Mon Sep 30 17:44:06 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019 /usr/local/freesurfer/bin/recon-all -s KING_LUCAS_JAVIER_25-09-2019 -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 -all -parallel subjid KING_LUCAS_JAVIER_25-09-2019 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects 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 fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 4096 memorylocked 16384 kbytes maxproc 128196 maxlocks unlimited maxsignal 128196 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32866180 13676680 2708988 56360 16480512 18877676 Swap: 2097148 0 2097148 ######################################## 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: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/30-20:44:06-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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 ####################################### /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019 mri_convert /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig/001.mgz mri_convert.bin /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58... Starting DICOMRead2() dcmfile = /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 dcmdir = /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR Ref Series No = 4 Found 144 files, checking for dicoms Found 142 dicom files in series. First Sorting Computing Slice Direction Vs: 0.012 -0.041 1.0992 Vs: 0.0109088 -0.0372717 0.999246 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 142 ndcmfiles = 142 PE Dir = ROW (dicom read) Loading pixel data TR=8.27, TE=3.26, TI=450.00, flip angle=12.00 i_ras = (-0.99934, -0.0349, -0.00991) j_ras = (0.03451, -0.99872, 0.0369) k_ras = (-0.0109088, 0.0372717, 0.999246) writing to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Sep 30 17:44:09 -03 2019 Found 1 runs /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig/001.mgz /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/rawavg.mgz /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019 mri_convert /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/rawavg.mgz /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/rawavg.mgz /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/rawavg.mgz... TR=8.27, TE=3.26, TI=450.00, flip angle=12.00 i_ras = (-0.99934, -0.0349, -0.00991) j_ras = (0.03451, -0.99872, 0.0369) k_ras = (-0.0109088, 0.0372717, 0.999246) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig.mgz /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Sep 30 17:44:14 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Mon Sep 30 17:44:14 -03 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.29449 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29449/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29449/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.27, TE=3.26, TI=450.00, flip angle=12.00 i_ras = (-1, 1.10595e-09, 0) j_ras = (0, 0, -1) k_ras = (-1.07684e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.29449/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Sep 30 17:44:16 -03 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.29449/nu0.mnc ./tmp.mri_nu_correct.mni.29449/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29449/0/ -iterations 1000 -distance 50 [fisicos@fisicos-ub2:/usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/] [2019-09-30 17:44:16] 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.29449/0/ ./tmp.mri_nu_correct.mni.29449/nu0.mnc ./tmp.mri_nu_correct.mni.29449/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.000953585 mri_convert ./tmp.mri_nu_correct.mni.29449/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.29449/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.29449/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.10595e-09, 0) j_ras = (0, 0, -1) k_ras = (-1.07684e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Sep 30 17:44:39 -03 2019 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Sep 30 17:44:39 -03 2019 Ended at Mon Sep 30 17:44:54 -03 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Sep 30 17:44:56 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6928, pval=0.4932 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/transforms/talairach_avi.log TalAviQA: 0.98248 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Sep 30 17:44:56 -03 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Mon Sep 30 17:44:56 -03 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.29948 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29948/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29948/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.27, TE=3.26, TI=450.00, flip angle=12.00 i_ras = (-1, 1.10595e-09, 0) j_ras = (0, 0, -1) k_ras = (-1.07684e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.29948/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Sep 30 17:44:57 -03 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.29948/nu0.mnc ./tmp.mri_nu_correct.mni.29948/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29948/0/ [fisicos@fisicos-ub2:/usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/] [2019-09-30 17:44:57] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.29948/0/ ./tmp.mri_nu_correct.mni.29948/nu0.mnc ./tmp.mri_nu_correct.mni.29948/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 15 CV of field change: 0.000940238 -------------------------------------------------------- Iteration 2 Mon Sep 30 17:45:14 -03 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.29948/nu1.mnc ./tmp.mri_nu_correct.mni.29948/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.29948/1/ [fisicos@fisicos-ub2:/usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/] [2019-09-30 17:45:14] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.29948/1/ ./tmp.mri_nu_correct.mni.29948/nu1.mnc ./tmp.mri_nu_correct.mni.29948/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000945273 mri_binarize --i ./tmp.mri_nu_correct.mni.29948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29948/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.29948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29948/ones.mgz sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos input ./tmp.mri_nu_correct.mni.29948/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.29948/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.29948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29948/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.29948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29948/input.mean.dat sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 Loading ./tmp.mri_nu_correct.mni.29948/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.29948/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29948/ones.mgz --i ./tmp.mri_nu_correct.mni.29948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29948/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.29948/ones.mgz --i ./tmp.mri_nu_correct.mni.29948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29948/output.mean.dat sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 Loading ./tmp.mri_nu_correct.mni.29948/ones.mgz Loading ./tmp.mri_nu_correct.mni.29948/nu2.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.29948/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.29948/nu2.mnc ./tmp.mri_nu_correct.mni.29948/nu2.mnc mul .95947425414232750165 Saving result to './tmp.mri_nu_correct.mni.29948/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.29948/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.29948/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.29948/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.10595e-09, 0) j_ras = (0, 0, -1) k_ras = (-1.07684e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 3 seconds. mapping ( 6, 99) to ( 3, 110) Mon Sep 30 17:45:44 -03 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Sep 30 17:45:45 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 1.01528 0.03768 0.00891 3.07866; -0.04113 0.96125 0.10343 -43.42776; -0.00963 -0.07248 1.07652 -62.43872; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 22 Starting OpenSpline(): npoints = 22 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 73 (73), valley at 39 (39) csf peak at 37, setting threshold to 61 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 76 (76), valley at 39 (39) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 0 minutes and 55 seconds. #-------------------------------------------- #@# Skull Stripping Mon Sep 30 17:46:40 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_em_register -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 = 4 == 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=25.0 skull bounding box = (40, 51, 19) --> (211, 196, 232) using (97, 99, 126) as brain centroid... mean wm in atlas = 108, using box (76,81,100) --> (118, 116,152) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 110 +- 3.2 after smoothing, mri peak at 110, scaling input intensities by 0.982 scaling channel 0 by 0.981818 initial log_p = -4.276 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.245054 @ (0.000, 0.000, 0.000) max log p = -4.093009 @ (4.545, -4.545, -13.636) max log p = -3.984200 @ (-2.273, 2.273, 2.273) max log p = -3.953464 @ (-3.409, -1.136, -1.136) max log p = -3.930782 @ (0.568, -0.568, 0.568) max log p = -3.930782 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -4.0, -11.9): log p = -3.931 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.896, old_max_log_p =-3.931 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.07500 0.00000 -14.93864; 0.00000 0.00000 0.92500 -2.71770; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.896, old_max_log_p =-3.896 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.07500 0.00000 -14.93864; 0.00000 0.00000 0.92500 -2.71770; 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=-3.805, old_max_log_p =-3.896 (thresh=-3.9) 0.99894 0.03988 -0.02797 -0.82437; -0.03558 1.13489 0.03301 -19.46758; 0.03448 -0.03578 0.94061 -3.61052; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.805, old_max_log_p =-3.805 (thresh=-3.8) 1.01767 0.04063 -0.02850 -3.18123; -0.03625 1.15617 0.03363 -22.49835; 0.03448 -0.03578 0.94061 -3.61052; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.797, old_max_log_p =-3.805 (thresh=-3.8) 1.01402 0.03183 -0.03644 -1.42291; -0.02616 1.15331 0.07953 -28.50605; 0.04411 -0.09202 0.93427 2.57554; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.792, old_max_log_p =-3.797 (thresh=-3.8) 1.01023 0.02322 -0.04471 1.76936; -0.01717 1.15188 0.09444 -30.80517; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.790, old_max_log_p =-3.792 (thresh=-3.8) 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 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 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.790 (old=-4.276) transform before final EM align: 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 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 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.00905 0.02319 -0.04466 1.91362; -0.01710 1.14783 0.09411 -30.19751; 0.05287 -0.11074 0.93361 4.23049; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 523.124084 mri_em_register stimesec 0.943985 mri_em_register ru_maxrss 614544 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161777 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 27 mri_em_register ru_nivcsw 965 registration took 2 minutes and 30 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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=125 y=120 z=124 r=74 first estimation of the main basin volume: 1743871 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=106, y=93, z=89, Imax=255 CSF=21, 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=9394106668 voxels, voxel volume =1.000 = 9394106668 mmm3 = 9394106.368 cm3 done. PostAnalyze...Basin Prior 93 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=125,y=125, z=118, r=10457 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=51 , nb = 44703 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = -1069101665 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = 1094261351 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=55 , nb = -1064980418 LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=64 , nb = 1078481222 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = 1072729578 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 51, 46, 44, 71 after analyzing : 33, 46, 46, 52 RIGHT_CER before analyzing : 18, 28, 48, 80 after analyzing : 18, 41, 48, 50 LEFT_CER before analyzing : 26, 39, 54, 79 after analyzing : 26, 49, 54, 56 RIGHT_BRAIN before analyzing : 55, 47, 44, 70 after analyzing : 35, 47, 47, 52 LEFT_BRAIN before analyzing : 64, 50, 45, 71 after analyzing : 37, 50, 50, 55 OTHER before analyzing : 11, 42, 80, 91 after analyzing : 11, 67, 80, 73 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 74.141, std = 8.075 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.68, sigma = 3.75 after rotation: sse = 2.68, sigma = 3.75 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.79, its var is 3.24 before Erosion-Dilatation 0.12% of inacurate vertices after Erosion-Dilatation 0.00% 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...45 iterations mri_strip_skull: done peeling brain Brain Size = 1996227 voxels, voxel volume = 1.000 mm3 = 1996227 mmm3 = 1996.227 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 17.145212 mri_watershed stimesec 0.140468 mri_watershed ru_maxrss 841736 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 208817 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2992 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 3904 mri_watershed ru_nivcsw 28 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Sep 30 17:49:20 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_em_register -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 = 4 == 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=26.1 skull bounding box = (55, 59, 31) --> (196, 187, 215) using (102, 102, 123) as brain centroid... mean wm in atlas = 107, using box (85,86,100) --> (119, 117,145) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 110 +- 3.4 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 initial log_p = -4.003 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.952906 @ (0.000, 0.000, 0.000) max log p = -3.705983 @ (4.545, -4.545, -13.636) max log p = -3.514677 @ (-2.273, 2.273, 2.273) max log p = -3.482355 @ (-1.136, -1.136, -1.136) max log p = -3.466692 @ (-0.568, 1.705, -0.568) max log p = -3.466692 @ (0.000, 0.000, 0.000) Found translation: (0.6, -1.7, -13.1): log p = -3.467 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.387, old_max_log_p =-3.467 (thresh=-3.5) 1.00000 0.00000 0.00000 0.56818; 0.00000 1.07500 0.00000 -10.77914; 0.00000 0.00000 0.92500 -4.17974; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.387, old_max_log_p =-3.387 (thresh=-3.4) 1.00000 0.00000 0.00000 0.56818; 0.00000 1.07500 0.00000 -10.77914; 0.00000 0.00000 0.92500 -4.17974; 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=-3.258, old_max_log_p =-3.387 (thresh=-3.4) 0.98072 -0.03422 -0.00388 7.71989; 0.03211 1.04526 0.11841 -27.05927; 0.00000 -0.14295 0.93428 14.14086; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.256, old_max_log_p =-3.258 (thresh=-3.3) 0.99911 -0.03486 -0.00395 5.48833; 0.03211 1.04526 0.11841 -27.05927; 0.00000 -0.14295 0.93428 