Sat Jan 12 01:30:03 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115 /opt/freesurfer/bin/recon-all -autorecon1 -i /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/working_bids_fmripreprest/fmriprep_wf/single_subject_ADS5115_wf/anat_preproc_wf/anat_template_wf/t1_reorient/sub-ADS5115_ses-wave2_T1w_template_ras.nii.gz -noskullstrip -hires -openmp 8 -subjid sub-ADS5115 -sd /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer -expert /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/working_bids_fmripreprest/fmriprep_wf/single_subject_ADS5115_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts subjid sub-ADS5115 setenv SUBJECTS_DIR /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/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 n018 3.10.0-862.14.4.el7.x86_64 #1 SMP Fri Sep 21 09:07:21 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 104857600 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 515220 maxlocks unlimited maxsignal 515220 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131915620 16212712 109859308 216908 5843600 113797956 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: 2019/01/12-01:30:04-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-01:30:04-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-01:30:05-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:05-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:06-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:06-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:06-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:07-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:07-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:07-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:08-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:08-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:08-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:08-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:09-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:09-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:10-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:10-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:13-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:13-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:14-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-01:30:15-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:15-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:16-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:16-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:17-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-01:30:17-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-01:30:17-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:17-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:18-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:18-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:18-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-01:30:19-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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 ####################################### /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115 mri_convert /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/working_bids_fmripreprest/fmriprep_wf/single_subject_ADS5115_wf/anat_preproc_wf/anat_template_wf/t1_reorient/sub-ADS5115_ses-wave2_T1w_template_ras.nii.gz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig/001.mgz mri_convert.bin /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/working_bids_fmripreprest/fmriprep_wf/single_subject_ADS5115_wf/anat_preproc_wf/anat_template_wf/t1_reorient/sub-ADS5115_ses-wave2_T1w_template_ras.nii.gz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/working_bids_fmripreprest/fmriprep_wf/single_subject_ADS5115_wf/anat_preproc_wf/anat_template_wf/t1_reorient/sub-ADS5115_ses-wave2_T1w_template_ras.nii.gz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998096, -0.0598177, 0.0150545) j_ras = (0.0598251, 0.998209, -3.80946e-05) k_ras = (-0.0150253, 0.000938661, 0.999887) writing to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Jan 12 01:32:30 UTC 2019 Found 1 runs /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig/001.mgz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/rawavg.mgz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115 mri_convert /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/rawavg.mgz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig.mgz --conform_min mri_convert.bin /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/rawavg.mgz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/rawavg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998096, -0.0598177, 0.0150545) j_ras = (0.0598251, 0.998209, -3.80946e-05) k_ras = (-0.0150253, 0.000938661, 0.999887) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig.mgz... mri_add_xform_to_header -c /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/transforms/talairach.xfm /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig.mgz /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Jan 12 01:44:20 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 n018 3.10.0-862.14.4.el7.x86_64 #1 SMP Fri Sep 21 09:07:21 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sat Jan 12 01:44:22 UTC 2019 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.122795 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.122795/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.122795/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.7108e-09, 1.0366e-09) j_ras = (-1.0366e-09, 6.47877e-11, -1) k_ras = (-5.85721e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.122795/nu0.mnc... Outputting Volume: 12% done. (32223/262144) Time: 20 sec out of approx 3 min Outputting Volume: 37% done. (98271/262144) Time: 43 sec out of approx 114.7 sec Outputting Volume: 59% done. (153567/262144) Time: 63 sec out of approx 106.3 sec Outputting Volume: 80% done. (209631/262144) Time: 83 sec out of approx 103.2 sec Outputting Volume: DONE in 99 sec -------------------------------------------------------- Iteration 1 Sat Jan 12 01:52:09 UTC 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.122795/nu0.mnc ./tmp.mri_nu_correct.mni.122795/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.122795/0/ -iterations 1000 -distance 50 [pettitta@n018:/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/] [2019-01-12 01:52:10] 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.122795/0/ ./tmp.mri_nu_correct.mni.122795/nu0.mnc ./tmp.mri_nu_correct.mni.122795/nu1.imp Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Processing:.................................................................................................................................Done Fitting splines: .............................................................. Fitting splines: .............................................................. Number of iterations: 24 CV of field change: 0.000984531 Smoothing volume: ............................................................. Outputting Volume: ............................................................ Outputting Volume: 0% done. (112/262144) Time: 20 sec out of approx 12.9 hrs Outputting Volume: 0% done. (302/262144) Time: 40 sec out of approx 9.9 hrs Outputting Volume: 0% done. (424/262144) Time: 60 sec out of approx 10.3 hrs Outputting Volume: 2% done. (4600/262144) Time: 2.3 min out of approx 2.2 hrs Outputting Volume: 4% done. (9208/262144) Time: 3.5 min out of approx 95.9 min Outputting Volume: 6% done. (16376/262144) Time: 4.6 min out of approx 75.2 min Outputting Volume: 7% done. (18424/262144) Time: 5.7 min out of approx 78.7 min Outputting Volume: 8% done. (20984/262144) Time: 6.8 min out of approx 81.1 min Outputting Volume: 10% done. (25336/262144) Time: 7.9 min out of approx 80.6 min Outputting Volume: 12% done. (32504/262144) Time: 8.8 min out of approx 72.9 min Outputting Volume: 14% done. (37112/262144) Time: 9.3 min out of approx 66.6 min Outputting Volume: 16% done. (41464/262144) Time: 11 min out of approx 67.6 min Outputting Volume: 18% done. (46072/262144) Time: 12.5 min out of approx 69 min Outputting Volume: 19% done. (50168/262144) Time: 14 min out of approx 70.6 min Outputting Volume: 21% done. (53752/262144) Time: 15.4 min out of approx 73.1 min Outputting Volume: 22% done. (58360/262144) Time: 16.8 min out of approx 74 min Outputting Volume: 25% done. (65528/262144) Time: 18.2 min out of approx 72.9 min Outputting Volume: 26% done. (67576/262144) Time: 19.7 min out of approx 74.7 min Outputting Volume: 27% done. (70648/262144) Time: 21 min out of approx 76.4 min Outputting Volume: 30% done. (77816/262144) Time: 22.3 min out of approx 75.2 min Outputting Volume: 30% done. (79864/262144) Time: 23.5 min out of approx 76.3 min Outputting Volume: 33% done. (87544/262144) Time: 24.8 min out of approx 75 min Outputting Volume: 39% done. (102904/262144) Time: 26.2 min out of approx 67.3 min Outputting Volume: 46% done. (119800/262144) Time: 27.5 min out of approx 60.6 min Outputting Volume: 55% done. (143096/262144) Time: 29.1 min out of approx 54 min Outputting Volume: 61% done. (160504/262144) Time: 30.7 min out of approx 50.4 min Outputting Volume: 69% done. (182008/262144) Time: 32.3 min out of approx 46.8 min Outputting Volume: 79% done. (208376/262144) Time: 34.2 min out of approx 43.4 min Outputting Volume: 89% done. (232952/262144) Time: 36.1 min out of approx 40.9 min Outputting Volume: 98% done. (257528/262144) Time: 38 min out of approx 38.9 min Outputting Volume: DONE in 38.4 min Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.122795/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.122795/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.122795/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.7108e-09, 1.0366e-09) j_ras = (-1.0366e-09, 6.47876e-11, -1) k_ras = (-5.85721e-09, 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... Sat Jan 12 06:01:29 UTC 2019 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 Sat Jan 12 06:01:29 UTC 2019 Ended at Sat Jan 12 06:08:08 UTC 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Jan 12 06:08:10 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7836, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/transforms/talairach_avi.log tal_QC_AZS /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/transforms/talairach_avi.log TalAviQA: 0.97756 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Jan 12 06:08:11 UTC 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 n018 3.10.0-862.14.4.el7.x86_64 #1 SMP Fri Sep 21 09:07:21 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sat Jan 12 06:08:11 UTC 2019 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.101244 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.101244/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.101244/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.7108e-09, 1.0366e-09) j_ras = (-1.0366e-09, 6.47877e-11, -1) k_ras = (-5.85721e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.101244/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Sat Jan 12 06:11:27 UTC 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.101244/nu0.mnc ./tmp.mri_nu_correct.mni.101244/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.101244/0/ [pettitta@n018:/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/] [2019-01-12 06:11:28] 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.101244/0/ ./tmp.mri_nu_correct.mni.101244/nu0.mnc ./tmp.mri_nu_correct.mni.101244/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 Number of iterations: 16 CV of field change: 0.000957486 Smoothing volume: ............................................................. Outputting Volume: ............................................................ Outputting Volume: 4% done. (11767/262144) Time: 28 sec out of approx 10.8 min Outputting Volume: 9% done. (24055/262144) Time: 56 sec out of approx 10.4 min Outputting Volume: 14% done. (36343/262144) Time: 84 sec out of approx 10.3 min Outputting Volume: 16% done. (42487/262144) Time: 104 sec out of approx 10.7 min Outputting Volume: 21% done. (55287/262144) Time: 2.2 min out of approx 10.3 min Outputting Volume: 26% done. (67575/262144) Time: 2.7 min out of approx 10.2 min Outputting Volume: 30% done. (79863/262144) Time: 3.1 min out of approx 10.2 min Outputting Volume: 35% done. (92151/262144) Time: 3.6 min out of approx 10.2 min Outputting Volume: 40% done. (104439/262144) Time: 4.1 min out of approx 10.2 min Outputting Volume: 45% done. (116727/262144) Time: 4.6 min out of approx 10.2 min Outputting Volume: 49% done. (129015/262144) Time: 5 min out of approx 10.1 min Outputting Volume: 54% done. (141303/262144) Time: 5.5 min out of approx 10.1 min Outputting Volume: 59% done. (153591/262144) Time: 6 min out of approx 10.1 min Outputting Volume: 63% done. (165879/262144) Time: 6.4 min out of approx 10.1 min Outputting Volume: 68% done. (178167/262144) Time: 6.9 min out of approx 10.1 min Outputting Volume: 73% done. (190455/262144) Time: 7.4 min out of approx 10.1 min Outputting Volume: 77% done. (202743/262144) Time: 7.8 min out of approx 10.1 min Outputting Volume: 82% done. (215031/262144) Time: 8.3 min out of approx 10.1 min Outputting Volume: 87% done. (227319/262144) Time: 8.7 min out of approx 10 min Outputting Volume: 91% done. (239607/262144) Time: 9.2 min out of approx 10 min Outputting Volume: 96% done. (250359/262144) Time: 9.7 min out of approx 10.1 min Outputting Volume: DONE in 10 min Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Sat Jan 12 07:00:50 UTC 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.101244/nu1.mnc ./tmp.mri_nu_correct.mni.101244/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.101244/1/ [pettitta@n018:/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/] [2019-01-12 07:00:50] 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.101244/1/ ./tmp.mri_nu_correct.mni.101244/nu1.mnc ./tmp.mri_nu_correct.mni.101244/nu2.imp Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Number of iterations: 10 CV of field change: 0.000988347 Smoothing volume: ............................................................. Outputting Volume: 4% done. (11792/262144) Time: 28 sec out of approx 10.8 min Outputting Volume: 9% done. (24080/262144) Time: 56 sec out of approx 10.4 min Outputting Volume: 14% done. (36368/262144) Time: 85 sec out of approx 10.3 min Outputting Volume: 17% done. (45584/262144) Time: 113 sec out of approx 10.6 min Outputting Volume: 22% done. (58384/262144) Time: 2.4 min out of approx 10.5 min Outputting Volume: 27% done. (70672/262144) Time: 2.8 min out of approx 10.3 min Outputting Volume: 33% done. (85520/262144) Time: 3.3 min out of approx 10.1 min Outputting Volume: 37% done. (97808/262144) Time: 3.8 min out of approx 10.1 min Outputting Volume: 42% done. (110096/262144) Time: 4.2 min out of approx 10.1 min Outputting Volume: 47% done. (122384/262144) Time: 4.7 min out of approx 10.1 min Outputting Volume: 51% done. (134672/262144) Time: 5.2 min out of approx 10.1 min Outputting Volume: 55% done. (144400/262144) Time: 5.6 min out of approx 10.2 min Outputting Volume: 60% done. (156688/262144) Time: 6.1 min out of approx 10.2 min Outputting Volume: 65% done. (171536/262144) Time: 6.6 min out of approx 10.1 min Outputting Volume: 70% done. (183824/262144) Time: 7.1 min out of approx 10.1 min Outputting Volume: 75% done. (196112/262144) Time: 7.5 min out of approx 10.1 min Outputting Volume: 79% done. (208400/262144) Time: 8 min out of approx 10.1 min Outputting Volume: 84% done. (220688/262144) Time: 8.5 min out of approx 10.1 min Outputting Volume: 89% done. (232976/262144) Time: 8.9 min out of approx 10.1 min Outputting Volume: 94% done. (245264/262144) Time: 9.4 min out of approx 10.1 min Outputting Volume: 99% done. (259600/262144) Time: 10 min out of approx 10.1 min Outputting Volume: DONE in 10 min Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.101244/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.101244/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.101244/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.101244/ones.mgz sysname Linux hostname n018 machine x86_64 user pettitta input ./tmp.mri_nu_correct.mni.101244/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.101244/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 134217728 values in range Counting number of voxels in first frame Found 134217728 voxels in final mask Count: 134217728 12167000.000000 134217728 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.101244/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.101244/sum.junk --avgwf ./tmp.mri_nu_correct.mni.101244/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.101244/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.101244/sum.junk --avgwf ./tmp.mri_nu_correct.mni.101244/input.mean.dat sysname Linux hostname n018 machine x86_64 user pettitta UseRobust 0 Loading ./tmp.mri_nu_correct.mni.101244/ones.mgz Loading orig.mgz Voxel Volume is 0.0906512 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.101244/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.101244/ones.mgz --i ./tmp.mri_nu_correct.mni.101244/nu2.mnc --sum ./tmp.mri_nu_correct.mni.101244/sum.junk --avgwf ./tmp.mri_nu_correct.mni.101244/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.101244/ones.mgz --i ./tmp.mri_nu_correct.mni.101244/nu2.mnc --sum ./tmp.mri_nu_correct.mni.101244/sum.junk --avgwf ./tmp.mri_nu_correct.mni.101244/output.mean.dat sysname Linux hostname n018 machine x86_64 user pettitta UseRobust 0 Loading ./tmp.mri_nu_correct.mni.101244/ones.mgz Loading ./tmp.mri_nu_correct.mni.101244/nu2.mnc Voxel Volume is 0.0906512 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.101244/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.101244/nu2.mnc ./tmp.mri_nu_correct.mni.101244/nu2.mnc mul .99805932849368644778 Saving result to './tmp.mri_nu_correct.mni.101244/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.101244/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.101244/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.101244/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.7108e-09, 1.0366e-09) j_ras = (-1.0366e-09, 6.47876e-11, -1) k_ras = (-5.85721e-09, 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 1 minutes and 45 seconds. mapping ( 5, 108) to ( 3, 110) Sat Jan 12 08:32:17 UTC 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Jan 12 08:32:31 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 1.08806 -0.04577 0.00207 1.35489; 0.01907 1.01789 0.20832 -47.91590; -0.00683 -0.12010 1.09834 -31.80229; 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 = 7 Starting OpenSpline(): npoints = 7 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 84 (84), valley at 52 (52) csf peak at 39, setting threshold to 69 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 84 (84), valley at 58 (58) csf peak at 37, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- ******* WARNING - forcing scaling of values to prevent cropping of input [ 0, 272] ***** DISABLING forcing and not doing scaling ******** writing output to T1.mgz 3D bias adjustment took 60 minutes and 29 seconds. Started at Sat Jan 12 01:30:02 UTC 2019 Ended at Sat Jan 12 09:33:13 UTC 2019 #@#%# recon-all-run-time-hours 8.053 recon-all -s sub-ADS5115 finished without error at Sat Jan 12 09:33:13 UTC 2019 New invocation of recon-all Sat Jan 12 09:34:35 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-ADS5115 -sd /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer subjid sub-ADS5115 setenv SUBJECTS_DIR /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/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 n018 3.10.0-862.14.4.el7.x86_64 #1 SMP Fri Sep 21 09:07:21 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 104857600 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 515220 maxlocks unlimited maxsignal 515220 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131915620 19030512 106269524 216908 6615584 110979664 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: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:35-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/12-09:34:36-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/12-09:34:36-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/12-09:34:37-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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 Sat Jan 12 09:34:37 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_em_register -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.9 skull bounding box = (118, 56, 81) --> (406, 335, 438) using (214, 149, 260) as brain centroid... mean wm in atlas = 107, using box (178,114,216) --> (249, 183,304) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.629 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.957535 @ (9.091, 27.273, -9.091) max log p = -3.925889 @ (-4.545, 4.545, 4.545) max log p = -3.881389 @ (2.273, 2.273, 2.273) max log p = -3.877730 @ (3.409, -5.682, -1.136) max log p = -3.863899 @ (-0.568, 1.705, -0.568) max log p = -3.846753 @ (-0.284, -0.284, 0.284) Found translation: (9.4, 29.8, -3.7): log p = -3.847 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.826, old_max_log_p =-3.847 (thresh=-3.8) 0.48291 0.00000 0.00000 -1.49716; 0.00000 0.44922 0.00000 29.82955; 0.00000 0.00000 0.44922 -3.69318; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.826, old_max_log_p =-3.826 (thresh=-3.8) 0.48291 0.00000 0.00000 -1.49716; 0.00000 0.44922 0.00000 29.82955; 0.00000 0.00000 0.44922 -3.69318; 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=-3.790, old_max_log_p =-3.826 (thresh=-3.8) 0.46430 0.01594 -0.01320 5.54388; -0.01520 0.42824 0.05910 25.37383; 0.01549 -0.05970 0.47064 -0.36785; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.764, old_max_log_p =-3.790 (thresh=-3.8) 0.45585 