, invalid=762 0362: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=762 0363: dt=0.028000, rms=0.441 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=762 0364: dt=0.048000, rms=0.441 (0.109%), neg=0, invalid=762 0365: dt=0.001750, rms=0.441 (0.004%), neg=0, invalid=762 0366: dt=0.001750, rms=0.441 (0.000%), neg=0, invalid=762 0367: dt=0.001750, rms=0.441 (0.000%), neg=0, invalid=762 0368: dt=0.001750, rms=0.441 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 0369: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 0370: dt=23.120000, rms=0.425 (0.002%), neg=0, invalid=762 0371: dt=2.023000, rms=0.425 (0.000%), neg=0, invalid=762 0372: dt=2.023000, rms=0.425 (0.000%), neg=0, invalid=762 0373: dt=2.023000, rms=0.425 (-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=0.425, neg=0, invalid=762 0374: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 0375: dt=25.920000, rms=0.425 (0.012%), neg=0, invalid=762 0376: dt=31.104000, rms=0.425 (0.005%), neg=0, invalid=762 0377: dt=31.104000, rms=0.425 (0.004%), neg=0, invalid=762 0378: dt=31.104000, rms=0.425 (-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=0.426, neg=0, invalid=762 0379: dt=8.000000, rms=0.426 (0.053%), neg=0, invalid=762 0380: dt=2.800000, rms=0.426 (0.005%), neg=0, invalid=762 0381: dt=2.800000, rms=0.426 (0.001%), neg=0, invalid=762 0382: dt=2.800000, rms=0.426 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0383: dt=38.400000, rms=0.424 (0.369%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0384: dt=25.600000, rms=0.423 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0385: dt=25.600000, rms=0.423 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0386: dt=25.600000, rms=0.422 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 5 iterations, nbhd size=0, neg = 0 0387: dt=25.600000, rms=0.422 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0388: dt=25.600000, rms=0.422 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=0, neg = 0 0389: dt=25.600000, rms=0.421 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 5 iterations, nbhd size=0, neg = 0 0390: dt=25.600000, rms=0.421 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0391: dt=32.000000, rms=0.421 (0.044%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0392: dt=4.476190, rms=0.424 (0.085%), neg=0, invalid=762 0393: dt=1.750000, rms=0.424 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0394: dt=1.750000, rms=0.424 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0395: dt=13.355932, rms=0.423 (0.290%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0396: dt=21.333333, rms=0.422 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0397: dt=21.333333, rms=0.422 (-0.229%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0398: dt=0.000063, rms=0.429 (0.000%), neg=0, invalid=762 0399: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0400: dt=0.000000, rms=0.429 (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=0.418, neg=0, invalid=762 iter 0, gcam->neg = 401 after 18 iterations, nbhd size=1, neg = 0 0401: dt=1.093347, rms=0.410 (1.886%), neg=0, invalid=762 0402: dt=0.000027, rms=0.410 (0.000%), neg=0, invalid=762 0403: dt=0.000027, rms=0.410 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0404: dt=0.112000, rms=0.410 (0.113%), neg=0, invalid=762 0405: dt=0.112000, rms=0.409 (0.077%), neg=0, invalid=762 0406: dt=0.112000, rms=0.409 (0.067%), neg=0, invalid=762 0407: dt=0.112000, rms=0.409 (0.057%), neg=0, invalid=762 0408: dt=0.112000, rms=0.409 (-0.013%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 30 minutes and 8 seconds. mri_ca_register utimesec 6879.949314 mri_ca_register stimesec 23.110616 mri_ca_register ru_maxrss 1608500 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 20414331 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63472 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 17070 mri_ca_register ru_nivcsw 5321 FSRUNTIME@ mri_ca_register 1.5022 hours 8 threads #-------------------------------------- #@# SubCort Seg Tue May 25 19:21:53 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 blg6114.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-06/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 12.73 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 = 0.12827 (27) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (6106 voxels, overlap=0.391) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (6106 voxels, peak = 26), gca=26.1 gca peak = 0.17677 (13) mri peak = 0.13709 (25) Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (7193 voxels, overlap=0.249) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (7193 voxels, peak = 24), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.11128 (99) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (1595 voxels, overlap=0.797) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (1595 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.07914 (100) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (1815 voxels, overlap=1.020) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (1815 voxels, peak = 102), gca=102.2 gca peak = 0.24553 (55) mri peak = 0.09547 (76) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2328 voxels, overlap=0.023) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (2328 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.09327 (74) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (2167 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (2167 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.09728 (98) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (113426 voxels, overlap=0.773) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (113426 voxels, peak = 100), gca=100.4 gca peak = 0.07714 (104) mri peak = 0.08843 (99) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (108965 voxels, overlap=0.776) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (108965 voxels, peak = 102), gca=102.4 gca peak = 0.09712 (58) mri peak = 0.04637 (72) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (76583 voxels, overlap=0.008) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (76583 voxels, peak = 73), gca=73.4 gca peak = 0.11620 (58) mri peak = 0.04872 (72) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (71870 voxels, overlap=0.033) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (71870 voxels, peak = 72), gca=72.2 gca peak = 0.30970 (66) mri peak = 0.09307 (80) Right_Caudate (50): linear fit = 1.17 x + 0.0 (2754 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.17 x + 0.0 (2754 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.12349 (80) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2257 voxels, overlap=0.507) Left_Caudate (11): linear fit = 1.12 x + 0.0 (2257 voxels, peak = 77), gca=76.9 gca peak = 0.13902 (56) mri peak = 0.04373 (72) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (35287 voxels, overlap=0.002) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (35287 voxels, peak = 74), gca=74.2 gca peak = 0.14777 (55) mri peak = 0.04326 (72) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (39939 voxels, overlap=0.004) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (39939 voxels, peak = 73), gca=72.9 gca peak = 0.16765 (84) mri peak = 0.10711 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (15451 voxels, overlap=0.530) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (15451 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.11806 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (15116 voxels, overlap=0.466) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (15116 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.10131 (78) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (916 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (916 voxels, peak = 76), gca=75.5 gca peak = 0.33601 (57) mri peak = 0.08895 (76) Right_Amygdala (54): linear fit = 1.33 x + 0.0 (1113 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.33 x + 0.0 (1113 voxels, peak = 76), gca=75.5 gca peak = 0.11131 (90) mri peak = 0.06381 (98) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (9842 voxels, overlap=0.284) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (9842 voxels, peak = 102), gca=102.2 gca peak = 0.11793 (83) mri peak = 0.08320 (95) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (8953 voxels, overlap=0.098) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (8953 voxels, peak = 95), gca=95.0 gca peak = 0.08324 (81) mri peak = 0.08818 (87) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2798 voxels, overlap=0.427) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2798 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.08213 (87) Right_Putamen (51): linear fit = 1.11 x + 0.0 (3932 voxels, overlap=0.530) Right_Putamen (51): linear fit = 1.11 x + 0.0 (3932 voxels, peak = 85), gca=85.1 gca peak = 0.08424 (78) mri peak = 0.06692 (88) Brain_Stem (16): linear fit = 1.12 x + 0.0 (25721 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (25721 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.07504 (102) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (3005 voxels, overlap=0.014) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (3005 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.07399 (101) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (3192 voxels, overlap=0.088) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (3192 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.15038 (28) Third_Ventricle (14): linear fit = 1.12 x + 0.0 (122 voxels, overlap=0.588) Third_Ventricle (14): linear fit = 1.12 x + 0.0 (122 voxels, peak = 27), gca=27.0 gca peak = 0.19357 (14) mri peak = 0.13955 (28) Fourth_Ventricle (15): linear fit = 1.66 x + 0.0 (812 voxels, overlap=0.195) Fourth_Ventricle (15): linear fit = 1.66 x + 0.0 (812 voxels, peak = 23), gca=23.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.29 x + 0.0 estimating mean wm scale to be 0.98 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 Left_Pallidum too bright - rescaling by 0.962 (from 1.065) to 98.4 (was 102.2) Right_Pallidum too bright - rescaling by 0.991 (from 1.045) to 98.4 (was 99.