Sun Jun 16 14:59:32 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline /usr/local/freesurfer/bin/recon-all -all -s sub-3811ses-Session_baseline -i /scratch/vferrer/PD_ANALYSIS/BIDS_PPMI/sub-3811/ses-Session_baseline/anat/sub-3811_ses-Session_baseline_T1w.nii.gz -sd /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI -hippocampal-subfields-T1 -brainstem-structures -3T -openmp 1 subjid sub-3811ses-Session_baseline setenv SUBJECTS_DIR /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux atlas-210 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize 4194304 kbytes stacksize unlimited coredumpsize 0 kbytes memoryuse 4194304 kbytes vmemoryuse unlimited descriptors 32768 memorylocked unlimited maxproc 514525 maxlocks unlimited maxsignal 514525 maxmessage unlimited maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131743240 8512884 103912356 141008 19318000 122450868 Swap: 8388604 203476 8185128 ######################################## 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: 2019/06/16-12:59:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.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: 2019/06/16-12:59:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.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: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.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: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.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: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/06/16-12:59:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: vferrer Machine: atlas-210 Platform: Linux PlatformVersion: 3.10.0-514.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/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 /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline mri_convert /scratch/vferrer/PD_ANALYSIS/BIDS_PPMI/sub-3811/ses-Session_baseline/anat/sub-3811_ses-Session_baseline_T1w.nii.gz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig/001.mgz mri_convert.bin /scratch/vferrer/PD_ANALYSIS/BIDS_PPMI/sub-3811/ses-Session_baseline/anat/sub-3811_ses-Session_baseline_T1w.nii.gz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /scratch/vferrer/PD_ANALYSIS/BIDS_PPMI/sub-3811/ses-Session_baseline/anat/sub-3811_ses-Session_baseline_T1w.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.9986, 0.0453484, 0.0272351) j_ras = (-0.0507324, 0.966842, 0.250287) k_ras = (-0.0149819, -0.251318, 0.967789) writing to /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Jun 16 14:59:50 CEST 2019 Found 1 runs /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/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 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig/001.mgz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/rawavg.mgz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline mri_convert /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/rawavg.mgz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig.mgz --conform mri_convert.bin /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/rawavg.mgz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/rawavg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.9986, 0.0453484, 0.0272351) j_ras = (-0.0507324, 0.966842, 0.250287) k_ras = (-0.0149819, -0.251318, 0.967789) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig.mgz... mri_add_xform_to_header -c /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/transforms/talairach.xfm /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig.mgz /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Jun 16 15:00:25 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri /usr/local/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 atlas-210 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Sun Jun 16 15:00:25 CEST 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.94614 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.94614/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.94614/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-9.31323e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.94614/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jun 16 15:00:36 CEST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.94614/nu0.mnc ./tmp.mri_nu_correct.mni.94614/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.94614/0/ -iterations 1000 -distance 50 [vferrer@atlas-210:/scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/] [2019-06-16 15:00:36] running: /usr/local/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.94614/0/ ./tmp.mri_nu_correct.mni.94614/nu0.mnc ./tmp.mri_nu_correct.mni.94614/nu1.imp 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Reading Volume: ............................................................... mri_convert ./tmp.mri_nu_correct.mni.94614/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.94614/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.94614/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-9.31323e-10, 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... Sun Jun 16 15:02:51 CEST 2019 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Sun Jun 16 15:02:51 CEST 2019 Ended at Sun Jun 16 15:04:25 CEST 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Jun 16 15:04:27 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4680, pval=0.1049 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/transforms/talairach_avi.log tal_QC_AZS /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/transforms/talairach_avi.log TalAviQA: 0.94156 z-score: -8 #-------------------------------------------- #@# Nu Intensity Correction Sun Jun 16 15:04:27 CEST 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux atlas-210 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Sun Jun 16 15:04:27 CEST 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.95463 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.95463/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.95463/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-9.31323e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.95463/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jun 16 15:04:39 CEST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.95463/nu0.mnc ./tmp.mri_nu_correct.mni.95463/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.95463/0/ -iterations 1000 -distance 50 [vferrer@atlas-210:/scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/] [2019-06-16 15:04:39] running: /usr/local/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.95463/0/ ./tmp.mri_nu_correct.mni.95463/nu0.mnc ./tmp.mri_nu_correct.mni.95463/nu1.imp 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Reading Volume: ............................................................... mri_binarize --i ./tmp.mri_nu_correct.mni.95463/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.95463/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.95463/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.95463/ones.mgz sysname Linux hostname atlas-210 machine x86_64 user vferrer input ./tmp.mri_nu_correct.mni.95463/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.95463/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.95463/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.95463/sum.junk --avgwf ./tmp.mri_nu_correct.mni.95463/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.95463/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.95463/sum.junk --avgwf ./tmp.mri_nu_correct.mni.95463/input.mean.dat sysname Linux hostname atlas-210 machine x86_64 user vferrer UseRobust 0 Loading ./tmp.mri_nu_correct.mni.95463/ones.mgz Loading orig.mgz Voxel Volume is 1 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.95463/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.95463/ones.mgz --i ./tmp.mri_nu_correct.mni.95463/nu1.mnc --sum ./tmp.mri_nu_correct.mni.95463/sum.junk --avgwf ./tmp.mri_nu_correct.mni.95463/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.95463/ones.mgz --i ./tmp.mri_nu_correct.mni.95463/nu1.mnc --sum ./tmp.mri_nu_correct.mni.95463/sum.junk --avgwf ./tmp.mri_nu_correct.mni.95463/output.mean.dat sysname Linux hostname atlas-210 machine x86_64 user vferrer UseRobust 0 Loading ./tmp.mri_nu_correct.mni.95463/ones.mgz Loading ./tmp.mri_nu_correct.mni.95463/nu1.mnc Voxel Volume is 1 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.95463/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.95463/nu1.mnc ./tmp.mri_nu_correct.mni.95463/nu1.mnc mul 1.02231487828961801646 Saving result to './tmp.mri_nu_correct.mni.95463/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.95463/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.95463/nu1.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.95463/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-9.31323e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 18 seconds. mapping (10, 104) to ( 3, 110) Sun Jun 16 15:08:56 CEST 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sun Jun 16 15:09:00 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.05151 0.06807 0.02696 3.51155; -0.03121 0.94622 0.44405 -33.06954; -0.02381 -0.45838 0.96557 -15.67186; 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 = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 67 (67), valley at 24 (24) csf peak at 10, setting threshold to 48 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 65 (65), valley at 24 (24) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 24 seconds. #-------------------------------------------- #@# Skull Stripping Sun Jun 16 15:12:28 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_em_register -rusage /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (50, 10, 12) --> (206, 255, 230) using (102, 92, 121) as brain centroid... mean wm in atlas = 108, using box (83,62,94) --> (121, 122,147) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 10.3 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.660 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.498743 @ (-9.091, 27.273, -9.091) max log p = -4.410786 @ (4.545, 4.545, 13.636) max log p = -4.409192 @ (2.273, -2.273, -6.818) max log p = -4.377048 @ (1.136, -7.955, 1.136) max log p = -4.377048 @ (0.000, 0.000, 0.000) max log p = -4.377048 @ (0.000, 0.000, 0.000) Found translation: (-1.1, 21.6, -1.1): log p = -4.377 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.195, old_max_log_p =-4.377 (thresh=-4.4) 0.99144 0.13934 0.05497 -21.07970; -0.13053 1.05840 0.41757 -1.05123; 0.00000 -0.40160 0.91881 54.42929; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.194, old_max_log_p =-4.195 (thresh=-4.2) 1.06596 0.05460 -0.12832 -1.39726; -0.00119 1.15478 0.43587 -29.74582; 0.12941 -0.37997 0.91813 35.86165; 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=-4.098, old_max_log_p =-4.194 (thresh=-4.2) 1.02879 0.00387 -0.11075 3.35332; 0.03015 1.10230 0.38043 -19.96547; 0.09343 -0.34092 0.91657 34.54763; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.082, old_max_log_p =-4.098 (thresh=-4.1) 1.02923 0.03993 -0.09824 -0.01167; -0.00346 1.08093 0.37666 -12.93862; 0.09343 -0.34092 0.91657 34.54763; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.076, old_max_log_p =-4.082 (thresh=-4.1) 1.00930 0.00525 -0.11034 5.65029; 0.03565 1.03724 0.42424 -20.40653; 0.09346 -0.41089 0.88997 44.85602; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.076, old_max_log_p =-4.076 (thresh=-4.1) 1.00930 0.00525 -0.11034 5.65029; 0.03565 1.03724 0.42424 -20.40653; 0.09346 -0.41089 0.88997 44.85602; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.069, old_max_log_p =-4.076 (thresh=-4.1) 1.00851 -0.00659 -0.10657 6.60818; 0.04450 1.03026 0.42899 -21.32832; 0.08538 -0.42077 0.89049 46.43674; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.066, old_max_log_p =-4.069 (thresh=-4.1) 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.066 (old=-4.660) transform before final EM align: 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 1.00856 -0.01157 -0.11749 8.34207; 0.05270 1.02900 0.42754 -22.56433; 0.09385 -0.42179 0.89167 45.78668; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 3253.012744 mri_em_register stimesec 13.624007 mri_em_register ru_maxrss 610616 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1323141 mri_em_register ru_majflt 4 mri_em_register ru_nswap 0 mri_em_register ru_inblock 43391 mri_em_register ru_oublock 3 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 502 mri_em_register ru_nivcsw 2224 registration took 54 minutes and 27 seconds. mri_watershed -rusage /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=130 y=91 z=102 r=100 first estimation of the main basin volume: 4203118 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=106, y=79, z=59, Imax=255 CSF=17, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=2288907813 voxels, voxel volume =1.000 = 2288907813 mmm3 = 2288907.776 cm3 done. PostAnalyze...Basin Prior 91 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=95, z=98, r=9756 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = 40998 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=35 , nb = -1032510563 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=30 , nb = 1075015046 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=46 , nb = -1064718247 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = 1066425272 OTHER CSF_MIN=0, CSF_intensity=15, CSF_MAX=41 , nb = 1083503578 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 34, 34, 35, 65 after analyzing : 23, 34, 35, 41 RIGHT_CER before analyzing : 35, 31, 26, 81 after analyzing : 23, 31, 31, 43 LEFT_CER before analyzing : 30, 34, 39, 66 after analyzing : 30, 37, 39, 44 RIGHT_BRAIN before analyzing : 46, 39, 35, 65 after analyzing : 27, 39, 39, 45 LEFT_BRAIN before analyzing : 29, 31, 35, 65 after analyzing : 29, 33, 35, 41 OTHER before analyzing : 41, 48, 59, 93 after analyzing : 41, 55, 59, 64 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...73 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 71.755, std = 7.523 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 6.19, sigma = 14.22 after rotation: sse = 6.19, sigma = 14.22 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.56, its var is 19.08 before Erosion-Dilatation 9.31% of inacurate vertices after Erosion-Dilatation 15.32% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...48 iterations mri_strip_skull: done peeling brain Brain Size = 1815601 voxels, voxel volume = 1.000 mm3 = 1815601 mmm3 = 1815.601 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 63.909761 mri_watershed stimesec 1.724966 mri_watershed ru_maxrss 843460 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 472423 mri_watershed ru_majflt 4 mri_watershed ru_nswap 0 mri_watershed ru_inblock 24536 mri_watershed ru_oublock 2970 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 144 mri_watershed ru_nivcsw 157 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Jun 16 16:08:03 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_em_register -rusage /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/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 = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/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'... 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=10.0 skull bounding box = (59, 23, 25) --> (198, 174, 185) using (105, 73, 105) as brain centroid... mean wm in atlas = 107, using box (88,54,85) --> (122, 91,124) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 6.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.685 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.159966 @ (-9.091, 27.273, 9.091) max log p = -4.008220 @ (4.545, 4.545, -4.545) max log p = -4.006704 @ (2.273, -2.273, -2.273) max log p = -3.956043 @ (-1.136, 1.136, 1.136) max log p = -3.946769 @ (0.568, -0.568, -0.568) max log p = -3.946769 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 30.1, 2.8): log p = -3.947 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.747, old_max_log_p =-3.947 (thresh=-3.9) 0.99144 0.04995 -0.12059 6.18626; 0.00000 0.92388 0.38268 -2.36286; 0.13053 -0.37941 0.91598 35.88314; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.747, old_max_log_p =-3.747 (thresh=-3.7) 0.99144 0.04995 -0.12059 6.18626; 0.00000 0.92388 0.38268 -2.36286; 0.13053 -0.37941 0.91598 35.88314; 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=-3.629, old_max_log_p =-3.747 (thresh=-3.7) 0.98020 0.04305 -0.01690 -3.53475; -0.03270 0.95760 0.39781 -2.70886; 0.03333 -0.38965 0.94070 46.95770; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.622, old_max_log_p =-3.629 (thresh=-3.6) 0.99749 0.02488 -0.06180 0.17975; -0.00067 0.95891 0.39604 -6.84102; 0.06416 -0.38076 0.92202 43.90260; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.622, old_max_log_p =-3.622 (thresh=-3.6) 0.99749 0.02488 -0.06180 0.17975; -0.00067 0.95891 0.39604 -6.84102; 0.06416 -0.38076 0.92202 43.90260; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.583, old_max_log_p =-3.622 (thresh=-3.6) 0.99719 0.02659 -0.04338 -1.71716; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.574, old_max_log_p =-3.583 (thresh=-3.6) 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.574, old_max_log_p =-3.574 (thresh=-3.6) 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 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 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.574 (old=-4.685) transform before final EM align: 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 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 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.0 tol 0.000000 final transform: 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 2652.205980 mri_em_register stimesec 9.418014 mri_em_register ru_maxrss 599924 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 949054 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 39448 mri_em_register ru_oublock 3 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 508 mri_em_register ru_nivcsw 1911 registration took 44 minutes and 22 seconds. #-------------------------------------- #@# CA Normalize Sun Jun 16 16:52:25 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/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 '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (59, 23, 25) --> (198, 174, 185) using (105, 73, 105) as brain centroid... mean wm in atlas = 107, using box (88,54,85) --> (122, 91,124) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 6.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 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 (126, 27, 23) --> (196, 149, 185) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 68 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 26, 24) --> (134, 139, 185) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 102 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 120, 57) --> (178, 163, 111) Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 0 of 24 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 120, 55) --> (128, 160, 112) Right_Cerebellum_White_Matter: limiting intensities to 107.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 102, 89) --> (148, 170, 121) Brain_Stem: limiting intensities to 111.0 --> 132.0 4 of 9 (44.4%) samples deleted using 215 total control points for intensity normalization... bias field = 0.896 +- 0.093 0 of 211 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 27, 23) --> (196, 149, 185) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 189 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 26, 24) --> (134, 139, 185) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 280 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 120, 57) --> (178, 163, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 86 (15.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 120, 55) --> (128, 160, 112) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 70 (4.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 102, 89) --> (148, 170, 121) Brain_Stem: limiting intensities to 88.0 --> 132.0 51 of 103 (49.5%) samples deleted using 728 total control points for intensity normalization... bias field = 0.992 +- 0.071 0 of 656 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 27, 23) --> (196, 149, 185) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 324 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 26, 24) --> (134, 139, 185) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 297 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 120, 57) --> (178, 163, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 61 of 92 (66.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 120, 55) --> (128, 160, 112) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 86 (54.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 102, 89) --> (148, 170, 121) Brain_Stem: limiting intensities to 88.0 --> 132.0 122 of 170 (71.8%) samples deleted using 969 total control points for intensity normalization... bias field = 1.005 +- 0.051 0 of 728 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 8 seconds. #-------------------------------------- #@# CA Reg Sun Jun 16 16:54:33 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_ca_register -rusage /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/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 = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.04 (predicted orig area = 7.