14.14086; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.249, old_max_log_p =-3.256 (thresh=-3.3) 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04437 0.11161 -23.47519; 0.01695 -0.13578 0.93716 11.27987; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.248, old_max_log_p =-3.249 (thresh=-3.2) 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.248 (old=-4.003) transform before final EM align: 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 366.672050 mri_em_register stimesec 1.607930 mri_em_register ru_maxrss 604160 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 166548 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 42 mri_em_register ru_nivcsw 6240 registration took 1 minutes and 43 seconds. #-------------------------------------- #@# CA Normalize Mon Sep 30 17:51:04 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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=26.1 skull bounding box = (55, 59, 31) --> (196, 187, 215) using (102, 102, 123) as brain centroid... mean wm in atlas = 107, using box (85,86,100) --> (119, 117,145) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 110 +- 3.4 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 using 246344 sample points... INFO: compute sample coordinates transform 0.99949 0.00134 -0.01585 1.90902; -0.00031 1.04315 0.11148 -23.30789; 0.01693 -0.13563 0.93606 11.39022; 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 (125, 60, 33) --> (192, 172, 211) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 12 of 9197 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 62, 33) --> (128, 172, 211) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 5 of 8999 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 146, 61) --> (175, 186, 119) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 514 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 146, 59) --> (125, 185, 121) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 370 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 135, 100) --> (144, 202, 131) Brain_Stem: limiting intensities to 91.0 --> 132.0 1 of 982 (0.1%) samples deleted using 20062 total control points for intensity normalization... bias field = 0.974 +- 0.069 69 of 20044 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 60, 33) --> (192, 172, 211) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 21 of 9267 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 62, 33) --> (128, 172, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 9109 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 146, 61) --> (175, 186, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 539 (3.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 146, 59) --> (125, 185, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 404 (5.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 135, 100) --> (144, 202, 131) Brain_Stem: limiting intensities to 88.0 --> 132.0 45 of 1039 (4.3%) samples deleted using 20358 total control points for intensity normalization... bias field = 1.021 +- 0.051 75 of 20179 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 60, 33) --> (192, 172, 211) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 22 of 9272 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 62, 33) --> (128, 172, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 9099 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 146, 61) --> (175, 186, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 110 of 551 (20.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 146, 59) --> (125, 185, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 111 of 423 (26.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 135, 100) --> (144, 202, 131) Brain_Stem: limiting intensities to 88.0 --> 132.0 245 of 1036 (23.6%) samples deleted using 20381 total control points for intensity normalization... bias field = 1.018 +- 0.040 68 of 19752 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 43 seconds. #-------------------------------------- #@# CA Reg Mon Sep 30 17:51:46 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 = 4 == 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) = 0.99 (predicted orig area = 8.1) 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=0.812, neg=0, invalid=762 0001: dt=129.472000, rms=0.758 (6.727%), neg=0, invalid=762 0002: dt=327.689046, rms=0.730 (3.610%), neg=0, invalid=762 0003: dt=188.235294, rms=0.724 (0.897%), neg=0, invalid=762 0004: dt=369.920000, rms=0.717 (0.954%), neg=0, invalid=762 0005: dt=129.472000, rms=0.714 (0.390%), neg=0, invalid=762 0006: dt=1183.744000, rms=0.705 (1.287%), neg=0, invalid=762 0007: dt=110.976000, rms=0.703 (0.275%), neg=0, invalid=762 0008: dt=1479.680000, rms=0.698 (0.714%), neg=0, invalid=762 0009: dt=295.936000, rms=0.694 (0.531%), neg=0, invalid=762 0010: dt=129.472000, rms=0.694 (0.079%), neg=0, invalid=762 0011: dt=129.472000, rms=0.693 (0.076%), neg=0, invalid=762 0012: dt=129.472000, rms=0.692 (0.120%), neg=0, invalid=762 0013: dt=129.472000, rms=0.691 (0.161%), neg=0, invalid=762 0014: dt=129.472000, rms=0.690 (0.185%), neg=0, invalid=762 0015: dt=129.472000, rms=0.689 (0.177%), neg=0, invalid=762 0016: dt=129.472000, rms=0.688 (0.172%), neg=0, invalid=762 0017: dt=129.472000, rms=0.686 (0.180%), neg=0, invalid=762 0018: dt=129.472000, rms=0.685 (0.184%), neg=0, invalid=762 0019: dt=129.472000, rms=0.684 (0.169%), neg=0, invalid=762 0020: dt=129.472000, rms=0.683 (0.160%), neg=0, invalid=762 0021: dt=129.472000, rms=0.682 (0.133%), neg=0, invalid=762 0022: dt=129.472000, rms=0.681 (0.136%), neg=0, invalid=762 0023: dt=129.472000, rms=0.680 (0.145%), neg=0, invalid=762 0024: dt=129.472000, rms=0.679 (0.146%), neg=0, invalid=762 0025: dt=129.472000, rms=0.678 (0.122%), neg=0, invalid=762 0026: dt=129.472000, rms=0.678 (0.090%), neg=0, invalid=762 0027: dt=887.808000, rms=0.677 (0.079%), neg=0, invalid=762 0028: dt=887.808000, rms=0.677 (-1.672%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0029: dt=129.472000, rms=0.677 (0.154%), neg=0, invalid=762 0030: dt=129.472000, rms=0.676 (0.016%), neg=0, invalid=762 0031: dt=129.472000, rms=0.676 (0.023%), neg=0, invalid=762 0032: dt=129.472000, rms=0.676 (0.022%), neg=0, invalid=762 0033: dt=129.472000, rms=0.676 (0.038%), neg=0, invalid=762 0034: dt=129.472000, rms=0.676 (0.053%), neg=0, invalid=762 0035: dt=129.472000, rms=0.675 (0.075%), neg=0, invalid=762 0036: dt=129.472000, rms=0.675 (0.071%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0037: dt=145.152000, rms=0.672 (1.134%), neg=0, invalid=762 0038: dt=275.461988, rms=0.661 (1.617%), neg=0, invalid=762 0039: dt=62.978723, rms=0.656 (0.786%), neg=0, invalid=762 0040: dt=145.152000, rms=0.653 (0.453%), neg=0, invalid=762 0041: dt=124.416000, rms=0.651 (0.267%), neg=0, invalid=762 0042: dt=124.416000, rms=0.648 (0.454%), neg=0, invalid=762 0043: dt=36.288000, rms=0.648 (0.121%), neg=0, invalid=762 0044: dt=36.288000, rms=0.647 (0.085%), neg=0, invalid=762 0045: dt=36.288000, rms=0.646 (0.136%), neg=0, invalid=762 0046: dt=36.288000, rms=0.645 (0.208%), neg=0, invalid=762 0047: dt=36.288000, rms=0.643 (0.279%), neg=0, invalid=762 0048: dt=36.288000, rms=0.641 (0.313%), neg=0, invalid=762 0049: dt=36.288000, rms=0.639 (0.300%), neg=0, invalid=762 0050: dt=36.288000, rms=0.637 (0.289%), neg=0, invalid=762 0051: dt=36.288000, rms=0.636 (0.272%), neg=0, invalid=762 0052: dt=36.288000, rms=0.634 (0.259%), neg=0, invalid=762 0053: dt=36.288000, rms=0.632 (0.247%), neg=0, invalid=762 0054: dt=36.288000, rms=0.631 (0.235%), neg=0, invalid=762 0055: dt=36.288000, rms=0.630 (0.219%), neg=0, invalid=762 0056: dt=36.288000, rms=0.628 (0.206%), neg=0, invalid=762 0057: dt=36.288000, rms=0.627 (0.180%), neg=0, invalid=762 0058: dt=36.288000, rms=0.626 (0.158%), neg=0, invalid=762 0059: dt=36.288000, rms=0.625 (0.140%), neg=0, invalid=762 0060: dt=36.288000, rms=0.624 (0.128%), neg=0, invalid=762 0061: dt=36.288000, rms=0.624 (0.133%), neg=0, invalid=762 0062: dt=36.288000, rms=0.623 (0.127%), neg=0, invalid=762 0063: dt=36.288000, rms=0.622 (0.118%), neg=0, invalid=762 0064: dt=36.288000, rms=0.621 (0.098%), neg=0, invalid=762 0065: dt=31.104000, rms=0.621 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0066: dt=36.288000, rms=0.621 (0.179%), neg=0, invalid=762 0067: dt=36.288000, rms=0.621 (0.031%), neg=0, invalid=762 0068: dt=36.288000, rms=0.621 (0.028%), neg=0, invalid=762 0069: dt=36.288000, rms=0.620 (0.032%), neg=0, invalid=762 0070: dt=36.288000, rms=0.620 (0.030%), neg=0, invalid=762 0071: dt=36.288000, rms=0.620 (0.044%), neg=0, invalid=762 0072: dt=36.288000, rms=0.620 (0.054%), neg=0, invalid=762 0073: dt=36.288000, rms=0.619 (0.066%), neg=0, invalid=762 0074: dt=36.288000, rms=0.619 (0.069%), neg=0, invalid=762 0075: dt=36.288000, rms=0.618 (0.050%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.641, neg=0, invalid=762 0076: dt=8.000000, rms=0.640 (0.190%), neg=0, invalid=762 0077: dt=2.800000, rms=0.640 (0.012%), neg=0, invalid=762 0078: dt=2.800000, rms=0.640 (0.002%), neg=0, invalid=762 0079: dt=2.800000, rms=0.640 (-0.021%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=762 0080: dt=0.000000, rms=0.640 (0.090%), neg=0, invalid=762 0081: dt=0.000000, rms=0.640 (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=0.697, neg=0, invalid=762 0082: dt=5.888889, rms=0.681 (2.300%), neg=0, invalid=762 0083: dt=3.371429, rms=0.680 (0.105%), neg=0, invalid=762 0084: dt=3.371429, rms=0.680 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=762 0085: dt=0.000000, rms=0.680 (0.079%), neg=0, invalid=762 0086: dt=0.000000, rms=0.680 (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=0.736, neg=0, invalid=762 0087: dt=0.768000, rms=0.734 (0.267%), neg=0, invalid=762 0088: dt=1.792000, rms=0.731 (0.383%), neg=0, invalid=762 0089: dt=3.125307, rms=0.727 (0.526%), neg=0, invalid=762 0090: dt=0.448000, rms=0.727 (0.028%), neg=0, invalid=762 0091: dt=0.448000, rms=0.727 (0.007%), neg=0, invalid=762 0092: dt=0.448000, rms=0.727 (0.004%), neg=0, invalid=762 0093: dt=0.448000, rms=0.727 (0.015%), neg=0, invalid=762 0094: dt=0.448000, rms=0.727 (0.029%), neg=0, invalid=762 0095: dt=0.448000, rms=0.727 (0.015%), neg=0, invalid=762 0096: dt=4.096000, rms=0.726 (0.146%), neg=0, invalid=762 0097: dt=0.000000, rms=0.726 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.726, neg=0, invalid=762 0098: dt=0.448000, rms=0.725 (0.097%), neg=0, invalid=762 0099: dt=0.192000, rms=0.725 (0.000%), neg=0, invalid=762 0100: dt=0.192000, rms=0.725 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.698, neg=0, invalid=762 0101: dt=0.820717, rms=0.681 (2.457%), neg=0, invalid=762 0102: dt=0.080000, rms=0.680 (0.133%), neg=0, invalid=762 0103: dt=0.080000, rms=0.680 (-0.072%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0104: dt=0.028000, rms=0.680 (0.094%), neg=0, invalid=762 0105: dt=0.007000, rms=0.680 (0.001%), neg=0, invalid=762 0106: dt=0.007000, rms=0.680 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.17170 (29) Left_Lateral_Ventricle (4): linear fit = 1.63 x + 0.0 (1884 voxels, overlap=0.274) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1884 voxels, peak = 33), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.18012 (31) Right_Lateral_Ventricle (43): linear fit = 1.90 x + 0.0 (1864 voxels, overlap=0.065) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1864 voxels, peak = 30), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.08639 (99) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (1308 voxels, overlap=0.785) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (1308 voxels, peak = 104), gca=104.2 gca peak = 0.20183 (93) mri peak = 0.07366 (102) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1163 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1163 voxels, peak = 95), gca=95.3 gca peak = 0.21683 (55) mri peak = 0.06951 (66) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (1541 voxels, overlap=0.024) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (1541 voxels, peak = 65), gca=65.2 gca peak = 0.30730 (58) mri peak = 0.09233 (70) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (1474 voxels, overlap=0.015) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (1474 voxels, peak = 69), gca=68.7 gca peak = 0.11430 (101) mri peak = 0.15768 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (88566 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (88566 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.15728 (106) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (92148 voxels, overlap=0.510) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (92148 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03932 (71) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (45114 voxels, overlap=0.285) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (45114 voxels, peak = 71), gca=70.5 gca peak = 0.15082 (58) mri peak = 0.04246 (71) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (51738 voxels, overlap=0.385) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (51738 voxels, peak = 68), gca=67.6 gca peak = 0.14161 (67) mri peak = 0.10549 (73) Right_Caudate (50): linear fit = 1.12 x + 0.0 (938 voxels, overlap=0.333) Right_Caudate (50): linear fit = 1.12 x + 0.0 (938 voxels, peak = 75), gca=75.4 gca peak = 0.15243 (71) mri peak = 0.07543 (89) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1470 voxels, overlap=0.106) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1470 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.04747 (65) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (31700 voxels, overlap=0.086) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (31700 voxels, peak = 68), gca=67.5 gca peak = 0.13252 (56) mri peak = 0.04314 (68) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (40252 voxels, overlap=0.036) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (40252 voxels, peak = 67), gca=67.5 gca peak = 0.18181 (84) mri peak = 0.07089 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (12630 voxels, overlap=0.253) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (12630 voxels, peak = 91), gca=91.1 gca peak = 0.20573 (83) mri peak = 0.06292 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (10633 voxels, overlap=0.458) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (10633 voxels, peak = 89), gca=89.2 gca peak = 0.21969 (57) mri peak = 0.10297 (69) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (616 voxels, overlap=0.041) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (616 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 0.18130 (67) Right_Amygdala (54): linear fit = 1.17 x + 0.0 (722 voxels, overlap=0.004) Right_Amygdala (54): linear fit = 1.17 x + 0.0 (722 voxels, peak = 66), gca=65.8 gca peak = 0.14181 (85) mri peak = 0.06661 (95) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (7035 voxels, overlap=0.340) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (7035 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.06552 (96) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5208 voxels, overlap=0.740) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5208 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.05664 (84) Left_Putamen (12): linear fit = 1.10 x + 0.0 (3213 voxels, overlap=0.604) Left_Putamen (12): linear fit = 1.10 x + 0.0 (3213 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.05909 (89) Right_Putamen (51): linear fit = 1.14 x + 0.0 (3314 voxels, overlap=0.764) Right_Putamen (51): linear fit = 1.14 x + 0.0 (3314 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.10258 (91) Brain_Stem (16): linear fit = 1.13 x + 0.0 (15157 voxels, overlap=0.203) Brain_Stem (16): linear fit = 1.13 x + 0.0 (15157 voxels, peak = 91), gca=90.8 gca peak = 0.13281 (86) mri peak = 0.13004 (99) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1620 voxels, overlap=0.017) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1620 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.11227 (99) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (2025 voxels, overlap=0.088) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (2025 voxels, peak = 98), gca=98.3 gca peak = 0.20494 (23) mri peak = 0.50000 (42) Third_Ventricle (14): linear fit = 1.76 x + 0.0 (94 voxels, overlap=1.996) Third_Ventricle (14): linear fit = 1.76 x + 0.0 (94 voxels, peak = 41), gca=40.6 gca peak = 0.15061 (21) mri peak = 0.29386 (24) Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (751 voxels, overlap=0.246) Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (751 voxels, peak = 30), gca=29.