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15817 (24) mri peak = 0.12827 (27) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (6106 voxels, overlap=0.803) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (6106 voxels, peak = 25), gca=25.3 gca peak = 0.14041 (19) mri peak = 0.13709 (25) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (7193 voxels, overlap=0.444) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (7193 voxels, peak = 23), gca=22.5 gca peak = 0.28305 (99) mri peak = 0.11128 (99) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1595 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1595 voxels, peak = 100), gca=100.5 gca peak = 0.17907 (97) mri peak = 0.07914 (100) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1815 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1815 voxels, peak = 101), gca=101.4 gca peak = 0.24553 (71) mri peak = 0.09547 (76) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (2328 voxels, overlap=1.004) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (2328 voxels, peak = 73), gca=73.5 gca peak = 0.26891 (73) mri peak = 0.09327 (74) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (2167 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (2167 voxels, peak = 73), gca=73.0 gca peak = 0.07847 (101) mri peak = 0.09728 (98) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (113426 voxels, overlap=0.764) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (113426 voxels, peak = 101), gca=101.0 gca peak = 0.07986 (103) mri peak = 0.08843 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (108965 voxels, overlap=0.770) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (108965 voxels, peak = 102), gca=102.5 gca peak = 0.07778 (73) mri peak = 0.04637 (72) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (76583 voxels, overlap=0.936) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (76583 voxels, peak = 73), gca=73.0 gca peak = 0.09555 (72) mri peak = 0.04872 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (71870 voxels, overlap=0.950) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (71870 voxels, peak = 71), gca=70.9 gca peak = 0.23747 (78) mri peak = 0.09307 (80) Right_Caudate (50): linear fit = 1.01 x + 0.0 (2754 voxels, overlap=1.009) Right_Caudate (50): linear fit = 1.01 x + 0.0 (2754 voxels, peak = 79), gca=79.2 gca peak = 0.12966 (76) mri peak = 0.12349 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (2257 voxels, overlap=0.936) Left_Caudate (11): linear fit = 1.00 x + 0.0 (2257 voxels, peak = 76), gca=76.0 gca peak = 0.10956 (73) mri peak = 0.04373 (72) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (35287 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (35287 voxels, peak = 73), gca=72.6 gca peak = 0.11418 (73) mri peak = 0.04326 (72) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (39939 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (39939 voxels, peak = 72), gca=71.9 gca peak = 0.15948 (90) mri peak = 0.10711 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (15451 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (15451 voxels, peak = 90), gca=89.6 gca peak = 0.15241 (90) mri peak = 0.11806 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (15116 voxels, overlap=0.868) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (15116 voxels, peak = 90), gca=89.6 gca peak = 0.27936 (77) mri peak = 0.10131 (78) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (916 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (916 voxels, peak = 76), gca=75.8 gca peak = 0.25156 (74) mri peak = 0.08895 (76) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1113 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1113 voxels, peak = 74), gca=74.0 gca peak = 0.11222 (100) mri peak = 0.06381 (98) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (9842 voxels, overlap=0.929) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (9842 voxels, peak = 100), gca=100.5 gca peak = 0.09829 (95) mri peak = 0.08320 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (8953 voxels, overlap=0.907) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (8953 voxels, peak = 95), gca=95.5 gca peak = 0.08060 (90) mri peak = 0.08818 (87) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2798 voxels, overlap=0.820) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2798 voxels, peak = 90), gca=89.6 gca peak = 0.08526 (85) mri peak = 0.08213 (87) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3932 voxels, overlap=0.928) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3932 voxels, peak = 85), gca=85.0 gca peak = 0.07944 (88) mri peak = 0.06692 (88) Brain_Stem (16): linear fit = 0.99 x + 0.0 (25721 voxels, overlap=0.824) Brain_Stem (16): linear fit = 0.99 x + 0.0 (25721 voxels, peak = 87), gca=86.7 gca peak = 0.09682 (96) mri peak = 0.07504 (102) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (3005 voxels, overlap=0.791) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (3005 voxels, peak = 97), gca=97.4 gca peak = 0.14435 (97) mri peak = 0.07399 (101) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (3192 voxels, overlap=0.889) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (3192 voxels, peak = 98), gca=98.5 gca peak = 0.16820 (29) mri peak = 0.15038 (28) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (122 voxels, overlap=0.813) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (122 voxels, peak = 29), gca=29.0 gca peak = 0.16542 (21) mri peak = 0.13955 (28) Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (812 voxels, overlap=0.468) Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (812 voxels, peak = 27), gca=26.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.36646 (101) gca peak CSF = 0.18586 (47) gca peak Left_Accumbens_area = 0.48173 (70) gca peak Left_undetermined = 0.96707 (30) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.29796 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14509 (37) gca peak Fifth_Ventricle = 0.86987 (41) gca peak WM_hypointensities = 0.08196 (75) gca peak non_WM_hypointensities = 0.07893 (57) gca peak Optic_Chiasm = 0.63169 (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 1.13 x + 0.0 Left_Pallidum too bright - rescaling by 0.974 (from 1.045) to 98.7 (was 101.4) Right_Pallidum too bright - rescaling by 0.982 (from 1.015) to 98.7 (was 100.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 144903 voxels changed in iteration 0 of unlikely voxel relabeling 741 voxels changed in iteration 1 of unlikely voxel relabeling 35 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 161028 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 481 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 123473 changed. image ll: -2.081, PF=0.500 pass 2: 32640 changed. image ll: -2.080, PF=0.500 pass 3: 10615 changed. pass 4: 4395 changed. 152894 voxels changed in iteration 0 of unlikely voxel relabeling 906 voxels changed in iteration 1 of unlikely voxel relabeling 55 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 13005 voxels changed in iteration 0 of unlikely voxel relabeling 250 voxels changed in iteration 1 of unlikely voxel relabeling 53 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 12090 voxels changed in iteration 0 of unlikely voxel relabeling 109 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 7 voxels changed in iteration 3 of unlikely voxel relabeling 5 voxels changed in iteration 4 of unlikely voxel relabeling 10556 voxels changed in iteration 0 of unlikely voxel relabeling 66 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4884.824412 mri_ca_label stimesec 14.365924 mri_ca_label ru_maxrss 3155604 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 16381483 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 4456 mri_ca_label ru_oublock 736 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 603 mri_ca_label ru_nivcsw 3284 auto-labeling took 80 minutes and 24 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/cc_up.lta sub-06 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-06/mri/transforms/cc_up.lta reading aseg from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/aseg.auto_noCCseg.mgz reading norm from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/norm.mgz 58053 voxels in left wm, 56633 in right wm, xrange [156, 166] searching rotation angles z=[-8 6], y=[-5 9] searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 global minimum found at slice 161.0, rotations (2.19, -0.87) final transformation (x=161.0, yr=2.189, zr=-0.872): 0.99915 0.01521 0.03819 -39.26532; -0.01520 0.99988 -0.00058 18.53152; -0.03820 -0.00000 0.99927 11.23973; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 131] in xformed coordinates best xformed slice 127 cc center is found at 127 112 123 eigenvectors: 0.00121 0.00142 1.00000; -0.04510 -0.99898 0.00147; 0.99898 -0.04510 -0.00115; error in mid anterior detected - correcting... writing aseg with callosum to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/aseg.auto.mgz... corpus callosum segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Tue May 25 20:43:16 UTC 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue May 25 20:43:17 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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... 756 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 78 (78), valley at 43 (43) csf peak at 26, setting threshold to 60 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 77 (77), valley at 43 (43) csf peak at 25, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 55 seconds. #-------------------------------------------- #@# Mask BFS Tue May 25 20:48:19 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2612862 voxels in mask (pct= 7.97) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue May 25 20:48:28 UTC 2021 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.2 +- 6.6 [79.0 --> 125.0] GM (77.0) : 76.0 +- 9.7 [30.0 --> 95.0] setting bottom of white matter range to 85.7 setting top of gray matter range to 95.4 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, 2103 filled 11 bright non-wm voxels segmented. 8809 diagonally connected voxels added... white matter segmentation took 2.0 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... 