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.955, neg=0, invalid=762 0001: dt=246.139535, rms=0.883 (7.558%), neg=0, invalid=762 0002: dt=271.752198, rms=0.857 (2.910%), neg=0, invalid=762 0003: dt=221.952000, rms=0.846 (1.328%), neg=0, invalid=762 0004: dt=295.936000, rms=0.837 (1.113%), neg=0, invalid=762 0005: dt=172.246914, rms=0.831 (0.637%), neg=0, invalid=762 0006: dt=887.808000, rms=0.820 (1.293%), neg=0, invalid=762 0007: dt=133.549133, rms=0.814 (0.757%), neg=0, invalid=762 0008: dt=4734.976000, rms=0.796 (2.232%), neg=0, invalid=762 0009: dt=135.337580, rms=0.790 (0.753%), neg=0, invalid=762 0010: dt=443.904000, rms=0.787 (0.416%), neg=0, invalid=762 0011: dt=129.472000, rms=0.786 (0.159%), neg=0, invalid=762 0012: dt=129.472000, rms=0.785 (0.068%), neg=0, invalid=762 0013: dt=129.472000, rms=0.784 (0.099%), neg=0, invalid=762 0014: dt=129.472000, rms=0.783 (0.109%), neg=0, invalid=762 0015: dt=129.472000, rms=0.782 (0.123%), neg=0, invalid=762 0016: dt=129.472000, rms=0.781 (0.144%), neg=0, invalid=762 0017: dt=129.472000, rms=0.780 (0.153%), neg=0, invalid=762 0018: dt=129.472000, rms=0.779 (0.156%), neg=0, invalid=762 0019: dt=129.472000, rms=0.778 (0.147%), neg=0, invalid=762 0020: dt=129.472000, rms=0.777 (0.152%), neg=0, invalid=762 0021: dt=129.472000, rms=0.775 (0.163%), neg=0, invalid=762 0022: dt=129.472000, rms=0.774 (0.185%), neg=0, invalid=762 0023: dt=129.472000, rms=0.772 (0.220%), neg=0, invalid=762 0024: dt=129.472000, rms=0.770 (0.239%), neg=0, invalid=762 0025: dt=129.472000, rms=0.768 (0.247%), neg=0, invalid=762 0026: dt=129.472000, rms=0.767 (0.239%), neg=0, invalid=762 0027: dt=129.472000, rms=0.765 (0.236%), neg=0, invalid=762 0028: dt=129.472000, rms=0.763 (0.231%), neg=0, invalid=762 0029: dt=129.472000, rms=0.761 (0.232%), neg=0, invalid=762 0030: dt=129.472000, rms=0.760 (0.222%), neg=0, invalid=762 0031: dt=129.472000, rms=0.758 (0.207%), neg=0, invalid=762 0032: dt=129.472000, rms=0.757 (0.192%), neg=0, invalid=762 0033: dt=129.472000, rms=0.755 (0.176%), neg=0, invalid=762 0034: dt=129.472000, rms=0.754 (0.173%), neg=0, invalid=762 0035: dt=129.472000, rms=0.753 (0.170%), neg=0, invalid=762 0036: dt=129.472000, rms=0.751 (0.160%), neg=0, invalid=762 0037: dt=129.472000, rms=0.750 (0.142%), neg=0, invalid=762 0038: dt=129.472000, rms=0.749 (0.134%), neg=0, invalid=762 0039: dt=129.472000, rms=0.748 (0.128%), neg=0, invalid=762 0040: dt=129.472000, rms=0.747 (0.117%), neg=0, invalid=762 0041: dt=129.472000, rms=0.747 (0.116%), neg=0, invalid=762 0042: dt=2071.552000, rms=0.746 (0.105%), neg=0, invalid=762 0043: dt=2071.552000, rms=0.746 (-4.372%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.746, neg=0, invalid=762 0044: dt=8.092000, rms=0.746 (0.060%), neg=0, invalid=762 0045: dt=5.780000, rms=0.746 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.753, neg=0, invalid=762 0046: dt=414.720000, rms=0.734 (2.539%), neg=0, invalid=762 0047: dt=100.655308, rms=0.720 (1.943%), neg=0, invalid=762 0048: dt=102.895028, rms=0.715 (0.572%), neg=0, invalid=762 0049: dt=172.281081, rms=0.710 (0.728%), neg=0, invalid=762 0050: dt=70.826667, rms=0.707 (0.448%), neg=0, invalid=762 0051: dt=580.608000, rms=0.697 (1.456%), neg=0, invalid=762 0052: dt=66.222222, rms=0.693 (0.589%), neg=0, invalid=762 0053: dt=414.720000, rms=0.689 (0.496%), neg=0, invalid=762 0054: dt=36.288000, rms=0.688 (0.243%), neg=0, invalid=762 0055: dt=36.288000, rms=0.687 (0.081%), neg=0, invalid=762 0056: dt=36.288000, rms=0.687 (0.068%), neg=0, invalid=762 0057: dt=36.288000, rms=0.686 (0.098%), neg=0, invalid=762 0058: dt=36.288000, rms=0.685 (0.175%), neg=0, invalid=762 0059: dt=36.288000, rms=0.683 (0.228%), neg=0, invalid=762 0060: dt=36.288000, rms=0.682 (0.225%), neg=0, invalid=762 0061: dt=36.288000, rms=0.680 (0.225%), neg=0, invalid=762 0062: dt=36.288000, rms=0.679 (0.222%), neg=0, invalid=762 0063: dt=36.288000, rms=0.677 (0.214%), neg=0, invalid=762 0064: dt=36.288000, rms=0.676 (0.225%), neg=0, invalid=762 0065: dt=36.288000, rms=0.674 (0.237%), neg=0, invalid=762 0066: dt=36.288000, rms=0.672 (0.238%), neg=0, invalid=762 0067: dt=36.288000, rms=0.671 (0.219%), neg=0, invalid=762 0068: dt=36.288000, rms=0.670 (0.193%), neg=0, invalid=762 0069: dt=36.288000, rms=0.668 (0.184%), neg=0, invalid=762 0070: dt=36.288000, rms=0.667 (0.154%), neg=0, invalid=762 0071: dt=36.288000, rms=0.666 (0.144%), neg=0, invalid=762 0072: dt=36.288000, rms=0.665 (0.153%), neg=0, invalid=762 0073: dt=36.288000, rms=0.664 (0.159%), neg=0, invalid=762 0074: dt=36.288000, rms=0.663 (0.143%), neg=0, invalid=762 0075: dt=36.288000, rms=0.662 (0.130%), neg=0, invalid=762 0076: dt=36.288000, rms=0.662 (0.118%), neg=0, invalid=762 0077: dt=36.288000, rms=0.661 (0.106%), neg=0, invalid=762 0078: dt=248.832000, rms=0.661 (0.058%), neg=0, invalid=762 0079: dt=248.832000, rms=0.661 (-0.314%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=762 0080: dt=9.072000, rms=0.661 (0.094%), neg=0, invalid=762 0081: dt=0.000000, rms=0.661 (-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=0.690, neg=0, invalid=762 0082: dt=0.043750, rms=0.689 (0.083%), neg=0, invalid=762 0083: dt=0.043750, rms=0.689 (0.000%), neg=0, invalid=762 0084: dt=0.043750, rms=0.689 (0.000%), neg=0, invalid=762 0085: dt=0.043750, rms=0.689 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.690, neg=0, invalid=762 0086: dt=0.000000, rms=0.689 (0.083%), neg=0, invalid=762 0087: dt=0.000000, rms=0.689 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.774, neg=0, invalid=762 0088: dt=5.741294, rms=0.749 (3.314%), neg=0, invalid=762 0089: dt=1.900000, rms=0.748 (0.063%), neg=0, invalid=762 0090: dt=1.900000, rms=0.748 (-0.061%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.748, neg=0, invalid=762 0091: dt=0.000000, rms=0.748 (0.060%), neg=0, invalid=762 0092: dt=0.000000, rms=0.748 (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=0.832, neg=0, invalid=762 0093: dt=1.536000, rms=0.826 (0.741%), neg=0, invalid=762 0094: dt=1.990050, rms=0.819 (0.856%), neg=0, invalid=762 0095: dt=0.112000, rms=0.819 (0.006%), neg=0, invalid=762 0096: dt=0.112000, rms=0.819 (0.002%), neg=0, invalid=762 0097: dt=0.112000, rms=0.819 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.819, neg=0, invalid=762 0098: dt=0.384000, rms=0.819 (0.077%), neg=0, invalid=762 0099: dt=0.448000, rms=0.818 (0.016%), neg=0, invalid=762 0100: dt=0.448000, rms=0.818 (0.013%), neg=0, invalid=762 0101: dt=0.448000, rms=0.818 (-0.016%), 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=0.745, neg=0, invalid=762 0102: dt=0.996603, rms=0.721 (3.223%), neg=0, invalid=762 0103: dt=0.112000, rms=0.720 (0.218%), neg=0, invalid=762 0104: dt=0.112000, rms=0.720 (-0.112%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.720, neg=0, invalid=762 0105: dt=0.028000, rms=0.719 (0.080%), neg=0, invalid=762 0106: dt=0.016000, rms=0.719 (0.002%), neg=0, invalid=762 0107: dt=0.016000, rms=0.719 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10898 (13) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (2965 voxels, overlap=0.414) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (2965 voxels, peak = 14), gca=13.7 gca peak = 0.15565 (16) mri peak = 0.12619 (17) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (2264 voxels, overlap=0.717) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (2264 voxels, peak = 15), gca=14.6 gca peak = 0.26829 (96) mri peak = 0.07748 (101) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (972 voxels, overlap=0.789) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (972 voxels, peak = 102), gca=102.2 gca peak = 0.20183 (93) mri peak = 0.08460 (101) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (885 voxels, overlap=0.603) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (885 voxels, peak = 100), gca=100.0 gca peak = 0.21683 (55) mri peak = 0.08296 (67) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (823 voxels, overlap=0.045) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (823 voxels, peak = 64), gca=63.5 gca peak = 0.30730 (58) mri peak = 0.07427 (66) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (650 voxels, overlap=0.585) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (650 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.08748 (102) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (64349 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (64349 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.08244 (104) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (64349 voxels, overlap=0.779) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (64349 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.04141 (61) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (21907 voxels, overlap=0.973) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (21907 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.04372 (63) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (25585 voxels, overlap=0.955) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (25585 voxels, peak = 61), gca=60.6 gca peak = 0.14161 (67) mri peak = 0.18421 (70) Right_Caudate (50): linear fit = 1.03 x + 0.0 (891 voxels, overlap=0.818) Right_Caudate (50): linear fit = 1.03 x + 0.0 (891 voxels, peak = 69), gca=69.3 gca peak = 0.15243 (71) mri peak = 0.11357 (72) Left_Caudate (11): linear fit = 0.99 x + 0.0 (687 voxels, overlap=0.967) Left_Caudate (11): linear fit = 0.99 x + 0.0 (687 voxels, peak = 70), gca=69.9 gca peak = 0.13336 (57) mri peak = 0.04313 (57) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (24519 voxels, overlap=0.936) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (24519 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.03866 (65) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (24627 voxels, overlap=0.555) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (24627 voxels, peak = 64), gca=63.6 gca peak = 0.18181 (84) mri peak = 0.07992 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (10078 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (10078 voxels, peak = 86), gca=86.1 gca peak = 0.20573 (83) mri peak = 0.07710 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8165 voxels, overlap=0.679) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8165 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.09446 (63) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (313 voxels, overlap=0.670) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (313 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.09290 (65) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (505 voxels, overlap=0.255) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (505 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.06215 (87) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4631 voxels, overlap=0.967) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4631 voxels, peak = 86), gca=86.3 gca peak = 0.11978 (83) mri peak = 0.07523 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3833 voxels, overlap=0.920) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3833 voxels, peak = 83), gca=82.6 gca peak = 0.13399 (79) mri peak = 0.06075 (84) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2543 voxels, overlap=0.921) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2543 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.05081 (84) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2469 voxels, overlap=0.784) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2469 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.10197 (82) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13339 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13339 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.08310 (93) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1336 voxels, overlap=0.329) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1336 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.08867 (94) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1561 voxels, overlap=0.539) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1561 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.13932 (20) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (174 voxels, overlap=0.513) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (174 voxels, peak = 18), gca=17.8 gca peak = 0.15061 (21) mri peak = 0.14552 (18) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (558 voxels, overlap=0.783) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (558 voxels, peak = 19), gca=19.