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak 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 1.18 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.47 x + 0.0 Right_Pallidum too bright - rescaling by 0.978 (from 1.085) to 101.9 (was 104.2) 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=0.670, neg=0, invalid=762 0107: dt=129.472000, rms=0.660 (1.489%), neg=0, invalid=762 0108: dt=443.904000, rms=0.653 (1.173%), neg=0, invalid=762 0109: dt=165.415385, rms=0.649 (0.617%), neg=0, invalid=762 0110: dt=129.472000, rms=0.647 (0.180%), neg=0, invalid=762 0111: dt=887.808000, rms=0.643 (0.749%), neg=0, invalid=762 0112: dt=73.984000, rms=0.642 (0.148%), neg=0, invalid=762 0113: dt=110.976000, rms=0.641 (0.037%), neg=0, invalid=762 0114: dt=110.976000, rms=0.641 (0.068%), neg=0, invalid=762 0115: dt=110.976000, rms=0.640 (0.107%), neg=0, invalid=762 0116: dt=110.976000, rms=0.639 (0.132%), neg=0, invalid=762 0117: dt=110.976000, rms=0.638 (0.153%), neg=0, invalid=762 0118: dt=110.976000, rms=0.637 (0.178%), neg=0, invalid=762 0119: dt=110.976000, rms=0.636 (0.177%), neg=0, invalid=762 0120: dt=110.976000, rms=0.635 (0.167%), neg=0, invalid=762 0121: dt=110.976000, rms=0.634 (0.151%), neg=0, invalid=762 0122: dt=110.976000, rms=0.633 (0.155%), neg=0, invalid=762 0123: dt=110.976000, rms=0.632 (0.147%), neg=0, invalid=762 0124: dt=110.976000, rms=0.631 (0.146%), neg=0, invalid=762 0125: dt=110.976000, rms=0.630 (0.144%), neg=0, invalid=762 0126: dt=110.976000, rms=0.629 (0.147%), neg=0, invalid=762 0127: dt=110.976000, rms=0.629 (0.146%), neg=0, invalid=762 0128: dt=110.976000, rms=0.628 (0.147%), neg=0, invalid=762 0129: dt=110.976000, rms=0.627 (0.145%), neg=0, invalid=762 0130: dt=110.976000, rms=0.626 (0.148%), neg=0, invalid=762 0131: dt=110.976000, rms=0.625 (0.131%), neg=0, invalid=762 0132: dt=110.976000, rms=0.624 (0.108%), neg=0, invalid=762 0133: dt=110.976000, rms=0.624 (0.083%), neg=0, invalid=762 0134: dt=110.976000, rms=0.623 (0.078%), neg=0, invalid=762 0135: dt=110.976000, rms=0.623 (0.085%), neg=0, invalid=762 0136: dt=110.976000, rms=0.622 (0.089%), neg=0, invalid=762 0137: dt=110.976000, rms=0.622 (0.086%), neg=0, invalid=762 0138: dt=110.976000, rms=0.621 (0.075%), neg=0, invalid=762 0139: dt=110.976000, rms=0.621 (0.063%), neg=0, invalid=762 0140: dt=110.976000, rms=0.620 (0.064%), neg=0, invalid=762 0141: dt=110.976000, rms=0.620 (0.069%), neg=0, invalid=762 0142: dt=110.976000, rms=0.620 (0.064%), neg=0, invalid=762 0143: dt=110.976000, rms=0.619 (0.051%), neg=0, invalid=762 0144: dt=110.976000, rms=0.619 (0.044%), neg=0, invalid=762 0145: dt=110.976000, rms=0.619 (0.047%), neg=0, invalid=762 0146: dt=110.976000, rms=0.618 (0.050%), neg=0, invalid=762 0147: dt=110.976000, rms=0.618 (0.051%), neg=0, invalid=762 0148: dt=110.976000, rms=0.618 (0.049%), neg=0, invalid=762 0149: dt=110.976000, rms=0.618 (0.046%), neg=0, invalid=762 0150: dt=110.976000, rms=0.617 (0.046%), neg=0, invalid=762 0151: dt=110.976000, rms=0.617 (0.049%), neg=0, invalid=762 0152: dt=110.976000, rms=0.617 (0.046%), neg=0, invalid=762 0153: dt=110.976000, rms=0.616 (0.043%), neg=0, invalid=762 0154: dt=110.976000, rms=0.616 (0.040%), neg=0, invalid=762 0155: dt=110.976000, rms=0.616 (0.042%), neg=0, invalid=762 0156: dt=110.976000, rms=0.616 (0.044%), neg=0, invalid=762 0157: dt=110.976000, rms=0.615 (0.039%), neg=0, invalid=762 0158: dt=110.976000, rms=0.615 (0.035%), neg=0, invalid=762 0159: dt=110.976000, rms=0.615 (0.034%), neg=0, invalid=762 0160: dt=110.976000, rms=0.615 (0.034%), neg=0, invalid=762 0161: dt=110.976000, rms=0.615 (0.035%), neg=0, invalid=762 0162: dt=110.976000, rms=0.614 (0.036%), neg=0, invalid=762 0163: dt=110.976000, rms=0.614 (0.034%), neg=0, invalid=762 0164: dt=110.976000, rms=0.614 (0.029%), neg=0, invalid=762 0165: dt=110.976000, rms=0.614 (0.030%), neg=0, invalid=762 0166: dt=110.976000, rms=0.614 (0.034%), neg=0, invalid=762 0167: dt=110.976000, rms=0.613 (0.035%), neg=0, invalid=762 0168: dt=110.976000, rms=0.613 (0.029%), neg=0, invalid=762 0169: dt=110.976000, rms=0.613 (0.022%), neg=0, invalid=762 0170: dt=110.976000, rms=0.613 (0.019%), neg=0, invalid=762 0171: dt=1775.616000, rms=0.612 (0.082%), neg=0, invalid=762 0172: dt=23.120000, rms=0.612 (-0.002%), neg=0, invalid=762 0173: dt=23.120000, rms=0.612 (0.003%), neg=0, invalid=762 0174: dt=23.120000, rms=0.612 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0175: dt=6.936000, rms=0.612 (0.046%), neg=0, invalid=762 0176: dt=2.023000, rms=0.612 (0.001%), neg=0, invalid=762 0177: dt=2.023000, rms=0.612 (0.000%), neg=0, invalid=762 0178: dt=2.023000, rms=0.612 (-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=0.614, neg=0, invalid=762 0179: dt=248.832000, rms=0.607 (1.127%), neg=0, invalid=762 0180: dt=81.441109, rms=0.602 (0.908%), neg=0, invalid=762 0181: dt=78.295533, rms=0.600 (0.290%), neg=0, invalid=762 0182: dt=145.152000, rms=0.596 (0.570%), neg=0, invalid=762 0183: dt=36.288000, rms=0.595 (0.199%), neg=0, invalid=762 0184: dt=145.152000, rms=0.593 (0.345%), neg=0, invalid=762 0185: dt=110.169154, rms=0.591 (0.392%), neg=0, invalid=762 0186: dt=36.288000, rms=0.590 (0.131%), neg=0, invalid=762 0187: dt=145.152000, rms=0.589 (0.256%), neg=0, invalid=762 0188: dt=112.000000, rms=0.587 (0.329%), neg=0, invalid=762 0189: dt=36.288000, rms=0.586 (0.111%), neg=0, invalid=762 0190: dt=145.152000, rms=0.585 (0.183%), neg=0, invalid=762 0191: dt=111.888112, rms=0.583 (0.292%), neg=0, invalid=762 0192: dt=36.288000, rms=0.583 (0.089%), neg=0, invalid=762 0193: dt=145.152000, rms=0.582 (0.157%), neg=0, invalid=762 0194: dt=103.680000, rms=0.580 (0.269%), neg=0, invalid=762 0195: dt=36.288000, rms=0.580 (0.061%), neg=0, invalid=762 0196: dt=145.152000, rms=0.579 (0.140%), neg=0, invalid=762 0197: dt=124.416000, rms=0.578 (0.235%), neg=0, invalid=762 0198: dt=36.288000, rms=0.577 (0.059%), neg=0, invalid=762 0199: dt=145.152000, rms=0.577 (0.097%), neg=0, invalid=762 0200: dt=103.680000, rms=0.576 (0.208%), neg=0, invalid=762 0201: dt=36.288000, rms=0.575 (0.039%), neg=0, invalid=762 0202: dt=36.288000, rms=0.575 (0.044%), neg=0, invalid=762 0203: dt=36.288000, rms=0.575 (0.067%), neg=0, invalid=762 0204: dt=36.288000, rms=0.574 (0.108%), neg=0, invalid=762 0205: dt=36.288000, rms=0.573 (0.144%), neg=0, invalid=762 0206: dt=36.288000, rms=0.572 (0.164%), neg=0, invalid=762 0207: dt=36.288000, rms=0.571 (0.173%), neg=0, invalid=762 0208: dt=36.288000, rms=0.570 (0.176%), neg=0, invalid=762 0209: dt=36.288000, rms=0.569 (0.177%), neg=0, invalid=762 0210: dt=36.288000, rms=0.568 (0.180%), neg=0, invalid=762 0211: dt=36.288000, rms=0.567 (0.181%), neg=0, invalid=762 0212: dt=36.288000, rms=0.566 (0.181%), neg=0, invalid=762 0213: dt=36.288000, rms=0.565 (0.171%), neg=0, invalid=762 0214: dt=36.288000, rms=0.564 (0.163%), neg=0, invalid=762 0215: dt=36.288000, rms=0.563 (0.150%), neg=0, invalid=762 0216: dt=36.288000, rms=0.563 (0.142%), neg=0, invalid=762 0217: dt=36.288000, rms=0.562 (0.134%), neg=0, invalid=762 0218: dt=36.288000, rms=0.561 (0.131%), neg=0, invalid=762 0219: dt=36.288000, rms=0.560 (0.127%), neg=0, invalid=762 0220: dt=36.288000, rms=0.560 (0.121%), neg=0, invalid=762 0221: dt=36.288000, rms=0.559 (0.121%), neg=0, invalid=762 0222: dt=36.288000, rms=0.558 (0.112%), neg=0, invalid=762 0223: dt=36.288000, rms=0.558 (0.112%), neg=0, invalid=762 0224: dt=36.288000, rms=0.557 (0.107%), neg=0, invalid=762 0225: dt=36.288000, rms=0.557 (0.103%), neg=0, invalid=762 0226: dt=36.288000, rms=0.556 (0.096%), neg=0, invalid=762 0227: dt=36.288000, rms=0.556 (0.092%), neg=0, invalid=762 0228: dt=36.288000, rms=0.555 (0.089%), neg=0, invalid=762 0229: dt=36.288000, rms=0.555 (0.086%), neg=0, invalid=762 0230: dt=36.288000, rms=0.554 (0.083%), neg=0, invalid=762 0231: dt=36.288000, rms=0.554 (0.082%), neg=0, invalid=762 0232: dt=36.288000, rms=0.553 (0.081%), neg=0, invalid=762 0233: dt=36.288000, rms=0.553 (0.079%), neg=0, invalid=762 0234: dt=36.288000, rms=0.552 (0.076%), neg=0, invalid=762 0235: dt=36.288000, rms=0.552 (0.073%), neg=0, invalid=762 0236: dt=36.288000, rms=0.552 (0.067%), neg=0, invalid=762 0237: dt=36.288000, rms=0.551 (0.065%), neg=0, invalid=762 0238: dt=36.288000, rms=0.551 (0.057%), neg=0, invalid=762 0239: dt=36.288000, rms=0.551 (0.053%), neg=0, invalid=762 0240: dt=36.288000, rms=0.550 (0.056%), neg=0, invalid=762 0241: dt=36.288000, rms=0.550 (0.055%), neg=0, invalid=762 0242: dt=36.288000, rms=0.550 (0.055%), neg=0, invalid=762 0243: dt=36.288000, rms=0.549 (0.054%), neg=0, invalid=762 0244: dt=36.288000, rms=0.549 (0.050%), neg=0, invalid=762 0245: dt=36.288000, rms=0.549 (0.051%), neg=0, invalid=762 0246: dt=36.288000, rms=0.549 (0.048%), neg=0, invalid=762 0247: dt=36.288000, rms=0.548 (0.051%), neg=0, invalid=762 0248: dt=36.288000, rms=0.548 (0.049%), neg=0, invalid=762 0249: dt=36.288000, rms=0.548 (0.049%), neg=0, invalid=762 0250: dt=36.288000, rms=0.548 (0.047%), neg=0, invalid=762 0251: dt=36.288000, rms=0.547 (0.047%), neg=0, invalid=762 0252: dt=36.288000, rms=0.547 (0.045%), neg=0, invalid=762 0253: dt=36.288000, rms=0.547 (0.039%), neg=0, invalid=762 0254: dt=36.288000, rms=0.547 (0.040%), neg=0, invalid=762 0255: dt=36.288000, rms=0.546 (0.038%), neg=0, invalid=762 0256: dt=36.288000, rms=0.546 (0.039%), neg=0, invalid=762 0257: dt=36.288000, rms=0.546 (0.036%), neg=0, invalid=762 0258: dt=36.288000, rms=0.546 (0.036%), neg=0, invalid=762 0259: dt=36.288000, rms=0.546 (0.033%), neg=0, invalid=762 0260: dt=36.288000, rms=0.545 (0.034%), neg=0, invalid=762 0261: dt=36.288000, rms=0.545 (0.033%), neg=0, invalid=762 0262: dt=36.288000, rms=0.545 (0.033%), neg=0, invalid=762 0263: dt=36.288000, rms=0.545 (0.030%), neg=0, invalid=762 0264: dt=36.288000, rms=0.545 (0.029%), neg=0, invalid=762 0265: dt=36.288000, rms=0.545 (0.029%), neg=0, invalid=762 0266: dt=36.288000, rms=0.544 (0.030%), neg=0, invalid=762 0267: dt=36.288000, rms=0.544 (0.030%), neg=0, invalid=762 0268: dt=36.288000, rms=0.544 (0.028%), neg=0, invalid=762 0269: dt=36.288000, rms=0.544 (0.026%), neg=0, invalid=762 0270: dt=36.288000, rms=0.544 (0.025%), neg=0, invalid=762 0271: dt=36.288000, rms=0.544 (0.024%), neg=0, invalid=762 0272: dt=36.288000, rms=0.544 (0.024%), neg=0, invalid=762 0273: dt=580.608000, rms=0.543 (0.018%), neg=0, invalid=762 0274: dt=580.608000, rms=0.543 (-0.544%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=762 0275: dt=103.680000, rms=0.542 (0.306%), neg=0, invalid=762 0276: dt=124.416000, rms=0.542 (0.127%), neg=0, invalid=762 0277: dt=62.208000, rms=0.541 (0.088%), neg=0, invalid=762 0278: dt=82.944000, rms=0.541 (0.025%), neg=0, invalid=762 0279: dt=82.944000, rms=0.541 (0.066%), neg=0, invalid=762 0280: dt=82.944000, rms=0.540 (0.074%), neg=0, invalid=762 0281: dt=82.944000, rms=0.540 (0.066%), neg=0, invalid=762 0282: dt=82.944000, rms=0.539 (0.093%), neg=0, invalid=762 0283: dt=82.944000, rms=0.539 (0.073%), neg=0, invalid=762 0284: dt=82.944000, rms=0.539 (0.047%), neg=0, invalid=762 0285: dt=82.944000, rms=0.539 (0.031%), neg=0, invalid=762 0286: dt=82.944000, rms=0.538 (0.068%), neg=0, invalid=762 0287: dt=82.944000, rms=0.538 (0.062%), neg=0, invalid=762 0288: dt=82.944000, rms=0.538 (0.054%), neg=0, invalid=762 0289: dt=82.944000, rms=0.537 (0.046%), neg=0, invalid=762 0290: dt=82.944000, rms=0.537 (0.059%), neg=0, invalid=762 0291: dt=82.944000, rms=0.537 (0.056%), neg=0, invalid=762 0292: dt=82.944000, rms=0.536 (0.057%), neg=0, invalid=762 0293: dt=82.944000, rms=0.536 (0.051%), neg=0, invalid=762 0294: dt=82.944000, rms=0.536 (0.048%), neg=0, invalid=762 0295: dt=82.944000, rms=0.536 (0.043%), neg=0, invalid=762 0296: dt=82.944000, rms=0.535 (0.040%), neg=0, invalid=762 0297: dt=82.944000, rms=0.535 (0.044%), neg=0, invalid=762 0298: dt=82.944000, rms=0.535 (0.048%), neg=0, invalid=762 0299: dt=82.944000, rms=0.535 (0.044%), neg=0, invalid=762 0300: dt=82.944000, rms=0.534 (0.046%), neg=0, invalid=762 0301: dt=82.944000, rms=0.534 (0.056%), neg=0, invalid=762 0302: dt=82.944000, rms=0.534 (0.053%), neg=0, invalid=762 0303: dt=82.944000, rms=0.534 (0.047%), neg=0, invalid=762 0304: dt=82.944000, rms=0.533 (0.042%), neg=0, invalid=762 0305: dt=82.944000, rms=0.533 (0.048%), neg=0, invalid=762 0306: dt=82.944000, rms=0.533 (0.048%), neg=0, invalid=762 0307: dt=82.944000, rms=0.533 (0.045%), neg=0, invalid=762 0308: dt=82.944000, rms=0.532 (0.041%), neg=0, invalid=762 0309: dt=82.944000, rms=0.532 (0.037%), neg=0, invalid=762 0310: dt=82.944000, rms=0.532 (0.032%), neg=0, invalid=762 0311: dt=82.944000, rms=0.532 (0.030%), neg=0, invalid=762 0312: dt=82.944000, rms=0.532 (0.032%), neg=0, invalid=762 0313: dt=82.944000, rms=0.532 (0.028%), neg=0, invalid=762 0314: dt=82.944000, rms=0.531 (0.026%), neg=0, invalid=762 0315: dt=82.944000, rms=0.531 (0.029%), neg=0, invalid=762 0316: dt=82.944000, rms=0.531 (0.035%), neg=0, invalid=762 0317: dt=82.944000, rms=0.531 (0.031%), neg=0, invalid=762 0318: dt=82.944000, rms=0.531 (0.028%), neg=0, invalid=762 0319: dt=82.944000, rms=0.531 (0.029%), neg=0, invalid=762 0320: dt=82.944000, rms=0.530 (0.030%), neg=0, invalid=762 0321: dt=82.944000, rms=0.530 (0.028%), neg=0, invalid=762 0322: dt=82.944000, rms=0.530 (0.023%), neg=0, invalid=762 0323: dt=82.944000, rms=0.530 (0.024%), neg=0, invalid=762 0324: dt=82.944000, rms=0.530 (0.025%), neg=0, invalid=762 0325: dt=82.944000, rms=0.530 (0.024%), neg=0, invalid=762 0326: dt=82.944000, rms=0.530 (0.027%), neg=0, invalid=762 0327: dt=82.944000, rms=0.529 (0.029%), neg=0, invalid=762 0328: dt=82.944000, rms=0.529 (0.024%), neg=0, invalid=762 0329: dt=82.944000, rms=0.529 (0.019%), neg=0, invalid=762 0330: dt=145.152000, rms=0.529 (0.010%), neg=0, invalid=762 0331: dt=145.152000, rms=0.529 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.540, neg=0, invalid=762 0332: dt=23.405714, rms=0.539 (0.202%), neg=0, invalid=762 0333: dt=25.600000, rms=0.539 (0.071%), neg=0, invalid=762 0334: dt=44.800000, rms=0.538 (0.122%), neg=0, invalid=762 0335: dt=179.200000, rms=0.535 (0.590%), neg=0, invalid=762 0336: dt=44.800000, rms=0.533 (0.331%), neg=0, invalid=762 0337: dt=44.800000, rms=0.531 (0.315%), neg=0, invalid=762 0338: dt=0.700000, rms=0.532 (-0.008%), neg=0, invalid=762 0339: dt=0.700000, rms=0.532 (0.007%), neg=0, invalid=762 0340: dt=0.043750, rms=0.532 (0.003%), neg=0, invalid=762 0341: dt=0.021875, rms=0.532 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0342: dt=38.400000, rms=0.529 (0.482%), neg=0, invalid=762 0343: dt=44.800000, rms=0.527 (0.386%), neg=0, invalid=762 0344: dt=32.000000, rms=0.526 (0.155%), neg=0, invalid=762 0345: dt=44.800000, rms=0.525 (0.223%), neg=0, invalid=762 0346: dt=38.400000, rms=0.525 (0.118%), neg=0, invalid=762 0347: dt=38.400000, rms=0.524 (0.140%), neg=0, invalid=762 0348: dt=32.000000, rms=0.523 (0.118%), neg=0, invalid=762 0349: dt=38.400000, rms=0.523 (0.109%), neg=0, invalid=762 0350: dt=32.000000, rms=0.522 (0.109%), neg=0, invalid=762 0351: dt=32.000000, rms=0.522 (0.083%), neg=0, invalid=762 0352: dt=38.400000, rms=0.521 (0.112%), neg=0, invalid=762 0353: dt=25.600000, rms=0.521 (0.073%), neg=0, invalid=762 0354: dt=44.800000, rms=0.520 (0.120%), neg=0, invalid=762 0355: dt=32.000000, rms=0.520 (0.064%), neg=0, invalid=762 0356: dt=38.400000, rms=0.519 (0.101%), neg=0, invalid=762 0357: dt=25.600000, rms=0.519 (0.063%), neg=0, invalid=762 0358: dt=38.400000, rms=0.518 (0.102%), neg=0, invalid=762 0359: dt=2.000000, rms=0.518 (0.006%), neg=0, invalid=762 0360: dt=0.125000, rms=0.518 (0.003%), neg=0, invalid=762 0361: dt=0.015625, rms=0.518 (0.000%), neg=0, invalid=762 0362: dt=0.003906, rms=0.518 (0.000%), neg=0, invalid=762 0363: dt=0.000684, rms=0.518 (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=0.538, neg=0, invalid=762 0364: dt=0.000000, rms=0.538 (0.067%), neg=0, invalid=762 0365: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 0366: dt=0.150000, rms=0.538 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0367: dt=0.000000, rms=0.538 (0.067%), neg=0, invalid=762 0368: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 0369: dt=0.150000, rms=0.538 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0370: dt=1.837037, rms=0.572 (0.777%), neg=0, invalid=762 0371: dt=0.448000, rms=0.572 (0.035%), neg=0, invalid=762 0372: dt=0.448000, rms=0.572 (0.005%), neg=0, invalid=762 0373: dt=0.448000, rms=0.572 (-0.056%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.573, neg=0, invalid=762 0374: dt=1.536000, rms=0.571 (0.230%), neg=0, invalid=762 0375: dt=0.448000, rms=0.571 (0.016%), neg=0, invalid=762 0376: dt=0.448000, rms=0.571 (0.004%), neg=0, invalid=762 0377: dt=0.448000, rms=0.571 (-0.022%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0378: dt=0.448000, rms=0.518 (2.629%), neg=0, invalid=762 0379: dt=0.448000, rms=0.514 (0.783%), neg=0, invalid=762 0380: dt=0.448000, rms=0.512 (0.443%), neg=0, invalid=762 0381: dt=0.448000, rms=0.510 (0.268%), neg=0, invalid=762 0382: dt=0.448000, rms=0.509 (0.188%), neg=0, invalid=762 0383: dt=0.448000, rms=0.509 (0.144%), neg=0, invalid=762 0384: dt=0.448000, rms=0.508 (0.116%), neg=0, invalid=762 0385: dt=0.448000, rms=0.508 (0.091%), neg=0, invalid=762 0386: dt=0.448000, rms=0.507 (0.080%), neg=0, invalid=762 0387: dt=0.448000, rms=0.507 (0.065%), neg=0, invalid=762 0388: dt=0.448000, rms=0.507 (0.057%), neg=0, invalid=762 0389: dt=0.448000, rms=0.506 (0.049%), neg=0, invalid=762 0390: dt=0.448000, rms=0.506 (0.043%), neg=0, invalid=762 0391: dt=0.448000, rms=0.506 (0.074%), neg=0, invalid=762 0392: dt=0.448000, rms=0.505 (0.096%), neg=0, invalid=762 0393: dt=0.448000, rms=0.505 (0.109%), neg=0, invalid=762 0394: dt=0.448000, rms=0.505 (0.008%), neg=0, invalid=762 0395: dt=0.448000, rms=0.505 (0.011%), neg=0, invalid=762 0396: dt=0.448000, rms=0.504 (0.022%), neg=0, invalid=762 0397: dt=0.448000, rms=0.504 (0.031%), neg=0, invalid=762 0398: dt=0.448000, rms=0.504 (0.009%), neg=0, invalid=762 0399: dt=0.448000, rms=0.504 (0.007%), neg=0, invalid=762 0400: dt=0.448000, rms=0.504 (0.006%), neg=0, invalid=762 0401: dt=0.448000, rms=0.504 (0.006%), neg=0, invalid=762 0402: dt=0.448000, rms=0.504 (0.011%), neg=0, invalid=762 0403: dt=0.448000, rms=0.504 (0.014%), neg=0, invalid=762 0404: dt=0.448000, rms=0.504 (0.015%), neg=0, invalid=762 0405: dt=0.448000, rms=0.504 (0.017%), neg=0, invalid=762 0406: dt=0.448000, rms=0.504 (0.018%), neg=0, invalid=762 0407: dt=0.448000, rms=0.504 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0408: dt=0.448000, rms=0.499 (0.963%), neg=0, invalid=762 0409: dt=0.448000, rms=0.498 (0.185%), neg=0, invalid=762 0410: dt=0.448000, rms=0.498 (0.092%), neg=0, invalid=762 0411: dt=0.448000, rms=0.498 (0.044%), neg=0, invalid=762 0412: dt=0.448000, rms=0.498 (0.025%), neg=0, invalid=762 0413: dt=0.448000, rms=0.497 (0.041%), neg=0, invalid=762 0414: dt=0.448000, rms=0.497 (-0.017%), neg=0, invalid=762 0415: dt=0.000000, rms=0.497 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0416: dt=27.744000, rms=0.495 (0.096%), neg=0, invalid=762 0417: dt=18.496000, rms=0.495 (0.000%), neg=0, invalid=762 0418: dt=18.496000, rms=0.495 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0419: dt=92.480000, rms=0.495 (0.109%), neg=0, invalid=762 0420: dt=517.888000, rms=0.494 (0.097%), neg=0, invalid=762 0421: dt=517.888000, rms=0.494 (-0.459%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0422: dt=36.288000, rms=0.494 (0.261%), neg=0, invalid=762 0423: dt=36.288000, rms=0.493 (0.066%), neg=0, invalid=762 0424: dt=36.288000, rms=0.493 (0.052%), neg=0, invalid=762 0425: dt=36.288000, rms=0.493 (0.043%), neg=0, invalid=762 0426: dt=36.288000, rms=0.493 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0427: dt=107.192118, rms=0.491 (0.536%), neg=0, invalid=762 0428: dt=103.680000, rms=0.489 (0.282%), neg=0, invalid=762 0429: dt=36.288000, rms=0.489 (0.056%), neg=0, invalid=762 0430: dt=36.288000, rms=0.489 (0.038%), neg=0, invalid=762 0431: dt=36.288000, rms=0.488 (0.066%), neg=0, invalid=762 0432: dt=36.288000, rms=0.488 (0.100%), neg=0, invalid=762 0433: dt=36.288000, rms=0.487 (0.128%), neg=0, invalid=762 0434: dt=36.288000, rms=0.487 (0.135%), neg=0, invalid=762 0435: dt=36.288000, rms=0.486 (0.125%), neg=0, invalid=762 0436: dt=36.288000, rms=0.485 (0.113%), neg=0, invalid=762 0437: dt=36.288000, rms=0.485 (0.104%), neg=0, invalid=762 0438: dt=580.608000, rms=0.484 (0.172%), neg=0, invalid=762 0439: dt=36.288000, rms=0.484 (0.069%), neg=0, invalid=762 0440: dt=36.288000, rms=0.484 (0.021%), neg=0, invalid=762 0441: dt=36.288000, rms=0.484 (0.021%), neg=0, invalid=762 0442: dt=36.288000, rms=0.483 (0.030%), neg=0, invalid=762 0443: dt=36.288000, rms=0.483 (0.042%), neg=0, invalid=762 0444: dt=36.288000, rms=0.483 (0.049%), neg=0, invalid=762 0445: dt=36.288000, rms=0.483 (0.050%), neg=0, invalid=762 0446: dt=36.288000, rms=0.483 (0.047%), neg=0, invalid=762 0447: dt=36.288000, rms=0.482 (0.052%), neg=0, invalid=762 0448: dt=36.288000, rms=0.482 (0.051%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0449: dt=29.639344, rms=0.481 (0.417%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 10 iterations, nbhd size=1, neg = 0 0450: dt=85.333333, rms=0.479 (0.384%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0451: dt=32.000000, rms=0.478 (0.322%), neg=0, invalid=762 0452: dt=32.000000, rms=0.477 (0.259%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0453: dt=25.600000, rms=0.476 (0.137%), neg=0, invalid=762 0454: dt=25.600000, rms=0.475 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0455: dt=25.600000, rms=0.474 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0456: dt=25.600000, rms=0.473 (0.203%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 0457: dt=25.600000, rms=0.472 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0458: dt=25.600000, rms=0.472 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0459: dt=25.600000, rms=0.471 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 25 after 12 iterations, nbhd size=1, neg = 0 0460: dt=25.600000, rms=0.470 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 13 iterations, nbhd size=1, neg = 0 0461: dt=25.600000, rms=0.469 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 14 iterations, nbhd size=1, neg = 0 0462: dt=25.600000, rms=0.469 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 13 iterations, nbhd size=1, neg = 0 0463: dt=25.600000, rms=0.468 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 8 iterations, nbhd size=0, neg = 0 0464: dt=25.600000, rms=0.467 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 33 after 16 iterations, nbhd size=1, neg = 0 0465: dt=25.600000, rms=0.466 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 37 after 8 iterations, nbhd size=0, neg = 0 0466: dt=25.600000, rms=0.466 (0.031%), neg=0, invalid=762 0467: dt=11.200000, rms=0.466 (0.038%), neg=0, invalid=762 0468: dt=32.000000, rms=0.466 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0469: dt=32.000000, rms=0.466 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0470: dt=44.800000, rms=0.462 (0.806%), neg=0, invalid=762 0471: dt=32.000000, rms=0.461 (0.310%), neg=0, invalid=762 0472: dt=25.600000, rms=0.460 (0.150%), neg=0, invalid=762 0473: dt=25.600000, rms=0.460 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0474: dt=25.600000, rms=0.459 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0475: dt=25.600000, rms=0.458 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=0, neg = 0 0476: dt=25.600000, rms=0.458 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 0477: dt=25.600000, rms=0.457 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 7 iterations, nbhd size=0, neg = 0 0478: dt=25.600000, rms=0.457 (0.042%), neg=0, invalid=762 0479: dt=25.600000, rms=0.457 (0.054%), neg=0, invalid=762 0480: dt=11.200000, rms=0.457 (0.031%), neg=0, invalid=762 0481: dt=11.200000, rms=0.457 (0.019%), neg=0, invalid=762 0482: dt=11.200000, rms=0.457 (0.022%), neg=0, invalid=762 0483: dt=11.200000, rms=0.456 (0.030%), neg=0, invalid=762 0484: dt=11.200000, rms=0.456 (0.036%), neg=0, invalid=762 0485: dt=11.200000, rms=0.456 (0.036%), neg=0, invalid=762 0486: dt=11.200000, rms=0.456 (0.036%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0487: dt=0.000000, rms=0.463 (0.100%), neg=0, invalid=762 0488: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0489: dt=1.008000, rms=0.463 (0.110%), neg=0, invalid=762 0490: dt=1.008000, rms=0.463 (0.004%), neg=0, invalid=762 0491: dt=1.008000, rms=0.463 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0492: dt=1.280000, rms=0.476 (0.407%), neg=0, invalid=762 0493: dt=0.384000, rms=0.476 (0.018%), neg=0, invalid=762 0494: dt=0.384000, rms=0.476 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0495: dt=1.536000, rms=0.475 (0.328%), neg=0, invalid=762 0496: dt=0.768000, rms=0.475 (0.028%), neg=0, invalid=762 0497: dt=0.768000, rms=0.475 (0.001%), neg=0, invalid=762 0498: dt=0.768000, rms=0.475 (-0.071%), 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=0.465, neg=0, invalid=762 iter 0, gcam->neg = 460 after 14 iterations, nbhd size=1, neg = 0 0499: dt=2.170414, rms=0.437 (6.031%), neg=0, invalid=762 0500: dt=0.096000, rms=0.437 (0.060%), neg=0, invalid=762 0501: dt=0.096000, rms=0.437 (-0.071%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.437, neg=0, invalid=762 0502: dt=0.080000, rms=0.437 (0.168%), neg=0, invalid=762 0503: dt=0.004000, rms=0.437 (0.004%), neg=0, invalid=762 0504: dt=0.004000, rms=0.437 (0.001%), neg=0, invalid=762 0505: dt=0.004000, rms=0.437 (0.000%), neg=0, invalid=762 0506: dt=0.004000, rms=0.437 (-0.002%), 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=0.424, neg=0, invalid=762 0507: dt=0.000000, rms=0.424 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0508: dt=32.368000, rms=0.424 (0.003%), neg=0, invalid=762 0509: dt=32.368000, rms=0.424 (0.001%), neg=0, invalid=762 0510: dt=32.368000, rms=0.424 (0.001%), neg=0, invalid=762 0511: dt=32.368000, rms=0.424 (-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=0.424, neg=0, invalid=762 0512: dt=5.184000, rms=0.424 (0.001%), neg=0, invalid=762 0513: dt=0.001012, rms=0.424 (0.000%), neg=0, invalid=762 0514: dt=0.001012, rms=0.424 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0515: dt=103.680000, rms=0.424 (0.081%), neg=0, invalid=762 0516: dt=124.416000, rms=0.423 (0.072%), neg=0, invalid=762 0517: dt=124.416000, rms=0.423 (-0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0518: dt=11.200000, rms=0.423 (0.130%), neg=0, invalid=762 0519: dt=11.200000, rms=0.423 (0.061%), neg=0, invalid=762 0520: dt=11.200000, rms=0.423 (0.035%), neg=0, invalid=762 0521: dt=11.200000, rms=0.423 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=762 0522: dt=44.800000, rms=0.420 (0.660%), neg=0, invalid=762 0523: dt=32.000000, rms=0.419 (0.303%), neg=0, invalid=762 0524: dt=25.600000, rms=0.418 (0.155%), neg=0, invalid=762 0525: dt=25.600000, rms=0.418 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0526: dt=25.600000, rms=0.417 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0527: dt=25.600000, rms=0.416 (0.239%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 12 iterations, nbhd size=1, neg = 0 0528: dt=25.600000, rms=0.415 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0529: dt=25.600000, rms=0.414 (0.242%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0530: dt=25.600000, rms=0.413 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0531: dt=25.600000, rms=0.412 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0532: dt=25.600000, rms=0.412 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0533: dt=25.600000, rms=0.411 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0534: dt=25.600000, rms=0.411 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0535: dt=25.600000, rms=0.410 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 5 iterations, nbhd size=0, neg = 0 0536: dt=25.600000, rms=0.410 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=0, neg = 0 0537: dt=44.800000, rms=0.410 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 3 iterations, nbhd size=0, neg = 0 0538: dt=44.800000, rms=0.410 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0539: dt=0.432000, rms=0.415 (0.001%), neg=0, invalid=762 0540: dt=0.063000, rms=0.415 (0.000%), neg=0, invalid=762 0541: dt=0.063000, rms=0.415 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0542: dt=4.032000, rms=0.415 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0543: dt=1.008000, rms=0.415 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0544: dt=1.008000, rms=0.415 (0.002%), neg=0, invalid=762 0545: dt=1.008000, rms=0.415 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0546: dt=0.000040, rms=0.424 (0.000%), neg=0, invalid=762 0547: dt=0.000000, rms=0.424 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0548: dt=0.000000, rms=0.424 (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=0.409, neg=0, invalid=762 iter 0, gcam->neg = 508 after 14 iterations, nbhd size=1, neg = 0 0549: dt=1.280000, rms=0.398 (2.548%), neg=0, invalid=762 0550: dt=0.000015, rms=0.398 (0.000%), neg=0, invalid=762 0551: dt=0.000015, rms=0.398 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 0552: dt=0.080000, rms=0.398 (0.028%), neg=0, invalid=762 0553: dt=0.028000, rms=0.398 (0.004%), neg=0, invalid=762 0554: dt=0.028000, rms=0.398 (0.001%), neg=0, invalid=762 0555: dt=0.028000, rms=0.398 (-0.007%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 11 minutes and 20 seconds. mri_ca_register utimesec 5008.690356 mri_ca_register stimesec 3.300275 mri_ca_register ru_maxrss 1338296 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4909474 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62792 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 8582 mri_ca_register ru_nivcsw 12112 FSRUNTIME@ mri_ca_register 1.1888 hours 4 threads #-------------------------------------- #@# SubCort Seg Mon Sep 30 19:03:06 -03 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 