208 voxels added to wm to prevent paths from MTL structures to cortex 6181 additional wm voxels added 0 additional wm voxels added SEG EDIT: 87944 voxels turned on, 110658 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 108 new 108 115,126,128 old 108 new 108 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 51 found - 51 modified | TOTAL: 51 pass 2 (xy+): 0 found - 51 modified | TOTAL: 51 pass 1 (xy-): 28 found - 28 modified | TOTAL: 79 pass 2 (xy-): 0 found - 28 modified | TOTAL: 79 pass 1 (yz+): 58 found - 58 modified | TOTAL: 137 pass 2 (yz+): 0 found - 58 modified | TOTAL: 137 pass 1 (yz-): 66 found - 66 modified | TOTAL: 203 pass 2 (yz-): 0 found - 66 modified | TOTAL: 203 pass 1 (xz+): 40 found - 40 modified | TOTAL: 243 pass 2 (xz+): 0 found - 40 modified | TOTAL: 243 pass 1 (xz-): 39 found - 39 modified | TOTAL: 282 pass 2 (xz-): 0 found - 39 modified | TOTAL: 282 Iteration Number : 1 pass 1 (+++): 27 found - 27 modified | TOTAL: 27 pass 2 (+++): 0 found - 27 modified | TOTAL: 27 pass 1 (+++): 31 found - 31 modified | TOTAL: 58 pass 2 (+++): 0 found - 31 modified | TOTAL: 58 pass 1 (+++): 35 found - 35 modified | TOTAL: 93 pass 2 (+++): 0 found - 35 modified | TOTAL: 93 pass 1 (+++): 40 found - 40 modified | TOTAL: 133 pass 2 (+++): 0 found - 40 modified | TOTAL: 133 Iteration Number : 1 pass 1 (++): 166 found - 166 modified | TOTAL: 166 pass 2 (++): 0 found - 166 modified | TOTAL: 166 pass 1 (+-): 223 found - 223 modified | TOTAL: 389 pass 2 (+-): 0 found - 223 modified | TOTAL: 389 pass 1 (--): 157 found - 157 modified | TOTAL: 546 pass 2 (--): 0 found - 157 modified | TOTAL: 546 pass 1 (-+): 170 found - 170 modified | TOTAL: 716 pass 2 (-+): 0 found - 170 modified | TOTAL: 716 Iteration Number : 2 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 19 found - 19 modified | TOTAL: 36 pass 2 (xy-): 0 found - 19 modified | TOTAL: 36 pass 1 (yz+): 18 found - 18 modified | TOTAL: 54 pass 2 (yz+): 0 found - 18 modified | TOTAL: 54 pass 1 (yz-): 16 found - 16 modified | TOTAL: 70 pass 2 (yz-): 0 found - 16 modified | TOTAL: 70 pass 1 (xz+): 19 found - 19 modified | TOTAL: 89 pass 2 (xz+): 0 found - 19 modified | TOTAL: 89 pass 1 (xz-): 13 found - 13 modified | TOTAL: 102 pass 2 (xz-): 0 found - 13 modified | TOTAL: 102 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 10 found - 10 modified | TOTAL: 12 pass 2 (+++): 0 found - 10 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 pass 1 (+++): 8 found - 8 modified | TOTAL: 20 pass 2 (+++): 0 found - 8 modified | TOTAL: 20 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 5 found - 5 modified | TOTAL: 10 pass 2 (+-): 0 found - 5 modified | TOTAL: 10 pass 1 (--): 8 found - 8 modified | TOTAL: 18 pass 2 (--): 0 found - 8 modified | TOTAL: 18 pass 1 (-+): 4 found - 4 modified | TOTAL: 22 pass 2 (-+): 0 found - 4 modified | TOTAL: 22 Iteration Number : 3 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 1 found - 1 modified | TOTAL: 7 pass 2 (xy-): 0 found - 1 modified | TOTAL: 7 pass 1 (yz+): 0 found - 0 modified | TOTAL: 7 pass 1 (yz-): 0 found - 0 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 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 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1285 (out of 1021285: 0.125822) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue May 25 20:51:13 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 1.05030 0.03252 0.07536 -26.80139; -0.03747 1.08588 0.17768 -10.61394; -0.08022 -0.16913 1.04170 22.53868; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05030 0.03252 0.07536 -26.80139; -0.03747 1.08588 0.17768 -10.61394; -0.08022 -0.16913 1.04170 22.53868; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (546, 2188) area[0] = 1914 (min = 546, max = 2188), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (157, 151, 185), TAL = (2.4, 20.0, 7.2) talairach voxel to voxel transform 0.94602 -0.03798 -0.06196 26.34811; 0.02018 0.89627 -0.15433 13.53236; 0.07613 0.14259 0.93014 -17.41042; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (157, 151, 185) --> (2.4, 20.0, 7.2) done. writing output to filled.mgz... filling took 1.1 minutes talairach cc position changed to (2.40, 20.00, 7.20) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(20.40, 20.00, 7.20) SRC: (136.39, 123.03, 186.44) search lh wm seed point around talairach space (-15.60, 20.00, 7.20), SRC: (178.96, 123.94, 189.86) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... Started at Tue May 25 17:44:49 UTC 2021 Ended at Tue May 25 20:52:18 UTC 2021 #@#%# recon-all-run-time-hours 3.125 recon-all -s sub-06 finished without error at Tue May 25 20:52:18 UTC 2021 New invocation of recon-all Tue May 25 22:48:08 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 /opt/freesurfer/bin/recon-all -parallel -subjid sub-06 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -T2pial -cortribbon subjid sub-06 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 blg6114.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 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 139370432 3709056 2232764 53558772 48573808 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-22:48:08-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-22:48:09-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: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue May 25 22:48:12 UTC 2021 bbregister --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.lta --init-coreg --T2 tmp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970 Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.dat.log Tue May 25 22:48:12 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-06/scripts /opt/freesurfer/bin/bbregister --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg6114.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-06/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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-06/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-06/mri/transforms/tmp.bbregister.263970/template.nii... mri_coreg --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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-06/scripts cmdline mri_coreg --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg6114.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-06/mri/transforms/tmp.bbregister.263970/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.8000 0.0000 -0.8000 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 = 116.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0352140471 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.80001; 0.00000 1.00000 0.00000 0.00001; 0.00000 0.00000 1.00000 -0.80000; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -1.00000 0.00000 0.00000 262.99997; 0.00000 0.00000 1.00000 -9.99998; 0.00000 -1.00000 0.00000 318.99997; 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 -0.80001 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0313114 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0357244015 #@# 4 188 -0.80001 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0357244 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.035724 #@# 4 190 0.19999 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0360961 #@# 4 195 0.16250 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0360968 #@# 4 196 0.15250 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0360969 #@# 4 206 0.13023 0.38197 1.20000 0.00000 0.00000 0.00000 -1.0361168 #@# 4 207 0.13023 0.30600 1.20000 0.00000 0.00000 0.00000 -1.0361189 #@# 4 214 0.13023 0.29219 0.58196 0.00000 0.00000 0.00000 -1.0361660 #@# 4 216 0.13023 0.29219 0.75323 0.00000 0.00000 0.00000 -1.0361716 #@# 4 217 0.13023 0.29219 0.73470 0.00000 0.00000 0.00000 -1.0361718 #@# 4 218 0.13023 0.29219 0.72241 0.00000 0.00000 0.00000 -1.0361719 #@# 4 226 0.13023 0.29219 0.72241 0.38197 0.00000 0.00000 -1.0361809 #@# 4 227 0.13023 0.29219 0.72241 0.24212 0.00000 0.00000 -1.0361845 #@# 4 247 0.13023 0.29219 0.72241 0.26212 -0.01430 0.09870 -1.0361869 #@# 4 252 0.13023 0.29219 0.72241 0.26212 -0.01430 0.13337 -1.0361871 powell nthiter 1: fret = -1.036187 #@# 4 261 0.12023 0.29219 0.72241 0.26212 -0.01430 0.13337 -1.0361872 #@# 4 269 0.12023 0.13939 0.72241 0.26212 -0.01430 0.13337 -1.0361925 #@# 4 270 0.12023 0.14939 0.72241 0.26212 -0.01430 0.13337 -1.0361927 #@# 4 281 0.12023 0.17249 0.80086 0.26212 -0.01430 0.13337 -1.0361941 #@# 4 282 0.12023 0.17249 0.79086 0.26212 -0.01430 0.13337 -1.0361942 #@# 4 292 0.12023 0.17249 0.78086 0.34279 -0.01430 0.13337 -1.0361953 #@# 4 297 0.12023 0.17249 0.78086 0.36383 -0.01430 0.13337 -1.0361954 #@# 4 305 0.12023 0.17249 0.78086 0.36383 -0.07726 0.13337 -1.0361961 Powell done niters total = 1 OptTimeSec 9.9 sec OptTimeMin 0.17 min nEvals 319 Final parameters 0.12023165 0.17248644 0.78086489 0.36382699 -0.08772265 0.12100271 Final cost -1.036196141705566 --------------------------------- mri_coreg utimesec 201.449723 mri_coreg stimesec 1.120573 mri_coreg ru_maxrss 890536 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 880456 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10064 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 802 mri_coreg ru_nivcsw 135 Final RefRAS-to-MovRAS 1.00000 0.00211 -0.00153 0.12023; -0.00210 0.99998 0.00635 0.17249; 0.00154 -0.00635 0.99998 0.78086; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -1.00000 0.00153 0.00211 263.66193; 0.00210 -0.00635 0.99998 -9.21173; -0.00154 -0.99998 -0.00635 322.02945; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.1202 0.1725 0.7809 0.3638 -0.0877 0.1210 nhits = 307655 out of 32768000, Percent Overlap: 60.1 mri_coreg RunTimeSec 78.6 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/mri_coreg.lta --s sub-06 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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-06/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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 blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat subject sub-06 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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 1622974622 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -1.00000 -0.00211 0.00153 -0.19631; 0.00154 -0.00635 0.99998 0.61626; 0.00210 -0.99998 -0.00635 -0.08401; 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 0.938148 1 -25.0 -25.0 25.0 0.945252 2 -25.0 25.0 -25.0 0.975470 3 -25.0 25.0 25.0 0.941900 4 25.0 -25.0 -25.0 0.972514 5 25.0 -25.0 25.0 0.990208 6 25.0 25.0 -25.0 0.973561 7 25.0 25.0 25.0 0.993441 REL: 8 0.108777 7.730496 0.966312 rel = 0.112569 Initial costs ---------------- Number of surface hits 4125 WM Intensity 729.7891 +/- 223.7845 Ctx Intensity 1002.3210 +/- 233.5627 Pct Contrast 32.8407 +/- 19.2404 Cost 0.1088 RelCost 0.1126 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9322 0.9322 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9116 0.9116 