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.10 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.82 x + 0.0 Right_Pallidum too bright - rescaling by 0.992 (from 1.065) to 101.4 (was 102.2) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.727, neg=0, invalid=762 0108: dt=73.984000, rms=0.724 (0.359%), neg=0, invalid=762 0109: dt=129.472000, rms=0.722 (0.287%), neg=0, invalid=762 0110: dt=517.888000, rms=0.715 (0.954%), neg=0, invalid=762 0111: dt=129.472000, rms=0.715 (0.073%), neg=0, invalid=762 0112: dt=1479.680000, rms=0.706 (1.266%), neg=0, invalid=762 0113: dt=32.368000, rms=0.705 (0.046%), neg=0, invalid=762 0114: dt=32.368000, rms=0.705 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.706, neg=0, invalid=762 0115: dt=13.872000, rms=0.705 (0.058%), neg=0, invalid=762 0116: dt=5.780000, rms=0.705 (0.004%), neg=0, invalid=762 0117: dt=5.780000, rms=0.705 (0.002%), neg=0, invalid=762 0118: dt=5.780000, rms=0.705 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=762 0119: dt=173.607282, rms=0.684 (3.146%), neg=0, invalid=762 0120: dt=111.541579, rms=0.667 (2.475%), neg=0, invalid=762 0121: dt=74.105263, rms=0.663 (0.598%), neg=0, invalid=762 0122: dt=181.621622, rms=0.656 (1.074%), neg=0, invalid=762 0123: dt=68.645161, rms=0.652 (0.556%), neg=0, invalid=762 0124: dt=145.152000, rms=0.648 (0.665%), neg=0, invalid=762 0125: dt=36.288000, rms=0.646 (0.213%), neg=0, invalid=762 0126: dt=145.152000, rms=0.644 (0.420%), neg=0, invalid=762 0127: dt=124.416000, rms=0.641 (0.372%), neg=0, invalid=762 0128: dt=36.288000, rms=0.640 (0.161%), neg=0, invalid=762 0129: dt=145.152000, rms=0.638 (0.285%), neg=0, invalid=762 0130: dt=36.288000, rms=0.637 (0.157%), neg=0, invalid=762 0131: dt=36.288000, rms=0.637 (0.082%), neg=0, invalid=762 0132: dt=36.288000, rms=0.636 (0.078%), neg=0, invalid=762 0133: dt=25.920000, rms=0.636 (0.050%), neg=0, invalid=762 0134: dt=0.567000, rms=0.636 (0.002%), neg=0, invalid=762 0135: dt=0.283500, rms=0.636 (0.001%), neg=0, invalid=762 0136: dt=0.141750, rms=0.636 (0.000%), neg=0, invalid=762 0137: dt=0.035437, rms=0.636 (0.000%), neg=0, invalid=762 0138: dt=0.000000, rms=0.636 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.637, neg=0, invalid=762 0139: dt=82.944000, rms=0.635 (0.266%), neg=0, invalid=762 0140: dt=248.832000, rms=0.632 (0.413%), neg=0, invalid=762 0141: dt=36.288000, rms=0.632 (0.087%), neg=0, invalid=762 0142: dt=145.152000, rms=0.631 (0.168%), neg=0, invalid=762 0143: dt=145.152000, rms=0.629 (0.256%), neg=0, invalid=762 0144: dt=36.288000, rms=0.629 (0.073%), neg=0, invalid=762 0145: dt=145.152000, rms=0.628 (0.102%), neg=0, invalid=762 0146: dt=82.944000, rms=0.627 (0.116%), neg=0, invalid=762 0147: dt=82.944000, rms=0.626 (0.132%), neg=0, invalid=762 0148: dt=36.288000, rms=0.626 (0.053%), neg=0, invalid=762 0149: dt=580.608000, rms=0.624 (0.372%), neg=0, invalid=762 0150: dt=36.288000, rms=0.622 (0.214%), neg=0, invalid=762 0151: dt=82.944000, rms=0.622 (0.104%), neg=0, invalid=762 0152: dt=82.944000, rms=0.621 (0.075%), neg=0, invalid=762 0153: dt=103.680000, rms=0.621 (0.092%), neg=0, invalid=762 0154: dt=36.288000, rms=0.620 (0.037%), neg=0, invalid=762 0155: dt=36.288000, rms=0.620 (0.027%), neg=0, invalid=762 0156: dt=36.288000, rms=0.620 (0.051%), neg=0, invalid=762 0157: dt=36.288000, rms=0.620 (0.030%), neg=0, invalid=762 0158: dt=18.144000, rms=0.620 (0.012%), neg=0, invalid=762 0159: dt=0.283500, rms=0.620 (0.001%), neg=0, invalid=762 0160: dt=0.141750, rms=0.620 (0.000%), neg=0, invalid=762 0161: dt=0.017719, rms=0.620 (0.000%), neg=0, invalid=762 0162: dt=0.004430, rms=0.620 (0.000%), neg=0, invalid=762 0163: dt=0.001107, rms=0.620 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=762 0164: dt=32.000000, rms=0.610 (2.103%), neg=0, invalid=762 0165: dt=2.800000, rms=0.609 (0.138%), neg=0, invalid=762 0166: dt=0.700000, rms=0.609 (0.032%), neg=0, invalid=762 0167: dt=0.175000, rms=0.609 (0.011%), neg=0, invalid=762 0168: dt=0.043750, rms=0.609 (0.002%), neg=0, invalid=762 0169: dt=0.021875, rms=0.609 (0.001%), neg=0, invalid=762 0170: dt=0.010937, rms=0.609 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.610, neg=0, invalid=762 0171: dt=62.416961, rms=0.601 (1.357%), neg=0, invalid=762 0172: dt=48.801484, rms=0.591 (1.650%), neg=0, invalid=762 0173: dt=2.800000, rms=0.591 (0.130%), neg=0, invalid=762 0174: dt=0.700000, rms=0.590 (0.030%), neg=0, invalid=762 0175: dt=0.043750, rms=0.590 (0.002%), neg=0, invalid=762 0176: dt=0.010937, rms=0.590 (0.002%), neg=0, invalid=762 0177: dt=0.005469, rms=0.590 (0.000%), neg=0, invalid=762 0178: dt=0.001367, rms=0.590 (0.000%), neg=0, invalid=762 0179: dt=0.000488, rms=0.590 (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=0.602, neg=0, invalid=762 0180: dt=4.032000, rms=0.595 (1.136%), neg=0, invalid=762 0181: dt=4.032000, rms=0.590 (0.766%), neg=0, invalid=762 0182: dt=13.824000, rms=0.580 (1.779%), neg=0, invalid=762 0183: dt=4.032000, rms=0.578 (0.255%), neg=0, invalid=762 0184: dt=16.128000, rms=0.574 (0.759%), neg=0, invalid=762 0185: dt=16.128000, rms=0.572 (0.329%), neg=0, invalid=762 0186: dt=18.509804, rms=0.571 (0.194%), neg=0, invalid=762 0187: dt=7.666667, rms=0.570 (0.139%), neg=0, invalid=762 0188: dt=4.032000, rms=0.570 (0.045%), neg=0, invalid=762 0189: dt=2.016000, rms=0.570 (0.018%), neg=0, invalid=762 0190: dt=1.008000, rms=0.570 (0.007%), neg=0, invalid=762 0191: dt=0.504000, rms=0.570 (0.003%), neg=0, invalid=762 0192: dt=0.216000, rms=0.570 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=762 0193: dt=0.000000, rms=0.570 (0.083%), neg=0, invalid=762 0194: dt=0.000000, rms=0.570 (0.000%), neg=0, invalid=762 0195: dt=0.150000, rms=0.570 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.592, neg=0, invalid=762 0196: dt=0.000000, rms=0.591 (0.077%), neg=0, invalid=762 0197: dt=0.000000, rms=0.591 (0.000%), neg=0, invalid=762 0198: dt=0.100000, rms=0.591 (-0.094%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=762 0199: dt=0.000000, rms=0.591 (0.077%), neg=0, invalid=762 0200: dt=0.000000, rms=0.591 (0.000%), neg=0, invalid=762 0201: dt=0.100000, rms=0.591 (-0.068%), 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=0.555, neg=0, invalid=762 0202: dt=0.448000, rms=0.539 (2.851%), neg=0, invalid=762 0203: dt=0.448000, rms=0.535 (0.801%), neg=0, invalid=762 0204: dt=0.448000, rms=0.533 (0.443%), neg=0, invalid=762 0205: dt=0.384000, rms=0.531 (0.228%), neg=0, invalid=762 0206: dt=0.448000, rms=0.530 (0.214%), neg=0, invalid=762 0207: dt=0.384000, rms=0.530 (0.119%), neg=0, invalid=762 0208: dt=0.384000, rms=0.529 (0.118%), neg=0, invalid=762 0209: dt=0.384000, rms=0.529 (0.076%), neg=0, invalid=762 0210: dt=0.384000, rms=0.528 (0.081%), neg=0, invalid=762 0211: dt=0.384000, rms=0.528 (0.050%), neg=0, invalid=762 0212: dt=0.384000, rms=0.528 (0.063%), neg=0, invalid=762 0213: dt=0.384000, rms=0.527 (0.031%), neg=0, invalid=762 0214: dt=0.384000, rms=0.527 (0.048%), neg=0, invalid=762 0215: dt=0.384000, rms=0.527 (0.071%), neg=0, invalid=762 0216: dt=0.384000, rms=0.527 (0.024%), neg=0, invalid=762 0217: dt=0.384000, rms=0.526 (0.054%), neg=0, invalid=762 0218: dt=0.384000, rms=0.526 (0.022%), neg=0, invalid=762 0219: dt=0.384000, rms=0.526 (0.036%), neg=0, invalid=762 0220: dt=0.384000, rms=0.526 (0.020%), neg=0, invalid=762 0221: dt=0.384000, rms=0.526 (0.026%), neg=0, invalid=762 0222: dt=0.384000, rms=0.526 (0.013%), neg=0, invalid=762 0223: dt=0.384000, rms=0.526 (0.003%), neg=0, invalid=762 0224: dt=0.320000, rms=0.526 (0.015%), neg=0, invalid=762 0225: dt=0.256000, rms=0.526 (0.008%), neg=0, invalid=762 0226: dt=0.256000, rms=0.526 (0.010%), neg=0, invalid=762 0227: dt=0.256000, rms=0.526 (0.013%), neg=0, invalid=762 0228: dt=0.256000, rms=0.526 (0.004%), neg=0, invalid=762 0229: dt=0.256000, rms=0.525 (0.006%), neg=0, invalid=762 0230: dt=0.256000, rms=0.525 (0.010%), neg=0, invalid=762 0231: dt=0.256000, rms=0.525 (0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=762 0232: dt=0.320000, rms=0.522 (0.827%), neg=0, invalid=762 0233: dt=0.384000, rms=0.520 (0.340%), neg=0, invalid=762 0234: dt=0.384000, rms=0.519 (0.095%), neg=0, invalid=762 0235: dt=0.384000, rms=0.519 (0.027%), neg=0, invalid=762 0236: dt=0.192000, rms=0.519 (0.008%), neg=0, invalid=762 0237: dt=0.192000, rms=0.519 (0.016%), neg=0, invalid=762 0238: dt=0.192000, rms=0.519 (0.007%), neg=0, invalid=762 0239: dt=0.192000, rms=0.519 (0.003%), neg=0, invalid=762 0240: dt=0.000000, rms=0.519 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0241: dt=0.000000, rms=0.517 (0.100%), neg=0, invalid=762 0242: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0243: dt=8.092000, rms=0.517 (0.100%), neg=0, invalid=762 0244: dt=8.092000, rms=0.517 (0.000%), neg=0, invalid=762 0245: dt=8.092000, rms=0.517 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0246: dt=82.944000, rms=0.516 (0.237%), neg=0, invalid=762 0247: dt=145.152000, rms=0.514 (0.287%), neg=0, invalid=762 0248: dt=31.104000, rms=0.514 (0.028%), neg=0, invalid=762 0249: dt=31.104000, rms=0.514 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0250: dt=31.104000, rms=0.514 (0.044%), neg=0, invalid=762 0251: dt=31.104000, rms=0.513 (0.074%), neg=0, invalid=762 0252: dt=31.104000, rms=0.513 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0253: dt=31.104000, rms=0.513 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=0, neg = 0 0254: dt=414.720000, rms=0.512 (0.151%), neg=0, invalid=762 0255: dt=31.104000, rms=0.512 (0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=762 0256: dt=77.012448, rms=0.510 (0.381%), neg=0, invalid=762 0257: dt=83.636364, rms=0.509 (0.272%), neg=0, invalid=762 0258: dt=19.555556, rms=0.509 (0.033%), neg=0, invalid=762 0259: dt=19.555556, rms=0.509 (0.012%), neg=0, invalid=762 0260: dt=19.555556, rms=0.509 (0.010%), neg=0, invalid=762 0261: dt=19.555556, rms=0.509 (0.023%), neg=0, invalid=762 0262: dt=19.555556, rms=0.508 (0.060%), neg=0, invalid=762 0263: dt=19.555556, rms=0.508 (0.086%), neg=0, invalid=762 0264: dt=19.555556, rms=0.507 (0.072%), neg=0, invalid=762 0265: dt=9.072000, rms=0.507 (0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.508, neg=0, invalid=762 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 0266: dt=44.800000, rms=0.504 (0.797%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 7 iterations, nbhd size=0, neg = 0 0267: dt=60.127389, rms=0.501 (0.718%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0268: dt=11.200000, rms=0.499 (0.294%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 4 iterations, nbhd size=0, neg = 0 0269: dt=25.600000, rms=0.499 (0.144%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 4 iterations, nbhd size=0, neg = 0 0270: dt=25.600000, rms=0.498 (0.202%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 18 iterations, nbhd size=1, neg = 0 0271: dt=25.600000, rms=0.496 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 65 after 12 iterations, nbhd size=0, neg = 0 0272: dt=25.600000, rms=0.495 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 118 