fisicos-ub2 machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 = 4 == 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 8.07 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 = 0.16764 (30) Left_Lateral_Ventricle (4): linear fit = 1.42 x + 0.0 (2404 voxels, overlap=0.147) Left_Lateral_Ventricle (4): linear fit = 1.42 x + 0.0 (2404 voxels, peak = 28), gca=28.5 gca peak = 0.17677 (13) mri peak = 0.12055 (29) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (3957 voxels, overlap=0.285) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3957 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.18528 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (788 voxels, overlap=0.271) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (788 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.15707 (102) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (764 voxels, overlap=0.499) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (764 voxels, peak = 102), gca=102.2 gca peak = 0.24553 (55) mri peak = 0.10897 (67) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1404 voxels, overlap=0.023) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1404 voxels, peak = 66), gca=66.3 gca peak = 0.30264 (59) mri peak = 0.13594 (70) Left_Hippocampus (17): linear fit = 1.21 x + 0.0 (1172 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.21 x + 0.0 (1172 voxels, peak = 71), gca=71.1 gca peak = 0.07580 (103) mri peak = 0.18193 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (65920 voxels, overlap=0.493) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (65920 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.18018 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (63105 voxels, overlap=0.519) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (63105 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04715 (71) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (54260 voxels, overlap=0.357) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (54260 voxels, peak = 69), gca=68.7 gca peak = 0.11620 (58) mri peak = 0.05001 (70) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (51635 voxels, overlap=0.432) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (51635 voxels, peak = 68), gca=67.6 gca peak = 0.30970 (66) mri peak = 0.11101 (80) Right_Caudate (50): linear fit = 1.21 x + 0.0 (1089 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.21 x + 0.0 (1089 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.08627 (86) Left_Caudate (11): linear fit = 1.15 x + 0.0 (1136 voxels, overlap=0.216) Left_Caudate (11): linear fit = 1.15 x + 0.0 (1136 voxels, peak = 80), gca=79.7 gca peak = 0.13902 (56) mri peak = 0.06522 (65) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (36402 voxels, overlap=0.331) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (36402 voxels, peak = 66), gca=66.4 gca peak = 0.14777 (55) mri peak = 0.06695 (68) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (36770 voxels, overlap=0.227) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (36770 voxels, peak = 66), gca=65.7 gca peak = 0.16765 (84) mri peak = 0.14629 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6623 voxels, overlap=0.530) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6623 voxels, peak = 90), gca=90.3 gca peak = 0.18739 (84) mri peak = 0.15361 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7388 voxels, overlap=0.326) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7388 voxels, peak = 91), gca=91.1 gca peak = 0.29869 (57) mri peak = 0.13468 (68) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (593 voxels, overlap=0.032) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (593 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.22826 (67) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (644 voxels, overlap=0.042) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (644 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.08485 (95) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5571 voxels, overlap=0.529) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5571 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.09638 (95) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4453 voxels, overlap=0.449) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4453 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.06600 (87) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1694 voxels, overlap=0.636) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1694 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.08691 (89) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2094 voxels, overlap=0.635) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2094 voxels, peak = 86), gca=85.9 gca peak = 0.08424 (78) mri peak = 0.09375 (91) Brain_Stem (16): linear fit = 1.11 x + 0.0 (17161 voxels, overlap=0.414) Brain_Stem (16): linear fit = 1.11 x + 0.0 (17161 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.12666 (101) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1991 voxels, overlap=0.010) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1991 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.10508 (101) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2086 voxels, overlap=0.085) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2086 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.21053 (31) Third_Ventricle (14): linear fit = 1.14 x + 0.0 (74 voxels, overlap=0.712) Third_Ventricle (14): linear fit = 1.14 x + 0.0 (74 voxels, peak = 27), gca=27.5 gca peak = 0.19357 (14) mri peak = 0.23791 (25) Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (515 voxels, overlap=0.158) Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (515 voxels, peak = 23), gca=22.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.19 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 Left_Pallidum too bright - rescaling by 0.997 (from 1.065) to 101.9 (was 102.2) Right_Pallidum too bright - rescaling by 0.998 (from 1.075) to 101.9 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15428 (26) mri peak = 0.16764 (30) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2404 voxels, overlap=0.668) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2404 voxels, peak = 26), gca=26.0 gca peak = 0.13981 (19) mri peak = 0.12055 (29) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (3957 voxels, overlap=0.625) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (3957 voxels, peak = 27), gca=26.5 gca peak = 0.22472 (102) mri peak = 0.18528 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (788 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (788 voxels, peak = 103), gca=102.5 gca peak = 0.16006 (100) mri peak = 0.15707 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (764 voxels, overlap=0.996) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (764 voxels, peak = 100), gca=100.0 gca peak = 0.28157 (67) mri peak = 0.10897 (67) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1404 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1404 voxels, peak = 66), gca=66.0 gca peak = 0.28060 (68) mri peak = 0.13594 (70) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1172 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1172 voxels, peak = 67), gca=67.0 gca peak = 0.07791 (104) mri peak = 0.18193 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (65920 voxels, overlap=0.550) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (65920 voxels, peak = 104), gca=104.0 gca peak = 0.07820 (106) mri peak = 0.18018 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63105 voxels, overlap=0.579) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63105 voxels, peak = 106), gca=106.0 gca peak = 0.08213 (69) mri peak = 0.04715 (71) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (54260 voxels, overlap=0.952) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (54260 voxels, peak = 69), gca=69.0 gca peak = 0.09800 (68) mri peak = 0.05001 (70) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (51635 voxels, overlap=0.959) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (51635 voxels, peak = 68), gca=68.0 gca peak = 0.21553 (80) mri peak = 0.11101 (80) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1089 voxels, overlap=0.958) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1089 voxels, peak = 79), gca=78.8 gca peak = 0.14387 (79) mri peak = 0.08627 (86) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1136 voxels, overlap=1.000) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1136 voxels, peak = 78), gca=77.8 gca peak = 0.11937 (66) mri peak = 0.06522 (65) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36402 voxels, overlap=0.972) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36402 voxels, peak = 66), gca=66.0 gca peak = 0.12206 (66) mri peak = 0.06695 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (36770 voxels, overlap=0.979) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (36770 voxels, peak = 66), gca=66.0 gca peak = 0.16303 (91) mri peak = 0.14629 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6623 voxels, overlap=0.928) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6623 voxels, peak = 91), gca=91.0 gca peak = 0.14985 (91) mri peak = 0.15361 (91) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7388 voxels, overlap=0.887) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7388 voxels, peak = 90), gca=89.6 gca peak = 0.29148 (69) mri peak = 0.13468 (68) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (593 voxels, overlap=0.981) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (593 voxels, peak = 68), gca=68.0 gca peak = 0.29009 (68) mri peak = 0.22826 (67) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (644 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (644 voxels, peak = 68), gca=68.0 gca peak = 0.09797 (97) mri peak = 0.08485 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5571 voxels, overlap=0.895) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5571 voxels, peak = 97), gca=97.5 gca peak = 0.10420 (90) mri peak = 0.09638 (95) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4453 voxels, overlap=0.948) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4453 voxels, peak = 91), gca=91.3 gca peak = 0.07894 (84) mri peak = 0.06600 (87) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1694 voxels, overlap=0.981) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1694 voxels, peak = 84), gca=84.0 gca peak = 0.09434 (84) mri peak = 0.08691 (89) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2094 voxels, overlap=0.996) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2094 voxels, peak = 86), gca=86.1 gca peak = 0.07201 (90) mri peak = 0.09375 (91) Brain_Stem (16): linear fit = 1.01 x + 0.0 (17161 voxels, overlap=0.754) Brain_Stem (16): linear fit = 1.01 x + 0.0 (17161 voxels, peak = 91), gca=91.3 gca peak = 0.10170 (96) mri peak = 0.12666 (101) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1991 voxels, overlap=0.780) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1991 voxels, peak = 97), gca=97.4 gca peak = 0.15846 (97) mri peak = 0.10508 (101) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (2086 voxels, overlap=0.842) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (2086 voxels, peak = 96), gca=95.5 gca peak = 0.13199 (29) mri peak = 0.21053 (31) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (74 voxels, overlap=0.918) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (74 voxels, peak = 29), gca=29.4 gca peak = 0.17375 (20) mri peak = 0.23791 (25) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (515 voxels, overlap=0.393) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (515 voxels, peak = 24), gca=23.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.14113 (32) gca peak Left_Thalamus = 0.36646 (103) gca peak CSF = 0.21405 (49) gca peak Left_Accumbens_area = 0.49711 (72) gca peak Left_undetermined = 0.96707 (33) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12606 (35) gca peak Right_Inf_Lat_Vent = 0.24202 (28) gca peak Right_Accumbens_area = 0.29896 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14505 (37) gca peak Fifth_Ventricle = 0.51669 (42) gca peak WM_hypointensities = 0.07717 (78) gca peak non_WM_hypointensities = 0.09744 (44) gca peak Optic_Chiasm = 0.49672 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.15 x + 0.0 Right_Pallidum too bright - rescaling by 0.994 (from 1.005) to 101.8 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 80346 voxels changed in iteration 0 of unlikely voxel relabeling 403 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 54850 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 371 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 78292 changed. image ll: -2.175, PF=0.500 pass 2: 23105 changed. image ll: -2.174, PF=0.500 pass 3: 7613 changed. pass 4: 2914 changed. 65236 voxels changed in iteration 0 of unlikely voxel relabeling 386 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8458 voxels changed in iteration 0 of unlikely voxel relabeling 188 voxels changed in iteration 1 of unlikely voxel relabeling 12 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 6654 voxels changed in iteration 0 of unlikely voxel relabeling 56 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 6176 voxels changed in iteration 0 of unlikely voxel relabeling 24 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 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 1838.600534 mri_ca_label stimesec 0.472005 mri_ca_label ru_maxrss 2108400 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 730594 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 520 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 235 mri_ca_label ru_nivcsw 3209 auto-labeling took 30 minutes and 13 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/transforms/cc_up.lta KING_LUCAS_JAVIER_25-09-2019 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/norm.mgz 29544 voxels in left wm, 52187 in right wm, xrange [121, 129] searching rotation angles z=[-7 7], y=[-9 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 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 global minimum found at slice 125.5, rotations (-1.70, -0.23) final transformation (x=125.5, yr=-1.704, zr=-0.227): 0.99955 0.00396 -0.02974 5.79169; -0.00396 0.99999 0.00012 23.48274; 0.02974 -0.00000 0.99956 1.32222; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 105 123 eigenvectors: 0.00026 0.00156 1.00000; 0.01448 -0.99989 0.00155; 0.99990 0.01448 -0.00028; writing aseg with callosum to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg Mon Sep 30 19:33:40 -03 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Sep 30 19:33:40 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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... 489 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 75 (75), valley at 41 (41) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 75 (75), valley at 41 (41) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 26 seconds. #-------------------------------------------- #@# Mask BFS Mon Sep 30 19:35:08 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1956910 voxels in mask (pct= 11.66) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Sep 30 19:35:08 -03 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 (102.0): 101.5 +- 7.3 [79.0 --> 125.0] GM (74.0) : 71.7 +- 12.2 [30.0 --> 95.0] setting bottom of white matter range to 83.9 setting top of gray matter range to 96.1 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... 