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8737 0.8737 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8094 0.8094 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7559 0.7559 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7259 0.7259 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6361 0.6361 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.5915 0.5915 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1088 0.1088 0.0 Brute Force -------------------------- Min cost was 0.108777 Number of iterations 729 Search time 1.968000 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 = 0.108777 7 -0.075 0.000 0.000 0.000 0.000 0.000 0.1078655362 8 -0.099 0.000 0.000 0.000 0.000 0.000 0.1075977237 11 -0.133 0.000 0.000 0.000 0.000 0.000 0.1075635888 12 -0.127 0.000 0.000 0.000 0.000 0.000 0.1075605991 13 -0.126 0.000 0.000 0.000 0.000 0.000 0.1075570166 14 -0.115 0.000 0.000 0.000 0.000 0.000 0.1075444865 16 -0.117 0.000 0.000 0.000 0.000 0.000 0.1075438823 22 -0.117 -0.618 0.000 0.000 0.000 0.000 0.0764554062 24 -0.117 -0.507 0.000 0.000 0.000 0.000 0.0754279906 25 -0.117 -0.529 0.000 0.000 0.000 0.000 0.0753597247 27 -0.117 -0.522 0.000 0.000 0.000 0.000 0.0753387735 36 -0.117 -0.522 0.382 0.000 0.000 0.000 0.0588365137 37 -0.117 -0.522 0.403 0.000 0.000 0.000 0.0586650939 39 -0.117 -0.522 0.411 0.000 0.000 0.000 0.0586559325 40 -0.117 -0.522 0.409 0.000 0.000 0.000 0.0586555977 48 -0.117 -0.522 0.409 0.056 0.000 0.000 0.0578889440 52 -0.117 -0.522 0.409 0.048 0.000 0.000 0.0578871941 53 -0.117 -0.522 0.409 0.050 0.000 0.000 0.0578837951 54 -0.117 -0.522 0.409 0.052 0.000 0.000 0.0578829048 62 -0.117 -0.522 0.409 0.052 0.148 0.000 0.0567980266 63 -0.117 -0.522 0.409 0.052 0.126 0.000 0.0567397169 65 -0.117 -0.522 0.409 0.052 0.134 0.000 0.0567198316 66 -0.117 -0.522 0.409 0.052 0.133 0.000 0.0567193190 74 -0.117 -0.522 0.409 0.052 0.133 -0.037 0.0559333640 76 -0.117 -0.522 0.409 0.052 0.133 -0.084 0.0558933730 77 -0.117 -0.522 0.409 0.052 0.133 -0.062 0.0558092599 80 -0.117 -0.522 0.409 0.052 0.133 -0.059 0.0558062664 powell nthiter 1: fret = 0.055806 90 -0.021 -0.522 0.409 0.052 0.133 -0.059 0.0557302883 92 0.088 -0.522 0.409 0.052 0.133 -0.059 0.0549374314 96 0.071 -0.522 0.409 0.052 0.133 -0.059 0.0548324139 105 0.071 -0.489 0.409 0.052 0.133 -0.059 0.0548275235 106 0.071 -0.505 0.409 0.052 0.133 -0.059 0.0548117464 107 0.071 -0.504 0.409 0.052 0.133 -0.059 0.0548099356 108 0.071 -0.499 0.409 0.052 0.133 -0.059 0.0548077826 111 0.071 -0.501 0.409 0.052 0.133 -0.059 0.0548075311 119 0.071 -0.501 0.328 0.052 0.133 -0.059 0.0531633859 121 0.071 -0.501 0.310 0.052 0.133 -0.059 0.0529819631 123 0.071 -0.501 0.309 0.052 0.133 -0.059 0.0529815270 131 0.071 -0.501 0.309 0.121 0.133 -0.059 0.0517641867 132 0.071 -0.501 0.309 0.127 0.133 -0.059 0.0517551752 134 0.071 -0.501 0.309 0.125 0.133 -0.059 0.0517538355 144 0.071 -0.501 0.309 0.125 0.126 -0.059 0.0517263903 158 0.071 -0.501 0.309 0.125 0.126 -0.054 0.0517137343 powell nthiter 2: fret = 0.051714 172 0.084 -0.501 0.309 0.125 0.126 -0.054 0.0517016723 173 0.078 -0.501 0.309 0.125 0.126 -0.054 0.0516886587 184 0.078 -0.495 0.309 0.125 0.126 -0.054 0.0516793157 185 0.078 -0.496 0.309 0.125 0.126 -0.054 0.0516781690 193 0.078 -0.496 0.265 0.125 0.126 -0.054 0.0512447295 194 0.078 -0.496 0.245 0.125 0.126 -0.054 0.0511358878 197 0.078 -0.496 0.239 0.125 0.126 -0.054 0.0511200552 198 0.078 -0.496 0.236 0.125 0.126 -0.054 0.0511156996 208 0.078 -0.496 0.236 0.162 0.126 -0.054 0.0511069517 209 0.078 -0.496 0.236 0.144 0.126 -0.054 0.0510461324 210 0.078 -0.496 0.236 0.143 0.126 -0.054 0.0510450670 211 0.078 -0.496 0.236 0.140 0.126 -0.054 0.0510450030 214 0.078 -0.496 0.236 0.141 0.126 -0.054 0.0510442426 215 0.078 -0.496 0.236 0.142 0.126 -0.054 0.0510441648 224 0.078 -0.496 0.236 0.142 0.120 -0.054 0.0510062011 227 0.078 -0.496 0.236 0.142 0.117 -0.054 0.0510015919 228 0.078 -0.496 0.236 0.142 0.116 -0.054 0.0510013665 238 0.078 -0.496 0.236 0.142 0.116 -0.021 0.0509045465 239 0.078 -0.496 0.236 0.142 0.116 -0.033 0.0508254250 240 0.078 -0.496 0.236 0.142 0.116 -0.034 0.0508247208 248 0.081 -0.494 0.208 0.148 0.112 -0.027 0.0507533703 249 0.081 -0.494 0.211 0.147 0.112 -0.028 0.0507479241 250 0.080 -0.495 0.215 0.146 0.113 -0.029 0.0507423866 253 0.080 -0.495 0.216 0.146 0.113 -0.029 0.0507422261 powell nthiter 3: fret = 0.050742 267 0.098 -0.495 0.216 0.146 0.113 -0.029 0.0506926649 268 0.092 -0.495 0.216 0.146 0.113 -0.029 0.0506780812 277 0.092 -0.469 0.216 0.146 0.113 -0.029 0.0503306083 279 0.092 -0.466 0.216 0.146 0.113 -0.029 0.0503269879 292 0.092 -0.466 0.216 0.146 0.113 -0.026 0.0503195315 293 0.092 -0.466 0.216 0.146 0.113 -0.025 0.0503191804 302 0.092 -0.466 0.216 0.159 0.113 -0.025 0.0502043282 303 0.092 -0.466 0.216 0.161 0.113 -0.025 0.0502030357 313 0.092 -0.466 0.216 0.161 0.122 -0.025 0.0502008420 314 0.092 -0.466 0.216 0.161 0.118 -0.025 0.0501920799 318 0.099 -0.461 0.143 0.177 0.107 -0.005 0.0501401161 322 0.096 -0.463 0.171 0.171 0.111 -0.012 0.0499932596 324 0.096 -0.463 0.172 0.170 0.111 -0.013 0.0499923532 328 0.096 -0.463 0.172 0.170 0.111 -0.013 0.0499922617 powell nthiter 4: fret = 0.049992 339 0.098 -0.463 0.172 0.170 0.111 -0.013 0.0499819159 342 0.100 -0.463 0.172 0.170 0.111 -0.013 0.0499777623 351 0.100 -0.460 0.172 0.170 0.111 -0.013 0.0499489072 353 0.100 -0.450 0.172 0.170 0.111 -0.013 0.0499177998 354 0.100 -0.453 0.172 0.170 0.111 -0.013 0.0499152048 367 0.100 -0.453 0.172 0.170 0.111 -0.019 0.0499053006 368 0.100 -0.453 0.172 0.170 0.111 -0.018 0.0499051823 377 0.100 -0.453 0.172 0.180 0.111 -0.018 0.0498214789 378 0.100 -0.453 0.172 0.183 0.111 -0.018 0.0498197247 389 0.100 -0.453 0.172 0.183 0.117 -0.018 0.0497901165 390 0.100 -0.453 0.172 0.183 0.119 -0.018 0.0497898343 398 0.102 -0.452 0.159 0.185 0.117 -0.014 0.0497552229 399 0.102 -0.452 0.159 0.186 0.117 -0.014 0.0497552129 powell nthiter 5: fret = 0.049755 419 0.102 -0.451 0.159 0.186 0.117 -0.014 0.0497486287 421 0.102 -0.444 0.159 0.186 0.117 -0.014 0.0497321380 422 0.102 -0.445 0.159 0.186 0.117 -0.014 0.0497314184 435 0.102 -0.445 0.159 0.186 0.117 -0.018 0.0497247339 446 0.102 -0.445 0.159 0.190 0.117 -0.018 0.0497176017 447 0.102 -0.445 0.159 0.189 0.117 -0.018 0.0497172015 471 0.102 -0.438 0.159 0.192 0.117 -0.022 0.0497100503 478 0.102 -0.439 0.159 0.191 0.117 -0.021 0.0497099721 481 0.102 -0.439 0.159 0.191 0.117 -0.021 0.0497099228 484 0.102 -0.440 0.159 0.191 0.117 -0.021 0.0497098372 powell nthiter 6: fret = 0.049710 495 0.097 -0.440 0.159 0.191 0.117 -0.021 0.0497064349 496 0.098 -0.440 0.159 0.191 0.117 -0.021 0.0497049338 497 0.099 -0.440 0.159 0.191 0.117 -0.021 0.0497045737 505 0.099 -0.439 0.156 0.192 0.117 -0.021 0.0497034388 506 0.099 -0.439 0.157 0.192 0.117 -0.021 0.0497034227 507 0.099 -0.439 0.157 0.191 0.117 -0.021 0.0497033674 509 0.099 -0.439 0.157 0.191 0.117 -0.021 0.0497031999 524 0.099 -0.439 0.157 0.191 0.117 -0.022 0.0497022130 534 0.099 -0.439 0.157 0.193 0.117 -0.022 0.0497010227 544 0.099 -0.439 0.157 0.193 0.115 -0.022 0.0496994252 552 0.099 -0.437 0.157 0.194 0.115 -0.024 0.0496947543 555 0.099 -0.437 0.157 0.194 0.115 -0.024 0.0496945590 557 0.099 -0.437 0.157 0.194 0.115 -0.024 0.0496944603 powell nthiter 7: fret = 0.049694 573 0.098 -0.437 0.157 0.194 0.115 -0.024 0.0496941633 630 0.098 -0.436 0.157 0.195 0.115 -0.025 0.0496939136 631 0.098 -0.436 0.157 0.195 0.115 -0.024 0.0496938930 634 0.098 -0.436 0.157 0.195 0.115 -0.024 0.0496938178 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.937009 1 -25.0 -25.0 25.0 0.949760 2 -25.0 25.0 -25.0 0.942077 3 -25.0 25.0 25.0 0.950495 4 25.0 -25.0 -25.0 0.960005 5 25.0 -25.0 25.0 0.992166 6 25.0 25.0 -25.0 0.971376 7 25.0 25.0 25.0 0.980256 REL: 8 0.049694 7.683145 0.960393 rel = 0.0517432 Number of iterations 7 Min cost was 0.049694 Number of FunctionCalls 639 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.457000 sec Parameters at optimum (transmm) 0.09777 -0.43578 0.15703 Parameters at optimum (rotdeg) 0.19480 0.11478 -0.02443 Final costs ---------------- Number of surface hits 4125 WM Intensity 721.7407 +/- 217.0764 Ctx Intensity 996.4421 +/- 220.2374 Pct Contrast 33.4733 +/- 17.2933 Cost 0.0497 RelCost 0.1126 Reg at min cost was -0.99999 -0.00412 0.00195 -0.09845; 0.00196 -0.00295 0.99999 0.18084; 0.00411 -0.99999 -0.00295 0.07552; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat, type = 14 Original Reg -1.00000 -0.00211 0.00153 -0.19631; 0.00154 -0.00635 0.99998 0.61626; 0.00210 -0.99998 -0.00635 -0.08401; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 0.00200 -0.00042 -0.09786; -0.00042 -0.00340 -0.00002 0.43542; -0.00201 0.00001 -0.00340 -0.15952; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.578499 Computing change in rh position Surface-RMS-Diff-mm 0.598816 0.130064 0.839589 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/tmp.bbregister.263970/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-06/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/tmp.bbregister.263970/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat subject sub-06 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 1622417094 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 -0.00412 0.00195 -0.09845; 0.00196 -0.00295 0.99999 0.18084; 0.00411 -0.99999 -0.00295 0.07552; 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 0.961865 1 -25.0 -25.0 25.0 0.969815 2 -25.0 25.0 -25.0 0.962056 3 -25.0 25.0 25.0 0.949137 4 25.0 -25.0 -25.0 0.962483 5 25.0 -25.0 25.0 0.982092 6 25.0 25.0 -25.0 0.965111 7 25.0 25.0 25.0 0.961618 REL: 8 0.060522 7.714178 0.964272 rel = 0.0627639 Initial costs ---------------- Number of surface hits 410587 WM Intensity 729.0519 +/- 217.4000 Ctx Intensity 1003.3675 +/- 221.1589 Pct Contrast 33.1290 +/- 17.5346 Cost 0.0605 RelCost 0.0628 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0634 0.0634 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0594 0.0594 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0579 0.0579 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0568 0.0568 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0556 0.0556 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0553 0.0553 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0545 0.0545 0.0 16 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0541 0.0541 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0539 0.0539 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.0528 