after 20 iterations, nbhd size=1, neg = 0 0273: dt=25.600000, rms=0.494 (0.257%), neg=0, invalid=762 iter 0, gcam->neg = 156 after 17 iterations, nbhd size=1, neg = 0 0274: dt=25.600000, rms=0.492 (0.238%), neg=0, invalid=762 iter 0, gcam->neg = 202 after 22 iterations, nbhd size=1, neg = 0 0275: dt=25.600000, rms=0.491 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 245 after 24 iterations, nbhd size=1, neg = 0 0276: dt=25.600000, rms=0.491 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 293 after 20 iterations, nbhd size=1, neg = 0 0277: dt=25.600000, rms=0.490 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 341 after 22 iterations, nbhd size=1, neg = 0 0278: dt=25.600000, rms=0.490 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 343 after 33 iterations, nbhd size=2, neg = 0 0279: dt=25.600000, rms=0.489 (-0.125%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0280: dt=11.200000, rms=0.489 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 21 iterations, nbhd size=1, neg = 0 0281: dt=25.600000, rms=0.489 (0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 iter 0, gcam->neg = 20 after 13 iterations, nbhd size=0, neg = 0 0282: dt=32.000000, rms=0.487 (0.632%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 8 iterations, nbhd size=0, neg = 0 0283: dt=32.000000, rms=0.485 (0.309%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 0284: dt=11.200000, rms=0.485 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0285: dt=11.200000, rms=0.484 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0286: dt=11.200000, rms=0.484 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 0287: dt=11.200000, rms=0.483 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 6 iterations, nbhd size=0, neg = 0 0288: dt=11.200000, rms=0.483 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 10 iterations, nbhd size=0, neg = 0 0289: dt=11.200000, rms=0.483 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 7 iterations, nbhd size=0, neg = 0 0290: dt=11.200000, rms=0.482 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 3 iterations, nbhd size=0, neg = 0 0291: dt=44.800000, rms=0.482 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0292: dt=25.600000, rms=0.482 (0.061%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0293: dt=4.000000, rms=0.488 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0294: dt=1.333333, rms=0.488 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0295: dt=1.333333, rms=0.488 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=0, neg = 0 0296: dt=1.333333, rms=0.488 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=0, neg = 0 0297: dt=4.032000, rms=0.488 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0298: dt=5.777778, rms=0.488 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=0, neg = 0 0299: dt=5.777778, rms=0.487 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 8 iterations, nbhd size=0, neg = 0 0300: dt=5.777778, rms=0.487 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 66 after 10 iterations, nbhd size=0, neg = 0 0301: dt=5.777778, rms=0.487 (0.008%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0302: dt=0.000000, rms=0.492 (0.107%), neg=0, invalid=762 0303: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0304: dt=0.000040, rms=0.492 (0.107%), neg=0, invalid=762 0305: dt=0.000000, rms=0.492 (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=0.484, neg=0, invalid=762 iter 0, gcam->neg = 1548 after 18 iterations, nbhd size=1, neg = 0 0306: dt=1.792000, rms=0.456 (5.702%), neg=0, invalid=762 0307: dt=0.000013, rms=0.456 (0.005%), neg=0, invalid=762 0308: dt=0.000013, rms=0.456 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0309: dt=0.064000, rms=0.456 (0.168%), neg=0, invalid=762 0310: dt=0.000000, rms=0.456 (0.001%), neg=0, invalid=762 0311: dt=0.050000, rms=0.456 (-0.017%), 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=0.443, neg=0, invalid=762 0312: dt=2.023000, rms=0.443 (0.000%), neg=0, invalid=762 0313: dt=0.000000, rms=0.443 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 0314: dt=92.480000, rms=0.443 (0.007%), neg=0, invalid=762 0315: dt=295.936000, rms=0.443 (0.009%), neg=0, invalid=762 0316: dt=8.092000, rms=0.443 (0.000%), neg=0, invalid=762 0317: dt=8.092000, rms=0.443 (0.000%), neg=0, invalid=762 0318: dt=8.092000, rms=0.443 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 0319: dt=9.072000, rms=0.443 (0.007%), neg=0, invalid=762 0320: dt=5.184000, rms=0.443 (0.001%), neg=0, invalid=762 0321: dt=5.184000, rms=0.443 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 0322: dt=124.416000, rms=0.443 (0.082%), neg=0, invalid=762 0323: dt=82.944000, rms=0.443 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0324: dt=82.944000, rms=0.443 (-0.102%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 iter 0, gcam->neg = 22 after 11 iterations, nbhd size=1, neg = 0 0325: dt=29.875519, rms=0.442 (0.328%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 19 iterations, nbhd size=1, neg = 0 0326: dt=38.400000, rms=0.441 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 85 after 21 iterations, nbhd size=1, neg = 0 0327: dt=38.400000, rms=0.441 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 276 after 26 iterations, nbhd size=1, neg = 0 0328: dt=38.400000, rms=0.441 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=762 iter 0, gcam->neg = 70 after 9 iterations, nbhd size=0, neg = 0 0329: dt=32.000000, rms=0.438 (0.597%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 13 iterations, nbhd size=0, neg = 0 0330: dt=23.404959, rms=0.437 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 37 after 18 iterations, nbhd size=1, neg = 0 0331: dt=23.404959, rms=0.437 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 59 after 22 iterations, nbhd size=1, neg = 0 0332: dt=23.404959, rms=0.436 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 85 after 22 iterations, nbhd size=1, neg = 0 0333: dt=23.404959, rms=0.436 (0.144%), neg=0, invalid=762 iter 0, gcam->neg = 122 after 20 iterations, nbhd size=1, neg = 0 0334: dt=23.404959, rms=0.436 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 158 after 18 iterations, nbhd size=0, neg = 0 0335: dt=23.404959, rms=0.435 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 221 after 22 iterations, nbhd size=1, neg = 0 0336: dt=23.404959, rms=0.435 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 293 after 23 iterations, nbhd size=1, neg = 0 0337: dt=23.404959, rms=0.435 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 86 after 11 iterations, nbhd size=0, neg = 0 0338: dt=44.800000, rms=0.434 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 10 iterations, nbhd size=0, neg = 0 0339: dt=8.000000, rms=0.434 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 8 iterations, nbhd size=0, neg = 0 0340: dt=8.000000, rms=0.434 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 iter 0, gcam->neg = 56 after 11 iterations, nbhd size=0, neg = 0 0341: dt=6.105263, rms=0.438 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 10 iterations, nbhd size=0, neg = 0 0342: dt=4.888889, rms=0.437 (0.028%), neg=0, invalid=762 iter 0, gcam->neg = 33 after 22 iterations, nbhd size=1, neg = 0 0343: dt=4.888889, rms=0.437 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 71 after 23 iterations, nbhd size=1, neg = 0 0344: dt=4.888889, rms=0.437 (-0.052%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.437, neg=0, invalid=762 iter 0, gcam->neg = 82 after 10 iterations, nbhd size=0, neg = 0 0345: dt=11.816993, rms=0.436 (0.288%), neg=0, invalid=762 iter 0, gcam->neg = 199 after 20 iterations, nbhd size=1, neg = 0 0346: dt=23.692308, rms=0.435 (0.283%), neg=0, invalid=762 iter 0, gcam->neg = 64 after 11 iterations, nbhd size=0, neg = 0 0347: dt=7.942857, rms=0.434 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 74 after 17 iterations, nbhd size=0, neg = 0 0348: dt=7.942857, rms=0.434 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 152 after 13 iterations, nbhd size=0, neg = 0 0349: dt=7.942857, rms=0.433 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 180 after 17 iterations, nbhd size=0, neg = 0 0350: dt=7.942857, rms=0.433 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 260 after 15 iterations, nbhd size=0, neg = 0 0351: dt=7.942857, rms=0.433 (0.073%), neg=0, invalid=762 iter 0, gcam->neg = 116 after 12 iterations, nbhd size=0, neg = 0 0352: dt=10.980392, rms=0.432 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 80 after 11 iterations, nbhd size=0, neg = 0 0353: dt=9.422222, rms=0.432 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 83 after 9 iterations, nbhd size=0, neg = 0 0354: dt=9.422222, rms=0.432 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 139 after 22 iterations, nbhd size=1, neg = 0 0355: dt=9.422222, rms=0.432 (-0.074%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0356: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0357: dt=0.000050, rms=0.438 (0.000%), neg=0, invalid=762 0358: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 iter 0, gcam->neg = 978 after 25 iterations, nbhd size=1, neg = 0 0359: dt=1.035703, rms=0.419 (2.026%), neg=0, invalid=762 0360: dt=0.000020, rms=0.419 (0.000%), neg=0, invalid=762 0361: dt=0.000020, rms=0.419 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0362: dt=0.112000, rms=0.419 (0.081%), neg=0, invalid=762 0363: dt=0.112000, rms=0.418 (0.053%), neg=0, invalid=762 0364: dt=0.112000, rms=0.418 (0.056%), neg=0, invalid=762 0365: dt=0.112000, rms=0.418 (0.058%), neg=0, invalid=762 0366: dt=0.112000, rms=0.418 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0367: dt=0.112000, rms=0.418 (-0.036%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 9 hours, 51 minutes and 10 seconds. mri_ca_register utimesec 35426.485634 mri_ca_register stimesec 42.589892 mri_ca_register ru_maxrss 1345408 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 9477995 mri_ca_register ru_majflt 5 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 6878 mri_ca_register ru_oublock 64128 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 235 mri_ca_register ru_nivcsw 26337 FSRUNTIME@ mri_ca_register 9.8527 hours 1 threads #-------------------------------------- #@# SubCort Seg Mon Jun 17 02:45:43 CEST 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname atlas-210 machine x86_64 setenv SUBJECTS_DIR /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI cd /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == 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 /usr/local/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 7.73 Atlas used for the 3D morph was /usr/local/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 = 0.10736 (13) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (17412 voxels, overlap=0.391) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (17412 voxels, peak = 13), gca=13.1 gca peak = 0.17677 (13) mri peak = 0.11396 (15) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (16073 voxels, overlap=0.713) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (16073 voxels, peak = 13), gca=13.5 gca peak = 0.28129 (95) mri peak = 0.08036 (101) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (659 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (659 