0.01371 0.00217 3.68438; -0.01607 0.45263 0.06246 18.97319; 0.00029 -0.06019 0.47082 6.00842; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.718, old_max_log_p =-3.764 (thresh=-3.8) 0.46440 0.01397 0.00221 0.85966; -0.01634 0.45869 0.07811 14.36789; 0.00084 -0.07464 0.45925 11.77017; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.708, old_max_log_p =-3.718 (thresh=-3.7) 0.46440 0.01397 0.00221 0.85966; -0.01664 0.46729 0.07957 12.05432; 0.00084 -0.07464 0.45925 11.77017; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.708, old_max_log_p =-3.708 (thresh=-3.7) 0.46440 0.01397 0.00221 0.85966; -0.01664 0.46729 0.07957 12.05432; 0.00084 -0.07464 0.45925 11.77017; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.688, old_max_log_p =-3.708 (thresh=-3.7) 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.688, old_max_log_p =-3.688 (thresh=-3.7) 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 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 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.688 (old=-4.629) transform before final EM align: 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 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 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.1 tol 0.000000 final transform: 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 2632.851493 mri_em_register stimesec 139.688016 mri_em_register ru_maxrss 1752444 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 2046579 mri_em_register ru_majflt 4 mri_em_register ru_nswap 0 mri_em_register ru_inblock 26830 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 46219003 mri_em_register ru_nivcsw 27482 registration took 56 minutes and 52 seconds. #-------------------------------------- #@# CA Normalize Sat Jan 12 10:31:29 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... INFO: MRImask() using MRImaskDifferentGeometry() resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.9 skull bounding box = (118, 56, 81) --> (406, 335, 438) using (214, 149, 260) as brain centroid... mean wm in atlas = 107, using box (178,114,216) --> (249, 183,304) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 0.46405 0.00578 0.00478 3.21134; -0.00910 0.46748 0.07588 10.71496; -0.00318 -0.07123 0.46146 9.97942; 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 (260, 56, 74) --> (403, 303, 430) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 13 of 8103 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (121, 60, 71) --> (264, 301, 430) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 16 of 8369 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (263, 248, 131) --> (367, 340, 247) Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 390 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (164, 248, 125) --> (260, 334, 249) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 304 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (224, 222, 208) --> (298, 372, 272) Brain_Stem: limiting intensities to 88.0 --> 132.0 6 of 816 (0.7%) samples deleted using 17982 total control points for intensity normalization... bias field = 0.952 +- 0.063 33 of 17947 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (260, 56, 74) --> (403, 303, 430) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 14 of 8637 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (121, 60, 71) --> (264, 301, 430) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 16 of 8870 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (263, 248, 131) --> (367, 340, 247) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 259 of 495 (52.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (164, 248, 125) --> (260, 334, 249) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 221 of 367 (60.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (224, 222, 208) --> (298, 372, 272) Brain_Stem: limiting intensities to 88.0 --> 132.0 923 of 1064 (86.7%) samples deleted using 19433 total control points for intensity normalization... bias field = 1.030 +- 0.039 37 of 17982 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (260, 56, 74) --> (403, 303, 430) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 54 of 8645 (0.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (121, 60, 71) --> (264, 301, 430) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 40 of 8797 (0.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (263, 248, 131) --> (367, 340, 247) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 487 of 616 (79.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (164, 248, 125) --> (260, 334, 249) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 424 of 470 (90.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (224, 222, 208) --> (298, 372, 272) Brain_Stem: limiting intensities to 88.0 --> 132.0 1082 of 1105 (97.9%) samples deleted using 19633 total control points for intensity normalization... bias field = 1.020 +- 0.033 31 of 17494 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 16 minutes and 45 seconds. #-------------------------------------- #@# CA Reg Sat Jan 12 10:48:15 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_ca_register -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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) = 0.10 (predicted orig area = 77.9) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.929, neg=0, invalid=762 0001: dt=887.808000, rms=0.820 (11.712%), neg=0, invalid=762 0002: dt=517.888000, rms=0.805 (1.829%), neg=0, invalid=762 0003: dt=1479.680000, rms=0.788 (2.053%), neg=0, invalid=762 0004: dt=295.936000, rms=0.783 (0.740%), neg=0, invalid=762 0005: dt=2071.552000, rms=0.775 (0.902%), neg=0, invalid=762 0006: dt=517.888000, rms=0.771 (0.518%), neg=0, invalid=762 0007: dt=129.472000, rms=0.771 (0.022%), neg=0, invalid=762 0008: dt=129.472000, rms=0.771 (0.035%), neg=0, invalid=762 0009: dt=129.472000, rms=0.771 (0.040%), neg=0, invalid=762 0010: dt=129.472000, rms=0.770 (0.050%), neg=0, invalid=762 0011: dt=129.472000, rms=0.770 (0.106%), neg=0, invalid=762 0012: dt=129.472000, rms=0.768 (0.135%), neg=0, invalid=762 0013: dt=129.472000, rms=0.767 (0.177%), neg=0, invalid=762 0014: dt=129.472000, rms=0.766 (0.182%), neg=0, invalid=762 0015: dt=129.472000, rms=0.764 (0.192%), neg=0, invalid=762 0016: dt=129.472000, rms=0.763 (0.155%), neg=0, invalid=762 0017: dt=129.472000, rms=0.762 (0.127%), neg=0, invalid=762 0018: dt=129.472000, rms=0.761 (0.098%), neg=0, invalid=762 0019: dt=129.472000, rms=0.761 (0.106%), neg=0, invalid=762 0020: dt=129.472000, rms=0.760 (0.115%), neg=0, invalid=762 0021: dt=129.472000, rms=0.759 (0.103%), neg=0, invalid=762 0022: dt=2071.552000, rms=0.758 (0.160%), neg=0, invalid=762 0023: dt=129.472000, rms=0.758 (0.012%), neg=0, invalid=762 0024: dt=129.472000, rms=0.758 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.758, neg=0, invalid=762 0025: dt=517.888000, rms=0.757 (0.107%), neg=0, invalid=762 0026: dt=2071.552000, rms=0.755 (0.308%), neg=0, invalid=762 0027: dt=221.952000, rms=0.755 (0.038%), neg=0, invalid=762 0028: dt=221.952000, rms=0.755 (0.014%), neg=0, invalid=762 0029: dt=221.952000, rms=0.754 (0.026%), neg=0, invalid=762 0030: dt=221.952000, rms=0.754 (0.068%), neg=0, invalid=762 0031: dt=221.952000, rms=0.753 (0.076%), neg=0, invalid=762 0032: dt=221.952000, rms=0.753 (0.082%), neg=0, invalid=762 0033: dt=221.952000, rms=0.752 (0.061%), neg=0, invalid=762 0034: dt=221.952000, rms=0.752 (0.056%), neg=0, invalid=762 0035: dt=0.000000, rms=0.752 (0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0036: dt=145.152000, rms=0.762 (0.480%), neg=0, invalid=762 0037: dt=580.608000, rms=0.753 (1.166%), neg=0, invalid=762 0038: dt=414.720000, rms=0.746 (0.891%), neg=0, invalid=762 0039: dt=145.152000, rms=0.742 (0.518%), neg=0, invalid=762 0040: dt=145.152000, rms=0.741 (0.096%), neg=0, invalid=762 0041: dt=145.152000, rms=0.740 (0.143%), neg=0, invalid=762 0042: dt=145.152000, rms=0.739 (0.212%), neg=0, invalid=762 0043: dt=145.152000, rms=0.737 (0.308%), neg=0, invalid=762 0044: dt=145.152000, rms=0.734 (0.313%), neg=0, invalid=762 0045: dt=145.152000, rms=0.732 (0.355%), neg=0, invalid=762 0046: dt=145.152000, rms=0.729 (0.362%), neg=0, invalid=762 0047: dt=145.152000, rms=0.727 (0.325%), neg=0, invalid=762 0048: dt=145.152000, rms=0.725 (0.232%), neg=0, invalid=762 0049: dt=145.152000, rms=0.724 (0.155%), neg=0, invalid=762 0050: dt=145.152000, rms=0.722 (0.227%), neg=0, invalid=762 0051: dt=145.152000, rms=0.721 (0.211%), neg=0, invalid=762 0052: dt=145.152000, rms=0.720 (0.149%), neg=0, invalid=762 0053: dt=145.152000, rms=0.719 (0.094%), neg=0, invalid=762 0054: dt=145.152000, rms=0.718 (0.160%), neg=0, invalid=762 0055: dt=145.152000, rms=0.717 (0.157%), neg=0, invalid=762 0056: dt=145.152000, rms=0.716 (0.114%), neg=0, invalid=762 0057: dt=145.152000, rms=0.715 (0.052%), neg=0, invalid=762 0058: dt=103.680000, rms=0.715 (0.010%), neg=0, invalid=762 0059: dt=103.680000, rms=0.715 (0.035%), neg=0, invalid=762 0060: dt=103.680000, rms=0.715 (0.010%), neg=0, invalid=762 0061: dt=103.680000, rms=0.715 (0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.716, neg=0, invalid=762 0062: dt=248.832000, rms=0.712 (0.493%), neg=0, invalid=762 0063: dt=0.000000, rms=0.712 (-0.004%), neg=0, invalid=762 0064: dt=0.450000, rms=0.712 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.783, neg=0, invalid=762 0065: dt=38.400000, rms=0.771 (1.612%), neg=0, invalid=762 0066: dt=78.682353, rms=0.764 (0.860%), neg=0, invalid=762 0067: dt=124.363636, rms=0.761 (0.377%), neg=0, invalid=762 0068: dt=44.800000, rms=0.759 (0.269%), neg=0, invalid=762 0069: dt=44.800000, rms=0.759 (0.045%), neg=0, invalid=762 0070: dt=44.800000, rms=0.758 (0.043%), neg=0, invalid=762 0071: dt=44.800000, rms=0.758 (0.071%), neg=0, invalid=762 0072: dt=44.800000, rms=0.757 (0.081%), neg=0, invalid=762 0073: dt=44.800000, rms=0.757 (0.074%), neg=0, invalid=762 0074: dt=44.800000, rms=0.756 (0.053%), neg=0, invalid=762 0075: dt=38.400000, rms=0.756 (0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.757, neg=0, invalid=762 0076: dt=0.000000, rms=0.756 (0.067%), neg=0, invalid=762 0077: dt=0.000000, rms=0.756 (0.000%), neg=0, invalid=762 0078: dt=0.250000, rms=0.756 (-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=0.820, neg=0, invalid=762 0079: dt=4.692308, rms=0.813 (0.856%), neg=0, invalid=762 0080: dt=4.032000, rms=0.812 (0.114%), neg=0, invalid=762 0081: dt=4.032000, rms=0.811 (0.048%), neg=0, invalid=762 0082: dt=4.032000, rms=0.811 (-0.029%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.812, neg=0, invalid=762 0083: dt=0.000000, rms=0.811 (0.066%), neg=0, invalid=762 0084: dt=0.000000, rms=0.811 (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=0.881, neg=0, invalid=762 0085: dt=1.280000, rms=0.877 (0.490%), neg=0, invalid=762 0086: dt=2.275229, rms=0.871 (0.640%), neg=0, invalid=762 0087: dt=0.448000, rms=0.870 (0.104%), neg=0, invalid=762 0088: dt=0.448000, rms=0.870 (0.058%), neg=0, invalid=762 0089: dt=0.448000, rms=0.869 (0.094%), neg=0, invalid=762 0090: dt=0.448000, rms=0.868 (0.122%), neg=0, invalid=762 0091: dt=0.448000, rms=0.866 (0.160%), neg=0, invalid=762 0092: dt=0.448000, rms=0.865 (0.170%), neg=0, invalid=762 0093: dt=0.448000, rms=0.864 (0.143%), neg=0, invalid=762 0094: dt=0.448000, rms=0.863 (0.098%), neg=0, invalid=762 0095: dt=0.448000, rms=0.862 (0.059%), neg=0, invalid=762 0096: dt=1.792000, rms=0.862 (0.060%), neg=0, invalid=762 0097: dt=1.792000, rms=0.861 (0.133%), neg=0, invalid=762 0098: dt=0.448000, rms=0.861 (0.008%), neg=0, invalid=762 0099: dt=0.448000, rms=0.861 (0.008%), neg=0, invalid=762 0100: dt=0.448000, rms=0.860 (0.016%), neg=0, invalid=762 0101: dt=0.448000, rms=0.860 (0.020%), neg=0, invalid=762 0102: dt=0.448000, rms=0.860 (0.047%), neg=0, invalid=762 0103: dt=0.448000, rms=0.859 (0.051%), neg=0, invalid=762 0104: dt=0.448000, rms=0.859 (0.058%), neg=0, invalid=762 0105: dt=0.448000, rms=0.859 (0.044%), neg=0, invalid=762 0106: dt=0.448000, rms=0.858 (0.038%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.859, neg=0, invalid=762 0107: dt=0.000000, rms=0.858 (0.058%), neg=0, invalid=762 0108: 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=0.801, neg=0, invalid=762 0109: dt=0.384000, rms=0.796 (0.557%), neg=0, invalid=762 0110: dt=0.064000, rms=0.796 (0.035%), neg=0, invalid=762 0111: dt=0.064000, rms=0.796 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.797, neg=0, invalid=762 0112: dt=0.028000, rms=0.796 (0.075%), neg=0, invalid=762 0113: dt=0.020000, rms=0.796 (0.005%), neg=0, invalid=762 0114: dt=0.020000, rms=0.796 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.08943 (33) Left_Lateral_Ventricle (4): linear fit = 1.86 x + 0.0 (51059 voxels, overlap=0.132) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (51059 voxels, peak = 37), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.09665 (33) Right_Lateral_Ventricle (43): linear fit = 2.12 x + 0.0 (43176 voxels, overlap=0.041) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (43176 voxels, peak = 34), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06289 (102) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (19936 voxels, overlap=0.742) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (19936 voxels, peak = 103), gca=103.2 gca peak = 0.20183 (93) mri peak = 0.05252 (105) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (18842 voxels, overlap=1.020) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (18842 voxels, peak = 102), gca=101.8 gca peak = 0.21683 (55) mri peak = 0.07019 (73) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (27677 voxels, overlap=0.023) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (27677 voxels, peak = 71), gca=71.2 gca peak = 0.30730 (58) mri peak = 0.07584 (75) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (28450 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (28450 voxels, peak = 73), gca=73.4 gca peak = 0.11430 (101) mri peak = 0.08579 (106) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (1801463 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (1801463 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.09176 (106) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (1820438 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (1820438 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.04782 (77) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (1506729 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (1506729 voxels, peak = 78), gca=78.2 gca peak = 0.15082 (58) mri peak = 0.05206 (77) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (1447190 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (1447190 voxels, peak = 77), gca=76.9 gca peak = 0.14161 (67) mri peak = 0.10762 (86) Right_Caudate (50): linear fit = 1.27 x + 0.0 (25703 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.27 x + 0.0 (25703 voxels, peak = 85), gca=85.4 gca peak = 0.15243 (71) mri peak = 0.10816 (86) Left_Caudate (11): linear fit = 1.17 x + 0.0 (26051 voxels, overlap=0.015) Left_Caudate (11): linear fit = 1.17 x + 0.0 (26051 voxels, peak = 83), gca=83.4 gca peak = 0.13336 (57) mri peak = 0.05334 (80) Left_Cerebellum_Cortex (8): linear fit = 1.45 x + 0.0 (326211 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.45 x + 0.0 (326211 voxels, peak = 82), gca=82.4 gca peak = 0.13252 (56) mri peak = 0.06459 (78) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (325183 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (325183 voxels, peak = 77), gca=77.0 gca peak = 0.18181 (84) mri peak = 0.05618 (82) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (177675 voxels, overlap=0.990) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (177675 voxels, peak = 82), gca=81.9 gca peak = 0.20573 (83) mri peak = 0.05285 (71) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (154045 voxels, overlap=0.997) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (154045 voxels, peak = 81), gca=80.9 gca peak = 0.21969 (57) mri peak = 0.09107 (73) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (10695 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (10695 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.10414 (77) Right_Amygdala (54): linear fit = 1.37 x + 0.0 (12464 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.37 x + 0.0 (12464 voxels, peak = 76), gca=76.4 gca peak = 0.14181 (85) mri peak = 0.06240 (95) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (87427 voxels, overlap=0.486) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (87427 voxels, peak = 94), gca=93.9 gca peak = 0.11978 (83) mri peak = 0.06722 (95) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (78144 voxels, overlap=0.250) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (78144 voxels, peak = 95), gca=95.0 gca peak = 0.13399 (79) mri peak = 0.07242 (95) Left_Putamen (12): linear fit = 1.22 x + 0.0 (47702 voxels, overlap=0.010) Left_Putamen (12): linear fit = 1.22 x + 0.0 (47702 voxels, peak = 96), gca=96.0 gca peak = 0.14159 (79) mri peak = 0.06765 (93) Right_Putamen (51): linear fit = 1.20 x + 0.0 (47830 voxels, overlap=0.049) Right_Putamen (51): linear fit = 1.20 x + 0.0 (47830 voxels, peak = 94), gca=94.4 gca peak = 0.10025 (80) mri peak = 0.18537 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (193587 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.05 x + 0.0 (193587 voxels, peak = 84), gca=84.4 gca peak = 0.13281 (86) mri peak = 0.07221 (88) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (35020 voxels, overlap=0.725) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (35020 voxels, peak = 89), gca=89.0 gca peak = 0.12801 (89) mri peak = 0.07361 (89) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (35802 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (35802 voxels, peak = 91), gca=91.2 gca peak = 0.20494 (23) mri peak = 0.09717 (52) Third_Ventricle (14): linear fit = 2.07 x + 0.0 (4644 voxels, overlap=0.060) Third_Ventricle (14): linear fit = 2.07 x + 0.0 (4644 voxels, peak = 47), gca=47.5 gca peak = 0.15061 (21) mri peak = 0.06141 (50) Fourth_Ventricle (15): linear fit = 2.14 x + 0.0 (17564 voxels, overlap=0.213) Fourth_Ventricle (15): linear fit = 2.14 x + 0.0 (17564 voxels, peak = 45), gca=45.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.31 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Left_Putamen too bright - rescaling by 0.990 (from 1.215) to 95.0 (was 96.0) Right_Pallidum too bright - rescaling by 0.992 (from 1.075) to 102.4 (was 103.2) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.794, neg=0, invalid=762 0115: dt=577.141784, rms=0.712 (10.393%), neg=0, invalid=762 0116: dt=517.888000, rms=0.692 (2.783%), neg=0, invalid=762 0117: dt=517.888000, rms=0.681 (1.650%), neg=0, invalid=762 0118: dt=517.888000, rms=0.676 (0.737%), neg=0, invalid=762 0119: dt=517.888000, rms=0.671 (0.711%), neg=0, invalid=762 0120: dt=443.904000, rms=0.669 (0.331%), neg=0, invalid=762 0121: dt=443.904000, rms=0.666 (0.372%), neg=0, invalid=762 0122: dt=369.920000, rms=0.665 (0.216%), neg=0, invalid=762 0123: dt=517.888000, rms=0.663 (0.234%), neg=0, invalid=762 0124: dt=369.920000, rms=0.662 (0.181%), neg=0, invalid=762 0125: dt=517.888000, rms=0.661 (0.154%), neg=0, invalid=762 0126: dt=443.904000, rms=0.660 (0.190%), neg=0, invalid=762 0127: dt=369.920000, rms=0.659 (0.113%), neg=0, invalid=762 0128: dt=517.888000, rms=0.658 (0.148%), neg=0, invalid=762 0129: dt=369.920000, rms=0.657 (0.107%), neg=0, invalid=762 0130: dt=517.888000, rms=0.656 (0.122%), neg=0, invalid=762 0131: dt=369.920000, rms=0.656 (0.074%), neg=0, invalid=762 0132: dt=517.888000, rms=0.655 (0.145%), neg=0, invalid=762 0133: dt=221.952000, rms=0.655 (0.025%), neg=0, invalid=762 0134: dt=221.952000, rms=0.654 (0.061%), neg=0, invalid=762 0135: dt=221.952000, rms=0.654 (0.074%), neg=0, invalid=762 0136: dt=221.952000, rms=0.653 (0.090%), neg=0, invalid=762 0137: dt=221.952000, rms=0.653 (0.103%), neg=0, invalid=762 0138: dt=221.952000, rms=0.652 (0.120%), neg=0, invalid=762 0139: dt=221.952000, rms=0.651 (0.140%), neg=0, invalid=762 0140: dt=221.952000, rms=0.650 (0.126%), neg=0, invalid=762 0141: dt=221.952000, rms=0.649 (0.128%), neg=0, invalid=762 0142: dt=221.952000, rms=0.649 (0.109%), neg=0, invalid=762 0143: dt=221.952000, rms=0.648 (0.123%), neg=0, invalid=762 0144: dt=221.952000, rms=0.647 (0.097%), neg=0, invalid=762 0145: dt=221.952000, rms=0.647 (0.097%), neg=0, invalid=762 0146: dt=221.952000, rms=0.646 (0.083%), neg=0, invalid=762 0147: dt=221.952000, rms=0.646 (0.066%), neg=0, invalid=762 0148: dt=221.952000, rms=0.645 (0.055%), neg=0, invalid=762 0149: dt=221.952000, rms=0.645 (0.042%), neg=0, invalid=762 0150: dt=221.952000, rms=0.645 (0.054%), neg=0, invalid=762 0151: dt=221.952000, rms=0.644 (0.063%), neg=0, invalid=762 0152: dt=221.952000, rms=0.644 (0.053%), neg=0, invalid=762 0153: dt=221.952000, rms=0.644 (0.053%), neg=0, invalid=762 0154: dt=221.952000, rms=0.643 (0.050%), neg=0, invalid=762 0155: dt=221.952000, rms=0.643 (0.052%), neg=0, invalid=762 0156: dt=221.952000, rms=0.642 (0.065%), neg=0, invalid=762 0157: dt=221.952000, rms=0.642 (0.049%), neg=0, invalid=762 0158: dt=221.952000, rms=0.642 (0.045%), neg=0, invalid=762 0159: dt=221.952000, rms=0.642 (0.040%), neg=0, invalid=762 0160: dt=221.952000, rms=0.641 (0.046%), neg=0, invalid=762 0161: dt=221.952000, rms=0.641 (0.053%), neg=0, invalid=762 0162: dt=221.952000, rms=0.641 (0.065%), neg=0, invalid=762 0163: dt=221.952000, rms=0.640 (0.050%), neg=0, invalid=762 0164: dt=221.952000, rms=0.640 (0.036%), neg=0, invalid=762 0165: dt=221.952000, rms=0.640 (0.034%), neg=0, invalid=762 0166: dt=221.952000, rms=0.640 (0.035%), neg=0, invalid=762 0167: dt=221.952000, rms=0.639 (0.050%), neg=0, invalid=762 0168: dt=221.952000, rms=0.639 (0.049%), neg=0, invalid=762 0169: dt=221.952000, rms=0.639 (0.047%), neg=0, invalid=762 0170: dt=221.952000, rms=0.638 (0.043%), neg=0, invalid=762 0171: dt=221.952000, rms=0.638 (0.037%), neg=0, invalid=762 0172: dt=221.952000, rms=0.638 (0.046%), neg=0, invalid=762 0173: dt=221.952000, rms=0.637 (0.050%), neg=0, invalid=762 0174: dt=221.952000, rms=0.637 (0.035%), neg=0, invalid=762 0175: dt=221.952000, rms=0.637 (0.022%), neg=0, invalid=762 0176: dt=221.952000, rms=0.637 (0.030%), neg=0, invalid=762 0177: dt=221.952000, rms=0.637 (0.041%), neg=0, invalid=762 0178: dt=221.952000, rms=0.636 (0.038%), neg=0, invalid=762 0179: dt=221.952000, rms=0.636 (0.039%), neg=0, invalid=762 0180: dt=221.952000, rms=0.636 (0.038%), neg=0, invalid=762 0181: dt=221.952000, rms=0.636 (0.038%), neg=0, invalid=762 0182: dt=221.952000, rms=0.636 (0.024%), neg=0, invalid=762 0183: dt=221.952000, rms=0.635 (0.025%), neg=0, invalid=762 0184: dt=221.952000, rms=0.635 (0.029%), neg=0, invalid=762 0185: dt=221.952000, rms=0.635 (0.025%), neg=0, invalid=762 0186: dt=221.952000, rms=0.635 (0.041%), neg=0, invalid=762 0187: dt=221.952000, rms=0.635 (0.041%), neg=0, invalid=762 0188: dt=221.952000, rms=0.634 (0.042%), neg=0, invalid=762 0189: dt=221.952000, rms=0.634 (0.038%), neg=0, invalid=762 0190: dt=221.952000, rms=0.634 (0.042%), neg=0, invalid=762 0191: dt=221.952000, rms=0.634 (0.036%), neg=0, invalid=762 0192: dt=221.952000, rms=0.633 (0.038%), neg=0, invalid=762 0193: dt=221.952000, rms=0.633 (0.028%), neg=0, invalid=762 0194: dt=221.952000, rms=0.633 (0.021%), neg=0, invalid=762 0195: dt=221.952000, rms=0.633 (0.013%), neg=0, invalid=762 0196: dt=2071.552000, rms=0.633 (0.053%), neg=0, invalid=762 0197: dt=73.984000, rms=0.633 (-0.007%), neg=0, invalid=762 0198: dt=73.984000, rms=0.633 (0.003%), neg=0, invalid=762 0199: dt=73.984000, rms=0.633 (0.000%), neg=0, invalid=762 0200: dt=73.984000, rms=0.633 (-0.016%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0201: dt=517.888000, rms=0.632 (0.071%), neg=0, invalid=762 0202: dt=887.808000, rms=0.632 (0.106%), neg=0, invalid=762 0203: dt=110.976000, rms=0.632 (-0.011%), neg=0, invalid=762 0204: dt=110.976000, rms=0.632 (0.004%), neg=0, invalid=762 0205: dt=110.976000, rms=0.632 (-0.007%), 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 0206: dt=497.664000, rms=0.632 (0.749%), neg=0, invalid=762 0207: dt=248.832000, rms=0.625 (1.001%), neg=0, invalid=762 0208: dt=145.152000, rms=0.624 (0.253%), neg=0, invalid=762 0209: dt=580.608000, rms=0.619 (0.809%), neg=0, invalid=762 0210: dt=124.416000, rms=0.617 (0.245%), neg=0, invalid=762 0211: dt=1327.104000, rms=0.613 (0.762%), neg=0, invalid=762 0212: dt=124.081633, rms=0.609 (0.649%), neg=0, invalid=762 0213: dt=414.720000, rms=0.607 (0.310%), neg=0, invalid=762 0214: dt=145.152000, rms=0.606 (0.155%), neg=0, invalid=762 0215: dt=331.776000, rms=0.605 (0.169%), neg=0, invalid=762 0216: dt=103.680000, rms=0.604 (0.086%), neg=0, invalid=762 0217: dt=1327.104000, rms=0.601 (0.465%), neg=0, invalid=762 0218: dt=124.416000, rms=0.600 (0.212%), neg=0, invalid=762 0219: dt=145.152000, rms=0.600 (0.085%), neg=0, invalid=762 0220: dt=580.608000, rms=0.599 (0.185%), neg=0, invalid=762 0221: dt=124.416000, rms=0.598 (0.092%), neg=0, invalid=762 0222: dt=580.608000, rms=0.597 (0.148%), neg=0, invalid=762 0223: dt=124.416000, rms=0.597 (0.100%), neg=0, invalid=762 0224: dt=331.776000, rms=0.596 (0.086%), neg=0, invalid=762 0225: dt=124.416000, rms=0.596 (0.053%), neg=0, invalid=762 0226: dt=414.720000, rms=0.595 (0.104%), neg=0, invalid=762 0227: dt=124.416000, rms=0.595 (0.049%), neg=0, invalid=762 0228: dt=124.416000, rms=0.594 (0.066%), neg=0, invalid=762 0229: dt=124.416000, rms=0.594 (0.059%), neg=0, invalid=762 0230: dt=124.416000, rms=0.593 (0.094%), neg=0, invalid=762 0231: dt=124.416000, rms=0.593 (0.108%), neg=0, invalid=762 0232: dt=124.416000, rms=0.592 (0.127%), neg=0, invalid=762 0233: dt=124.416000, rms=0.591 (0.143%), neg=0, invalid=762 0234: dt=124.416000, rms=0.590 (0.156%), neg=0, invalid=762 0235: dt=124.416000, rms=0.589 (0.163%), neg=0, invalid=762 0236: dt=124.416000, rms=0.588 (0.162%), neg=0, invalid=762 0237: dt=124.416000, rms=0.588 (0.152%), neg=0, invalid=762 0238: dt=124.416000, rms=0.587 (0.137%), neg=0, invalid=762 0239: dt=124.416000, rms=0.586 (0.139%), neg=0, invalid=762 0240: dt=124.416000, rms=0.585 (0.161%), neg=0, invalid=762 0241: dt=124.416000, rms=0.584 (0.138%), neg=0, invalid=762 0242: dt=124.416000, rms=0.583 (0.128%), neg=0, invalid=762 0243: dt=124.416000, rms=0.583 (0.102%), neg=0, invalid=762 0244: dt=124.416000, rms=0.582 (0.095%), neg=0, invalid=762 0245: dt=124.416000, rms=0.582 (0.121%), neg=0, invalid=762 0246: dt=124.416000, rms=0.581 (0.110%), neg=0, invalid=762 0247: dt=124.416000, rms=0.580 (0.087%), neg=0, invalid=762 0248: dt=124.416000, rms=0.580 (0.089%), neg=0, invalid=762 0249: dt=124.416000, rms=0.579 (0.088%), neg=0, invalid=762 0250: dt=124.416000, rms=0.579 (0.104%), neg=0, invalid=762 0251: dt=124.416000, rms=0.578 (0.070%), neg=0, invalid=762 0252: dt=124.416000, rms=0.578 (0.051%), neg=0, invalid=762 0253: dt=124.416000, rms=0.578 (0.068%), neg=0, invalid=762 0254: dt=124.416000, rms=0.577 (0.070%), neg=0, invalid=762 0255: dt=124.416000, rms=0.577 (0.066%), neg=0, invalid=762 0256: dt=124.416000, rms=0.577 (0.051%), neg=0, invalid=762 0257: dt=124.416000, rms=0.576 (0.060%), neg=0, invalid=762 0258: dt=124.416000, rms=0.576 (0.063%), neg=0, invalid=762 0259: dt=124.416000, rms=0.576 (0.022%), neg=0, invalid=762 0260: dt=124.416000, rms=0.575 (0.053%), neg=0, invalid=762 0261: dt=124.416000, rms=0.575 (0.048%), neg=0, invalid=762 0262: dt=124.416000, rms=0.575 (0.057%), neg=0, invalid=762 0263: dt=124.416000, rms=0.575 (0.036%), neg=0, invalid=762 0264: dt=124.416000, rms=0.574 (0.031%), neg=0, invalid=762 0265: dt=124.416000, rms=0.574 (0.050%), neg=0, invalid=762 0266: dt=124.416000, rms=0.574 (0.041%), neg=0, invalid=762 0267: dt=124.416000, rms=0.574 (0.000%), neg=0, invalid=762 0268: dt=124.416000, rms=0.574 (0.030%), neg=0, invalid=762 0269: dt=124.416000, rms=0.574 (0.042%), neg=0, invalid=762 0270: dt=124.416000, rms=0.573 (0.039%), neg=0, invalid=762 0271: dt=124.416000, rms=0.573 (0.031%), neg=0, invalid=762 0272: dt=124.416000, rms=0.573 (0.015%), neg=0, invalid=762 0273: dt=124.416000, rms=0.573 (0.039%), neg=0, invalid=762 0274: dt=124.416000, rms=0.573 (0.040%), neg=0, invalid=762 0275: dt=124.416000, rms=0.572 (0.029%), neg=0, invalid=762 0276: dt=124.416000, rms=0.572 (0.004%), neg=0, invalid=762 0277: dt=124.416000, rms=0.572 (0.012%), neg=0, invalid=762 0278: dt=124.416000, rms=0.572 (0.030%), neg=0, invalid=762 0279: dt=124.416000, rms=0.572 (0.031%), neg=0, invalid=762 0280: dt=124.416000, rms=0.572 (0.027%), neg=0, invalid=762 0281: dt=124.416000, rms=0.572 (0.014%), neg=0, invalid=762 0282: dt=124.416000, rms=0.572 (0.031%), neg=0, invalid=762 0283: dt=124.416000, rms=0.571 (0.031%), neg=0, invalid=762 0284: dt=124.416000, rms=0.571 (0.021%), neg=0, invalid=762 0285: dt=124.416000, rms=0.571 (0.025%), neg=0, invalid=762 0286: dt=124.416000, rms=0.571 (0.021%), neg=0, invalid=762 0287: dt=124.416000, rms=0.571 (0.023%), neg=0, invalid=762 0288: dt=124.416000, rms=0.571 (0.022%), neg=0, invalid=762 0289: dt=24.000000, rms=0.571 (0.001%), neg=0, invalid=762 0290: dt=24.000000, 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 0291: dt=331.776000, rms=0.569 (0.321%), neg=0, invalid=762 0292: dt=82.944000, rms=0.569 (0.033%), neg=0, invalid=762 0293: dt=82.944000, rms=0.569 (0.010%), neg=0, invalid=762 0294: dt=82.944000, rms=0.569 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.600, neg=0, invalid=762 0295: dt=44.800000, rms=0.598 (0.389%), neg=0, invalid=762 0296: dt=128.000000, rms=0.595 (0.511%), neg=0, invalid=762 0297: dt=227.984906, rms=0.588 (1.090%), neg=0, invalid=762 0298: dt=44.800000, rms=0.587 (0.230%), neg=0, invalid=762 0299: dt=102.400000, rms=0.585 (0.298%), neg=0, invalid=762 0300: dt=102.400000, rms=0.583 (0.346%), neg=0, invalid=762 0301: dt=44.800000, rms=0.582 (0.196%), neg=0, invalid=762 0302: dt=179.200000, rms=0.580 (0.337%), neg=0, invalid=762 0303: dt=44.800000, rms=0.579 (0.120%), neg=0, invalid=762 0304: dt=179.200000, rms=0.578 (0.280%), neg=0, invalid=762 0305: dt=38.400000, rms=0.577 (0.101%), neg=0, invalid=762 0306: dt=409.600000, rms=0.575 (0.264%), neg=0, invalid=762 0307: dt=38.400000, rms=0.575 (0.130%), neg=0, invalid=762 0308: dt=153.600000, rms=0.574 (0.178%), neg=0, invalid=762 0309: dt=44.800000, rms=0.573 (0.028%), neg=0, invalid=762 0310: dt=44.800000, rms=0.573 (0.078%), neg=0, invalid=762 0311: dt=44.800000, rms=0.573 (0.045%), neg=0, invalid=762 0312: dt=44.800000, rms=0.572 (0.055%), neg=0, invalid=762 0313: dt=44.800000, rms=0.572 (0.112%), neg=0, invalid=762 0314: dt=44.800000, rms=0.571 (0.119%), neg=0, invalid=762 0315: dt=44.800000, rms=0.570 (0.120%), neg=0, invalid=762 0316: dt=44.800000, rms=0.570 (0.138%), neg=0, invalid=762 0317: dt=44.800000, rms=0.569 (0.134%), neg=0, invalid=762 0318: dt=44.800000, rms=0.568 (0.115%), neg=0, invalid=762 0319: dt=44.800000, rms=0.568 (0.111%), neg=0, invalid=762 0320: dt=44.800000, rms=0.567 (0.096%), neg=0, invalid=762 0321: dt=44.800000, rms=0.566 (0.108%), neg=0, invalid=762 0322: dt=44.800000, rms=0.566 (0.103%), neg=0, invalid=762 0323: dt=44.800000, rms=0.565 (0.082%), neg=0, invalid=762 0324: dt=44.800000, rms=0.565 (0.090%), neg=0, invalid=762 0325: dt=44.800000, rms=0.564 (0.080%), neg=0, invalid=762 0326: dt=44.800000, rms=0.564 (0.075%), neg=0, invalid=762 0327: dt=44.800000, rms=0.564 (0.066%), neg=0, invalid=762 0328: dt=44.800000, rms=0.563 (0.063%), neg=0, invalid=762 0329: dt=44.800000, rms=0.563 (0.056%), neg=0, invalid=762 0330: dt=44.800000, rms=0.563 (0.021%), neg=0, invalid=762 0331: dt=44.800000, rms=0.563 (0.024%), neg=0, invalid=762 0332: dt=44.800000, rms=0.563 (0.017%), neg=0, invalid=762 0333: dt=2.000000, rms=0.563 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0334: dt=32.000000, rms=0.562 (0.086%), neg=0, invalid=762 0335: dt=0.000000, rms=0.562 (0.004%), neg=0, invalid=762 0336: dt=0.250000, rms=0.562 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0337: dt=6.232558, rms=0.611 (0.301%), neg=0, invalid=762 0338: dt=2.880000, rms=0.611 (0.022%), neg=0, invalid=762 0339: dt=2.880000, rms=0.611 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=762 0340: dt=2.000000, rms=0.611 (0.052%), neg=0, invalid=762 0341: dt=0.180000, rms=0.611 (-0.001%), neg=0, invalid=762 0342: dt=0.180000, rms=0.611 (0.000%), neg=0, invalid=762 0343: dt=0.180000, rms=0.611 (-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=0.681, neg=0, invalid=762 0344: dt=4.232735, rms=0.664 (2.484%), neg=0, invalid=762 0345: dt=6.144000, rms=0.658 (0.903%), neg=0, invalid=762 0346: dt=6.144000, rms=0.656 (0.280%), neg=0, invalid=762 0347: dt=7.168000, rms=0.655 (0.254%), neg=0, invalid=762 0348: dt=1.792000, rms=0.655 (0.015%), neg=0, invalid=762 0349: dt=1.792000, rms=0.655 (0.016%), neg=0, invalid=762 0350: dt=1.792000, rms=0.654 (0.019%), neg=0, invalid=762 0351: dt=1.792000, rms=0.654 (0.015%), neg=0, invalid=762 0352: dt=1.792000, rms=0.654 (0.014%), neg=0, invalid=762 0353: dt=7.168000, rms=0.654 (0.077%), neg=0, invalid=762 0354: dt=0.320000, rms=0.654 (-0.003%), neg=0, invalid=762 0355: dt=0.320000, rms=0.654 (0.000%), neg=0, invalid=762 0356: dt=0.320000, rms=0.654 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=762 0357: dt=0.000000, rms=0.654 (0.033%), neg=0, invalid=762 0358: dt=0.000000, rms=0.654 (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=0.624, neg=0, invalid=762 0359: dt=2.103152, rms=0.600 (3.861%), neg=0, invalid=762 0360: dt=0.256000, rms=0.598 (0.193%), neg=0, invalid=762 0361: dt=0.000000, rms=0.598 (-0.000%), neg=0, invalid=762 0362: dt=0.050000, rms=0.598 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.599, neg=0, invalid=762 0363: dt=0.028000, rms=0.598 (0.056%), neg=0, invalid=762 0364: dt=0.004000, rms=0.598 (0.000%), neg=0, invalid=762 0365: dt=0.004000, rms=0.598 (0.000%), neg=0, invalid=762 0366: dt=0.004000, rms=0.598 (-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=0.586, neg=0, invalid=762 0367: dt=295.936000, rms=0.583 (0.486%), neg=0, invalid=762 0368: dt=517.888000, rms=0.581 (0.383%), neg=0, invalid=762 0369: dt=129.472000, rms=0.580 (0.111%), neg=0, invalid=762 0370: dt=129.472000, rms=0.580 (0.029%), neg=0, invalid=762 0371: dt=129.472000, rms=0.580 (0.038%), neg=0, invalid=762 0372: dt=129.472000, rms=0.579 (0.079%), neg=0, invalid=762 0373: dt=129.472000, rms=0.579 (0.101%), neg=0, invalid=762 0374: dt=129.472000, rms=0.578 (0.099%), neg=0, invalid=762 0375: dt=129.472000, rms=0.578 (0.071%), neg=0, invalid=762 0376: dt=443.904000, rms=0.577 (0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=762 0377: dt=517.888000, rms=0.576 (0.289%), neg=0, invalid=762 0378: dt=129.472000, rms=0.576 (0.019%), neg=0, invalid=762 0379: dt=129.472000, rms=0.576 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0380: dt=145.152000, rms=0.573 (0.556%), neg=0, invalid=762 0381: dt=580.608000, rms=0.566 (1.317%), neg=0, invalid=762 0382: dt=82.944000, rms=0.565 (0.128%), neg=0, invalid=762 0383: dt=82.944000, rms=0.564 (0.121%), neg=0, invalid=762 0384: dt=82.944000, rms=0.563 (0.164%), neg=0, invalid=762 0385: dt=82.944000, rms=0.562 (0.236%), neg=0, invalid=762 0386: dt=82.944000, rms=0.561 (0.280%), neg=0, invalid=762 0387: dt=82.944000, rms=0.559 (0.272%), neg=0, invalid=762 0388: dt=82.944000, rms=0.558 (0.236%), neg=0, invalid=762 0389: dt=82.944000, rms=0.557 (0.174%), neg=0, invalid=762 0390: dt=82.944000, rms=0.556 (0.135%), neg=0, invalid=762 0391: dt=82.944000, rms=0.555 (0.128%), neg=0, invalid=762 0392: dt=82.944000, rms=0.554 (0.137%), neg=0, invalid=762 0393: dt=82.944000, rms=0.554 (0.148%), neg=0, invalid=762 0394: dt=82.944000, rms=0.553 (0.145%), neg=0, invalid=762 0395: dt=82.944000, rms=0.552 (0.139%), neg=0, invalid=762 0396: dt=82.944000, rms=0.551 (0.123%), neg=0, invalid=762 0397: dt=82.944000, rms=0.551 (0.111%), neg=0, invalid=762 0398: dt=145.152000, rms=0.551 (0.036%), neg=0, invalid=762 0399: dt=145.152000, rms=0.550 (0.036%), neg=0, invalid=762 0400: dt=145.152000, rms=0.550 (0.063%), neg=0, invalid=762 0401: dt=145.152000, rms=0.550 (0.087%), neg=0, invalid=762 0402: dt=145.152000, rms=0.549 (0.097%), neg=0, invalid=762 0403: dt=145.152000, rms=0.549 (0.097%), neg=0, invalid=762 0404: dt=145.152000, rms=0.548 (0.091%), neg=0, invalid=762 0405: dt=145.152000, rms=0.548 (0.090%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0406: dt=331.776000, rms=0.545 (0.442%), neg=0, invalid=762 0407: dt=62.208000, rms=0.545 (0.046%), neg=0, invalid=762 0408: dt=62.208000, rms=0.545 (0.039%), neg=0, invalid=762 0409: dt=62.208000, rms=0.545 (-0.030%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.554, neg=0, invalid=762 0410: dt=100.392157, rms=0.551 (0.492%), neg=0, invalid=762 0411: dt=126.838284, rms=0.543 (1.613%), neg=0, invalid=762 0412: dt=31.331010, rms=0.541 (0.297%), neg=0, invalid=762 0413: dt=32.000000, rms=0.540 (0.100%), neg=0, invalid=762 0414: dt=32.000000, rms=0.540 (0.119%), neg=0, invalid=762 0415: dt=32.000000, rms=0.539 (0.178%), neg=0, invalid=762 0416: dt=32.000000, rms=0.537 (0.274%), neg=0, invalid=762 0417: dt=32.000000, rms=0.535 (0.345%), neg=0, invalid=762 0418: dt=32.000000, rms=0.533 (0.390%), neg=0, invalid=762 0419: dt=32.000000, rms=0.531 (0.367%), neg=0, invalid=762 0420: dt=32.000000, rms=0.530 (0.283%), neg=0, invalid=762 0421: dt=32.000000, rms=0.529 (0.199%), neg=0, invalid=762 0422: dt=32.000000, rms=0.528 (0.170%), neg=0, invalid=762 0423: dt=32.000000, rms=0.527 (0.158%), neg=0, invalid=762 0424: dt=32.000000, rms=0.526 (0.154%), neg=0, invalid=762 0425: dt=32.000000, rms=0.526 (0.141%), neg=0, invalid=762 0426: dt=32.000000, rms=0.525 (0.124%), neg=0, invalid=762 0427: dt=32.000000, rms=0.524 (0.100%), neg=0, invalid=762 0428: dt=11.200000, rms=0.524 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0429: dt=44.800000, rms=0.523 (0.243%), neg=0, invalid=762 0430: dt=25.600000, rms=0.523 (0.012%), neg=0, invalid=762 0431: dt=25.600000, rms=0.523 (0.018%), neg=0, invalid=762 0432: dt=25.600000, rms=0.523 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.551, neg=0, invalid=762 0433: dt=8.505092, rms=0.549 (0.430%), neg=0, invalid=762 0434: dt=4.032000, rms=0.549 (0.032%), neg=0, invalid=762 0435: dt=4.032000, rms=0.549 (0.001%), neg=0, invalid=762 0436: dt=4.032000, rms=0.549 (-0.094%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.549, neg=0, invalid=762 0437: dt=2.304000, rms=0.549 (0.064%), neg=0, invalid=762 0438: dt=0.252000, rms=0.549 (-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=0.580, neg=0, invalid=762 0439: dt=1.876543, rms=0.577 (0.547%), neg=0, invalid=762 0440: dt=1.536000, rms=0.576 (0.104%), neg=0, invalid=762 0441: dt=1.536000, rms=0.576 (0.013%), neg=0, invalid=762 0442: dt=1.536000, rms=0.576 (-0.188%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0443: dt=1.024000, rms=0.576 (0.080%), neg=0, invalid=762 0444: dt=0.448000, rms=0.576 (0.002%), neg=0, invalid=762 0445: dt=0.448000, rms=0.576 (0.007%), neg=0, invalid=762 0446: dt=0.448000, rms=0.576 (-0.009%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0447: dt=1.892285, rms=0.534 (3.477%), neg=0, invalid=762 0448: dt=0.112000, rms=0.533 (0.090%), neg=0, invalid=762 0449: dt=0.112000, rms=0.533 (-0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0450: dt=0.080000, rms=0.533 (0.085%), neg=0, invalid=762 0451: dt=0.000000, rms=0.533 (0.003%), neg=0, invalid=762 0452: dt=0.050000, rms=0.533 (-0.008%), 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=0.522, neg=0, invalid=762 0453: dt=0.000000, rms=0.522 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0454: dt=369.920000, rms=0.521 (0.099%), neg=0, invalid=762 0455: dt=55.488000, rms=0.521 (0.003%), neg=0, invalid=762 0456: dt=55.488000, rms=0.521 (0.001%), neg=0, invalid=762 0457: dt=55.488000, rms=0.521 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.521, neg=0, invalid=762 0458: dt=82.944000, rms=0.521 (0.085%), neg=0, invalid=762 0459: dt=145.152000, rms=0.520 (0.119%), neg=0, invalid=762 0460: dt=497.664000, rms=0.519 (0.210%), neg=0, invalid=762 0461: dt=497.664000, rms=0.518 (0.280%), neg=0, invalid=762 0462: dt=62.208000, rms=0.517 (0.086%), neg=0, invalid=762 0463: dt=62.208000, rms=0.517 (0.015%), neg=0, invalid=762 0464: dt=62.208000, rms=0.517 (0.013%), neg=0, invalid=762 0465: dt=62.208000, rms=0.517 (0.023%), neg=0, invalid=762 0466: dt=62.208000, rms=0.517 (0.051%), neg=0, invalid=762 0467: dt=62.208000, rms=0.517 (0.065%), neg=0, invalid=762 0468: dt=62.208000, rms=0.516 (0.063%), neg=0, invalid=762 0469: dt=248.832000, rms=0.516 (0.039%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0470: dt=145.152000, rms=0.514 (0.379%), neg=0, invalid=762 0471: dt=145.152000, rms=0.514 (0.051%), neg=0, invalid=762 0472: dt=145.152000, rms=0.513 (0.101%), neg=0, invalid=762 0473: dt=145.152000, rms=0.513 (0.100%), neg=0, invalid=762 0474: dt=145.152000, rms=0.512 (0.079%), neg=0, invalid=762 0475: dt=580.608000, rms=0.512 (0.077%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0476: dt=44.800000, rms=0.512 (0.338%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0477: dt=179.200000, rms=0.506 (1.229%), neg=0, invalid=762 0478: dt=44.800000, rms=0.505 (0.214%), neg=0, invalid=762 0479: dt=44.800000, rms=0.504 (0.199%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0480: dt=44.800000, rms=0.502 (0.278%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0481: dt=44.800000, rms=0.501 (0.297%), neg=0, invalid=762 0482: dt=44.800000, rms=0.500 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0483: dt=44.800000, rms=0.498 (0.253%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0484: dt=44.800000, rms=0.497 (0.247%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0485: dt=44.800000, rms=0.496 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0486: dt=44.800000, rms=0.495 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0487: dt=44.800000, rms=0.494 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0488: dt=44.800000, rms=0.494 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0489: dt=44.800000, rms=0.493 (0.104%), neg=0, invalid=762 0490: dt=44.800000, rms=0.493 (0.005%), neg=0, invalid=762 0491: dt=44.800000, rms=0.493 (0.000%), neg=0, invalid=762 0492: dt=44.800000, rms=0.493 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0493: dt=95.262055, rms=0.491 (0.403%), neg=0, invalid=762 0494: dt=25.600000, rms=0.491 (0.024%), neg=0, invalid=762 0495: dt=25.600000, rms=0.491 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.508, neg=0, invalid=762 0496: dt=8.304348, rms=0.507 (0.297%), neg=0, invalid=762 0497: dt=4.032000, rms=0.506 (0.026%), neg=0, invalid=762 0498: dt=4.032000, rms=0.506 (0.001%), neg=0, invalid=762 0499: dt=4.032000, rms=0.506 (-0.060%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=762 0500: dt=4.032000, rms=0.506 (0.048%), neg=0, invalid=762 0501: dt=4.032000, rms=0.506 (0.017%), neg=0, invalid=762 0502: dt=4.032000, rms=0.506 (0.000%), neg=0, invalid=762 0503: dt=4.032000, rms=0.506 (-0.044%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.521, neg=0, invalid=762 0504: dt=0.112000, rms=0.521 (0.001%), neg=0, invalid=762 0505: dt=0.024000, rms=0.521 (0.000%), neg=0, invalid=762 0506: dt=0.024000, rms=0.521 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=762 0507: dt=0.448000, rms=0.521 (0.016%), neg=0, invalid=762 0508: dt=0.112000, rms=0.521 (0.001%), neg=0, invalid=762 0509: dt=0.112000, rms=0.521 (0.000%), neg=0, invalid=762 0510: dt=0.112000, rms=0.521 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.499, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0511: dt=1.733124, rms=0.484 (2.950%), neg=0, invalid=762 0512: dt=0.080000, rms=0.484 (0.028%), neg=0, invalid=762 0513: dt=0.080000, rms=0.484 (-0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0514: dt=0.028000, rms=0.484 (0.006%), neg=0, invalid=762 0515: dt=0.016000, rms=0.484 (0.001%), neg=0, invalid=762 0516: dt=0.016000, rms=0.484 (-0.001%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 