0.0528 0.0 117 -0.1000 0.0000 0.0000 0.0000 -0.1000 -0.1000 0.0524 0.0524 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.0516 0.0516 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0497 0.0497 0.0 Brute Force -------------------------- Min cost was 0.049694 Number of iterations 729 Search time 1.677000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.060522 7 -0.126 0.000 0.000 0.000 0.000 0.000 0.0592212289 8 -0.114 0.000 0.000 0.000 0.000 0.000 0.0592141076 9 -0.117 0.000 0.000 0.000 0.000 0.000 0.0592131121 18 -0.117 -0.021 0.000 0.000 0.000 0.000 0.0591193945 19 -0.117 -0.028 0.000 0.000 0.000 0.000 0.0591121746 20 -0.117 -0.029 0.000 0.000 0.000 0.000 0.0591120606 28 -0.117 -0.029 -0.002 0.000 0.000 0.000 0.0591010127 29 -0.117 -0.029 -0.022 0.000 0.000 0.000 0.0590529973 31 -0.117 -0.029 -0.026 0.000 0.000 0.000 0.0590527345 32 -0.117 -0.029 -0.024 0.000 0.000 0.000 0.0590523965 40 -0.117 -0.029 -0.024 0.016 0.000 0.000 0.0590320904 41 -0.117 -0.029 -0.024 0.011 0.000 0.000 0.0590303150 42 -0.117 -0.029 -0.024 0.012 0.000 0.000 0.0590300561 50 -0.117 -0.029 -0.024 0.012 -0.052 0.000 0.0586889825 51 -0.117 -0.029 -0.024 0.012 -0.054 0.000 0.0586868768 52 -0.117 -0.029 -0.024 0.012 -0.057 0.000 0.0586845702 55 -0.117 -0.029 -0.024 0.012 -0.059 0.000 0.0586843821 56 -0.117 -0.029 -0.024 0.012 -0.060 0.000 0.0586843627 63 -0.117 -0.029 -0.024 0.012 -0.060 0.079 0.0582940669 64 -0.117 -0.029 -0.024 0.012 -0.060 0.065 0.0582750526 powell nthiter 1: fret = 0.058275 74 -0.061 -0.029 -0.024 0.012 -0.060 0.065 0.0579056364 75 -0.059 -0.029 -0.024 0.012 -0.060 0.065 0.0579045465 76 -0.058 -0.029 -0.024 0.012 -0.060 0.065 0.0579043257 85 -0.058 -0.026 -0.024 0.012 -0.060 0.065 0.0579017969 86 -0.058 -0.025 -0.024 0.012 -0.060 0.065 0.0579017802 95 -0.058 -0.025 -0.037 0.012 -0.060 0.065 0.0578904478 96 -0.058 -0.025 -0.034 0.012 -0.060 0.065 0.0578892025 106 -0.058 -0.025 -0.034 0.016 -0.060 0.065 0.0578856798 116 -0.058 -0.025 -0.034 0.016 -0.062 0.065 0.0578854056 124 -0.058 -0.025 -0.034 0.016 -0.062 0.115 0.0577840918 125 -0.058 -0.025 -0.034 0.016 -0.062 0.101 0.0577555435 126 -0.058 -0.025 -0.034 0.016 -0.062 0.099 0.0577553285 128 0.002 -0.020 -0.044 0.020 -0.063 0.133 0.0577283636 134 -0.021 -0.022 -0.040 0.019 -0.063 0.120 0.0576586043 136 -0.024 -0.022 -0.040 0.019 -0.062 0.119 0.0576575352 137 -0.024 -0.022 -0.040 0.019 -0.062 0.119 0.0576575255 139 -0.024 -0.022 -0.040 0.019 -0.063 0.119 0.0576575177 powell nthiter 2: fret = 0.057658 157 -0.024 -0.016 -0.040 0.019 -0.063 0.119 0.0576548775 158 -0.024 -0.017 -0.040 0.019 -0.063 0.119 0.0576543002 178 -0.024 -0.017 -0.040 0.020 -0.063 0.119 0.0576541750 188 -0.024 -0.017 -0.040 0.020 -0.064 0.119 0.0576539420 197 -0.023 -0.017 -0.040 0.020 -0.064 0.119 0.0576538346 198 -0.023 -0.017 -0.040 0.020 -0.064 0.119 0.0576538201 201 -0.022 -0.017 -0.040 0.020 -0.064 0.119 0.0576538195 202 -0.023 -0.017 -0.040 0.020 -0.064 0.119 0.0576538060 powell nthiter 3: fret = 0.057654 249 -0.023 -0.017 -0.040 0.020 -0.065 0.119 0.0576538025 258 -0.022 -0.017 -0.040 0.020 -0.065 0.119 0.0576537731 267 -0.022 -0.017 -0.040 0.020 -0.065 0.120 0.0576537694 powell nthiter 4: fret = 0.057654 329 -0.022 -0.017 -0.040 0.020 -0.065 0.120 0.0576537647 powell nthiter 5: fret = 0.057654 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.962578 1 -25.0 -25.0 25.0 0.969735 2 -25.0 25.0 -25.0 0.963039 3 -25.0 25.0 25.0 0.949601 4 25.0 -25.0 -25.0 0.961506 5 25.0 -25.0 25.0 0.980436 6 25.0 25.0 -25.0 0.964538 7 25.0 25.0 25.0 0.961307 REL: 8 0.057654 7.712740 0.964093 rel = 0.0598011 Number of iterations 5 Min cost was 0.057654 Number of FunctionCalls 388 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 44.335000 sec Parameters at optimum (transmm) -0.02194 -0.01726 -0.04028 Parameters at optimum (rotdeg) 0.01976 -0.06506 0.11975 Final costs ---------------- Number of surface hits 410587 WM Intensity 728.7081 +/- 216.9927 Ctx Intensity 1002.8839 +/- 220.3977 Pct Contrast 33.1325 +/- 17.4295 Cost 0.0577 RelCost 0.0628 Reg at min cost was -1.00000 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 -0.00412 0.00195 -0.09845; 0.00196 -0.00295 0.99999 0.18084; 0.00411 -0.99999 -0.00295 0.07552; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 -0.00114 0.00209 0.02241; 0.00209 -0.00034 -0.00000 0.01750; 0.00113 0.00000 -0.00035 0.04033; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.129204 Computing change in rh position Surface-RMS-Diff-mm 0.146713 0.053455 0.252195 mri_segreg done MinCost: 0.057654 728.708102 1002.883896 33.132550 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-06 RegMat --------------------------- -1.00000 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 22:48:12 UTC 2021 Ended at Tue May 25 22:50:44 UTC 2021 BBR-Run-Time-Sec 152 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.lta --surfs cp /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.lta mri_convert -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/T2.prenorm.mgz mri_convert.bin -odt float -at /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.lta -rl /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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-06/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz... INFO: Applying transformation from file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.00000 -0.00298 -0.00013 -0.04551; 0.00298 0.99999 -0.00261 -0.00019; 0.00014 0.00261 1.00000 -0.23087; 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-06/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-06/mri/aseg.presurf.mgz -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.white identity.nofile -surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white identity.nofile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/T2.prenorm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/T2.prenorm.mgz... computing distance transform computing distance transform 102048 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-06/mri/T2.norm.mgz mri_mask /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/T2.norm.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brainmask.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/T2.mgz DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/T2.mgz...done. /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts cp -v /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.pial /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.woT2.pial '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.pial' -> '/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 rh Waiting for PID 265405 of (265405 265411) to complete... Waiting for PID 265411 of (265405 265411) 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-06 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-06/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... 43072 bright wm thresholded. 19 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.orig... computing class statistics... border white: 444165 voxels (1.36%) border gray 461455 voxels (1.41%) WM (102.0): 102.0 +- 6.9 [70.0 --> 110.0] GM (80.0) : 79.3 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.0 (was 70) setting MAX_BORDER_WHITE to 115.9 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 56.1 (was 40) setting MAX_GRAY to 102.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=76+-5.2 mean inside = 100.1, mean outside = 81.2 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 44 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 31 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 209 points - only 0.00% unknown deleting segment 6 with 86 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 18 points - only 0.00% unknown deleting segment 10 with 52 points - only 0.00% unknown deleting segment 12 with 45 points - only 0.00% unknown deleting segment 16 with 43 points - only 0.00% unknown deleting segment 17 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 2 points - only 0.00% unknown deleting segment 19 with 82 points - only 0.00% unknown deleting segment 20 with 29 points - only 0.00% unknown deleting segment 21 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 22 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 23 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) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (box.dx, box.dy, box.dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) locating cortical regions not in the range [82.00 216.40], gm=178.00+-19.20, and vertices in regions > 168.4 174351 surface locations found to contain inconsistent values (61814 in, 112537 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg61, 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=147740.1, rms=0.373 001: dt: 0.0500, sse=147752.1, rms=0.372 (0.151%) 002: dt: 0.0500, sse=147759.2, rms=0.372 (0.172%) 003: dt: 0.0500, sse=147765.6, rms=0.371 (0.168%) 004: dt: 0.0500, sse=147771.9, rms=0.371 (0.166%) 005: dt: 0.0500, sse=147778.0, rms=0.370 (0.165%) 006: dt: 0.0500, sse=147783.4, rms=0.369 (0.164%) 007: dt: 0.0500, sse=147788.8, rms=0.369 (0.162%) 008: dt: 0.0500, sse=147794.1, rms=0.368 (0.161%) 009: dt: 0.0500, sse=147798.9, rms=0.368 (0.160%) 010: dt: 0.0500, sse=147803.5, rms=0.367 (0.159%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg61, 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=147224.8, rms=0.367 011: dt: 0.0500, sse=147229.0, rms=0.366 (0.158%) 012: dt: 0.0500, sse=147233.2, rms=0.366 (0.156%) 013: dt: 0.0500, sse=147237.1, rms=0.365 (0.155%) 014: dt: 0.0500, sse=147240.8, rms=0.365 (0.154%) 015: dt: 0.0500, sse=147244.8, rms=0.364 (0.153%) 016: dt: 0.0500, sse=147248.4, rms=0.364 (0.152%) 017: dt: 0.0500, sse=147251.8, rms=0.363 (0.151%) 018: dt: 0.0500, sse=147254.7, rms=0.363 (0.149%) 019: dt: 0.0500, sse=147257.7, rms=0.362 (0.147%) 020: dt: 0.0500, sse=147260.4, rms=0.361 (0.147%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg61, 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=146758.5, rms=0.361 021: dt: 0.0500, sse=146761.0, rms=0.361 (0.146%) 022: dt: 0.0500, sse=146763.2, rms=0.360 (0.145%) 023: dt: 0.0500, sse=146765.4, rms=0.360 (0.144%) 024: dt: 0.0500, sse=146767.7, rms=0.359 (0.142%) 025: dt: 0.0500, sse=146769.8, rms=0.359 (0.142%) 026: dt: 0.0500, sse=146771.7, rms=0.358 (0.141%) 027: dt: 0.0500, sse=146773.3, rms=0.358 (0.140%) 028: dt: 0.0500, sse=146774.6, rms=0.357 (0.139%) 029: dt: 0.0500, sse=146776.0, rms=0.357 (0.138%) 030: dt: 0.0500, sse=146777.1, rms=0.356 (0.137%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg61, 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=146335.6, rms=0.356 031: dt: 0.5000, sse=146344.7, rms=0.352 (1.321%) 032: dt: 0.5000, sse=146356.2, rms=0.347 (1.230%) 033: dt: 0.5000, sse=146344.6, rms=0.343 (1.136%) 034: dt: 0.5000, sse=146330.6, rms=0.340 (1.071%) 035: dt: 0.5000, sse=146310.1, rms=0.336 (1.003%) 036: dt: 0.5000, sse=146291.1, rms=0.333 (0.940%) 037: dt: 0.5000, sse=146269.2, rms=0.330 (0.882%) 038: dt: 0.5000, sse=146250.6, rms=0.327 (0.831%) 039: dt: 0.5000, sse=146233.9, rms=0.325 (0.791%) 040: dt: 0.5000, sse=146218.7, rms=0.322 (0.734%) 041: dt: 0.5000, sse=146192.9, rms=0.320 (0.710%) 042: dt: 0.5000, sse=146173.1, rms=0.318 (0.665%) 043: dt: 0.5000, sse=146147.3, rms=0.316 (0.645%) 044: dt: 0.5000, sse=146126.3, rms=0.314 (0.612%) 045: dt: 0.5000, sse=146102.0, rms=0.312 (0.591%) 046: dt: 0.5000, sse=146078.6, rms=0.310 (0.553%) 047: dt: 0.5000, sse=146058.2, rms=0.309 (0.535%) 048: dt: 0.5000, sse=146040.2, rms=0.307 (0.503%) 049: dt: 0.5000, sse=146019.9, rms=0.306 (0.483%) 050: dt: 0.5000, sse=145999.0, rms=0.304 (0.456%) 051: dt: 0.5000, sse=145979.2, rms=0.303 (0.442%) 052: dt: 0.5000, sse=145957.6, rms=0.302 (0.418%) 053: dt: 0.5000, sse=145941.6, rms=0.301 (0.392%) 054: dt: 0.5000, sse=145923.2, rms=0.299 (0.386%) 055: dt: 0.5000, sse=145902.3, rms=0.298 (0.366%) 056: dt: 0.5000, sse=145889.8, rms=0.297 (0.349%) 057: dt: 0.5000, sse=145875.3, rms=0.296 (0.332%) 058: dt: 0.5000, sse=145864.0, rms=0.295 (0.313%) 059: dt: 0.5000, sse=145848.1, rms=0.294 (0.306%) 060: dt: 0.5000, sse=145836.4, rms=0.294 (0.280%) positioning took 4.9 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (box.dx, box.dy, box.dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) locating cortical regions not in the range [80.00 218.60], gm=179.00+-19.80, and vertices in regions > 169.1 168126 surface locations found to contain inconsistent values (39757 in, 128369 out) tol=1.0e-04, sigma=1.0, host=blg61, 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=141215.2, rms=0.297 061: dt: 0.5000, sse=141180.7, rms=0.294 (1.036%) 062: dt: 0.5000, sse=141111.0, rms=0.291 (1.235%) 063: dt: 0.5000, sse=141049.0, rms=0.288 (1.044%) 064: dt: 0.5000, sse=140992.8, rms=0.285 (0.948%) 065: dt: 0.5000, sse=140944.5, rms=0.283 (0.852%) 066: dt: 0.5000, sse=140899.8, rms=0.280 (0.769%) 067: dt: 0.5000, sse=140861.0, rms=0.278 (0.694%) 068: dt: 0.5000, sse=140828.9, rms=0.277 (0.628%) 069: dt: 0.5000, sse=140798.4, rms=0.275 (0.568%) 070: dt: 0.5000, sse=140766.1, rms=0.274 (0.532%) 071: dt: 0.5000, sse=140741.2, rms=0.272 (0.496%) 072: dt: 0.5000, sse=140723.5, rms=0.271 (0.468%) 073: dt: 0.5000, sse=140704.9, rms=0.270 (0.447%) 074: dt: 0.5000, sse=140687.5, rms=0.269 (0.425%) 075: dt: 0.5000, sse=140671.2, rms=0.268 (0.405%) 076: dt: 0.5000, sse=140655.1, rms=0.267 (0.387%) 077: dt: 0.5000, sse=140638.3, rms=0.265 (0.375%) 078: dt: 0.5000, sse=140621.2, rms=0.265 (0.357%) 079: dt: 0.5000, sse=140604.6, rms=0.264 (0.340%) 080: dt: 0.5000, sse=140590.0, rms=0.263 (0.326%) 081: dt: 0.5000, sse=140575.3, rms=0.262 (0.309%) 082: dt: 0.5000, sse=140560.7, rms=0.261 (0.303%) 083: dt: 0.5000, sse=140546.4, rms=0.260 (0.293%) 084: dt: 0.5000, sse=140535.0, rms=0.260 (0.271%) 085: dt: 0.5000, sse=140521.9, rms=0.259 (0.262%) 086: dt: 0.5000, sse=140512.5, rms=0.258 (0.250%) 087: dt: 0.5000, sse=140497.7, rms=0.258 (0.245%) 088: dt: 0.5000, sse=140486.5, rms=0.257 (0.234%) 089: dt: 0.5000, sse=140473.6, rms=0.257 (0.224%) 090: dt: 0.5000, sse=140460.2, rms=0.256 (0.218%) positioning took 5.9 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (box.dx, box.dy, box.dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) locating cortical regions not in the range [78.00 219.40], gm=179.00+-20.20, and vertices in regions > 168.9 164701 surface locations found to contain inconsistent values (35051 in, 129650 out) tol=1.0e-04, sigma=0.5, host=blg61, 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=140537.7, rms=0.272 091: dt: 0.5000, sse=140520.8, rms=0.270 (0.773%) 092: dt: 0.5000, sse=140469.0, rms=0.267 (0.923%) 093: dt: 0.5000, sse=140420.0, rms=0.265 (0.756%) 094: dt: 0.5000, sse=140375.2, rms=0.263 (0.669%) 095: dt: 0.5000, sse=140332.9, rms=0.262 (0.591%) 096: dt: 0.5000, sse=140299.0, rms=0.260 (0.525%) 097: dt: 0.5000, sse=140267.4, rms=0.259 (0.463%) 098: dt: 0.5000, sse=140239.7, rms=0.258 (0.411%) 099: dt: 0.5000, sse=140216.6, rms=0.257 (0.374%) 100: dt: 0.5000, sse=140194.6, rms=0.256 (0.347%) 101: dt: 0.5000, sse=140174.2, rms=0.256 (0.323%) 102: dt: 0.5000, sse=140157.1, rms=0.255 (0.303%) 103: dt: 0.5000, sse=140140.2, rms=0.254 (0.283%) 104: dt: 0.5000, sse=140126.2, rms=0.253 (0.268%) 105: dt: 0.5000, sse=140110.2, rms=0.253 (0.259%) 106: dt: 0.5000, sse=140095.8, rms=0.252 (0.243%) 107: dt: 0.5000, sse=140082.0, rms=0.251 (0.231%) 108: dt: 0.5000, sse=140069.4, rms=0.251 (0.221%) 109: dt: 0.5000, sse=140057.8, rms=0.250 (0.212%) 110: dt: 0.5000, sse=140046.7, rms=0.250 (0.202%) 111: dt: 0.5000, sse=140035.5, rms=0.249 (0.194%) 112: dt: 0.5000, sse=140024.5, rms=0.249 (0.183%) 113: dt: 0.5000, sse=140013.8, rms=0.249 (0.177%) 114: dt: 0.5000, sse=140004.5, rms=0.248 (0.168%) 115: dt: 0.5000, sse=139995.7, rms=0.248 (0.164%) 116: dt: 0.5000, sse=139987.1, rms=0.247 (0.154%) 117: dt: 0.5000, sse=139977.8, rms=0.247 (0.145%) 118: dt: 0.5000, sse=139969.5, rms=0.247 (0.145%) 119: dt: 0.5000, sse=139961.6, rms=0.246 (0.140%) 120: dt: 0.5000, sse=139953.0, rms=0.246 (0.132%) positioning took 6.8 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (region->dx, region->dy, region->dz) = (170, 383, 268) (box.dx, box.dy, box.dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) (region->dx, region->dy, region->dz) = (173, 396, 285) locating cortical regions not in the range [76.00 220.20], gm=179.00+-20.60, and vertices in regions > 168.7 163353 surface locations found to contain inconsistent values (32339 in, 131014 out) tol=1.0e-04, sigma=0.2, host=blg61, 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-06/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=140999.8, rms=0.261 121: dt: 0.5000, sse=140995.4, rms=0.260 (0.584%) 122: dt: 0.5000, sse=140952.0, rms=0.258 (0.696%) 123: dt: 0.5000, sse=140910.6, rms=0.257 (0.557%) 124: dt: 0.5000, sse=140872.0, rms=0.255 (0.488%) 125: dt: 0.5000, sse=140838.2, rms=0.254 (0.422%) 126: dt: 0.5000, sse=140807.3, rms=0.253 (0.372%) 127: dt: 0.5000, sse=140780.3, rms=0.253 (0.327%) 128: dt: 0.5000, sse=140756.6, rms=0.252 (0.290%) 129: dt: 0.5000, sse=140736.4, rms=0.251 (0.260%) 130: dt: 0.5000, sse=140719.8, rms=0.251 (0.242%) 131: dt: 0.5000, sse=140703.2, rms=0.250 (0.225%) 132: dt: 0.5000, sse=140688.3, rms=0.249 (0.208%) 133: dt: 0.5000, sse=140674.9, rms=0.249 (0.198%) 134: dt: 0.5000, sse=140662.8, rms=0.249 (0.184%) 135: dt: 0.5000, sse=140650.0, rms=0.248 (0.172%) 136: dt: 0.5000, sse=140638.3, rms=0.248 (0.165%) 137: dt: 0.5000, sse=140628.3, rms=0.247 (0.154%) 138: dt: 0.5000, sse=140620.7, rms=0.247 (0.143%) 139: dt: 0.5000, sse=140612.6, rms=0.247 (0.138%) 140: dt: 0.5000, sse=140602.8, rms=0.246 (0.136%) 141: dt: 0.5000, sse=140594.7, rms=0.246 (0.126%) 142: dt: 0.5000, sse=140586.1, rms=0.246 (0.118%) 143: dt: 0.5000, sse=140579.5, rms=0.245 (0.114%) 144: dt: 0.5000, sse=140573.2, rms=0.245 (0.110%) 145: dt: 0.5000, sse=140567.2, rms=0.245 (0.102%) 146: dt: 0.5000, sse=140561.0, rms=0.245 (0.099%) 147: dt: 0.5000, sse=140554.0, rms=0.244 (0.099%) 148: dt: 0.5000, sse=140549.1, rms=0.244 (0.090%) 149: dt: 0.5000, sse=140544.4, rms=0.244 (0.085%) 150: dt: 0.5000, sse=140540.6, rms=0.244 (0.086%) positioning took 7.4 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.area.pial vertex spacing 0.79 +- 0.35 (0.03-->6.30) (max @ vno 144920 --> 144891) face area 0.24 +- 0.20 (0.00-->5.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 213589 vertices processed 25000 of 213589 vertices processed 50000 of 213589 vertices processed 75000 of 213589 vertices processed 100000 of 213589 vertices processed 125000 of 213589 vertices processed 150000 of 213589 vertices processed 175000 of 213589 vertices processed 200000 of 213589 vertices processed 0 of 213589 vertices processed 25000 of 213589 vertices processed 50000 of 213589 vertices processed 75000 of 213589 vertices processed 100000 of 213589 vertices processed 125000 of 213589 vertices processed 150000 of 213589 vertices processed 175000 of 213589 vertices processed 200000 of 213589 vertices processed thickness calculation complete, 371:791 truncations. 36480 vertices at 0 distance 119076 vertices at 1 distance 131074 vertices at 2 distance 73967 vertices at 3 distance 30832 vertices at 4 distance 10904 vertices at 5 distance 3497 vertices at 6 distance 1079 vertices at 7 distance 359 vertices at 8 distance 156 vertices at 9 distance 118 vertices at 10 distance 83 vertices at 11 distance 54 vertices at 12 distance 30 vertices at 13 distance 29 vertices at 14 distance 20 vertices at 15 distance 21 vertices at 16 distance 16 vertices at 17 distance 18 vertices at 18 distance 16 vertices at 19 distance 27 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.thickness positioning took 54.1 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-06 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-06/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... 43072 bright wm thresholded. 19 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.orig... computing class statistics... border white: 444165 voxels (1.36%) border gray 461455 voxels (1.41%) WM (102.0): 102.0 +- 6.9 [70.0 --> 110.0] GM (80.0) : 79.3 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.0 (was 70) setting MAX_BORDER_WHITE to 115.9 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 56.1 (was 40) setting MAX_GRAY to 102.