voxels, peak = 100), gca=100.2 gca peak = 0.16930 (96) mri peak = 0.08470 (100) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (673 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (673 voxels, peak = 101), gca=101.3 gca peak = 0.24553 (55) mri peak = 0.08828 (67) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1019 voxels, overlap=0.281) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1019 voxels, peak = 62), gca=62.4 gca peak = 0.30264 (59) mri peak = 0.07659 (66) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (940 voxels, overlap=0.590) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (940 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.09565 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43211 voxels, overlap=0.774) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43211 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.08471 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (42499 voxels, overlap=0.704) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (42499 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04494 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24019 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24019 voxels, peak = 59), gca=59.4 gca peak = 0.11620 (58) mri peak = 0.04733 (63) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (22807 voxels, overlap=0.944) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (22807 voxels, peak = 62), gca=62.4 gca peak = 0.30970 (66) mri peak = 0.08211 (72) Right_Caudate (50): linear fit = 1.10 x + 0.0 (1296 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.10 x + 0.0 (1296 voxels, peak = 72), gca=72.3 gca peak = 0.15280 (69) mri peak = 0.09120 (72) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1111 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1111 voxels, peak = 69), gca=69.0 gca peak = 0.13902 (56) mri peak = 0.05456 (60) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (20526 voxels, overlap=0.914) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (20526 voxels, peak = 60), gca=59.6 gca peak = 0.14777 (55) mri peak = 0.05272 (65) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (20465 voxels, overlap=0.721) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (20465 voxels, peak = 64), gca=63.5 gca peak = 0.16765 (84) mri peak = 0.11022 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6586 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6586 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.10816 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6592 voxels, overlap=0.672) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6592 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.09004 (65) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (522 voxels, overlap=0.212) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (522 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.08081 (67) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (594 voxels, overlap=0.060) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (594 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.06465 (88) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4370 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4370 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.07424 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4310 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4310 voxels, peak = 85), gca=85.1 gca peak = 0.08324 (81) mri peak = 0.06279 (84) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1814 voxels, overlap=0.813) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1814 voxels, peak = 85), gca=85.5 gca peak = 0.10360 (77) mri peak = 0.06117 (84) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1928 voxels, overlap=0.882) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1928 voxels, peak = 81), gca=81.2 gca peak = 0.08424 (78) mri peak = 0.08693 (82) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12856 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12856 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.07687 (96) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1427 voxels, overlap=0.393) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1427 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.07681 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1468 voxels, overlap=0.246) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1468 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.14485 (20) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (787 voxels, overlap=0.482) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (787 voxels, peak = 18), gca=17.9 gca peak = 0.19357 (14) mri peak = 0.14855 (18) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (650 voxels, overlap=0.841) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (650 voxels, peak = 17), gca=16.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak 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 1.12 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.90 x + 0.0 Left_Pallidum too bright - rescaling by 0.996 (from 1.055) to 100.9 (was 101.3) Right_Pallidum too bright - rescaling by 1.007 (from 1.055) to 100.9 (was 100.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21122 (13) mri peak = 0.10736 (13) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (17412 voxels, overlap=0.963) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (17412 voxels, peak = 13), gca=13.5 gca peak = 0.19081 (13) mri peak = 0.11396 (15) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (16073 voxels, overlap=0.671) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (16073 voxels, peak = 12), gca=11.9 gca peak = 0.22871 (101) mri peak = 0.08036 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (659 voxels, peak = 102), gca=101.5 gca peak = 0.14808 (100) mri peak = 0.08470 (100) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (673 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (673 voxels, peak = 102), gca=101.5 gca peak = 0.26834 (63) mri peak = 0.08828 (67) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1019 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1019 voxels, peak = 62), gca=62.1 gca peak = 0.27962 (67) mri peak = 0.07659 (66) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (940 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (940 voxels, peak = 67), gca=67.0 gca peak = 0.07874 (102) mri peak = 0.09565 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43211 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43211 voxels, peak = 102), gca=102.0 gca peak = 0.07854 (106) mri peak = 0.08471 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42499 voxels, overlap=0.769) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42499 voxels, peak = 105), gca=105.5 gca peak = 0.09517 (59) mri peak = 0.04494 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24019 voxels, overlap=0.970) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24019 voxels, peak = 60), gca=60.5 gca peak = 0.11125 (62) mri peak = 0.04733 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (22807 voxels, overlap=0.978) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (22807 voxels, peak = 61), gca=61.1 gca peak = 0.25592 (73) mri peak = 0.08211 (72) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1296 voxels, overlap=1.007) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1296 voxels, peak = 72), gca=71.9 gca peak = 0.15280 (69) mri peak = 0.09120 (72) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1111 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1111 voxels, peak = 69), gca=69.0 gca peak = 0.13236 (60) mri peak = 0.05456 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (20526 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (20526 voxels, peak = 62), gca=61.5 gca peak = 0.12984 (63) mri peak = 0.05272 (65) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (20465 voxels, overlap=0.990) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (20465 voxels, peak = 63), gca=63.0 gca peak = 0.15819 (86) mri peak = 0.11022 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6586 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6586 voxels, peak = 86), gca=85.6 gca peak = 0.15153 (90) mri peak = 0.10816 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6592 voxels, overlap=0.940) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6592 voxels, peak = 89), gca=88.7 gca peak = 0.24259 (69) mri peak = 0.09004 (65) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (522 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (522 voxels, peak = 70), gca=70.0 gca peak = 0.29908 (68) mri peak = 0.08081 (67) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (594 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (594 voxels, peak = 66), gca=65.6 gca peak = 0.10567 (90) mri peak = 0.06465 (88) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4370 voxels, overlap=0.991) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4370 voxels, peak = 89), gca=88.7 gca peak = 0.11776 (83) mri peak = 0.07424 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4310 voxels, overlap=0.986) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4310 voxels, peak = 83), gca=82.6 gca peak = 0.08452 (87) mri peak = 0.06279 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1814 voxels, overlap=0.954) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1814 voxels, peak = 87), gca=86.6 gca peak = 0.08162 (81) mri peak = 0.06117 (84) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1928 voxels, overlap=0.979) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1928 voxels, peak = 80), gca=79.8 gca peak = 0.07279 (83) mri peak = 0.08693 (82) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12856 voxels, overlap=0.725) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12856 voxels, peak = 82), gca=81.8 gca peak = 0.11382 (92) mri peak = 0.07687 (96) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1427 voxels, overlap=0.801) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1427 voxels, peak = 93), gca=93.4 gca peak = 0.14934 (94) mri peak = 0.07681 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1468 voxels, overlap=0.871) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1468 voxels, peak = 94), gca=93.5 gca peak = 0.21286 (19) mri peak = 0.14485 (20) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (787 voxels, overlap=1.013) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (787 voxels, peak = 19), gca=19.0 gca peak = 0.17387 (17) mri peak = 0.14855 (18) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (650 voxels, overlap=0.776) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (650 voxels, peak = 17), gca=17.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15127 (30) gca peak Left_Thalamus = 0.64095 (102) gca peak CSF = 0.25901 (33) gca peak Left_Accumbens_area = 0.70064 (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 = 0.21972 (26) gca peak Right_Accumbens_area = 0.32007 (71) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (29) gca peak WM_hypointensities = 0.07758 (76) gca peak non_WM_hypointensities = 0.07897 (44) gca peak Optic_Chiasm = 0.68944 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 Left_Pallidum too bright - rescaling by 0.991 (from 1.015) to 100.6 (was 101.5) Right_Pallidum too bright - rescaling by 0.991 (from 1.005) to 100.6 (was 101.