20 minutes and 21 seconds. mri_ca_register utimesec 10979.764378 mri_ca_register stimesec 29.471728 mri_ca_register ru_maxrss 3564312 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 18494939 mri_ca_register ru_majflt 5 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 738 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 98861 mri_ca_register ru_nivcsw 362672 FSRUNTIME@ mri_ca_register 3.3391 hours 8 threads #-------------------------------------- #@# SubCort Seg Sat Jan 12 14:08:35 UTC 2019 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 n018 machine x86_64 setenv SUBJECTS_DIR /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer cd /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 77.94 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 = 0.10224 (33) Left_Lateral_Ventricle (4): linear fit = 1.74 x + 0.0 (26341 voxels, overlap=0.052) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (26341 voxels, peak = 35), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.10907 (33) Right_Lateral_Ventricle (43): linear fit = 2.38 x + 0.0 (19314 voxels, overlap=0.044) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (19314 voxels, peak = 31), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.13605 (102) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (14877 voxels, overlap=0.102) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (14877 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.11475 (105) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (14362 voxels, overlap=0.197) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (14362 voxels, peak = 104), gca=104.2 gca peak = 0.24553 (55) mri peak = 0.11349 (76) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (21787 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (21787 voxels, peak = 73), gca=73.4 gca peak = 0.30264 (59) mri peak = 0.11095 (77) Left_Hippocampus (17): linear fit = 1.32 x + 0.0 (21899 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.32 x + 0.0 (21899 voxels, peak = 78), gca=77.6 gca peak = 0.07580 (103) mri peak = 0.09387 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (1346804 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (1346804 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.09993 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (1373418 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (1373418 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.05623 (77) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (1631091 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (1631091 voxels, peak = 77), gca=76.9 gca peak = 0.11620 (58) mri peak = 0.05981 (77) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (1589662 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (1589662 voxels, peak = 77), gca=76.9 gca peak = 0.30970 (66) mri peak = 0.14635 (86) Right_Caudate (50): linear fit = 1.29 x + 0.0 (18512 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.29 x + 0.0 (18512 voxels, peak = 85), gca=85.5 gca peak = 0.15280 (69) mri peak = 0.14600 (86) Left_Caudate (11): linear fit = 1.13 x + 0.0 (19230 voxels, overlap=0.016) Left_Caudate (11): linear fit = 1.13 x + 0.0 (19230 voxels, peak = 78), gca=78.3 gca peak = 0.13902 (56) mri peak = 0.06050 (79) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (473356 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (473356 voxels, peak = 79), gca=78.7 gca peak = 0.14777 (55) mri peak = 0.07106 (75) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (490840 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (490840 voxels, peak = 74), gca=74.0 gca peak = 0.16765 (84) mri peak = 0.08377 (83) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (132173 voxels, overlap=0.937) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (132173 voxels, peak = 85), gca=85.3 gca peak = 0.18739 (84) mri peak = 0.08934 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (114625 voxels, overlap=0.968) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (114625 voxels, peak = 85), gca=85.3 gca peak = 0.29869 (57) mri peak = 0.12338 (78) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (9128 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (9128 voxels, peak = 77), gca=76.7 gca peak = 0.33601 (57) mri peak = 0.12078 (77) Right_Amygdala (54): linear fit = 1.35 x + 0.0 (10614 voxels, overlap=0.042) Right_Amygdala (54): linear fit = 1.35 x + 0.0 (10614 voxels, peak = 77), gca=76.7 gca peak = 0.11131 (90) mri peak = 0.07582 (95) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (70323 voxels, overlap=0.668) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (70323 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.07916 (95) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (65933 voxels, overlap=0.309) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (65933 voxels, peak = 95), gca=95.0 gca peak = 0.08324 (81) mri peak = 0.09461 (97) Left_Putamen (12): linear fit = 1.18 x + 0.0 (37186 voxels, overlap=0.010) Left_Putamen (12): linear fit = 1.18 x + 0.0 (37186 voxels, peak = 96), gca=96.0 gca peak = 0.10360 (77) mri peak = 0.08415 (93) Right_Putamen (51): linear fit = 1.17 x + 0.0 (39165 voxels, overlap=0.099) Right_Putamen (51): linear fit = 1.17 x + 0.0 (39165 voxels, peak = 90), gca=90.5 gca peak = 0.08424 (78) mri peak = 0.14083 (80) Brain_Stem (16): linear fit = 1.03 x + 0.0 (178823 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.03 x + 0.0 (178823 voxels, peak = 81), gca=80.7 gca peak = 0.12631 (89) mri peak = 0.07054 (90) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (27616 voxels, overlap=0.739) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (27616 voxels, peak = 94), gca=93.9 gca peak = 0.14500 (87) mri peak = 0.06933 (94) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (28212 voxels, overlap=0.843) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (28212 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.06148 (32) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (1584 voxels, overlap=0.546) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (1584 voxels, peak = 31), gca=30.6 gca peak = 0.19357 (14) mri peak = 0.06140 (28) Fourth_Ventricle (15): linear fit = 1.89 x + 0.0 (8462 voxels, overlap=0.179) Fourth_Ventricle (15): linear fit = 1.89 x + 0.0 (8462 voxels, peak = 27), gca=26.5 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 1.33 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.43 x + 0.0 Left_Putamen too bright - rescaling by 0.985 (from 1.185) to 94.5 (was 96.0) Left_Pallidum too bright - rescaling by 0.978 (from 1.085) to 101.9 (was 104.2) Right_Pallidum too bright - rescaling by 0.998 (from 1.075) to 101.9 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.10224 (33) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (26341 voxels, overlap=0.582) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (26341 voxels, peak = 35), gca=35.5 gca peak = 0.13981 (19) mri peak = 0.10907 (33) Right_Lateral_Ventricle (43): linear fit = 1.62 x + 0.0 (19314 voxels, overlap=0.278) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (19314 voxels, peak = 31), gca=28.5 gca peak = 0.21676 (102) mri peak = 0.13605 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (14877 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (14877 voxels, peak = 103), gca=102.5 gca peak = 0.14994 (100) mri peak = 0.11475 (105) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (14362 voxels, overlap=0.927) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (14362 voxels, peak = 102), gca=102.5 gca peak = 0.20773 (74) mri peak = 0.11349 (76) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (21787 voxels, overlap=0.976) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (21787 voxels, peak = 74), gca=74.0 gca peak = 0.28644 (74) mri peak = 0.11095 (77) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (21899 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (21899 voxels, peak = 74), gca=74.0 gca peak = 0.07781 (104) mri peak = 0.09387 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (1346804 voxels, overlap=0.711) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (1346804 voxels, peak = 105), gca=104.5 gca peak = 0.07820 (106) mri peak = 0.09993 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (1373418 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (1373418 voxels, peak = 106), gca=106.0 gca peak = 0.07413 (77) mri peak = 0.05623 (77) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (1631091 voxels, overlap=0.862) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (1631091 voxels, peak = 76), gca=75.8 gca peak = 0.09055 (77) mri peak = 0.05981 (77) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (1589662 voxels, overlap=0.886) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (1589662 voxels, peak = 76), gca=75.8 gca peak = 0.21576 (85) mri peak = 0.14635 (86) Right_Caudate (50): linear fit = 0.99 x + 0.0 (18512 voxels, overlap=0.999) Right_Caudate (50): linear fit = 0.99 x + 0.0 (18512 voxels, peak = 84), gca=83.7 gca peak = 0.14928 (88) mri peak = 0.14600 (86) Left_Caudate (11): linear fit = 1.00 x + 0.0 (19230 voxels, overlap=0.712) Left_Caudate (11): linear fit = 1.00 x + 0.0 (19230 voxels, peak = 88), gca=88.0 gca peak = 0.10495 (79) mri peak = 0.06050 (79) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (473356 voxels, overlap=0.930) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (473356 voxels, peak = 79), gca=78.6 gca peak = 0.11243 (74) mri peak = 0.07106 (75) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (490840 voxels, overlap=0.946) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (490840 voxels, peak = 74), gca=74.0 gca peak = 0.17351 (86) mri peak = 0.08377 (83) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (132173 voxels, overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (132173 voxels, peak = 86), gca=85.6 gca peak = 0.15537 (85) mri peak = 0.08934 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (114625 voxels, overlap=0.986) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (114625 voxels, peak = 85), gca=85.0 gca peak = 0.29164 (78) mri peak = 0.12338 (78) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (9128 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (9128 voxels, peak = 77), gca=76.8 gca peak = 0.26214 (76) mri peak = 0.12078 (77) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (10614 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (10614 voxels, peak = 76), gca=76.0 gca peak = 0.09966 (96) mri peak = 0.07582 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (70323 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (70323 voxels, peak = 96), gca=96.5 gca peak = 0.09821 (95) mri peak = 0.07916 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (65933 voxels, overlap=0.919) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (65933 voxels, peak = 95), gca=95.0 gca peak = 0.07569 (88) mri peak = 0.09461 (97) Left_Putamen (12): linear fit = 1.02 x + 0.0 (37186 voxels, overlap=0.745) Left_Putamen (12): linear fit = 1.02 x + 0.0 (37186 voxels, peak = 90), gca=90.2 gca peak = 0.08774 (92) mri peak = 0.08415 (93) Right_Putamen (51): linear fit = 1.00 x + 0.0 (39165 voxels, overlap=0.883) Right_Putamen (51): linear fit = 1.00 x + 0.0 (39165 voxels, peak = 92), gca=91.5 gca peak = 0.08646 (81) mri peak = 0.14083 (80) Brain_Stem (16): linear fit = 1.01 x + 0.0 (178823 voxels, overlap=0.625) Brain_Stem (16): linear fit = 1.01 x + 0.0 (178823 voxels, peak = 82), gca=82.2 gca peak = 0.12863 (94) mri peak = 0.07054 (90) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (27616 voxels, overlap=0.825) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (27616 voxels, peak = 94), gca=93.5 gca peak = 0.13948 (91) mri peak = 0.06933 (94) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (28212 voxels, overlap=0.932) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (28212 voxels, peak = 91), gca=90.5 gca peak = 0.16815 (33) mri peak = 0.06148 (32) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (1584 voxels, overlap=0.941) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (1584 voxels, peak = 33), gca=33.5 gca peak = 0.17373 (21) mri peak = 0.06140 (28) Fourth_Ventricle (15): linear fit = 1.33 x + 0.0 (8462 voxels, overlap=0.472) Fourth_Ventricle (15): linear fit = 1.33 x + 0.0 (8462 voxels, peak = 28), gca=27.