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=76+-6.1 mean inside = 99.8, mean outside = 81.0 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) 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 43 points - only 0.00% unknown deleting segment 1 with 159 points - only 0.00% unknown deleting segment 2 with 58 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 39 points - only 0.00% unknown deleting segment 6 with 26 points - only 0.00% unknown deleting segment 7 with 28 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 19 points - only 0.00% unknown deleting segment 11 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 43 points - only 0.00% unknown deleting segment 16 with 60 points - only 0.00% unknown deleting segment 17 with 16 points - only 0.00% unknown deleting segment 18 with 5 points - only 0.00% unknown deleting segment 19 with 6 points - only 0.00% unknown reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (box.dx, box.dy, box.dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) locating cortical regions not in the range [93.50 218.80], gm=183.00+-17.90, and vertices in regions > 174.0 179094 surface locations found to contain inconsistent values (74769 in, 104325 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg61, 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=151096.1, rms=0.384 001: dt: 0.0500, sse=151105.3, rms=0.384 (0.151%) 002: dt: 0.0500, sse=151110.3, rms=0.383 (0.171%) 003: dt: 0.0500, sse=151114.7, rms=0.382 (0.166%) 004: dt: 0.0500, sse=151118.5, rms=0.382 (0.165%) 005: dt: 0.0500, sse=151122.4, rms=0.381 (0.164%) 006: dt: 0.0500, sse=151125.5, rms=0.381 (0.163%) 007: dt: 0.0500, sse=151128.9, rms=0.380 (0.161%) 008: dt: 0.0500, sse=151131.3, rms=0.379 (0.160%) 009: dt: 0.0500, sse=151134.2, rms=0.379 (0.159%) 010: dt: 0.0500, sse=151136.1, rms=0.378 (0.158%) positioning took 1.4 minutes tol=1.0e-04, sigma=2.0, host=blg61, 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=150558.8, rms=0.378 011: dt: 0.0500, sse=150560.9, rms=0.378 (0.157%) 012: dt: 0.0500, sse=150562.3, rms=0.377 (0.156%) 013: dt: 0.0500, sse=150564.1, rms=0.376 (0.155%) 014: dt: 0.0500, sse=150565.2, rms=0.376 (0.154%) 015: dt: 0.0500, sse=150566.5, rms=0.375 (0.152%) 016: dt: 0.0500, sse=150567.5, rms=0.375 (0.152%) 017: dt: 0.0500, sse=150568.1, rms=0.374 (0.151%) 018: dt: 0.0500, sse=150568.5, rms=0.373 (0.150%) 019: dt: 0.0500, sse=150568.7, rms=0.373 (0.149%) 020: dt: 0.0500, sse=150568.5, rms=0.372 (0.147%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg61, 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=150065.3, rms=0.372 021: dt: 0.0500, sse=150064.8, rms=0.372 (0.146%) 022: dt: 0.0500, sse=150064.5, rms=0.371 (0.146%) 023: dt: 0.0500, sse=150064.0, rms=0.371 (0.145%) 024: dt: 0.0500, sse=150063.4, rms=0.370 (0.144%) 025: dt: 0.0500, sse=150062.6, rms=0.370 (0.143%) 026: dt: 0.0500, sse=150062.0, rms=0.369 (0.142%) 027: dt: 0.0500, sse=150060.6, rms=0.369 (0.141%) 028: dt: 0.0500, sse=150059.4, rms=0.368 (0.140%) 029: dt: 0.0500, sse=150057.9, rms=0.368 (0.139%) 030: dt: 0.0500, sse=150056.4, rms=0.367 (0.138%) positioning took 1.5 minutes tol=1.0e-04, sigma=2.0, host=blg61, 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=149615.3, rms=0.367 031: dt: 0.5000, sse=149597.4, rms=0.362 (1.340%) 032: dt: 0.5000, sse=149570.2, rms=0.358 (1.263%) 033: dt: 0.5000, sse=149528.9, rms=0.353 (1.194%) 034: dt: 0.5000, sse=149490.4, rms=0.349 (1.109%) 035: dt: 0.5000, sse=149444.7, rms=0.346 (1.050%) 036: dt: 0.5000, sse=149404.8, rms=0.342 (0.979%) 037: dt: 0.5000, sse=149356.5, rms=0.339 (0.934%) 038: dt: 0.5000, sse=149307.5, rms=0.336 (0.891%) 039: dt: 0.5000, sse=149264.7, rms=0.333 (0.841%) 040: dt: 0.5000, sse=149221.9, rms=0.331 (0.805%) 041: dt: 0.5000, sse=149173.6, rms=0.328 (0.760%) 042: dt: 0.5000, sse=149132.4, rms=0.326 (0.730%) 043: dt: 0.5000, sse=149090.4, rms=0.323 (0.691%) 044: dt: 0.5000, sse=149046.9, rms=0.321 (0.668%) 045: dt: 0.5000, sse=149014.6, rms=0.319 (0.629%) 046: dt: 0.5000, sse=148969.4, rms=0.317 (0.610%) 047: dt: 0.5000, sse=148938.9, rms=0.316 (0.581%) 048: dt: 0.5000, sse=148900.8, rms=0.314 (0.559%) 049: dt: 0.5000, sse=148875.5, rms=0.312 (0.520%) 050: dt: 0.5000, sse=148840.4, rms=0.311 (0.516%) 051: dt: 0.5000, sse=148810.0, rms=0.309 (0.486%) 052: dt: 0.5000, sse=148775.2, rms=0.308 (0.472%) 053: dt: 0.5000, sse=148743.1, rms=0.306 (0.451%) 054: dt: 0.5000, sse=148707.6, rms=0.305 (0.453%) 055: dt: 0.5000, sse=148680.7, rms=0.303 (0.430%) 056: dt: 0.5000, sse=148646.7, rms=0.302 (0.404%) 057: dt: 0.5000, sse=148620.1, rms=0.301 (0.407%) 058: dt: 0.5000, sse=148591.9, rms=0.300 (0.388%) 059: dt: 0.5000, sse=148560.9, rms=0.299 (0.366%) 060: dt: 0.5000, sse=148539.9, rms=0.298 (0.353%) positioning took 5.0 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (box.dx, box.dy, box.dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) locating cortical regions not in the range [94.00 220.00], gm=184.00+-18.00, and vertices in regions > 175.0 170415 surface locations found to contain inconsistent values (51908 in, 118507 out) tol=1.0e-04, sigma=1.0, host=blg61, 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=143890.1, rms=0.300 061: dt: 0.5000, sse=143848.4, rms=0.297 (0.971%) 062: dt: 0.5000, sse=143762.8, rms=0.294 (1.200%) 063: dt: 0.5000, sse=143682.5, rms=0.291 (1.016%) 064: dt: 0.5000, sse=143610.0, rms=0.288 (0.935%) 065: dt: 0.5000, sse=143544.2, rms=0.286 (0.839%) 066: dt: 0.5000, sse=143481.9, rms=0.283 (0.787%) 067: dt: 0.5000, sse=143433.6, rms=0.281 (0.702%) 068: dt: 0.5000, sse=143380.9, rms=0.279 (0.666%) 069: dt: 0.5000, sse=143338.4, rms=0.278 (0.606%) 070: dt: 0.5000, sse=143298.9, rms=0.276 (0.574%) 071: dt: 0.5000, sse=143259.7, rms=0.275 (0.542%) 072: dt: 0.5000, sse=143235.5, rms=0.273 (0.497%) 073: dt: 0.5000, sse=143202.6, rms=0.272 (0.496%) 074: dt: 0.5000, sse=143172.5, rms=0.271 (0.458%) 075: dt: 0.5000, sse=143143.8, rms=0.269 (0.447%) 076: dt: 0.5000, sse=143113.8, rms=0.268 (0.441%) 077: dt: 0.5000, sse=143091.5, rms=0.267 (0.402%) 078: dt: 0.5000, sse=143065.6, rms=0.266 (0.411%) 079: dt: 0.5000, sse=143042.5, rms=0.265 (0.369%) 080: dt: 0.5000, sse=143024.2, rms=0.264 (0.344%) 081: dt: 0.5000, sse=143003.6, rms=0.263 (0.362%) 082: dt: 0.5000, sse=142974.7, rms=0.262 (0.359%) 083: dt: 0.5000, sse=142964.0, rms=0.261 (0.303%) 084: dt: 0.5000, sse=142940.4, rms=0.261 (0.330%) 085: dt: 0.5000, sse=142922.2, rms=0.260 (0.309%) 086: dt: 0.5000, sse=142910.9, rms=0.259 (0.284%) 087: dt: 0.5000, sse=142886.8, rms=0.258 (0.295%) 088: dt: 0.5000, sse=142866.6, rms=0.258 (0.286%) 089: dt: 0.5000, sse=142845.9, rms=0.257 (0.269%) 090: dt: 0.5000, sse=142828.9, rms=0.256 (0.264%) positioning took 5.9 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (box.dx, box.dy, box.dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) locating cortical regions not in the range [91.00 221.20], gm=184.00+-18.60, and vertices in regions > 174.7 167555 surface locations found to contain inconsistent values (40396 in, 127159 out) tol=1.0e-04, sigma=0.5, host=blg61, 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=142692.7, rms=0.266 091: dt: 0.5000, sse=142685.5, rms=0.264 (0.724%) 092: dt: 0.5000, sse=142629.6, rms=0.262 (0.915%) 093: dt: 0.5000, sse=142581.7, rms=0.260 (0.741%) 094: dt: 0.5000, sse=142534.0, rms=0.258 (0.666%) 095: dt: 0.5000, sse=142490.2, rms=0.257 (0.588%) 096: dt: 0.5000, sse=142452.5, rms=0.255 (0.536%) 097: dt: 0.5000, sse=142421.0, rms=0.254 (0.478%) 098: dt: 0.5000, sse=142389.5, rms=0.253 (0.436%) 099: dt: 0.5000, sse=142362.7, rms=0.252 (0.398%) 100: dt: 0.5000, sse=142344.5, rms=0.251 (0.373%) 101: dt: 0.5000, sse=142318.5, rms=0.250 (0.343%) 102: dt: 0.5000, sse=142298.9, rms=0.249 (0.328%) 103: dt: 0.5000, sse=142276.6, rms=0.248 (0.314%) 104: dt: 0.5000, sse=142259.9, rms=0.248 (0.289%) 105: dt: 0.5000, sse=142237.7, rms=0.247 (0.287%) 106: dt: 0.5000, sse=142222.4, rms=0.246 (0.274%) 107: dt: 0.5000, sse=142209.1, rms=0.246 (0.255%) 108: dt: 0.5000, sse=142193.0, rms=0.245 (0.248%) 109: dt: 0.5000, sse=142178.8, rms=0.245 (0.237%) 110: dt: 0.5000, sse=142165.5, rms=0.244 (0.233%) 111: dt: 0.5000, sse=142146.3, rms=0.243 (0.219%) 112: dt: 0.5000, sse=142140.3, rms=0.243 (0.197%) 113: dt: 0.5000, sse=142121.1, rms=0.242 (0.204%) 114: dt: 0.5000, sse=142105.4, rms=0.242 (0.191%) 115: dt: 0.5000, sse=142096.8, rms=0.242 (0.195%) 116: dt: 0.5000, sse=142088.9, rms=0.241 (0.176%) 117: dt: 0.5000, sse=142075.8, rms=0.241 (0.183%) 118: dt: 0.5000, sse=142063.4, rms=0.240 (0.173%) 119: dt: 0.5000, sse=142052.2, rms=0.240 (0.148%) 120: dt: 0.5000, sse=142047.7, rms=0.239 (0.164%) positioning took 6.6 minutes repositioning pial surface locations using ../mri/T2.mgz (box.dx, box.dy, box.dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (region->dx, region->dy, region->dz) = (160, 387, 261) (box.dx, box.dy, box.dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) (region->dx, region->dy, region->dz) = (175, 400, 279) locating cortical regions not in the range [87.50 222.60], gm=184.00+-19.30, and vertices in regions > 174.3 167638 surface locations found to contain inconsistent values (34674 in, 132964 out) tol=1.0e-04, sigma=0.2, host=blg61, 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-06/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=142908.1, rms=0.250 121: dt: 0.5000, sse=142914.1, rms=0.249 (0.554%) 122: dt: 0.5000, sse=142867.9, rms=0.247 (0.723%) 123: dt: 0.5000, sse=142823.2, rms=0.246 (0.579%) 124: dt: 0.5000, sse=142781.0, rms=0.244 (0.506%) 125: dt: 0.5000, sse=142753.7, rms=0.243 (0.436%) 126: dt: 0.5000, sse=142718.8, rms=0.242 (0.392%) 127: dt: 0.5000, sse=142694.0, rms=0.242 (0.344%) 128: dt: 0.5000, sse=142672.8, rms=0.241 (0.308%) 129: dt: 0.5000, sse=142653.1, rms=0.240 (0.275%) 130: dt: 0.5000, sse=142635.6, rms=0.240 (0.255%) 131: dt: 0.5000, sse=142618.8, rms=0.239 (0.232%) 132: dt: 0.5000, sse=142605.4, rms=0.239 (0.217%) 133: dt: 0.5000, sse=142599.0, rms=0.238 (0.205%) 134: dt: 0.5000, sse=142583.5, rms=0.238 (0.191%) 135: dt: 0.5000, sse=142575.8, rms=0.237 (0.185%) 136: dt: 0.5000, sse=142561.6, rms=0.237 (0.174%) 137: dt: 0.5000, sse=142555.2, rms=0.236 (0.163%) 138: dt: 0.5000, sse=142544.2, rms=0.236 (0.156%) 139: dt: 0.5000, sse=142537.2, rms=0.236 (0.145%) 140: dt: 0.5000, sse=142532.6, rms=0.235 (0.147%) 141: dt: 0.5000, sse=142524.2, rms=0.235 (0.136%) 142: dt: 0.5000, sse=142525.5, rms=0.235 (0.128%) 143: dt: 0.5000, sse=142519.7, rms=0.234 (0.125%) 144: dt: 0.5000, sse=142510.5, rms=0.234 (0.118%) 145: dt: 0.5000, sse=142504.1, rms=0.234 (0.114%) 146: dt: 0.5000, sse=142502.6, rms=0.234 (0.111%) 147: dt: 0.5000, sse=142494.9, rms=0.233 (0.105%) 148: dt: 0.5000, sse=142494.6, rms=0.233 (0.100%) 149: dt: 0.5000, sse=142488.4, rms=0.233 (0.095%) 150: dt: 0.5000, sse=142483.9, rms=0.233 (0.095%) positioning took 7.2 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.area.pial vertex spacing 0.78 +- 0.35 (0.02-->7.08) (max @ vno 165715 --> 220413) face area 0.24 +- 0.20 (0.00-->8.23) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 220453 vertices processed 25000 of 220453 vertices processed 50000 of 220453 vertices processed 75000 of 220453 vertices processed 100000 of 220453 vertices processed 125000 of 220453 vertices processed 150000 of 220453 vertices processed 175000 of 220453 vertices processed 200000 of 220453 vertices processed 0 of 220453 vertices processed 25000 of 220453 vertices processed 50000 of 220453 vertices processed 75000 of 220453 vertices processed 100000 of 220453 vertices processed 125000 of 220453 vertices processed 150000 of 220453 vertices processed 175000 of 220453 vertices processed 200000 of 220453 vertices processed thickness calculation complete, 202:610 truncations. 