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 87378 voxels changed in iteration 0 of unlikely voxel relabeling 315 voxels changed in iteration 1 of unlikely voxel relabeling 15 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 47189 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 320 hippocampal voxels changed. 3 amygdala voxels changed. pass 1: 86894 changed. image ll: -2.160, PF=0.500 pass 2: 25260 changed. image ll: -2.160, PF=0.500 pass 3: 7489 changed. pass 4: 2619 changed. 57778 voxels changed in iteration 0 of unlikely voxel relabeling 347 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 9224 voxels changed in iteration 0 of unlikely voxel relabeling 72 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7755 voxels changed in iteration 0 of unlikely voxel relabeling 89 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 10 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6463 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 5867.296784 mri_ca_label stimesec 13.748997 mri_ca_label ru_maxrss 2106424 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 5686059 mri_ca_label ru_majflt 5 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 68141 mri_ca_label ru_oublock 515 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 455 mri_ca_label ru_nivcsw 4436 auto-labeling took 98 minutes and 2 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/transforms/cc_up.lta sub-3811ses-Session_baseline will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/transforms/cc_up.lta reading aseg from /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/aseg.auto_noCCseg.mgz reading norm from /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/norm.mgz 49198 voxels in left wm, 86250 in right wm, xrange [121, 135] searching rotation angles z=[-10 4], y=[-10 4] searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 global minimum found at slice 129.0, rotations (-3.36, -2.75) final transformation (x=129.0, yr=-3.362, zr=-2.747): 0.99713 0.04793 -0.05857 0.78070; -0.04785 0.99885 0.00281 62.02189; 0.05864 0.00000 0.99828 37.57798; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 72 83 eigenvectors: 0.00292 0.03218 0.99948; 0.06111 -0.99762 0.03194; 0.99813 0.06099 -0.00488; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri/aseg.auto.mgz... corpus callosum segmentation took 1.8 minutes #-------------------------------------- #@# Merge ASeg Mon Jun 17 04:25:36 CEST 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Jun 17 04:25:36 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/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... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1314 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 109 gm peak at 66 (66), valley at 28 (28) csf peak at 15, setting threshold to 49 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 68 (68), valley at 28 (28) csf peak at 15, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 7 minutes and 37 seconds. #-------------------------------------------- #@# Mask BFS Mon Jun 17 04:33:24 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1772566 voxels in mask (pct= 10.57) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jun 17 04:33:33 CEST 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 (105.0): 105.5 +- 5.9 [79.0 --> 125.0] GM (70.0) : 67.4 +- 11.5 [30.0 --> 95.0] setting bottom of white matter range to 78.9 setting top of gray matter range to 90.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 8994 sparsely connected voxels removed... thickening thin strands.... 20 segments, 9364 filled 3320 bright non-wm voxels segmented. 4679 diagonally connected voxels added... white matter segmentation took 1.8 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 1.03 minutes reading wm segmentation from wm.seg.mgz... 41 voxels added to wm to prevent paths from MTL structures to cortex 5597 additional wm voxels added 0 additional wm voxels added SEG EDIT: 150206 voxels turned on, 43466 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+): 35 found - 35 modified | TOTAL: 35 pass 2 (xy+): 0 found - 35 modified | TOTAL: 35 pass 1 (xy-): 48 found - 48 modified | TOTAL: 83 pass 2 (xy-): 0 found - 48 modified | TOTAL: 83 pass 1 (yz+): 41 found - 41 modified | TOTAL: 124 pass 2 (yz+): 0 found - 41 modified | TOTAL: 124 pass 1 (yz-): 36 found - 36 modified | TOTAL: 160 pass 2 (yz-): 0 found - 36 modified | TOTAL: 160 pass 1 (xz+): 33 found - 33 modified | TOTAL: 193 pass 2 (xz+): 0 found - 33 modified | TOTAL: 193 pass 1 (xz-): 29 found - 29 modified | TOTAL: 222 pass 2 (xz-): 0 found - 29 modified | TOTAL: 222 Iteration Number : 1 pass 1 (+++): 24 found - 24 modified | TOTAL: 24 pass 2 (+++): 0 found - 24 modified | TOTAL: 24 pass 1 (+++): 22 found - 22 modified | TOTAL: 46 pass 2 (+++): 0 found - 22 modified | TOTAL: 46 pass 1 (+++): 31 found - 31 modified | TOTAL: 77 pass 2 (+++): 0 found - 31 modified | TOTAL: 77 pass 1 (+++): 37 found - 37 modified | TOTAL: 114 pass 2 (+++): 0 found - 37 modified | TOTAL: 114 Iteration Number : 1 pass 1 (++): 139 found - 139 modified | TOTAL: 139 pass 2 (++): 0 found - 139 modified | TOTAL: 139 pass 1 (+-): 139 found - 139 modified | TOTAL: 278 pass 2 (+-): 0 found - 139 modified | TOTAL: 278 pass 1 (--): 131 found - 131 modified | TOTAL: 409 pass 2 (--): 0 found - 131 modified | TOTAL: 409 pass 1 (-+): 95 found - 95 modified | TOTAL: 504 pass 2 (-+): 0 found - 95 modified | TOTAL: 504 Iteration Number : 2 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 7 found - 7 modified | TOTAL: 21 pass 2 (xy-): 0 found - 7 modified | TOTAL: 21 pass 1 (yz+): 5 found - 5 modified | TOTAL: 26 pass 2 (yz+): 0 found - 5 modified | TOTAL: 26 pass 1 (yz-): 5 found - 5 modified | TOTAL: 31 pass 2 (yz-): 0 found - 5 modified | TOTAL: 31 pass 1 (xz+): 9 found - 9 modified | TOTAL: 40 pass 2 (xz+): 0 found - 9 modified | TOTAL: 40 pass 1 (xz-): 3 found - 3 modified | TOTAL: 43 pass 2 (xz-): 0 found - 3 modified | TOTAL: 43 Iteration Number : 2 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 : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 5 found - 5 modified | TOTAL: 6 pass 2 (+-): 0 found - 5 modified | TOTAL: 6 pass 1 (--): 7 found - 7 modified | TOTAL: 13 pass 2 (--): 0 found - 7 modified | TOTAL: 13 pass 1 (-+): 2 found - 2 modified | TOTAL: 15 pass 2 (-+): 0 found - 2 modified | TOTAL: 15 Iteration Number : 3 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 899 (out of 680267: 0.132154) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Jun 17 04:36:35 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/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 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.00070 0.02669 -0.04354 -2.16910; -0.00934 0.95956 0.38792 -4.98454; 0.04781 -0.37284 0.92502 44.08404; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1291 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (126, 116, 94), TAL = (2.0, -34.0, 12.0) talairach voxel to voxel transform 0.99682 -0.00817 0.05034 -0.09763; 0.02625 0.89591 -0.37447 21.03100; -0.04094 0.36152 0.92752 -39.17542; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 116, 94) --> (2.0, -34.0, 12.0) done. writing output to filled.mgz... filling took 1.6 minutes talairach cc position changed to (2.00, -34.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -34.00, 12.00) SRC: (111.34, 92.59, 85.53) search lh wm seed point around talairach space (-16.00, -34.00, 12.00), SRC: (147.23, 93.54, 84.05) 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 ... #-------------------------------------------- #@# Tessellate lh Mon Jun 17 04:38:13 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 Iteration Number : 1 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 : 1 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 (-+): 2 found - 2 modified | TOTAL: 2 pass 2 (-+): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 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 : 2 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 : 2 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 = 8 (out of 322007: 0.002484) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 57 vertices, 77 faces slice 40: 6655 vertices, 7060 faces slice 50: 20588 vertices, 21102 faces slice 60: 36526 vertices, 37091 faces slice 70: 51884 vertices, 52378 faces slice 80: 64631 vertices, 65151 faces slice 90: 77426 vertices, 77979 faces slice 100: 90605 vertices, 91143 faces slice 110: 102665 vertices, 103217 faces slice 120: 114577 vertices, 115086 faces slice 130: 124822 vertices, 125270 faces slice 140: 133779 vertices, 134175 faces slice 150: 141743 vertices, 142112 faces slice 160: 148432 vertices, 148725 faces slice 170: 153610 vertices, 153856 faces slice 180: 156919 vertices, 157107 faces slice 190: 157528 vertices, 157624 faces slice 200: 157528 vertices, 157624 faces slice 210: 157528 vertices, 157624 faces slice 220: 157528 vertices, 157624 faces slice 230: 157528 vertices, 157624 faces slice 240: 157528 vertices, 157624 faces slice 250: 157528 vertices, 157624 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 157528 voxel in cpt #1: X=-96 [v=157528,e=472872,f=315248] located at (-30.176363, -34.447998, 44.250774) For the whole surface: X=-96 [v=157528,e=472872,f=315248] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Jun 17 04:38:34 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 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 : 1 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 : 2 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 : 2 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 : 2 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 = 3 (out of 330954: 0.000906) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 4506 vertices, 4795 faces slice 50: 16893 vertices, 17408 faces slice 60: 32798 vertices, 33352 faces slice 70: 48391 vertices, 48909 faces slice 80: 61481 vertices, 61956 faces slice 90: 74648 vertices, 75195 faces slice 100: 87955 vertices, 88546 faces slice 110: 101058 vertices, 101644 faces slice 120: 113746 vertices, 114291 faces slice 130: 125114 vertices, 125606 faces slice 140: 134280 vertices, 134705 faces slice 150: 142063 vertices, 142475 faces slice 160: 148719 vertices, 149055 faces slice 170: 154373 vertices, 154679 faces slice 180: 158210 vertices, 158434 faces slice 190: 158768 vertices, 158900 faces slice 200: 158768 vertices, 158900 faces slice 210: 158768 vertices, 158900 faces slice 220: 158768 vertices, 158900 faces slice 230: 158768 vertices, 158900 faces slice 240: 158768 vertices, 158900 faces slice 250: 158768 vertices, 158900 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 158768 voxel in cpt #1: X=-132 [v=158768,e=476700,f=317800] located at (28.314787, -32.449970, 47.403023) For the whole surface: X=-132 [v=158768,e=476700,f=317800] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Jun 17 04:38:55 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Mon Jun 17 04:39:07 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Jun 17 04:39:18 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 50.6 mm, total surface area = 82977 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 2.3 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.055 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.051 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 134.697666 mris_inflate stimesec 0.457992 mris_inflate ru_maxrss 201964 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 200123 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11609 mris_inflate ru_oublock 11083 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 58 mris_inflate ru_nivcsw 111 #-------------------------------------------- #@# Inflation1 rh Mon Jun 17 04:41:33 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.7 mm, total surface area = 83937 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 2.3 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.060 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.056 (target=0.015) step 045: RMS=0.055 (target=0.015) step 050: RMS=0.054 (target=0.015) step 055: RMS=0.054 (target=0.015) step 060: RMS=0.054 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 137.276414 mris_inflate stimesec 0.458981 mris_inflate ru_maxrss 203656 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 199040 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11191 mris_inflate ru_oublock 11172 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 64 mris_inflate ru_nivcsw 108 #-------------------------------------------- #@# QSphere lh Mon Jun 17 04:43:51 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.58 (0.00-->7.50) (max @ vno 67471 --> 68701) face area 0.03 +- 0.04 (-0.16-->0.96) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.344... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=173.652, avgs=0 005/300: dt: 0.9000, rms radial error=173.403, avgs=0 010/300: dt: 0.9000, rms radial error=172.869, avgs=0 015/300: dt: 0.9000, rms radial error=172.167, avgs=0 020/300: dt: 0.9000, rms radial error=171.365, avgs=0 025/300: dt: 0.9000, rms radial error=170.506, avgs=0 030/300: dt: 0.9000, rms radial error=169.615, avgs=0 035/300: dt: 0.9000, rms radial error=168.708, avgs=0 040/300: dt: 0.9000, rms radial error=167.793, avgs=0 045/300: dt: 0.9000, rms radial error=166.875, avgs=0 050/300: dt: 0.9000, rms radial error=165.957, avgs=0 055/300: dt: 0.9000, rms radial error=165.041, avgs=0 060/300: dt: 0.9000, rms radial error=164.127, avgs=0 065/300: dt: 0.9000, rms radial error=163.217, avgs=0 070/300: dt: 0.9000, rms radial error=162.312, avgs=0 075/300: dt: 0.9000, rms radial error=161.410, avgs=0 080/300: dt: 0.9000, rms radial error=160.513, avgs=0 085/300: dt: 0.9000, rms radial error=159.621, avgs=0 090/300: dt: 0.9000, rms radial error=158.732, avgs=0 095/300: dt: 0.9000, rms radial error=157.848, avgs=0 100/300: dt: 0.9000, rms radial error=156.968, avgs=0 105/300: dt: 0.9000, rms radial error=156.093, avgs=0 110/300: dt: 0.9000, rms radial error=155.223, avgs=0 115/300: dt: 0.9000, rms radial error=154.357, avgs=0 120/300: dt: 0.9000, rms radial error=153.497, avgs=0 125/300: dt: 0.9000, rms radial error=152.641, avgs=0 130/300: dt: 0.9000, rms radial error=151.790, avgs=0 135/300: dt: 0.9000, rms radial error=150.944, avgs=0 140/300: dt: 0.9000, rms radial error=150.102, avgs=0 145/300: dt: 0.9000, rms radial error=149.265, avgs=0 150/300: dt: 0.9000, rms radial error=148.432, avgs=0 155/300: dt: 0.9000, rms radial error=147.605, avgs=0 160/300: dt: 0.9000, rms radial error=146.781, avgs=0 165/300: dt: 0.9000, rms radial error=145.962, avgs=0 170/300: dt: 0.9000, rms radial error=145.147, avgs=0 175/300: dt: 0.9000, rms radial error=144.337, avgs=0 180/300: dt: 0.9000, rms radial error=143.531, avgs=0 185/300: dt: 0.9000, rms radial error=142.729, avgs=0 190/300: dt: 0.9000, rms radial error=141.932, avgs=0 195/300: dt: 0.9000, rms radial error=141.139, avgs=0 200/300: dt: 0.9000, rms radial error=140.349, avgs=0 205/300: dt: 0.9000, rms radial error=139.564, avgs=0 210/300: dt: 0.9000, rms radial error=138.784, avgs=0 215/300: dt: 0.9000, rms radial error=138.007, avgs=0 220/300: dt: 0.9000, rms radial error=137.235, avgs=0 225/300: dt: 0.9000, rms radial error=136.467, avgs=0 230/300: dt: 0.9000, rms radial error=135.704, avgs=0 235/300: dt: 0.9000, rms radial error=134.944, avgs=0 240/300: dt: 0.9000, rms radial error=134.189, avgs=0 245/300: dt: 0.9000, rms radial error=133.437, avgs=0 250/300: dt: 0.9000, rms radial error=132.690, avgs=0 255/300: dt: 0.9000, rms radial error=131.948, avgs=0 260/300: dt: 0.9000, rms radial error=131.210, avgs=0 265/300: dt: 0.9000, rms radial error=130.476, avgs=0 270/300: dt: 0.9000, rms radial error=129.745, avgs=0 275/300: dt: 0.9000, rms radial error=129.019, avgs=0 280/300: dt: 0.9000, rms radial error=128.297, avgs=0 285/300: dt: 0.9000, rms radial error=127.579, avgs=0 290/300: dt: 0.9000, rms radial error=126.865, avgs=0 295/300: dt: 0.9000, rms radial error=126.155, avgs=0 300/300: dt: 0.9000, rms radial error=125.449, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17967.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 3049.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00045 epoch 3 (K=160.0), pass 1, starting sse = 448.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.00996 epoch 4 (K=640.0), pass 1, starting sse = 127.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.26/16 = 0.01596 final distance error %28.75 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.22 hours mris_sphere utimesec 803.269778 mris_sphere stimesec 0.675995 mris_sphere ru_maxrss 202160 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 348965 mris_sphere ru_majflt 3 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11620 mris_sphere ru_oublock 11084 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 60 mris_sphere ru_nivcsw 549 FSRUNTIME@ mris_sphere 0.2233 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Jun 17 04:57:15 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.55 (0.00-->6.79) (max @ vno 128771 --> 128772) face area 0.03 +- 0.04 (-0.19-->0.77) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.341... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=173.834, avgs=0 005/300: dt: 0.9000, rms radial error=173.585, avgs=0 010/300: dt: 0.9000, rms radial error=173.049, avgs=0 015/300: dt: 0.9000, rms radial error=172.345, avgs=0 020/300: dt: 0.9000, rms radial error=171.546, avgs=0 025/300: dt: 0.9000, rms radial error=170.688, avgs=0 030/300: dt: 0.9000, rms radial error=169.799, avgs=0 035/300: dt: 0.9000, rms radial error=168.893, avgs=0 040/300: dt: 0.9000, rms radial error=167.978, avgs=0 045/300: dt: 0.9000, rms radial error=167.060, avgs=0 050/300: dt: 0.9000, rms radial error=166.141, avgs=0 055/300: dt: 0.9000, rms radial error=165.225, avgs=0 060/300: dt: 0.9000, rms radial error=164.310, avgs=0 065/300: dt: 0.9000, rms radial error=163.399, avgs=0 070/300: dt: 0.9000, rms radial error=162.492, avgs=0 075/300: dt: 0.9000, rms radial error=161.590, avgs=0 080/300: dt: 0.9000, rms radial error=160.691, avgs=0 085/300: dt: 0.9000, rms radial error=159.799, avgs=0 090/300: dt: 0.9000, rms radial error=158.910, avgs=0 095/300: dt: 0.9000, rms radial error=158.026, avgs=0 100/300: dt: 0.9000, rms radial error=157.146, avgs=0 105/300: dt: 0.9000, rms radial error=156.271, avgs=0 110/300: dt: 0.9000, rms radial error=155.400, avgs=0 115/300: dt: 0.9000, rms radial error=154.533, avgs=0 120/300: dt: 0.9000, rms radial error=153.671, avgs=0 125/300: dt: 0.9000, rms radial error=152.813, avgs=0 130/300: dt: 0.9000, rms radial error=151.959, avgs=0 135/300: dt: 0.9000, rms radial error=151.109, avgs=0 140/300: dt: 0.9000, rms radial error=150.264, avgs=0 145/300: dt: 0.9000, rms radial error=149.424, avgs=0 150/300: dt: 0.9000, rms radial error=148.588, avgs=0 155/300: dt: 0.9000, rms radial error=147.756, avgs=0 160/300: dt: 0.9000, rms radial error=146.929, avgs=0 165/300: dt: 0.9000, rms radial error=146.107, avgs=0 170/300: dt: 0.9000, rms radial error=145.289, avgs=0 175/300: dt: 0.9000, rms radial error=144.475, avgs=0 180/300: dt: 0.9000, rms radial error=143.666, avgs=0 185/300: dt: 0.9000, rms radial error=142.862, avgs=0 190/300: dt: 0.9000, rms radial error=142.062, avgs=0 195/300: dt: 0.9000, rms radial error=141.266, avgs=0 200/300: dt: 0.9000, rms radial error=140.474, avgs=0 205/300: dt: 0.9000, rms radial error=139.687, avgs=0 210/300: dt: 0.9000, rms radial error=138.904, avgs=0 215/300: dt: 0.9000, rms radial error=138.125, avgs=0 220/300: dt: 0.9000, rms radial error=137.351, avgs=0 225/300: dt: 0.9000, rms radial error=136.580, avgs=0 230/300: dt: 0.9000, rms radial error=135.814, avgs=0 235/300: dt: 0.9000, rms radial error=135.052, avgs=0 240/300: dt: 0.9000, rms radial error=134.294, avgs=0 245/300: dt: 0.9000, rms radial error=133.541, avgs=0 250/300: dt: 0.9000, rms radial error=132.792, avgs=0 255/300: dt: 0.9000, rms radial error=132.047, avgs=0 260/300: dt: 0.9000, rms radial error=131.306, avgs=0 265/300: dt: 0.9000, rms radial error=130.569, avgs=0 270/300: dt: 0.9000, rms radial error=129.835, avgs=0 275/300: dt: 0.9000, rms radial error=129.106, avgs=0 280/300: dt: 0.9000, rms radial error=128.381, avgs=0 285/300: dt: 0.9000, rms radial error=127.660, avgs=0 290/300: dt: 0.9000, rms radial error=126.943, avgs=0 295/300: dt: 0.9000, rms radial error=126.230, avgs=0 300/300: dt: 0.9000, rms radial error=125.521, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18083.22 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2994.95 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00051 epoch 3 (K=160.0), pass 1, starting sse = 395.76 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00682 epoch 4 (K=640.0), pass 1, starting sse = 96.46 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/14 = 0.01281 final distance error %26.88 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.22 hours mris_sphere utimesec 780.040873 mris_sphere stimesec 0.658999 mris_sphere ru_maxrss 203844 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 330138 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11192 mris_sphere ru_oublock 11172 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 58 mris_sphere ru_nivcsw 551 FSRUNTIME@ mris_sphere 0.2169 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Jun 17 05:10:16 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Jun 17 05:10:16 CEST 2019 /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Jun 17 05:10:16 CEST 2019 mris_fix_topology -rusage /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-3811ses-Session_baseline lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-96 (nv=157528, nf=315248, ne=472872, g=49) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 42563 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 22 defects to be corrected 0 vertices coincident reading input surface /scratch/vferrer/PD_ANALYSIS/FREESURFER_PPMI/sub-3811ses-Session_baseline/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5944 (-4.7972) -vertex loglikelihood: -6.4141 (-3.2071) -normal dot loglikelihood: -3.6181 (-3.6181) -quad curv loglikelihood: -6.1087 (-3.0544) Total Loglikelihood : -25.7353 CORRECTING DEFECT 0 (vertices=20853, convex hull=1865, v0=368) XL defect detected...