6119 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4124 filled 7207 bright non-wm voxels segmented. 2574 diagonally connected voxels added... white matter segmentation took 0.9 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.21 minutes reading wm segmentation from wm.seg.mgz... 54 voxels added to wm to prevent paths from MTL structures to cortex 3082 additional wm voxels added 0 additional wm voxels added SEG EDIT: 55729 voxels turned on, 60599 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 22 found - 22 modified | TOTAL: 34 pass 2 (xy-): 0 found - 22 modified | TOTAL: 34 pass 1 (yz+): 14 found - 14 modified | TOTAL: 48 pass 2 (yz+): 0 found - 14 modified | TOTAL: 48 pass 1 (yz-): 21 found - 21 modified | TOTAL: 69 pass 2 (yz-): 0 found - 21 modified | TOTAL: 69 pass 1 (xz+): 18 found - 18 modified | TOTAL: 87 pass 2 (xz+): 0 found - 18 modified | TOTAL: 87 pass 1 (xz-): 13 found - 13 modified | TOTAL: 100 pass 2 (xz-): 0 found - 13 modified | TOTAL: 100 Iteration Number : 1 pass 1 (+++): 28 found - 28 modified | TOTAL: 28 pass 2 (+++): 0 found - 28 modified | TOTAL: 28 pass 1 (+++): 42 found - 42 modified | TOTAL: 70 pass 2 (+++): 0 found - 42 modified | TOTAL: 70 pass 1 (+++): 43 found - 43 modified | TOTAL: 113 pass 2 (+++): 0 found - 43 modified | TOTAL: 113 pass 1 (+++): 54 found - 54 modified | TOTAL: 167 pass 2 (+++): 0 found - 54 modified | TOTAL: 167 Iteration Number : 1 pass 1 (++): 43 found - 43 modified | TOTAL: 43 pass 2 (++): 0 found - 43 modified | TOTAL: 43 pass 1 (+-): 24 found - 24 modified | TOTAL: 67 pass 2 (+-): 0 found - 24 modified | TOTAL: 67 pass 1 (--): 53 found - 53 modified | TOTAL: 120 pass 2 (--): 0 found - 53 modified | TOTAL: 120 pass 1 (-+): 36 found - 36 modified | TOTAL: 156 pass 2 (-+): 0 found - 36 modified | TOTAL: 156 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 7 found - 7 modified | TOTAL: 13 pass 2 (xy-): 0 found - 7 modified | TOTAL: 13 pass 1 (yz+): 2 found - 2 modified | TOTAL: 15 pass 2 (yz+): 0 found - 2 modified | TOTAL: 15 pass 1 (yz-): 12 found - 12 modified | TOTAL: 27 pass 2 (yz-): 0 found - 12 modified | TOTAL: 27 pass 1 (xz+): 4 found - 4 modified | TOTAL: 31 pass 2 (xz+): 0 found - 4 modified | TOTAL: 31 pass 1 (xz-): 8 found - 8 modified | TOTAL: 39 pass 2 (xz-): 0 found - 8 modified | TOTAL: 39 Iteration Number : 2 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 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 2 found - 2 modified | TOTAL: 4 pass 2 (+-): 0 found - 2 modified | TOTAL: 4 pass 1 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 0 found - 0 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 473 (out of 720039: 0.065691) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Sep 30 19:36:15 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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 0.99949 0.00134 -0.01585 1.90903; -0.00031 1.04315 0.11148 -23.30788; 0.01693 -0.13563 0.93606 11.39024; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.99949 0.00134 -0.01585 1.90903; -0.00031 1.04315 0.11148 -23.30788; 0.01693 -0.13563 0.93606 11.39024; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1082 (min = 350, max = 1400), aspect = 0.39 (min = 0.10, max = 0.75) no need to search using seed (125, 122, 151), TAL = (3.0, 23.0, 6.0) talairach voxel to voxel transform 1.00023 0.00090 0.01683 -2.08017; 0.00220 0.94402 -0.11239 23.27909; -0.01777 0.13676 1.05172 -8.75777; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 122, 151) --> (3.0, 23.0, 6.0) done. writing output to filled.mgz... filling took 0.3 minutes talairach cc position changed to (3.00, 23.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 23.00, 6.00) SRC: (107.60, 121.71, 164.84) search lh wm seed point around talairach space (-15.00, 23.00, 6.00), SRC: (143.60, 121.79, 164.20) 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 Sep 30 19:36:31 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 2 found - 2 modified | TOTAL: 8 pass 2 (yz+): 0 found - 2 modified | TOTAL: 8 pass 1 (yz-): 0 found - 0 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 2 found - 2 modified | TOTAL: 11 pass 2 (xz-): 0 found - 2 modified | TOTAL: 11 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 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 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 = 14 (out of 340668: 0.004110) 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 40: 420 vertices, 477 faces slice 50: 4937 vertices, 5141 faces slice 60: 12899 vertices, 13234 faces slice 70: 23382 vertices, 23754 faces slice 80: 33510 vertices, 33849 faces slice 90: 44878 vertices, 45266 faces slice 100: 55979 vertices, 56352 faces slice 110: 69006 vertices, 69436 faces slice 120: 81549 vertices, 81986 faces slice 130: 93741 vertices, 94169 faces slice 140: 104998 vertices, 105416 faces slice 150: 115738 vertices, 116074 faces slice 160: 124162 vertices, 124439 faces slice 170: 131310 vertices, 131604 faces slice 180: 138866 vertices, 139135 faces slice 190: 145233 vertices, 145470 faces slice 200: 150732 vertices, 150933 faces slice 210: 153823 vertices, 153898 faces slice 220: 154018 vertices, 154054 faces slice 230: 154018 vertices, 154054 faces slice 240: 154018 vertices, 154054 faces slice 250: 154018 vertices, 154054 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... 154018 voxel in cpt #1: X=-36 [v=154018,e=462162,f=308108] located at (-26.127796, -10.425197, 11.434852) For the whole surface: X=-36 [v=154018,e=462162,f=308108] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Sep 30 19:36:34 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/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-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 1 (out of 348812: 0.000287) 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: 360 vertices, 419 faces slice 50: 4745 vertices, 4945 faces slice 60: 11994 vertices, 12276 faces slice 70: 21757 vertices, 22128 faces slice 80: 32580 vertices, 32938 faces slice 90: 43408 vertices, 43797 faces slice 100: 54078 vertices, 54451 faces slice 110: 66495 vertices, 66913 faces slice 120: 78410 vertices, 78801 faces slice 130: 90088 vertices, 90475 faces slice 140: 101535 vertices, 101932 faces slice 150: 112433 vertices, 112780 faces slice 160: 121572 vertices, 121895 faces slice 170: 129676 vertices, 129952 faces slice 180: 137269 vertices, 137549 faces slice 190: 143821 vertices, 144031 faces slice 200: 149585 vertices, 149784 faces slice 210: 153228 vertices, 153304 faces slice 220: 153592 vertices, 153608 faces slice 230: 153592 vertices, 153608 faces slice 240: 153592 vertices, 153608 faces slice 250: 153592 vertices, 153608 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... 153592 voxel in cpt #1: X=-16 [v=153592,e=460824,f=307216] located at (31.667547, -8.614446, 12.442725) For the whole surface: X=-16 [v=153592,e=460824,f=307216] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Sep 30 19:36:36 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Mon Sep 30 19:36:36 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 1762 of (1762 1765) to complete... Waiting for PID 1765 of (1762 1765) to complete... 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... 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... PIDs (1762 1765) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Mon Sep 30 19:36:39 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Mon Sep 30 19:36:39 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 1884 of (1884 1890) to complete... Waiting for PID 1890 of (1884 1890) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 50.0 mm, total surface area = 83205 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.147 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 43.371391 mris_inflate stimesec 0.180163 mris_inflate ru_maxrss 242072 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 58896 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10840 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 34140 mris_inflate ru_nivcsw 82 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 50.2 mm, total surface area = 83716 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.143 (target=0.015) step 005: RMS=0.107 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.053 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 44.270148 mris_inflate stimesec 0.204175 mris_inflate ru_maxrss 241032 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 58697 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10808 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 37894 mris_inflate ru_nivcsw 40 PIDs (1884 1890) completed and logs appended. #-------------------------------------------- #@# QSphere lh Mon Sep 30 19:36:54 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Mon Sep 30 19:36:54 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 2028 of (2028 2032) to complete... Waiting for PID 2032 of (2028 2032) to complete... 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 0.94 +- 0.54 (0.00-->6.89) (max @ vno 108211 --> 109358) face area 0.02 +- 0.03 (-0.21-->0.54) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.836, avgs=0 005/300: dt: 0.9000, rms radial error=176.578, avgs=0 010/300: dt: 0.9000, rms radial error=176.024, avgs=0 015/300: dt: 0.9000, rms radial error=175.295, avgs=0 020/300: dt: 0.9000, rms radial error=174.465, avgs=0 025/300: dt: 0.9000, rms radial error=173.577, avgs=0 030/300: dt: 0.9000, rms radial error=172.657, avgs=0 035/300: dt: 0.9000, rms radial error=171.720, avgs=0 040/300: dt: 0.9000, rms radial error=170.776, avgs=0 045/300: dt: 0.9000, rms radial error=169.829, avgs=0 050/300: dt: 0.9000, rms radial error=168.883, avgs=0 055/300: dt: 0.9000, rms radial error=167.940, avgs=0 060/300: dt: 0.9000, rms radial error=167.000, avgs=0 065/300: dt: 0.9000, rms radial error=166.065, avgs=0 070/300: dt: 0.9000, rms radial error=165.135, avgs=0 075/300: dt: 0.9000, rms radial error=164.210, avgs=0 080/300: dt: 0.9000, rms radial error=163.290, avgs=0 085/300: dt: 0.9000, rms radial error=162.375, avgs=0 090/300: dt: 0.9000, rms radial error=161.465, avgs=0 095/300: dt: 0.9000, rms radial error=160.560, avgs=0 100/300: dt: 0.9000, rms radial error=159.660, avgs=0 105/300: dt: 0.9000, rms radial error=158.765, avgs=0 110/300: dt: 0.9000, rms radial error=157.874, avgs=0 115/300: dt: 0.9000, rms radial error=156.989, avgs=0 120/300: dt: 0.9000, rms radial error=156.108, avgs=0 125/300: dt: 0.9000, rms radial error=155.232, avgs=0 130/300: dt: 0.9000, rms radial error=154.361, avgs=0 135/300: dt: 0.9000, rms radial error=153.495, avgs=0 140/300: dt: 0.9000, rms radial error=152.633, avgs=0 145/300: dt: 0.9000, rms radial error=151.776, avgs=0 150/300: dt: 0.9000, rms radial error=150.923, avgs=0 155/300: dt: 0.9000, rms radial error=150.075, avgs=0 160/300: dt: 0.9000, rms radial error=149.232, avgs=0 165/300: dt: 0.9000, rms radial error=148.394, avgs=0 170/300: dt: 0.9000, rms radial error=147.560, avgs=0 175/300: dt: 0.9000, rms radial error=146.731, avgs=0 180/300: dt: 0.9000, rms radial error=145.906, avgs=0 185/300: dt: 0.9000, rms radial error=145.086, avgs=0 190/300: dt: 0.9000, rms radial error=144.270, avgs=0 195/300: dt: 0.9000, rms radial error=143.459, avgs=0 200/300: dt: 0.9000, rms radial error=142.653, avgs=0 205/300: dt: 0.9000, rms radial error=141.850, avgs=0 210/300: dt: 0.9000, rms radial error=141.053, avgs=0 215/300: dt: 0.9000, rms radial error=140.259, avgs=0 220/300: dt: 0.9000, rms radial error=139.470, avgs=0 225/300: dt: 0.9000, rms radial error=138.686, avgs=0 230/300: dt: 0.9000, rms radial error=137.906, avgs=0 235/300: dt: 0.9000, rms radial error=137.130, avgs=0 240/300: dt: 0.9000, rms radial error=136.358, avgs=0 245/300: dt: 0.9000, rms radial error=135.591, avgs=0 250/300: dt: 0.9000, rms radial error=134.828, avgs=0 255/300: dt: 0.9000, rms radial error=134.070, avgs=0 260/300: dt: 0.9000, rms radial error=133.315, avgs=0 265/300: dt: 0.9000, rms radial error=132.565, avgs=0 270/300: dt: 0.9000, rms radial error=131.819, avgs=0 275/300: dt: 0.9000, rms radial error=131.077, avgs=0 280/300: dt: 0.9000, rms radial error=130.339, avgs=0 285/300: dt: 0.9000, rms radial error=129.606, avgs=0 290/300: dt: 0.9000, rms radial error=128.876, avgs=0 295/300: dt: 0.9000, rms radial error=128.151, avgs=0 300/300: dt: 0.9000, rms radial error=127.429, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18324.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 3140.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 326.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00650 epoch 4 (K=640.0), pass 1, starting sse = 18.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00781 final distance error %27.26 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 247.085825 mris_sphere stimesec 0.268119 mris_sphere ru_maxrss 242040 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 58910 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10864 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 37456 mris_sphere ru_nivcsw 399 FSRUNTIME@ mris_sphere 0.0249 hours 1 threads 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 0.94 +- 0.52 (0.00-->8.25) (max @ vno 62425 --> 62426) face area 0.02 +- 0.03 (-0.31-->0.83) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.287... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.925, avgs=0 005/300: dt: 0.9000, rms radial error=176.665, avgs=0 010/300: dt: 0.9000, rms radial error=176.105, avgs=0 015/300: dt: 0.9000, rms radial error=175.371, avgs=0 020/300: dt: 0.9000, rms radial error=174.536, avgs=0 025/300: dt: 0.9000, rms radial error=173.644, avgs=0 030/300: dt: 0.9000, rms radial error=172.722, avgs=0 035/300: dt: 0.9000, rms radial error=171.784, avgs=0 040/300: dt: 0.9000, rms radial error=170.839, avgs=0 045/300: dt: 0.9000, rms radial error=169.891, avgs=0 050/300: dt: 0.9000, rms radial error=168.945, avgs=0 055/300: dt: 0.9000, rms radial error=168.001, avgs=0 060/300: dt: 0.9000, rms radial error=167.061, avgs=0 065/300: dt: 0.9000, rms radial error=166.125, avgs=0 070/300: dt: 0.9000, rms radial error=165.193, avgs=0 075/300: dt: 0.9000, rms radial error=164.267, avgs=0 080/300: dt: 0.9000, rms radial error=163.345, avgs=0 085/300: dt: 0.9000, rms radial error=162.429, avgs=0 090/300: dt: 0.9000, rms radial error=161.517, avgs=0 095/300: dt: 0.9000, rms radial error=160.611, avgs=0 100/300: dt: 0.9000, rms radial error=159.709, avgs=0 105/300: dt: 0.9000, rms radial error=158.813, avgs=0 110/300: dt: 0.9000, rms radial error=157.921, avgs=0 115/300: dt: 0.9000, rms radial error=157.034, avgs=0 120/300: dt: 0.9000, rms radial error=156.152, avgs=0 125/300: dt: 0.9000, rms radial error=155.275, avgs=0 130/300: dt: 0.9000, rms radial error=154.403, avgs=0 135/300: dt: 0.9000, rms radial error=153.536, avgs=0 140/300: dt: 0.9000, rms radial error=152.673, avgs=0 145/300: dt: 0.9000, rms radial error=151.815, avgs=0 150/300: dt: 0.9000, rms radial error=150.963, avgs=0 155/300: dt: 0.9000, rms radial error=150.115, avgs=0 160/300: dt: 0.9000, rms radial error=149.272, avgs=0 165/300: dt: 0.9000, rms radial error=148.434, avgs=0 170/300: dt: 0.9000, rms radial error=147.600, avgs=0 175/300: dt: 0.9000, rms radial error=146.771, avgs=0 180/300: dt: 0.9000, rms radial error=145.946, avgs=0 185/300: dt: 0.9000, rms radial error=145.125, avgs=0 190/300: dt: 0.9000, rms radial error=144.309, avgs=0 195/300: dt: 0.9000, rms radial error=143.498, avgs=0 200/300: dt: 0.9000, rms radial error=142.691, avgs=0 205/300: dt: 0.9000, rms radial error=141.888, avgs=0 210/300: dt: 0.9000, rms radial error=141.090, avgs=0 215/300: dt: 0.9000, rms radial error=140.296, avgs=0 220/300: dt: 0.9000, rms radial error=139.507, avgs=0 225/300: dt: 0.9000, rms radial error=138.722, avgs=0 230/300: dt: 0.9000, rms radial error=137.941, avgs=0 235/300: dt: 0.9000, rms radial error=137.164, avgs=0 240/300: dt: 0.9000, rms radial error=136.392, avgs=0 245/300: dt: 0.9000, rms radial error=135.624, avgs=0 250/300: dt: 0.9000, rms radial error=134.861, avgs=0 255/300: dt: 0.9000, rms radial error=134.101, avgs=0 260/300: dt: 0.9000, rms radial error=133.346, avgs=0 265/300: dt: 0.9000, rms radial error=132.595, avgs=0 270/300: dt: 0.9000, rms radial error=131.848, avgs=0 275/300: dt: 0.9000, rms radial error=131.106, avgs=0 280/300: dt: 0.9000, rms radial error=130.367, avgs=0 285/300: dt: 0.9000, rms radial error=129.633, avgs=0 290/300: dt: 0.9000, rms radial error=128.902, avgs=0 295/300: dt: 0.9000, rms radial error=128.176, avgs=0 300/300: dt: 0.9000, rms radial error=127.454, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18284.62 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 = 3124.