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.12777 (42) gca peak Left_Thalamus = 0.36646 (104) gca peak CSF = 0.18992 (52) gca peak Left_Accumbens_area = 0.59345 (71) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.24572 (31) gca peak Right_Accumbens_area = 0.29821 (84) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (44) gca peak WM_hypointensities = 0.08024 (78) gca peak non_WM_hypointensities = 0.09187 (44) gca peak Optic_Chiasm = 0.68992 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.25 x + 0.0 Left_Pallidum too bright - rescaling by 0.996 (from 1.025) to 102.1 (was 102.5) Right_Pallidum too bright - rescaling by 0.996 (from 1.005) to 102.1 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 554763 voxels changed in iteration 0 of unlikely voxel relabeling 3739 voxels changed in iteration 1 of unlikely voxel relabeling 425 voxels changed in iteration 2 of unlikely voxel relabeling 238 voxels changed in iteration 3 of unlikely voxel relabeling 28 voxels changed in iteration 4 of unlikely voxel relabeling 741709 gm and wm labels changed (%42 to gray, %58 to white out of all changed labels) 3006 hippocampal voxels changed. 18 amygdala voxels changed. pass 1: 80999 changed. image ll: -2.136, PF=0.500 pass 2: 322878 changed. image ll: -2.131, PF=0.500 pass 3: 123716 changed. pass 4: 64338 changed. pass 5: 39230 changed. pass 6: 25601 changed. pass 7: 17310 changed. pass 8: 12123 changed. pass 9: 8755 changed. pass 10: 6285 changed. pass 11: 4588 changed. 843105 voxels changed in iteration 0 of unlikely voxel relabeling 5260 voxels changed in iteration 1 of unlikely voxel relabeling 528 voxels changed in iteration 2 of unlikely voxel relabeling 144 voxels changed in iteration 3 of unlikely voxel relabeling 42 voxels changed in iteration 4 of unlikely voxel relabeling 77906 voxels changed in iteration 0 of unlikely voxel relabeling 1114 voxels changed in iteration 1 of unlikely voxel relabeling 139 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 70876 voxels changed in iteration 0 of unlikely voxel relabeling 623 voxels changed in iteration 1 of unlikely voxel relabeling 85 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 1 voxels changed in iteration 4 of unlikely voxel relabeling 55633 voxels changed in iteration 0 of unlikely voxel relabeling 292 voxels changed in iteration 1 of unlikely voxel relabeling 33 voxels changed in iteration 2 of unlikely voxel relabeling 4 voxels changed in iteration 3 of unlikely voxel relabeling 3 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 30037.270593 mri_ca_label stimesec 35.015166 mri_ca_label ru_maxrss 9962244 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 32631867 mri_ca_label ru_majflt 5 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 850 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 3852 mri_ca_label ru_nivcsw 553585 auto-labeling took 559 minutes and 52 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/transforms/cc_up.lta sub-ADS5115 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/transforms/cc_up.lta reading aseg from /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/aseg.auto_noCCseg.mgz reading norm from /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/norm.mgz 329278 voxels in left wm, 331585 in right wm, xrange [255, 269] searching rotation angles z=[-8 6], y=[-6 8] searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 global minimum found at slice 262.0, rotations (1.46, -0.80) final transformation (x=262.0, yr=1.458, zr=-0.801): 0.99958 0.01398 0.02545 -142.17976; -0.01397 0.99990 -0.00036 -26.23896; -0.02545 0.00000 0.99968 -104.25470; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 134] in xformed coordinates best xformed slice 128 cc center is found at 128 158 239 eigenvectors: 0.00003 -0.00126 1.00000; 0.05064 -0.99872 -0.00126; 0.99872 0.05064 0.00004; writing aseg with callosum to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/aseg.auto.mgz... corpus callosum segmentation took 7.8 minutes #-------------------------------------- #@# Merge ASeg Sat Jan 12 23:36:17 UTC 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Jan 12 23:36:17 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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... 2343 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 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 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 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 59 minutes and 58 seconds. #-------------------------------------------- #@# Mask BFS Sun Jan 13 00:37:31 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 15313153 voxels in mask (pct= 11.41) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Jan 13 00:38:46 UTC 2019 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 (99.0): 99.0 +- 5.1 [79.0 --> 125.0] GM (86.0) : 85.0 +- 6.1 [30.0 --> 95.0] setting bottom of white matter range to 91.1 setting top of gray matter range to 97.3 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... thickening thin strands.... 20 segments, 2244 filled 45 bright non-wm voxels segmented. 10601 diagonally connected voxels added... white matter segmentation took 13.2 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 5.94 minutes reading wm segmentation from wm.seg.mgz... 754 voxels added to wm to prevent paths from MTL structures to cortex 37610 additional wm voxels added 0 additional wm voxels added SEG EDIT: 304759 voxels turned on, 708191 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 221 found - 221 modified | TOTAL: 221 pass 2 (xy+): 0 found - 221 modified | TOTAL: 221 pass 1 (xy-): 135 found - 135 modified | TOTAL: 356 pass 2 (xy-): 0 found - 135 modified | TOTAL: 356 pass 1 (yz+): 186 found - 186 modified | TOTAL: 542 pass 2 (yz+): 0 found - 186 modified | TOTAL: 542 pass 1 (yz-): 182 found - 182 modified | TOTAL: 724 pass 2 (yz-): 0 found - 182 modified | TOTAL: 724 pass 1 (xz+): 154 found - 154 modified | TOTAL: 878 pass 2 (xz+): 0 found - 154 modified | TOTAL: 878 pass 1 (xz-): 125 found - 125 modified | TOTAL: 1003 pass 2 (xz-): 0 found - 125 modified | TOTAL: 1003 Iteration Number : 1 pass 1 (+++): 40 found - 40 modified | TOTAL: 40 pass 2 (+++): 0 found - 40 modified | TOTAL: 40 pass 1 (+++): 63 found - 63 modified | TOTAL: 103 pass 2 (+++): 0 found - 63 modified | TOTAL: 103 pass 1 (+++): 44 found - 44 modified | TOTAL: 147 pass 2 (+++): 0 found - 44 modified | TOTAL: 147 pass 1 (+++): 77 found - 77 modified | TOTAL: 224 pass 2 (+++): 0 found - 77 modified | TOTAL: 224 Iteration Number : 1 pass 1 (++): 134 found - 134 modified | TOTAL: 134 pass 2 (++): 0 found - 134 modified | TOTAL: 134 pass 1 (+-): 164 found - 164 modified | TOTAL: 298 pass 2 (+-): 0 found - 164 modified | TOTAL: 298 pass 1 (--): 143 found - 143 modified | TOTAL: 441 pass 2 (--): 2 found - 145 modified | TOTAL: 443 pass 3 (--): 0 found - 145 modified | TOTAL: 443 pass 1 (-+): 137 found - 137 modified | TOTAL: 580 pass 2 (-+): 0 found - 137 modified | TOTAL: 580 Iteration Number : 2 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 10 found - 10 modified | TOTAL: 25 pass 2 (xy-): 0 found - 10 modified | TOTAL: 25 pass 1 (yz+): 15 found - 15 modified | TOTAL: 40 pass 2 (yz+): 0 found - 15 modified | TOTAL: 40 pass 1 (yz-): 9 found - 9 modified | TOTAL: 49 pass 2 (yz-): 0 found - 9 modified | TOTAL: 49 pass 1 (xz+): 12 found - 12 modified | TOTAL: 61 pass 2 (xz+): 0 found - 12 modified | TOTAL: 61 pass 1 (xz-): 10 found - 10 modified | TOTAL: 71 pass 2 (xz-): 0 found - 10 modified | TOTAL: 71 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 1 found - 1 modified | TOTAL: 9 pass 2 (+++): 0 found - 1 modified | TOTAL: 9 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 8 found - 8 modified | TOTAL: 13 pass 2 (+-): 0 found - 8 modified | TOTAL: 13 pass 1 (--): 7 found - 7 modified | TOTAL: 20 pass 2 (--): 0 found - 7 modified | TOTAL: 20 pass 1 (-+): 7 found - 7 modified | TOTAL: 27 pass 2 (-+): 0 found - 7 modified | TOTAL: 27 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1919 (out of 5886732: 0.032599) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Jan 13 00:58:41 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 1.03302 0.01288 0.01063 -21.79037; -0.02026 1.04065 0.16891 -5.08670; -0.00708 -0.15857 1.02725 -6.72406; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03302 0.01288 0.01063 -21.79037; -0.02026 1.04065 0.16891 -5.08670; -0.00708 -0.15857 1.02725 -6.72406; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (1734, 6938) area[0] = 12255 (min = 1734, max = 6938), aspect = 1.16 (min = 0.10, max = 0.75) need search nearby using seed (251, 237, 310), TAL = (2.2, 24.3, 8.5) talairach voxel to voxel transform 0.96772 -0.01317 -0.00785 20.96736; 0.01733 0.93721 -0.15429 4.10741; 0.00935 0.14458 0.94960 7.32437; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (251, 237, 310) --> (2.2, 24.3, 8.5) done. writing output to filled.mgz... filling took 9.3 minutes badRH = 18158/2832280, badLH=0/2846449 Please check filled volume. Cerebellum may be included. talairach cc position changed to (2.25, 24.26, 8.54) Erasing brainstem...done. seed_search_size = 21, min_neighbors = 5 search rh wm seed point around talairach space:(20.25, 24.26, 8.54) SRC: (219.53, 182.05, 337.94) search lh wm seed point around talairach space (-15.75, 24.26, 8.54), SRC: (297.09, 183.44, 338.69) 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 Sat Jan 12 09:34:35 UTC 2019 Ended at Sun Jan 13 01:08:07 UTC 2019 #@#%# recon-all-run-time-hours 15.559 recon-all -s sub-ADS5115 finished without error at Sun Jan 13 01:08:07 UTC 2019