41192 vertices at 0 distance 126523 vertices at 1 distance 133536 vertices at 2 distance 73973 vertices at 3 distance 28999 vertices at 4 distance 9845 vertices at 5 distance 3232 vertices at 6 distance 1198 vertices at 7 distance 365 vertices at 8 distance 152 vertices at 9 distance 78 vertices at 10 distance 67 vertices at 11 distance 45 vertices at 12 distance 45 vertices at 13 distance 37 vertices at 14 distance 28 vertices at 15 distance 23 vertices at 16 distance 24 vertices at 17 distance 21 vertices at 18 distance 8 vertices at 19 distance 9 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.thickness positioning took 53.1 minutes PIDs (265405 265411) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Tue May 25 23:46:29 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf vertexvol --s sub-06 --lh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Total face volume 239272 Total vertex volume 236896 (mask=0) #@# sub-06 lh 236896 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue May 25 23:46:33 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf vertexvol --s sub-06 --rh --th3 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/rh.cortex.label Total face volume 236022 Total vertex volume 233821 (mask=0) #@# sub-06 rh 233821 vertexvol Done #-------------------------------------------- #@# Surf Volume lh Tue May 25 23:46:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Total face volume 239272 Total vertex volume 236896 (mask=0) #@# sub-06 lh 236896 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue May 25 23:46:42 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/rh.cortex.label Total face volume 236022 Total vertex volume 233821 (mask=0) #@# sub-06 rh 233821 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue May 25 23:46:46 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06 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 = 302 writing volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/ribbon.mgz mris_volmask took 24.10 minutes writing ribbon files Started at Tue May 25 22:48:05 UTC 2021 Ended at Wed May 26 00:10:52 UTC 2021 #@#%# recon-all-run-time-hours 1.380 recon-all -s sub-06 finished without error at Wed May 26 00:10:53 UTC 2021 New invocation of recon-all Wed May 26 00:21:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 /opt/freesurfer/bin/recon-all -autorecon3 -openmp 8 -subjid sub-06 -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-06 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 blg6114.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 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 139161636 6673312 2233864 50803312 48478428 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: 2021/05/26-00:21:16-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: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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: 2021/05/26-00:21:17-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: blg6114.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 00:21:17 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2795 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1405 voxels changed to hypointensity... 4143 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed May 26 00:21:50 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 mri_aparc2aseg --s sub-06 --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-06 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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-06/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 12.73 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 73 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 73 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 76 rescaling Left_Putamen from 80 --> 90 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 73 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 70 rescaling Left_VentralDC from 87 --> 98 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 71 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 72 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 97 rescaling Fifth_Ventricle from 40 --> 46 rescaling WM_hypointensities from 78 --> 75 rescaling non_WM_hypointensities from 40 --> 57 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 = 913784 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 295 changed. pass 2: 13 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Wed May 26 00:31:04 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 mri_aparc2aseg --s sub-06 --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-06 outvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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-06/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 12.73 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 73 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 73 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 76 rescaling Left_Putamen from 80 --> 90 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 73 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 70 rescaling Left_VentralDC from 87 --> 98 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 71 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 72 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 97 rescaling Fifth_Ventricle from 40 --> 46 rescaling WM_hypointensities from 78 --> 75 rescaling non_WM_hypointensities from 40 --> 57 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 = 913947 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 295 changed. pass 2: 13 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed May 26 00:40:24 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 mri_aparc2aseg --s sub-06 --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-06 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-06/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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-06/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 12.73 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 73 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 73 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 100 rescaling Left_Caudate from 75 --> 76 rescaling Left_Putamen from 80 --> 90 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 73 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 70 rescaling Left_VentralDC from 87 --> 98 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 71 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 72 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 97 rescaling Fifth_Ventricle from 40 --> 46 rescaling WM_hypointensities from 78 --> 75 rescaling non_WM_hypointensities from 40 --> 57 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 = 913947 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 295 changed. pass 2: 13 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Wed May 26 00:49:35 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Wed May 26 00:49:35 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-06/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 blg6114.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-06/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 blg6114.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 00:49:35 UTC 2021 Ended at Wed May 26 00:49:44 UTC 2021 Apas2aseg-Run-Time-Sec 9 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed May 26 00:49:44 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 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-06 $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-06 sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1492006 mm^3 (det: 1.305695 ) Computing euler number orig.nofix lheno = -76, rheno = -72 orig.nofix lhholes = 39, rhholes = 37 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 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 00:51:00 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 mri_aparc2aseg --s sub-06 --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-06 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-06/mri/aparc+aseg.mgz Reading lh white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading lh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial Loading lh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/surf/rh.white Reading rh pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/rh.pial Loading rh annotations from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/ribbon.mgz Loading filled from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 11426 vertices from left hemi Ripped 12124 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-06/mri/aseg.mgz Loading Ctx Seg File /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 = 1711346 Used brute-force search on 16 voxels Fixing Parahip LH WM Found 10 clusters 0 k 1.024000 1 k 0.512000 2 k 0.512000 3 k 1.024000 4 k 0.512000 5 k 0.512000 6 k 1351.163330 7 k 0.512000 8 k 0.512000 9 k 16.384001 Fixing Parahip RH WM Found 7 clusters 0 k 1321.981689 1 k 0.512000 2 k 0.512000 3 k 0.512000 4 k 25.087986 5 k 0.512000 6 k 0.512000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-06 --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-06 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 atlas_icv (eTIV) = 1492006 mm^3 (det: 1.305695 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 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 00:21:16 UTC 2021 Ended at Wed May 26 01:03:57 UTC 2021 #@#%# recon-all-run-time-hours 0.711 recon-all -s sub-06 finished without error at Wed May 26 01:03:58 UTC 2021