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 320.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00673 epoch 4 (K=640.0), pass 1, starting sse = 16.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/15 = 0.01111 final distance error %27.08 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 249.551290 mris_sphere stimesec 0.404005 mris_sphere ru_maxrss 241728 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 58719 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10832 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 35569 mris_sphere ru_nivcsw 259 FSRUNTIME@ mris_sphere 0.0252 hours 1 threads PIDs (2028 2032) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Mon Sep 30 19:38:25 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Sep 30 19:38:25 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Sep 30 19:38:25 -03 2019 mris_fix_topology -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 KING_LUCAS_JAVIER_25-09-2019 lh #@# Fix Topology rh Mon Sep 30 19:38:25 -03 2019 mris_fix_topology -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 KING_LUCAS_JAVIER_25-09-2019 rh Waiting for PID 2155 of (2155 2158) to complete... Waiting for PID 2158 of (2155 2158) to complete... mris_fix_topology -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 KING_LUCAS_JAVIER_25-09-2019 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=-36 (nv=154018, nf=308108, ne=462162, g=19) 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 7 iterations marking ambiguous vertices... 3862 ambiguous faces found in tessellation segmenting defects... 23 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 4 22 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9628 (-4.4814) -vertex loglikelihood: -5.8298 (-2.9149) -normal dot loglikelihood: -3.5477 (-3.5477) -quad curv loglikelihood: -6.2702 (-3.1351) Total Loglikelihood : -24.6105 CORRECTING DEFECT 0 (vertices=16, convex hull=18, v0=237) After retessellation of defect 0 (v0=237), euler #=-19 (151723,454413,302671) : difference with theory (-19) = 0 CORRECTING DEFECT 1 (vertices=7, convex hull=28, v0=23080) After retessellation of defect 1 (v0=23080), euler #=-18 (151724,454424,302682) : difference with theory (-18) = 0 CORRECTING DEFECT 2 (vertices=31, convex hull=57, v0=26091) After retessellation of defect 2 (v0=26091), euler #=-17 (151740,454495,302738) : difference with theory (-17) = 0 CORRECTING DEFECT 3 (vertices=21, convex hull=45, v0=28264) After retessellation of defect 3 (v0=28264), euler #=-16 (151743,454519,302760) : difference with theory (-16) = 0 CORRECTING DEFECT 4 (vertices=941, convex hull=469, v0=55608) XL defect detected... After retessellation of defect 4 (v0=55608), euler #=-15 (151996,455553,303542) : difference with theory (-15) = 0 CORRECTING DEFECT 5 (vertices=24, convex hull=54, v0=63179) After retessellation of defect 5 (v0=63179), euler #=-14 (152010,455615,303591) : difference with theory (-14) = 0 CORRECTING DEFECT 6 (vertices=156, convex hull=63, v0=87194) After retessellation of defect 6 (v0=87194), euler #=-13 (152020,455669,303636) : difference with theory (-13) = 0 CORRECTING DEFECT 7 (vertices=380, convex hull=126, v0=99445) After retessellation of defect 7 (v0=99445), euler #=-12 (152053,455825,303760) : difference with theory (-12) = 0 CORRECTING DEFECT 8 (vertices=66, convex hull=81, v0=101556) After retessellation of defect 8 (v0=101556), euler #=-11 (152080,455942,303851) : difference with theory (-11) = 0 CORRECTING DEFECT 9 (vertices=77, convex hull=82, v0=104689) After retessellation of defect 9 (v0=104689), euler #=-10 (152106,456054,303938) : difference with theory (-10) = 0 CORRECTING DEFECT 10 (vertices=19, convex hull=32, v0=106066) After retessellation of defect 10 (v0=106066), euler #=-9 (152109,456076,303958) : difference with theory (-9) = 0 CORRECTING DEFECT 11 (vertices=104, convex hull=46, v0=111551) After retessellation of defect 11 (v0=111551), euler #=-8 (152115,456111,303988) : difference with theory (-8) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=28, v0=112424) After retessellation of defect 12 (v0=112424), euler #=-7 (152123,456141,304011) : difference with theory (-7) = 0 CORRECTING DEFECT 13 (vertices=49, convex hull=92, v0=126430) After retessellation of defect 13 (v0=126430), euler #=-6 (152156,456281,304119) : difference with theory (-6) = 0 CORRECTING DEFECT 14 (vertices=53, convex hull=49, v0=135876) After retessellation of defect 14 (v0=135876), euler #=-5 (152163,456324,304156) : difference with theory (-5) = 0 CORRECTING DEFECT 15 (vertices=39, convex hull=58, v0=137160) After retessellation of defect 15 (v0=137160), euler #=-4 (152177,456385,304204) : difference with theory (-4) = 0 CORRECTING DEFECT 16 (vertices=61, convex hull=71, v0=141549) After retessellation of defect 16 (v0=141549), euler #=-3 (152193,456464,304268) : difference with theory (-3) = 0 CORRECTING DEFECT 17 (vertices=110, convex hull=85, v0=145831) After retessellation of defect 17 (v0=145831), euler #=-2 (152208,456550,304340) : difference with theory (-2) = 0 CORRECTING DEFECT 18 (vertices=10, convex hull=24, v0=147079) After retessellation of defect 18 (v0=147079), euler #=-1 (152209,456561,304351) : difference with theory (-1) = 0 CORRECTING DEFECT 19 (vertices=33, convex hull=61, v0=148715) After retessellation of defect 19 (v0=148715), euler #=0 (152218,456610,304392) : difference with theory (0) = 0 CORRECTING DEFECT 20 (vertices=35, convex hull=82, v0=151936) After retessellation of defect 20 (v0=151936), euler #=1 (152239,456704,304466) : difference with theory (1) = 0 CORRECTING DEFECT 21 (vertices=29, convex hull=24, v0=153969) After retessellation of defect 21 (v0=153969), euler #=2 (152242,456720,304480) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.06-->10.50) (max @ vno 71367 --> 73711) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.06-->10.50) (max @ vno 71367 --> 73711) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 66 mutations (32.0%), 140 crossovers (68.0%), 195 vertices were eliminated building final representation... 1776 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=152242, nf=304480, ne=456720, g=0) writing corrected surface to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 7.4 minutes 0 defective edges removing intersecting faces 000: 285 intersecting 001: 2 intersecting mris_fix_topology utimesec 452.225331 mris_fix_topology stimesec 0.108001 mris_fix_topology ru_maxrss 526300 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 130610 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 14416 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 664 mris_fix_topology ru_nivcsw 1243 FSRUNTIME@ mris_fix_topology lh 0.1241 hours 1 threads mris_fix_topology -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 KING_LUCAS_JAVIER_25-09-2019 rh 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=-16 (nv=153592, nf=307216, ne=460824, g=9) 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... 1227 ambiguous faces found in tessellation segmenting defects... 18 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 18 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9741 (-4.4871) -vertex loglikelihood: -5.8255 (-2.9127) -normal dot loglikelihood: -3.6401 (-3.6401) -quad curv loglikelihood: -6.4112 (-3.2056) Total Loglikelihood : -24.8509 CORRECTING DEFECT 0 (vertices=23, convex hull=70, v0=29174) After retessellation of defect 0 (v0=29174), euler #=-15 (152800,457981,305166) : difference with theory (-15) = 0 CORRECTING DEFECT 1 (vertices=19, convex hull=51, v0=56096) After retessellation of defect 1 (v0=56096), euler #=-14 (152809,458035,305212) : difference with theory (-14) = 0 CORRECTING DEFECT 2 (vertices=11, convex hull=45, v0=58488) After retessellation of defect 2 (v0=58488), euler #=-13 (152813,458064,305238) : difference with theory (-13) = 0 CORRECTING DEFECT 3 (vertices=189, convex hull=151, v0=58496) normal vector of length zero at vertex 153016 with 3 faces After retessellation of defect 3 (v0=58496), euler #=-12 (152824,458165,305329) : difference with theory (-12) = 0 CORRECTING DEFECT 4 (vertices=6, convex hull=34, v0=62563) After retessellation of defect 4 (v0=62563), euler #=-11 (152827,458185,305347) : difference with theory (-11) = 0 CORRECTING DEFECT 5 (vertices=136, convex hull=223, v0=68796) normal vector of length zero at vertex 153067 with 3 faces normal vector of length zero at vertex 153067 with 3 faces normal vector of length zero at vertex 153067 with 3 faces After retessellation of defect 5 (v0=68796), euler #=-10 (152890,458483,305583) : difference with theory (-10) = 0 CORRECTING DEFECT 6 (vertices=5, convex hull=30, v0=69900) After retessellation of defect 6 (v0=69900), euler #=-9 (152891,458493,305593) : difference with theory (-9) = 0 CORRECTING DEFECT 7 (vertices=22, convex hull=23, v0=94337) After retessellation of defect 7 (v0=94337), euler #=-8 (152896,458513,305609) : difference with theory (-8) = 0 CORRECTING DEFECT 8 (vertices=149, convex hull=60, v0=99174) After retessellation of defect 8 (v0=99174), euler #=-7 (152907,458569,305655) : difference with theory (-7) = 0 CORRECTING DEFECT 9 (vertices=30, convex hull=23, v0=99927) After retessellation of defect 9 (v0=99927), euler #=-6 (152910,458582,305666) : difference with theory (-6) = 0 CORRECTING DEFECT 10 (vertices=27, convex hull=34, v0=104608) After retessellation of defect 10 (v0=104608), euler #=-5 (152918,458614,305691) : difference with theory (-5) = 0 CORRECTING DEFECT 11 (vertices=28, convex hull=66, v0=109952) After retessellation of defect 11 (v0=109952), euler #=-4 (152934,458685,305747) : difference with theory (-4) = 0 CORRECTING DEFECT 12 (vertices=13, convex hull=23, v0=111017) After retessellation of defect 12 (v0=111017), euler #=-3 (152936,458698,305759) : difference with theory (-3) = 0 CORRECTING DEFECT 13 (vertices=37, convex hull=56, v0=128936) After retessellation of defect 13 (v0=128936), euler #=-2 (152951,458767,305814) : difference with theory (-2) = 0 CORRECTING DEFECT 14 (vertices=21, convex hull=49, v0=132637) After retessellation of defect 14 (v0=132637), euler #=-1 (152960,458816,305855) : difference with theory (-1) = 0 CORRECTING DEFECT 15 (vertices=27, convex hull=27, v0=144453) After retessellation of defect 15 (v0=144453), euler #=0 (152961,458830,305869) : difference with theory (0) = 0 CORRECTING DEFECT 16 (vertices=45, convex hull=71, v0=145127) After retessellation of defect 16 (v0=145127), euler #=1 (152979,458913,305935) : difference with theory (1) = 0 CORRECTING DEFECT 17 (vertices=18, convex hull=48, v0=151515) After retessellation of defect 17 (v0=151515), euler #=2 (152989,458961,305974) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.14-->8.01) (max @ vno 144418 --> 147318) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.14-->8.01) (max @ vno 144418 --> 147318) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 77 mutations (33.2%), 155 crossovers (66.8%), 112 vertices were eliminated building final representation... 603 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=152989, nf=305974, ne=458961, g=0) writing corrected surface to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 6.4 minutes 0 defective edges removing intersecting faces 000: 137 intersecting 001: 2 intersecting mris_fix_topology utimesec 387.205781 mris_fix_topology stimesec 0.100003 mris_fix_topology ru_maxrss 525880 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 130395 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 14432 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 1111 mris_fix_topology ru_nivcsw 144 FSRUNTIME@ mris_fix_topology rh 0.1062 hours 1 threads PIDs (2155 2158) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 152242 - 456720 + 304480 = 2 --> 0 holes F =2V-4: 304480 = 304484-4 (0) 2E=3F: 913440 = 913440 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 152989 - 458961 + 305974 = 2 --> 0 holes F =2V-4: 305974 = 305978-4 (0) 2E=3F: 917922 = 917922 (0) total defect index = 0 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 58 intersecting 001: 22 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 9 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Sep 30 19:45:57 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs KING_LUCAS_JAVIER_25-09-2019 lh #-------------------------------------------- #@# Make White Surf rh Mon Sep 30 19:45:57 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs KING_LUCAS_JAVIER_25-09-2019 rh Waiting for PID 2291 of (2291 2294) to complete... Waiting for PID 2294 of (2291 2294) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs KING_LUCAS_JAVIER_25-09-2019 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/wm.mgz... 18209 bright wm thresholded. 8738 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/lh.orig... computing class statistics... border white: 300224 voxels (1.79%) border gray 341596 voxels (2.04%) WM (101.0): 100.6 +- 6.8 [70.0 --> 110.0] GM (79.0) : 77.7 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.0 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.0 (was 40) setting MAX_GRAY to 97.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.04-->5.43) (max @ vno 71367 --> 73711) face area 0.28 +- 0.12 (0.00-->3.12) mean absolute distance = 0.79 +- 0.99 3669 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=75+-7.8 mean inside = 96.8, mean outside = 81.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=85.0, 42 (42) missing vertices, mean dist 0.3 [0.7 (%34.8)->0.9 (%65.2))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.24 (0.07-->4.56) (max @ vno 151810 --> 151880) face area 0.28 +- 0.13 (0.00-->3.02) mean absolute distance = 0.39 +- 0.70 3668 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3022720.8, rms=9.039 001: dt: 0.5000, sse=1803884.5, rms=6.370 (29.528%) 002: dt: 0.5000, sse=1222877.1, rms=4.569 (28.276%) 003: dt: 0.5000, sse=959002.5, rms=3.444 (24.618%) 004: dt: 0.5000, sse=838976.6, rms=2.787 (19.078%) 005: dt: 0.5000, sse=794331.4, rms=2.494 (10.519%) 006: dt: 0.5000, sse=775076.1, rms=2.347 (5.904%) rms = 2.31, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=770503.7, rms=2.315 (1.354%) 008: dt: 0.2500, sse=679115.9, rms=1.337 (42.262%) 009: dt: 0.2500, sse=666585.2, rms=1.152 (13.801%) rms = 1.11, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=663904.6, rms=1.109 (3.700%) rms = 1.09, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=662678.4, rms=1.086 (2.135%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... mean border=87.6, 62 (14) missing vertices, mean dist -0.3 [0.5 (%71.6)->0.2 (%28.4))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.23 (0.11-->5.15) (max @ vno 151810 --> 151880) face area 0.36 +- 0.16 (0.00-->4.47) mean absolute distance = 0.29 +- 0.45 4143 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1306479.1, rms=4.209 012: dt: 0.5000, sse=987111.8, rms=2.630 (37.507%) 013: dt: 0.5000, sse=912182.6, rms=2.115 (19.599%) 014: dt: 0.5000, sse=886643.8, rms=1.883 (10.977%) rms = 1.96, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=841475.1, rms=1.405 (25.367%) 016: dt: 0.2500, sse=821586.3, rms=1.117 (20.534%) 017: dt: 0.2500, sse=816294.4, rms=1.021 (8.559%) rms = 0.98, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=813596.8, rms=0.984 (3.604%) rms = 0.96, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=812442.5, rms=0.963 (2.172%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.9, 71 (12) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.2 (%26.5))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.23 (0.06-->5.46) (max @ vno 151810 --> 151880) face area 0.35 +- 0.15 (0.00-->4.66) mean absolute distance = 0.22 +- 0.34 3582 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1055585.2, rms=3.197 020: dt: 0.5000, sse=861940.5, rms=1.878 (41.245%) 021: dt: 0.5000, sse=844746.8, rms=1.716 (8.648%) 022: dt: 0.5000, sse=836492.3, rms=1.665 (2.987%) rms = 1.89, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=795765.9, rms=1.143 (31.357%) 024: dt: 0.2500, sse=784147.8, rms=0.925 (19.082%) rms = 0.89, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=781568.3, rms=0.891 (3.641%) rms = 0.88, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=780509.3, rms=0.875 (1.779%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.6, 94 (11) missing vertices, mean dist -0.1 [0.2 (%58.6)->0.2 (%41.4))] %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=798212.2, rms=1.414 027: dt: 0.5000, sse=769618.6, rms=1.006 (28.889%) rms = 1.28, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=758258.8, rms=0.789 (21.514%) 029: dt: 0.2500, sse=755931.9, rms=0.731 (7.363%) rms = 0.71, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=754373.1, rms=0.705 (3.541%) rms = 0.71, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=753281.6, rms=0.705 (0.032%) positioning took 0.3 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7466 vertices erasing segment 1 (vno[0] = 61514) erasing segment 2 (vno[0] = 63558) erasing segment 3 (vno[0] = 76958) erasing segment 4 (vno[0] = 85702) erasing segment 5 (vno[0] = 91837) erasing segment 6 (vno[0] = 105306) erasing segment 7 (vno[0] = 107647) erasing segment 8 (vno[0] = 111410) erasing segment 9 (vno[0] = 111626) erasing segment 10 (vno[0] = 114443) erasing segment 11 (vno[0] = 114474) erasing segment 12 (vno[0] = 117164) writing cortex label to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/lh.area vertex spacing 0.89 +- 0.24 (0.04-->5.54) (max @ vno 151810 --> 151880) face area 0.34 +- 0.15 (0.00-->4.67) refinement took 2.7 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs KING_LUCAS_JAVIER_25-09-2019 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/mri/wm.mgz... 18209 bright wm thresholded. 8738 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/rh.orig... computing class statistics... border white: 300224 voxels (1.79%) border gray 341596 voxels (2.04%) WM (101.0): 100.6 +- 6.8 [70.0 --> 110.0] GM (79.0) : 77.7 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.0 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 54.0 (was 40) setting MAX_GRAY to 97.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.04-->4.73) (max @ vno 58475 --> 152823) face area 0.29 +- 0.12 (0.00-->5.11) mean absolute distance = 0.74 +- 0.95 4181 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=76+-7.0 mean inside = 96.9, mean outside = 82.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=85.7, 43 (43) missing vertices, mean dist 0.3 [0.6 (%36.7)->0.8 (%63.3))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.24 (0.15-->5.09) (max @ vno 58475 --> 59703) face area 0.29 +- 0.12 (0.00-->3.34) mean absolute distance = 0.35 +- 0.65 2946 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2862329.5, rms=8.699 001: dt: 0.5000, sse=1714333.1, rms=6.088 (30.017%) 002: dt: 0.5000, sse=1179132.0, rms=4.363 (28.340%) 003: dt: 0.5000, sse=936968.6, rms=3.294 (24.502%) 004: dt: 0.5000, sse=829571.3, rms=2.683 (18.533%) 005: dt: 0.5000, sse=791564.1, rms=2.426 (9.603%) 006: dt: 0.5000, sse=776241.9, rms=2.312 (4.691%) rms = 2.29, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=773741.4, rms=2.290 (0.934%) 008: dt: 0.2500, sse=682373.3, rms=1.296 (43.419%) 009: dt: 0.2500, sse=669929.0, rms=1.112 (14.170%) rms = 1.07, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=667671.2, rms=1.073 (3.554%) rms = 1.05, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=666300.0, rms=1.049 (2.250%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=87.9, 59 (30) missing vertices, mean dist -0.2 [0.4 (%69.8)->0.2 (%30.2))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.23 (0.08-->5.23) (max @ vno 58475 --> 59703) face area 0.36 +- 0.15 (0.00-->4.51) mean absolute distance = 0.29 +- 0.45 3967 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1193217.4, rms=3.697 012: dt: 0.5000, sse=930301.0, rms=2.202 (40.439%) 013: dt: 0.5000, sse=886068.2, rms=1.854 (15.817%) 014: dt: 0.5000, sse=869709.2, rms=1.721 (7.152%) rms = 1.86, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=831825.8, rms=1.236 (28.214%) 016: dt: 0.2500, sse=818474.6, rms=1.004 (18.761%) rms = 0.95, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=814994.6, rms=0.954 (4.907%) rms = 0.93, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=814015.6, rms=0.935 (2.039%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.2, 37 (30) missing vertices, mean dist -0.2 [0.3 (%73.0)->0.2 (%27.0))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.23 (0.10-->5.21) (max @ vno 58475 --> 59703) face area 0.35 +- 0.15 (0.00-->4.96) mean absolute distance = 0.22 +- 0.34 3618 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1062633.9, rms=3.179 019: dt: 0.5000, sse=871509.9, rms=1.884 (40.738%) 020: dt: 0.5000, sse=849573.5, rms=1.695 (9.994%) 021: dt: 0.5000, sse=841148.4, rms=1.635 (3.588%) rms = 1.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=802916.0, rms=1.122 (31.334%) 023: dt: 0.2500, sse=791560.4, rms=0.911 (18.800%) rms = 0.88, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=789359.6, rms=0.880 (3.479%) rms = 0.86, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=788393.9, rms=0.862 (1.983%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=91.0, 47 (29) missing vertices, mean dist -0.1 [0.2 (%58.8)->0.2 (%41.2))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=809722.2, rms=1.442 026: dt: 0.5000, sse=778267.4, rms=0.995 (30.998%) rms = 1.27, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=767044.6, rms=0.772 (22.449%) 028: dt: 0.2500, sse=764041.1, rms=0.713 (7.600%) rms = 0.69, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=762548.2, rms=0.690 (3.151%) rms = 0.69, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=761932.1, rms=0.688 (0.399%) positioning took 0.3 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7623 vertices erasing segment 1 (vno[0] = 65638) erasing segment 2 (vno[0] = 106105) erasing segment 3 (vno[0] = 108303) erasing segment 4 (vno[0] = 111525) erasing segment 5 (vno[0] = 112478) erasing segment 6 (vno[0] = 114172) writing cortex label to /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf/rh.area vertex spacing 0.90 +- 0.24 (0.04-->5.33) (max @ vno 58475 --> 59703) face area 0.34 +- 0.15 (0.00-->5.08) refinement took 2.6 minutes PIDs (2291 2294) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Mon Sep 30 19:48:37 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Mon Sep 30 19:48:37 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 2390 of (2390 2401) to complete... Waiting for PID 2401 of (2390 2401) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (2390 2401) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Mon Sep 30 19:48:40 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Mon Sep 30 19:48:40 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 2530 of (2530 2533) to complete... Waiting for PID 2533 of (2530 2533) to complete... mris_inflate -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 50.0 mm, total surface area = 93418 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.169 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.2 minutes mris_inflate utimesec 44.740224 mris_inflate stimesec 0.236254 mris_inflate ru_maxrss 239288 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 58260 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11904 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 33278 mris_inflate ru_nivcsw 122 mris_inflate -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 50.3 mm, total surface area = 94497 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.168 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.019 (target=0.015) inflation complete. inflation took 0.2 minutes mris_inflate utimesec 43.704843 mris_inflate stimesec 0.208576 mris_inflate ru_maxrss 239604 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 58478 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11968 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 35024 mris_inflate ru_nivcsw 459 PIDs (2530 2533) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Mon Sep 30 19:48:54 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Mon Sep 30 19:48:54 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf mris_curvature -w rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf reconbatchjobs /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 2625 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2628 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2631 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2634 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2637 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2640 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2643 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2646 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2649 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2652 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2655 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... Waiting for PID 2658 of (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 3.848*4pi (48.360) --> -3 handles ICI = 154.1, FI = 1615.7, variation=25402.308 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 184 vertices thresholded to be in k1 ~ [-0.17 0.66], k2 ~ [-0.09 0.05] total integrated curvature = 0.568*4pi (7.140) --> 0 handles ICI = 1.6, FI = 10.0, variation=172.014 137 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 159 vertices thresholded to be in [-0.12 0.26] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.014, std = 0.024 done. mris_curvature -w rh.white.preaparc total integrated curvature = 6.704*4pi (84.243) --> -6 handles ICI = 153.5, FI = 1581.5, variation=24907.527 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 261 vertices thresholded to be in k1 ~ [-0.16 0.53], k2 ~ [-0.08 0.04] total integrated curvature = 0.611*4pi (7.682) --> 0 handles ICI = 1.5, FI = 10.7, variation=176.719 137 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 165 vertices thresholded to be in [-0.10 0.24] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.024 done. PIDs (2625 2628 2631 2634 2637 2640 2643 2646 2649 2652 2655 2658) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Mon Sep 30 19:49:35 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm KING_LUCAS_JAVIER_25-09-2019 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ KING_LUCAS_JAVIER_25-09-2019/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 268 ] Gb_filter = 0 WARN: S lookup min: -0.176654 WARN: S explicit min: 0.000000 vertex = 42 #----------------------------------------- #@# Curvature Stats rh Mon Sep 30 19:49:37 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm KING_LUCAS_JAVIER_25-09-2019 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ KING_LUCAS_JAVIER_25-09-2019/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 256 ] Gb_filter = 0 WARN: S lookup min: -0.729228 WARN: S explicit min: 0.000000 vertex = 223 #-------------------------------------------- #@# Sphere lh Mon Sep 30 19:49:39 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Mon Sep 30 19:49:39 -03 2019 /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 2778 of (2778 2781) to complete... /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fault (core dumped) exec $JOB >> $LOG 2>&1 Waiting for PID 2781 of (2778 2781) to complete... mris_sphere -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 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... == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.273... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 mris_sphere -rusage /usr/local/freesurfer/subjects/KING_LUCAS_JAVIER_25-09-2019/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 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... == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.269... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.66 pass 1: epoch 2 of 3 starting distance error %18.60 unfolding complete - removing small folds... starting distance error %18.57 removing remaining folds... final distance error %18.57 MRISunfold() return, current seed 1234 -01: dt=0.0000, 239 negative triangles 089: dt=0.9900, 239 negative triangles 090: dt=0.9900, 78 negative triangles 091: dt=0.9900, 42 negative triangles 092: dt=0.9900, 29 negative triangles 093: dt=0.9900, 23 negative triangles 094: dt=0.9900, 13 negative triangles 095: dt=0.9900, 18 negative triangles 096: dt=0.9900, 8 negative triangles 097: dt=0.9900, 4 negative triangles 098: dt=0.9900, 6 negative triangles 099: dt=0.9900, 5 negative triangles 100: dt=0.9900, 5 negative triangles 101: dt=0.9900, 8 negative triangles 102: dt=0.9900, 5 negative triangles 103: dt=0.9900, 8 negative triangles 104: dt=0.9900, 5 negative triangles 105: dt=0.9900, 2 negative triangles 106: dt=0.9900, 6 negative triangles 107: dt=0.9900, 2 negative triangles 108: dt=0.9900, 4 negative triangles 109: dt=0.9900, 2 negative triangles 110: dt=0.9900, 2 negative triangles 111: dt=0.9900, 5 negative triangles 112: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.15 hours mris_sphere utimesec 2016.893461 mris_sphere stimesec 2.239939 mris_sphere ru_maxrss 334064 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 81950 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10784 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 46405 mris_sphere ru_nivcsw 5266 FSRUNTIME@ mris_sphere 0.1534 hours 1 threads PIDs (2778 2781) completed and logs appended. Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s KING_LUCAS_JAVIER_25-09-2019 exited with ERRORS at Mon Sep 30 20:00:58 -03 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting