Wed Oct 2 18:38:25 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/6.0.0/bin/recon-all -s 2012-646-010-KK -noskullstrip -all subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux n511 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 52428800 kbytes descriptors 102400 memorylocked unlimited maxproc 63708 total used free shared buffers cached Mem: 264563032 119453580 145109452 140172 0 4132636 -/+ buffers/cache: 115320944 149242088 Swap: 8388604 0 8388604 ######################################## 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: 2019/10/02-22:38:26-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:26-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:27-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:28-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:28-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:29-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:29-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:30-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:30-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:30-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:31-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:31-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:32-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:32-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:33-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:33-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:33-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:34-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:34-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:34-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:35-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:35-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:36-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/02-22:38:38-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:38-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:38-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:39-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:39-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:40-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:40-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:41-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:41-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:42-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:42-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/02-22:38:42-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: mwagshul Machine: n511 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /public/apps/freesurfer/6.0.0/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 /public/apps/freesurfer/6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Oct 2 18:38:45 EDT 2019 Found 1 runs /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform mri_convert.bin /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261116, -0.041979) j_ras = (-0.0224984, 0.996182, -0.0843504) k_ras = (-0.0440213, 0.0833028, 0.995551) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Oct 2 18:38:55 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/6.0.0/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 n511 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 2 18:38:58 EDT 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.250543 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.250543/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.250543/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.250543/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Oct 2 18:39:01 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.250543/nu0.mnc ./tmp.mri_nu_correct.mni.250543/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.250543/0/ -iterations 1000 -distance 50 [mwagshul@n511:/gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/] [2019-10-02 18:39:01] running: /public/apps/freesurfer/6.0.0/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.250543/0/ ./tmp.mri_nu_correct.mni.250543/nu0.mnc ./tmp.mri_nu_correct.mni.250543/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 38 CV of field change: 0.000957607 mri_convert ./tmp.mri_nu_correct.mni.250543/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.250543/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.250543/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31322e-10, 1, -7.45058e-09) 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... Wed Oct 2 18:39:58 EDT 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 Wed Oct 2 18:39:59 EDT 2019 Ended at Wed Oct 2 18:40:33 EDT 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Oct 2 18:40:36 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5199, pval=0.1531 >= threshold=0.0050) awk -f /public/apps/freesurfer/6.0.0/bin/extract_talairach_avi_QA.awk /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log tal_QC_AZS /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log TalAviQA: 0.96057 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Wed Oct 2 18:40:38 EDT 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/6.0.0/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 n511 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 2 18:40:40 EDT 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.255424 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.255424/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.255424/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.255424/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Oct 2 18:40:43 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.255424/nu0.mnc ./tmp.mri_nu_correct.mni.255424/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.255424/0/ [mwagshul@n511:/gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/] [2019-10-02 18:40:44] running: /public/apps/freesurfer/6.0.0/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.255424/0/ ./tmp.mri_nu_correct.mni.255424/nu0.mnc ./tmp.mri_nu_correct.mni.255424/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 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./tmp.mri_nu_correct.mni.255424/1/ [mwagshul@n511:/gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/] [2019-10-02 18:41:22] running: /public/apps/freesurfer/6.0.0/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.255424/1/ ./tmp.mri_nu_correct.mni.255424/nu1.mnc ./tmp.mri_nu_correct.mni.255424/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 12 CV of field change: 0.000928496 mri_binarize --i ./tmp.mri_nu_correct.mni.255424/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.255424/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.255424/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.255424/ones.mgz sysname Linux hostname n511 machine x86_64 user mwagshul input ./tmp.mri_nu_correct.mni.255424/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.255424/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.255424/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.255424/sum.junk --avgwf ./tmp.mri_nu_correct.mni.255424/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.255424/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.255424/sum.junk --avgwf ./tmp.mri_nu_correct.mni.255424/input.mean.dat sysname Linux hostname n511 machine x86_64 user mwagshul UseRobust 0 Loading ./tmp.mri_nu_correct.mni.255424/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.255424/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.255424/ones.mgz --i ./tmp.mri_nu_correct.mni.255424/nu2.mnc --sum ./tmp.mri_nu_correct.mni.255424/sum.junk --avgwf ./tmp.mri_nu_correct.mni.255424/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.255424/ones.mgz --i ./tmp.mri_nu_correct.mni.255424/nu2.mnc --sum ./tmp.mri_nu_correct.mni.255424/sum.junk --avgwf ./tmp.mri_nu_correct.mni.255424/output.mean.dat sysname Linux hostname n511 machine x86_64 user mwagshul UseRobust 0 Loading ./tmp.mri_nu_correct.mni.255424/ones.mgz Loading ./tmp.mri_nu_correct.mni.255424/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.255424/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.255424/nu2.mnc ./tmp.mri_nu_correct.mni.255424/nu2.mnc mul .92093046833416844900 Saving result to './tmp.mri_nu_correct.mni.255424/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.255424/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.255424/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.255424/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31322e-10, 1, -7.45058e-09) 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 6 seconds. mapping (12, 180) to ( 3, 110) Wed Oct 2 18:42:19 EDT 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed Oct 2 18:42:21 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/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 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 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 = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 61 (61), valley at 24 (24) csf peak at 31, setting threshold to 51 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 62 (62), valley at 0 (-1) csf peak at 31, setting threshold to 51 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 39 seconds. #-------------------------------------------- #@# Skull Stripping Wed Oct 2 18:44:02 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /public/apps/freesurfer/6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/public/apps/freesurfer/6.0.0/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=26.1 skull bounding box = (58, 73, 27) --> (196, 168, 189) using (104, 105, 108) as brain centroid... mean wm in atlas = 108, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 5.9 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.467 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.467209 @ (0.000, 0.000, 0.000) max log p = -4.467209 @ (0.000, 0.000, 0.000) max log p = -4.435071 @ (-2.273, -6.818, 2.273) max log p = -4.425727 @ (1.136, 1.136, -1.136) max log p = -4.414628 @ (-0.568, 0.568, -1.705) max log p = -4.414628 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -5.1, -0.6): log p = -4.415 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.076, old_max_log_p =-4.415 (thresh=-4.4) 1.15000 0.00000 0.00000 -20.69151; 0.00000 1.23625 0.00000 -32.41039; 0.00000 0.00000 1.07500 -8.93004; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.027, old_max_log_p =-4.076 (thresh=-4.1) 1.06375 0.00000 0.00000 -9.77400; 0.00000 1.52831 0.00000 -73.65601; 0.00000 0.00000 1.07500 -8.93004; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.027, old_max_log_p =-4.027 (thresh=-4.0) 1.06375 0.00000 0.00000 -9.77400; 0.00000 1.52831 0.00000 -73.65601; 0.00000 0.00000 1.07500 -8.93004; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.981, old_max_log_p =-4.027 (thresh=-4.0) 1.08311 0.05075 0.00356 -19.79255; -0.03542 1.55543 0.03447 -74.84545; -0.00228 -0.05386 1.11462 -9.20172; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.981, old_max_log_p =-3.981 (thresh=-4.0) 1.08311 0.05075 0.00356 -19.79255; -0.03542 1.55543 0.03447 -74.84545; -0.00228 -0.05386 1.11462 -9.20172; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.958, old_max_log_p =-3.981 (thresh=-4.0) 1.08528 0.04901 0.03093 -22.49664; -0.03525 1.55312 0.04354 -76.05417; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.957, old_max_log_p =-3.958 (thresh=-4.0) 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 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 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.957 (old=-4.467) transform before final EM align: 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 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 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.08274 0.04889 0.03085 -22.15124; -0.03533 1.55676 0.04364 -76.56564; -0.02857 -0.06773 1.11257 -4.17282; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 951.532345 mri_em_register stimesec 1.018845 mri_em_register ru_maxrss 609808 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157575 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 35 mri_em_register ru_nivcsw 4658 registration took 15 minutes and 53 seconds. mri_watershed -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mri_watershed.dat -T1 -brain_atlas /public/apps/freesurfer/6.0.0/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=129 y=123 z=113 r=56 first estimation of the main basin volume: 752026 voxels Looking for seedpoints 2 found in the cerebellum 13 found in the rest of the brain global maximum in x=110, y=108, z=86, Imax=255 CSF=12, 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=7081542858 voxels, voxel volume =1.000 = 7081542858 mmm3 = 7081542.656 cm3 done. PostAnalyze...Basin Prior 33 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=128,y=126, z=106, r=8763 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 46034 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1048890145 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1055634642 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1067776255 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1071012918 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1074431868 (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 4, 36, 56 after analyzing : 3, 25, 36, 32 RIGHT_CER before analyzing : 3, 4, 39, 57 after analyzing : 3, 27, 39, 34 LEFT_CER before analyzing : 3, 4, 40, 59 after analyzing : 3, 28, 40, 35 RIGHT_BRAIN before analyzing : 3, 4, 36, 56 after analyzing : 3, 25, 36, 32 LEFT_BRAIN before analyzing : 3, 4, 35, 56 after analyzing : 3, 24, 35, 32 OTHER before analyzing : 3, 3, 26, 56 after analyzing : 3, 18, 26, 27 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 67.475, std = 9.955 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.32, sigma = 7.22 after rotation: sse = 5.32, sigma = 7.22 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.47, its var is 8.57 before Erosion-Dilatation 3.25% of inacurate vertices after Erosion-Dilatation 5.02% 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...35 iterations mri_strip_skull: done peeling brain Brain Size = 1467567 voxels, voxel volume = 1.000 mm3 = 1467567 mmm3 = 1467.567 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 15.053711 mri_watershed stimesec 0.344947 mri_watershed ru_maxrss 816836 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 208167 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 35 mri_watershed ru_nivcsw 193 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Oct 2 19:00:13 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/public/apps/freesurfer/6.0.0/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 = (58, 73, 27) --> (196, 168, 189) using (104, 105, 108) as brain centroid... mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 5.9 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -3.901 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.875418 @ (0.000, 0.000, 0.000) max log p = -3.854017 @ (-4.545, -4.545, 4.545) max log p = -3.772842 @ (2.273, 2.273, -6.818) max log p = -3.755873 @ (-1.136, -1.136, 1.136) max log p = -3.736387 @ (-0.568, 1.705, 0.568) max log p = -3.736387 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -1.7, -0.6): log p = -3.736 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.575, old_max_log_p =-3.736 (thresh=-3.7) 1.00000 0.00000 0.00000 -3.97727; 0.00000 1.23625 0.00000 -37.78951; 0.00000 0.00000 1.00000 -0.56818; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.575, old_max_log_p =-3.575 (thresh=-3.6) 1.00000 0.00000 0.00000 -3.97727; 0.00000 1.23625 0.00000 -37.78951; 0.00000 0.00000 1.00000 -0.56818; 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=-3.490, old_max_log_p =-3.575 (thresh=-3.6) 1.01742 0.04249 0.00436 -10.23956; -0.03194 1.25886 0.00001 -34.61284; -0.00420 -0.00017 0.98124 0.11569; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.490, old_max_log_p =-3.490 (thresh=-3.5) 1.01742 0.04249 0.00436 -10.23956; -0.03194 1.25886 0.00001 -34.61284; -0.00420 -0.00017 0.98124 0.11569; 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=-3.474, old_max_log_p =-3.490 (thresh=-3.5) 1.01645 0.03210 0.00435 -8.81055; -0.02374 1.26360 0.00004 -36.26847; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.470, old_max_log_p =-3.474 (thresh=-3.5) 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.470, old_max_log_p =-3.470 (thresh=-3.5) 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.470 (old=-3.901) transform before final EM align: 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 808.973017 mri_em_register stimesec 0.953854 mri_em_register ru_maxrss 599036 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159465 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 16 mri_em_register ru_nivcsw 2087 registration took 13 minutes and 30 seconds. #-------------------------------------- #@# CA Normalize Wed Oct 2 19:13:44 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /public/apps/freesurfer/6.0.0/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 '/public/apps/freesurfer/6.0.0/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=25.1 skull bounding box = (58, 72, 27) --> (196, 169, 190) using (104, 104, 109) as brain centroid... mean wm in atlas = 107, using box (87,92,89) --> (120, 115,129) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 5.8 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246344 sample points... INFO: compute sample coordinates transform 1.01764 0.03214 0.00436 -8.96939; -0.02380 1.26656 0.00004 -36.63306; -0.00421 -0.00017 0.98469 -0.25489; 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 (128, 73, 27) --> (194, 168, 198) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 1601 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 72, 27) --> (131, 167, 198) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 917 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 140, 50) --> (176, 174, 104) Left_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0 5 of 12 (41.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 140, 47) --> (128, 173, 106) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 20 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 134, 84) --> (145, 189, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 2 of 28 (7.1%) samples deleted using 2578 total control points for intensity normalization... bias field = 0.972 +- 0.043 20 of 2571 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 73, 27) --> (194, 168, 198) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 1939 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 72, 27) --> (131, 167, 198) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 1296 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 140, 50) --> (176, 174, 104) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 29 of 84 (34.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 140, 47) --> (128, 173, 106) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 73 (23.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 134, 84) --> (145, 189, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 41 of 107 (38.3%) samples deleted using 3499 total control points for intensity normalization... bias field = 1.024 +- 0.047 27 of 3387 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 73, 27) --> (194, 168, 198) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 1955 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 72, 27) --> (131, 167, 198) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 1 of 1378 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 140, 50) --> (176, 174, 104) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 70 of 128 (54.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 140, 47) --> (128, 173, 106) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 105 (46.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 134, 84) --> (145, 189, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 96 of 142 (67.6%) samples deleted using 3708 total control points for intensity normalization... bias field = 1.024 +- 0.044 21 of 3415 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 23 seconds. #-------------------------------------- #@# CA Reg Wed Oct 2 19:15:07 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_register -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.27 (predicted orig area = 6.3) 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=0.946, neg=0, invalid=762 0001: dt=221.952000, rms=0.803 (15.156%), neg=0, invalid=762 0002: dt=212.789809, rms=0.776 (3.351%), neg=0, invalid=762 0003: dt=191.433628, rms=0.759 (2.127%), neg=0, invalid=762 0004: dt=157.138211, rms=0.753 (0.828%), neg=0, invalid=762 0005: dt=443.904000, rms=0.742 (1.437%), neg=0, invalid=762 0006: dt=110.976000, rms=0.737 (0.661%), neg=0, invalid=762 0007: dt=2071.552000, rms=0.718 (2.547%), neg=0, invalid=762 0008: dt=369.920000, rms=0.714 (0.571%), neg=0, invalid=762 0009: dt=129.472000, rms=0.713 (0.219%), neg=0, invalid=762 0010: dt=129.472000, rms=0.712 (0.107%), neg=0, invalid=762 0011: dt=129.472000, rms=0.711 (0.168%), neg=0, invalid=762 0012: dt=129.472000, rms=0.709 (0.220%), neg=0, invalid=762 0013: dt=129.472000, rms=0.708 (0.233%), neg=0, invalid=762 0014: dt=129.472000, rms=0.706 (0.228%), neg=0, invalid=762 0015: dt=129.472000, rms=0.704 (0.229%), neg=0, invalid=762 0016: dt=129.472000, rms=0.703 (0.227%), neg=0, invalid=762 0017: dt=129.472000, rms=0.701 (0.227%), neg=0, invalid=762 0018: dt=129.472000, rms=0.700 (0.223%), neg=0, invalid=762 0019: dt=129.472000, rms=0.698 (0.207%), neg=0, invalid=762 0020: dt=129.472000, rms=0.697 (0.185%), neg=0, invalid=762 0021: dt=129.472000, rms=0.696 (0.178%), neg=0, invalid=762 0022: dt=129.472000, rms=0.694 (0.165%), neg=0, invalid=762 0023: dt=129.472000, rms=0.693 (0.145%), neg=0, invalid=762 0024: dt=129.472000, rms=0.693 (0.134%), neg=0, invalid=762 0025: dt=129.472000, rms=0.692 (0.135%), neg=0, invalid=762 0026: dt=129.472000, rms=0.691 (0.140%), neg=0, invalid=762 0027: dt=129.472000, rms=0.690 (0.137%), neg=0, invalid=762 0028: dt=129.472000, rms=0.689 (0.128%), neg=0, invalid=762 0029: dt=129.472000, rms=0.688 (0.114%), neg=0, invalid=762 0030: dt=129.472000, rms=0.687 (0.101%), neg=0, invalid=762 0031: dt=517.888000, rms=0.687 (0.029%), neg=0, invalid=762 0032: dt=517.888000, rms=0.687 (-0.154%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=762 0033: dt=110.976000, rms=0.687 (0.122%), neg=0, invalid=762 0034: dt=295.936000, rms=0.686 (0.055%), neg=0, invalid=762 0035: dt=295.936000, rms=0.686 (0.092%), neg=0, invalid=762 0036: dt=295.936000, rms=0.685 (0.090%), neg=0, invalid=762 0037: dt=295.936000, rms=0.685 (0.059%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.692, neg=0, invalid=762 0038: dt=159.319149, rms=0.683 (1.369%), neg=0, invalid=762 0039: dt=144.601504, rms=0.672 (1.523%), neg=0, invalid=762 0040: dt=66.810540, rms=0.668 (0.570%), neg=0, invalid=762 0041: dt=580.608000, rms=0.654 (2.221%), neg=0, invalid=762 0042: dt=57.546218, rms=0.648 (0.793%), neg=0, invalid=762 0043: dt=414.720000, rms=0.644 (0.673%), neg=0, invalid=762 0044: dt=74.926829, rms=0.641 (0.419%), neg=0, invalid=762 0045: dt=93.775401, rms=0.640 (0.251%), neg=0, invalid=762 0046: dt=36.288000, rms=0.639 (0.086%), neg=0, invalid=762 0047: dt=36.288000, rms=0.639 (0.054%), neg=0, invalid=762 0048: dt=36.288000, rms=0.638 (0.099%), neg=0, invalid=762 0049: dt=36.288000, rms=0.637 (0.147%), neg=0, invalid=762 0050: dt=36.288000, rms=0.636 (0.187%), neg=0, invalid=762 0051: dt=36.288000, rms=0.635 (0.212%), neg=0, invalid=762 0052: dt=36.288000, rms=0.633 (0.225%), neg=0, invalid=762 0053: dt=36.288000, rms=0.632 (0.231%), neg=0, invalid=762 0054: dt=36.288000, rms=0.630 (0.233%), neg=0, invalid=762 0055: dt=36.288000, rms=0.629 (0.228%), neg=0, invalid=762 0056: dt=36.288000, rms=0.627 (0.223%), neg=0, invalid=762 0057: dt=36.288000, rms=0.626 (0.218%), neg=0, invalid=762 0058: dt=36.288000, rms=0.625 (0.209%), neg=0, invalid=762 0059: dt=36.288000, rms=0.624 (0.195%), neg=0, invalid=762 0060: dt=36.288000, rms=0.622 (0.184%), neg=0, invalid=762 0061: dt=36.288000, rms=0.621 (0.170%), neg=0, invalid=762 0062: dt=36.288000, rms=0.620 (0.161%), neg=0, invalid=762 0063: dt=36.288000, rms=0.619 (0.153%), neg=0, invalid=762 0064: dt=36.288000, rms=0.619 (0.138%), neg=0, invalid=762 0065: dt=36.288000, rms=0.618 (0.131%), neg=0, invalid=762 0066: dt=36.288000, rms=0.617 (0.115%), neg=0, invalid=762 0067: dt=36.288000, rms=0.616 (0.106%), neg=0, invalid=762 0068: dt=580.608000, rms=0.616 (0.075%), neg=0, invalid=762 0069: dt=580.608000, rms=0.616 (-4.223%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=762 0070: dt=36.288000, rms=0.615 (0.219%), neg=0, invalid=762 0071: dt=62.208000, rms=0.615 (0.037%), neg=0, invalid=762 0072: dt=62.208000, rms=0.615 (0.021%), neg=0, invalid=762 0073: dt=62.208000, rms=0.615 (0.007%), neg=0, invalid=762 0074: dt=62.208000, rms=0.615 (-0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.643, neg=0, invalid=762 0075: dt=0.000000, rms=0.642 (0.085%), neg=0, invalid=762 0076: dt=0.000000, rms=0.642 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.643, neg=0, invalid=762 0077: dt=0.000000, rms=0.642 (0.085%), neg=0, invalid=762 0078: dt=0.000000, rms=0.642 (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=0.724, neg=0, invalid=762 0079: dt=5.175824, rms=0.705 (2.654%), neg=0, invalid=762 0080: dt=2.415584, rms=0.704 (0.112%), neg=0, invalid=762 0081: dt=2.415584, rms=0.704 (-0.052%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0082: dt=0.000000, rms=0.704 (0.069%), neg=0, invalid=762 0083: dt=0.000000, rms=0.704 (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=0.794, neg=0, invalid=762 0084: dt=1.280000, rms=0.789 (0.557%), neg=0, invalid=762 0085: dt=2.191781, rms=0.783 (0.832%), neg=0, invalid=762 0086: dt=0.448000, rms=0.782 (0.042%), neg=0, invalid=762 0087: dt=0.448000, rms=0.782 (0.054%), neg=0, invalid=762 0088: dt=0.448000, rms=0.781 (0.079%), neg=0, invalid=762 0089: dt=0.448000, rms=0.781 (0.080%), neg=0, invalid=762 0090: dt=0.448000, rms=0.780 (0.038%), neg=0, invalid=762 0091: dt=0.448000, rms=0.780 (-0.062%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.781, neg=0, invalid=762 0092: dt=1.792000, rms=0.778 (0.353%), neg=0, invalid=762 0093: dt=0.000000, rms=0.778 (0.003%), neg=0, invalid=762 0094: dt=0.100000, rms=0.778 (-0.009%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.713, neg=0, invalid=762 0095: dt=1.024000, rms=0.688 (3.523%), neg=0, invalid=762 0096: dt=0.096000, rms=0.687 (0.218%), neg=0, invalid=762 0097: dt=0.096000, rms=0.687 (-0.083%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.687, neg=0, invalid=762 0098: dt=0.028000, rms=0.687 (0.102%), neg=0, invalid=762 0099: dt=0.016000, rms=0.687 (0.003%), neg=0, invalid=762 0100: dt=0.016000, rms=0.687 (-0.003%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.05065 (53) Left_Lateral_Ventricle (4): linear fit = 1.91 x + 0.0 (809 voxels, overlap=0.019) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (809 voxels, peak = 38), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.06410 (24) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (307 voxels, overlap=0.414) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (307 voxels, peak = 23), gca=23.3 gca peak = 0.26829 (96) mri peak = 0.07729 (90) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (633 voxels, overlap=0.245) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (633 voxels, peak = 89), gca=88.8 gca peak = 0.20183 (93) mri peak = 0.06992 (86) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (616 voxels, overlap=0.603) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (616 voxels, peak = 82), gca=82.3 gca peak = 0.21683 (55) mri peak = 0.09696 (54) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (755 voxels, overlap=0.996) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (755 voxels, peak = 53), gca=53.1 gca peak = 0.30730 (58) mri peak = 0.08225 (55) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (543 voxels, overlap=0.966) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (543 voxels, peak = 56), gca=56.0 gca peak = 0.11430 (101) mri peak = 0.12251 (103) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (51360 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (51360 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.10820 (104) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (50034 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (50034 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.03926 (57) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (17235 voxels, overlap=0.995) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (17235 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.04767 (56) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (18881 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (18881 voxels, peak = 56), gca=56.0 gca peak = 0.14161 (67) mri peak = 0.08902 (75) Right_Caudate (50): linear fit = 1.09 x + 0.0 (891 voxels, overlap=0.880) Right_Caudate (50): linear fit = 1.09 x + 0.0 (891 voxels, peak = 73), gca=72.7 gca peak = 0.15243 (71) mri peak = 0.06534 (77) Left_Caudate (11): linear fit = 1.03 x + 0.0 (937 voxels, overlap=0.868) Left_Caudate (11): linear fit = 1.03 x + 0.0 (937 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.03901 (56) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (24764 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (24764 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.03938 (56) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (22062 voxels, overlap=0.984) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (22062 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.08482 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (8443 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (8443 voxels, peak = 86), gca=86.1 gca peak = 0.20573 (83) mri peak = 0.09713 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7314 voxels, overlap=0.749) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7314 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.18406 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (397 voxels, overlap=0.728) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (397 voxels, peak = 51), gca=51.0 gca peak = 0.39313 (56) mri peak = 0.11623 (51) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (506 voxels, overlap=0.826) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (506 voxels, peak = 50), gca=50.1 gca peak = 0.14181 (85) mri peak = 0.05692 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4804 voxels, overlap=0.991) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4804 voxels, peak = 85), gca=84.6 gca peak = 0.11978 (83) mri peak = 0.06359 (88) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3978 voxels, overlap=0.895) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3978 voxels, peak = 87), gca=86.7 gca peak = 0.13399 (79) mri peak = 0.05799 (77) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2218 voxels, overlap=0.997) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2218 voxels, peak = 77), gca=77.0 gca peak = 0.14159 (79) mri peak = 0.06812 (75) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2071 voxels, overlap=0.961) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2071 voxels, peak = 76), gca=76.2 gca peak = 0.10025 (80) mri peak = 0.09670 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9941 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9941 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07022 (84) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (680 voxels, overlap=0.727) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (680 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.06995 (90) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (874 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (874 voxels, peak = 92), gca=92.1 gca peak = 0.20494 (23) mri peak = 0.05508 (36) gca peak = 0.15061 (21) mri peak = 1.00000 (55) Fourth_Ventricle (15): linear fit = 2.60 x + 0.0 (236 voxels, overlap=1.519) Fourth_Ventricle (15): linear fit = 2.60 x + 0.0 (236 voxels, peak = 54), gca=54.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.95 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.48 x + 0.0 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=0.698, neg=0, invalid=762 0101: dt=129.472000, rms=0.689 (1.342%), neg=0, invalid=762 0102: dt=134.400000, rms=0.685 (0.512%), neg=0, invalid=762 0103: dt=129.472000, rms=0.683 (0.336%), neg=0, invalid=762 0104: dt=129.472000, rms=0.681 (0.212%), neg=0, invalid=762 0105: dt=221.952000, rms=0.680 (0.244%), neg=0, invalid=762 0106: dt=110.976000, rms=0.679 (0.164%), neg=0, invalid=762 0107: dt=129.472000, rms=0.678 (0.133%), neg=0, invalid=762 0108: dt=295.936000, rms=0.677 (0.163%), neg=0, invalid=762 0109: dt=92.480000, rms=0.676 (0.145%), neg=0, invalid=762 0110: dt=295.936000, rms=0.675 (0.138%), neg=0, invalid=762 0111: dt=92.480000, rms=0.674 (0.101%), neg=0, invalid=762 0112: dt=443.904000, rms=0.673 (0.144%), neg=0, invalid=762 0113: dt=73.984000, rms=0.672 (0.118%), neg=0, invalid=762 0114: dt=2071.552000, rms=0.668 (0.556%), neg=0, invalid=762 0115: dt=517.888000, rms=0.668 (0.091%), neg=0, invalid=762 0116: dt=110.976000, rms=0.668 (0.039%), neg=0, invalid=762 0117: dt=110.976000, rms=0.667 (0.024%), neg=0, invalid=762 0118: dt=110.976000, rms=0.667 (0.041%), neg=0, invalid=762 0119: dt=110.976000, rms=0.667 (0.050%), neg=0, invalid=762 0120: dt=110.976000, rms=0.666 (0.058%), neg=0, invalid=762 0121: dt=110.976000, rms=0.666 (0.064%), neg=0, invalid=762 0122: dt=110.976000, rms=0.666 (0.069%), neg=0, invalid=762 0123: dt=110.976000, rms=0.665 (0.071%), neg=0, invalid=762 0124: dt=110.976000, rms=0.665 (0.070%), neg=0, invalid=762 0125: dt=110.976000, rms=0.664 (0.070%), neg=0, invalid=762 0126: dt=110.976000, rms=0.664 (0.070%), neg=0, invalid=762 0127: dt=110.976000, rms=0.663 (0.067%), neg=0, invalid=762 0128: dt=110.976000, rms=0.663 (0.062%), neg=0, invalid=762 0129: dt=110.976000, rms=0.662 (0.058%), neg=0, invalid=762 0130: dt=110.976000, rms=0.662 (0.055%), neg=0, invalid=762 0131: dt=110.976000, rms=0.662 (0.056%), neg=0, invalid=762 0132: dt=110.976000, rms=0.661 (0.061%), neg=0, invalid=762 0133: dt=110.976000, rms=0.661 (0.062%), neg=0, invalid=762 0134: dt=110.976000, rms=0.660 (0.063%), neg=0, invalid=762 0135: dt=110.976000, rms=0.660 (0.062%), neg=0, invalid=762 0136: dt=110.976000, rms=0.660 (0.061%), neg=0, invalid=762 0137: dt=110.976000, rms=0.659 (0.058%), neg=0, invalid=762 0138: dt=110.976000, rms=0.659 (0.058%), neg=0, invalid=762 0139: dt=110.976000, rms=0.658 (0.055%), neg=0, invalid=762 0140: dt=110.976000, rms=0.658 (0.055%), neg=0, invalid=762 0141: dt=110.976000, rms=0.658 (0.054%), neg=0, invalid=762 0142: dt=110.976000, rms=0.657 (0.055%), neg=0, invalid=762 0143: dt=110.976000, rms=0.657 (0.057%), neg=0, invalid=762 0144: dt=110.976000, rms=0.657 (0.059%), neg=0, invalid=762 0145: dt=110.976000, rms=0.656 (0.060%), neg=0, invalid=762 0146: dt=110.976000, rms=0.656 (0.057%), neg=0, invalid=762 0147: dt=110.976000, rms=0.656 (0.056%), neg=0, invalid=762 0148: dt=110.976000, rms=0.655 (0.054%), neg=0, invalid=762 0149: dt=110.976000, rms=0.655 (0.054%), neg=0, invalid=762 0150: dt=110.976000, rms=0.654 (0.051%), neg=0, invalid=762 0151: dt=110.976000, rms=0.654 (0.048%), neg=0, invalid=762 0152: dt=110.976000, rms=0.654 (0.044%), neg=0, invalid=762 0153: dt=110.976000, rms=0.654 (0.040%), neg=0, invalid=762 0154: dt=110.976000, rms=0.653 (0.043%), neg=0, invalid=762 0155: dt=110.976000, rms=0.653 (0.042%), neg=0, invalid=762 0156: dt=110.976000, rms=0.653 (0.041%), neg=0, invalid=762 0157: dt=110.976000, rms=0.653 (0.039%), neg=0, invalid=762 0158: dt=110.976000, rms=0.652 (0.039%), neg=0, invalid=762 0159: dt=110.976000, rms=0.652 (0.037%), neg=0, invalid=762 0160: dt=110.976000, rms=0.652 (0.035%), neg=0, invalid=762 0161: dt=110.976000, rms=0.652 (0.033%), neg=0, invalid=762 0162: dt=110.976000, rms=0.651 (0.033%), neg=0, invalid=762 0163: dt=110.976000, rms=0.651 (0.031%), neg=0, invalid=762 0164: dt=110.976000, rms=0.651 (0.028%), neg=0, invalid=762 0165: dt=110.976000, rms=0.651 (0.029%), neg=0, invalid=762 0166: dt=110.976000, rms=0.651 (0.029%), neg=0, invalid=762 0167: dt=110.976000, rms=0.650 (0.030%), neg=0, invalid=762 0168: dt=110.976000, rms=0.650 (0.029%), neg=0, invalid=762 0169: dt=110.976000, rms=0.650 (0.029%), neg=0, invalid=762 0170: dt=110.976000, rms=0.650 (0.027%), neg=0, invalid=762 0171: dt=110.976000, rms=0.650 (0.025%), neg=0, invalid=762 0172: dt=110.976000, rms=0.650 (0.025%), neg=0, invalid=762 0173: dt=110.976000, rms=0.649 (0.026%), neg=0, invalid=762 0174: dt=110.976000, rms=0.649 (0.026%), neg=0, invalid=762 0175: dt=110.976000, rms=0.649 (0.025%), neg=0, invalid=762 0176: dt=110.976000, rms=0.649 (0.024%), neg=0, invalid=762 0177: dt=110.976000, rms=0.649 (0.024%), neg=0, invalid=762 0178: dt=110.976000, rms=0.649 (0.024%), neg=0, invalid=762 0179: dt=4734.976000, rms=0.648 (0.052%), neg=0, invalid=762 0180: dt=110.976000, rms=0.648 (0.041%), neg=0, invalid=762 0181: dt=110.976000, rms=0.648 (0.002%), neg=0, invalid=762 0182: dt=110.976000, rms=0.648 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.649, neg=0, invalid=762 0183: dt=129.472000, rms=0.648 (0.172%), neg=0, invalid=762 0184: dt=369.920000, rms=0.647 (0.094%), neg=0, invalid=762 0185: dt=92.480000, rms=0.647 (0.038%), neg=0, invalid=762 0186: dt=92.480000, rms=0.646 (0.025%), neg=0, invalid=762 0187: dt=92.480000, rms=0.646 (0.028%), neg=0, invalid=762 0188: dt=92.480000, rms=0.646 (0.035%), neg=0, invalid=762 0189: dt=92.480000, rms=0.646 (0.038%), neg=0, invalid=762 0190: dt=92.480000, rms=0.646 (0.039%), neg=0, invalid=762 0191: dt=92.480000, rms=0.645 (0.043%), neg=0, invalid=762 0192: dt=92.480000, rms=0.645 (0.036%), neg=0, invalid=762 0193: dt=92.480000, rms=0.645 (0.032%), neg=0, invalid=762 0194: dt=92.480000, rms=0.645 (0.036%), neg=0, invalid=762 0195: dt=92.480000, rms=0.644 (0.032%), neg=0, invalid=762 0196: dt=92.480000, rms=0.644 (0.030%), neg=0, invalid=762 0197: dt=92.480000, rms=0.644 (0.026%), neg=0, invalid=762 0198: dt=92.480000, rms=0.644 (0.021%), neg=0, invalid=762 0199: dt=92.480000, rms=0.644 (0.018%), neg=0, invalid=762 0200: dt=887.808000, rms=0.644 (0.014%), neg=0, invalid=762 0201: dt=887.808000, rms=0.644 (-0.146%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0202: dt=114.549153, rms=0.641 (0.695%), neg=0, invalid=762 0203: dt=164.641221, rms=0.635 (1.001%), neg=0, invalid=762 0204: dt=55.688312, rms=0.631 (0.532%), neg=0, invalid=762 0205: dt=145.152000, rms=0.628 (0.570%), neg=0, invalid=762 0206: dt=67.121951, rms=0.625 (0.372%), neg=0, invalid=762 0207: dt=73.194366, rms=0.623 (0.346%), neg=0, invalid=762 0208: dt=78.035088, rms=0.621 (0.295%), neg=0, invalid=762 0209: dt=75.264000, rms=0.620 (0.265%), neg=0, invalid=762 0210: dt=76.800000, rms=0.618 (0.256%), neg=0, invalid=762 0211: dt=72.977376, rms=0.617 (0.219%), neg=0, invalid=762 0212: dt=78.712644, rms=0.615 (0.220%), neg=0, invalid=762 0213: dt=67.869767, rms=0.614 (0.187%), neg=0, invalid=762 0214: dt=82.944000, rms=0.613 (0.201%), neg=0, invalid=762 0215: dt=67.918367, rms=0.612 (0.163%), neg=0, invalid=762 0216: dt=82.944000, rms=0.611 (0.183%), neg=0, invalid=762 0217: dt=62.757282, rms=0.610 (0.142%), neg=0, invalid=762 0218: dt=103.680000, rms=0.609 (0.189%), neg=0, invalid=762 0219: dt=36.288000, rms=0.608 (0.112%), neg=0, invalid=762 0220: dt=145.152000, rms=0.607 (0.257%), neg=0, invalid=762 0221: dt=103.680000, rms=0.606 (0.167%), neg=0, invalid=762 0222: dt=36.288000, rms=0.605 (0.093%), neg=0, invalid=762 0223: dt=36.288000, rms=0.605 (0.066%), neg=0, invalid=762 0224: dt=0.141750, rms=0.605 (0.004%), neg=0, invalid=762 0225: dt=0.035437, rms=0.605 (0.000%), neg=0, invalid=762 0226: dt=0.008859, rms=0.605 (0.000%), neg=0, invalid=762 0227: dt=0.002215, rms=0.605 (0.000%), neg=0, invalid=762 0228: dt=0.000000, rms=0.605 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0229: dt=121.367876, rms=0.602 (0.579%), neg=0, invalid=762 0230: dt=75.811159, rms=0.600 (0.251%), neg=0, invalid=762 0231: dt=82.944000, rms=0.599 (0.182%), neg=0, invalid=762 0232: dt=36.288000, rms=0.599 (0.076%), neg=0, invalid=762 0233: dt=2.268000, rms=0.599 (0.007%), neg=0, invalid=762 0234: dt=0.035437, rms=0.599 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0235: dt=0.000488, rms=0.604 (0.129%), neg=0, invalid=762 0236: dt=0.000000, rms=0.604 (-0.000%), neg=0, invalid=762 0237: dt=0.000031, rms=0.604 (0.000%), neg=0, invalid=762 0238: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0239: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0240: dt=32.000000, rms=0.591 (2.268%), neg=0, invalid=762 0241: dt=2.400000, rms=0.590 (0.127%), neg=0, invalid=762 0242: dt=0.043750, rms=0.590 (0.002%), neg=0, invalid=762 0243: dt=0.021875, rms=0.590 (0.001%), neg=0, invalid=762 0244: dt=0.005469, rms=0.590 (0.000%), neg=0, invalid=762 0245: dt=0.002734, rms=0.590 (0.000%), neg=0, invalid=762 0246: dt=0.001250, rms=0.590 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.607, neg=0, invalid=762 0247: dt=1.008000, rms=0.603 (0.601%), neg=0, invalid=762 0248: dt=1.008000, rms=0.600 (0.451%), neg=0, invalid=762 0249: dt=0.252000, rms=0.600 (0.107%), neg=0, invalid=762 0250: dt=0.216000, rms=0.599 (0.091%), neg=0, invalid=762 0251: dt=0.002813, rms=0.599 (-0.000%), neg=0, invalid=762 0252: dt=0.002813, rms=0.599 (0.001%), neg=0, invalid=762 0253: dt=0.000176, rms=0.599 (0.000%), neg=0, invalid=762 0254: dt=0.000022, rms=0.599 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=762 0255: dt=4.032000, rms=0.591 (1.577%), neg=0, invalid=762 0256: dt=3.456000, rms=0.585 (0.996%), neg=0, invalid=762 0257: dt=0.252000, rms=0.584 (0.063%), neg=0, invalid=762 0258: dt=0.216000, rms=0.584 (0.052%), neg=0, invalid=762 0259: dt=0.015750, rms=0.584 (0.004%), neg=0, invalid=762 0260: dt=0.003938, rms=0.584 (0.001%), neg=0, invalid=762 0261: dt=0.000492, rms=0.584 (0.000%), neg=0, invalid=762 0262: dt=0.000031, rms=0.584 (0.000%), neg=0, invalid=762 0263: dt=0.000000, rms=0.584 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.616, neg=0, invalid=762 0264: dt=4.596237, rms=0.608 (1.229%), neg=0, invalid=762 0265: dt=1.792000, rms=0.608 (0.080%), neg=0, invalid=762 0266: dt=6.144000, rms=0.607 (0.101%), neg=0, invalid=762 0267: dt=1.792000, rms=0.607 (0.027%), neg=0, invalid=762 0268: dt=1.792000, rms=0.607 (0.028%), neg=0, invalid=762 0269: dt=1.792000, rms=0.607 (0.036%), neg=0, invalid=762 0270: dt=1.792000, rms=0.607 (0.017%), neg=0, invalid=762 0271: dt=1.792000, rms=0.607 (-0.009%), neg=0, invalid=762 0272: dt=7.168000, rms=0.606 (0.064%), neg=0, invalid=762 0273: dt=1.792000, rms=0.606 (0.017%), neg=0, invalid=762 0274: dt=1.792000, rms=0.606 (0.011%), neg=0, invalid=762 0275: dt=1.792000, rms=0.606 (0.024%), neg=0, invalid=762 0276: dt=1.792000, rms=0.606 (0.034%), neg=0, invalid=762 0277: dt=1.792000, rms=0.606 (0.026%), neg=0, invalid=762 0278: dt=1.792000, rms=0.605 (0.021%), neg=0, invalid=762 0279: dt=1.792000, rms=0.605 (0.002%), neg=0, invalid=762 0280: dt=0.256000, rms=0.605 (0.002%), neg=0, invalid=762 0281: dt=0.768000, rms=0.605 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0282: dt=7.168000, rms=0.601 (0.848%), neg=0, invalid=762 0283: dt=0.028000, rms=0.601 (0.006%), neg=0, invalid=762 0284: dt=0.028000, rms=0.601 (-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=0.583, neg=0, invalid=762 0285: dt=0.448000, rms=0.564 (3.325%), neg=0, invalid=762 0286: dt=0.448000, rms=0.558 (1.082%), neg=0, invalid=762 0287: dt=0.448000, rms=0.554 (0.665%), neg=0, invalid=762 0288: dt=0.448000, rms=0.552 (0.433%), neg=0, invalid=762 0289: dt=0.448000, rms=0.550 (0.340%), neg=0, invalid=762 0290: dt=0.448000, rms=0.549 (0.248%), neg=0, invalid=762 0291: dt=0.448000, rms=0.547 (0.218%), neg=0, invalid=762 0292: dt=0.448000, rms=0.547 (0.163%), neg=0, invalid=762 0293: dt=0.448000, rms=0.546 (0.154%), neg=0, invalid=762 0294: dt=0.448000, rms=0.545 (0.114%), neg=0, invalid=762 0295: dt=0.448000, rms=0.544 (0.116%), neg=0, invalid=762 0296: dt=0.448000, rms=0.544 (0.082%), neg=0, invalid=762 0297: dt=0.448000, rms=0.544 (0.090%), neg=0, invalid=762 0298: dt=0.448000, rms=0.543 (0.066%), neg=0, invalid=762 0299: dt=0.448000, rms=0.543 (0.071%), neg=0, invalid=762 0300: dt=0.448000, rms=0.542 (0.051%), neg=0, invalid=762 0301: dt=0.448000, rms=0.542 (0.059%), neg=0, invalid=762 0302: dt=0.448000, rms=0.542 (0.039%), neg=0, invalid=762 0303: dt=0.448000, rms=0.542 (0.049%), neg=0, invalid=762 0304: dt=0.448000, rms=0.541 (0.075%), neg=0, invalid=762 0305: dt=0.448000, rms=0.541 (0.100%), neg=0, invalid=762 0306: dt=0.448000, rms=0.540 (0.113%), neg=0, invalid=762 0307: dt=0.448000, rms=0.540 (0.020%), neg=0, invalid=762 0308: dt=0.448000, rms=0.540 (0.023%), neg=0, invalid=762 0309: dt=0.448000, rms=0.540 (0.022%), neg=0, invalid=762 0310: dt=0.448000, rms=0.540 (0.008%), neg=0, invalid=762 0311: dt=0.448000, rms=0.540 (0.013%), neg=0, invalid=762 0312: dt=0.448000, rms=0.540 (0.022%), neg=0, invalid=762 0313: dt=0.448000, rms=0.539 (0.026%), neg=0, invalid=762 0314: dt=0.448000, rms=0.539 (0.036%), neg=0, invalid=762 0315: dt=0.448000, rms=0.539 (0.039%), neg=0, invalid=762 0316: dt=0.448000, rms=0.539 (0.033%), neg=0, invalid=762 0317: dt=0.448000, rms=0.539 (0.004%), neg=0, invalid=762 0318: dt=0.448000, rms=0.539 (0.009%), neg=0, invalid=762 0319: dt=0.448000, rms=0.539 (0.009%), neg=0, invalid=762 0320: dt=0.448000, rms=0.539 (0.008%), neg=0, invalid=762 0321: dt=0.320000, rms=0.539 (0.002%), neg=0, invalid=762 0322: dt=0.320000, rms=0.539 (0.005%), neg=0, invalid=762 0323: dt=0.320000, rms=0.539 (0.007%), neg=0, invalid=762 0324: dt=0.320000, rms=0.539 (0.001%), neg=0, invalid=762 0325: dt=0.320000, rms=0.539 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0326: dt=0.448000, rms=0.534 (1.043%), neg=0, invalid=762 0327: dt=0.384000, rms=0.534 (0.024%), neg=0, invalid=762 0328: dt=0.384000, rms=0.534 (-0.002%), 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=0.531, neg=0, invalid=762 0329: dt=0.007902, rms=0.530 (0.161%), neg=0, invalid=762 0330: dt=0.000000, rms=0.530 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0331: dt=55.488000, rms=0.530 (0.183%), neg=0, invalid=762 0332: dt=129.472000, rms=0.530 (0.021%), neg=0, invalid=762 0333: dt=129.472000, rms=0.529 (0.036%), neg=0, invalid=762 0334: dt=129.472000, rms=0.529 (0.032%), neg=0, invalid=762 0335: dt=129.472000, rms=0.529 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.530, neg=0, invalid=762 0336: dt=36.288000, rms=0.528 (0.368%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0337: dt=78.117647, rms=0.527 (0.162%), neg=0, invalid=762 0338: dt=78.117647, rms=0.526 (0.159%), neg=0, invalid=762 0339: dt=78.117647, rms=0.526 (0.126%), neg=0, invalid=762 0340: dt=78.117647, rms=0.526 (-0.055%), neg=0, invalid=762 0341: dt=124.416000, rms=0.525 (0.113%), neg=0, invalid=762 0342: dt=36.288000, rms=0.524 (0.138%), neg=0, invalid=762 0343: dt=145.152000, rms=0.524 (0.085%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0344: dt=69.333333, rms=0.522 (0.595%), neg=0, invalid=762 0345: dt=36.288000, rms=0.520 (0.316%), neg=0, invalid=762 0346: dt=145.152000, rms=0.519 (0.294%), neg=0, invalid=762 0347: dt=31.104000, rms=0.518 (0.134%), neg=0, invalid=762 0348: dt=31.104000, rms=0.518 (0.051%), neg=0, invalid=762 0349: dt=31.104000, rms=0.517 (0.059%), neg=0, invalid=762 0350: dt=31.104000, rms=0.517 (0.080%), neg=0, invalid=762 0351: dt=31.104000, rms=0.517 (0.090%), neg=0, invalid=762 0352: dt=31.104000, rms=0.516 (0.094%), neg=0, invalid=762 0353: dt=31.104000, rms=0.516 (0.098%), neg=0, invalid=762 0354: dt=31.104000, rms=0.515 (0.099%), neg=0, invalid=762 0355: dt=31.104000, rms=0.515 (0.093%), neg=0, invalid=762 0356: dt=31.104000, rms=0.514 (0.087%), neg=0, invalid=762 0357: dt=124.416000, rms=0.514 (0.039%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 iter 0, gcam->neg = 16 after 5 iterations, nbhd size=0, neg = 0 0358: dt=42.947368, rms=0.510 (1.124%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0359: dt=42.845938, rms=0.505 (0.900%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0360: dt=23.192182, rms=0.503 (0.481%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0361: dt=67.298969, rms=0.500 (0.595%), neg=0, invalid=762 0362: dt=21.132075, rms=0.498 (0.360%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0363: dt=38.400000, rms=0.496 (0.419%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0364: dt=11.200000, rms=0.495 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0365: dt=11.200000, rms=0.495 (0.085%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0366: dt=11.200000, rms=0.494 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0367: dt=11.200000, rms=0.493 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=1, neg = 0 0368: dt=11.200000, rms=0.492 (0.244%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0369: dt=11.200000, rms=0.491 (0.264%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0370: dt=11.200000, rms=0.489 (0.258%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 10 iterations, nbhd size=0, neg = 0 0371: dt=11.200000, rms=0.488 (0.231%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 4 iterations, nbhd size=0, neg = 0 0372: dt=11.200000, rms=0.487 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 3 iterations, nbhd size=0, neg = 0 0373: dt=11.200000, rms=0.486 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 7 iterations, nbhd size=0, neg = 0 0374: dt=11.200000, rms=0.485 (0.199%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=0, neg = 0 0375: dt=11.200000, rms=0.484 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 8 iterations, nbhd size=0, neg = 0 0376: dt=11.200000, rms=0.484 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 4 iterations, nbhd size=0, neg = 0 0377: dt=11.200000, rms=0.483 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 11 iterations, nbhd size=0, neg = 0 0378: dt=11.200000, rms=0.482 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0379: dt=11.200000, rms=0.482 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 13 iterations, nbhd size=1, neg = 0 0380: dt=11.200000, rms=0.481 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0381: dt=44.800000, rms=0.481 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=0, neg = 0 0382: dt=44.800000, rms=0.481 (-0.117%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0383: dt=38.400000, rms=0.478 (0.821%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=0, neg = 0 0384: dt=24.026230, rms=0.477 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0385: dt=24.592593, rms=0.476 (0.140%), neg=0, invalid=762 0386: dt=24.592593, rms=0.476 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0387: dt=24.592593, rms=0.475 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0388: dt=24.592593, rms=0.475 (0.049%), neg=0, invalid=762 0389: dt=24.592593, rms=0.475 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0390: dt=24.592593, rms=0.475 (-0.047%), neg=0, invalid=762 0391: dt=11.200000, rms=0.474 (0.046%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0392: dt=128.000000, rms=0.474 (0.152%), neg=0, invalid=762 0393: dt=11.200000, rms=0.474 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0394: dt=0.000000, rms=0.483 (0.184%), neg=0, invalid=762 0395: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0396: dt=0.000023, rms=0.483 (0.184%), neg=0, invalid=762 0397: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762 0398: dt=0.150000, rms=0.483 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 0399: dt=1.280000, rms=0.502 (0.571%), neg=0, invalid=762 0400: dt=0.448000, rms=0.502 (0.029%), neg=0, invalid=762 0401: dt=0.448000, rms=0.502 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=762 0402: dt=1.024000, rms=0.501 (0.289%), neg=0, invalid=762 0403: dt=0.384000, rms=0.501 (0.012%), neg=0, invalid=762 0404: dt=0.384000, rms=0.501 (-0.003%), 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=0.482, neg=0, invalid=762 iter 0, gcam->neg = 1527 after 14 iterations, nbhd size=1, neg = 0 0405: dt=2.460800, rms=0.446 (7.625%), neg=0, invalid=762 0406: dt=0.112000, rms=0.445 (0.167%), neg=0, invalid=762 0407: dt=0.112000, rms=0.445 (-0.065%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=762 0408: dt=0.096000, rms=0.445 (0.281%), neg=0, invalid=762 0409: dt=0.000094, rms=0.445 (-0.000%), neg=0, invalid=762 0410: dt=0.000094, rms=0.445 (0.000%), neg=0, invalid=762 0411: dt=0.000094, rms=0.445 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0412: dt=0.000000, rms=0.428 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0413: dt=32.368000, rms=0.428 (0.005%), neg=0, invalid=762 0414: dt=27.744000, rms=0.428 (0.001%), neg=0, invalid=762 0415: dt=27.744000, rms=0.428 (0.000%), neg=0, invalid=762 0416: dt=27.744000, rms=0.428 (-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=0.428, neg=0, invalid=762 0417: dt=2.268000, rms=0.428 (0.001%), neg=0, invalid=762 0418: dt=0.567000, rms=0.428 (0.000%), neg=0, invalid=762 0419: dt=0.567000, rms=0.428 (0.000%), neg=0, invalid=762 0420: dt=0.567000, rms=0.428 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0421: dt=82.944000, rms=0.428 (0.077%), neg=0, invalid=762 0422: dt=103.680000, rms=0.427 (0.067%), neg=0, invalid=762 0423: dt=103.680000, rms=0.427 (-0.021%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0424: dt=19.200000, rms=0.427 (0.241%), neg=0, invalid=762 0425: dt=25.600000, rms=0.427 (0.142%), neg=0, invalid=762 0426: dt=25.600000, rms=0.426 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 0427: dt=25.600000, rms=0.426 (0.036%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 7 iterations, nbhd size=0, neg = 0 0428: dt=25.600000, rms=0.426 (-0.116%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0429: dt=44.800000, rms=0.422 (0.974%), neg=0, invalid=762 0430: dt=25.600000, rms=0.421 (0.226%), neg=0, invalid=762 0431: dt=25.600000, rms=0.420 (0.138%), neg=0, invalid=762 0432: dt=25.600000, rms=0.419 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0433: dt=25.600000, rms=0.419 (0.223%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0434: dt=25.600000, rms=0.418 (0.206%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0435: dt=25.600000, rms=0.417 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0436: dt=25.600000, rms=0.416 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 12 iterations, nbhd size=1, neg = 0 0437: dt=25.600000, rms=0.415 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 15 iterations, nbhd size=1, neg = 0 0438: dt=25.600000, rms=0.415 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=0, neg = 0 0439: dt=25.600000, rms=0.414 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 12 iterations, nbhd size=0, neg = 0 0440: dt=25.600000, rms=0.414 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=0, neg = 0 0441: dt=25.600000, rms=0.413 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 0442: dt=44.800000, rms=0.413 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0443: dt=44.800000, rms=0.413 (-0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0444: dt=0.500000, rms=0.419 (0.001%), neg=0, invalid=762 0445: dt=0.013500, rms=0.419 (0.000%), neg=0, invalid=762 0446: dt=0.013500, rms=0.419 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0447: dt=1.008000, rms=0.419 (0.007%), neg=0, invalid=762 0448: dt=1.008000, rms=0.419 (0.003%), neg=0, invalid=762 0449: dt=1.008000, rms=0.419 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 0450: dt=0.000000, rms=0.430 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 0451: dt=0.000000, rms=0.430 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 iter 0, gcam->neg = 466 after 19 iterations, nbhd size=1, neg = 0 0452: dt=0.992361, rms=0.404 (1.731%), neg=0, invalid=762 0453: dt=0.028000, rms=0.404 (0.009%), neg=0, invalid=762 0454: dt=0.028000, rms=0.404 (0.005%), neg=0, invalid=762 0455: dt=0.028000, rms=0.404 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0456: dt=0.320000, rms=0.403 (0.282%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0457: dt=0.488506, rms=0.402 (0.244%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 1 iterations, nbhd size=0, neg = 0 0458: dt=0.488506, rms=0.402 (-0.022%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 7 minutes and 57 seconds. mri_ca_register utimesec 7671.574743 mri_ca_register stimesec 7.285892 mri_ca_register ru_maxrss 1323640 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4037180 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 108 mri_ca_register ru_nivcsw 25835 FSRUNTIME@ mri_ca_register 2.1324 hours 1 threads #-------------------------------------- #@# SubCort Seg Wed Oct 2 21:23:05 EDT 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname n511 machine x86_64 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /public/apps/freesurfer/6.0.0/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 6.30 Atlas used for the 3D morph was /public/apps/freesurfer/6.0.0/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 = 0.07599 (15) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (117 voxels, overlap=0.442) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (117 voxels, peak = 13), gca=13.1 gca peak = 0.17677 (13) mri peak = 0.04788 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.60 x + 0.0 (176 voxels, overlap=0.428) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (176 voxels, peak = 21), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.09198 (91) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (509 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (509 voxels, peak = 92), gca=91.7 gca peak = 0.16930 (96) mri peak = 0.09026 (96) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (698 voxels, overlap=1.016) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (698 voxels, peak = 95), gca=94.6 gca peak = 0.24553 (55) mri peak = 0.11722 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (664 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (664 voxels, peak = 55), gca=55.0 gca peak = 0.30264 (59) mri peak = 0.10182 (56) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (670 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (670 voxels, peak = 58), gca=58.1 gca peak = 0.07580 (103) mri peak = 0.12923 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24862 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24862 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.10507 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (27968 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (27968 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.03944 (58) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (22168 voxels, overlap=0.992) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (22168 voxels, peak = 56), gca=56.0 gca peak = 0.11620 (58) mri peak = 0.04620 (58) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (21314 voxels, overlap=0.992) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (21314 voxels, peak = 56), gca=56.0 gca peak = 0.30970 (66) mri peak = 0.11146 (75) Right_Caudate (50): linear fit = 1.11 x + 0.0 (742 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.11 x + 0.0 (742 voxels, peak = 73), gca=72.9 gca peak = 0.15280 (69) mri peak = 0.10565 (74) Left_Caudate (11): linear fit = 1.00 x + 0.0 (672 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.00 x + 0.0 (672 voxels, peak = 69), gca=69.0 gca peak = 0.13902 (56) mri peak = 0.04819 (56) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (28385 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (28385 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.04448 (56) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (25527 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (25527 voxels, peak = 54), gca=54.2 gca peak = 0.16765 (84) mri peak = 0.12464 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5631 voxels, overlap=0.903) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5631 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.11577 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5371 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5371 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.18116 (52) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (519 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (519 voxels, peak = 51), gca=51.0 gca peak = 0.33601 (57) mri peak = 0.14618 (52) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (466 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (466 voxels, peak = 51), gca=51.0 gca peak = 0.11131 (90) mri peak = 0.06939 (89) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3778 voxels, overlap=0.972) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3778 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.07216 (88) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3144 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3144 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.08932 (74) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1658 voxels, overlap=0.790) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1658 voxels, peak = 78), gca=78.2 gca peak = 0.10360 (77) mri peak = 0.07900 (76) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1677 voxels, overlap=0.829) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1677 voxels, peak = 74), gca=74.3 gca peak = 0.08424 (78) mri peak = 0.10140 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11451 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11451 voxels, peak = 82), gca=82.3 gca peak = 0.12631 (89) mri peak = 0.06801 (99) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1287 voxels, overlap=0.828) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1287 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.05617 (94) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1463 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1463 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.07814 (16) gca peak = 0.19357 (14) mri peak = 0.13637 (10) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (104 voxels, overlap=0.566) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (104 voxels, peak = 8), gca=8.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) 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 0.95 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.08 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.23253 (13) mri peak = 0.07599 (15) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (117 voxels, overlap=0.887) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (117 voxels, peak = 14), gca=14.5 gca peak = 0.13417 (19) mri peak = 0.04788 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (176 voxels, overlap=0.583) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (176 voxels, peak = 20), gca=19.7 gca peak = 0.24970 (91) mri peak = 0.09198 (91) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (509 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (509 voxels, peak = 91), gca=90.5 gca peak = 0.20279 (95) mri peak = 0.09026 (96) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (698 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (698 voxels, peak = 95), gca=94.5 gca peak = 0.23255 (55) mri peak = 0.11722 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (664 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (664 voxels, peak = 55), gca=55.0 gca peak = 0.30642 (58) mri peak = 0.10182 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (670 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (670 voxels, peak = 55), gca=54.8 gca peak = 0.07876 (103) mri peak = 0.12923 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24862 voxels, overlap=0.668) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24862 voxels, peak = 104), gca=103.5 gca peak = 0.07821 (106) mri peak = 0.10507 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27968 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27968 voxels, peak = 106), gca=106.0 gca peak = 0.10056 (56) mri peak = 0.03944 (58) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22168 voxels, overlap=0.991) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22168 voxels, peak = 57), gca=57.4 gca peak = 0.11995 (56) mri peak = 0.04620 (58) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21314 voxels, overlap=0.995) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21314 voxels, peak = 57), gca=57.4 gca peak = 0.26552 (73) mri peak = 0.11146 (75) Right_Caudate (50): linear fit = 1.00 x + 0.0 (742 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.00 x + 0.0 (742 voxels, peak = 73), gca=73.0 gca peak = 0.15150 (69) mri peak = 0.10565 (74) Left_Caudate (11): linear fit = 1.00 x + 0.0 (672 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.00 x + 0.0 (672 voxels, peak = 69), gca=69.0 gca peak = 0.13262 (57) mri peak = 0.04819 (56) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (28385 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (28385 voxels, peak = 55), gca=55.0 gca peak = 0.14692 (54) mri peak = 0.04448 (56) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (25527 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (25527 voxels, peak = 56), gca=56.4 gca peak = 0.15784 (86) mri peak = 0.12464 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5631 voxels, overlap=0.959) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5631 voxels, peak = 86), gca=86.0 gca peak = 0.18253 (87) mri peak = 0.11577 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5371 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5371 voxels, peak = 87), gca=86.6 gca peak = 0.24274 (52) mri peak = 0.18116 (52) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (519 voxels, overlap=1.007) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (519 voxels, peak = 52), gca=52.0 gca peak = 0.30267 (51) mri peak = 0.14618 (52) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (466 voxels, overlap=1.005) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (466 voxels, peak = 51), gca=51.0 gca peak = 0.11039 (86) mri peak = 0.06939 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3778 voxels, overlap=0.994) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3778 voxels, peak = 86), gca=85.6 gca peak = 0.09389 (90) mri peak = 0.07216 (88) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3144 voxels, overlap=0.981) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3144 voxels, peak = 89), gca=88.7 gca peak = 0.08891 (78) mri peak = 0.08932 (74) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1658 voxels, overlap=0.929) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1658 voxels, peak = 77), gca=76.8 gca peak = 0.09183 (72) mri peak = 0.07900 (76) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1677 voxels, overlap=0.912) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1677 voxels, peak = 73), gca=73.1 gca peak = 0.07537 (83) mri peak = 0.10140 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11451 voxels, overlap=0.677) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11451 voxels, peak = 83), gca=82.6 gca peak = 0.11598 (92) mri peak = 0.06801 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1287 voxels, overlap=0.935) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1287 voxels, peak = 92), gca=92.0 gca peak = 0.16995 (91) mri peak = 0.05617 (94) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1463 voxels, overlap=0.975) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1463 voxels, peak = 92), gca=92.4 gca peak = 0.14469 (28) mri peak = 0.07814 (16) gca peak = 0.17386 (16) mri peak = 0.13637 (10) Fourth_Ventricle (15): linear fit = 0.55 x + 0.0 (104 voxels, overlap=0.403) Fourth_Ventricle (15): linear fit = 0.55 x + 0.0 (104 voxels, peak = 9), gca=8.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18140 (33) gca peak Left_Thalamus = 0.64095 (89) gca peak Third_Ventricle = 0.14469 (28) gca peak Fourth_Ventricle = 0.17386 (16) gca peak CSF = 0.21669 (39) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75881 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.37907 (71) gca peak Right_vessel = 0.83204 (52) gca peak Right_choroid_plexus = 0.14511 (37) gca peak Fifth_Ventricle = 0.54107 (35) gca peak WM_hypointensities = 0.08125 (77) gca peak non_WM_hypointensities = 0.12165 (55) gca peak Optic_Chiasm = 0.70608 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.08 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 59146 voxels changed in iteration 0 of unlikely voxel relabeling 205 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 34537 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 313 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 60098 changed. image ll: -2.086, PF=0.500 pass 2: 17423 changed. image ll: -2.085, PF=0.500 pass 3: 5444 changed. pass 4: 1969 changed. 38977 voxels changed in iteration 0 of unlikely voxel relabeling 199 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6479 voxels changed in iteration 0 of unlikely voxel relabeling 154 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 5580 voxels changed in iteration 0 of unlikely voxel relabeling 67 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 4541 voxels changed in iteration 0 of unlikely voxel relabeling 29 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 2541.109692 mri_ca_label stimesec 1.584759 mri_ca_label ru_maxrss 2103432 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 750486 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 57 mri_ca_label ru_nivcsw 3672 auto-labeling took 42 minutes and 22 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/cc_up.lta 2012-646-010-KK will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/cc_up.lta reading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.auto_noCCseg.mgz reading norm from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/norm.mgz 14543 voxels in left wm, 53304 in right wm, xrange [121, 131] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 global minimum found at slice 128.0, rotations (-0.46, -0.02) final transformation (x=128.0, yr=-0.464, zr=-0.018): 0.99997 0.00032 -0.00810 0.86769; -0.00032 1.00000 0.00000 15.04069; 0.00810 -0.00000 0.99997 15.96622; 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 128 113 111 eigenvectors: 0.01904 0.02024 0.99961; 0.06977 -0.99738 0.01887; 0.99738 0.06938 -0.02040; error in mid anterior detected - correcting... writing aseg with callosum to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Wed Oct 2 22:06:07 EDT 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Oct 2 22:06:07 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/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... 996 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 62 (62), valley at 0 (-1) csf peak at 31, setting threshold to 51 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 62 (62), valley at 0 (-1) csf peak at 31, setting threshold to 51 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 43 seconds. #-------------------------------------------- #@# Mask BFS Wed Oct 2 22:08:53 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1304683 voxels in mask (pct= 7.78) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Oct 2 22:08:56 EDT 2019 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.5 +- 4.9 [79.0 --> 125.0] GM (70.0) : 68.4 +- 9.1 [30.0 --> 95.0] setting bottom of white matter range to 77.5 setting top of gray matter range to 86.5 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... 4670 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4976 filled 44 bright non-wm voxels segmented. 2752 diagonally connected voxels added... white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.44 minutes reading wm segmentation from wm.seg.mgz... 522 voxels added to wm to prevent paths from MTL structures to cortex 3553 additional wm voxels added 0 additional wm voxels added SEG EDIT: 43792 voxels turned on, 44198 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+): 23 found - 23 modified | TOTAL: 23 pass 2 (xy+): 0 found - 23 modified | TOTAL: 23 pass 1 (xy-): 20 found - 20 modified | TOTAL: 43 pass 2 (xy-): 0 found - 20 modified | TOTAL: 43 pass 1 (yz+): 33 found - 33 modified | TOTAL: 76 pass 2 (yz+): 0 found - 33 modified | TOTAL: 76 pass 1 (yz-): 27 found - 27 modified | TOTAL: 103 pass 2 (yz-): 0 found - 27 modified | TOTAL: 103 pass 1 (xz+): 20 found - 20 modified | TOTAL: 123 pass 2 (xz+): 0 found - 20 modified | TOTAL: 123 pass 1 (xz-): 17 found - 17 modified | TOTAL: 140 pass 2 (xz-): 0 found - 17 modified | TOTAL: 140 Iteration Number : 1 pass 1 (+++): 11 found - 11 modified | TOTAL: 11 pass 2 (+++): 0 found - 11 modified | TOTAL: 11 pass 1 (+++): 19 found - 19 modified | TOTAL: 30 pass 2 (+++): 0 found - 19 modified | TOTAL: 30 pass 1 (+++): 13 found - 13 modified | TOTAL: 43 pass 2 (+++): 0 found - 13 modified | TOTAL: 43 pass 1 (+++): 13 found - 13 modified | TOTAL: 56 pass 2 (+++): 0 found - 13 modified | TOTAL: 56 Iteration Number : 1 pass 1 (++): 123 found - 123 modified | TOTAL: 123 pass 2 (++): 0 found - 123 modified | TOTAL: 123 pass 1 (+-): 142 found - 142 modified | TOTAL: 265 pass 2 (+-): 0 found - 142 modified | TOTAL: 265 pass 1 (--): 115 found - 115 modified | TOTAL: 380 pass 2 (--): 0 found - 115 modified | TOTAL: 380 pass 1 (-+): 101 found - 101 modified | TOTAL: 481 pass 2 (-+): 0 found - 101 modified | TOTAL: 481 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 4 found - 4 modified | TOTAL: 9 pass 2 (xy-): 0 found - 4 modified | TOTAL: 9 pass 1 (yz+): 5 found - 5 modified | TOTAL: 14 pass 2 (yz+): 0 found - 5 modified | TOTAL: 14 pass 1 (yz-): 6 found - 6 modified | TOTAL: 20 pass 2 (yz-): 0 found - 6 modified | TOTAL: 20 pass 1 (xz+): 7 found - 7 modified | TOTAL: 27 pass 2 (xz+): 0 found - 7 modified | TOTAL: 27 pass 1 (xz-): 4 found - 4 modified | TOTAL: 31 pass 2 (xz-): 0 found - 4 modified | TOTAL: 31 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 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 (+-): 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 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 718 (out of 467271: 0.153658) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Oct 2 22:10:38 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01764 0.03214 0.00436 -8.96941; -0.02380 1.26656 0.00004 -36.63304; -0.00421 -0.00017 0.98469 -0.25488; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01764 0.03214 0.00436 -8.96941; -0.02380 1.26656 0.00004 -36.63304; -0.00421 -0.00017 0.98469 -0.25488; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 996 (min = 350, max = 1400), aspect = 0.38 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 149), TAL = (2.0, 21.0, 8.0) talairach voxel to voxel transform 0.98206 -0.02492 -0.00434 7.89448; 0.01845 0.78907 -0.00011 29.07163; 0.00420 0.00003 1.01553 0.29764; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 120, 149) --> (2.0, 21.0, 8.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (2.00, 21.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 8.00) SRC: (110.32, 125.74, 152.07) search lh wm seed point around talairach space (-16.00, 21.00, 8.00), SRC: (145.67, 126.40, 152.22) 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 Wed Oct 2 22:11:12 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 0 found - 0 modified | TOTAL: 5 pass 1 (yz+): 3 found - 3 modified | TOTAL: 8 pass 2 (yz+): 0 found - 3 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 1 found - 1 modified | TOTAL: 10 pass 2 (xz+): 0 found - 1 modified | TOTAL: 10 pass 1 (xz-): 2 found - 2 modified | TOTAL: 12 pass 2 (xz-): 0 found - 2 modified | TOTAL: 12 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 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 = 13 (out of 229180: 0.005672) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 539 vertices, 625 faces slice 40: 4847 vertices, 5032 faces slice 50: 10548 vertices, 10730 faces slice 60: 16788 vertices, 17030 faces slice 70: 24668 vertices, 24982 faces slice 80: 33370 vertices, 33710 faces slice 90: 43236 vertices, 43613 faces slice 100: 54563 vertices, 54941 faces slice 110: 66786 vertices, 67212 faces slice 120: 78213 vertices, 78620 faces slice 130: 89627 vertices, 90046 faces slice 140: 100323 vertices, 100708 faces slice 150: 109709 vertices, 110079 faces slice 160: 118263 vertices, 118650 faces slice 170: 126251 vertices, 126540 faces slice 180: 132853 vertices, 133103 faces slice 190: 136119 vertices, 136204 faces slice 200: 136192 vertices, 136256 faces slice 210: 136192 vertices, 136256 faces slice 220: 136192 vertices, 136256 faces slice 230: 136192 vertices, 136256 faces slice 240: 136192 vertices, 136256 faces slice 250: 136192 vertices, 136256 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... 136192 voxel in cpt #1: X=-64 [v=136192,e=408768,f=272512] located at (-28.580570, -18.179907, 6.651815) For the whole surface: X=-64 [v=136192,e=408768,f=272512] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Oct 2 22:11:18 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 13 (out of 218156: 0.005959) 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 30: 288 vertices, 337 faces slice 40: 3999 vertices, 4158 faces slice 50: 10022 vertices, 10272 faces slice 60: 17342 vertices, 17586 faces slice 70: 25519 vertices, 25848 faces slice 80: 35261 vertices, 35614 faces slice 90: 45161 vertices, 45494 faces slice 100: 56171 vertices, 56567 faces slice 110: 68077 vertices, 68475 faces slice 120: 79102 vertices, 79518 faces slice 130: 90101 vertices, 90520 faces slice 140: 100834 vertices, 101203 faces slice 150: 108789 vertices, 109104 faces slice 160: 116834 vertices, 117140 faces slice 170: 123708 vertices, 123993 faces slice 180: 130285 vertices, 130573 faces slice 190: 133763 vertices, 133846 faces slice 200: 133788 vertices, 133860 faces slice 210: 133788 vertices, 133860 faces slice 220: 133788 vertices, 133860 faces slice 230: 133788 vertices, 133860 faces slice 240: 133788 vertices, 133860 faces slice 250: 133788 vertices, 133860 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... 133788 voxel in cpt #1: X=-72 [v=133788,e=401580,f=267720] located at (28.128794, -19.606459, 8.465117) For the whole surface: X=-72 [v=133788,e=401580,f=267720] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Oct 2 22:11:25 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Wed Oct 2 22:11:29 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Oct 2 22:11:34 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.7 mm, total surface area = 71113 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.159 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.050 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.046 (target=0.015) step 055: RMS=0.046 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 29.709483 mris_inflate stimesec 0.079987 mris_inflate ru_maxrss 175320 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22755 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 38 mris_inflate ru_nivcsw 75 #-------------------------------------------- #@# Inflation1 rh Wed Oct 2 22:12:05 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.3 mm, total surface area = 69913 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.159 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.062 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.052 (target=0.015) step 040: RMS=0.049 (target=0.015) step 045: RMS=0.046 (target=0.015) step 050: RMS=0.045 (target=0.015) step 055: RMS=0.045 (target=0.015) step 060: RMS=0.044 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 31.128267 mris_inflate stimesec 0.082987 mris_inflate ru_maxrss 172396 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23047 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 30 mris_inflate ru_nivcsw 71 #-------------------------------------------- #@# QSphere lh Wed Oct 2 22:12:37 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.59 (0.00-->5.99) (max @ vno 92711 --> 92712) face area 0.02 +- 0.03 (-0.07-->0.57) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.480, avgs=0 005/300: dt: 0.9000, rms radial error=177.222, avgs=0 010/300: dt: 0.9000, rms radial error=176.668, avgs=0 015/300: dt: 0.9000, rms radial error=175.941, avgs=0 020/300: dt: 0.9000, rms radial error=175.114, avgs=0 025/300: dt: 0.9000, rms radial error=174.228, avgs=0 030/300: dt: 0.9000, rms radial error=173.310, avgs=0 035/300: dt: 0.9000, rms radial error=172.374, avgs=0 040/300: dt: 0.9000, rms radial error=171.431, avgs=0 045/300: dt: 0.9000, rms radial error=170.485, avgs=0 050/300: dt: 0.9000, rms radial error=169.538, avgs=0 055/300: dt: 0.9000, rms radial error=168.593, avgs=0 060/300: dt: 0.9000, rms radial error=167.651, avgs=0 065/300: dt: 0.9000, rms radial error=166.713, avgs=0 070/300: dt: 0.9000, rms radial error=165.779, avgs=0 075/300: dt: 0.9000, rms radial error=164.849, avgs=0 080/300: dt: 0.9000, rms radial error=163.924, avgs=0 085/300: dt: 0.9000, rms radial error=163.003, avgs=0 090/300: dt: 0.9000, rms radial error=162.085, avgs=0 095/300: dt: 0.9000, rms radial error=161.173, avgs=0 100/300: dt: 0.9000, rms radial error=160.265, avgs=0 105/300: dt: 0.9000, rms radial error=159.362, avgs=0 110/300: dt: 0.9000, rms radial error=158.464, avgs=0 115/300: dt: 0.9000, rms radial error=157.571, avgs=0 120/300: dt: 0.9000, rms radial error=156.683, avgs=0 125/300: dt: 0.9000, rms radial error=155.799, avgs=0 130/300: dt: 0.9000, rms radial error=154.921, avgs=0 135/300: dt: 0.9000, rms radial error=154.047, avgs=0 140/300: dt: 0.9000, rms radial error=153.177, avgs=0 145/300: dt: 0.9000, rms radial error=152.313, avgs=0 150/300: dt: 0.9000, rms radial error=151.454, avgs=0 155/300: dt: 0.9000, rms radial error=150.599, avgs=0 160/300: dt: 0.9000, rms radial error=149.749, avgs=0 165/300: dt: 0.9000, rms radial error=148.903, avgs=0 170/300: dt: 0.9000, rms radial error=148.062, avgs=0 175/300: dt: 0.9000, rms radial error=147.226, avgs=0 180/300: dt: 0.9000, rms radial error=146.395, avgs=0 185/300: dt: 0.9000, rms radial error=145.568, avgs=0 190/300: dt: 0.9000, rms radial error=144.746, avgs=0 195/300: dt: 0.9000, rms radial error=143.928, avgs=0 200/300: dt: 0.9000, rms radial error=143.115, avgs=0 205/300: dt: 0.9000, rms radial error=142.307, avgs=0 210/300: dt: 0.9000, rms radial error=141.503, avgs=0 215/300: dt: 0.9000, rms radial error=140.703, avgs=0 220/300: dt: 0.9000, rms radial error=139.908, avgs=0 225/300: dt: 0.9000, rms radial error=139.118, avgs=0 230/300: dt: 0.9000, rms radial error=138.331, avgs=0 235/300: dt: 0.9000, rms radial error=137.550, avgs=0 240/300: dt: 0.9000, rms radial error=136.772, avgs=0 245/300: dt: 0.9000, rms radial error=135.999, avgs=0 250/300: dt: 0.9000, rms radial error=135.230, avgs=0 255/300: dt: 0.9000, rms radial error=134.466, avgs=0 260/300: dt: 0.9000, rms radial error=133.706, avgs=0 265/300: dt: 0.9000, rms radial error=132.950, avgs=0 270/300: dt: 0.9000, rms radial error=132.199, avgs=0 275/300: dt: 0.9000, rms radial error=131.451, avgs=0 280/300: dt: 0.9000, rms radial error=130.708, avgs=0 285/300: dt: 0.9000, rms radial error=129.970, avgs=0 290/300: dt: 0.9000, rms radial error=129.235, avgs=0 295/300: dt: 0.9000, rms radial error=128.504, avgs=0 300/300: dt: 0.9000, rms radial error=127.778, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16119.68 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 = 2774.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 331.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00602 epoch 4 (K=640.0), pass 1, starting sse = 30.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00722 final distance error %29.84 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 168.877326 mris_sphere stimesec 0.088986 mris_sphere ru_maxrss 175512 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22804 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 42 mris_sphere ru_nivcsw 184 FSRUNTIME@ mris_sphere 0.0470 hours 1 threads #-------------------------------------------- #@# QSphere rh Wed Oct 2 22:15:27 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.60 (0.00-->8.21) (max @ vno 41051 --> 41992) face area 0.02 +- 0.03 (-0.14-->0.77) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.602, avgs=0 005/300: dt: 0.9000, rms radial error=177.342, avgs=0 010/300: dt: 0.9000, rms radial error=176.783, avgs=0 015/300: dt: 0.9000, rms radial error=176.052, avgs=0 020/300: dt: 0.9000, rms radial error=175.219, avgs=0 025/300: dt: 0.9000, rms radial error=174.328, avgs=0 030/300: dt: 0.9000, rms radial error=173.404, avgs=0 035/300: dt: 0.9000, rms radial error=172.464, avgs=0 040/300: dt: 0.9000, rms radial error=171.516, avgs=0 045/300: dt: 0.9000, rms radial error=170.565, avgs=0 050/300: dt: 0.9000, rms radial error=169.615, avgs=0 055/300: dt: 0.9000, rms radial error=168.667, avgs=0 060/300: dt: 0.9000, rms radial error=167.723, avgs=0 065/300: dt: 0.9000, rms radial error=166.783, avgs=0 070/300: dt: 0.9000, rms radial error=165.847, avgs=0 075/300: dt: 0.9000, rms radial error=164.916, avgs=0 080/300: dt: 0.9000, rms radial error=163.990, avgs=0 085/300: dt: 0.9000, rms radial error=163.069, avgs=0 090/300: dt: 0.9000, rms radial error=162.152, avgs=0 095/300: dt: 0.9000, rms radial error=161.240, avgs=0 100/300: dt: 0.9000, rms radial error=160.333, avgs=0 105/300: dt: 0.9000, rms radial error=159.430, avgs=0 110/300: dt: 0.9000, rms radial error=158.533, avgs=0 115/300: dt: 0.9000, rms radial error=157.639, avgs=0 120/300: dt: 0.9000, rms radial error=156.751, avgs=0 125/300: dt: 0.9000, rms radial error=155.867, avgs=0 130/300: dt: 0.9000, rms radial error=154.988, avgs=0 135/300: dt: 0.9000, rms radial error=154.113, avgs=0 140/300: dt: 0.9000, rms radial error=153.244, avgs=0 145/300: dt: 0.9000, rms radial error=152.379, avgs=0 150/300: dt: 0.9000, rms radial error=151.519, avgs=0 155/300: dt: 0.9000, rms radial error=150.664, avgs=0 160/300: dt: 0.9000, rms radial error=149.813, avgs=0 165/300: dt: 0.9000, rms radial error=148.967, avgs=0 170/300: dt: 0.9000, rms radial error=148.126, avgs=0 175/300: dt: 0.9000, rms radial error=147.289, avgs=0 180/300: dt: 0.9000, rms radial error=146.457, avgs=0 185/300: dt: 0.9000, rms radial error=145.630, avgs=0 190/300: dt: 0.9000, rms radial error=144.807, avgs=0 195/300: dt: 0.9000, rms radial error=143.989, avgs=0 200/300: dt: 0.9000, rms radial error=143.175, avgs=0 205/300: dt: 0.9000, rms radial error=142.366, avgs=0 210/300: dt: 0.9000, rms radial error=141.562, avgs=0 215/300: dt: 0.9000, rms radial error=140.761, avgs=0 220/300: dt: 0.9000, rms radial error=139.966, avgs=0 225/300: dt: 0.9000, rms radial error=139.175, avgs=0 230/300: dt: 0.9000, rms radial error=138.388, avgs=0 235/300: dt: 0.9000, rms radial error=137.605, avgs=0 240/300: dt: 0.9000, rms radial error=136.827, avgs=0 245/300: dt: 0.9000, rms radial error=136.053, avgs=0 250/300: dt: 0.9000, rms radial error=135.284, avgs=0 255/300: dt: 0.9000, rms radial error=134.519, avgs=0 260/300: dt: 0.9000, rms radial error=133.758, avgs=0 265/300: dt: 0.9000, rms radial error=133.002, avgs=0 270/300: dt: 0.9000, rms radial error=132.250, avgs=0 275/300: dt: 0.9000, rms radial error=131.502, avgs=0 280/300: dt: 0.9000, rms radial error=130.758, avgs=0 285/300: dt: 0.9000, rms radial error=130.018, avgs=0 290/300: dt: 0.9000, rms radial error=129.283, avgs=0 295/300: dt: 0.9000, rms radial error=128.551, avgs=0 300/300: dt: 0.9000, rms radial error=127.824, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15828.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2720.36 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 324.29 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00642 epoch 4 (K=640.0), pass 1, starting sse = 28.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/15 = 0.00813 final distance error %29.60 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 172.445784 mris_sphere stimesec 0.103984 mris_sphere ru_maxrss 172588 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22586 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 30 mris_sphere ru_nivcsw 190 FSRUNTIME@ mris_sphere 0.0479 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Wed Oct 2 22:18:20 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Wed Oct 2 22:18:21 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Oct 2 22:18:22 EDT 2019 mris_fix_topology -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 2012-646-010-KK 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=-64 (nv=136192, nf=272512, ne=408768, g=33) 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... 10404 ambiguous faces found in tessellation segmenting defects... 43 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 42 defects to be corrected 0 vertices coincident reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4383 (-4.7192) -vertex loglikelihood: -6.5314 (-3.2657) -normal dot loglikelihood: -3.6382 (-3.6382) -quad curv loglikelihood: -6.5139 (-3.2570) Total Loglikelihood : -26.1218 CORRECTING DEFECT 0 (vertices=17, convex hull=28, v0=10248) After retessellation of defect 0 (v0=10248), euler #=-40 (130023,388015,257952) : difference with theory (-39) = 1 CORRECTING DEFECT 1 (vertices=131, convex hull=141, v0=11329) After retessellation of defect 1 (v0=11329), euler #=-39 (130050,388168,258079) : difference with theory (-38) = 1 CORRECTING DEFECT 2 (vertices=34, convex hull=43, v0=14604) After retessellation of defect 2 (v0=14604), euler #=-38 (130058,388207,258111) : difference with theory (-37) = 1 CORRECTING DEFECT 3 (vertices=93, convex hull=67, v0=20059) After retessellation of defect 3 (v0=20059), euler #=-37 (130082,388304,258185) : difference with theory (-36) = 1 CORRECTING DEFECT 4 (vertices=24, convex hull=60, v0=22134) After retessellation of defect 4 (v0=22134), euler #=-36 (130091,388354,258227) : difference with theory (-35) = 1 CORRECTING DEFECT 5 (vertices=219, convex hull=222, v0=35269) After retessellation of defect 5 (v0=35269), euler #=-35 (130146,388627,258446) : difference with theory (-34) = 1 CORRECTING DEFECT 6 (vertices=713, convex hull=377, v0=35837) After retessellation of defect 6 (v0=35837), euler #=-34 (130342,389399,259023) : difference with theory (-33) = 1 CORRECTING DEFECT 7 (vertices=23, convex hull=24, v0=56383) After retessellation of defect 7 (v0=56383), euler #=-33 (130344,389418,259041) : difference with theory (-32) = 1 CORRECTING DEFECT 8 (vertices=177, convex hull=192, v0=59196) After retessellation of defect 8 (v0=59196), euler #=-32 (130441,389800,259327) : difference with theory (-31) = 1 CORRECTING DEFECT 9 (vertices=149, convex hull=63, v0=64118) After retessellation of defect 9 (v0=64118), euler #=-31 (130468,389911,259412) : difference with theory (-30) = 1 CORRECTING DEFECT 10 (vertices=351, convex hull=319, v0=75992) After retessellation of defect 10 (v0=75992), euler #=-29 (130652,390633,259952) : difference with theory (-29) = 0 CORRECTING DEFECT 11 (vertices=20, convex hull=28, v0=84289) After retessellation of defect 11 (v0=84289), euler #=-28 (130654,390651,259969) : difference with theory (-28) = 0 CORRECTING DEFECT 12 (vertices=40, convex hull=79, v0=87026) After retessellation of defect 12 (v0=87026), euler #=-27 (130674,390747,260046) : difference with theory (-27) = 0 CORRECTING DEFECT 13 (vertices=50, convex hull=87, v0=88024) After retessellation of defect 13 (v0=88024), euler #=-26 (130703,390871,260142) : difference with theory (-26) = 0 CORRECTING DEFECT 14 (vertices=33, convex hull=68, v0=88403) After retessellation of defect 14 (v0=88403), euler #=-25 (130720,390951,260206) : difference with theory (-25) = 0 CORRECTING DEFECT 15 (vertices=10, convex hull=22, v0=90195) After retessellation of defect 15 (v0=90195), euler #=-24 (130722,390964,260218) : difference with theory (-24) = 0 CORRECTING DEFECT 16 (vertices=275, convex hull=216, v0=90439) After retessellation of defect 16 (v0=90439), euler #=-23 (130822,391370,260525) : difference with theory (-23) = 0 CORRECTING DEFECT 17 (vertices=379, convex hull=135, v0=90694) After retessellation of defect 17 (v0=90694), euler #=-22 (130869,391572,260681) : difference with theory (-22) = 0 CORRECTING DEFECT 18 (vertices=23, convex hull=37, v0=90713) After retessellation of defect 18 (v0=90713), euler #=-21 (130873,391596,260702) : difference with theory (-21) = 0 CORRECTING DEFECT 19 (vertices=42, convex hull=32, v0=91277) After retessellation of defect 19 (v0=91277), euler #=-20 (130883,391636,260733) : difference with theory (-20) = 0 CORRECTING DEFECT 20 (vertices=313, convex hull=207, v0=91358) After retessellation of defect 20 (v0=91358), euler #=-19 (130937,391898,260942) : difference with theory (-19) = 0 CORRECTING DEFECT 21 (vertices=76, convex hull=72, v0=91463) After retessellation of defect 21 (v0=91463), euler #=-18 (130965,392007,261024) : difference with theory (-18) = 0 CORRECTING DEFECT 22 (vertices=40, convex hull=64, v0=91602) After retessellation of defect 22 (v0=91602), euler #=-17 (130992,392110,261101) : difference with theory (-17) = 0 CORRECTING DEFECT 23 (vertices=6, convex hull=24, v0=95233) After retessellation of defect 23 (v0=95233), euler #=-16 (130992,392115,261107) : difference with theory (-16) = 0 CORRECTING DEFECT 24 (vertices=1669, convex hull=850, v0=97348) XL defect detected... After retessellation of defect 24 (v0=97348), euler #=-15 (131292,393457,262150) : difference with theory (-15) = 0 CORRECTING DEFECT 25 (vertices=18, convex hull=35, v0=97971) After retessellation of defect 25 (v0=97971), euler #=-14 (131295,393480,262171) : difference with theory (-14) = 0 CORRECTING DEFECT 26 (vertices=20, convex hull=33, v0=98075) After retessellation of defect 26 (v0=98075), euler #=-13 (131299,393502,262190) : difference with theory (-13) = 0 CORRECTING DEFECT 27 (vertices=74, convex hull=52, v0=99294) After retessellation of defect 27 (v0=99294), euler #=-12 (131312,393563,262239) : difference with theory (-12) = 0 CORRECTING DEFECT 28 (vertices=119, convex hull=42, v0=100026) After retessellation of defect 28 (v0=100026), euler #=-11 (131318,393602,262273) : difference with theory (-11) = 0 CORRECTING DEFECT 29 (vertices=29, convex hull=52, v0=101928) After retessellation of defect 29 (v0=101928), euler #=-10 (131333,393670,262327) : difference with theory (-10) = 0 CORRECTING DEFECT 30 (vertices=158, convex hull=39, v0=102044) After retessellation of defect 30 (v0=102044), euler #=-9 (131343,393713,262361) : difference with theory (-9) = 0 CORRECTING DEFECT 31 (vertices=339, convex hull=283, v0=102075) After retessellation of defect 31 (v0=102075), euler #=-8 (131496,394313,262809) : difference with theory (-8) = 0 CORRECTING DEFECT 32 (vertices=57, convex hull=53, v0=104934) After retessellation of defect 32 (v0=104934), euler #=-7 (131508,394371,262856) : difference with theory (-7) = 0 CORRECTING DEFECT 33 (vertices=9, convex hull=25, v0=105435) After retessellation of defect 33 (v0=105435), euler #=-6 (131509,394381,262866) : difference with theory (-6) = 0 CORRECTING DEFECT 34 (vertices=19, convex hull=31, v0=111323) After retessellation of defect 34 (v0=111323), euler #=-5 (131513,394404,262886) : difference with theory (-5) = 0 CORRECTING DEFECT 35 (vertices=15, convex hull=30, v0=113817) After retessellation of defect 35 (v0=113817), euler #=-4 (131515,394420,262901) : difference with theory (-4) = 0 CORRECTING DEFECT 36 (vertices=196, convex hull=84, v0=114724) After retessellation of defect 36 (v0=114724), euler #=-3 (131548,394554,263003) : difference with theory (-3) = 0 CORRECTING DEFECT 37 (vertices=94, convex hull=64, v0=115517) After retessellation of defect 37 (v0=115517), euler #=-2 (131562,394624,263060) : difference with theory (-2) = 0 CORRECTING DEFECT 38 (vertices=8, convex hull=28, v0=134453) After retessellation of defect 38 (v0=134453), euler #=-1 (131563,394635,263071) : difference with theory (-1) = 0 CORRECTING DEFECT 39 (vertices=30, convex hull=28, v0=135498) After retessellation of defect 39 (v0=135498), euler #=0 (131564,394648,263084) : difference with theory (0) = 0 CORRECTING DEFECT 40 (vertices=44, convex hull=37, v0=135717) After retessellation of defect 40 (v0=135717), euler #=1 (131570,394679,263110) : difference with theory (1) = 0 CORRECTING DEFECT 41 (vertices=32, convex hull=62, v0=135916) After retessellation of defect 41 (v0=135916), euler #=2 (131581,394737,263158) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.04-->13.18) (max @ vno 100669 --> 107567) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.04-->13.18) (max @ vno 100669 --> 107567) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 145 mutations (36.4%), 253 crossovers (63.6%), 450 vertices were eliminated building final representation... 4611 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=131581, nf=263158, ne=394737, g=0) writing corrected surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 28.7 minutes 0 defective edges removing intersecting faces 000: 582 intersecting 001: 10 intersecting mris_fix_topology utimesec 1719.662571 mris_fix_topology stimesec 0.190970 mris_fix_topology ru_maxrss 445864 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 59409 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 97 mris_fix_topology ru_nivcsw 2302 FSRUNTIME@ mris_fix_topology lh 0.4777 hours 1 threads #@# Fix Topology rh Wed Oct 2 22:47:03 EDT 2019 mris_fix_topology -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 2012-646-010-KK 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=-72 (nv=133788, nf=267720, ne=401580, g=37) 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 12 iterations marking ambiguous vertices... 7862 ambiguous faces found in tessellation segmenting defects... 48 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 48 defects to be corrected 0 vertices coincident reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5504 (-4.7752) -vertex loglikelihood: -6.4660 (-3.2330) -normal dot loglikelihood: -3.6131 (-3.6131) -quad curv loglikelihood: -5.9802 (-2.9901) Total Loglikelihood : -25.6096 CORRECTING DEFECT 0 (vertices=32, convex hull=25, v0=1499) After retessellation of defect 0 (v0=1499), euler #=-41 (128942,384819,255836) : difference with theory (-45) = -4 CORRECTING DEFECT 1 (vertices=501, convex hull=309, v0=1837) After retessellation of defect 1 (v0=1837), euler #=-41 (129103,385485,256341) : difference with theory (-44) = -3 CORRECTING DEFECT 2 (vertices=882, convex hull=764, v0=3350) XL defect detected... After retessellation of defect 2 (v0=3350), euler #=-40 (129430,386853,257383) : difference with theory (-43) = -3 CORRECTING DEFECT 3 (vertices=20, convex hull=54, v0=17414) After retessellation of defect 3 (v0=17414), euler #=-39 (129443,386907,257425) : difference with theory (-42) = -3 CORRECTING DEFECT 4 (vertices=39, convex hull=73, v0=21262) After retessellation of defect 4 (v0=21262), euler #=-38 (129466,387006,257502) : difference with theory (-41) = -3 CORRECTING DEFECT 5 (vertices=60, convex hull=43, v0=22568) After retessellation of defect 5 (v0=22568), euler #=-37 (129475,387049,257537) : difference with theory (-40) = -3 CORRECTING DEFECT 6 (vertices=232, convex hull=199, v0=37357) After retessellation of defect 6 (v0=37357), euler #=-36 (129511,387254,257707) : difference with theory (-39) = -3 CORRECTING DEFECT 7 (vertices=26, convex hull=60, v0=46041) After retessellation of defect 7 (v0=46041), euler #=-35 (129526,387321,257760) : difference with theory (-38) = -3 CORRECTING DEFECT 8 (vertices=37, convex hull=73, v0=49611) After retessellation of defect 8 (v0=49611), euler #=-34 (129548,387416,257834) : difference with theory (-37) = -3 CORRECTING DEFECT 9 (vertices=20, convex hull=26, v0=51222) After retessellation of defect 9 (v0=51222), euler #=-33 (129553,387439,257853) : difference with theory (-36) = -3 CORRECTING DEFECT 10 (vertices=142, convex hull=157, v0=56153) After retessellation of defect 10 (v0=56153), euler #=-32 (129648,387801,258121) : difference with theory (-35) = -3 CORRECTING DEFECT 11 (vertices=46, convex hull=19, v0=59436) After retessellation of defect 11 (v0=59436), euler #=-31 (129650,387815,258134) : difference with theory (-34) = -3 CORRECTING DEFECT 12 (vertices=127, convex hull=148, v0=60753) After retessellation of defect 12 (v0=60753), euler #=-30 (129734,388137,258373) : difference with theory (-33) = -3 CORRECTING DEFECT 13 (vertices=58, convex hull=115, v0=60773) After retessellation of defect 13 (v0=60773), euler #=-30 (129773,388308,258505) : difference with theory (-32) = -2 CORRECTING DEFECT 14 (vertices=18, convex hull=12, v0=61846) After retessellation of defect 14 (v0=61846), euler #=-29 (129773,388310,258508) : difference with theory (-31) = -2 CORRECTING DEFECT 15 (vertices=47, convex hull=60, v0=66159) After retessellation of defect 15 (v0=66159), euler #=-28 (129805,388431,258598) : difference with theory (-30) = -2 CORRECTING DEFECT 16 (vertices=18, convex hull=43, v0=71160) After retessellation of defect 16 (v0=71160), euler #=-27 (129814,388474,258633) : difference with theory (-29) = -2 CORRECTING DEFECT 17 (vertices=65, convex hull=36, v0=74059) After retessellation of defect 17 (v0=74059), euler #=-26 (129818,388502,258658) : difference with theory (-28) = -2 CORRECTING DEFECT 18 (vertices=151, convex hull=71, v0=74610) After retessellation of defect 18 (v0=74610), euler #=-25 (129837,388591,258729) : difference with theory (-27) = -2 CORRECTING DEFECT 19 (vertices=5, convex hull=23, v0=75675) After retessellation of defect 19 (v0=75675), euler #=-24 (129837,388597,258736) : difference with theory (-26) = -2 CORRECTING DEFECT 20 (vertices=137, convex hull=121, v0=79029) After retessellation of defect 20 (v0=79029), euler #=-23 (129884,388792,258885) : difference with theory (-25) = -2 CORRECTING DEFECT 21 (vertices=22, convex hull=54, v0=82015) After retessellation of defect 21 (v0=82015), euler #=-22 (129895,388848,258931) : difference with theory (-24) = -2 CORRECTING DEFECT 22 (vertices=38, convex hull=72, v0=82500) After retessellation of defect 22 (v0=82500), euler #=-21 (129914,388932,258997) : difference with theory (-23) = -2 CORRECTING DEFECT 23 (vertices=115, convex hull=79, v0=83506) After retessellation of defect 23 (v0=83506), euler #=-20 (129963,389110,259127) : difference with theory (-22) = -2 CORRECTING DEFECT 24 (vertices=30, convex hull=28, v0=83731) After retessellation of defect 24 (v0=83731), euler #=-19 (129966,389129,259144) : difference with theory (-21) = -2 CORRECTING DEFECT 25 (vertices=32, convex hull=66, v0=84460) After retessellation of defect 25 (v0=84460), euler #=-18 (129980,389197,259199) : difference with theory (-20) = -2 CORRECTING DEFECT 26 (vertices=38, convex hull=54, v0=85531) After retessellation of defect 26 (v0=85531), euler #=-17 (130003,389289,259269) : difference with theory (-19) = -2 CORRECTING DEFECT 27 (vertices=339, convex hull=186, v0=88685) After retessellation of defect 27 (v0=88685), euler #=-16 (130016,389421,259389) : difference with theory (-18) = -2 CORRECTING DEFECT 28 (vertices=13, convex hull=31, v0=89893) After retessellation of defect 28 (v0=89893), euler #=-15 (130019,389439,259405) : difference with theory (-17) = -2 CORRECTING DEFECT 29 (vertices=29, convex hull=30, v0=89975) After retessellation of defect 29 (v0=89975), euler #=-14 (130028,389477,259435) : difference with theory (-16) = -2 CORRECTING DEFECT 30 (vertices=186, convex hull=72, v0=90860) After retessellation of defect 30 (v0=90860), euler #=-13 (130050,389569,259506) : difference with theory (-15) = -2 CORRECTING DEFECT 31 (vertices=35, convex hull=64, v0=92007) After retessellation of defect 31 (v0=92007), euler #=-12 (130062,389628,259554) : difference with theory (-14) = -2 CORRECTING DEFECT 32 (vertices=6, convex hull=28, v0=93393) After retessellation of defect 32 (v0=93393), euler #=-11 (130062,389637,259564) : difference with theory (-13) = -2 CORRECTING DEFECT 33 (vertices=27, convex hull=33, v0=94053) After retessellation of defect 33 (v0=94053), euler #=-11 (130066,389663,259586) : difference with theory (-12) = -1 CORRECTING DEFECT 34 (vertices=19, convex hull=23, v0=95553) After retessellation of defect 34 (v0=95553), euler #=-10 (130066,389671,259595) : difference with theory (-11) = -1 CORRECTING DEFECT 35 (vertices=288, convex hull=219, v0=99925) After retessellation of defect 35 (v0=99925), euler #=-9 (130142,389997,259846) : difference with theory (-10) = -1 CORRECTING DEFECT 36 (vertices=60, convex hull=84, v0=100695) After retessellation of defect 36 (v0=100695), euler #=-8 (130159,390082,259915) : difference with theory (-9) = -1 CORRECTING DEFECT 37 (vertices=421, convex hull=273, v0=103855) After retessellation of defect 37 (v0=103855), euler #=-8 (130278,390583,260297) : difference with theory (-8) = 0 CORRECTING DEFECT 38 (vertices=70, convex hull=66, v0=105436) After retessellation of defect 38 (v0=105436), euler #=-7 (130293,390654,260354) : difference with theory (-7) = 0 CORRECTING DEFECT 39 (vertices=38, convex hull=48, v0=112084) After retessellation of defect 39 (v0=112084), euler #=-6 (130307,390716,260403) : difference with theory (-6) = 0 CORRECTING DEFECT 40 (vertices=100, convex hull=73, v0=124355) After retessellation of defect 40 (v0=124355), euler #=-5 (130317,390778,260456) : difference with theory (-5) = 0 CORRECTING DEFECT 41 (vertices=10, convex hull=26, v0=125711) After retessellation of defect 41 (v0=125711), euler #=-4 (130319,390793,260470) : difference with theory (-4) = 0 CORRECTING DEFECT 42 (vertices=7, convex hull=19, v0=127551) After retessellation of defect 42 (v0=127551), euler #=-3 (130320,390802,260479) : difference with theory (-3) = 0 CORRECTING DEFECT 43 (vertices=114, convex hull=137, v0=130227) After retessellation of defect 43 (v0=130227), euler #=-2 (130352,390960,260606) : difference with theory (-2) = 0 CORRECTING DEFECT 44 (vertices=44, convex hull=51, v0=131753) After retessellation of defect 44 (v0=131753), euler #=-1 (130360,391006,260645) : difference with theory (-1) = 0 CORRECTING DEFECT 45 (vertices=39, convex hull=81, v0=132093) After retessellation of defect 45 (v0=132093), euler #=0 (130379,391096,260717) : difference with theory (0) = 0 CORRECTING DEFECT 46 (vertices=55, convex hull=80, v0=133053) After retessellation of defect 46 (v0=133053), euler #=1 (130391,391163,260773) : difference with theory (1) = 0 CORRECTING DEFECT 47 (vertices=5, convex hull=14, v0=133777) After retessellation of defect 47 (v0=133777), euler #=2 (130392,391170,260780) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.05-->12.84) (max @ vno 17903 --> 20244) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.05-->12.84) (max @ vno 17903 --> 20244) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 146 mutations (31.6%), 316 crossovers (68.4%), 336 vertices were eliminated building final representation... 3396 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=130392, nf=260780, ne=391170, g=0) writing corrected surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.8 minutes 0 defective edges removing intersecting faces 000: 618 intersecting 001: 26 intersecting 002: 10 intersecting mris_fix_topology utimesec 1610.354188 mris_fix_topology stimesec 0.176973 mris_fix_topology ru_maxrss 425360 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55953 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 69 mris_fix_topology ru_nivcsw 1846 FSRUNTIME@ mris_fix_topology rh 0.4473 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 131581 - 394737 + 263158 = 2 --> 0 holes F =2V-4: 263158 = 263162-4 (0) 2E=3F: 789474 = 789474 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 130392 - 391170 + 260780 = 2 --> 0 holes F =2V-4: 260780 = 260784-4 (0) 2E=3F: 782340 = 782340 (0) total defect index = 0 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 153 intersecting 001: 23 intersecting 002: 4 intersecting expanding nbhd size to 2 003: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 126 intersecting 001: 7 intersecting 002: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Oct 2 23:14:07 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 2012-646-010-KK 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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/filled.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/../mri/aseg.presurf.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... 17706 bright wm thresholded. 97 bright non-wm voxels segmented. reading original surface position from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig... computing class statistics... border white: 240382 voxels (1.43%) border gray 280733 voxels (1.67%) WM (97.0): 97.1 +- 9.3 [70.0 --> 110.0] GM (67.0) : 67.3 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.5 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 42.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->5.90) (max @ vno 130196 --> 130227) face area 0.28 +- 0.14 (0.00-->12.00) mean absolute distance = 0.68 +- 0.89 3399 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=103+-6.1, GM=63+-7.8 mean inside = 91.8, mean outside = 71.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=76.6, 336 (336) missing vertices, mean dist 0.3 [0.6 (%35.5)->0.7 (%64.5))] %68 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, 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 0.92 +- 0.27 (0.07-->6.04) (max @ vno 89266 --> 89369) face area 0.28 +- 0.14 (0.00-->8.38) mean absolute distance = 0.36 +- 0.59 3481 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3985684.2, rms=11.699 001: dt: 0.5000, sse=2414145.8, rms=8.670 (25.890%) 002: dt: 0.5000, sse=1740661.8, rms=6.973 (19.575%) 003: dt: 0.5000, sse=1396108.4, rms=5.904 (15.329%) 004: dt: 0.5000, sse=1200155.5, rms=5.195 (12.008%) 005: dt: 0.5000, sse=1096190.9, rms=4.756 (8.456%) 006: dt: 0.5000, sse=1018288.9, rms=4.447 (6.482%) 007: dt: 0.5000, sse=988527.9, rms=4.291 (3.523%) 008: dt: 0.5000, sse=976502.7, rms=4.229 (1.443%) 009: dt: 0.5000, sse=959560.9, rms=4.166 (1.492%) 010: dt: 0.5000, sse=948281.8, rms=4.113 (1.273%) rms = 4.09, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=948969.6, rms=4.090 (0.541%) 012: dt: 0.2500, sse=752343.6, rms=2.942 (28.085%) 013: dt: 0.2500, sse=710065.2, rms=2.638 (10.328%) 014: dt: 0.2500, sse=703590.9, rms=2.570 (2.565%) 015: dt: 0.2500, sse=693505.6, rms=2.498 (2.823%) rms = 2.46, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=688912.6, rms=2.462 (1.430%) 017: dt: 0.1250, sse=681369.2, rms=2.379 (3.382%) rms = 2.36, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=679410.1, rms=2.360 (0.778%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.4, 246 (104) missing vertices, mean dist -0.2 [0.4 (%76.2)->0.3 (%23.8))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n511, 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 0.90 +- 0.26 (0.07-->5.86) (max @ vno 130193 --> 130218) face area 0.35 +- 0.18 (0.00-->10.24) mean absolute distance = 0.25 +- 0.40 3434 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1465723.4, rms=5.616 019: dt: 0.5000, sse=1070229.9, rms=3.926 (30.088%) rms = 3.97, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=930847.1, rms=3.205 (18.361%) 021: dt: 0.2500, sse=865750.1, rms=2.690 (16.061%) 022: dt: 0.2500, sse=830207.6, rms=2.448 (9.030%) 023: dt: 0.2500, sse=807288.8, rms=2.319 (5.240%) 024: dt: 0.2500, sse=798516.1, rms=2.251 (2.951%) rms = 2.21, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=796354.4, rms=2.207 (1.926%) 026: dt: 0.1250, sse=787756.2, rms=2.152 (2.513%) rms = 2.11, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=801019.7, rms=2.110 (1.963%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.8, 287 (56) missing vertices, mean dist -0.1 [0.3 (%72.0)->0.2 (%28.0))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n511, 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 0.89 +- 0.26 (0.07-->5.92) (max @ vno 130309 --> 130310) face area 0.34 +- 0.18 (0.00-->9.87) mean absolute distance = 0.21 +- 0.33 2701 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1015024.6, rms=3.718 028: dt: 0.5000, sse=955750.0, rms=3.388 (8.884%) rms = 3.66, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=813355.7, rms=2.496 (26.322%) 030: dt: 0.2500, sse=768982.0, rms=2.138 (14.345%) 031: dt: 0.2500, sse=778006.4, rms=2.035 (4.811%) rms = 2.00, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=752396.8, rms=2.004 (1.544%) 033: dt: 0.1250, sse=742482.5, rms=1.914 (4.468%) rms = 1.90, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=741049.5, rms=1.899 (0.782%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.7, 301 (39) missing vertices, mean dist -0.0 [0.2 (%57.5)->0.2 (%42.5))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n511, 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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=763631.6, rms=2.223 rms = 2.45, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=723753.2, rms=1.830 (17.695%) 036: dt: 0.2500, sse=724414.4, rms=1.683 (7.995%) rms = 1.69, time step reduction 2 of 3 to 0.125... rms = 1.65, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=717936.9, rms=1.649 (2.025%) positioning took 0.3 minutes generating cortex label... 18 non-cortical segments detected only using segment with 6824 vertices erasing segment 0 (vno[0] = 34762) erasing segment 2 (vno[0] = 43210) erasing segment 3 (vno[0] = 48346) erasing segment 4 (vno[0] = 49741) erasing segment 5 (vno[0] = 74870) erasing segment 6 (vno[0] = 76865) erasing segment 7 (vno[0] = 81092) erasing segment 8 (vno[0] = 88295) erasing segment 9 (vno[0] = 89268) erasing segment 10 (vno[0] = 90304) erasing segment 11 (vno[0] = 93191) erasing segment 12 (vno[0] = 93259) erasing segment 13 (vno[0] = 97894) erasing segment 14 (vno[0] = 99215) erasing segment 15 (vno[0] = 99569) erasing segment 16 (vno[0] = 100822) erasing segment 17 (vno[0] = 130897) writing cortex label to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label... writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.curv writing smoothed area to lh.area writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.area vertex spacing 0.89 +- 0.27 (0.03-->6.04) (max @ vno 89266 --> 89369) face area 0.33 +- 0.18 (0.00-->9.77) refinement took 4.4 minutes #-------------------------------------------- #@# Make White Surf rh Wed Oct 2 23:18:34 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 2012-646-010-KK 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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/filled.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/../mri/aseg.presurf.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... 17706 bright wm thresholded. 97 bright non-wm voxels segmented. reading original surface position from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig... computing class statistics... border white: 240382 voxels (1.43%) border gray 280733 voxels (1.67%) WM (97.0): 97.1 +- 9.3 [70.0 --> 110.0] GM (67.0) : 67.3 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.5 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 42.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->5.92) (max @ vno 17903 --> 20244) face area 0.28 +- 0.13 (0.00-->5.02) mean absolute distance = 0.69 +- 0.85 3633 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=103+-7.0, GM=63+-7.0 mean inside = 92.0, mean outside = 71.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=75.9, 188 (188) missing vertices, mean dist 0.3 [0.6 (%34.5)->0.8 (%65.5))] %66 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, 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 +- 0.27 (0.04-->6.52) (max @ vno 17903 --> 20244) face area 0.28 +- 0.14 (0.00-->4.36) mean absolute distance = 0.34 +- 0.56 2747 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3885749.5, rms=11.570 001: dt: 0.5000, sse=2231176.8, rms=8.275 (28.477%) 002: dt: 0.5000, sse=1523524.4, rms=6.357 (23.177%) 003: dt: 0.5000, sse=1190247.1, rms=5.206 (18.114%) 004: dt: 0.5000, sse=1044638.8, rms=4.572 (12.172%) 005: dt: 0.5000, sse=966795.4, rms=4.263 (6.772%) 006: dt: 0.5000, sse=934938.1, rms=4.098 (3.867%) 007: dt: 0.5000, sse=931360.6, rms=3.990 (2.625%) 008: dt: 0.5000, sse=891062.6, rms=3.873 (2.935%) 009: dt: 0.5000, sse=877181.2, rms=3.797 (1.955%) rms = 3.75, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=869765.5, rms=3.748 (1.288%) 011: dt: 0.2500, sse=683014.9, rms=2.454 (34.536%) 012: dt: 0.2500, sse=639510.9, rms=2.089 (14.874%) 013: dt: 0.2500, sse=631661.9, rms=2.010 (3.790%) 014: dt: 0.2500, sse=626486.2, rms=1.955 (2.734%) rms = 1.94, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=624465.1, rms=1.935 (1.006%) 016: dt: 0.1250, sse=617123.8, rms=1.858 (4.000%) rms = 1.84, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=615976.1, rms=1.844 (0.726%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=79.7, 199 (54) missing vertices, mean dist -0.2 [0.4 (%76.0)->0.2 (%24.0))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n511, 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 +- 0.26 (0.09-->6.53) (max @ vno 17903 --> 20244) face area 0.35 +- 0.17 (0.00-->6.04) mean absolute distance = 0.24 +- 0.37 3028 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1377736.1, rms=5.300 018: dt: 0.5000, sse=980025.9, rms=3.476 (34.417%) rms = 3.62, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=850529.9, rms=2.646 (23.865%) 020: dt: 0.2500, sse=782252.1, rms=2.060 (22.146%) 021: dt: 0.2500, sse=761479.4, rms=1.791 (13.077%) 022: dt: 0.2500, sse=747109.2, rms=1.687 (5.821%) 023: dt: 0.2500, sse=744187.1, rms=1.630 (3.328%) rms = 1.59, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=738566.9, rms=1.589 (2.560%) 025: dt: 0.1250, sse=733685.8, rms=1.526 (3.933%) rms = 1.52, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=732879.4, rms=1.516 (0.641%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.3, 206 (32) missing vertices, mean dist -0.1 [0.3 (%72.0)->0.2 (%28.0))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n511, 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 +- 0.26 (0.11-->6.48) (max @ vno 17903 --> 20244) face area 0.34 +- 0.17 (0.00-->6.10) mean absolute distance = 0.20 +- 0.30 2735 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=968220.9, rms=3.560 027: dt: 0.5000, sse=898412.1, rms=3.096 (13.021%) rms = 3.44, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=760798.6, rms=2.064 (33.338%) 029: dt: 0.2500, sse=720576.8, rms=1.588 (23.055%) 030: dt: 0.2500, sse=706697.1, rms=1.438 (9.439%) rms = 1.43, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=704736.9, rms=1.425 (0.893%) 032: dt: 0.1250, sse=698190.8, rms=1.334 (6.385%) rms = 1.33, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=696320.9, rms=1.330 (0.353%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=83.2, 229 (27) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n511, 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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=714105.8, rms=1.730 rms = 2.05, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=678086.5, rms=1.233 (28.698%) 035: dt: 0.2500, sse=668490.9, rms=1.050 (14.913%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=666770.6, rms=1.036 (1.317%) positioning took 0.3 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6843 vertices erasing segment 1 (vno[0] = 42221) erasing segment 2 (vno[0] = 75464) erasing segment 3 (vno[0] = 83704) erasing segment 4 (vno[0] = 86785) erasing segment 5 (vno[0] = 90962) erasing segment 6 (vno[0] = 93075) erasing segment 7 (vno[0] = 94046) erasing segment 8 (vno[0] = 94102) erasing segment 9 (vno[0] = 94137) erasing segment 10 (vno[0] = 129552) writing cortex label to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label... writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.curv writing smoothed area to rh.area writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.area vertex spacing 0.90 +- 0.26 (0.05-->6.43) (max @ vno 17903 --> 20244) face area 0.34 +- 0.17 (0.00-->6.20) refinement took 4.4 minutes #-------------------------------------------- #@# Smooth2 lh Wed Oct 2 23:22:59 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts 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... #-------------------------------------------- #@# Smooth2 rh Wed Oct 2 23:23:04 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts 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... #-------------------------------------------- #@# Inflation2 lh Wed Oct 2 23:23:09 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.7 mm, total surface area = 79142 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.180 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 25.809076 mris_inflate stimesec 0.077988 mris_inflate ru_maxrss 169728 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22514 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 36 mris_inflate ru_nivcsw 49 #-------------------------------------------- #@# Inflation2 rh Wed Oct 2 23:23:35 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.2 mm, total surface area = 79090 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.181 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 25.835072 mris_inflate stimesec 0.076988 mris_inflate ru_maxrss 168268 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22150 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 30 mris_inflate ru_nivcsw 55 #-------------------------------------------- #@# Curv .H and .K lh Wed Oct 2 23:24:02 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature -w lh.white.preaparc total integrated curvature = 8.856*4pi (111.286) --> -8 handles ICI = 167.1, FI = 1736.6, variation=27287.314 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 136 vertices thresholded to be in k1 ~ [-0.30 0.52], k2 ~ [-0.12 0.08] total integrated curvature = 0.452*4pi (5.676) --> 1 handles ICI = 1.5, FI = 8.9, variation=155.283 113 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 125 vertices thresholded to be in [-0.16 0.21] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.023 done. #-------------------------------------------- #@# Curv .H and .K rh Wed Oct 2 23:25:11 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature -w rh.white.preaparc total integrated curvature = 6.294*4pi (79.094) --> -5 handles ICI = 159.1, FI = 1716.6, variation=26793.151 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 150 vertices thresholded to be in k1 ~ [-0.38 0.61], k2 ~ [-0.14 0.10] total integrated curvature = 0.318*4pi (3.991) --> 1 handles ICI = 1.4, FI = 9.8, variation=164.850 115 vertices thresholded to be in [-0.02 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 144 vertices thresholded to be in [-0.19 0.26] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Wed Oct 2 23:26:18 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 2012-646-010-KK 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 [ 2012-646-010-KK/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 [ 235 ] Gb_filter = 0 WARN: S lookup min: -0.330964 WARN: S explicit min: 0.000000 vertex = 1072 #----------------------------------------- #@# Curvature Stats rh Wed Oct 2 23:26:22 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 2012-646-010-KK 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 [ 2012-646-010-KK/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 [ 230 ] Gb_filter = 0 WARN: S lookup min: -0.114380 WARN: S explicit min: 0.000000 vertex = 466 #-------------------------------------------- #@# Sphere lh Wed Oct 2 23:26:26 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/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 = 1 == scaling brain by 0.282... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n511, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.39 pass 1: epoch 2 of 3 starting distance error %21.36 unfolding complete - removing small folds... starting distance error %21.24 removing remaining folds... final distance error %21.27 MRISunfold() return, current seed 1234 -01: dt=0.0000, 116 negative triangles 197: dt=0.9900, 116 negative triangles 198: dt=0.9900, 58 negative triangles 199: dt=0.9900, 47 negative triangles 200: dt=0.9900, 47 negative triangles 201: dt=0.9900, 42 negative triangles 202: dt=0.9900, 32 negative triangles 203: dt=0.9900, 25 negative triangles 204: dt=0.9900, 28 negative triangles 205: dt=0.9900, 24 negative triangles 206: dt=0.9900, 20 negative triangles 207: dt=0.9900, 21 negative triangles 208: dt=0.9900, 23 negative triangles 209: dt=0.9900, 19 negative triangles 210: dt=0.9900, 17 negative triangles 211: dt=0.9900, 13 negative triangles 212: dt=0.9900, 13 negative triangles 213: dt=0.9900, 14 negative triangles 214: dt=0.9900, 11 negative triangles 215: dt=0.9900, 12 negative triangles 216: dt=0.9900, 15 negative triangles 217: dt=0.9900, 8 negative triangles 218: dt=0.9900, 8 negative triangles 219: dt=0.9900, 5 negative triangles 220: dt=0.9900, 4 negative triangles 221: dt=0.9900, 2 negative triangles 222: dt=0.9900, 4 negative triangles 223: dt=0.9900, 3 negative triangles 224: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.64 hours mris_sphere utimesec 2319.856328 mris_sphere stimesec 0.186971 mris_sphere ru_maxrss 233260 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38010 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 29 mris_sphere ru_nivcsw 9537 FSRUNTIME@ mris_sphere 0.6443 hours 1 threads #-------------------------------------------- #@# Sphere rh Thu Oct 3 00:05:06 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/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 = 1 == scaling brain by 0.281... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n511, 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 %22.27 pass 1: epoch 2 of 3 starting distance error %22.26 unfolding complete - removing small folds... starting distance error %22.11 removing remaining folds... final distance error %22.14 MRISunfold() return, current seed 1234 -01: dt=0.0000, 138 negative triangles 210: dt=0.9900, 138 negative triangles 211: dt=0.9900, 44 negative triangles 212: dt=0.9900, 32 negative triangles 213: dt=0.9900, 27 negative triangles 214: dt=0.9900, 25 negative triangles 215: dt=0.9900, 20 negative triangles 216: dt=0.9900, 18 negative triangles 217: dt=0.9900, 23 negative triangles 218: dt=0.9900, 21 negative triangles 219: dt=0.9900, 18 negative triangles 220: dt=0.9900, 8 negative triangles 221: dt=0.9900, 6 negative triangles 222: dt=0.9900, 9 negative triangles 223: dt=0.9900, 7 negative triangles 224: dt=0.9900, 4 negative triangles 225: dt=0.9900, 7 negative triangles 226: dt=0.9900, 6 negative triangles 227: dt=0.9900, 4 negative triangles 228: dt=0.9900, 3 negative triangles 229: dt=0.9900, 2 negative triangles 230: dt=0.9900, 2 negative triangles 231: dt=0.9900, 5 negative triangles 232: dt=0.9900, 2 negative triangles 233: dt=0.9900, 1 negative triangles 234: dt=0.9900, 1 negative triangles 235: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.59 hours mris_sphere utimesec 2142.402305 mris_sphere stimesec 0.234964 mris_sphere ru_maxrss 231204 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38011 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 31 mris_sphere ru_nivcsw 3012 FSRUNTIME@ mris_sphere 0.5950 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Thu Oct 3 00:40:48 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /public/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n511, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n511, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.448 curvature mean = 0.017, std = 0.812 curvature mean = 0.022, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 347932.9, tmin=0.8088 d=32.00 min @ (0.00, -8.00, -8.00) sse = 264722.8, tmin=1.6550 d=8.00 min @ (-2.00, 2.00, 0.00) sse = 261419.5, tmin=3.3500 d=4.00 min @ (0.00, -1.00, 0.00) sse = 260266.5, tmin=4.1978 d=2.00 min @ (0.50, 0.00, 0.00) sse = 260049.3, tmin=5.0599 d=1.00 min @ (0.00, 0.00, -0.25) sse = 260005.0, tmin=5.9148 d=0.50 min @ (0.00, 0.12, 0.00) sse = 260002.6, tmin=6.7845 tol=1.0e+00, sigma=0.5, host= n511, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.78 min curvature mean = -0.012, std = 0.837 curvature mean = 0.007, std = 0.948 curvature mean = -0.015, std = 0.848 curvature mean = 0.003, std = 0.979 curvature mean = -0.017, std = 0.851 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.034, std = 0.301 curvature mean = 0.036, std = 0.249 curvature mean = 0.069, std = 0.350 curvature mean = 0.030, std = 0.308 curvature mean = 0.038, std = 0.537 curvature mean = 0.029, std = 0.335 curvature mean = 0.021, std = 0.678 curvature mean = 0.029, std = 0.346 curvature mean = 0.007, std = 0.788 MRISregister() return, current seed 0 -01: dt=0.0000, 66 negative triangles 112: dt=0.9900, 66 negative triangles expanding nbhd size to 1 113: dt=0.9900, 86 negative triangles 114: dt=0.9900, 71 negative triangles 115: dt=0.9900, 80 negative triangles 116: dt=0.9900, 75 negative triangles 117: dt=0.9900, 74 negative triangles 118: dt=0.9900, 69 negative triangles 119: dt=0.9900, 59 negative triangles 120: dt=0.9900, 60 negative triangles 121: dt=0.9900, 52 negative triangles 122: dt=0.9900, 56 negative triangles 123: dt=0.9900, 47 negative triangles 124: dt=0.9900, 53 negative triangles 125: dt=0.9900, 44 negative triangles 126: dt=0.9900, 48 negative triangles 127: dt=0.9900, 41 negative triangles 128: dt=0.9900, 39 negative triangles 129: dt=0.9900, 37 negative triangles 130: dt=0.9900, 38 negative triangles 131: dt=0.9900, 37 negative triangles 132: dt=0.9900, 33 negative triangles 133: dt=0.9900, 34 negative triangles 134: dt=0.9900, 30 negative triangles 135: dt=0.9900, 28 negative triangles 136: dt=0.9900, 26 negative triangles 137: dt=0.9900, 20 negative triangles 138: dt=0.9900, 14 negative triangles 139: dt=0.9900, 14 negative triangles 140: dt=0.9900, 13 negative triangles 141: dt=0.9900, 12 negative triangles 142: dt=0.9900, 10 negative triangles 143: dt=0.9900, 11 negative triangles 144: dt=0.9900, 12 negative triangles 145: dt=0.9900, 7 negative triangles 146: dt=0.9900, 7 negative triangles 147: dt=0.9900, 6 negative triangles 148: dt=0.9900, 5 negative triangles 149: dt=0.9900, 8 negative triangles 150: dt=0.9900, 6 negative triangles 151: dt=0.9900, 5 negative triangles 152: dt=0.9900, 6 negative triangles 153: dt=0.9900, 3 negative triangles 154: dt=0.9900, 2 negative triangles 155: dt=0.9900, 2 negative triangles 156: dt=0.9900, 3 negative triangles 157: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.68 hours mris_register utimesec 2459.398114 mris_register stimesec 0.352946 mris_register ru_maxrss 222992 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 28052 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 86 mris_register ru_nivcsw 2664 FSRUNTIME@ mris_register 0.6831 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Oct 3 01:21:48 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /public/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n511, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n511, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.637 curvature mean = 0.037, std = 0.811 curvature mean = 0.021, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 331237.9, tmin=0.9299 d=32.00 min @ (-8.00, 0.00, -8.00) sse = 306612.9, tmin=1.8588 d=16.00 min @ (0.00, 4.00, 4.00) sse = 286036.9, tmin=2.7899 d=8.00 min @ (0.00, -2.00, 0.00) sse = 285248.9, tmin=3.7422 d=4.00 min @ (1.00, 1.00, 0.00) sse = 284416.4, tmin=4.7001 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 284178.7, tmin=5.5745 d=1.00 min @ (0.25, 0.00, 0.25) sse = 284096.7, tmin=6.4439 d=0.50 min @ (0.00, 0.12, 0.00) sse = 284096.0, tmin=7.3124 tol=1.0e+00, sigma=0.5, host= n511, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.31 min curvature mean = -0.002, std = 0.831 curvature mean = 0.007, std = 0.949 curvature mean = -0.009, std = 0.840 curvature mean = 0.003, std = 0.979 curvature mean = -0.011, std = 0.842 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.034, std = 0.296 curvature mean = 0.034, std = 0.242 curvature mean = 0.071, std = 0.358 curvature mean = 0.025, std = 0.301 curvature mean = 0.040, std = 0.545 curvature mean = 0.024, std = 0.328 curvature mean = 0.022, std = 0.688 curvature mean = 0.024, std = 0.339 curvature mean = 0.008, std = 0.799 MRISregister() return, current seed 0 -01: dt=0.0000, 43 negative triangles 118: dt=0.9900, 43 negative triangles expanding nbhd size to 1 119: dt=0.9900, 66 negative triangles 120: dt=0.9405, 47 negative triangles 121: dt=0.9405, 42 negative triangles 122: dt=0.9405, 44 negative triangles 123: dt=0.9405, 41 negative triangles 124: dt=0.9405, 39 negative triangles 125: dt=0.9405, 41 negative triangles 126: dt=0.9405, 38 negative triangles 127: dt=0.9405, 37 negative triangles 128: dt=0.9405, 41 negative triangles 129: dt=0.9405, 39 negative triangles 130: dt=0.9405, 36 negative triangles 131: dt=0.9405, 35 negative triangles 132: dt=0.9405, 31 negative triangles 133: dt=0.9405, 27 negative triangles 134: dt=0.9405, 25 negative triangles 135: dt=0.9405, 28 negative triangles 136: dt=0.9405, 26 negative triangles 137: dt=0.9405, 25 negative triangles 138: dt=0.9405, 25 negative triangles 139: dt=0.9405, 23 negative triangles 140: dt=0.9405, 21 negative triangles 141: dt=0.9405, 16 negative triangles 142: dt=0.9405, 15 negative triangles 143: dt=0.9405, 15 negative triangles 144: dt=0.9405, 16 negative triangles 145: dt=0.9405, 14 negative triangles 146: dt=0.9405, 13 negative triangles 147: dt=0.9405, 11 negative triangles 148: dt=0.9405, 12 negative triangles 149: dt=0.9405, 11 negative triangles 150: dt=0.9405, 8 negative triangles 151: dt=0.9405, 7 negative triangles 152: dt=0.9405, 8 negative triangles 153: dt=0.9405, 8 negative triangles 154: dt=0.9405, 6 negative triangles 155: dt=0.9405, 3 negative triangles 156: dt=0.9405, 4 negative triangles 157: dt=0.9405, 4 negative triangles 158: dt=0.9405, 5 negative triangles 159: dt=0.9405, 7 negative triangles 160: dt=0.9405, 3 negative triangles 161: dt=0.9405, 4 negative triangles 162: dt=0.9405, 3 negative triangles 163: dt=0.9405, 4 negative triangles 164: dt=0.9405, 3 negative triangles 165: dt=0.9405, 2 negative triangles 166: dt=0.9405, 2 negative triangles 167: dt=0.9405, 3 negative triangles 168: dt=0.9405, 5 negative triangles 169: dt=0.9405, 2 negative triangles 170: dt=0.9405, 1 negative triangles 171: dt=0.9405, 1 negative triangles 172: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.89 hours mris_register utimesec 3212.528621 mris_register stimesec 0.686895 mris_register ru_maxrss 222056 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 30365 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 49 mris_register ru_nivcsw 7280 FSRUNTIME@ mris_register 0.8924 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Thu Oct 3 02:15:22 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Thu Oct 3 02:15:24 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Oct 3 02:15:27 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /public/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Thu Oct 3 02:15:29 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /public/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Oct 3 02:15:31 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK lh ../surf/lh.sphere.reg /public/apps/freesurfer/6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /public/apps/freesurfer/6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1041 labels changed using aseg relabeling using gibbs priors... 000: 3031 changed, 131581 examined... 001: 679 changed, 12552 examined... 002: 144 changed, 3742 examined... 003: 53 changed, 889 examined... 004: 15 changed, 308 examined... 005: 8 changed, 83 examined... 006: 3 changed, 52 examined... 007: 1 changed, 17 examined... 008: 0 changed, 7 examined... 235 labels changed using aseg 000: 113 total segments, 72 labels (341 vertices) changed 001: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2131 vertices marked for relabeling... 2131 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Cortical Parc rh Thu Oct 3 02:15:43 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK rh ../surf/rh.sphere.reg /public/apps/freesurfer/6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /public/apps/freesurfer/6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1052 labels changed using aseg relabeling using gibbs priors... 000: 2654 changed, 130392 examined... 001: 613 changed, 11664 examined... 002: 149 changed, 3508 examined... 003: 53 changed, 902 examined... 004: 20 changed, 306 examined... 005: 11 changed, 122 examined... 006: 3 changed, 72 examined... 007: 2 changed, 23 examined... 008: 0 changed, 8 examined... 142 labels changed using aseg 000: 86 total segments, 48 labels (206 vertices) changed 001: 41 total segments, 3 labels (5 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1405 vertices marked for relabeling... 1405 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 12 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Oct 3 02:15:56 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 2012-646-010-KK lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/filled.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/../mri/aseg.presurf.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... 17706 bright wm thresholded. 97 bright non-wm voxels segmented. reading original surface position from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig... computing class statistics... border white: 240382 voxels (1.43%) border gray 280733 voxels (1.67%) WM (97.0): 97.1 +- 9.3 [70.0 --> 110.0] GM (67.0) : 67.3 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.5 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 42.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=63+-7.8 mean inside = 91.8, mean outside = 71.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.27 (0.03-->6.04) (max @ vno 89266 --> 89369) face area 0.33 +- 0.18 (0.00-->9.72) mean absolute distance = 0.61 +- 0.85 2647 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 70 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 64 points - only 0.00% unknown deleting segment 4 with 58 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 150 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 47 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=76.4, 375 (362) missing vertices, mean dist 0.4 [0.9 (%12.9)->0.6 (%87.1))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, 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 0.92 +- 0.27 (0.05-->5.93) (max @ vno 130193 --> 130218) face area 0.33 +- 0.17 (0.00-->9.05) mean absolute distance = 0.36 +- 0.59 3325 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2764414.0, rms=9.173 001: dt: 0.5000, sse=1419487.8, rms=5.566 (39.317%) 002: dt: 0.5000, sse=1079320.6, rms=4.225 (24.097%) 003: dt: 0.5000, sse=1030777.2, rms=3.994 (5.469%) 004: dt: 0.5000, sse=983601.9, rms=3.750 (6.107%) rms = 3.87, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=836478.9, rms=2.844 (24.171%) 006: dt: 0.2500, sse=792855.1, rms=2.449 (13.878%) 007: dt: 0.2500, sse=776325.7, rms=2.327 (4.973%) 008: dt: 0.2500, sse=772609.2, rms=2.276 (2.186%) rms = 2.25, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=767271.4, rms=2.248 (1.242%) 010: dt: 0.1250, sse=757291.5, rms=2.193 (2.468%) rms = 2.18, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=756611.6, rms=2.178 (0.667%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 77 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 55 points - only 0.00% unknown deleting segment 4 with 55 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 64 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 39 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown mean border=80.3, 224 (88) missing vertices, mean dist -0.2 [0.4 (%76.7)->0.2 (%23.3))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n511, 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 0.90 +- 0.27 (0.09-->5.96) (max @ vno 130215 --> 130221) face area 0.35 +- 0.19 (0.00-->9.86) mean absolute distance = 0.25 +- 0.40 2971 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1435887.8, rms=5.477 012: dt: 0.5000, sse=1057609.1, rms=3.796 (30.698%) rms = 3.80, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=918850.6, rms=3.066 (19.228%) 014: dt: 0.2500, sse=848973.2, rms=2.500 (18.454%) 015: dt: 0.2500, sse=810756.7, rms=2.254 (9.859%) 016: dt: 0.2500, sse=797402.6, rms=2.149 (4.644%) 017: dt: 0.2500, sse=800357.0, rms=2.098 (2.389%) rms = 2.05, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=791778.4, rms=2.055 (2.059%) 019: dt: 0.1250, sse=784966.9, rms=1.997 (2.807%) rms = 1.99, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=781510.9, rms=1.988 (0.460%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 73 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 54 points - only 0.00% unknown deleting segment 3 with 61 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown deleting segment 6 with 66 points - only 0.00% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 44 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown mean border=82.8, 256 (57) missing vertices, mean dist -0.1 [0.3 (%72.3)->0.2 (%27.7))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n511, 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 0.89 +- 0.27 (0.10-->6.19) (max @ vno 130215 --> 130221) face area 0.34 +- 0.18 (0.00-->9.96) mean absolute distance = 0.21 +- 0.33 2635 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=999897.9, rms=3.691 021: dt: 0.5000, sse=960975.4, rms=3.344 (9.393%) rms = 3.60, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=813411.7, rms=2.449 (26.773%) 023: dt: 0.2500, sse=783985.8, rms=2.087 (14.759%) 024: dt: 0.2500, sse=760324.3, rms=1.984 (4.976%) rms = 1.97, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=758741.0, rms=1.966 (0.867%) 026: dt: 0.1250, sse=748922.5, rms=1.883 (4.260%) rms = 1.87, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=744478.5, rms=1.866 (0.883%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 89 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 53 points - only 0.00% unknown deleting segment 3 with 64 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown deleting segment 6 with 64 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 44 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown mean border=83.6, 305 (45) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n511, 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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=763599.5, rms=2.169 rms = 2.42, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=723582.1, rms=1.761 (18.838%) 029: dt: 0.2500, sse=728699.2, rms=1.625 (7.703%) rms = 1.61, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=712404.1, rms=1.612 (0.830%) 031: dt: 0.1250, sse=703538.9, rms=1.533 (4.893%) rms = 1.50, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=704584.8, rms=1.500 (2.122%) positioning took 0.4 minutes generating cortex label... 15 non-cortical segments detected only using segment with 6792 vertices erasing segment 0 (vno[0] = 34751) erasing segment 2 (vno[0] = 48346) erasing segment 3 (vno[0] = 49741) erasing segment 4 (vno[0] = 76865) erasing segment 5 (vno[0] = 81092) erasing segment 6 (vno[0] = 88295) erasing segment 7 (vno[0] = 89287) erasing segment 8 (vno[0] = 90304) erasing segment 9 (vno[0] = 93191) erasing segment 10 (vno[0] = 93259) erasing segment 11 (vno[0] = 97894) erasing segment 12 (vno[0] = 99234) erasing segment 13 (vno[0] = 99569) erasing segment 14 (vno[0] = 130897) writing cortex label to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label... writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.curv writing smoothed area to lh.area writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.area vertex spacing 0.89 +- 0.27 (0.03-->6.39) (max @ vno 130215 --> 130221) face area 0.33 +- 0.18 (0.00-->10.63) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 91 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.5, 240 (240) missing vertices, mean dist 1.7 [1.0 (%0.1)->2.8 (%99.9))] %12 local maxima, %45 large gradients and %39 min vals, 332 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=29532406.0, rms=33.878 001: dt: 0.0500, sse=26023192.0, rms=31.755 (6.268%) 002: dt: 0.0500, sse=23533156.0, rms=30.157 (5.031%) 003: dt: 0.0500, sse=21633780.0, rms=28.879 (4.238%) 004: dt: 0.0500, sse=20102538.0, rms=27.806 (3.716%) 005: dt: 0.0500, sse=18819546.0, rms=26.874 (3.353%) 006: dt: 0.0500, sse=17711578.0, rms=26.042 (3.096%) 007: dt: 0.0500, sse=16734505.0, rms=25.285 (2.905%) 008: dt: 0.0500, sse=15859005.0, rms=24.588 (2.759%) 009: dt: 0.0500, sse=15066335.0, rms=23.938 (2.640%) 010: dt: 0.0500, sse=14340719.0, rms=23.328 (2.549%) positioning took 0.7 minutes mean border=50.3, 150 (108) missing vertices, mean dist 1.4 [0.8 (%0.2)->2.3 (%99.8))] %12 local maxima, %45 large gradients and %38 min vals, 284 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=15090194.0, rms=23.951 011: dt: 0.0500, sse=14416275.0, rms=23.385 (2.360%) 012: dt: 0.0500, sse=13792595.0, rms=22.850 (2.291%) 013: dt: 0.0500, sse=13213699.0, rms=22.341 (2.227%) 014: dt: 0.0500, sse=12674987.0, rms=21.857 (2.167%) 015: dt: 0.0500, sse=12172866.0, rms=21.396 (2.110%) 016: dt: 0.0500, sse=11703969.0, rms=20.956 (2.056%) 017: dt: 0.0500, sse=11265595.0, rms=20.536 (2.004%) 018: dt: 0.0500, sse=10855700.0, rms=20.135 (1.951%) 019: dt: 0.0500, sse=10471331.0, rms=19.752 (1.903%) 020: dt: 0.0500, sse=10110264.0, rms=19.385 (1.857%) positioning took 0.7 minutes mean border=50.2, 154 (77) missing vertices, mean dist 1.2 [0.2 (%1.1)->2.0 (%98.9))] %13 local maxima, %45 large gradients and %38 min vals, 294 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=10248808.0, rms=19.530 021: dt: 0.0500, sse=9900961.0, rms=19.173 (1.830%) 022: dt: 0.0500, sse=9574492.0, rms=18.831 (1.782%) 023: dt: 0.0500, sse=9265916.0, rms=18.503 (1.746%) 024: dt: 0.0500, sse=8975946.0, rms=18.188 (1.699%) 025: dt: 0.0500, sse=8702791.0, rms=17.887 (1.657%) 026: dt: 0.0500, sse=8445071.0, rms=17.598 (1.616%) 027: dt: 0.0500, sse=8200432.5, rms=17.319 (1.585%) 028: dt: 0.0500, sse=7966572.5, rms=17.048 (1.565%) 029: dt: 0.0500, sse=7741849.5, rms=16.783 (1.553%) 030: dt: 0.0500, sse=7526101.0, rms=16.525 (1.538%) positioning took 0.7 minutes mean border=50.1, 194 (66) missing vertices, mean dist 1.0 [0.1 (%7.4)->1.8 (%92.6))] %13 local maxima, %45 large gradients and %38 min vals, 247 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_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 = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7622877.5, rms=16.641 031: dt: 0.5000, sse=6048206.0, rms=14.636 (12.047%) 032: dt: 0.5000, sse=4903364.0, rms=12.979 (11.325%) 033: dt: 0.5000, sse=3989834.0, rms=11.487 (11.490%) 034: dt: 0.5000, sse=3315585.2, rms=10.242 (10.839%) 035: dt: 0.5000, sse=2795754.8, rms=9.168 (10.484%) 036: dt: 0.5000, sse=2398510.8, rms=8.249 (10.028%) 037: dt: 0.5000, sse=2091138.4, rms=7.465 (9.509%) 038: dt: 0.5000, sse=1871505.9, rms=6.846 (8.282%) 039: dt: 0.5000, sse=1737810.4, rms=6.443 (5.898%) 040: dt: 0.5000, sse=1647253.6, rms=6.150 (4.535%) 041: dt: 0.5000, sse=1590244.1, rms=5.962 (3.069%) 042: dt: 0.5000, sse=1546038.0, rms=5.807 (2.592%) 043: dt: 0.5000, sse=1518861.8, rms=5.714 (1.608%) 044: dt: 0.5000, sse=1493605.0, rms=5.621 (1.619%) rms = 5.58, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1480627.8, rms=5.577 (0.785%) 046: dt: 0.2500, sse=1345955.5, rms=5.024 (9.924%) 047: dt: 0.2500, sse=1298051.8, rms=4.831 (3.825%) rms = 4.85, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1280017.8, rms=4.753 (1.625%) 049: dt: 0.1250, sse=1256480.6, rms=4.648 (2.219%) rms = 4.63, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1252877.5, rms=4.630 (0.369%) positioning took 2.0 minutes mean border=48.8, 1999 (26) missing vertices, mean dist 0.2 [0.2 (%49.8)->0.7 (%50.2))] %21 local maxima, %38 large gradients and %36 min vals, 140 gradients ignored tol=1.0e-04, sigma=1.0, host= n511, nav=8, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1528852.6, rms=5.105 rms = 5.11, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1404115.5, rms=4.575 (10.374%) 052: dt: 0.2500, sse=1339503.6, rms=4.272 (6.620%) rms = 4.22, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1327786.4, rms=4.223 (1.162%) 054: dt: 0.1250, sse=1260189.0, rms=3.877 (8.178%) 055: dt: 0.1250, sse=1243223.5, rms=3.791 (2.230%) rms = 3.76, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1236253.9, rms=3.756 (0.925%) positioning took 0.7 minutes mean border=48.0, 2222 (24) missing vertices, mean dist 0.1 [0.2 (%49.7)->0.5 (%50.3))] %33 local maxima, %26 large gradients and %35 min vals, 162 gradients ignored tol=1.0e-04, sigma=0.5, host= n511, nav=4, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1288012.6, rms=4.028 rms = 4.51, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1248041.6, rms=3.822 (5.128%) 058: dt: 0.2500, sse=1230781.5, rms=3.738 (2.175%) rms = 3.79, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1221324.2, rms=3.685 (1.428%) 060: dt: 0.1250, sse=1208415.6, rms=3.614 (1.922%) rms = 3.57, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1199986.2, rms=3.570 (1.234%) positioning took 0.8 minutes mean border=47.5, 4163 (21) missing vertices, mean dist 0.1 [0.2 (%50.6)->0.4 (%49.4))] %37 local maxima, %21 large gradients and %35 min vals, 168 gradients ignored tol=1.0e-04, sigma=0.2, host= n511, nav=2, nbrs=2, l_surf_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 pial surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1217637.0, rms=3.643 rms = 4.06, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1195426.6, rms=3.518 (3.429%) 063: dt: 0.2500, sse=1182275.0, rms=3.460 (1.667%) rms = 3.51, time step reduction 2 of 3 to 0.125... rms = 3.41, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1174418.4, rms=3.411 (1.395%) positioning took 0.5 minutes writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.area.pial vertex spacing 1.01 +- 0.44 (0.08-->6.58) (max @ vno 130193 --> 130218) face area 0.40 +- 0.31 (0.00-->13.20) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 131581 vertices processed 25000 of 131581 vertices processed 50000 of 131581 vertices processed 75000 of 131581 vertices processed 100000 of 131581 vertices processed 125000 of 131581 vertices processed 0 of 131581 vertices processed 25000 of 131581 vertices processed 50000 of 131581 vertices processed 75000 of 131581 vertices processed 100000 of 131581 vertices processed 125000 of 131581 vertices processed thickness calculation complete, 218:585 truncations. 32538 vertices at 0 distance 95993 vertices at 1 distance 76655 vertices at 2 distance 31313 vertices at 3 distance 10225 vertices at 4 distance 3424 vertices at 5 distance 1074 vertices at 6 distance 419 vertices at 7 distance 178 vertices at 8 distance 132 vertices at 9 distance 68 vertices at 10 distance 51 vertices at 11 distance 28 vertices at 12 distance 29 vertices at 13 distance 27 vertices at 14 distance 19 vertices at 15 distance 15 vertices at 16 distance 7 vertices at 17 distance 7 vertices at 18 distance 7 vertices at 19 distance 13 vertices at 20 distance writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.thickness positioning took 11.8 minutes #-------------------------------------------- #@# Make Pial Surf rh Thu Oct 3 02:27:47 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 2012-646-010-KK rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/filled.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/../mri/aseg.presurf.mgz... reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... 17706 bright wm thresholded. 97 bright non-wm voxels segmented. reading original surface position from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig... computing class statistics... border white: 240382 voxels (1.43%) border gray 280733 voxels (1.67%) WM (97.0): 97.1 +- 9.3 [70.0 --> 110.0] GM (67.0) : 67.3 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.5 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 42.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.0, GM=63+-7.0 mean inside = 92.0, mean outside = 71.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.05-->6.43) (max @ vno 17903 --> 20244) face area 0.33 +- 0.17 (0.00-->6.16) mean absolute distance = 0.61 +- 0.81 2541 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 29 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 152 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown mean border=75.6, 211 (211) missing vertices, mean dist 0.4 [0.9 (%11.9)->0.6 (%88.1))] %64 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, 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 +- 0.27 (0.10-->6.75) (max @ vno 17903 --> 20244) face area 0.33 +- 0.17 (0.00-->5.62) mean absolute distance = 0.34 +- 0.56 2534 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2770111.5, rms=9.236 001: dt: 0.5000, sse=1384569.1, rms=5.454 (40.951%) 002: dt: 0.5000, sse=1033468.5, rms=3.996 (26.724%) 003: dt: 0.5000, sse=977475.9, rms=3.730 (6.663%) 004: dt: 0.5000, sse=931261.4, rms=3.491 (6.405%) rms = 3.62, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=785424.4, rms=2.477 (29.052%) 006: dt: 0.2500, sse=736423.7, rms=2.020 (18.427%) 007: dt: 0.2500, sse=733416.8, rms=1.871 (7.413%) rms = 1.84, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=720243.5, rms=1.837 (1.804%) 009: dt: 0.1250, sse=714833.7, rms=1.767 (3.785%) rms = 1.76, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=713726.7, rms=1.755 (0.688%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 46 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown mean border=79.6, 194 (88) missing vertices, mean dist -0.2 [0.4 (%76.5)->0.2 (%23.5))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n511, 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 +- 0.26 (0.10-->6.64) (max @ vno 17903 --> 20244) face area 0.36 +- 0.18 (0.00-->6.42) mean absolute distance = 0.24 +- 0.38 3075 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1384013.0, rms=5.291 011: dt: 0.5000, sse=977777.9, rms=3.402 (35.708%) rms = 3.50, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=849162.8, rms=2.571 (24.431%) 013: dt: 0.2500, sse=777722.6, rms=1.928 (25.014%) 014: dt: 0.2500, sse=755553.4, rms=1.634 (15.258%) 015: dt: 0.2500, sse=743556.7, rms=1.532 (6.203%) rms = 1.49, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=749158.9, rms=1.488 (2.873%) 017: dt: 0.1250, sse=738638.8, rms=1.426 (4.179%) rms = 1.42, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=735401.6, rms=1.423 (0.207%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 28 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 48 points - only 0.00% unknown deleting segment 3 with 28 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown mean border=82.2, 208 (67) missing vertices, mean dist -0.1 [0.3 (%72.5)->0.2 (%27.5))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n511, 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 +- 0.26 (0.05-->6.57) (max @ vno 17903 --> 20244) face area 0.34 +- 0.18 (0.00-->6.44) mean absolute distance = 0.20 +- 0.30 2833 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=971714.8, rms=3.547 019: dt: 0.5000, sse=902050.2, rms=3.072 (13.396%) rms = 3.40, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=765136.1, rms=2.030 (33.911%) 021: dt: 0.2500, sse=721513.5, rms=1.550 (23.660%) 022: dt: 0.2500, sse=708180.8, rms=1.398 (9.761%) rms = 1.39, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=707605.6, rms=1.386 (0.898%) 024: dt: 0.1250, sse=708769.4, rms=1.301 (6.135%) rms = 1.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=700683.6, rms=1.297 (0.328%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 49 points - only 0.00% unknown deleting segment 4 with 34 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown mean border=83.1, 233 (58) missing vertices, mean dist -0.0 [0.2 (%57.5)->0.2 (%42.5))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n511, 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 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=721072.0, rms=1.739 rms = 2.06, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=683183.2, rms=1.226 (29.538%) 027: dt: 0.2500, sse=673283.0, rms=1.028 (16.161%) rms = 1.05, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=671143.4, rms=1.014 (1.341%) positioning took 0.3 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6813 vertices erasing segment 1 (vno[0] = 75464) erasing segment 2 (vno[0] = 83704) erasing segment 3 (vno[0] = 86785) erasing segment 4 (vno[0] = 90962) erasing segment 5 (vno[0] = 93075) erasing segment 6 (vno[0] = 94046) erasing segment 7 (vno[0] = 94102) erasing segment 8 (vno[0] = 94137) writing cortex label to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label... writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.curv writing smoothed area to rh.area writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.area vertex spacing 0.90 +- 0.27 (0.05-->6.48) (max @ vno 17903 --> 20244) face area 0.34 +- 0.17 (0.00-->6.45) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.3, 192 (192) missing vertices, mean dist 1.7 [0.7 (%0.0)->2.7 (%100.0))] %12 local maxima, %50 large gradients and %34 min vals, 341 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=28804416.0, rms=33.576 001: dt: 0.0500, sse=25324758.0, rms=31.434 (6.380%) 002: dt: 0.0500, sse=22843282.0, rms=29.812 (5.159%) 003: dt: 0.0500, sse=20952428.0, rms=28.514 (4.353%) 004: dt: 0.0500, sse=19433160.0, rms=27.427 (3.813%) 005: dt: 0.0500, sse=18162872.0, rms=26.484 (3.440%) 006: dt: 0.0500, sse=17068840.0, rms=25.643 (3.173%) 007: dt: 0.0500, sse=16107018.0, rms=24.881 (2.973%) 008: dt: 0.0500, sse=15247392.0, rms=24.179 (2.820%) 009: dt: 0.0500, sse=14470548.0, rms=23.527 (2.697%) 010: dt: 0.0500, sse=13761650.0, rms=22.916 (2.598%) positioning took 0.7 minutes mean border=50.1, 151 (108) missing vertices, mean dist 1.4 [0.4 (%0.0)->2.2 (%100.0))] %12 local maxima, %50 large gradients and %34 min vals, 320 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14423649.0, rms=23.483 011: dt: 0.0500, sse=13767890.0, rms=22.918 (2.409%) 012: dt: 0.0500, sse=13162139.0, rms=22.382 (2.336%) 013: dt: 0.0500, sse=12600200.0, rms=21.874 (2.271%) 014: dt: 0.0500, sse=12077642.0, rms=21.390 (2.211%) 015: dt: 0.0500, sse=11590256.0, rms=20.929 (2.156%) 016: dt: 0.0500, sse=11135016.0, rms=20.489 (2.104%) 017: dt: 0.0500, sse=10709689.0, rms=20.069 (2.051%) 018: dt: 0.0500, sse=10311406.0, rms=19.667 (2.001%) 019: dt: 0.0500, sse=9938571.0, rms=19.283 (1.951%) 020: dt: 0.0500, sse=9589044.0, rms=18.917 (1.902%) positioning took 0.7 minutes mean border=50.0, 155 (81) missing vertices, mean dist 1.2 [0.1 (%0.5)->1.9 (%99.5))] %12 local maxima, %50 large gradients and %33 min vals, 323 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=9698801.0, rms=19.037 021: dt: 0.0500, sse=9363431.0, rms=18.680 (1.872%) 022: dt: 0.0500, sse=9049156.0, rms=18.340 (1.822%) 023: dt: 0.0500, sse=8752483.0, rms=18.013 (1.785%) 024: dt: 0.0500, sse=8473866.0, rms=17.700 (1.738%) 025: dt: 0.0500, sse=8211781.0, rms=17.400 (1.693%) 026: dt: 0.0500, sse=7964655.0, rms=17.113 (1.652%) 027: dt: 0.0500, sse=7730542.0, rms=16.836 (1.618%) 028: dt: 0.0500, sse=7506537.5, rms=16.566 (1.600%) 029: dt: 0.0500, sse=7292257.0, rms=16.305 (1.581%) 030: dt: 0.0500, sse=7087040.0, rms=16.050 (1.563%) positioning took 0.7 minutes mean border=49.9, 174 (66) missing vertices, mean dist 1.0 [0.1 (%6.7)->1.6 (%93.3))] %13 local maxima, %50 large gradients and %33 min vals, 288 gradients ignored tol=1.0e-04, sigma=2.0, host= n511, nav=16, nbrs=2, l_surf_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 = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7162209.0, rms=16.143 031: dt: 0.5000, sse=5675667.5, rms=14.175 (12.195%) 032: dt: 0.5000, sse=4634245.5, rms=12.607 (11.061%) 033: dt: 0.5000, sse=3819015.2, rms=11.230 (10.921%) 034: dt: 0.5000, sse=3190780.0, rms=10.033 (10.661%) 035: dt: 0.5000, sse=2689662.5, rms=8.965 (10.644%) 036: dt: 0.5000, sse=2298629.8, rms=8.029 (10.435%) 037: dt: 0.5000, sse=1999503.5, rms=7.236 (9.886%) 038: dt: 0.5000, sse=1784730.9, rms=6.604 (8.724%) 039: dt: 0.5000, sse=1646565.4, rms=6.165 (6.649%) 040: dt: 0.5000, sse=1552178.4, rms=5.844 (5.218%) 041: dt: 0.5000, sse=1494419.9, rms=5.640 (3.489%) 042: dt: 0.5000, sse=1453263.0, rms=5.486 (2.722%) 043: dt: 0.5000, sse=1425668.1, rms=5.385 (1.841%) 044: dt: 0.5000, sse=1405971.6, rms=5.306 (1.469%) rms = 5.26, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1393520.9, rms=5.260 (0.865%) 046: dt: 0.2500, sse=1257937.2, rms=4.658 (11.449%) 047: dt: 0.2500, sse=1212335.8, rms=4.458 (4.300%) rms = 4.47, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1195931.4, rms=4.379 (1.755%) 049: dt: 0.1250, sse=1173911.5, rms=4.271 (2.469%) rms = 4.25, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1169637.0, rms=4.250 (0.503%) positioning took 1.9 minutes mean border=48.6, 1644 (30) missing vertices, mean dist 0.1 [0.2 (%50.9)->0.6 (%49.1))] %22 local maxima, %41 large gradients and %31 min vals, 121 gradients ignored tol=1.0e-04, sigma=1.0, host= n511, nav=8, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1463674.9, rms=4.806 rms = 4.80, time step reduction 1 of 3 to 0.250... 051: dt: 0.5000, sse=1458925.1, rms=4.802 (0.079%) 052: dt: 0.2500, sse=1271396.9, rms=3.897 (18.845%) 053: dt: 0.2500, sse=1239764.2, rms=3.733 (4.206%) rms = 3.74, time step reduction 2 of 3 to 0.125... 054: dt: 0.1250, sse=1216581.5, rms=3.600 (3.562%) 055: dt: 0.1250, sse=1183936.5, rms=3.406 (5.382%) 056: dt: 0.1250, sse=1174120.4, rms=3.348 (1.700%) rms = 3.32, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1169799.6, rms=3.324 (0.728%) positioning took 0.8 minutes mean border=47.7, 1855 (26) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.4 (%50.5))] %37 local maxima, %27 large gradients and %31 min vals, 117 gradients ignored tol=1.0e-04, sigma=0.5, host= n511, nav=4, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1237366.0, rms=3.701 rms = 4.21, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1193923.9, rms=3.451 (6.761%) 059: dt: 0.2500, sse=1176704.6, rms=3.354 (2.819%) rms = 3.42, time step reduction 2 of 3 to 0.125... rms = 3.30, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1169026.8, rms=3.305 (1.455%) positioning took 0.5 minutes mean border=47.1, 3674 (25) missing vertices, mean dist 0.1 [0.2 (%50.6)->0.3 (%49.4))] %41 local maxima, %22 large gradients and %30 min vals, 136 gradients ignored tol=1.0e-04, sigma=0.2, host= n511, nav=2, nbrs=2, l_surf_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 pial surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1189383.5, rms=3.416 rms = 4.04, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1162920.1, rms=3.252 (4.822%) 062: dt: 0.2500, sse=1152162.9, rms=3.199 (1.601%) rms = 3.26, time step reduction 2 of 3 to 0.125... 063: dt: 0.1250, sse=1144358.0, rms=3.147 (1.630%) 064: dt: 0.1250, sse=1133071.2, rms=3.075 (2.296%) rms = 3.04, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1126922.8, rms=3.039 (1.161%) positioning took 0.7 minutes writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.area.pial vertex spacing 1.02 +- 0.44 (0.07-->8.23) (max @ vno 79702 --> 79701) face area 0.41 +- 0.32 (0.00-->6.44) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 130392 vertices processed 25000 of 130392 vertices processed 50000 of 130392 vertices processed 75000 of 130392 vertices processed 100000 of 130392 vertices processed 125000 of 130392 vertices processed 0 of 130392 vertices processed 25000 of 130392 vertices processed 50000 of 130392 vertices processed 75000 of 130392 vertices processed 100000 of 130392 vertices processed 125000 of 130392 vertices processed thickness calculation complete, 246:527 truncations. 32333 vertices at 0 distance 95327 vertices at 1 distance 76676 vertices at 2 distance 30809 vertices at 3 distance 9902 vertices at 4 distance 3158 vertices at 5 distance 1057 vertices at 6 distance 390 vertices at 7 distance 190 vertices at 8 distance 98 vertices at 9 distance 49 vertices at 10 distance 40 vertices at 11 distance 39 vertices at 12 distance 29 vertices at 13 distance 27 vertices at 14 distance 21 vertices at 15 distance 22 vertices at 16 distance 13 vertices at 17 distance 12 vertices at 18 distance 9 vertices at 19 distance 23 vertices at 20 distance writing curvature file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.thickness positioning took 11.7 minutes #-------------------------------------------- #@# Surf Volume lh Thu Oct 3 02:39:27 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 2012-646-010-KK lh /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.volume masking with /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label Total face volume 235186 Total vertex volume 232314 (mask=0) #@# 2012-646-010-KK lh 232314 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Thu Oct 3 02:39:31 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 2012-646-010-KK rh /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.volume masking with /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label Total face volume 237442 Total vertex volume 233740 (mask=0) #@# 2012-646-010-KK rh 233740 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Thu Oct 3 02:39:35 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 2012-646-010-KK SUBJECTS_DIR is /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 50 writing volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/ribbon.mgz mris_volmask took 7.75 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Oct 3 02:47:21 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 2012-646-010-KK lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 235186 Total vertex volume 232314 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1232 1193 2633 2.610 0.671 0.177 0.040 15 2.6 bankssts 709 464 1419 2.691 0.791 0.130 0.035 8 1.0 caudalanteriorcingulate 3665 2366 6937 2.546 0.596 0.123 0.032 45 5.3 caudalmiddlefrontal 2566 1641 3421 1.984 0.483 0.148 0.032 39 3.4 cuneus 659 435 1383 2.596 0.739 0.153 0.063 13 1.8 entorhinal 4564 3176 9593 2.698 0.653 0.133 0.034 73 6.1 fusiform 5610 3765 10327 2.547 0.473 0.126 0.026 75 5.8 inferiorparietal 4917 3295 9755 2.677 0.664 0.138 0.036 81 7.2 inferiortemporal 1528 946 2229 2.153 0.931 0.132 0.032 25 1.7 isthmuscingulate 7758 4742 11230 2.156 0.540 0.131 0.029 104 8.6 lateraloccipital 3825 2526 6367 2.503 0.735 0.145 0.047 60 8.2 lateralorbitofrontal 4645 3229 7856 2.312 0.642 0.158 0.037 78 7.5 lingual 2688 1800 4954 2.410 0.639 0.136 0.045 47 5.1 medialorbitofrontal 5371 3649 11045 2.592 0.761 0.134 0.040 81 9.9 middletemporal 1178 742 2100 2.512 0.703 0.092 0.026 7 1.4 parahippocampal 2356 1508 4184 2.578 0.530 0.115 0.023 23 2.3 paracentral 2278 1574 5062 2.786 0.446 0.123 0.028 31 2.7 parsopercularis 1079 675 1770 2.252 0.506 0.130 0.031 18 1.2 parsorbitalis 1978 1352 3867 2.489 0.501 0.131 0.028 28 2.2 parstriangularis 2136 1472 2396 1.819 0.502 0.123 0.031 21 2.8 pericalcarine 6412 4032 9897 2.221 0.653 0.108 0.020 61 5.1 postcentral 1575 1093 3055 2.514 0.723 0.136 0.033 24 2.2 posteriorcingulate 7261 4387 13523 2.762 0.530 0.099 0.018 54 5.1 precentral 5164 3518 9642 2.570 0.549 0.128 0.026 65 5.4 precuneus 862 595 2168 3.216 0.635 0.128 0.033 11 1.3 rostralanteriorcingulate 7825 5256 14896 2.442 0.616 0.143 0.040 146 13.6 rostralmiddlefrontal 10723 7404 23618 2.754 0.600 0.130 0.031 137 13.8 superiorfrontal 7933 5234 12993 2.309 0.423 0.125 0.024 98 7.5 superiorparietal 5697 3785 12120 2.677 0.734 0.109 0.030 70 7.5 superiortemporal 4894 3380 10805 2.886 0.561 0.133 0.028 70 5.9 supramarginal 361 231 833 2.792 0.813 0.162 0.051 8 0.9 frontalpole 573 386 1353 2.758 0.870 0.159 0.053 12 1.7 temporalpole 569 363 1074 2.754 0.327 0.123 0.019 6 0.4 transversetemporal 3720 2445 7789 2.982 0.863 0.130 0.043 53 6.6 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 2012-646-010-KK lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 235186 Total vertex volume 232314 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1232 977 2633 2.610 0.671 0.145 0.039 19 2.4 bankssts 709 652 1419 2.691 0.791 0.161 0.049 8 1.9 caudalanteriorcingulate 3665 2936 6937 2.546 0.596 0.145 0.034 51 5.8 caudalmiddlefrontal 2566 1915 3421 1.984 0.483 0.135 0.031 34 3.4 cuneus 659 651 1383 2.596 0.739 0.180 0.053 11 1.5 entorhinal 4564 3991 9593 2.698 0.653 0.153 0.037 69 7.8 fusiform 5610 4420 10327 2.547 0.473 0.140 0.034 74 9.0 inferiorparietal 4917 3953 9755 2.677 0.664 0.148 0.037 91 8.6 inferiortemporal 1528 1156 2229 2.153 0.931 0.159 0.055 72 4.2 isthmuscingulate 7758 5733 11230 2.156 0.540 0.127 0.028 108 10.1 lateraloccipital 3825 2607 6367 2.503 0.735 0.143 0.047 72 8.6 lateralorbitofrontal 4645 3803 7856 2.312 0.642 0.152 0.039 80 8.0 lingual 2688 2300 4954 2.410 0.639 0.159 0.041 39 5.2 medialorbitofrontal 5371 4755 11045 2.592 0.761 0.155 0.038 75 9.4 middletemporal 1178 973 2100 2.512 0.703 0.131 0.033 14 2.0 parahippocampal 2356 1767 4184 2.578 0.530 0.126 0.029 25 2.9 paracentral 2278 2047 5062 2.786 0.446 0.148 0.029 27 3.1 parsopercularis 1079 899 1770 2.252 0.506 0.147 0.031 14 1.6 parsorbitalis 1978 1695 3867 2.489 0.501 0.151 0.033 27 2.8 parstriangularis 2136 1233 2396 1.819 0.502 0.117 0.035 35 3.0 pericalcarine 6412 4976 9897 2.221 0.653 0.126 0.024 59 7.0 postcentral 1575 1351 3055 2.514 0.723 0.153 0.037 22 2.6 posteriorcingulate 7261 5301 13523 2.762 0.530 0.111 0.022 72 7.1 precentral 5164 3879 9642 2.570 0.549 0.136 0.032 74 7.2 precuneus 862 794 2168 3.216 0.635 0.182 0.042 19 1.7 rostralanteriorcingulate 7825 6740 14896 2.442 0.616 0.166 0.041 119 15.6 rostralmiddlefrontal 10723 9512 23618 2.754 0.600 0.150 0.035 146 17.1 superiorfrontal 7933 6029 12993 2.309 0.423 0.136 0.031 108 11.0 superiorparietal 5697 5056 12120 2.677 0.734 0.146 0.055 73 8.7 superiortemporal 4894 4060 10805 2.886 0.561 0.148 0.035 68 7.9 supramarginal 361 379 833 2.792 0.813 0.207 0.062 5 1.0 frontalpole 573 600 1353 2.758 0.870 0.191 0.043 9 1.3 temporalpole 569 438 1074 2.754 0.327 0.129 0.029 5 0.7 transversetemporal 3720 2544 7789 2.982 0.863 0.154 0.054 93 9.2 insula #----------------------------------------- #@# Parcellation Stats rh Thu Oct 3 02:48:27 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 2012-646-010-KK rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 237442 Total vertex volume 233740 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1631 1159 3327 2.877 0.486 0.128 0.023 17 1.6 bankssts 1022 722 2262 2.584 0.722 0.163 0.040 24 1.7 caudalanteriorcingulate 3177 2120 6492 2.770 0.467 0.121 0.024 38 3.1 caudalmiddlefrontal 2324 1477 3391 2.027 0.479 0.137 0.030 30 2.8 cuneus 578 419 1411 2.576 0.742 0.155 0.042 10 1.2 entorhinal 4719 3214 9094 2.566 0.640 0.135 0.034 69 6.2 fusiform 7470 5105 14945 2.588 0.526 0.120 0.023 88 7.1 inferiorparietal 5134 3534 9977 2.520 0.729 0.151 0.047 109 10.4 inferiortemporal 1213 794 2118 2.292 0.885 0.134 0.034 19 1.4 isthmuscingulate 7550 4778 11094 2.117 0.543 0.137 0.032 110 10.0 lateraloccipital 3939 2771 7283 2.567 0.705 0.135 0.037 51 5.8 lateralorbitofrontal 4396 3067 7107 2.112 0.616 0.150 0.038 68 7.1 lingual 2599 1794 4909 2.494 0.729 0.131 0.041 39 4.0 medialorbitofrontal 5284 3630 12267 2.844 0.752 0.126 0.033 69 7.6 middletemporal 992 647 1727 2.347 0.656 0.091 0.016 7 0.5 parahippocampal 2121 1369 3543 2.393 0.547 0.106 0.019 16 1.6 paracentral 1772 1186 3828 2.831 0.438 0.111 0.027 20 1.7 parsopercularis 1328 856 2456 2.407 0.586 0.136 0.035 21 1.8 parsorbitalis 1968 1375 4202 2.633 0.494 0.117 0.023 21 1.8 parstriangularis 2286 1571 2768 1.970 0.547 0.141 0.034 27 3.2 pericalcarine 5386 3474 8078 2.127 0.635 0.114 0.021 53 4.4 postcentral 1552 1069 3011 2.474 0.710 0.148 0.040 27 2.6 posteriorcingulate 7021 4504 13199 2.640 0.518 0.107 0.021 60 6.1 precentral 5237 3590 9176 2.410 0.557 0.133 0.029 70 6.2 precuneus 892 624 2145 2.773 0.843 0.129 0.031 16 1.0 rostralanteriorcingulate 8243 5562 15625 2.486 0.573 0.136 0.033 137 11.3 rostralmiddlefrontal 10017 6868 22372 2.823 0.598 0.128 0.030 123 12.1 superiorfrontal 7312 4796 11901 2.217 0.465 0.129 0.025 97 7.5 superiorparietal 5753 3781 12499 2.916 0.657 0.109 0.022 60 5.2 superiortemporal 5481 3750 11279 2.779 0.543 0.136 0.028 78 6.4 supramarginal 498 357 1169 2.576 0.605 0.174 0.073 11 1.7 frontalpole 680 427 1358 2.422 0.765 0.143 0.052 11 1.5 temporalpole 450 284 896 2.738 0.350 0.119 0.026 6 0.4 transversetemporal 3021 2061 6744 3.056 0.696 0.127 0.033 32 4.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 2012-646-010-KK rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 237442 Total vertex volume 233740 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1631 1114 3327 2.877 0.486 0.143 0.041 30 3.0 bankssts 1022 954 2262 2.584 0.722 0.173 0.043 26 1.9 caudalanteriorcingulate 3177 2542 6492 2.770 0.467 0.136 0.028 52 4.0 caudalmiddlefrontal 2324 1909 3391 2.027 0.479 0.143 0.030 25 3.2 cuneus 578 681 1411 2.576 0.742 0.216 0.051 9 1.5 entorhinal 4719 4002 9094 2.566 0.640 0.158 0.042 87 9.0 fusiform 7470 6303 14945 2.588 0.526 0.148 0.032 91 11.4 inferiorparietal 5134 4277 9977 2.520 0.729 0.158 0.042 89 10.4 inferiortemporal 1213 970 2118 2.292 0.885 0.142 0.038 22 2.0 isthmuscingulate 7550 5869 11094 2.117 0.543 0.136 0.032 104 10.7 lateraloccipital 3939 2939 7283 2.567 0.705 0.139 0.038 65 6.8 lateralorbitofrontal 4396 3803 7107 2.112 0.616 0.157 0.040 92 8.5 lingual 2599 2185 4909 2.494 0.729 0.163 0.044 50 4.9 medialorbitofrontal 5284 4885 12267 2.844 0.752 0.149 0.033 79 7.9 middletemporal 992 800 1727 2.347 0.656 0.128 0.031 10 1.3 parahippocampal 2121 1560 3543 2.393 0.547 0.119 0.024 22 2.0 paracentral 1772 1509 3828 2.831 0.438 0.148 0.034 20 2.7 parsopercularis 1328 1172 2456 2.407 0.586 0.145 0.035 17 1.9 parsorbitalis 1968 1799 4202 2.633 0.494 0.153 0.032 22 2.8 parstriangularis 2286 1389 2768 1.970 0.547 0.128 0.038 44 3.9 pericalcarine 5386 4187 8078 2.127 0.635 0.131 0.025 57 5.8 postcentral 1552 1283 3011 2.474 0.710 0.144 0.032 24 2.2 posteriorcingulate 7021 5352 13199 2.640 0.518 0.121 0.025 73 7.8 precentral 5237 3946 9176 2.410 0.557 0.145 0.034 80 8.1 precuneus 892 888 2145 2.773 0.843 0.169 0.038 15 1.4 rostralanteriorcingulate 8243 6898 15625 2.486 0.573 0.156 0.036 122 13.9 rostralmiddlefrontal 10017 8704 22372 2.823 0.598 0.148 0.034 133 15.4 superiorfrontal 7312 5963 11901 2.217 0.465 0.144 0.028 91 9.0 superiorparietal 5753 4753 12499 2.916 0.657 0.140 0.032 64 8.5 superiortemporal 5481 4389 11279 2.779 0.543 0.145 0.035 76 9.1 supramarginal 498 527 1169 2.576 0.605 0.216 0.056 11 1.5 frontalpole 680 696 1358 2.422 0.765 0.199 0.055 8 2.0 temporalpole 450 362 896 2.738 0.350 0.122 0.025 3 0.5 transversetemporal 3021 2119 6744 3.056 0.696 0.148 0.039 54 5.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Oct 3 02:49:26 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK lh ../surf/lh.sphere.reg /public/apps/freesurfer/6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /public/apps/freesurfer/6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 91 labels changed using aseg relabeling using gibbs priors... 000: 8650 changed, 131581 examined... 001: 2020 changed, 33594 examined... 002: 578 changed, 10524 examined... 003: 265 changed, 3356 examined... 004: 133 changed, 1506 examined... 005: 78 changed, 726 examined... 006: 39 changed, 404 examined... 007: 19 changed, 235 examined... 008: 9 changed, 117 examined... 009: 6 changed, 48 examined... 010: 3 changed, 33 examined... 011: 0 changed, 23 examined... 29 labels changed using aseg 000: 263 total segments, 176 labels (2440 vertices) changed 001: 95 total segments, 9 labels (23 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 23 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1429 vertices marked for relabeling... 1429 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Thu Oct 3 02:49:42 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK rh ../surf/rh.sphere.reg /public/apps/freesurfer/6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /public/apps/freesurfer/6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1 labels changed using aseg relabeling using gibbs priors... 000: 8733 changed, 130392 examined... 001: 2004 changed, 34054 examined... 002: 560 changed, 10617 examined... 003: 250 changed, 3222 examined... 004: 113 changed, 1424 examined... 005: 46 changed, 640 examined... 006: 31 changed, 271 examined... 007: 15 changed, 175 examined... 008: 6 changed, 84 examined... 009: 4 changed, 37 examined... 010: 1 changed, 24 examined... 011: 0 changed, 8 examined... 3 labels changed using aseg 000: 269 total segments, 178 labels (2058 vertices) changed 001: 100 total segments, 9 labels (73 vertices) changed 002: 92 total segments, 1 labels (1 vertices) changed 003: 91 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 46 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 994 vertices marked for relabeling... 994 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Oct 3 02:49:58 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 2012-646-010-KK lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 235186 Total vertex volume 232314 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1283 877 2412 2.480 0.780 0.171 0.052 28 3.4 G&S_frontomargin 1512 1000 2849 2.455 0.592 0.136 0.027 21 1.6 G&S_occipital_inf 1831 1068 3234 2.511 0.636 0.115 0.024 20 1.8 G&S_paracentral 1496 960 3053 2.681 0.571 0.120 0.022 15 1.3 G&S_subcentral 650 429 1454 2.402 0.676 0.156 0.068 22 2.2 G&S_transv_frontopol 2097 1458 4547 2.873 0.582 0.118 0.025 23 2.2 G&S_cingul-Ant 1159 803 1995 2.447 0.634 0.126 0.032 11 1.7 G&S_cingul-Mid-Ant 1253 877 2273 2.520 0.491 0.113 0.026 11 1.4 G&S_cingul-Mid-Post 562 365 1467 3.090 0.653 0.164 0.045 13 0.9 G_cingul-Post-dorsal 330 199 665 2.565 0.748 0.156 0.039 7 0.5 G_cingul-Post-ventral 2357 1494 3186 1.920 0.506 0.154 0.037 38 3.6 G_cuneus 1213 802 3085 3.002 0.476 0.130 0.033 19 1.6 G_front_inf-Opercular 507 308 1100 2.608 0.460 0.167 0.041 13 1.0 G_front_inf-Orbital 1107 721 2838 2.799 0.471 0.142 0.037 21 1.5 G_front_inf-Triangul 4714 3000 10684 2.607 0.648 0.148 0.043 94 9.0 G_front_middle 7878 5216 19110 2.859 0.607 0.140 0.035 125 11.6 G_front_sup 578 388 1670 3.428 0.814 0.147 0.047 10 1.1 G_Ins_lg&S_cent_ins 728 473 2513 3.621 0.700 0.140 0.038 16 1.2 G_insular_short 2289 1342 4272 2.459 0.426 0.140 0.035 43 2.9 G_occipital_middle 1800 1020 2514 2.191 0.451 0.124 0.030 19 2.1 G_occipital_sup 1907 1274 4577 2.857 0.754 0.151 0.040 43 3.0 G_oc-temp_lat-fusifor 3143 2090 5400 2.247 0.742 0.163 0.041 60 5.4 G_oc-temp_med-Lingual 1604 1031 3189 2.506 0.722 0.132 0.054 23 3.8 G_oc-temp_med-Parahip 2494 1563 4390 2.269 0.728 0.155 0.050 56 5.3 G_orbital 2209 1437 4845 2.688 0.488 0.152 0.040 50 3.4 G_pariet_inf-Angular 2519 1725 6634 3.044 0.575 0.145 0.030 43 3.2 G_pariet_inf-Supramar 3099 2041 5879 2.369 0.419 0.137 0.028 54 3.5 G_parietal_sup 2486 1426 3963 2.240 0.563 0.112 0.022 30 2.2 G_postcentral 2747 1468 5779 2.959 0.452 0.089 0.018 21 2.0 G_precentral 2481 1658 5403 2.588 0.546 0.143 0.031 44 3.1 G_precuneus 946 620 1837 2.198 0.676 0.166 0.075 25 3.1 G_rectus 942 589 1377 2.351 0.915 0.142 0.073 20 2.7 G_subcallosal 361 210 780 2.879 0.314 0.126 0.021 5 0.2 G_temp_sup-G_T_transv 2201 1376 5230 2.604 0.856 0.141 0.053 50 5.5 G_temp_sup-Lateral 806 544 2188 3.255 0.779 0.085 0.019 3 0.6 G_temp_sup-Plan_polar 803 568 2059 3.000 0.647 0.115 0.024 10 0.9 G_temp_sup-Plan_tempo 2587 1647 5911 2.707 0.773 0.146 0.045 54 4.8 G_temporal_inf 2973 1911 6614 2.564 0.872 0.147 0.050 57 6.6 G_temporal_middle 235 175 340 2.232 0.291 0.091 0.010 1 0.1 Lat_Fis-ant-Horizont 348 271 611 2.513 0.565 0.127 0.018 2 0.3 Lat_Fis-ant-Vertical 836 567 1281 2.857 0.482 0.095 0.015 4 0.5 Lat_Fis-post 2228 1249 2350 1.795 0.453 0.135 0.032 34 2.8 Pole_occipital 1269 859 2938 2.577 0.694 0.169 0.061 36 3.6 Pole_temporal 2373 1643 3054 2.132 0.657 0.128 0.028 24 2.9 S_calcarine 3026 2037 3600 1.983 0.536 0.100 0.019 17 2.1 S_central 1230 846 1825 2.366 0.475 0.105 0.016 9 0.8 S_cingul-Marginalis 633 435 1040 3.009 0.526 0.105 0.022 3 0.6 S_circular_insula_ant 1155 776 1831 2.901 0.561 0.098 0.018 6 1.0 S_circular_insula_inf 1564 1074 2364 2.733 0.496 0.104 0.021 8 1.5 S_circular_insula_sup 778 562 1328 2.769 0.584 0.103 0.020 6 0.4 S_collat_transv_ant 606 432 817 2.251 0.473 0.135 0.025 6 0.6 S_collat_transv_post 2196 1505 3464 2.363 0.481 0.106 0.020 17 1.8 S_front_inf 1367 959 2322 2.397 0.567 0.130 0.028 18 1.5 S_front_middle 2563 1899 4325 2.479 0.504 0.113 0.023 20 2.4 S_front_sup 323 226 497 2.365 0.452 0.115 0.018 2 0.3 S_interm_prim-Jensen 2494 1737 3604 2.328 0.398 0.110 0.019 19 1.8 S_intrapariet&P_trans 867 596 999 2.042 0.356 0.119 0.020 6 0.7 S_oc_middle&Lunatus 1202 821 1535 2.110 0.402 0.109 0.017 8 0.8 S_oc_sup&transversal 683 500 1241 2.519 0.427 0.124 0.025 7 0.6 S_occipital_ant 819 581 1407 2.695 0.482 0.123 0.022 8 0.8 S_oc-temp_lat 2542 1860 4083 2.438 0.493 0.123 0.024 24 2.8 S_oc-temp_med&Lingual 356 239 457 2.310 0.455 0.119 0.027 3 0.3 S_orbital_lateral 820 549 1016 2.140 0.594 0.142 0.056 13 2.3 S_orbital_med-olfact 1266 854 2053 2.533 0.561 0.127 0.031 12 1.6 S_orbital-H_Shaped 2249 1529 3482 2.481 0.516 0.123 0.023 22 2.2 S_parieto_occipital 1160 724 1072 1.828 0.966 0.116 0.028 16 1.1 S_pericallosal 2775 1937 4671 2.601 0.519 0.102 0.017 18 1.9 S_postcentral 1802 1239 2996 2.557 0.476 0.113 0.019 16 1.4 S_precentral-inf-part 1094 755 1874 2.727 0.339 0.088 0.012 5 0.4 S_precentral-sup-part 748 517 1243 2.505 0.548 0.122 0.026 7 0.9 S_suborbital 778 547 1199 2.472 0.493 0.110 0.016 5 0.5 S_subparietal 2071 1493 3301 2.524 0.470 0.117 0.021 16 2.0 S_temporal_inf 5935 4477 10583 2.545 0.563 0.121 0.024 51 6.6 S_temporal_sup 288 217 536 2.543 0.333 0.079 0.008 1 0.1 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Thu Oct 3 02:50:30 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 2012-646-010-KK rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 237442 Total vertex volume 233740 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1155 788 2086 2.390 0.699 0.160 0.049 25 2.3 G&S_frontomargin 1154 816 2258 2.472 0.614 0.149 0.038 20 1.7 G&S_occipital_inf 1409 844 2282 2.207 0.528 0.113 0.025 16 1.4 G&S_paracentral 1348 871 2728 2.684 0.527 0.125 0.025 16 1.3 G&S_subcentral 1329 906 3088 2.679 0.687 0.166 0.052 31 3.3 G&S_transv_frontopol 2682 1922 5765 2.783 0.610 0.124 0.029 33 2.9 G&S_cingul-Ant 1114 800 2429 2.674 0.619 0.142 0.037 20 1.6 G&S_cingul-Mid-Ant 1392 982 2752 2.706 0.531 0.124 0.026 14 1.5 G&S_cingul-Mid-Post 507 336 1401 3.112 0.504 0.179 0.062 14 1.0 G_cingul-Post-dorsal 300 190 707 2.818 0.849 0.136 0.036 5 0.3 G_cingul-Post-ventral 2285 1449 3351 1.979 0.504 0.139 0.033 32 3.0 G_cuneus 1220 793 3121 2.927 0.393 0.123 0.033 18 1.7 G_front_inf-Opercular 354 227 727 2.390 0.442 0.131 0.032 7 0.4 G_front_inf-Orbital 829 557 2290 2.906 0.454 0.139 0.032 13 1.0 G_front_inf-Triangul 3709 2444 9511 2.820 0.512 0.147 0.034 84 5.2 G_front_middle 7059 4675 17768 2.954 0.586 0.137 0.035 107 9.7 G_front_sup 551 400 1592 3.231 0.700 0.151 0.047 10 1.0 G_Ins_lg&S_cent_ins 503 318 1938 3.700 0.750 0.125 0.035 8 0.6 G_insular_short 2301 1438 4423 2.441 0.487 0.140 0.026 40 2.5 G_occipital_middle 1830 1119 2923 2.198 0.471 0.128 0.024 25 1.8 G_occipital_sup 2353 1521 5023 2.648 0.637 0.149 0.037 45 3.5 G_oc-temp_lat-fusifor 2850 1961 4985 2.142 0.659 0.163 0.044 52 5.3 G_oc-temp_med-Lingual 1315 895 3131 2.637 0.696 0.147 0.047 22 2.8 G_oc-temp_med-Parahip 2822 1890 5856 2.429 0.783 0.144 0.047 52 5.3 G_orbital 2950 1940 7567 2.844 0.579 0.137 0.028 49 3.4 G_pariet_inf-Angular 2413 1684 5937 2.867 0.520 0.152 0.034 48 3.5 G_pariet_inf-Supramar 2091 1369 4091 2.311 0.527 0.140 0.031 37 2.5 G_parietal_sup 1826 1121 3096 2.141 0.513 0.122 0.024 23 1.8 G_postcentral 2683 1559 6051 2.880 0.466 0.107 0.024 27 2.5 G_precentral 2070 1397 4612 2.478 0.548 0.150 0.036 42 3.0 G_precuneus 704 468 1391 2.207 0.734 0.150 0.066 17 1.9 G_rectus 376 257 658 2.424 0.724 0.086 0.034 2 0.3 G_subcallosal 404 247 863 2.799 0.355 0.117 0.027 6 0.3 G_temp_sup-G_T_transv 2142 1407 5870 3.086 0.665 0.140 0.034 39 2.8 G_temp_sup-Lateral 972 644 2204 3.177 0.561 0.103 0.031 6 1.2 G_temp_sup-Plan_polar 872 591 1945 2.795 0.444 0.100 0.020 10 0.5 G_temp_sup-Plan_tempo 2376 1628 5293 2.543 0.791 0.160 0.053 50 5.5 G_temporal_inf 3471 2307 8683 2.812 0.803 0.143 0.046 60 6.9 G_temporal_middle 350 245 553 2.541 0.439 0.085 0.012 1 0.2 Lat_Fis-ant-Horizont 141 115 291 2.806 0.367 0.130 0.024 1 0.1 Lat_Fis-ant-Vertical 1302 885 1944 2.720 0.444 0.111 0.019 8 1.0 Lat_Fis-post 3842 2302 4926 1.938 0.498 0.137 0.036 59 5.7 Pole_occipital 1755 1128 3268 2.297 0.712 0.143 0.052 34 3.9 Pole_temporal 2104 1508 2974 2.231 0.619 0.142 0.033 24 3.0 S_calcarine 2750 1888 3222 1.942 0.500 0.100 0.017 15 1.9 S_central 1157 789 1520 2.079 0.435 0.101 0.016 7 0.7 S_cingul-Marginalis 672 473 1161 2.895 0.471 0.126 0.023 5 0.8 S_circular_insula_ant 1096 715 1646 2.697 0.519 0.092 0.013 5 0.7 S_circular_insula_inf 1277 866 2078 2.752 0.525 0.099 0.019 6 1.1 S_circular_insula_sup 1019 720 1681 2.693 0.583 0.111 0.024 8 0.8 S_collat_transv_ant 354 308 535 2.097 0.434 0.182 0.036 6 0.6 S_collat_transv_post 2056 1401 3137 2.400 0.453 0.112 0.021 17 1.5 S_front_inf 2280 1612 3695 2.306 0.420 0.114 0.023 19 2.1 S_front_middle 2231 1588 3638 2.570 0.422 0.101 0.017 12 1.7 S_front_sup 628 432 867 2.609 0.395 0.121 0.025 4 0.6 S_interm_prim-Jensen 3127 2131 4255 2.194 0.439 0.116 0.019 27 2.6 S_intrapariet&P_trans 682 477 781 1.922 0.423 0.121 0.023 5 0.7 S_oc_middle&Lunatus 1298 885 1734 2.125 0.373 0.130 0.026 14 1.4 S_oc_sup&transversal 528 384 789 2.212 0.463 0.115 0.019 5 0.5 S_occipital_ant 1339 948 2156 2.414 0.490 0.134 0.030 34 1.6 S_oc-temp_lat 2119 1492 2904 2.168 0.600 0.103 0.019 13 1.6 S_oc-temp_med&Lingual 429 313 608 2.343 0.486 0.126 0.017 3 0.4 S_orbital_lateral 729 575 1050 2.241 0.602 0.142 0.030 8 0.9 S_orbital_med-olfact 1493 1016 2504 2.663 0.539 0.120 0.028 14 1.9 S_orbital-H_Shaped 2685 1835 3835 2.265 0.447 0.123 0.023 26 2.6 S_parieto_occipital 1522 943 1301 1.800 0.673 0.133 0.029 25 1.7 S_pericallosal 2291 1548 3114 2.277 0.494 0.121 0.021 21 2.0 S_postcentral 1689 1146 2669 2.663 0.443 0.108 0.019 13 1.3 S_precentral-inf-part 1236 869 1870 2.484 0.471 0.104 0.019 8 1.0 S_precentral-sup-part 156 111 291 3.119 0.468 0.153 0.023 2 0.2 S_suborbital 660 465 1083 2.542 0.530 0.119 0.022 5 0.6 S_subparietal 1275 953 2432 2.693 0.673 0.130 0.030 12 1.6 S_temporal_inf 6875 4768 12489 2.766 0.632 0.103 0.017 46 5.0 S_temporal_sup 217 152 343 2.506 0.340 0.127 0.016 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Oct 3 02:51:01 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK lh ../surf/lh.sphere.reg /public/apps/freesurfer/6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /public/apps/freesurfer/6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 853 labels changed using aseg relabeling using gibbs priors... 000: 1859 changed, 131581 examined... 001: 391 changed, 8647 examined... 002: 111 changed, 2295 examined... 003: 49 changed, 639 examined... 004: 34 changed, 288 examined... 005: 16 changed, 190 examined... 006: 9 changed, 104 examined... 007: 6 changed, 50 examined... 008: 8 changed, 36 examined... 009: 6 changed, 44 examined... 010: 2 changed, 33 examined... 011: 1 changed, 14 examined... 012: 1 changed, 7 examined... 013: 1 changed, 7 examined... 014: 2 changed, 9 examined... 015: 2 changed, 11 examined... 016: 2 changed, 10 examined... 017: 1 changed, 12 examined... 018: 0 changed, 7 examined... 211 labels changed using aseg 000: 60 total segments, 27 labels (201 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 970 vertices marked for relabeling... 970 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Oct 3 02:51:12 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK rh ../surf/rh.sphere.reg /public/apps/freesurfer/6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /public/apps/freesurfer/6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1004 labels changed using aseg relabeling using gibbs priors... 000: 1831 changed, 130392 examined... 001: 455 changed, 8846 examined... 002: 113 changed, 2562 examined... 003: 53 changed, 676 examined... 004: 22 changed, 306 examined... 005: 14 changed, 134 examined... 006: 5 changed, 71 examined... 007: 3 changed, 29 examined... 008: 1 changed, 24 examined... 009: 1 changed, 9 examined... 010: 1 changed, 5 examined... 011: 3 changed, 7 examined... 012: 2 changed, 13 examined... 013: 2 changed, 9 examined... 014: 4 changed, 14 examined... 015: 4 changed, 22 examined... 016: 4 changed, 21 examined... 017: 5 changed, 26 examined... 018: 3 changed, 23 examined... 019: 5 changed, 21 examined... 020: 5 changed, 30 examined... 021: 5 changed, 26 examined... 022: 1 changed, 23 examined... 023: 1 changed, 7 examined... 024: 0 changed, 7 examined... 175 labels changed using aseg 000: 47 total segments, 14 labels (103 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 756 vertices marked for relabeling... 756 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Oct 3 02:51:24 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 2012-646-010-KK lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 235186 Total vertex volume 232314 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1328 866 2450 2.595 0.708 0.127 0.035 15 1.9 caudalanteriorcingulate 3859 2508 7263 2.535 0.589 0.121 0.031 46 5.4 caudalmiddlefrontal 3445 2195 4713 2.074 0.490 0.142 0.030 48 4.3 cuneus 537 363 1143 2.512 0.736 0.154 0.060 10 1.5 entorhinal 4320 3016 8899 2.701 0.646 0.131 0.031 66 5.4 fusiform 5640 3780 10373 2.533 0.476 0.131 0.028 82 6.5 inferiorparietal 4800 3198 9671 2.661 0.686 0.139 0.038 82 7.7 inferiortemporal 1460 898 2163 2.172 0.935 0.133 0.032 24 1.7 isthmuscingulate 7813 4766 11241 2.155 0.538 0.132 0.030 107 9.0 lateraloccipital 4381 2860 7583 2.455 0.776 0.156 0.057 81 11.8 lateralorbitofrontal 4793 3304 8014 2.296 0.637 0.156 0.037 80 7.6 lingual 2388 1595 4116 2.308 0.703 0.135 0.053 42 5.0 medialorbitofrontal 6810 4767 13944 2.609 0.723 0.139 0.040 101 12.5 middletemporal 1241 790 2215 2.518 0.715 0.096 0.027 8 1.5 parahippocampal 2760 1770 4926 2.590 0.511 0.113 0.023 27 2.6 paracentral 2056 1426 4595 2.803 0.440 0.124 0.029 29 2.5 parsopercularis 1099 705 1993 2.536 0.522 0.125 0.023 15 1.1 parsorbitalis 2344 1614 4506 2.499 0.492 0.129 0.029 33 2.6 parstriangularis 2087 1436 2341 1.824 0.500 0.122 0.031 20 2.7 pericalcarine 7093 4505 11065 2.242 0.642 0.109 0.020 67 5.8 postcentral 1740 1213 3243 2.494 0.726 0.133 0.033 25 2.4 posteriorcingulate 7223 4366 13481 2.770 0.530 0.100 0.018 53 5.1 precentral 5057 3447 9717 2.576 0.558 0.130 0.026 68 5.3 precuneus 1295 888 2966 3.029 0.661 0.119 0.030 15 1.6 rostralanteriorcingulate 5996 3971 11409 2.420 0.610 0.140 0.035 105 8.7 rostralmiddlefrontal 11526 7950 25261 2.716 0.622 0.135 0.034 171 16.7 superiorfrontal 6284 4191 10288 2.312 0.420 0.123 0.023 74 5.5 superiorparietal 7208 5033 15343 2.680 0.740 0.118 0.033 92 10.6 superiortemporal 4488 3089 9969 2.913 0.549 0.128 0.026 59 4.8 supramarginal 556 351 1039 2.753 0.328 0.123 0.019 6 0.4 transversetemporal 2704 1810 6386 3.267 0.700 0.126 0.033 34 3.8 insula #----------------------------------------- #@# Parcellation Stats 3 rh Thu Oct 3 02:51:49 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 2012-646-010-KK rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 237442 Total vertex volume 233740 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1109 787 2404 2.547 0.726 0.163 0.041 26 1.8 caudalanteriorcingulate 3309 2209 6699 2.761 0.463 0.121 0.024 39 3.3 caudalmiddlefrontal 2895 1840 4236 2.071 0.460 0.135 0.029 36 3.4 cuneus 514 368 1373 2.709 0.704 0.167 0.047 10 1.2 entorhinal 4473 3050 8630 2.589 0.616 0.137 0.033 66 5.9 fusiform 7361 5013 14774 2.593 0.533 0.122 0.023 88 7.1 inferiorparietal 5426 3699 10308 2.483 0.729 0.147 0.046 111 10.2 inferiortemporal 1226 798 2135 2.309 0.877 0.133 0.034 19 1.4 isthmuscingulate 7393 4710 10752 2.089 0.540 0.135 0.031 104 9.4 lateraloccipital 4419 3075 7923 2.491 0.731 0.138 0.039 59 7.2 lateralorbitofrontal 4364 3070 7083 2.110 0.622 0.152 0.039 69 7.2 lingual 2044 1390 4049 2.493 0.715 0.137 0.046 35 3.7 medialorbitofrontal 6506 4490 14826 2.841 0.724 0.126 0.033 82 9.4 middletemporal 1067 699 1878 2.391 0.702 0.095 0.017 7 0.6 parahippocampal 2270 1463 3754 2.372 0.554 0.106 0.019 17 1.7 paracentral 2013 1362 4424 2.816 0.475 0.115 0.027 24 2.2 parsopercularis 1168 766 2334 2.572 0.527 0.125 0.026 15 1.2 parsorbitalis 1924 1337 3780 2.544 0.481 0.118 0.023 20 1.7 parstriangularis 2246 1526 2690 1.973 0.543 0.139 0.034 26 3.1 pericalcarine 5823 3762 8736 2.145 0.626 0.118 0.022 59 5.2 postcentral 1627 1120 3096 2.480 0.713 0.148 0.039 28 2.7 posteriorcingulate 6832 4370 12848 2.636 0.513 0.106 0.021 58 5.8 precentral 5435 3717 9666 2.401 0.556 0.134 0.029 75 6.5 precuneus 1123 785 2562 2.778 0.834 0.123 0.029 17 1.1 rostralanteriorcingulate 5727 3841 11121 2.503 0.553 0.134 0.032 98 7.4 rostralmiddlefrontal 12739 8740 27792 2.771 0.610 0.131 0.032 170 16.9 superiorfrontal 6052 3976 9806 2.211 0.459 0.128 0.025 81 6.1 superiorparietal 7574 5013 16125 2.861 0.658 0.117 0.027 86 8.0 superiortemporal 5229 3600 10789 2.769 0.525 0.134 0.027 75 5.9 supramarginal 446 285 896 2.753 0.352 0.124 0.026 6 0.4 transversetemporal 2751 1886 6253 3.080 0.697 0.125 0.030 28 3.4 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Oct 3 02:52:24 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts pctsurfcon --s 2012-646-010-KK --lh-only Log file is /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts/pctsurfcon.log Thu Oct 3 02:52:26 EDT 2019 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts /public/apps/freesurfer/6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux n511 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /public/apps/freesurfer/6.0.0 mri_vol2surf --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594577/lh.wm.mgh --regheader 2012-646-010-KK --cortex srcvol = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99878 0.02611 0.04198 -0.00002; -0.04402 0.08330 0.99555 0.00002; 0.02250 -0.99618 0.08435 -0.00006; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label Reading surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 69444 Masking with /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594577/lh.wm.mgh Dim: 131581 1 1 mri_vol2surf --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594577/lh.gm.mgh --projfrac 0.3 --regheader 2012-646-010-KK --cortex srcvol = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99878 0.02611 0.04198 -0.00002; -0.04402 0.08330 0.99555 0.00002; 0.02250 -0.99618 0.08435 -0.00006; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label Reading surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Done reading source surface Reading thickness /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 85189 Masking with /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.cortex.label Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594577/lh.gm.mgh Dim: 131581 1 1 mri_concat /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594577/lh.wm.mgh /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594577/lh.gm.mgh --paired-diff-norm --mul 100 --o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.w-g.pct.mgh mri_segstats --in /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.w-g.pct.mgh --annot 2012-646-010-KK lh aparc --sum /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.w-g.pct.mgh --annot 2012-646-010-KK lh aparc --sum /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/stats/lh.w-g.pct.stats --snr sysname Linux hostname n511 machine x86_64 user mwagshul UseRobust 0 Constructing seg from annotation Reading annotation /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.w-g.pct.mgh Vertex Area is 0.663325 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Thu Oct 3 02:52:33 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts pctsurfcon --s 2012-646-010-KK --rh-only Log file is /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts/pctsurfcon.log Thu Oct 3 02:52:34 EDT 2019 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts /public/apps/freesurfer/6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux n511 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /public/apps/freesurfer/6.0.0 mri_vol2surf --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594898/rh.wm.mgh --regheader 2012-646-010-KK --cortex srcvol = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99878 0.02611 0.04198 -0.00002; -0.04402 0.08330 0.99555 0.00002; 0.02250 -0.99618 0.08435 -0.00006; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label Reading surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 69008 Masking with /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594898/rh.wm.mgh Dim: 130392 1 1 mri_vol2surf --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594898/rh.gm.mgh --projfrac 0.3 --regheader 2012-646-010-KK --cortex srcvol = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99878 0.02611 0.04198 -0.00002; -0.04402 0.08330 0.99555 0.00002; 0.02250 -0.99618 0.08435 -0.00006; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label Reading surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Done reading source surface Reading thickness /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 85456 Masking with /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.cortex.label Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594898/rh.gm.mgh Dim: 130392 1 1 mri_concat /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594898/rh.wm.mgh /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/tmp.pctsurfcon.594898/rh.gm.mgh --paired-diff-norm --mul 100 --o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.w-g.pct.mgh mri_segstats --in /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.w-g.pct.mgh --annot 2012-646-010-KK rh aparc --sum /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.w-g.pct.mgh --annot 2012-646-010-KK rh aparc --sum /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/stats/rh.w-g.pct.stats --snr sysname Linux hostname n511 machine x86_64 user mwagshul UseRobust 0 Constructing seg from annotation Reading annotation /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.w-g.pct.mgh Vertex Area is 0.670808 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Thu Oct 3 02:52:41 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1548 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1143 voxels changed to hypointensity... 2663 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Oct 3 02:53:00 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_aparc2aseg --s 2012-646-010-KK --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING subject 2012-646-010-KK outvol /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading lh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial Loading lh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading rh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial Loading rh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.30 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 89 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 77 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 30 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 52 rescaling CSF from 32 --> 42 rescaling Left_Accumbens_area from 62 --> 62 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 57 rescaling Right_Lateral_Ventricle from 13 --> 20 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 56 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 38 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 462845 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 136 changed. pass 2: 6 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Oct 3 02:56:43 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_aparc2aseg --s 2012-646-010-KK --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING subject 2012-646-010-KK outvol /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading lh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial Loading lh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading rh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial Loading rh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.30 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 89 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 77 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 30 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 52 rescaling CSF from 32 --> 42 rescaling Left_Accumbens_area from 62 --> 62 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 57 rescaling Right_Lateral_Ventricle from 13 --> 20 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 56 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 38 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 462915 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 136 changed. pass 2: 6 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Oct 3 03:00:08 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_aparc2aseg --s 2012-646-010-KK --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /public/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING subject 2012-646-010-KK outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading lh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial Loading lh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading rh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial Loading rh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.30 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 89 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 77 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 30 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 52 rescaling CSF from 32 --> 42 rescaling Left_Accumbens_area from 62 --> 62 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 57 rescaling Right_Lateral_Ventricle from 13 --> 20 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 56 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 38 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 462915 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 136 changed. pass 2: 6 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Thu Oct 3 03:03:34 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Oct 3 03:03:37 EDT 2019 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/6.0.0/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux n511 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname n511 machine x86_64 user mwagshul input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Thu Oct 3 03:03:35 EDT 2019 Ended at Thu Oct 3 03:03:45 EDT 2019 Apas2aseg-Run-Time-Sec 9 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Oct 3 03:03:46 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /public/apps/freesurfer/6.0.0/ASegStatsLUT.txt --subject 2012-646-010-KK $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /public/apps/freesurfer/6.0.0/ASegStatsLUT.txt --subject 2012-646-010-KK sysname Linux hostname n511 machine x86_64 user mwagshul UseRobust 0 atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) Computing euler number orig.nofix lheno = -64, rheno = -72 orig.nofix lhholes = 33, rhholes = 37 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Thu Oct 3 03:05:25 EDT 2019 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_aparc2aseg --s 2012-646-010-KK --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING subject 2012-646-010-KK outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc+aseg.mgz Reading lh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading lh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial Loading lh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading rh pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial Loading rh annotations from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/ribbon.mgz Loading filled from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7270 vertices from left hemi Ripped 7346 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.mgz Loading Ctx Seg File /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 841625 Used brute-force search on 65 voxels Fixing Parahip LH WM Found 8 clusters 0 k 4.000000 1 k 1.000000 2 k 1493.000000 3 k 2.000000 4 k 24.000000 5 k 1.000000 6 k 2.000000 7 k 2.000000 Fixing Parahip RH WM Found 9 clusters 0 k 4.000000 1 k 1.000000 2 k 1466.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 4.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 2012-646-010-KK --surf-wm-vol --ctab /public/apps/freesurfer/6.0.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 2012-646-010-KK --surf-wm-vol --ctab /public/apps/freesurfer/6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname n511 machine x86_64 user mwagshul UseRobust 0 atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Oct 3 03:13:15 EDT 2019 mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA1_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4396 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA2_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 412 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8321 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4193 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 334 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6317 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 456 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6240 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4277 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA6_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 1484 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15073 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA44_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4488 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA45_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 597 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4019 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V1_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 1631 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6272 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V2_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 3225 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11339 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.MT_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2450 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1286 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1085 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2191 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1543 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2120 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2529 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1606 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 543 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2032 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1418 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 1122 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 1541 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4875 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 91 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 604 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 537 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 131581 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 488 mri_label2label: Done mris_label2annot --s 2012-646-010-KK --hemi lh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label cmdline mris_label2annot --s 2012-646-010-KK --hemi lh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname n511 machine x86_64 user mwagshul subject 2012-646-010-KK hemi lh SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING ColorTable /public/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89347 unhit vertices Writing annot to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.BA_exvivo.annot mris_label2annot --s 2012-646-010-KK --hemi lh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label cmdline mris_label2annot --s 2012-646-010-KK --hemi lh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname n511 machine x86_64 user mwagshul subject 2012-646-010-KK hemi lh SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING ColorTable /public/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 106674 unhit vertices Writing annot to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 2012-646-010-KK lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 235186 Total vertex volume 232314 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /public/apps/freesurfer/6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 1211 657 1869 2.252 0.442 0.126 0.027 18 1.2 BA1_exvivo 3774 2560 6645 2.569 0.502 0.101 0.017 26 2.7 BA2_exvivo 1035 706 1049 1.930 0.443 0.137 0.027 10 1.0 BA3a_exvivo 2501 1581 3339 1.919 0.631 0.112 0.022 25 2.3 BA3b_exvivo 1885 1019 3504 2.884 0.461 0.094 0.021 16 1.5 BA4a_exvivo 1160 786 1883 2.446 0.404 0.083 0.016 4 0.7 BA4p_exvivo 9730 6270 20862 2.798 0.551 0.119 0.027 105 11.5 BA6_exvivo 2240 1515 4878 2.790 0.506 0.122 0.027 29 2.4 BA44_exvivo 2940 2023 5998 2.524 0.506 0.133 0.033 47 3.8 BA45_exvivo 3764 2521 4222 1.727 0.491 0.133 0.034 47 5.4 V1_exvivo 8690 5398 12017 2.132 0.543 0.145 0.033 129 11.9 V2_exvivo 2049 1369 3779 2.486 0.448 0.134 0.032 34 2.4 MT_exvivo 592 387 1299 2.530 0.695 0.132 0.052 9 1.4 perirhinal_exvivo 663 470 1228 2.463 0.539 0.137 0.045 10 1.2 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 2012-646-010-KK lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 235186 Total vertex volume 232314 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /public/apps/freesurfer/6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 767 388 1220 2.340 0.434 0.122 0.028 10 0.8 BA1_exvivo 1514 976 2747 2.543 0.507 0.086 0.015 10 0.8 BA2_exvivo 878 589 843 1.921 0.461 0.140 0.030 9 0.9 BA3a_exvivo 1492 964 1622 1.601 0.367 0.096 0.018 11 1.1 BA3b_exvivo 1751 992 3247 2.812 0.461 0.089 0.019 12 1.3 BA4a_exvivo 977 652 1500 2.389 0.399 0.088 0.016 5 0.6 BA4p_exvivo 5330 3239 10965 2.836 0.509 0.107 0.022 49 5.2 BA6_exvivo 1357 949 3022 2.821 0.499 0.129 0.032 20 1.7 BA44_exvivo 1253 835 3074 2.748 0.508 0.143 0.035 22 1.7 BA45_exvivo 3956 2649 4499 1.732 0.494 0.134 0.035 50 5.8 V1_exvivo 4470 2716 5846 2.070 0.536 0.152 0.036 74 6.7 V2_exvivo 492 356 1025 2.571 0.421 0.125 0.027 6 0.4 MT_exvivo 315 206 640 2.370 0.769 0.132 0.060 5 0.9 perirhinal_exvivo 355 256 615 2.487 0.446 0.105 0.024 2 0.3 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Thu Oct 3 03:17:09 EDT 2019 mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA1_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4148 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA2_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6884 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4060 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4650 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 225 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 136 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4609 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA6_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 843 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13099 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA44_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 558 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7470 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA45_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 710 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6065 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V1_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 1827 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6554 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V2_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 2880 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10896 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.MT_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2196 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1107 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 2012-646-010-KK --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 848 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 935 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2753 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1741 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2233 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1465 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 431 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7390 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1083 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1259 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 1229 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4461 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 1420 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4857 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 300 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 738 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 2012-646-010-KK --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 2012-646-010-KK trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/6.0.0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white Reading target registration /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 130392 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 304 mri_label2label: Done mris_label2annot --s 2012-646-010-KK --hemi rh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label cmdline mris_label2annot --s 2012-646-010-KK --hemi rh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname n511 machine x86_64 user mwagshul subject 2012-646-010-KK hemi rh SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING ColorTable /public/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 91481 unhit vertices Writing annot to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.BA_exvivo.annot mris_label2annot --s 2012-646-010-KK --hemi rh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label cmdline mris_label2annot --s 2012-646-010-KK --hemi rh --ctab /public/apps/freesurfer/6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname n511 machine x86_64 user mwagshul subject 2012-646-010-KK hemi rh SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING ColorTable /public/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 108453 unhit vertices Writing annot to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 2012-646-010-KK rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 237442 Total vertex volume 233740 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /public/apps/freesurfer/6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 863 482 1515 2.259 0.432 0.135 0.029 13 1.1 BA1_exvivo 2684 1792 3949 2.245 0.514 0.115 0.020 23 2.3 BA2_exvivo 1011 666 942 1.830 0.399 0.120 0.024 8 1.0 BA3a_exvivo 1752 1145 2205 1.712 0.445 0.104 0.017 14 1.2 BA3b_exvivo 1424 865 2763 2.653 0.404 0.092 0.020 10 1.1 BA4a_exvivo 1132 739 1737 2.395 0.365 0.093 0.018 8 0.7 BA4p_exvivo 7872 5170 17099 2.805 0.556 0.120 0.027 83 8.7 BA6_exvivo 3399 2287 6725 2.749 0.474 0.115 0.024 36 3.2 BA44_exvivo 3900 2676 8215 2.581 0.515 0.128 0.026 50 4.1 BA45_exvivo 4125 2718 5707 1.988 0.573 0.138 0.035 56 6.1 V1_exvivo 8079 5237 11494 2.026 0.535 0.147 0.036 123 11.9 V2_exvivo 1746 1199 2937 2.370 0.447 0.121 0.022 19 1.6 MT_exvivo 536 372 1347 2.643 0.747 0.125 0.026 5 0.7 perirhinal_exvivo 388 269 829 2.547 0.698 0.105 0.037 4 0.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 2012-646-010-KK rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/wm.mgz... reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... reading input pial surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.pial... reading input white surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 237442 Total vertex volume 233740 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /public/apps/freesurfer/6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 929102 mm^3 (det: 2.096762 ) lhCtxGM: 231391.254 231007.000 diff= 384.3 pctdiff= 0.166 rhCtxGM: 233725.859 233270.000 diff= 455.9 pctdiff= 0.195 lhCtxWM: 193030.805 192557.000 diff= 473.8 pctdiff= 0.245 rhCtxWM: 185700.646 186844.000 diff=-1143.4 pctdiff=-0.616 SubCortGMVol 53008.000 SupraTentVol 912250.564 (910558.000) diff=1692.564 pctdiff=0.186 SupraTentVolNotVent 898400.564 (896708.000) diff=1692.564 pctdiff=0.188 BrainSegVol 1061919.000 (1058406.000) diff=3513.000 pctdiff=0.331 BrainSegVolNotVent 1043589.000 (1043662.564) diff=-73.564 pctdiff=-0.007 BrainSegVolNotVent 1043589.000 CerebellumVol 146784.000 VentChorVol 13850.000 3rd4th5thCSF 4480.000 CSFVol 967.000, OptChiasmVol 97.000 MaskVol 1321618.000 586 329 1038 2.206 0.424 0.140 0.029 10 0.7 BA1_exvivo 1508 1006 2366 2.200 0.524 0.107 0.018 13 1.1 BA2_exvivo 917 598 774 1.808 0.381 0.129 0.026 7 1.0 BA3a_exvivo 1336 915 1496 1.592 0.359 0.091 0.013 7 0.7 BA3b_exvivo 930 517 1853 2.855 0.390 0.100 0.025 8 0.8 BA4a_exvivo 871 606 1392 2.440 0.343 0.085 0.013 4 0.4 BA4p_exvivo 5005 3252 10747 2.772 0.566 0.121 0.027 54 5.5 BA6_exvivo 767 519 1756 2.898 0.418 0.126 0.035 11 1.1 BA44_exvivo 898 637 2441 2.878 0.463 0.136 0.030 12 1.1 BA45_exvivo 3898 2552 5303 1.999 0.575 0.136 0.035 51 5.7 V1_exvivo 4431 2883 5947 1.933 0.528 0.156 0.041 73 7.7 V2_exvivo 250 171 535 2.402 0.428 0.109 0.021 3 0.2 MT_exvivo 332 220 785 2.620 0.770 0.116 0.024 3 0.4 perirhinal_exvivo 210 161 441 2.676 0.644 0.119 0.026 2 0.1 entorhinal_exvivo Started at Wed Oct 2 18:38:22 EDT 2019 Ended at Thu Oct 3 03:21:07 EDT 2019 #@#%# recon-all-run-time-hours 8.712 recon-all -s 2012-646-010-KK finished without error at Thu Oct 3 03:21:09 EDT 2019 #New# invocation of recon-all Tue Jul 14 12:56:22 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -all -noskullstrip subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 1024 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:32-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:32-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:32-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:32-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/14-16:56:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Tue Jul 14 12:56:42 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:14:12:56:42 mri_convert N 4 e 10.90 S 0.04 U 1.97 P 18% M 53736 F 0 R 1525 W 0 c 2710 w 48 I 0 O 0 L 17.63 17.45 16.30 @#@FSLOADPOST 2020:07:14:12:56:53 mri_convert N 4 18.00 17.53 16.34 #-------------------------------------------- #@# MotionCor Tue Jul 14 12:56:53 EDT 2020 Found 1 runs /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261116, -0.041979) j_ras = (-0.0224984, 0.996182, -0.0843504) k_ras = (-0.0440213, 0.0833028, 0.995551) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 3297.37 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... @#@FSTIME 2020:07:14:12:56:58 mri_convert N 3 e 42.55 S 0.09 U 8.41 P 19% M 65732 F 0 R 3613 W 0 c 7354 w 28 I 0 O 0 L 18.24 17.59 16.36 @#@FSLOADPOST 2020:07:14:12:57:40 mri_convert N 3 19.32 17.92 16.53 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:07:14:12:57:41 mri_add_xform_to_header N 4 e 4.25 S 0.01 U 0.78 P 18% M 20492 F 0 R 1773 W 0 c 758 w 35 I 0 O 0 L 19.32 17.92 16.53 @#@FSLOADPOST 2020:07:14:12:57:46 mri_add_xform_to_header N 4 19.45 17.97 16.55 #-------------------------------------------- #@# Talairach Tue Jul 14 12:57:46 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Jul 14 12:57:47 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.15165 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.15165/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.15165/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.15165/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.15165/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Jul 14 13:13:27 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:14:12:57:46 mri_nu_correct.mni N 12 e 940.57 S 1.82 U 219.73 P 23% M 500280 F 0 R 40362 W 0 c 169665 w 267 I 0 O 0 L 19.45 17.97 16.55 @#@FSLOADPOST 2020:07:14:13:13:27 mri_nu_correct.mni N 12 16.41 16.97 17.03 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Jul 14 13:13:27 EDT 2020 Ended at Tue Jul 14 13:15:33 EDT 2020 talairach_avi done @#@FSTIME 2020:07:14:13:13:27 talairach_avi N 4 e 125.89 S 1.26 U 29.26 P 24% M 253940 F 0 R 41728 W 0 c 19549 w 995 I 0 O 32 L 16.41 16.97 17.03 @#@FSLOADPOST 2020:07:14:13:15:33 talairach_avi N 4 14.49 16.16 16.73 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm lta_convert --src orig.mgz --trg /public/apps/freesurfer/7.1.0/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.1.0 --src: orig.mgz src image (geometry). --trg: /public/apps/freesurfer/7.1.0/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Tue Jul 14 13:15:34 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5199, pval=0.1531 >= threshold=0.0050) @#@FSTIME 2020:07:14:13:15:34 talairach_afd N 4 e 0.25 S 0.00 U 0.00 P 2% M 2452 F 0 R 717 W 0 c 4 w 49 I 0 O 0 L 14.49 16.16 16.73 @#@FSLOADPOST 2020:07:14:13:15:34 talairach_afd N 4 14.49 16.16 16.73 awk -f /public/apps/freesurfer/7.1.0/bin/extract_talairach_avi_QA.awk /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log tal_QC_AZS /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log TalAviQA: 0.96317 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Tue Jul 14 13:15:35 EDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Jul 14 13:15:35 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.16731 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz sysname Linux hostname loginnode2 machine x86_64 user pankumar input /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.16731/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 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16731/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16731/input.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16731/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16731/input.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.16731/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 /dev/shm/tmp.mri_nu_correct.mni.16731/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16731/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16731/output.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16731/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16731/output.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.16731/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.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 /dev/shm/tmp.mri_nu_correct.mni.16731/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz mul 1.15054592399081702868 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.16731/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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 34 seconds. mapping (13, 196) to ( 3, 110) Tue Jul 14 13:32:36 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:14:13:15:35 mri_nu_correct.mni N 9 e 1020.76 S 2.94 U 275.39 P 27% M 611088 F 0 R 189963 W 0 c 165672 w 489 I 0 O 0 L 14.49 16.16 16.73 @#@FSLOADPOST 2020:07:14:13:32:36 mri_nu_correct.mni N 9 16.53 15.81 15.60 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2020:07:14:13:32:36 mri_add_xform_to_header N 4 e 3.89 S 0.01 U 0.89 P 23% M 20568 F 0 R 1793 W 0 c 333 w 31 I 0 O 0 L 16.53 15.81 15.60 @#@FSLOADPOST 2020:07:14:13:32:40 mri_add_xform_to_header N 4 16.53 15.81 15.60 #-------------------------------------------- #@# Intensity Normalization Tue Jul 14 13:32:41 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 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(): error: MRIhistogramRegion: input mri nu.mgz is blank MRIsplineNormalize(): npeaks = 12 Starting OpenSpline(): npoints = 12 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 56 (56), valley at 0 (-1) csf peak at 28, setting threshold to 46 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 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 8 minutes and 28 seconds. @#@FSTIME 2020:07:14:13:32:41 mri_normalize N 7 e 516.66 S 1.14 U 127.80 P 24% M 578872 F 0 R 14435 W 0 c 73708 w 48 I 0 O 0 L 16.65 15.85 15.61 @#@FSLOADPOST 2020:07:14:13:41:18 mri_normalize N 7 15.44 15.90 15.77 #------------------------------------- #@# EM Registration Tue Jul 14 13:41:18 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 6 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, 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=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -3.918 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (-2.632, -2.632, -2.632) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) Found translation: (-2.6, -2.6, -2.6): log p = -3.811 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.811 (thresh=-3.8) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; iteration took 9 minutes and 47 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.624 (thresh=-3.6) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 9 minutes and 3 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.624 (thresh=-3.6) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; iteration took 7 minutes and 2 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 7 minutes and 3 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.505, old_max_log_p =-3.534 (thresh=-3.5) 1.03379 0.01049 0.00809 -9.19070; -0.00869 1.28704 0.00797 -40.93967; -0.00832 -0.01033 0.99642 -0.34468; 0.00000 0.00000 0.00000 1.00000; iteration took 6 minutes and 59 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.505 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; iteration took 6 minutes and 41 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.488 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.488 (old=-3.918) transform before final EM align: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 886188 FSRUNTIME@ mri_em_register 1.0069 hours 1 threads registration took 60 minutes and 25 seconds. @#@FSTIME 2020:07:14:13:41:18 mri_em_register N 7 e 3625.18 S 7.40 U 1112.12 P 30% M 613104 F 0 R 112874 W 0 c 495357 w 98 I 0 O 0 L 15.44 15.90 15.77 @#@FSLOADPOST 2020:07:14:14:41:44 mri_em_register N 7 13.29 13.23 13.23 #-------------------------------------- #@# CA Normalize Tue Jul 14 14:41:44 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.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 '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 133 of 656 (20.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 395 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 15 (0.0%) samples deleted using 1091 total control points for intensity normalization... bias field = 0.959 +- 0.058 1 of 958 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 823 (1.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 533 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 64 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 53 (3.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 27 of 79 (34.2%) samples deleted using 1552 total control points for intensity normalization... bias field = 1.009 +- 0.066 3 of 1469 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 824 (1.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 626 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 84 (53.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 77 (32.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 86 of 139 (61.9%) samples deleted using 1750 total control points for intensity normalization... bias field = 1.002 +- 0.054 1 of 1545 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 4 minutes and 59 seconds. @#@FSTIME 2020:07:14:14:41:44 mri_ca_normalize N 8 e 299.68 S 1.15 U 91.79 P 31% M 927680 F 0 R 127921 W 0 c 50823 w 104 I 0 O 0 L 13.29 13.23 13.23 @#@FSLOADPOST 2020:07:14:14:46:44 mri_ca_normalize N 8 13.28 13.41 13.31 #-------------------------------------- #@# CA Reg Tue Jul 14 14:46:44 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.935117 #FOTS# QuadFit found better minimum quadopt=(dt=246.905,rms=0.794434) vs oldopt=(dt=92.48,rms=0.845465) #GCMRL# 0 dt 246.904762 rms 0.794 15.044% neg 0 invalid 762 tFOTS 83.6760 tGradient 27.3540 tsec 117.0020 #FOTS# QuadFit found better minimum quadopt=(dt=209.836,rms=0.765228) vs oldopt=(dt=92.48,rms=0.774396) #GCMRL# 1 dt 209.836066 rms 0.765 3.676% neg 0 invalid 762 tFOTS 85.4750 tGradient 33.1610 tsec 124.9890 #FOTS# QuadFit found better minimum quadopt=(dt=229.859,rms=0.750881) vs oldopt=(dt=92.48,rms=0.755764) #GCMRL# 2 dt 229.859155 rms 0.751 1.875% neg 0 invalid 762 tFOTS 79.3020 tGradient 30.3590 tsec 116.9560 #FOTS# QuadFit found better minimum quadopt=(dt=129.506,rms=0.74519) vs oldopt=(dt=92.48,rms=0.745844) #GCMRL# 3 dt 129.505882 rms 0.745 0.758% neg 0 invalid 762 tFOTS 77.9490 tGradient 31.3500 tsec 115.0340 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.734166) vs oldopt=(dt=369.92,rms=0.736011) #GCMRL# 4 dt 517.888000 rms 0.734 1.479% neg 0 invalid 762 tFOTS 85.4490 tGradient 25.2770 tsec 115.6660 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.7319) vs oldopt=(dt=92.48,rms=0.731939) #GCMRL# 5 dt 110.976000 rms 0.732 0.309% neg 0 invalid 762 tFOTS 83.3620 tGradient 26.3370 tsec 115.1670 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.716292) vs oldopt=(dt=1479.68,rms=0.718156) #GCMRL# 6 dt 2071.552000 rms 0.716 2.132% neg 0 invalid 762 tFOTS 77.2480 tGradient 26.3020 tsec 108.8800 #GCMRL# 7 dt 92.480000 rms 0.713 0.459% neg 0 invalid 762 tFOTS 87.8370 tGradient 35.5590 tsec 129.9620 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.712379) vs oldopt=(dt=369.92,rms=0.712527) #GCMRL# 8 dt 221.952000 rms 0.712 0.000% neg 0 invalid 762 tFOTS 92.4560 tGradient 31.9240 tsec 135.7330 #GCMRL# 9 dt 221.952000 rms 0.711 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.5640 tsec 49.8420 #GCMRL# 10 dt 221.952000 rms 0.710 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.7410 tsec 44.5070 #GCMRL# 11 dt 221.952000 rms 0.710 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 44.0320 tsec 52.3630 #GCMRL# 12 dt 221.952000 rms 0.708 0.284% neg 0 invalid 762 tFOTS 0.0000 tGradient 44.3650 tsec 50.6980 #GCMRL# 13 dt 221.952000 rms 0.706 0.288% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.3410 tsec 43.6140 #GCMRL# 14 dt 221.952000 rms 0.704 0.260% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.6280 tsec 46.3150 #GCMRL# 15 dt 221.952000 rms 0.702 0.307% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.0180 tsec 37.3550 #GCMRL# 16 dt 221.952000 rms 0.699 0.343% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.5040 tsec 36.0790 #GCMRL# 17 dt 221.952000 rms 0.697 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.5690 tsec 46.4570 #GCMRL# 18 dt 221.952000 rms 0.696 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 43.7330 tsec 50.5010 #GCMRL# 19 dt 221.952000 rms 0.695 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.9820 tsec 40.9020 #GCMRL# 20 dt 221.952000 rms 0.693 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.0190 tsec 47.2810 #GCMRL# 21 dt 221.952000 rms 0.693 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.2850 tsec 44.9520 #GCMRL# 22 dt 221.952000 rms 0.692 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.0290 tsec 45.9270 #GCMRL# 23 dt 221.952000 rms 0.691 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.1040 tsec 45.8120 #GCMRL# 24 dt 221.952000 rms 0.690 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 41.7400 tsec 49.2560 #GCMRL# 25 dt 221.952000 rms 0.690 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 44.0060 tsec 51.5250 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.689488) vs oldopt=(dt=369.92,rms=0.68951) #GCMRL# 26 dt 295.936000 rms 0.689 0.066% neg 0 invalid 762 tFOTS 99.3660 tGradient 36.1950 tsec 141.1960 #GCAMreg# pass 0 level1 5 level2 1 tsec 2186.6 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.689936 #GCMRL# 28 dt 92.480000 rms 0.689 0.112% neg 0 invalid 762 tFOTS 122.5910 tGradient 36.2520 tsec 166.5940 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.688749) vs oldopt=(dt=369.92,rms=0.688806) #GCMRL# 29 dt 295.936000 rms 0.689 0.000% neg 0 invalid 762 tFOTS 114.1300 tGradient 40.9460 tsec 162.7710 #GCMRL# 30 dt 295.936000 rms 0.688 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 46.3560 tsec 55.6840 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.706108 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704881) vs oldopt=(dt=25.92,rms=0.704889) #GCMRL# 32 dt 31.104000 rms 0.705 0.174% neg 0 invalid 762 tFOTS 114.1770 tGradient 31.6710 tsec 151.6870 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704506) vs oldopt=(dt=25.92,rms=0.704515) #GCMRL# 33 dt 31.104000 rms 0.705 0.000% neg 0 invalid 762 tFOTS 105.7890 tGradient 35.8530 tsec 147.8450 #GCMRL# 34 dt 31.104000 rms 0.704 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.0280 tsec 33.1790 #GCMRL# 35 dt 31.104000 rms 0.704 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.1670 tsec 38.2300 #GCAMreg# pass 0 level1 4 level2 1 tsec 432.027 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.704365 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.70353) vs oldopt=(dt=25.92,rms=0.703568) #GCMRL# 37 dt 36.288000 rms 0.704 0.119% neg 0 invalid 762 tFOTS 102.0670 tGradient 24.5890 tsec 132.3990 #FOTS# QuadFit found better minimum quadopt=(dt=15.552,rms=0.703504) vs oldopt=(dt=25.92,rms=0.703509) #GCMRL# 38 dt 15.552000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 110.2320 tGradient 26.5660 tsec 144.4790 #GCMRL# 39 dt 15.552000 rms 0.703 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.0090 tsec 37.3290 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.73685 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.735541) vs oldopt=(dt=8,rms=0.735619) #GCMRL# 41 dt 6.400000 rms 0.736 0.178% neg 0 invalid 762 tFOTS 104.2400 tGradient 21.2990 tsec 132.8540 #FOTS# QuadFit found better minimum quadopt=(dt=2.4,rms=0.735475) vs oldopt=(dt=2,rms=0.735476) #GCMRL# 42 dt 2.400000 rms 0.735 0.000% neg 0 invalid 762 tFOTS 97.4810 tGradient 24.7560 tsec 128.5890 #GCAMreg# pass 0 level1 3 level2 1 tsec 332.136 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.73596 #GCMRL# 44 dt 0.000000 rms 0.735 0.067% neg 0 invalid 762 tFOTS 92.4140 tGradient 26.6340 tsec 126.5360 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.817881 #FOTS# QuadFit found better minimum quadopt=(dt=3.31099,rms=0.806528) vs oldopt=(dt=2.88,rms=0.806715) #GCMRL# 46 dt 3.310987 rms 0.807 1.388% neg 0 invalid 762 tFOTS 93.4590 tGradient 25.5040 tsec 125.5380 #FOTS# QuadFit found better minimum quadopt=(dt=1.93269,rms=0.804898) vs oldopt=(dt=2.88,rms=0.805279) #GCMRL# 47 dt 1.932692 rms 0.805 0.000% neg 0 invalid 762 tFOTS 108.1390 tGradient 23.0760 tsec 140.2020 #GCMRL# 48 dt 1.932692 rms 0.803 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.6720 tsec 35.7940 #GCMRL# 49 dt 1.932692 rms 0.803 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.3100 tsec 34.9310 #GCMRL# 50 dt 1.932692 rms 0.803 -0.411% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.4340 tsec 42.7730 #GCAMreg# pass 0 level1 2 level2 1 tsec 552.86 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.803105 #GCMRL# 52 dt 0.000000 rms 0.803 0.068% neg 0 invalid 762 tFOTS 100.5800 tGradient 26.8810 tsec 136.6000 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.877757 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877204) vs oldopt=(dt=0.08,rms=0.877207) #GCMRL# 54 dt 0.064000 rms 0.877 0.063% neg 0 invalid 762 tFOTS 114.4430 tGradient 29.3570 tsec 151.8810 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877178) vs oldopt=(dt=0.08,rms=0.877183) #GCMRL# 55 dt 0.064000 rms 0.877 0.000% neg 0 invalid 762 tFOTS 110.1790 tGradient 24.9500 tsec 143.5720 #GCMRL# 56 dt 0.064000 rms 0.877 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.5420 tsec 32.3810 #GCMRL# 57 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.0930 tsec 33.1980 #GCMRL# 58 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.7870 tsec 37.1850 #GCMRL# 59 dt 0.064000 rms 0.877 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.7890 tsec 37.7980 #GCMRL# 60 dt 0.064000 rms 0.876 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.1380 tsec 34.2890 #GCMRL# 61 dt 0.064000 rms 0.875 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.4230 tsec 32.2380 #GCMRL# 62 dt 0.064000 rms 0.874 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.6730 tsec 34.2070 #GCMRL# 63 dt 0.064000 rms 0.872 0.191% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.9150 tsec 32.2020 #GCMRL# 64 dt 0.064000 rms 0.871 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.3710 tsec 36.1140 #GCMRL# 65 dt 0.064000 rms 0.869 0.179% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.3110 tsec 36.1800 #GCMRL# 66 dt 0.064000 rms 0.868 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.6970 tsec 35.5600 #GCMRL# 67 dt 0.064000 rms 0.867 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.8890 tsec 41.0830 #GCMRL# 68 dt 0.064000 rms 0.866 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.9020 tsec 34.1070 #GCMRL# 69 dt 0.064000 rms 0.865 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.5030 tsec 39.0280 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.862601) vs oldopt=(dt=1.28,rms=0.862653) #GCMRL# 70 dt 1.536000 rms 0.863 0.268% neg 0 invalid 762 tFOTS 121.9170 tGradient 29.9240 tsec 160.4890 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.861829) vs oldopt=(dt=0.32,rms=0.862083) #GCMRL# 71 dt 0.192000 rms 0.862 0.000% neg 0 invalid 762 tFOTS 123.3050 tGradient 35.7560 tsec 166.7530 #GCMRL# 72 dt 0.192000 rms 0.861 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.6670 tsec 36.5410 #GCMRL# 73 dt 0.192000 rms 0.860 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.8690 tsec 40.8240 #GCMRL# 74 dt 0.192000 rms 0.860 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.1670 tsec 35.0090 #GCMRL# 75 dt 0.192000 rms 0.859 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.5930 tsec 32.6630 #GCAMreg# pass 0 level1 1 level2 1 tsec 1449.56 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.859744 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.858997) vs oldopt=(dt=0.32,rms=0.859029) #GCMRL# 77 dt 0.192000 rms 0.859 0.087% neg 0 invalid 762 tFOTS 103.9920 tGradient 28.7110 tsec 141.0020 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.858993) vs oldopt=(dt=0.02,rms=0.858993) #GCMRL# 78 dt 0.028000 rms 0.859 0.000% neg 0 invalid 762 tFOTS 103.5840 tGradient 22.7380 tsec 134.4270 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.798691 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.792197) vs oldopt=(dt=0.32,rms=0.792517) #GCMRL# 80 dt 0.256000 rms 0.792 0.813% neg 0 invalid 762 tFOTS 110.1710 tGradient 18.3990 tsec 135.8960 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.791804) vs oldopt=(dt=0.02,rms=0.791836) #GCMRL# 81 dt 0.028000 rms 0.792 0.000% neg 0 invalid 762 tFOTS 104.4970 tGradient 16.4370 tsec 129.4410 #GCAMreg# pass 0 level1 0 level2 1 tsec 330.595 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.792455 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.791733) vs oldopt=(dt=0.02,rms=0.79174) #GCMRL# 83 dt 0.016000 rms 0.792 0.091% neg 0 invalid 762 tFOTS 120.6140 tGradient 27.1400 tsec 155.5250 GCAMregister done in 123.248 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.02912 ( 6) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, overlap=0.766) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, peak = 18), gca=18.5 gca peak = 0.17690 (16) mri peak = 0.06897 (30) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, overlap=0.426) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, peak = 23), gca=23.4 gca peak = 0.28275 (96) mri peak = 0.06787 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, overlap=0.966) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, peak = 93), gca=92.6 gca peak = 0.18948 (93) mri peak = 0.06458 (96) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, overlap=1.008) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, peak = 92), gca=91.6 gca peak = 0.20755 (55) mri peak = 0.11697 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, peak = 55), gca=55.0 gca peak = 0.31831 (58) mri peak = 0.08625 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, peak = 55), gca=54.8 gca peak = 0.11957 (102) mri peak = 0.06876 (109) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, peak = 110), gca=109.7 gca peak = 0.11429 (102) mri peak = 0.06805 (111) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, overlap=0.521) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, peak = 111), gca=110.7 gca peak = 0.14521 (59) mri peak = 0.03738 (55) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, overlap=0.966) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, peak = 54), gca=54.0 gca peak = 0.14336 (58) mri peak = 0.04502 (53) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, overlap=0.848) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, peak = 52), gca=51.9 gca peak = 0.13305 (70) mri peak = 0.08346 (76) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, overlap=0.651) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, peak = 77), gca=77.3 gca peak = 0.15761 (71) mri peak = 0.06809 (83) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, overlap=0.571) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, peak = 77), gca=77.0 gca peak = 0.13537 (57) mri peak = 0.03402 (55) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, overlap=0.918) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, peak = 55), gca=55.0 gca peak = 0.13487 (56) mri peak = 0.03585 (51) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, peak = 54), gca=54.0 gca peak = 0.19040 (84) mri peak = 0.06228 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, overlap=0.746) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, peak = 87), gca=86.9 gca peak = 0.18871 (83) mri peak = 0.08367 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, peak = 86), gca=85.9 gca peak = 0.24248 (57) mri peak = 0.13222 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, overlap=0.798) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, peak = 51), gca=51.0 gca peak = 0.35833 (56) mri peak = 0.11187 (55) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, overlap=0.978) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, peak = 54), gca=54.0 gca peak = 0.12897 (85) mri peak = 0.05445 (88) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, overlap=0.975) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, peak = 83), gca=82.9 gca peak = 0.13127 (83) mri peak = 0.05455 (82) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, overlap=0.920) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, peak = 86), gca=85.9 gca peak = 0.12974 (78) mri peak = 0.06301 (81) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, overlap=0.985) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, peak = 82), gca=81.5 gca peak = 0.17796 (79) mri peak = 0.07260 (81) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, overlap=0.934) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, peak = 82), gca=81.8 gca peak = 0.10999 (80) mri peak = 0.09164 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.05790 (86) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, overlap=0.730) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.05402 (89) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, overlap=0.853) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, peak = 97), gca=96.6 gca peak = 0.20775 (25) mri peak = 0.03183 (12) gca peak = 0.13297 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.08 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 32.3277 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.848745 #FOTS# QuadFit found better minimum quadopt=(dt=182.491,rms=0.80955) vs oldopt=(dt=92.48,rms=0.818919) #GCMRL# 85 dt 182.490818 rms 0.810 4.618% neg 0 invalid 762 tFOTS 128.5610 tGradient 55.0890 tsec 192.0200 #FOTS# QuadFit found better minimum quadopt=(dt=175.23,rms=0.798144) vs oldopt=(dt=92.48,rms=0.801288) #GCMRL# 86 dt 175.229947 rms 0.798 1.409% neg 0 invalid 762 tFOTS 129.0280 tGradient 56.5140 tsec 196.4830 #FOTS# QuadFit found better minimum quadopt=(dt=176.792,rms=0.790975) vs oldopt=(dt=92.48,rms=0.79302) #GCMRL# 87 dt 176.792079 rms 0.791 0.898% neg 0 invalid 762 tFOTS 125.9320 tGradient 56.2350 tsec 192.4560 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.787162) vs oldopt=(dt=92.48,rms=0.787957) #GCMRL# 88 dt 129.472000 rms 0.787 0.482% neg 0 invalid 762 tFOTS 122.3550 tGradient 61.9860 tsec 195.6560 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.779255) vs oldopt=(dt=369.92,rms=0.780123) #GCMRL# 89 dt 517.888000 rms 0.779 1.005% neg 0 invalid 762 tFOTS 124.0870 tGradient 57.5710 tsec 189.7260 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.775457) vs oldopt=(dt=92.48,rms=0.775669) #GCMRL# 90 dt 129.472000 rms 0.775 0.487% neg 0 invalid 762 tFOTS 125.8660 tGradient 49.2430 tsec 183.8620 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.772686) vs oldopt=(dt=369.92,rms=0.773004) #GCMRL# 91 dt 295.936000 rms 0.773 0.357% neg 0 invalid 762 tFOTS 116.8320 tGradient 50.9820 tsec 176.9080 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.770251) vs oldopt=(dt=92.48,rms=0.77046) #GCMRL# 92 dt 129.472000 rms 0.770 0.315% neg 0 invalid 762 tFOTS 134.0350 tGradient 54.3620 tsec 201.7020 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.768064) vs oldopt=(dt=369.92,rms=0.768174) #GCMRL# 93 dt 295.936000 rms 0.768 0.284% neg 0 invalid 762 tFOTS 130.4700 tGradient 53.2320 tsec 193.3850 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.766199) vs oldopt=(dt=92.48,rms=0.766423) #GCMRL# 94 dt 129.472000 rms 0.766 0.243% neg 0 invalid 762 tFOTS 132.3570 tGradient 59.3580 tsec 199.9160 #GCMRL# 95 dt 369.920000 rms 0.764 0.240% neg 0 invalid 762 tFOTS 129.4740 tGradient 54.9580 tsec 193.9720 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.762431) vs oldopt=(dt=92.48,rms=0.762576) #GCMRL# 96 dt 129.472000 rms 0.762 0.253% neg 0 invalid 762 tFOTS 123.5260 tGradient 48.0030 tsec 180.8850 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.761167) vs oldopt=(dt=369.92,rms=0.761516) #GCMRL# 97 dt 221.952000 rms 0.761 0.166% neg 0 invalid 762 tFOTS 86.7480 tGradient 39.1560 tsec 132.4160 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.760028) vs oldopt=(dt=92.48,rms=0.760234) #GCMRL# 98 dt 129.472000 rms 0.760 0.150% neg 0 invalid 762 tFOTS 124.1650 tGradient 39.0600 tsec 170.9030 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.758301) vs oldopt=(dt=369.92,rms=0.758399) #GCMRL# 99 dt 517.888000 rms 0.758 0.227% neg 0 invalid 762 tFOTS 86.8890 tGradient 39.3350 tsec 132.8900 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.75648) vs oldopt=(dt=92.48,rms=0.756592) #GCMRL# 100 dt 129.472000 rms 0.756 0.240% neg 0 invalid 762 tFOTS 87.7470 tGradient 31.0010 tsec 125.9610 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.755734) vs oldopt=(dt=92.48,rms=0.755844) #GCMRL# 101 dt 129.472000 rms 0.756 0.099% neg 0 invalid 762 tFOTS 80.9000 tGradient 32.0570 tsec 117.3420 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.753709) vs oldopt=(dt=369.92,rms=0.754086) #GCMRL# 102 dt 517.888000 rms 0.754 0.268% neg 0 invalid 762 tFOTS 81.3700 tGradient 35.1720 tsec 122.5230 #GCMRL# 103 dt 92.480000 rms 0.753 0.116% neg 0 invalid 762 tFOTS 87.5180 tGradient 31.4850 tsec 125.4330 #FOTS# QuadFit found better minimum quadopt=(dt=4734.98,rms=0.742561) vs oldopt=(dt=5918.72,rms=0.743082) #GCMRL# 104 dt 4734.976000 rms 0.743 1.365% neg 0 invalid 762 tFOTS 87.7920 tGradient 36.8150 tsec 129.4470 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.740244) vs oldopt=(dt=92.48,rms=0.740309) #GCMRL# 105 dt 73.984000 rms 0.740 0.312% neg 0 invalid 762 tFOTS 70.0540 tGradient 27.7680 tsec 102.4660 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.740078) vs oldopt=(dt=92.48,rms=0.740106) #GCMRL# 106 dt 129.472000 rms 0.740 0.000% neg 0 invalid 762 tFOTS 73.0070 tGradient 34.3660 tsec 111.6150 #GCMRL# 107 dt 129.472000 rms 0.740 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.1760 tsec 31.8800 #GCMRL# 108 dt 129.472000 rms 0.739 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.0970 tsec 39.4660 #GCMRL# 109 dt 129.472000 rms 0.739 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.7190 tsec 38.7590 #GCMRL# 110 dt 129.472000 rms 0.738 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.7850 tsec 42.2010 #GCMRL# 111 dt 129.472000 rms 0.737 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.0080 tsec 41.1850 #GCMRL# 112 dt 129.472000 rms 0.736 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.5020 tsec 39.8050 #GCMRL# 113 dt 129.472000 rms 0.735 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.6300 tsec 36.7780 #GCMRL# 114 dt 129.472000 rms 0.734 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.1990 tsec 36.1370 #GCMRL# 115 dt 129.472000 rms 0.733 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.2770 tsec 34.5810 #GCMRL# 116 dt 129.472000 rms 0.732 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.3090 tsec 35.1940 #GCMRL# 117 dt 129.472000 rms 0.731 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.1160 tsec 39.0730 #GCMRL# 118 dt 129.472000 rms 0.731 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.4950 tsec 36.8560 #GCMRL# 119 dt 129.472000 rms 0.730 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.6000 tsec 37.2240 #GCMRL# 120 dt 129.472000 rms 0.729 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.4510 tsec 40.4980 #GCMRL# 121 dt 129.472000 rms 0.728 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.8120 tsec 38.5560 #GCMRL# 122 dt 129.472000 rms 0.727 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.0540 tsec 37.6440 #GCMRL# 123 dt 129.472000 rms 0.726 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.1200 tsec 38.9260 #GCMRL# 124 dt 129.472000 rms 0.726 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.7340 tsec 38.0210 #GCMRL# 125 dt 129.472000 rms 0.725 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.9070 tsec 41.6100 #GCMRL# 126 dt 129.472000 rms 0.724 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.0550 tsec 38.6340 #GCMRL# 127 dt 129.472000 rms 0.724 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.9680 tsec 42.0030 #GCMRL# 128 dt 129.472000 rms 0.723 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.9620 tsec 38.2220 #GCMRL# 129 dt 129.472000 rms 0.723 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.7930 tsec 41.4320 #GCMRL# 130 dt 129.472000 rms 0.722 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.5700 tsec 39.5400 #GCMRL# 131 dt 129.472000 rms 0.721 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.1700 tsec 38.0360 #GCMRL# 132 dt 129.472000 rms 0.721 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.9710 tsec 34.6980 #GCMRL# 133 dt 129.472000 rms 0.720 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 40.1220 tsec 48.6880 #GCMRL# 134 dt 129.472000 rms 0.720 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.9590 tsec 45.7950 #GCMRL# 135 dt 129.472000 rms 0.719 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.9310 tsec 46.1670 #GCMRL# 136 dt 129.472000 rms 0.719 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 37.2440 tsec 42.6270 #GCMRL# 137 dt 129.472000 rms 0.718 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.4370 tsec 49.5080 #GCMRL# 138 dt 129.472000 rms 0.718 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.1580 tsec 47.7100 #GCMRL# 139 dt 129.472000 rms 0.718 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 37.4190 tsec 44.2660 #GCMRL# 140 dt 129.472000 rms 0.717 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 37.4290 tsec 42.9960 #GCMRL# 141 dt 129.472000 rms 0.717 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.4190 tsec 39.3210 #GCMRL# 142 dt 129.472000 rms 0.716 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.7660 tsec 40.0090 #GCMRL# 143 dt 129.472000 rms 0.716 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.4850 tsec 36.8560 #GCMRL# 144 dt 129.472000 rms 0.715 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.9670 tsec 40.2580 #GCMRL# 145 dt 129.472000 rms 0.715 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.0670 tsec 40.0680 #GCMRL# 146 dt 129.472000 rms 0.715 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.5140 tsec 42.2210 #GCMRL# 147 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.2520 tsec 38.8560 #GCMRL# 148 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.6170 tsec 40.5970 #GCMRL# 149 dt 129.472000 rms 0.714 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 37.8890 tsec 44.8610 #GCMRL# 150 dt 129.472000 rms 0.713 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.7020 tsec 41.1050 #GCMRL# 151 dt 129.472000 rms 0.713 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.2660 tsec 42.0910 #GCMRL# 152 dt 129.472000 rms 0.713 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.5030 tsec 42.1220 #GCMRL# 153 dt 129.472000 rms 0.712 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.9360 tsec 42.1030 #GCMRL# 154 dt 129.472000 rms 0.712 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.4770 tsec 41.9050 #GCMRL# 155 dt 129.472000 rms 0.712 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.4090 tsec 44.8250 #GCMRL# 156 dt 129.472000 rms 0.712 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 40.1370 tsec 46.7680 #GCMRL# 157 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 37.9620 tsec 44.9050 #GCMRL# 158 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.8060 tsec 38.3100 #GCMRL# 159 dt 129.472000 rms 0.711 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.6100 tsec 39.4180 #GCMRL# 160 dt 129.472000 rms 0.710 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.2930 tsec 39.6540 #GCMRL# 161 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 41.9120 tsec 47.3020 #GCMRL# 162 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.1890 tsec 45.1200 #GCMRL# 163 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.2940 tsec 41.0670 #GCMRL# 164 dt 129.472000 rms 0.710 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.7750 tsec 43.4610 #GCMRL# 165 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.6470 tsec 47.6050 #GCMRL# 166 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.1140 tsec 40.8940 #GCMRL# 167 dt 129.472000 rms 0.709 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.2170 tsec 42.0240 #GCMRL# 168 dt 129.472000 rms 0.709 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.6030 tsec 37.3090 #GCMRL# 169 dt 129.472000 rms 0.709 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.0550 tsec 38.8700 #GCMRL# 170 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.5270 tsec 36.3270 #GCMRL# 171 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.8160 tsec 40.1160 #GCMRL# 172 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.9850 tsec 38.2880 #GCMRL# 173 dt 129.472000 rms 0.708 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.0250 tsec 40.2990 #GCMRL# 174 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.2440 tsec 37.3440 #GCMRL# 175 dt 129.472000 rms 0.707 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.5310 tsec 39.9300 #GCMRL# 176 dt 129.472000 rms 0.707 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.2650 tsec 37.0860 #GCMRL# 177 dt 129.472000 rms 0.707 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.0510 tsec 37.3990 #GCMRL# 178 dt 129.472000 rms 0.707 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.3180 tsec 40.7390 #GCMRL# 179 dt 5918.720000 rms 0.706 0.071% neg 0 invalid 762 tFOTS 84.8930 tGradient 30.4560 tsec 120.7410 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.70616) vs oldopt=(dt=92.48,rms=0.706165) #GCMRL# 180 dt 73.984000 rms 0.706 0.000% neg 0 invalid 762 tFOTS 77.8890 tGradient 33.7560 tsec 117.9110 #GCMRL# 181 dt 73.984000 rms 0.706 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.4350 tsec 43.4960 #GCMRL# 182 dt 73.984000 rms 0.706 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.7640 tsec 45.5000 #GCAMreg# pass 0 level1 5 level2 1 tsec 6902.97 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.706908 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.705379) vs oldopt=(dt=92.48,rms=0.705528) #GCMRL# 184 dt 129.472000 rms 0.705 0.216% neg 0 invalid 762 tFOTS 101.5840 tGradient 41.3450 tsec 150.9480 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.704347) vs oldopt=(dt=369.92,rms=0.704522) #GCMRL# 185 dt 517.888000 rms 0.704 0.146% neg 0 invalid 762 tFOTS 107.0090 tGradient 41.3380 tsec 154.4980 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.704176) vs oldopt=(dt=92.48,rms=0.704194) #GCMRL# 186 dt 129.472000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 77.3700 tGradient 41.7050 tsec 125.0780 #GCMRL# 187 dt 129.472000 rms 0.704 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.7080 tsec 44.7410 #GCMRL# 188 dt 129.472000 rms 0.704 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.6950 tsec 44.8400 #GCMRL# 189 dt 129.472000 rms 0.704 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 43.6950 tsec 49.2860 #GCMRL# 190 dt 129.472000 rms 0.704 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.7960 tsec 40.9510 #GCMRL# 191 dt 129.472000 rms 0.703 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.8270 tsec 40.3190 #GCMRL# 192 dt 129.472000 rms 0.703 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.2840 tsec 44.6470 #GCMRL# 193 dt 129.472000 rms 0.703 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.5940 tsec 46.4300 #GCMRL# 194 dt 129.472000 rms 0.703 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 40.8530 tsec 48.2820 #GCMRL# 195 dt 129.472000 rms 0.703 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 41.2010 tsec 48.2050 #GCMRL# 196 dt 129.472000 rms 0.702 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 41.9930 tsec 48.9640 #GCMRL# 197 dt 129.472000 rms 0.702 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.9140 tsec 45.8200 #GCMRL# 198 dt 129.472000 rms 0.702 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.7810 tsec 50.5710 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.70213) vs oldopt=(dt=369.92,rms=0.702135) #GCMRL# 199 dt 295.936000 rms 0.702 0.000% neg 0 invalid 762 tFOTS 114.1010 tGradient 50.2680 tsec 171.6250 #GCMRL# 200 dt 295.936000 rms 0.702 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 46.2310 tsec 56.8700 #GCMRL# 201 dt 295.936000 rms 0.702 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.7860 tsec 49.9950 #GCMRL# 202 dt 295.936000 rms 0.702 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 48.2780 tsec 54.7130 #GCMRL# 203 dt 295.936000 rms 0.702 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 43.6150 tsec 49.9430 #GCMRL# 204 dt 295.936000 rms 0.702 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.3950 tsec 43.9320 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701437) vs oldopt=(dt=92.48,rms=0.701445) #GCMRL# 205 dt 129.472000 rms 0.701 0.019% neg 0 invalid 762 tFOTS 97.0030 tGradient 39.7100 tsec 143.7470 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701443) vs oldopt=(dt=92.48,rms=0.701444) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.704686 #FOTS# QuadFit found better minimum quadopt=(dt=169.475,rms=0.699018) vs oldopt=(dt=103.68,rms=0.699625) #GCMRL# 207 dt 169.474860 rms 0.699 0.804% neg 0 invalid 762 tFOTS 90.0810 tGradient 29.0140 tsec 125.8410 #FOTS# QuadFit found better minimum quadopt=(dt=192,rms=0.689646) vs oldopt=(dt=103.68,rms=0.691455) #GCMRL# 208 dt 192.000000 rms 0.690 1.341% neg 0 invalid 762 tFOTS 93.0500 tGradient 28.4370 tsec 127.8070 #FOTS# QuadFit found better minimum quadopt=(dt=67.7333,rms=0.686057) vs oldopt=(dt=25.92,rms=0.686985) #GCMRL# 209 dt 67.733333 rms 0.686 0.520% neg 0 invalid 762 tFOTS 92.1740 tGradient 27.6450 tsec 126.2460 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.678544) vs oldopt=(dt=414.72,rms=0.678631) #GCMRL# 210 dt 331.776000 rms 0.679 1.095% neg 0 invalid 762 tFOTS 84.8390 tGradient 27.1880 tsec 118.6020 #FOTS# QuadFit found better minimum quadopt=(dt=61.9221,rms=0.674719) vs oldopt=(dt=25.92,rms=0.675676) #GCMRL# 211 dt 61.922078 rms 0.675 0.564% neg 0 invalid 762 tFOTS 90.5830 tGradient 25.8860 tsec 122.9810 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.671901) vs oldopt=(dt=103.68,rms=0.672143) #GCMRL# 212 dt 145.152000 rms 0.672 0.418% neg 0 invalid 762 tFOTS 89.0010 tGradient 25.6440 tsec 121.2560 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.670285) vs oldopt=(dt=25.92,rms=0.670597) #GCMRL# 213 dt 36.288000 rms 0.670 0.241% neg 0 invalid 762 tFOTS 97.7290 tGradient 25.6490 tsec 129.7670 #GCMRL# 214 dt 414.720000 rms 0.666 0.585% neg 0 invalid 762 tFOTS 86.7520 tGradient 25.2770 tsec 119.0360 #FOTS# QuadFit found better minimum quadopt=(dt=58.022,rms=0.662064) vs oldopt=(dt=25.92,rms=0.663079) #GCMRL# 215 dt 58.021978 rms 0.662 0.646% neg 0 invalid 762 tFOTS 94.5460 tGradient 26.9530 tsec 128.6440 #FOTS# QuadFit found better minimum quadopt=(dt=68.6829,rms=0.661125) vs oldopt=(dt=103.68,rms=0.661322) #GCMRL# 216 dt 68.682927 rms 0.661 0.142% neg 0 invalid 762 tFOTS 98.6010 tGradient 28.8090 tsec 135.9090 #GCMRL# 217 dt 103.680000 rms 0.660 0.206% neg 0 invalid 762 tFOTS 89.0530 tGradient 29.2300 tsec 124.2190 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.659053) vs oldopt=(dt=25.92,rms=0.659202) #GCMRL# 218 dt 36.288000 rms 0.659 0.108% neg 0 invalid 762 tFOTS 81.7520 tGradient 25.9190 tsec 113.9250 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.654714) vs oldopt=(dt=414.72,rms=0.65545) #GCMRL# 219 dt 580.608000 rms 0.655 0.658% neg 0 invalid 762 tFOTS 91.2130 tGradient 26.7450 tsec 123.7040 #FOTS# QuadFit found better minimum quadopt=(dt=67.6364,rms=0.652369) vs oldopt=(dt=25.92,rms=0.652822) #GCMRL# 220 dt 67.636364 rms 0.652 0.358% neg 0 invalid 762 tFOTS 103.9930 tGradient 26.1180 tsec 136.7420 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.651527) vs oldopt=(dt=25.92,rms=0.651666) #GCMRL# 221 dt 36.288000 rms 0.652 0.129% neg 0 invalid 762 tFOTS 88.7140 tGradient 27.6650 tsec 122.7970 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.648123) vs oldopt=(dt=414.72,rms=0.648688) #GCMRL# 222 dt 580.608000 rms 0.648 0.522% neg 0 invalid 762 tFOTS 92.9620 tGradient 30.2790 tsec 130.0700 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.646406) vs oldopt=(dt=25.92,rms=0.646678) #GCMRL# 223 dt 36.288000 rms 0.646 0.265% neg 0 invalid 762 tFOTS 101.7450 tGradient 27.9500 tsec 135.9170 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.645724) vs oldopt=(dt=103.68,rms=0.645835) #GCMRL# 224 dt 145.152000 rms 0.646 0.105% neg 0 invalid 762 tFOTS 93.8400 tGradient 25.6400 tsec 124.7320 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.64461) vs oldopt=(dt=103.68,rms=0.644727) #GCMRL# 225 dt 145.152000 rms 0.645 0.173% neg 0 invalid 762 tFOTS 94.8570 tGradient 29.2160 tsec 131.1880 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.644212) vs oldopt=(dt=25.92,rms=0.6443) #GCMRL# 226 dt 36.288000 rms 0.644 0.062% neg 0 invalid 762 tFOTS 84.1000 tGradient 24.6610 tsec 114.9930 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.643363) vs oldopt=(dt=414.72,rms=0.643531) #GCMRL# 227 dt 248.832000 rms 0.643 0.132% neg 0 invalid 762 tFOTS 85.3900 tGradient 24.7670 tsec 115.7360 #FOTS# QuadFit found better minimum quadopt=(dt=85.3333,rms=0.642294) vs oldopt=(dt=103.68,rms=0.642346) #GCMRL# 228 dt 85.333333 rms 0.642 0.166% neg 0 invalid 762 tFOTS 79.0570 tGradient 25.1350 tsec 110.5290 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.641898) vs oldopt=(dt=103.68,rms=0.641953) #GCMRL# 229 dt 82.944000 rms 0.642 0.062% neg 0 invalid 762 tFOTS 88.6010 tGradient 25.7690 tsec 120.0450 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.641285) vs oldopt=(dt=103.68,rms=0.641286) #GCMRL# 230 dt 124.416000 rms 0.641 0.095% neg 0 invalid 762 tFOTS 90.5900 tGradient 26.5240 tsec 123.9670 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.64088) vs oldopt=(dt=25.92,rms=0.640968) #GCMRL# 231 dt 36.288000 rms 0.641 0.063% neg 0 invalid 762 tFOTS 92.2040 tGradient 24.9090 tsec 124.0130 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.639431) vs oldopt=(dt=414.72,rms=0.639473) #GCMRL# 232 dt 497.664000 rms 0.639 0.226% neg 0 invalid 762 tFOTS 98.4220 tGradient 25.6390 tsec 130.9700 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.638071) vs oldopt=(dt=25.92,rms=0.638305) #GCMRL# 233 dt 36.288000 rms 0.638 0.213% neg 0 invalid 762 tFOTS 99.2840 tGradient 28.5930 tsec 134.6830 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.637494) vs oldopt=(dt=103.68,rms=0.637549) #GCMRL# 234 dt 145.152000 rms 0.637 0.090% neg 0 invalid 762 tFOTS 103.7620 tGradient 30.3040 tsec 141.9790 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.637132) vs oldopt=(dt=25.92,rms=0.637209) #GCMRL# 235 dt 36.288000 rms 0.637 0.057% neg 0 invalid 762 tFOTS 93.4850 tGradient 35.7740 tsec 135.5990 #GCMRL# 236 dt 414.720000 rms 0.636 0.165% neg 0 invalid 762 tFOTS 84.9370 tGradient 26.5270 tsec 117.4780 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.635115) vs oldopt=(dt=25.92,rms=0.635299) #GCMRL# 237 dt 36.288000 rms 0.635 0.152% neg 0 invalid 762 tFOTS 78.9670 tGradient 26.2030 tsec 110.9740 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.634581) vs oldopt=(dt=103.68,rms=0.63463) #GCMRL# 238 dt 145.152000 rms 0.635 0.084% neg 0 invalid 762 tFOTS 82.6450 tGradient 24.4340 tsec 113.0100 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.63422) vs oldopt=(dt=103.68,rms=0.634322) #GCMRL# 239 dt 62.208000 rms 0.634 0.057% neg 0 invalid 762 tFOTS 85.3410 tGradient 25.3650 tsec 116.3970 #GCMRL# 240 dt 414.720000 rms 0.633 0.151% neg 0 invalid 762 tFOTS 88.0170 tGradient 23.8560 tsec 118.0630 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.63243) vs oldopt=(dt=25.92,rms=0.63257) #GCMRL# 241 dt 36.288000 rms 0.632 0.131% neg 0 invalid 762 tFOTS 87.9910 tGradient 24.9700 tsec 119.0160 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.632065) vs oldopt=(dt=103.68,rms=0.632075) #GCMRL# 242 dt 124.416000 rms 0.632 0.058% neg 0 invalid 762 tFOTS 92.9710 tGradient 26.6600 tsec 125.8690 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631657) vs oldopt=(dt=103.68,rms=0.631671) #GCMRL# 243 dt 82.944000 rms 0.632 0.065% neg 0 invalid 762 tFOTS 90.9740 tGradient 28.6140 tsec 126.5660 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631393) vs oldopt=(dt=103.68,rms=0.631399) #GCMRL# 244 dt 82.944000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 87.6660 tGradient 25.5180 tsec 119.3870 #GCMRL# 245 dt 82.944000 rms 0.631 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.2270 tsec 45.3030 #GCMRL# 246 dt 82.944000 rms 0.631 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.2780 tsec 35.1770 #GCMRL# 247 dt 82.944000 rms 0.630 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.1810 tsec 37.5500 #GCMRL# 248 dt 82.944000 rms 0.629 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.9540 tsec 34.4650 #GCMRL# 249 dt 82.944000 rms 0.628 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.1810 tsec 40.4670 #GCMRL# 250 dt 82.944000 rms 0.627 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.1690 tsec 30.8530 #GCMRL# 251 dt 82.944000 rms 0.625 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.0050 tsec 35.2100 #GCMRL# 252 dt 82.944000 rms 0.624 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.9880 tsec 37.7770 #GCMRL# 253 dt 82.944000 rms 0.623 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.8410 tsec 38.3060 #GCMRL# 254 dt 82.944000 rms 0.622 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.3060 tsec 32.3960 #GCMRL# 255 dt 82.944000 rms 0.621 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.7330 tsec 30.6840 #GCMRL# 256 dt 82.944000 rms 0.620 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.9060 tsec 30.2650 #GCMRL# 257 dt 82.944000 rms 0.619 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.2170 tsec 34.1760 #GCMRL# 258 dt 82.944000 rms 0.618 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.1120 tsec 34.5010 #GCMRL# 259 dt 82.944000 rms 0.617 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.7170 tsec 34.7200 #GCMRL# 260 dt 82.944000 rms 0.616 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.2000 tsec 31.6950 #GCMRL# 261 dt 82.944000 rms 0.615 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.6700 tsec 31.4870 #GCMRL# 262 dt 82.944000 rms 0.614 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.8790 tsec 32.6690 #GCMRL# 263 dt 82.944000 rms 0.614 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.8420 tsec 31.5750 #GCMRL# 264 dt 82.944000 rms 0.613 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.2170 tsec 40.9000 #GCMRL# 265 dt 82.944000 rms 0.612 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.7910 tsec 35.1260 #GCMRL# 266 dt 82.944000 rms 0.612 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.5840 tsec 36.0960 #GCMRL# 267 dt 82.944000 rms 0.612 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.1750 tsec 36.9650 #GCMRL# 268 dt 20.736000 rms 0.612 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.5880 tsec 42.2390 #GCMRL# 269 dt 5.184000 rms 0.612 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.5180 tsec 41.7670 #FOTS# QuadFit found better minimum quadopt=(dt=0.567,rms=0.611569) vs oldopt=(dt=0.405,rms=0.611569) #GCMRL# 270 dt 0.567000 rms 0.612 0.000% neg 0 invalid 762 tFOTS 62.0930 tGradient 25.6200 tsec 93.7200 #GCMRL# 271 dt 0.141750 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.9480 tsec 41.5150 #GCMRL# 272 dt 0.070875 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.8790 tsec 36.7900 #GCAMreg# pass 0 level1 4 level2 1 tsec 5846.16 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.612649 #FOTS# QuadFit found better minimum quadopt=(dt=0.0354375,rms=0.611567) vs oldopt=(dt=0.0253125,rms=0.611568) #GCMRL# 274 dt 0.035437 rms 0.612 0.176% neg 0 invalid 762 tFOTS 51.7000 tGradient 24.3170 tsec 81.6170 #FOTS# QuadFit found better minimum quadopt=(dt=0.00885937,rms=0.611567) vs oldopt=(dt=0.00632812,rms=0.611567) #GCMRL# 275 dt 0.008859 rms 0.612 0.000% neg 0 invalid 762 tFOTS 45.7220 tGradient 28.0760 tsec 80.2080 #GCMRL# 276 dt 0.002215 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.1100 tsec 37.1760 #GCMRL# 277 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.5020 tsec 34.6980 #GCMRL# 278 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.4590 tsec 31.9780 #GCMRL# 279 dt 0.000138 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.9690 tsec 43.9020 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.625485 #FOTS# QuadFit found better minimum quadopt=(dt=87.0701,rms=0.614414) vs oldopt=(dt=128,rms=0.616497) #GCMRL# 281 dt 87.070059 rms 0.614 1.770% neg 0 invalid 762 tFOTS 98.5550 tGradient 21.5540 tsec 127.1220 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.610965) vs oldopt=(dt=8,rms=0.61191) #GCMRL# 282 dt 11.200000 rms 0.611 0.561% neg 0 invalid 762 tFOTS 89.6910 tGradient 24.9130 tsec 122.0220 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.608422) vs oldopt=(dt=8,rms=0.609126) #GCMRL# 283 dt 11.200000 rms 0.608 0.416% neg 0 invalid 762 tFOTS 92.5870 tGradient 23.6210 tsec 123.7970 #GCMRL# 284 dt 32.000000 rms 0.603 0.902% neg 0 invalid 762 tFOTS 98.2840 tGradient 28.7320 tsec 136.8850 #FOTS# QuadFit found better minimum quadopt=(dt=153.6,rms=0.588486) vs oldopt=(dt=128,rms=0.590481) #GCMRL# 285 dt 153.600000 rms 0.588 2.396% neg 0 invalid 762 tFOTS 115.6670 tGradient 27.6540 tsec 150.0430 #GCMRL# 286 dt 32.000000 rms 0.586 0.367% neg 0 invalid 762 tFOTS 95.0680 tGradient 25.2300 tsec 127.4790 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.584802) vs oldopt=(dt=32,rms=0.58511) #GCMRL# 287 dt 44.800000 rms 0.585 0.260% neg 0 invalid 762 tFOTS 89.0330 tGradient 29.3220 tsec 125.5670 #GCMRL# 288 dt 32.000000 rms 0.583 0.332% neg 0 invalid 762 tFOTS 87.5490 tGradient 23.4280 tsec 118.0040 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.581944) vs oldopt=(dt=32,rms=0.581955) #GCMRL# 289 dt 38.400000 rms 0.582 0.157% neg 0 invalid 762 tFOTS 83.3960 tGradient 24.9860 tsec 116.3610 #GCMRL# 290 dt 32.000000 rms 0.580 0.313% neg 0 invalid 762 tFOTS 93.7590 tGradient 24.1440 tsec 124.0940 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.579347) vs oldopt=(dt=32,rms=0.579356) #GCMRL# 291 dt 25.600000 rms 0.579 0.133% neg 0 invalid 762 tFOTS 93.8950 tGradient 25.4820 tsec 126.8850 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.577879) vs oldopt=(dt=32,rms=0.578021) #GCMRL# 292 dt 38.400000 rms 0.578 0.253% neg 0 invalid 762 tFOTS 102.3280 tGradient 29.0860 tsec 137.8260 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.577186) vs oldopt=(dt=32,rms=0.5772) #GCMRL# 293 dt 25.600000 rms 0.577 0.120% neg 0 invalid 762 tFOTS 104.8970 tGradient 24.1320 tsec 136.5900 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.575765) vs oldopt=(dt=32,rms=0.575998) #GCMRL# 294 dt 44.800000 rms 0.576 0.246% neg 0 invalid 762 tFOTS 109.7700 tGradient 29.5810 tsec 146.1490 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.575121) vs oldopt=(dt=32,rms=0.575172) #GCMRL# 295 dt 25.600000 rms 0.575 0.112% neg 0 invalid 762 tFOTS 94.9910 tGradient 25.6040 tsec 127.9730 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.573811) vs oldopt=(dt=32,rms=0.574018) #GCMRL# 296 dt 44.800000 rms 0.574 0.228% neg 0 invalid 762 tFOTS 99.5360 tGradient 28.0030 tsec 136.0050 #FOTS# QuadFit found better minimum quadopt=(dt=24.9449,rms=0.573318) vs oldopt=(dt=32,rms=0.573419) #GCMRL# 297 dt 24.944882 rms 0.573 0.086% neg 0 invalid 762 tFOTS 91.9990 tGradient 23.8020 tsec 122.4050 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.572173) vs oldopt=(dt=32,rms=0.572327) #GCMRL# 298 dt 44.800000 rms 0.572 0.200% neg 0 invalid 762 tFOTS 86.1080 tGradient 22.2440 tsec 114.9390 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.571704) vs oldopt=(dt=32,rms=0.571867) #GCMRL# 299 dt 19.200000 rms 0.572 0.082% neg 0 invalid 762 tFOTS 86.3570 tGradient 23.3060 tsec 115.8220 #GCMRL# 300 dt 128.000000 rms 0.569 0.411% neg 0 invalid 762 tFOTS 84.8860 tGradient 23.5000 tsec 114.4140 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.56885) vs oldopt=(dt=8,rms=0.56897) #GCMRL# 301 dt 11.200000 rms 0.569 0.089% neg 0 invalid 762 tFOTS 86.4190 tGradient 22.3960 tsec 115.9780 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.568437) vs oldopt=(dt=32,rms=0.568504) #GCMRL# 302 dt 19.200000 rms 0.568 0.073% neg 0 invalid 762 tFOTS 88.3320 tGradient 23.4010 tsec 118.7500 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.566753) vs oldopt=(dt=128,rms=0.566905) #GCMRL# 303 dt 179.200000 rms 0.567 0.296% neg 0 invalid 762 tFOTS 91.9150 tGradient 21.9460 tsec 121.1820 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.565599) vs oldopt=(dt=32,rms=0.565671) #GCMRL# 304 dt 25.600000 rms 0.566 0.204% neg 0 invalid 762 tFOTS 95.6990 tGradient 27.5610 tsec 130.7450 #GCMRL# 305 dt 32.000000 rms 0.565 0.151% neg 0 invalid 762 tFOTS 90.4380 tGradient 26.1050 tsec 127.4490 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.564467) vs oldopt=(dt=32,rms=0.564525) #GCMRL# 306 dt 19.200000 rms 0.564 0.000% neg 0 invalid 762 tFOTS 108.9180 tGradient 27.9750 tsec 146.2340 #GCMRL# 307 dt 19.200000 rms 0.564 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.1070 tsec 36.9850 #GCMRL# 308 dt 19.200000 rms 0.564 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.6070 tsec 34.4450 #GCMRL# 309 dt 19.200000 rms 0.563 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.3970 tsec 32.7100 #GCMRL# 310 dt 19.200000 rms 0.562 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.9430 tsec 36.8740 #GCMRL# 311 dt 19.200000 rms 0.562 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.9950 tsec 34.1850 #GCMRL# 312 dt 19.200000 rms 0.561 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.0950 tsec 29.3860 #GCMRL# 313 dt 19.200000 rms 0.560 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.3320 tsec 29.9910 #GCMRL# 314 dt 19.200000 rms 0.559 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.7250 tsec 29.6840 #GCMRL# 315 dt 19.200000 rms 0.558 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.1930 tsec 30.2700 #GCMRL# 316 dt 19.200000 rms 0.558 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6900 tsec 31.4080 #GCMRL# 317 dt 19.200000 rms 0.557 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.9420 tsec 31.4830 #GCMRL# 318 dt 19.200000 rms 0.557 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.9060 tsec 22.6790 #GCMRL# 319 dt 19.200000 rms 0.557 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.2070 tsec 24.5310 #GCMRL# 320 dt 9.600000 rms 0.557 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.2570 tsec 26.4240 #GCMRL# 321 dt 1.200000 rms 0.557 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.7140 tsec 30.0600 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.556586) vs oldopt=(dt=0.5,rms=0.556587) #GCMRL# 322 dt 0.700000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 63.3900 tGradient 19.1430 tsec 89.0940 #GCMRL# 323 dt 0.350000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.1960 tsec 28.2180 #GCMRL# 324 dt 0.087500 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.4840 tsec 30.8800 #GCAMreg# pass 0 level1 3 level2 1 tsec 3969.75 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.557587 #FOTS# QuadFit found better minimum quadopt=(dt=56.5828,rms=0.55345) vs oldopt=(dt=32,rms=0.553854) #GCMRL# 326 dt 56.582781 rms 0.553 0.742% neg 0 invalid 762 tFOTS 67.4960 tGradient 17.6360 tsec 90.0650 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.552809) vs oldopt=(dt=8,rms=0.552932) #GCMRL# 327 dt 11.200000 rms 0.553 0.116% neg 0 invalid 762 tFOTS 73.6210 tGradient 19.4140 tsec 98.8220 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.552079) vs oldopt=(dt=32,rms=0.552132) #GCMRL# 328 dt 44.800000 rms 0.552 0.132% neg 0 invalid 762 tFOTS 88.0750 tGradient 20.0730 tsec 114.1560 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.551251) vs oldopt=(dt=32,rms=0.551272) #GCMRL# 329 dt 38.400000 rms 0.551 0.150% neg 0 invalid 762 tFOTS 82.0990 tGradient 22.3650 tsec 110.5980 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.551016) vs oldopt=(dt=8,rms=0.551061) #GCMRL# 330 dt 11.200000 rms 0.551 0.000% neg 0 invalid 762 tFOTS 75.1550 tGradient 18.7720 tsec 98.8900 #GCMRL# 331 dt 11.200000 rms 0.551 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.8770 tsec 32.1860 #GCMRL# 332 dt 11.200000 rms 0.551 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.3020 tsec 33.0840 #GCMRL# 333 dt 11.200000 rms 0.550 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.2640 tsec 25.7670 #GCMRL# 334 dt 11.200000 rms 0.550 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.4520 tsec 24.7660 #GCMRL# 335 dt 11.200000 rms 0.549 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.2770 tsec 29.7450 #GCMRL# 336 dt 11.200000 rms 0.549 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.8570 tsec 29.5280 #GCMRL# 337 dt 11.200000 rms 0.549 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.1390 tsec 29.5440 #GCMRL# 338 dt 11.200000 rms 0.548 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.5820 tsec 23.3220 #GCMRL# 339 dt 11.200000 rms 0.548 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3580 tsec 28.5610 #GCMRL# 340 dt 11.200000 rms 0.547 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6410 tsec 27.7200 #GCMRL# 341 dt 11.200000 rms 0.547 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.2690 tsec 27.4890 #GCMRL# 342 dt 11.200000 rms 0.546 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.6710 tsec 25.8380 #GCMRL# 343 dt 11.200000 rms 0.546 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.1270 tsec 25.4970 #GCMRL# 344 dt 11.200000 rms 0.545 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.1950 tsec 25.8290 #GCMRL# 345 dt 11.200000 rms 0.545 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.4040 tsec 25.9390 #GCMRL# 346 dt 11.200000 rms 0.545 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.0660 tsec 24.0900 #GCMRL# 347 dt 11.200000 rms 0.544 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.4940 tsec 24.5000 #GCMRL# 348 dt 11.200000 rms 0.544 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.5630 tsec 29.7640 #GCMRL# 349 dt 11.200000 rms 0.543 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.5640 tsec 25.4760 #GCMRL# 350 dt 11.200000 rms 0.543 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.8840 tsec 24.9120 #GCMRL# 351 dt 11.200000 rms 0.542 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.0110 tsec 32.2480 #GCMRL# 352 dt 11.200000 rms 0.542 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.0230 tsec 26.5270 #GCMRL# 353 dt 11.200000 rms 0.542 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.9340 tsec 29.0880 #GCMRL# 354 dt 11.200000 rms 0.541 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.0070 tsec 33.4400 #GCMRL# 355 dt 11.200000 rms 0.541 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.5330 tsec 32.8770 #GCMRL# 356 dt 11.200000 rms 0.541 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.4350 tsec 25.0700 #GCMRL# 357 dt 11.200000 rms 0.540 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.7080 tsec 24.9440 #GCMRL# 358 dt 11.200000 rms 0.540 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.1950 tsec 27.2210 #GCMRL# 359 dt 11.200000 rms 0.540 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.2130 tsec 24.8160 #GCMRL# 360 dt 11.200000 rms 0.539 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.2220 tsec 20.7360 #GCMRL# 361 dt 11.200000 rms 0.539 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.8680 tsec 23.1590 #GCMRL# 362 dt 11.200000 rms 0.539 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.0070 tsec 23.1120 #GCMRL# 363 dt 11.200000 rms 0.539 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3000 tsec 27.5850 #GCMRL# 364 dt 11.200000 rms 0.538 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.6990 tsec 25.2940 #GCMRL# 365 dt 11.200000 rms 0.538 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.9560 tsec 21.2520 #GCMRL# 366 dt 11.200000 rms 0.538 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.1680 tsec 23.6650 #GCMRL# 367 dt 11.200000 rms 0.538 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.9110 tsec 25.2170 #GCMRL# 368 dt 11.200000 rms 0.537 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.0770 tsec 24.0330 #GCMRL# 369 dt 11.200000 rms 0.537 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.9360 tsec 22.2390 #GCMRL# 370 dt 11.200000 rms 0.537 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.4910 tsec 21.1760 #GCMRL# 371 dt 11.200000 rms 0.537 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.9350 tsec 23.4070 #GCMRL# 372 dt 11.200000 rms 0.537 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.4030 tsec 22.7620 #GCMRL# 373 dt 11.200000 rms 0.536 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.8000 tsec 24.8040 #GCMRL# 374 dt 11.200000 rms 0.536 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.9220 tsec 26.9700 #GCMRL# 375 dt 11.200000 rms 0.536 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.3070 tsec 25.2330 #GCMRL# 376 dt 11.200000 rms 0.536 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.9200 tsec 25.4680 #GCMRL# 377 dt 11.200000 rms 0.536 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.7120 tsec 25.9960 #GCMRL# 378 dt 11.200000 rms 0.536 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.3240 tsec 25.4730 #GCMRL# 379 dt 11.200000 rms 0.535 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.3870 tsec 24.0180 #GCMRL# 380 dt 11.200000 rms 0.535 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.0110 tsec 22.7760 #GCMRL# 381 dt 11.200000 rms 0.535 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.1990 tsec 24.9270 #GCMRL# 382 dt 11.200000 rms 0.535 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.5130 tsec 26.1230 #GCMRL# 383 dt 11.200000 rms 0.535 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.6500 tsec 25.6060 #GCMRL# 384 dt 11.200000 rms 0.535 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.1950 tsec 24.4280 #GCMRL# 385 dt 11.200000 rms 0.534 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.4930 tsec 23.2480 #GCMRL# 386 dt 11.200000 rms 0.534 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1260 tsec 27.5130 #GCMRL# 387 dt 11.200000 rms 0.534 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.9980 tsec 28.0600 #GCMRL# 388 dt 11.200000 rms 0.534 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.0430 tsec 25.1370 #GCMRL# 389 dt 11.200000 rms 0.534 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.2130 tsec 24.3130 #GCMRL# 390 dt 11.200000 rms 0.534 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.8250 tsec 26.6080 #GCMRL# 391 dt 11.200000 rms 0.534 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.4180 tsec 24.9750 #GCMRL# 392 dt 11.200000 rms 0.534 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.5880 tsec 24.3580 #FOTS# QuadFit found better minimum quadopt=(dt=76.8,rms=0.533466) vs oldopt=(dt=128,rms=0.533478) #GCMRL# 393 dt 76.800000 rms 0.533 0.000% neg 0 invalid 762 tFOTS 68.4180 tGradient 19.5740 tsec 93.5030 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.564323 #GCMRL# 395 dt 0.000000 rms 0.563 0.169% neg 0 invalid 762 tFOTS 78.0240 tGradient 19.7510 tsec 105.1320 #GCMRL# 396 dt 0.150000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 92.2740 tGradient 17.9710 tsec 122.9050 #GCAMreg# pass 0 level1 2 level2 1 tsec 283.791 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.564323 #GCMRL# 398 dt 0.000000 rms 0.563 0.169% neg 0 invalid 762 tFOTS 82.1750 tGradient 21.7210 tsec 109.5330 #GCMRL# 399 dt 0.150000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 65.5810 tGradient 18.8690 tsec 93.9950 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.623015 #FOTS# QuadFit found better minimum quadopt=(dt=0.850794,rms=0.620011) vs oldopt=(dt=1.28,rms=0.620289) #GCMRL# 401 dt 0.850794 rms 0.620 0.482% neg 0 invalid 762 tFOTS 77.8460 tGradient 17.2490 tsec 100.4900 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.619967) vs oldopt=(dt=0.08,rms=0.619976) #GCMRL# 402 dt 0.112000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 74.8610 tGradient 19.8210 tsec 100.5880 #GCMRL# 403 dt 0.112000 rms 0.620 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.6830 tsec 23.2970 #GCAMreg# pass 0 level1 1 level2 1 tsec 274.93 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.620798 #GCMRL# 405 dt 0.320000 rms 0.620 0.163% neg 0 invalid 762 tFOTS 84.2240 tGradient 18.6830 tsec 114.5540 #FOTS# QuadFit found better minimum quadopt=(dt=0.048,rms=0.619772) vs oldopt=(dt=0.08,rms=0.619772) #GCMRL# 406 dt 0.048000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 85.2950 tGradient 23.0580 tsec 115.0120 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.538626 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.521641) vs oldopt=(dt=0.32,rms=0.526028) #GCMRL# 408 dt 0.448000 rms 0.522 3.153% neg 0 invalid 762 tFOTS 74.5920 tGradient 16.4250 tsec 96.5550 #GCMRL# 409 dt 0.320000 rms 0.519 0.500% neg 0 invalid 762 tFOTS 87.8240 tGradient 15.3920 tsec 108.8340 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.516828) vs oldopt=(dt=0.32,rms=0.517189) #GCMRL# 410 dt 0.384000 rms 0.517 0.425% neg 0 invalid 762 tFOTS 71.4220 tGradient 15.0500 tsec 91.8400 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.515466) vs oldopt=(dt=0.32,rms=0.515684) #GCMRL# 411 dt 0.384000 rms 0.515 0.264% neg 0 invalid 762 tFOTS 83.2010 tGradient 19.4870 tsec 110.8480 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.514442) vs oldopt=(dt=0.32,rms=0.514602) #GCMRL# 412 dt 0.384000 rms 0.514 0.199% neg 0 invalid 762 tFOTS 75.2630 tGradient 15.2920 tsec 96.5080 #FOTS# QuadFit found better minimum quadopt=(dt=0.395833,rms=0.513723) vs oldopt=(dt=0.32,rms=0.513848) #GCMRL# 413 dt 0.395833 rms 0.514 0.140% neg 0 invalid 762 tFOTS 73.9640 tGradient 15.2770 tsec 95.5620 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.513152) vs oldopt=(dt=0.32,rms=0.513241) #GCMRL# 414 dt 0.384000 rms 0.513 0.111% neg 0 invalid 762 tFOTS 101.6830 tGradient 16.3380 tsec 124.1630 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.5127) vs oldopt=(dt=0.32,rms=0.512757) #GCMRL# 415 dt 0.384000 rms 0.513 0.088% neg 0 invalid 762 tFOTS 106.5100 tGradient 18.3010 tsec 132.5870 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.512332) vs oldopt=(dt=0.32,rms=0.512386) #GCMRL# 416 dt 0.384000 rms 0.512 0.072% neg 0 invalid 762 tFOTS 104.6580 tGradient 19.0870 tsec 136.1700 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.512026) vs oldopt=(dt=0.32,rms=0.512057) #GCMRL# 417 dt 0.384000 rms 0.512 0.060% neg 0 invalid 762 tFOTS 125.4780 tGradient 20.6700 tsec 154.9140 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.511776) vs oldopt=(dt=0.32,rms=0.511811) #GCMRL# 418 dt 0.384000 rms 0.512 0.000% neg 0 invalid 762 tFOTS 124.8880 tGradient 24.4150 tsec 157.7930 #GCMRL# 419 dt 0.384000 rms 0.512 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.9170 tsec 36.0930 #GCMRL# 420 dt 0.384000 rms 0.511 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.5760 tsec 49.6710 #GCMRL# 421 dt 0.384000 rms 0.511 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.0060 tsec 36.0610 #GCMRL# 422 dt 0.384000 rms 0.511 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.0790 tsec 42.4690 #GCMRL# 423 dt 0.384000 rms 0.511 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3330 tsec 31.9190 #GCMRL# 424 dt 0.192000 rms 0.511 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.5440 tsec 36.3490 #GCMRL# 425 dt 0.192000 rms 0.510 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.5670 tsec 35.9810 #GCMRL# 426 dt 0.192000 rms 0.510 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.1670 tsec 35.9990 #GCMRL# 427 dt 0.192000 rms 0.510 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.1550 tsec 37.2350 #GCMRL# 428 dt 0.192000 rms 0.510 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.7740 tsec 33.8170 #GCMRL# 429 dt 0.192000 rms 0.510 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.9440 tsec 39.7860 #GCMRL# 430 dt 0.192000 rms 0.510 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.0560 tsec 42.7720 #GCMRL# 431 dt 0.192000 rms 0.510 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.7890 tsec 37.8160 #GCMRL# 432 dt 0.192000 rms 0.510 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.1670 tsec 41.6930 #GCMRL# 433 dt 0.192000 rms 0.510 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3500 tsec 32.7320 #GCMRL# 434 dt 0.192000 rms 0.509 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.2990 tsec 36.8590 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.509489) vs oldopt=(dt=0.08,rms=0.50949) #GCMRL# 435 dt 0.112000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 111.7860 tGradient 26.2850 tsec 146.3150 #GCMRL# 436 dt 0.112000 rms 0.509 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1230 tsec 34.9810 #GCMRL# 437 dt 0.112000 rms 0.509 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.8770 tsec 31.2720 #GCMRL# 438 dt 0.112000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.4630 tsec 29.1630 #GCMRL# 439 dt 0.112000 rms 0.509 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.8810 tsec 40.5830 #GCAMreg# pass 0 level1 0 level2 1 tsec 2263.44 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.510508 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.508267) vs oldopt=(dt=0.08,rms=0.508608) #GCMRL# 441 dt 0.112000 rms 0.508 0.439% neg 0 invalid 762 tFOTS 111.7080 tGradient 21.9250 tsec 143.9140 #FOTS# QuadFit found better minimum quadopt=(dt=0.177083,rms=0.506797) vs oldopt=(dt=0.08,rms=0.507584) #GCMRL# 442 dt 0.177083 rms 0.507 0.289% neg 0 invalid 762 tFOTS 96.0120 tGradient 25.5260 tsec 130.5910 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.506224) vs oldopt=(dt=0.08,rms=0.506389) #GCMRL# 443 dt 0.112000 rms 0.506 0.113% neg 0 invalid 762 tFOTS 99.9730 tGradient 20.6330 tsec 128.9010 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505762) vs oldopt=(dt=0.08,rms=0.50589) #GCMRL# 444 dt 0.112000 rms 0.506 0.091% neg 0 invalid 762 tFOTS 95.5940 tGradient 21.3040 tsec 124.2370 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505406) vs oldopt=(dt=0.08,rms=0.505506) #GCMRL# 445 dt 0.112000 rms 0.505 0.070% neg 0 invalid 762 tFOTS 104.5860 tGradient 22.5900 tsec 136.8300 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505143) vs oldopt=(dt=0.08,rms=0.50522) #GCMRL# 446 dt 0.112000 rms 0.505 0.052% neg 0 invalid 762 tFOTS 95.5720 tGradient 22.0700 tsec 126.9190 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.504924) vs oldopt=(dt=0.08,rms=0.504985) #GCMRL# 447 dt 0.112000 rms 0.505 0.000% neg 0 invalid 762 tFOTS 109.5690 tGradient 22.6830 tsec 140.3910 #GCMRL# 448 dt 0.112000 rms 0.505 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1550 tsec 31.1270 #GCMRL# 449 dt 0.112000 rms 0.504 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5460 tsec 31.5540 #GCMRL# 450 dt 0.112000 rms 0.504 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2950 tsec 30.5520 #GCMRL# 451 dt 0.112000 rms 0.504 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.1190 tsec 28.1760 #GCMRL# 452 dt 0.112000 rms 0.504 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.8050 tsec 29.6590 #GCMRL# 453 dt 0.112000 rms 0.504 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.4290 tsec 29.7840 #GCMRL# 454 dt 0.112000 rms 0.504 -0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.6020 tsec 40.9170 GCAMregister done in 429.785 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.502289 #GCMRL# 456 dt 0.000000 rms 0.501 0.212% neg 0 invalid 762 tFOTS 125.1130 tGradient 51.7280 tsec 186.1740 #GCAMreg# pass 0 level1 5 level2 1 tsec 426.976 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.502289 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.500834) vs oldopt=(dt=92.48,rms=0.500897) #GCMRL# 458 dt 129.472000 rms 0.501 0.290% neg 0 invalid 762 tFOTS 136.5530 tGradient 58.8870 tsec 204.7700 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.500631) vs oldopt=(dt=92.48,rms=0.500667) #GCMRL# 459 dt 129.472000 rms 0.501 0.000% neg 0 invalid 762 tFOTS 135.9930 tGradient 55.5230 tsec 200.4950 #GCMRL# 460 dt 129.472000 rms 0.501 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.8180 tsec 64.4230 #GCMRL# 461 dt 129.472000 rms 0.500 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 57.3840 tsec 65.1940 #GCMRL# 462 dt 129.472000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.8270 tsec 64.1770 #GCMRL# 463 dt 129.472000 rms 0.500 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.0420 tsec 64.2480 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.500115) vs oldopt=(dt=23.12,rms=0.500116) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.5012 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.500138) vs oldopt=(dt=1.62,rms=0.500139) #GCMRL# 465 dt 2.268000 rms 0.500 0.212% neg 0 invalid 762 tFOTS 144.2560 tGradient 41.9770 tsec 193.8130 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.500136) vs oldopt=(dt=1.62,rms=0.500136) #GCMRL# 466 dt 2.268000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 136.6990 tGradient 33.2120 tsec 180.2010 #GCMRL# 467 dt 2.268000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 39.8710 tsec 48.1950 #GCAMreg# pass 0 level1 4 level2 1 tsec 504.668 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.501191 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.498188) vs oldopt=(dt=103.68,rms=0.498518) #GCMRL# 469 dt 145.152000 rms 0.498 0.599% neg 0 invalid 762 tFOTS 131.4100 tGradient 35.2020 tsec 175.0280 #GCMRL# 470 dt 25.920000 rms 0.498 0.000% neg 0 invalid 762 tFOTS 163.2250 tGradient 39.8210 tsec 216.7720 #GCMRL# 471 dt 25.920000 rms 0.498 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 50.8450 tsec 60.9490 #GCMRL# 472 dt 25.920000 rms 0.498 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.9290 tsec 50.3380 #GCMRL# 473 dt 25.920000 rms 0.497 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 38.0580 tsec 46.3500 #GCMRL# 474 dt 25.920000 rms 0.497 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.0610 tsec 44.1840 #GCMRL# 475 dt 25.920000 rms 0.496 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.6840 tsec 44.6530 #GCMRL# 476 dt 25.920000 rms 0.496 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 40.9430 tsec 50.2450 #GCMRL# 477 dt 25.920000 rms 0.496 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 41.7680 tsec 54.6590 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.495277) vs oldopt=(dt=414.72,rms=0.495335) setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.496637 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.49411) vs oldopt=(dt=32,rms=0.494205) #GCMRL# 479 dt 25.600000 rms 0.494 0.509% neg 0 invalid 762 tFOTS 132.0350 tGradient 36.1420 tsec 176.9880 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49218) vs oldopt=(dt=32,rms=0.492438) #GCMRL# 480 dt 44.800000 rms 0.492 0.391% neg 0 invalid 762 tFOTS 123.1540 tGradient 30.4030 tsec 161.6510 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.49171) vs oldopt=(dt=8,rms=0.49179) #GCMRL# 481 dt 11.200000 rms 0.492 0.000% neg 0 invalid 762 tFOTS 107.5380 tGradient 25.1550 tsec 141.7660 #GCMRL# 482 dt 11.200000 rms 0.491 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.1340 tsec 32.0210 #GCMRL# 483 dt 11.200000 rms 0.491 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.8690 tsec 31.1620 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 484 dt 11.200000 rms 0.490 0.156% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.3040 tsec 39.6620 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 485 dt 11.200000 rms 0.489 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5830 tsec 45.6310 #GCMRL# 486 dt 11.200000 rms 0.489 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.5040 tsec 30.7300 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 487 dt 11.200000 rms 0.488 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7900 tsec 53.6780 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 488 dt 11.200000 rms 0.488 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.9960 tsec 45.9320 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 489 dt 11.200000 rms 0.487 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.3100 tsec 50.3340 #GCMRL# 490 dt 128.000000 rms 0.486 0.247% neg 0 invalid 762 tFOTS 90.6630 tGradient 19.7170 tsec 117.0160 #FOTS# QuadFit found better minimum quadopt=(dt=23.6883,rms=0.485417) vs oldopt=(dt=32,rms=0.485554) #GCMRL# 491 dt 23.688312 rms 0.485 0.000% neg 0 invalid 762 tFOTS 96.3280 tGradient 21.8170 tsec 122.8100 #GCMRL# 492 dt 23.688312 rms 0.485 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.6600 tsec 22.3610 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 493 dt 23.688312 rms 0.485 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.9440 tsec 25.3030 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 1167.84 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.485738 #FOTS# QuadFit found better minimum quadopt=(dt=44.2483,rms=0.480719) vs oldopt=(dt=32,rms=0.48093) #GCMRL# 495 dt 44.248276 rms 0.481 1.033% neg 0 invalid 762 tFOTS 101.6760 tGradient 19.6050 tsec 127.4850 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.479586) vs oldopt=(dt=8,rms=0.479781) #GCMRL# 496 dt 11.200000 rms 0.480 0.000% neg 0 invalid 762 tFOTS 89.5540 tGradient 20.5040 tsec 116.5360 #GCMRL# 497 dt 11.200000 rms 0.479 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.8050 tsec 27.4010 #GCMRL# 498 dt 11.200000 rms 0.479 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.8320 tsec 28.1760 #GCMRL# 499 dt 11.200000 rms 0.478 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.1600 tsec 30.9480 #GCMRL# 500 dt 11.200000 rms 0.477 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1550 tsec 30.0200 #GCMRL# 501 dt 11.200000 rms 0.476 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.1060 tsec 32.2780 #GCMRL# 502 dt 11.200000 rms 0.476 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.7980 tsec 29.8720 #GCMRL# 503 dt 11.200000 rms 0.475 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.4400 tsec 29.4290 #GCMRL# 504 dt 11.200000 rms 0.475 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.2700 tsec 27.3010 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.474794) vs oldopt=(dt=32,rms=0.474809) #GCMRL# 505 dt 25.600000 rms 0.475 0.000% neg 0 invalid 762 tFOTS 106.0240 tGradient 23.1690 tsec 136.3520 #GCMRL# 506 dt 25.600000 rms 0.475 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.1480 tsec 27.5610 #GCMRL# 507 dt 25.600000 rms 0.474 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.0290 tsec 31.3780 #GCMRL# 508 dt 25.600000 rms 0.474 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.3510 tsec 41.6600 #GCMRL# 509 dt 25.600000 rms 0.474 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.3130 tsec 31.3170 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.478517 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.47742) vs oldopt=(dt=0.72,rms=0.477423) #GCMRL# 511 dt 1.008000 rms 0.477 0.229% neg 0 invalid 762 tFOTS 106.3750 tGradient 22.0890 tsec 134.1910 #FOTS# QuadFit found better minimum quadopt=(dt=0.864,rms=0.477412) vs oldopt=(dt=0.72,rms=0.477412) #GCMRL# 512 dt 0.864000 rms 0.477 0.000% neg 0 invalid 762 tFOTS 120.3460 tGradient 22.4400 tsec 150.8460 #GCMRL# 513 dt 0.864000 rms 0.477 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.9170 tsec 28.8160 #GCAMreg# pass 0 level1 2 level2 1 tsec 377.126 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.478505 #FOTS# QuadFit found better minimum quadopt=(dt=8.44444,rms=0.476945) vs oldopt=(dt=2.88,rms=0.477088) #GCMRL# 515 dt 8.444444 rms 0.477 0.326% neg 0 invalid 762 tFOTS 121.3470 tGradient 22.6870 tsec 151.6950 #FOTS# QuadFit found better minimum quadopt=(dt=21.8182,rms=0.475445) vs oldopt=(dt=11.52,rms=0.475763) iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 516 dt 21.818182 rms 0.476 0.288% neg 0 invalid 762 tFOTS 116.2680 tGradient 25.7990 tsec 191.6160 #FOTS# QuadFit found better minimum quadopt=(dt=15.3287,rms=0.473825) vs oldopt=(dt=11.52,rms=0.473933) iter 0, gcam->neg = 130 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 517 dt 15.328671 rms 0.474 0.307% neg 0 invalid 762 tFOTS 107.8050 tGradient 21.9640 tsec 195.5680 #FOTS# QuadFit found better minimum quadopt=(dt=11.0983,rms=0.472941) vs oldopt=(dt=11.52,rms=0.472943) iter 0, gcam->neg = 18 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 518 dt 11.098266 rms 0.473 0.000% neg 0 invalid 762 tFOTS 118.8690 tGradient 25.9800 tsec 202.1460 iter 0, gcam->neg = 16 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 519 dt 11.098266 rms 0.472 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.7850 tsec 88.7950 iter 0, gcam->neg = 41 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 520 dt 11.098266 rms 0.471 0.285% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.8170 tsec 80.6510 iter 0, gcam->neg = 53 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 521 dt 11.098266 rms 0.469 0.314% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.1390 tsec 99.9310 iter 0, gcam->neg = 76 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 522 dt 11.098266 rms 0.468 0.373% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.7120 tsec 102.7910 iter 0, gcam->neg = 138 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 523 dt 11.098266 rms 0.466 0.269% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.0520 tsec 100.0880 iter 0, gcam->neg = 157 after 23 iterations, nbhd size=1, neg = 0 #GCMRL# 524 dt 11.098266 rms 0.466 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.8250 tsec 128.3080 iter 0, gcam->neg = 85 after 21 iterations, nbhd size=1, neg = 0 #GCMRL# 525 dt 11.098266 rms 0.465 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 25.5140 tsec 100.2270 iter 0, gcam->neg = 125 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 526 dt 11.098266 rms 0.464 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.5240 tsec 79.9400 iter 0, gcam->neg = 113 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 527 dt 11.098266 rms 0.464 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.3650 tsec 100.8360 #FOTS# QuadFit found better minimum quadopt=(dt=8.26144,rms=0.463143) vs oldopt=(dt=11.52,rms=0.46324) iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 528 dt 8.261438 rms 0.463 0.133% neg 0 invalid 762 tFOTS 107.4860 tGradient 22.9890 tsec 180.6860 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.463098) vs oldopt=(dt=2.88,rms=0.463104) iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 529 dt 4.032000 rms 0.463 0.000% neg 0 invalid 762 tFOTS 104.3180 tGradient 21.8570 tsec 144.4940 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 530 dt 4.032000 rms 0.463 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 26.2460 tsec 54.3680 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=0, neg = 0 #GCMRL# 531 dt 4.032000 rms 0.463 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.3050 tsec 69.9130 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.469979 #GCMRL# 533 dt 0.000000 rms 0.469 0.240% neg 0 invalid 762 tFOTS 104.5740 tGradient 17.5570 tsec 128.5890 #GCAMreg# pass 0 level1 1 level2 1 tsec 293.324 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.469979 #GCMRL# 535 dt 0.000000 rms 0.469 0.240% neg 0 invalid 762 tFOTS 99.2460 tGradient 21.0830 tsec 124.4910 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.460177 #FOTS# QuadFit found better minimum quadopt=(dt=1.7452,rms=0.43232) vs oldopt=(dt=1.28,rms=0.434429) iter 0, gcam->neg = 1479 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 537 dt 1.745196 rms 0.434 5.614% neg 0 invalid 762 tFOTS 108.3910 tGradient 16.8930 tsec 192.0860 #GCMRL# 538 dt 0.000013 rms 0.434 0.000% neg 0 invalid 762 tFOTS 123.5560 tGradient 16.1100 tsec 146.6130 #GCAMreg# pass 0 level1 0 level2 1 tsec 384.729 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.435572 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.434228) vs oldopt=(dt=0.02,rms=0.434236) #GCMRL# 540 dt 0.028000 rms 0.434 0.309% neg 0 invalid 762 tFOTS 84.7370 tGradient 14.3380 tsec 104.4740 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.434227) vs oldopt=(dt=0.005,rms=0.434227) #GCMRL# 541 dt 0.007000 rms 0.434 0.000% neg 0 invalid 762 tFOTS 90.6200 tGradient 14.2530 tsec 110.8060 label assignment complete, 0 changed (0.00%) GCAMregister done in 141.195 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.422819 #GCAMreg# pass 0 level1 5 level2 1 tsec 151.841 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.422819 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.422814) vs oldopt=(dt=5.78,rms=0.422815) #GCMRL# 544 dt 8.092000 rms 0.423 0.001% neg 0 invalid 762 tFOTS 90.6870 tGradient 32.4610 tsec 128.0100 #FOTS# QuadFit found better minimum quadopt=(dt=4.624,rms=0.422814) vs oldopt=(dt=5.78,rms=0.422814) #GCMRL# 545 dt 4.624000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 95.6960 tGradient 32.8800 tsec 134.8580 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.422963 #GCAMreg# pass 0 level1 4 level2 1 tsec 131.635 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.422963 #GCMRL# 548 dt 25.920000 rms 0.423 0.016% neg 0 invalid 762 tFOTS 87.0120 tGradient 18.7460 tsec 111.6120 #GCMRL# 549 dt 25.920000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 87.8420 tGradient 21.6240 tsec 116.8260 #GCMRL# 550 dt 25.920000 rms 0.423 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 24.1150 tsec 30.1540 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.42343 #GCMRL# 552 dt 8.000000 rms 0.423 0.044% neg 0 invalid 762 tFOTS 97.3940 tGradient 18.9390 tsec 121.1450 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.423222) vs oldopt=(dt=2,rms=0.423226) #GCMRL# 553 dt 2.800000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 90.9900 tGradient 18.6630 tsec 115.8170 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 554 dt 2.800000 rms 0.423 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.8070 tsec 28.8900 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 329.594 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.423218 #FOTS# QuadFit found better minimum quadopt=(dt=65.1852,rms=0.421087) vs oldopt=(dt=32,rms=0.421436) iter 0, gcam->neg = 34 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 556 dt 65.185185 rms 0.421 0.466% neg 0 invalid 762 tFOTS 98.3610 tGradient 19.9400 tsec 162.4260 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.42064) vs oldopt=(dt=8,rms=0.420762) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 557 dt 11.200000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 90.4940 tGradient 17.9480 tsec 128.8950 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 558 dt 11.200000 rms 0.420 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.1650 tsec 35.9200 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 559 dt 11.200000 rms 0.420 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 19.7650 tsec 40.6410 iter 0, gcam->neg = 18 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 560 dt 11.200000 rms 0.420 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.6530 tsec 42.5650 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.419479) vs oldopt=(dt=32,rms=0.419552) iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 561 dt 44.800000 rms 0.419 0.143% neg 0 invalid 762 tFOTS 100.0870 tGradient 22.4990 tsec 138.5190 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.419289) vs oldopt=(dt=32,rms=0.419343) iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.421623 #FOTS# QuadFit found better minimum quadopt=(dt=8.47059,rms=0.420838) vs oldopt=(dt=11.52,rms=0.420927) iter 0, gcam->neg = 25 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 563 dt 8.470588 rms 0.421 0.098% neg 0 invalid 762 tFOTS 77.7820 tGradient 14.5100 tsec 144.3540 #FOTS# QuadFit found better minimum quadopt=(dt=9.62963,rms=0.420905) vs oldopt=(dt=11.52,rms=0.420919) iter 0, gcam->neg = 35 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 564 dt 9.629630 rms 0.421 0.000% neg 0 invalid 762 tFOTS 85.0790 tGradient 13.8450 tsec 144.4000 iter 0, gcam->neg = 31 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 565 dt 9.629630 rms 0.421 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.4980 tsec 77.5610 iter 0, gcam->neg = 55 after 19 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 488.877 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.421004 #FOTS# QuadFit found better minimum quadopt=(dt=16.6667,rms=0.41788) vs oldopt=(dt=11.52,rms=0.418174) iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 567 dt 16.666667 rms 0.418 0.664% neg 0 invalid 762 tFOTS 93.1370 tGradient 18.9680 tsec 173.9000 #FOTS# QuadFit found better minimum quadopt=(dt=12.2051,rms=0.417036) vs oldopt=(dt=11.52,rms=0.417039) iter 0, gcam->neg = 47 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 568 dt 12.205128 rms 0.417 0.000% neg 0 invalid 762 tFOTS 101.6780 tGradient 16.1430 tsec 183.1930 iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 569 dt 12.205128 rms 0.417 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.6220 tsec 82.9940 iter 0, gcam->neg = 75 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 570 dt 12.205128 rms 0.416 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 18.4460 tsec 53.9480 iter 0, gcam->neg = 88 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 571 dt 12.205128 rms 0.415 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.1240 tsec 93.3390 iter 0, gcam->neg = 85 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 572 dt 12.205128 rms 0.415 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.7650 tsec 97.5870 #FOTS# QuadFit found better minimum quadopt=(dt=9.43284,rms=0.414861) vs oldopt=(dt=11.52,rms=0.414875) iter 0, gcam->neg = 30 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 573 dt 9.432836 rms 0.415 0.000% neg 0 invalid 762 tFOTS 121.0420 tGradient 17.0880 tsec 236.6650 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 574 dt 9.432836 rms 0.415 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 20.2710 tsec 55.3170 iter 0, gcam->neg = 17 after 16 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.420351 #FOTS# QuadFit found better minimum quadopt=(dt=6e-05,rms=0.420351) vs oldopt=(dt=5e-05,rms=0.420351) #GCMRL# 576 dt 0.000060 rms 0.420 0.000% neg 0 invalid 762 tFOTS 148.6440 tGradient 17.8800 tsec 175.5910 #GCAMreg# pass 0 level1 1 level2 1 tsec 342.296 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.420351 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.410936 #FOTS# QuadFit found better minimum quadopt=(dt=0.815789,rms=0.403298) vs oldopt=(dt=1.28,rms=0.406458) iter 0, gcam->neg = 715 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 579 dt 0.815789 rms 0.406 1.277% neg 0 invalid 762 tFOTS 111.1990 tGradient 14.9050 tsec 222.1060 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.405599) vs oldopt=(dt=0.08,rms=0.405599) #GCMRL# 580 dt 0.064000 rms 0.406 0.000% neg 0 invalid 762 tFOTS 117.3910 tGradient 14.2490 tsec 139.2450 #GCMRL# 581 dt 0.064000 rms 0.406 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.7460 tsec 23.6300 #GCAMreg# pass 0 level1 0 level2 1 tsec 439.818 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.405564 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.403535) vs oldopt=(dt=0.32,rms=0.403796) iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 583 dt 0.448000 rms 0.404 0.500% neg 0 invalid 762 tFOTS 120.3170 tGradient 15.0390 tsec 151.0590 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.402674) vs oldopt=(dt=0.32,rms=0.402728) iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 584 dt 0.448000 rms 0.403 0.000% neg 0 invalid 762 tFOTS 109.2260 tGradient 14.2810 tsec 181.2530 iter 0, gcam->neg = 28 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 585 dt 0.448000 rms 0.402 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 17.3680 tsec 73.7550 iter 0, gcam->neg = 63 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 586 dt 0.448000 rms 0.402 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1200 tsec 78.1120 iter 0, gcam->neg = 99 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 587 dt 0.448000 rms 0.402 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.6570 tsec 56.5560 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 588 dt 0.320000 rms 0.401 0.157% neg 0 invalid 762 tFOTS 109.5330 tGradient 12.4310 tsec 167.5470 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 GCAMregister done in 89.6803 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4656 tmin = 132.114 Calls to gcamLabelEnergy 4069 tmin = 9.40533 Calls to gcamJacobianEnergy 4656 tmin = 103.466 Calls to gcamSmoothnessEnergy 4656 tmin = 81.3001 Calls to gcamLogLikelihoodTerm 590 tmin = 33.6955 Calls to gcamLabelTerm 543 tmin = 35.537 Calls to gcamJacobianTerm 590 tmin = 64.7917 Calls to gcamSmoothnessTerm 590 tmin = 20.1353 Calls to gcamComputeGradient 590 tmin = 273.478 Calls to gcamComputeMetricProperties 6842 tmin = 110.297 mri_ca_register took 13 hours, 37 minutes and 29 seconds. #VMPC# mri_ca_register VmPeak 2076540 FSRUNTIME@ mri_ca_register 13.6247 hours 1 threads @#@FSTIME 2020:07:14:14:46:44 mri_ca_register N 9 e 49049.34 S 76.32 U 12610.53 P 25% M 1325332 F 22 R 439278 W 0 c 6382497 w 753 I 4496 O 0 L 13.28 13.41 13.31 @#@FSLOADPOST 2020:07:15:04:24:14 mri_ca_register N 9 16.85 16.97 16.53 #-------------------------------------- #@# SubCort Seg Wed Jul 15 04:24:14 EDT 2020 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname loginnode2 machine x86_64 user pankumar Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname loginnode2 machine x86_64 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz 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 == Number of threads available to for OpenMP = 1 == reading 1 input volumes reading classifier array from /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.06 Atlas used for the 3D morph was /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.08824 (13) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (130 voxels, overlap=0.461) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (130 voxels, peak = 12), gca=12.3 gca peak = 0.20380 (13) mri peak = 0.06250 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.67 x + 0.0 (143 voxels, overlap=0.597) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (143 voxels, peak = 22), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.09236 (95) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (535 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (535 voxels, peak = 95), gca=94.6 gca peak = 0.15814 (97) mri peak = 0.07971 (99) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (550 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (550 voxels, peak = 103), gca=103.3 gca peak = 0.27624 (56) mri peak = 0.09660 (58) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (699 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (699 voxels, peak = 55), gca=55.2 gca peak = 0.28723 (59) mri peak = 0.09704 (57) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (717 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (717 voxels, peak = 58), gca=58.1 gca peak = 0.07623 (103) mri peak = 0.07976 (109) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (23014 voxels, overlap=0.569) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (23014 voxels, peak = 110), gca=109.7 gca peak = 0.07837 (105) mri peak = 0.08482 (111) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (26382 voxels, overlap=0.474) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (26382 voxels, peak = 112), gca=111.8 gca peak = 0.10165 (58) mri peak = 0.04337 (53) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (21952 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (21952 voxels, peak = 53), gca=53.1 gca peak = 0.11113 (58) mri peak = 0.04690 (51) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (21548 voxels, overlap=0.903) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (21548 voxels, peak = 53), gca=53.1 gca peak = 0.27796 (67) mri peak = 0.11552 (78) Right_Caudate (50): linear fit = 1.12 x + 0.0 (831 voxels, overlap=0.429) Right_Caudate (50): linear fit = 1.12 x + 0.0 (831 voxels, peak = 75), gca=75.4 gca peak = 0.14473 (69) mri peak = 0.12928 (78) Left_Caudate (11): linear fit = 1.07 x + 0.0 (772 voxels, overlap=0.625) Left_Caudate (11): linear fit = 1.07 x + 0.0 (772 voxels, peak = 73), gca=73.5 gca peak = 0.14301 (56) mri peak = 0.04642 (53) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (28473 voxels, overlap=0.984) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (28473 voxels, peak = 53), gca=52.9 gca peak = 0.14610 (55) mri peak = 0.04243 (51) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (27216 voxels, overlap=0.902) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (27216 voxels, peak = 52), gca=52.0 gca peak = 0.16309 (85) mri peak = 0.10011 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5967 voxels, overlap=0.880) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5967 voxels, peak = 87), gca=87.1 gca peak = 0.15172 (84) mri peak = 0.09966 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5693 voxels, overlap=0.876) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5693 voxels, peak = 87), gca=86.9 gca peak = 0.30461 (58) mri peak = 0.17597 (51) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (498 voxels, overlap=0.546) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (498 voxels, peak = 51), gca=50.8 gca peak = 0.32293 (57) mri peak = 0.11029 (50) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (486 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (486 voxels, peak = 55), gca=55.0 gca peak = 0.11083 (90) mri peak = 0.06853 (89) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3692 voxels, overlap=0.995) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3692 voxels, peak = 88), gca=87.8 gca peak = 0.11393 (83) mri peak = 0.06793 (90) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3349 voxels, overlap=0.979) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3349 voxels, peak = 86), gca=85.9 gca peak = 0.08575 (81) mri peak = 0.08485 (80) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1816 voxels, overlap=0.880) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1816 voxels, peak = 82), gca=82.2 gca peak = 0.08618 (78) mri peak = 0.08421 (81) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1709 voxels, overlap=0.865) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1709 voxels, peak = 80), gca=79.9 gca peak = 0.08005 (78) mri peak = 0.09874 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11215 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11215 voxels, peak = 82), gca=82.3 gca peak = 0.12854 (88) mri peak = 0.05677 (86) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1128 voxels, overlap=0.809) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1128 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.05943 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1283 voxels, overlap=0.898) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1283 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.09795 (15) gca peak = 0.17113 (14) mri peak = 0.14773 ( 8) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, overlap=0.489) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, peak = 7), gca=6.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 1.06 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.22482 (13) mri peak = 0.08824 (13) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (130 voxels, overlap=0.673) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (130 voxels, peak = 14), gca=14.5 gca peak = 0.16078 (19) mri peak = 0.06250 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (143 voxels, overlap=0.355) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (143 voxels, peak = 20), gca=20.4 gca peak = 0.21116 (94) mri peak = 0.09236 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (535 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (535 voxels, peak = 95), gca=95.4 gca peak = 0.16875 (102) mri peak = 0.07971 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (550 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (550 voxels, peak = 103), gca=102.5 gca peak = 0.30937 (55) mri peak = 0.09660 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (699 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (699 voxels, peak = 55), gca=55.0 gca peak = 0.28941 (58) mri peak = 0.09704 (57) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (717 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (717 voxels, peak = 58), gca=58.0 gca peak = 0.07344 (110) mri peak = 0.07976 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (23014 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (23014 voxels, peak = 110), gca=110.0 gca peak = 0.07460 (112) mri peak = 0.08482 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26382 voxels, overlap=0.762) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26382 voxels, peak = 112), gca=112.0 gca peak = 0.10919 (53) mri peak = 0.04337 (53) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (21952 voxels, overlap=1.000) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (21952 voxels, peak = 55), gca=55.4 gca peak = 0.12331 (53) mri peak = 0.04690 (51) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (21548 voxels, overlap=0.990) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (21548 voxels, peak = 52), gca=52.2 gca peak = 0.22309 (75) mri peak = 0.11552 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (831 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (831 voxels, peak = 75), gca=75.0 gca peak = 0.12384 (73) mri peak = 0.12928 (78) Left_Caudate (11): linear fit = 1.01 x + 0.0 (772 voxels, overlap=0.956) Left_Caudate (11): linear fit = 1.01 x + 0.0 (772 voxels, peak = 74), gca=74.1 gca peak = 0.14626 (52) mri peak = 0.04642 (53) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28473 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28473 voxels, peak = 52), gca=52.0 gca peak = 0.15405 (52) mri peak = 0.04243 (51) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27216 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27216 voxels, peak = 51), gca=51.2 gca peak = 0.15741 (87) mri peak = 0.10011 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5967 voxels, overlap=0.950) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5967 voxels, peak = 87), gca=87.0 gca peak = 0.14534 (87) mri peak = 0.09966 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5693 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5693 voxels, peak = 87), gca=86.6 gca peak = 0.26052 (51) mri peak = 0.17597 (51) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (498 voxels, overlap=0.960) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (498 voxels, peak = 51), gca=51.0 gca peak = 0.35771 (55) mri peak = 0.11029 (50) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (486 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (486 voxels, peak = 55), gca=55.0 gca peak = 0.11203 (86) mri peak = 0.06853 (89) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3692 voxels, overlap=0.991) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3692 voxels, peak = 86), gca=85.6 gca peak = 0.11103 (86) mri peak = 0.06793 (90) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3349 voxels, overlap=0.994) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3349 voxels, peak = 86), gca=85.6 gca peak = 0.08210 (82) mri peak = 0.08485 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1816 voxels, overlap=0.900) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1816 voxels, peak = 82), gca=82.0 gca peak = 0.08445 (82) mri peak = 0.08421 (81) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1709 voxels, overlap=0.918) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1709 voxels, peak = 82), gca=82.0 gca peak = 0.08443 (83) mri peak = 0.09874 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11215 voxels, overlap=0.678) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11215 voxels, peak = 83), gca=82.6 gca peak = 0.11072 (97) mri peak = 0.05677 (86) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1128 voxels, overlap=0.936) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1128 voxels, peak = 97), gca=97.5 gca peak = 0.14298 (96) mri peak = 0.05943 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1283 voxels, overlap=0.928) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1283 voxels, peak = 96), gca=96.5 gca peak = 0.20054 (28) mri peak = 0.09795 (15) gca peak = 0.16806 (17) mri peak = 0.14773 ( 8) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, overlap=0.315) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, peak = 8), gca=7.9 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19362 (27) gca peak Third_Ventricle = 0.20054 (28) gca peak Fourth_Ventricle = 0.16806 (17) gca peak CSF = 0.20346 (38) gca peak Left_Accumbens_area = 0.65277 (66) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.85300 (53) gca peak Left_choroid_plexus = 0.11687 (35) gca peak Right_Inf_Lat_Vent = 0.25588 (23) gca peak Right_Accumbens_area = 0.29156 (73) gca peak Right_vessel = 0.77367 (52) gca peak Right_choroid_plexus = 0.13288 (38) gca peak Fifth_Ventricle = 0.60973 (35) gca peak WM_hypointensities = 0.10282 (82) gca peak non_WM_hypointensities = 0.13942 (43) gca peak Optic_Chiasm = 0.60484 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 51140 voxels changed in iteration 0 of unlikely voxel relabeling 189 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 24401 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 324 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 59768 changed. image ll: -2.087, PF=0.500 pass 2: 16880 changed. image ll: -2.086, PF=0.500 pass 3: 5473 changed. pass 4: 2005 changed. 30539 voxels changed in iteration 0 of unlikely voxel relabeling 123 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4831 voxels changed in iteration 0 of unlikely voxel relabeling 84 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 4989 voxels changed in iteration 0 of unlikely voxel relabeling 67 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4003 voxels changed in iteration 0 of unlikely voxel relabeling 11 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 2 with volume 5926 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 264 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 6676 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 7 with volume 131 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3295.253045 mri_ca_label stimesec 17.734303 mri_ca_label ru_maxrss 2160888 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 443847 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 196 mri_ca_label ru_nivcsw 1633281 auto-labeling took 203 minutes and 15 seconds. @#@FSTIME 2020:07:15:04:24:31 mri_ca_label N 10 e 12195.73 S 17.77 U 3295.25 P 27% M 2160888 F 0 R 443897 W 0 c 1633294 w 203 I 0 O 0 L 16.59 16.91 16.52 @#@FSLOADPOST 2020:07:15:07:47:46 mri_ca_label N 10 15.54 15.30 15.25 #-------------------------------------- #@# CC Seg Wed Jul 15 07:47:47 EDT 2020 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/cc_up.lta 2012-646-010-KK will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/cc_up.lta reading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.auto_noCCseg.mgz reading norm from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/norm.mgz 9626 voxels in left wm, 39757 in right wm, xrange [123, 130] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 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 128.0, rotations (-0.50, -0.20) final transformation (x=128.0, yr=-0.503, zr=-0.200): 0.99996 0.00349 -0.00878 0.58606; -0.00349 0.99999 0.00003 15.44415; 0.00878 0.00000 0.99996 15.88011; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 113 111 eigenvectors: 0.01165 0.00725 0.99991; 0.05494 -0.99847 0.00660; 0.99842 0.05486 -0.01203; error in mid anterior detected - correcting... writing aseg with callosum to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.auto.mgz... corpus callosum segmentation took 3.6 minutes @#@FSTIME 2020:07:15:07:47:47 mri_cc N 7 e 213.45 S 0.78 U 49.63 P 23% M 418404 F 4 R 14653 W 0 c 33733 w 80 I 832 O 0 L 15.54 15.30 15.25 @#@FSLOADPOST 2020:07:15:07:51:20 mri_cc N 7 15.84 15.91 15.53 #-------------------------------------- #@# Merge ASeg Wed Jul 15 07:51:20 EDT 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Jul 15 07:51:21 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 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 mri_src from norm.mgz... MRImask(): AllowDiffGeom = 1 Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 840 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 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 61 (61), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 14 minutes and 22 seconds. @#@FSTIME 2020:07:15:07:51:21 mri_normalize N 9 e 877.74 S 2.50 U 219.12 P 25% M 1258244 F 0 R 221220 W 0 c 102206 w 94 I 0 O 0 L 15.84 15.91 15.53 @#@FSLOADPOST 2020:07:15:08:05:59 mri_normalize N 9 18.24 17.11 16.06 #-------------------------------------------- #@# Mask BFS Wed Jul 15 08:05:59 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1304683 voxels in mask (pct= 7.78) MRImask(): AllowDiffGeom = 1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2020:07:15:08:05:59 mri_mask N 5 e 10.45 S 0.03 U 1.91 P 18% M 71420 F 0 R 3906 W 0 c 766 w 71 I 0 O 0 L 18.22 17.12 16.07 @#@FSLOADPOST 2020:07:15:08:06:10 mri_mask N 5 18.26 17.17 16.09 #-------------------------------------------- #@# WM Segmentation Wed Jul 15 08:06:10 EDT 2020 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname loginnode2 machine x86_64 user pankumar input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname loginnode2 machine x86_64 user pankumar input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: -1 deletes, -1 fills cp wm.mgz wm.seg.mgz AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2020:07:15:08:07:08 AntsDenoiseImageFs N 4 e 237.75 S 0.35 U 46.95 P 19% M 347800 F 0 R 4594 W 0 c 23199 w 57 I 0 O 0 L 18.63 17.45 16.25 @#@FSLOADPOST 2020:07:15:08:11:06 AntsDenoiseImageFs N 4 19.82 18.72 17.03 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz preserving editing changes in output volume... wsizemm = 13, voxres = 1, wsize = 13 WHITE_MATTER_MEAN 110 wsize 13 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm_low 79 wm_hi 125 gray_low 30 gray_hi 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (103.0): 103.7 +- 4.5 [79.0 --> 125.0] CCS GM (71.0) : 70.3 +- 9.1 [30.0 --> 95.0] white_mean 103.672 white_sigma 4.53265 gray_mean 70.2502 gray_sigma 9.09654 setting bottom of white matter range wm_low to 79.3 setting top of gray matter range gray_hi to 88.4 wm_low 79.3468 wm_hi 125 gray_low 30 gray_hi 88.4433 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 79.3468 wm_hi 125 gray_low 30 gray_hi 88.4433 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 88.4433, wm_low = 79.3468 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=88.4433, wmlow=79.3468 95483 voxels processed (0.57%) 44684 voxels white (0.27%) 50799 voxels non-white (0.30%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=74.3468, gray_hi=88.4433, wsize=13 162977 voxels tested (0.97%) 37597 voxels changed (0.22%) 39830 multi-scale searches (0.24%) Recovering bright white MRIrecoverBrightWhite() wm_low 79.3468 wm_hi 125 slack 4.53265 pct_thresh 0.33 intensity_thresh 129.533 nvox_thresh 8.58 14 voxels tested (0.00%) 14 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=74.3468, hithr=88.4433 smoothing input volume with sigma = 0.250 61941 voxels tested (0.37%) 12936 voxels changed (0.08%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1885 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1260 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3978 filled MRIfindBrightNonWM(): 2 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 7.4 minutes writing output to wm.seg.mgz... @#@FSTIME 2020:07:15:08:11:06 mri_segment N 6 e 451.49 S 1.45 U 82.54 P 18% M 153324 F 0 R 42589 W 0 c 63014 w 69 I 0 O 0 L 19.82 18.72 17.03 @#@FSLOADPOST 2020:07:15:08:18:37 mri_segment N 6 20.02 19.64 18.12 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 3.84 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 3894 additional wm voxels added 0 additional wm voxels added SEG EDIT: 47157 voxels turned on, 32990 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 103 new 103 115,126,128 old 103 new 103 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2020:07:15:08:18:38 mri_edit_wm_with_aseg N 5 e 230.49 S 0.79 U 43.49 P 19% M 474088 F 0 R 20007 W 0 c 26944 w 93 I 0 O 0 L 20.02 19.64 18.12 @#@FSLOADPOST 2020:07:15:08:22:28 mri_edit_wm_with_aseg N 5 19.73 19.88 18.56 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 24 found - 24 modified | TOTAL: 40 pass 2 (xy-): 0 found - 24 modified | TOTAL: 40 pass 1 (yz+): 24 found - 24 modified | TOTAL: 64 pass 2 (yz+): 0 found - 24 modified | TOTAL: 64 pass 1 (yz-): 11 found - 11 modified | TOTAL: 75 pass 2 (yz-): 0 found - 11 modified | TOTAL: 75 pass 1 (xz+): 11 found - 11 modified | TOTAL: 86 pass 2 (xz+): 0 found - 11 modified | TOTAL: 86 pass 1 (xz-): 12 found - 12 modified | TOTAL: 98 pass 2 (xz-): 0 found - 12 modified | TOTAL: 98 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 4 found - 4 modified | TOTAL: 14 pass 2 (+++): 0 found - 4 modified | TOTAL: 14 pass 1 (+++): 4 found - 4 modified | TOTAL: 18 pass 2 (+++): 0 found - 4 modified | TOTAL: 18 Iteration Number : 1 pass 1 (++): 62 found - 62 modified | TOTAL: 62 pass 2 (++): 0 found - 62 modified | TOTAL: 62 pass 1 (+-): 102 found - 102 modified | TOTAL: 164 pass 2 (+-): 0 found - 102 modified | TOTAL: 164 pass 1 (--): 59 found - 59 modified | TOTAL: 223 pass 2 (--): 0 found - 59 modified | TOTAL: 223 pass 1 (-+): 94 found - 94 modified | TOTAL: 317 pass 2 (-+): 0 found - 94 modified | TOTAL: 317 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 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 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 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 Total Number of Modified Voxels = 448 (out of 441090: 0.101567) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done @#@FSTIME 2020:07:15:08:22:29 mri_pretess N 5 e 28.96 S 0.18 U 4.66 P 16% M 54132 F 0 R 3732 W 0 c 5194 w 85 I 0 O 0 L 19.73 19.88 18.56 @#@FSLOADPOST 2020:07:15:08:22:58 mri_pretess N 5 19.56 19.82 18.58 #-------------------------------------------- #@# Fill Wed Jul 15 08:22:58 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.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.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03016 0.01046 0.00806 -8.71298; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22072; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03016 0.01046 0.00806 -8.71298; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22072; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1005 (min = 350, max = 1400), aspect = 0.42 (min = 0.10, max = 0.75) no need to search using seed (126, 121, 149), TAL = (2.0, 21.0, 7.0) talairach voxel to voxel transform 0.97060 -0.00795 -0.00779 8.12970; 0.00651 0.77688 -0.00627 31.86034; 0.00817 0.00799 1.00464 0.62001; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 121, 149) --> (2.0, 21.0, 7.0) done. writing output to filled.mgz... filling took 12.2 minutes talairach cc position changed to (2.00, 21.00, 7.00) Erasing brainstem...done. MRImask(): AllowDiffGeom = 1 seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 7.00) SRC: (110.83, 125.63, 152.16) search lh wm seed point around talairach space (-16.00, 21.00, 7.00), SRC: (145.77, 125.86, 152.45) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... @#@FSTIME 2020:07:15:08:22:58 mri_fill N 8 e 735.75 S 3.62 U 133.80 P 18% M 966676 F 0 R 292250 W 0 c 99230 w 82 I 0 O 0 L 19.56 19.82 18.58 @#@FSLOADPOST 2020:07:15:08:35:14 mri_fill N 8 20.43 20.17 19.42 #-------------------------------------------- #@# Tessellate lh Wed Jul 15 08:35:14 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 2 found - 2 modified | TOTAL: 6 pass 2 (xy-): 0 found - 2 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 4 found - 4 modified | TOTAL: 13 pass 2 (yz-): 0 found - 4 modified | TOTAL: 13 pass 1 (xz+): 0 found - 0 modified | TOTAL: 13 pass 1 (xz-): 4 found - 4 modified | TOTAL: 17 pass 2 (xz-): 0 found - 4 modified | TOTAL: 17 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (-+): 2 found - 2 modified | TOTAL: 2 pass 2 (-+): 0 found - 2 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 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 Total Number of Modified Voxels = 26 (out of 216539: 0.012007) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:15:08:35:15 mri_pretess N 4 e 16.18 S 0.02 U 3.40 P 21% M 37288 F 0 R 2391 W 0 c 1746 w 45 I 0 O 0 L 20.64 20.22 19.44 @#@FSLOADPOST 2020:07:15:08:35:31 mri_pretess N 4 20.80 20.27 19.47 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.1.0 7.1.0 slice 30: 318 vertices, 370 faces slice 40: 3905 vertices, 4066 faces slice 50: 9065 vertices, 9233 faces slice 60: 14611 vertices, 14834 faces slice 70: 21758 vertices, 22050 faces slice 80: 29683 vertices, 29997 faces slice 90: 38691 vertices, 39033 faces slice 100: 49124 vertices, 49481 faces slice 110: 60299 vertices, 60684 faces slice 120: 70412 vertices, 70774 faces slice 130: 80568 vertices, 80933 faces slice 140: 89583 vertices, 89910 faces slice 150: 97628 vertices, 97926 faces slice 160: 105102 vertices, 105425 faces slice 170: 112115 vertices, 112359 faces slice 180: 117690 vertices, 117885 faces slice 190: 120067 vertices, 120116 faces slice 200: 120086 vertices, 120126 faces slice 210: 120086 vertices, 120126 faces slice 220: 120086 vertices, 120126 faces slice 230: 120086 vertices, 120126 faces slice 240: 120086 vertices, 120126 faces slice 250: 120086 vertices, 120126 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; @#@FSTIME 2020:07:15:08:35:31 mri_tessellate N 3 e 20.49 S 0.16 U 2.43 P 12% M 38760 F 0 R 2956 W 0 c 4347 w 58 I 0 O 0 L 20.80 20.27 19.47 @#@FSLOADPOST 2020:07:15:08:35:52 mri_tessellate N 3 20.63 20.27 19.49 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 120086 voxel in cpt #1: X=-40 [v=120086,e=360378,f=240252] located at (-28.104359, -18.978382, 7.232117) For the whole surface: X=-40 [v=120086,e=360378,f=240252] One single component has been found nothing to do done @#@FSTIME 2020:07:15:08:35:52 mris_extract_main_component N 2 e 5.57 S 0.17 U 0.94 P 20% M 238104 F 1 R 28615 W 0 c 418 w 55 I 16 O 0 L 20.63 20.27 19.49 @#@FSLOADPOST 2020:07:15:08:35:58 mris_extract_main_component N 2 20.58 20.27 19.49 #-------------------------------------------- #@# Tessellate rh Wed Jul 15 08:35:58 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 0 found - 3 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 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 = 10 (out of 205883: 0.004857) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:15:08:35:58 mri_pretess N 4 e 10.61 S 0.02 U 2.07 P 19% M 37288 F 0 R 2392 W 0 c 923 w 48 I 0 O 0 L 20.58 20.27 19.49 @#@FSLOADPOST 2020:07:15:08:36:09 mri_pretess N 4 20.79 20.32 19.52 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.1.0 7.1.0 slice 30: 112 vertices, 142 faces slice 40: 2951 vertices, 3088 faces slice 50: 8335 vertices, 8560 faces slice 60: 15032 vertices, 15253 faces slice 70: 22425 vertices, 22730 faces slice 80: 31421 vertices, 31745 faces slice 90: 40636 vertices, 40953 faces slice 100: 50877 vertices, 51245 faces slice 110: 61610 vertices, 61967 faces slice 120: 71232 vertices, 71594 faces slice 130: 80664 vertices, 81021 faces slice 140: 89956 vertices, 90260 faces slice 150: 96668 vertices, 96933 faces slice 160: 103953 vertices, 104204 faces slice 170: 110088 vertices, 110310 faces slice 180: 115690 vertices, 115884 faces slice 190: 118150 vertices, 118186 faces slice 200: 118150 vertices, 118186 faces slice 210: 118150 vertices, 118186 faces slice 220: 118150 vertices, 118186 faces slice 230: 118150 vertices, 118186 faces slice 240: 118150 vertices, 118186 faces slice 250: 118150 vertices, 118186 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; @#@FSTIME 2020:07:15:08:36:10 mri_tessellate N 3 e 11.30 S 0.01 U 2.37 P 21% M 36604 F 0 R 2260 W 0 c 1128 w 26 I 0 O 0 L 20.65 20.30 19.51 @#@FSLOADPOST 2020:07:15:08:36:21 mri_tessellate N 3 20.46 20.27 19.51 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 118150 voxel in cpt #1: X=-36 [v=118150,e=354558,f=236372] located at (27.710352, -20.338045, 9.246179) For the whole surface: X=-36 [v=118150,e=354558,f=236372] One single component has been found nothing to do done @#@FSTIME 2020:07:15:08:36:22 mris_extract_main_component N 2 e 6.32 S 0.16 U 1.01 P 18% M 234280 F 0 R 29076 W 0 c 649 w 32 I 0 O 0 L 20.46 20.27 19.51 @#@FSLOADPOST 2020:07:15:08:36:28 mris_extract_main_component N 2 20.35 20.25 19.51 #-------------------------------------------- #@# Smooth1 lh Wed Jul 15 08:36:28 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2020:07:15:08:36:28 mris_smooth N 5 e 24.54 S 0.22 U 4.19 P 18% M 190084 F 0 R 35134 W 0 c 3481 w 62 I 0 O 0 L 20.35 20.25 19.51 @#@FSLOADPOST 2020:07:15:08:36:53 mris_smooth N 5 20.16 20.21 19.52 #-------------------------------------------- #@# Smooth1 rh Wed Jul 15 08:36:53 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2020:07:15:08:36:53 mris_smooth N 5 e 25.12 S 0.21 U 4.32 P 18% M 187064 F 0 R 33239 W 0 c 3192 w 36 I 0 O 0 L 20.16 20.21 19.52 @#@FSLOADPOST 2020:07:15:08:37:19 mris_smooth N 5 19.76 20.12 19.50 #-------------------------------------------- #@# Inflation1 lh Wed Jul 15 08:37:19 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.8 mm, total surface area = 64331 mm^2 step 000: RMS=0.153 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 2.4 minutes inflation complete. Not saving sulc mris_inflate utimesec 26.588957 mris_inflate stimesec 0.534918 mris_inflate ru_maxrss 251268 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49918 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 57 mris_inflate ru_nivcsw 17088 @#@FSTIME 2020:07:15:08:37:19 mris_inflate N 3 e 144.05 S 0.55 U 26.59 P 18% M 251268 F 0 R 49920 W 0 c 17095 w 60 I 0 O 0 L 19.76 20.12 19.50 @#@FSLOADPOST 2020:07:15:08:39:43 mris_inflate N 3 19.54 19.87 19.49 #-------------------------------------------- #@# Inflation1 rh Wed Jul 15 08:39:43 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.3 mm, total surface area = 63328 mm^2 step 000: RMS=0.152 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 2.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 26.427982 mris_inflate stimesec 0.389940 mris_inflate ru_maxrss 247304 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 47789 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 31 mris_inflate ru_nivcsw 13839 @#@FSTIME 2020:07:15:08:39:44 mris_inflate N 3 e 136.34 S 0.41 U 26.43 P 19% M 247304 F 0 R 47791 W 0 c 13848 w 35 I 0 O 0 L 19.54 19.87 19.49 @#@FSLOADPOST 2020:07:15:08:42:00 mris_inflate N 3 19.20 19.65 19.46 #-------------------------------------------- #@# QSphere lh Wed Jul 15 08:42:00 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.314... inflating... Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.549, avgs=0 005/300: dt: 0.9000, rms radial error=177.288, avgs=0 010/300: dt: 0.9000, rms radial error=176.730, avgs=0 015/300: dt: 0.9000, rms radial error=175.997, avgs=0 020/300: dt: 0.9000, rms radial error=175.162, avgs=0 025/300: dt: 0.9000, rms radial error=174.271, avgs=0 030/300: dt: 0.9000, rms radial error=173.347, avgs=0 035/300: dt: 0.9000, rms radial error=172.406, avgs=0 040/300: dt: 0.9000, rms radial error=171.457, avgs=0 045/300: dt: 0.9000, rms radial error=170.505, avgs=0 050/300: dt: 0.9000, rms radial error=169.554, avgs=0 055/300: dt: 0.9000, rms radial error=168.605, avgs=0 060/300: dt: 0.9000, rms radial error=167.659, avgs=0 065/300: dt: 0.9000, rms radial error=166.717, avgs=0 070/300: dt: 0.9000, rms radial error=165.780, avgs=0 075/300: dt: 0.9000, rms radial error=164.848, avgs=0 080/300: dt: 0.9000, rms radial error=163.920, avgs=0 085/300: dt: 0.9000, rms radial error=162.998, avgs=0 090/300: dt: 0.9000, rms radial error=162.080, avgs=0 095/300: dt: 0.9000, rms radial error=161.167, avgs=0 100/300: dt: 0.9000, rms radial error=160.258, avgs=0 105/300: dt: 0.9000, rms radial error=159.355, avgs=0 110/300: dt: 0.9000, rms radial error=158.457, avgs=0 115/300: dt: 0.9000, rms radial error=157.563, avgs=0 120/300: dt: 0.9000, rms radial error=156.675, avgs=0 125/300: dt: 0.9000, rms radial error=155.793, avgs=0 130/300: dt: 0.9000, rms radial error=154.915, avgs=0 135/300: dt: 0.9000, rms radial error=154.041, avgs=0 140/300: dt: 0.9000, rms radial error=153.173, avgs=0 145/300: dt: 0.9000, rms radial error=152.309, avgs=0 150/300: dt: 0.9000, rms radial error=151.450, avgs=0 155/300: dt: 0.9000, rms radial error=150.596, avgs=0 160/300: dt: 0.9000, rms radial error=149.746, avgs=0 165/300: dt: 0.9000, rms radial error=148.901, avgs=0 170/300: dt: 0.9000, rms radial error=148.061, avgs=0 175/300: dt: 0.9000, rms radial error=147.226, avgs=0 180/300: dt: 0.9000, rms radial error=146.395, avgs=0 185/300: dt: 0.9000, rms radial error=145.568, avgs=0 190/300: dt: 0.9000, rms radial error=144.747, avgs=0 195/300: dt: 0.9000, rms radial error=143.929, avgs=0 200/300: dt: 0.9000, rms radial error=143.117, avgs=0 205/300: dt: 0.9000, rms radial error=142.309, avgs=0 210/300: dt: 0.9000, rms radial error=141.505, avgs=0 215/300: dt: 0.9000, rms radial error=140.706, avgs=0 220/300: dt: 0.9000, rms radial error=139.911, avgs=0 225/300: dt: 0.9000, rms radial error=139.121, avgs=0 230/300: dt: 0.9000, rms radial error=138.335, avgs=0 235/300: dt: 0.9000, rms radial error=137.554, avgs=0 240/300: dt: 0.9000, rms radial error=136.777, avgs=0 245/300: dt: 0.9000, rms radial error=136.005, avgs=0 250/300: dt: 0.9000, rms radial error=135.236, avgs=0 255/300: dt: 0.9000, rms radial error=134.473, avgs=0 260/300: dt: 0.9000, rms radial error=133.713, avgs=0 265/300: dt: 0.9000, rms radial error=132.958, avgs=0 270/300: dt: 0.9000, rms radial error=132.207, avgs=0 275/300: dt: 0.9000, rms radial error=131.460, avgs=0 280/300: dt: 0.9000, rms radial error=130.717, avgs=0 285/300: dt: 0.9000, rms radial error=129.979, avgs=0 290/300: dt: 0.9000, rms radial error=129.245, avgs=0 295/300: dt: 0.9000, rms radial error=128.514, avgs=0 300/300: dt: 0.9000, rms radial error=127.788, avgs=0 spherical inflation complete. projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.05 +- 0.61 (0.00-->7.39) (max @ vno 83129 --> 83130) face area 0.03 +- 0.03 (-0.09-->0.60) epoch 1 (K=10.0), pass 1, starting sse = 13959.20 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00036 epoch 2 (K=40.0), pass 1, starting sse = 2262.17 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00036 epoch 3 (K=160.0), pass 1, starting sse = 237.19 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00733 epoch 4 (K=640.0), pass 1, starting sse = 18.37 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/22 = 0.00520 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix mris_sphere utimesec 204.918847 mris_sphere stimesec 2.681592 mris_sphere ru_maxrss 946392 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 317619 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 77 mris_sphere ru_nivcsw 133320 spherical transformation took 0.2363 hours FSRUNTIME@ mris_sphere 0.2363 hours 1 threads @#@FSTIME 2020:07:15:08:42:01 mris_sphere N 9 e 851.07 S 2.69 U 204.91 P 24% M 946392 F 0 R 317621 W 0 c 133326 w 81 I 0 O 0 L 19.20 19.65 19.46 @#@FSLOADPOST 2020:07:15:08:56:12 mris_sphere N 9 15.77 16.61 17.90 #-------------------------------------------- #@# QSphere rh Wed Jul 15 08:56:12 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.315... inflating... Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.552, avgs=0 005/300: dt: 0.9000, rms radial error=177.293, avgs=0 010/300: dt: 0.9000, rms radial error=176.737, avgs=0 015/300: dt: 0.9000, rms radial error=176.006, avgs=0 020/300: dt: 0.9000, rms radial error=175.174, avgs=0 025/300: dt: 0.9000, rms radial error=174.285, avgs=0 030/300: dt: 0.9000, rms radial error=173.362, avgs=0 035/300: dt: 0.9000, rms radial error=172.422, avgs=0 040/300: dt: 0.9000, rms radial error=171.475, avgs=0 045/300: dt: 0.9000, rms radial error=170.524, avgs=0 050/300: dt: 0.9000, rms radial error=169.574, avgs=0 055/300: dt: 0.9000, rms radial error=168.626, avgs=0 060/300: dt: 0.9000, rms radial error=167.682, avgs=0 065/300: dt: 0.9000, rms radial error=166.741, avgs=0 070/300: dt: 0.9000, rms radial error=165.805, avgs=0 075/300: dt: 0.9000, rms radial error=164.874, avgs=0 080/300: dt: 0.9000, rms radial error=163.947, avgs=0 085/300: dt: 0.9000, rms radial error=163.025, avgs=0 090/300: dt: 0.9000, rms radial error=162.107, avgs=0 095/300: dt: 0.9000, rms radial error=161.195, avgs=0 100/300: dt: 0.9000, rms radial error=160.287, avgs=0 105/300: dt: 0.9000, rms radial error=159.384, avgs=0 110/300: dt: 0.9000, rms radial error=158.486, avgs=0 115/300: dt: 0.9000, rms radial error=157.592, avgs=0 120/300: dt: 0.9000, rms radial error=156.704, avgs=0 125/300: dt: 0.9000, rms radial error=155.820, avgs=0 130/300: dt: 0.9000, rms radial error=154.941, avgs=0 135/300: dt: 0.9000, rms radial error=154.067, avgs=0 140/300: dt: 0.9000, rms radial error=153.197, avgs=0 145/300: dt: 0.9000, rms radial error=152.333, avgs=0 150/300: dt: 0.9000, rms radial error=151.473, avgs=0 155/300: dt: 0.9000, rms radial error=150.617, avgs=0 160/300: dt: 0.9000, rms radial error=149.767, avgs=0 165/300: dt: 0.9000, rms radial error=148.921, avgs=0 170/300: dt: 0.9000, rms radial error=148.080, avgs=0 175/300: dt: 0.9000, rms radial error=147.243, avgs=0 180/300: dt: 0.9000, rms radial error=146.411, avgs=0 185/300: dt: 0.9000, rms radial error=145.584, avgs=0 190/300: dt: 0.9000, rms radial error=144.761, avgs=0 195/300: dt: 0.9000, rms radial error=143.943, avgs=0 200/300: dt: 0.9000, rms radial error=143.129, avgs=0 205/300: dt: 0.9000, rms radial error=142.320, avgs=0 210/300: dt: 0.9000, rms radial error=141.515, avgs=0 215/300: dt: 0.9000, rms radial error=140.715, avgs=0 220/300: dt: 0.9000, rms radial error=139.919, avgs=0 225/300: dt: 0.9000, rms radial error=139.128, avgs=0 230/300: dt: 0.9000, rms radial error=138.341, avgs=0 235/300: dt: 0.9000, rms radial error=137.559, avgs=0 240/300: dt: 0.9000, rms radial error=136.781, avgs=0 245/300: dt: 0.9000, rms radial error=136.007, avgs=0 250/300: dt: 0.9000, rms radial error=135.238, avgs=0 255/300: dt: 0.9000, rms radial error=134.473, avgs=0 260/300: dt: 0.9000, rms radial error=133.712, avgs=0 265/300: dt: 0.9000, rms radial error=132.956, avgs=0 270/300: dt: 0.9000, rms radial error=132.204, avgs=0 275/300: dt: 0.9000, rms radial error=131.456, avgs=0 280/300: dt: 0.9000, rms radial error=130.712, avgs=0 285/300: dt: 0.9000, rms radial error=129.972, avgs=0 290/300: dt: 0.9000, rms radial error=129.237, avgs=0 295/300: dt: 0.9000, rms radial error=128.506, avgs=0 300/300: dt: 0.9000, rms radial error=127.779, avgs=0 spherical inflation complete. projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.61 (0.00-->6.76) (max @ vno 36866 --> 37701) face area 0.03 +- 0.03 (-0.09-->0.84) epoch 1 (K=10.0), pass 1, starting sse = 13706.98 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00027 epoch 2 (K=40.0), pass 1, starting sse = 2219.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00031 epoch 3 (K=160.0), pass 1, starting sse = 230.30 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/15 = 0.00683 epoch 4 (K=640.0), pass 1, starting sse = 17.33 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/20 = 0.00587 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix mris_sphere utimesec 196.502127 mris_sphere stimesec 2.319647 mris_sphere ru_maxrss 910912 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 302489 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 38 mris_sphere ru_nivcsw 133984 spherical transformation took 0.1818 hours FSRUNTIME@ mris_sphere 0.1818 hours 1 threads @#@FSTIME 2020:07:15:08:56:12 mris_sphere N 9 e 654.80 S 2.42 U 196.50 P 30% M 910912 F 0 R 302491 W 0 c 134047 w 41 I 0 O 0 L 15.77 16.61 17.90 @#@FSLOADPOST 2020:07:15:09:07:07 mris_sphere N 9 15.38 15.77 16.79 #@# Fix Topology lh Wed Jul 15 09:07:07 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 2012-646-010-KK lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.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 writing corrected surface to 'orig.premesh' 7.1.0 7.1.0 before topology correction, eno=-40 (nv=120086, nf=240252, ne=360378, g=21) 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 8 iterations marking ambiguous vertices... 6439 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 24 into 19 31 defects to be corrected 0 vertices coincident reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.4713 (-4.7356) -vertex loglikelihood: -6.6616 (-3.3308) -normal dot loglikelihood: -3.6454 (-3.6454) -quad curv loglikelihood: -5.9739 (-2.9870) Total Loglikelihood : -25.7522 CORRECTING DEFECT 0 (vertices=37, convex hull=88, v0=516) After retessellation of defect 0 (v0=516), euler #=-29 (116190,347100,230881) : difference with theory (-28) = 1 CORRECTING DEFECT 1 (vertices=33, convex hull=73, v0=1547) After retessellation of defect 1 (v0=1547), euler #=-28 (116208,347182,230946) : difference with theory (-27) = 1 CORRECTING DEFECT 2 (vertices=690, convex hull=375, v0=31979) After retessellation of defect 2 (v0=31979), euler #=-27 (116392,347920,231501) : difference with theory (-26) = 1 CORRECTING DEFECT 3 (vertices=26, convex hull=59, v0=44483) After retessellation of defect 3 (v0=44483), euler #=-26 (116407,347990,231557) : difference with theory (-25) = 1 CORRECTING DEFECT 4 (vertices=176, convex hull=178, v0=53367) After retessellation of defect 4 (v0=53367), euler #=-25 (116486,348316,231805) : difference with theory (-24) = 1 CORRECTING DEFECT 5 (vertices=17, convex hull=26, v0=60276) After retessellation of defect 5 (v0=60276), euler #=-24 (116489,348334,231821) : difference with theory (-23) = 1 CORRECTING DEFECT 6 (vertices=23, convex hull=47, v0=61852) After retessellation of defect 6 (v0=61852), euler #=-23 (116501,348384,231860) : difference with theory (-22) = 1 CORRECTING DEFECT 7 (vertices=65, convex hull=48, v0=69483) After retessellation of defect 7 (v0=69483), euler #=-22 (116517,348453,231914) : difference with theory (-21) = 1 CORRECTING DEFECT 8 (vertices=6, convex hull=31, v0=70345) After retessellation of defect 8 (v0=70345), euler #=-21 (116519,348467,231927) : difference with theory (-20) = 1 CORRECTING DEFECT 9 (vertices=53, convex hull=85, v0=78195) After retessellation of defect 9 (v0=78195), euler #=-20 (116538,348565,232007) : difference with theory (-19) = 1 CORRECTING DEFECT 10 (vertices=273, convex hull=209, v0=81313) After retessellation of defect 10 (v0=81313), euler #=-19 (116632,348947,232296) : difference with theory (-18) = 1 CORRECTING DEFECT 11 (vertices=277, convex hull=221, v0=82011) After retessellation of defect 11 (v0=82011), euler #=-18 (116641,349080,232421) : difference with theory (-17) = 1 CORRECTING DEFECT 12 (vertices=15, convex hull=35, v0=83113) After retessellation of defect 12 (v0=83113), euler #=-17 (116644,349101,232440) : difference with theory (-16) = 1 CORRECTING DEFECT 13 (vertices=13, convex hull=30, v0=84100) After retessellation of defect 13 (v0=84100), euler #=-16 (116647,349120,232457) : difference with theory (-15) = 1 CORRECTING DEFECT 14 (vertices=24, convex hull=32, v0=84822) After retessellation of defect 14 (v0=84822), euler #=-15 (116652,349143,232476) : difference with theory (-14) = 1 CORRECTING DEFECT 15 (vertices=55, convex hull=40, v0=86091) After retessellation of defect 15 (v0=86091), euler #=-14 (116661,349186,232511) : difference with theory (-13) = 1 CORRECTING DEFECT 16 (vertices=23, convex hull=27, v0=87683) After retessellation of defect 16 (v0=87683), euler #=-13 (116663,349199,232523) : difference with theory (-12) = 1 CORRECTING DEFECT 17 (vertices=108, convex hull=51, v0=87910) After retessellation of defect 17 (v0=87910), euler #=-12 (116671,349245,232562) : difference with theory (-11) = 1 CORRECTING DEFECT 18 (vertices=119, convex hull=74, v0=91823) After retessellation of defect 18 (v0=91823), euler #=-11 (116694,349351,232646) : difference with theory (-10) = 1 CORRECTING DEFECT 19 (vertices=1407, convex hull=922, v0=92999) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 19 (v0=92999), euler #=-9 (117122,351130,233999) : difference with theory (-9) = 0 CORRECTING DEFECT 20 (vertices=25, convex hull=66, v0=93365) After retessellation of defect 20 (v0=93365), euler #=-8 (117136,351197,234053) : difference with theory (-8) = 0 CORRECTING DEFECT 21 (vertices=124, convex hull=47, v0=93414) After retessellation of defect 21 (v0=93414), euler #=-7 (117151,351262,234104) : difference with theory (-7) = 0 CORRECTING DEFECT 22 (vertices=19, convex hull=32, v0=99854) After retessellation of defect 22 (v0=99854), euler #=-6 (117155,351286,234125) : difference with theory (-6) = 0 CORRECTING DEFECT 23 (vertices=49, convex hull=45, v0=101069) After retessellation of defect 23 (v0=101069), euler #=-5 (117164,351326,234157) : difference with theory (-5) = 0 CORRECTING DEFECT 24 (vertices=42, convex hull=35, v0=104253) After retessellation of defect 24 (v0=104253), euler #=-4 (117169,351354,234181) : difference with theory (-4) = 0 CORRECTING DEFECT 25 (vertices=48, convex hull=97, v0=107524) After retessellation of defect 25 (v0=107524), euler #=-3 (117186,351447,234258) : difference with theory (-3) = 0 CORRECTING DEFECT 26 (vertices=47, convex hull=101, v0=114830) After retessellation of defect 26 (v0=114830), euler #=-2 (117204,351544,234338) : difference with theory (-2) = 0 CORRECTING DEFECT 27 (vertices=46, convex hull=39, v0=116853) After retessellation of defect 27 (v0=116853), euler #=-1 (117210,351577,234366) : difference with theory (-1) = 0 CORRECTING DEFECT 28 (vertices=29, convex hull=31, v0=117813) After retessellation of defect 28 (v0=117813), euler #=0 (117214,351601,234387) : difference with theory (0) = 0 CORRECTING DEFECT 29 (vertices=17, convex hull=63, v0=118829) After retessellation of defect 29 (v0=118829), euler #=1 (117222,351648,234427) : difference with theory (1) = 0 CORRECTING DEFECT 30 (vertices=24, convex hull=39, v0=118959) After retessellation of defect 30 (v0=118959), euler #=2 (117225,351669,234446) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.04-->16.01) (max @ vno 91251 --> 98337) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.04-->16.01) (max @ vno 91251 --> 98337) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 119 mutations (35.7%), 214 crossovers (64.3%), 299 vertices were eliminated building final representation... 2861 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=117225, nf=234446, ne=351669, g=0) writing corrected surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 630 intersecting 001: 120 intersecting 002: 54 intersecting 003: 48 intersecting 004: 47 intersecting step 1 with no progress (num=47, old_num=47) 005: 47 intersecting step 2 with no progress (num=47, old_num=47) 006: 47 intersecting step 3 with no progress (num=47, old_num=47) 007: 47 intersecting step 4 with no progress (num=47, old_num=47) 008: 47 intersecting step 5 with no progress (num=47, old_num=47) 009: 47 intersecting step 6 with no progress (num=47, old_num=47) 010: 47 intersecting step 7 with no progress (num=47, old_num=47) 011: 47 intersecting step 8 with no progress (num=47, old_num=47) 012: 47 intersecting step 9 with no progress (num=47, old_num=47) 013: 47 intersecting step 10 with no progress (num=47, old_num=47) 014: 47 intersecting step 11 with no progress (num=47, old_num=47) 015: 47 intersecting step 12 with no progress (num=47, old_num=47) 016: 47 intersecting step 13 with no progress (num=47, old_num=47) 017: 47 intersecting step 14 with no progress (num=47, old_num=47) 018: 47 intersecting step 15 with no progress (num=47, old_num=47) 019: 47 intersecting step 16 with no progress (num=47, old_num=47) terminating search with 47 intersecting topology fixing took 15.7 minutes FSRUNTIME@ mris_fix_topology lh 0.2611 hours 1 threads #VMPC# mris_fix_topology VmPeak 857192 @#@FSTIME 2020:07:15:09:07:07 mris_fix_topology N 14 e 940.17 S 2.70 U 289.30 P 31% M 723096 F 0 R 165781 W 0 c 189514 w 248 I 0 O 0 L 15.38 15.77 16.79 @#@FSLOADPOST 2020:07:15:09:22:48 mris_fix_topology N 14 15.69 15.50 15.94 #@# Fix Topology rh Wed Jul 15 09:22:48 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 2012-646-010-KK rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.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 writing corrected surface to 'orig.premesh' 7.1.0 7.1.0 before topology correction, eno=-36 (nv=118150, nf=236372, ne=354558, 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 11 iterations marking ambiguous vertices... 5187 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 21 into 17 -merging segment 26 into 24 24 defects to be corrected 0 vertices coincident reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.6047 (-4.8023) -vertex loglikelihood: -6.6422 (-3.3211) -normal dot loglikelihood: -3.6567 (-3.6567) -quad curv loglikelihood: -6.2019 (-3.1009) Total Loglikelihood : -26.1054 CORRECTING DEFECT 0 (vertices=546, convex hull=388, v0=2225) After retessellation of defect 0 (v0=2225), euler #=-23 (115002,343819,228794) : difference with theory (-21) = 2 CORRECTING DEFECT 1 (vertices=760, convex hull=714, v0=2449) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 1 (v0=2449), euler #=-22 (115299,345062,229741) : difference with theory (-20) = 2 CORRECTING DEFECT 2 (vertices=102, convex hull=85, v0=17419) After retessellation of defect 2 (v0=17419), euler #=-21 (115325,345175,229829) : difference with theory (-19) = 2 CORRECTING DEFECT 3 (vertices=42, convex hull=64, v0=17693) After retessellation of defect 3 (v0=17693), euler #=-20 (115351,345281,229910) : difference with theory (-18) = 2 CORRECTING DEFECT 4 (vertices=13, convex hull=29, v0=20516) After retessellation of defect 4 (v0=20516), euler #=-19 (115354,345299,229926) : difference with theory (-17) = 2 CORRECTING DEFECT 5 (vertices=8, convex hull=20, v0=22931) After retessellation of defect 5 (v0=22931), euler #=-18 (115355,345307,229934) : difference with theory (-16) = 2 CORRECTING DEFECT 6 (vertices=23, convex hull=77, v0=27007) After retessellation of defect 6 (v0=27007), euler #=-17 (115370,345385,229998) : difference with theory (-15) = 2 CORRECTING DEFECT 7 (vertices=234, convex hull=199, v0=32457) After retessellation of defect 7 (v0=32457), euler #=-16 (115422,345640,230202) : difference with theory (-14) = 2 CORRECTING DEFECT 8 (vertices=55, convex hull=96, v0=42095) After retessellation of defect 8 (v0=42095), euler #=-15 (115450,345768,230303) : difference with theory (-13) = 2 CORRECTING DEFECT 9 (vertices=19, convex hull=22, v0=45786) After retessellation of defect 9 (v0=45786), euler #=-14 (115454,345790,230322) : difference with theory (-12) = 2 CORRECTING DEFECT 10 (vertices=17, convex hull=33, v0=50666) After retessellation of defect 10 (v0=50666), euler #=-13 (115459,345816,230344) : difference with theory (-11) = 2 CORRECTING DEFECT 11 (vertices=133, convex hull=138, v0=51920) After retessellation of defect 11 (v0=51920), euler #=-12 (115533,346101,230556) : difference with theory (-10) = 2 CORRECTING DEFECT 12 (vertices=56, convex hull=43, v0=52817) After retessellation of defect 12 (v0=52817), euler #=-11 (115545,346155,230599) : difference with theory (-9) = 2 CORRECTING DEFECT 13 (vertices=23, convex hull=44, v0=67426) After retessellation of defect 13 (v0=67426), euler #=-10 (115550,346186,230626) : difference with theory (-8) = 2 CORRECTING DEFECT 14 (vertices=6, convex hull=16, v0=75300) After retessellation of defect 14 (v0=75300), euler #=-9 (115551,346192,230632) : difference with theory (-7) = 2 CORRECTING DEFECT 15 (vertices=41, convex hull=40, v0=76865) After retessellation of defect 15 (v0=76865), euler #=-8 (115562,346239,230669) : difference with theory (-6) = 2 CORRECTING DEFECT 16 (vertices=635, convex hull=444, v0=80419) After retessellation of defect 16 (v0=80419), euler #=-6 (115752,347032,231274) : difference with theory (-5) = 1 CORRECTING DEFECT 17 (vertices=118, convex hull=66, v0=81382) After retessellation of defect 17 (v0=81382), euler #=-5 (115778,347138,231355) : difference with theory (-4) = 1 CORRECTING DEFECT 18 (vertices=9, convex hull=19, v0=83124) After retessellation of defect 18 (v0=83124), euler #=-4 (115781,347153,231368) : difference with theory (-3) = 1 CORRECTING DEFECT 19 (vertices=204, convex hull=201, v0=88314) After retessellation of defect 19 (v0=88314), euler #=-3 (115874,347531,231654) : difference with theory (-2) = 1 CORRECTING DEFECT 20 (vertices=27, convex hull=41, v0=103947) After retessellation of defect 20 (v0=103947), euler #=-2 (115878,347558,231678) : difference with theory (-1) = 1 CORRECTING DEFECT 21 (vertices=49, convex hull=55, v0=111278) After retessellation of defect 21 (v0=111278), euler #=-1 (115886,347605,231718) : difference with theory (0) = 1 CORRECTING DEFECT 22 (vertices=107, convex hull=68, v0=116433) After retessellation of defect 22 (v0=116433), euler #=1 (115907,347697,231791) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=19, convex hull=50, v0=117508) After retessellation of defect 23 (v0=117508), euler #=2 (115913,347733,231822) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.02-->9.15) (max @ vno 17829 --> 25251) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.02-->9.15) (max @ vno 17829 --> 25251) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 83 mutations (37.4%), 139 crossovers (62.6%), 284 vertices were eliminated building final representation... 2237 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=115913, nf=231822, ne=347733, g=0) writing corrected surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 425 intersecting 001: 51 intersecting 002: 12 intersecting 003: 4 intersecting step 1 with no progress (num=4, old_num=4) 004: 4 intersecting step 2 with no progress (num=4, old_num=4) 005: 4 intersecting step 3 with no progress (num=4, old_num=4) 006: 4 intersecting step 4 with no progress (num=4, old_num=4) 007: 4 intersecting step 5 with no progress (num=4, old_num=4) 008: 4 intersecting step 6 with no progress (num=4, old_num=4) 009: 4 intersecting step 7 with no progress (num=4, old_num=4) 010: 4 intersecting step 8 with no progress (num=4, old_num=4) 011: 4 intersecting step 9 with no progress (num=4, old_num=4) 012: 4 intersecting step 10 with no progress (num=4, old_num=4) 013: 4 intersecting step 11 with no progress (num=4, old_num=4) 014: 4 intersecting step 12 with no progress (num=4, old_num=4) 015: 4 intersecting step 13 with no progress (num=4, old_num=4) 016: 4 intersecting step 14 with no progress (num=4, old_num=4) 017: 4 intersecting step 15 with no progress (num=4, old_num=4) 018: 4 intersecting step 16 with no progress (num=4, old_num=4) terminating search with 4 intersecting topology fixing took 12.4 minutes FSRUNTIME@ mris_fix_topology rh 0.2071 hours 1 threads #VMPC# mris_fix_topology VmPeak 854848 @#@FSTIME 2020:07:15:09:22:48 mris_fix_topology N 14 e 745.70 S 1.24 U 251.14 P 33% M 716984 F 0 R 163748 W 0 c 113413 w 116 I 0 O 0 L 15.69 15.50 15.94 @#@FSLOADPOST 2020:07:15:09:35:14 mris_fix_topology N 14 15.05 14.98 15.36 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 117225 - 351669 + 234446 = 2 --> 0 holes F =2V-4: 234446 = 234450-4 (0) 2E=3F: 703338 = 703338 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 115913 - 347733 + 231822 = 2 --> 0 holes F =2V-4: 231822 = 231826-4 (0) 2E=3F: 695466 = 695466 (0) total defect index = 0 Wed Jul 15 09:35:18 EDT 2020 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts /public/apps/freesurfer/7.1.0/bin/defect2seg --s 2012-646-010-KK freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b defect2seg 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pid 20929 mri_label2vol --defects /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.nofix /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defect_labels /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz 1000 0 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mris_defects_pointset -s /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.nofix -d /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defect_labels -o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defects.pointset Reading in surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.nofix Reading in defect segmentation /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defect_labels #VMPC# mris_defects_pointset 178736 mris_defects_pointset done mri_label2vol --defects /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.nofix /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defect_labels /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz 2000 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mris_defects_pointset -s /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.nofix -d /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defect_labels -o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defects.pointset Reading in surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.nofix Reading in defect segmentation /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defect_labels #VMPC# mris_defects_pointset 176496 mris_defects_pointset done Started at Wed Jul 15 09:35:18 EDT 2020 Ended at Wed Jul 15 09:35:42 EDT 2020 Defect2seg-Run-Time-Sec 24 Defect2seg-Run-Time-Min 0.48 Defect2seg-Run-Time-Hours 0.01 tkmeditfv 2012-646-010-KK orig.mgz -defect -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/?h.defects.pointset defect2seg Done @#@FSTIME 2020:07:15:09:35:18 defect2seg N 2 e 24.38 S 0.55 U 7.14 P 31% M 223664 F 1 R 120246 W 0 c 3642 w 627 I 96 O 0 L 14.97 14.97 15.35 @#@FSLOADPOST 2020:07:15:09:35:42 defect2seg N 2 14.85 14.94 15.33 mris_remesh --remesh --iters 3 --input /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.premesh --output /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.714404 remeshing to edge length 0.714404 with 3 iterations avg qual before : 0.885761 after: 0.970733 Removing intersections removing intersecting faces 000: 33 intersecting 001: 23 intersecting 002: 15 intersecting 003: 14 intersecting 004: 13 intersecting step 1 with no progress (num=13, old_num=13) 005: 13 intersecting step 2 with no progress (num=13, old_num=13) 006: 13 intersecting step 3 with no progress (num=13, old_num=13) 007: 13 intersecting step 4 with no progress (num=13, old_num=13) 008: 13 intersecting step 5 with no progress (num=13, old_num=13) 009: 13 intersecting step 6 with no progress (num=13, old_num=13) 010: 13 intersecting step 7 with no progress (num=13, old_num=13) 011: 13 intersecting step 8 with no progress (num=13, old_num=13) 012: 13 intersecting step 9 with no progress (num=13, old_num=13) 013: 13 intersecting step 10 with no progress (num=13, old_num=13) 014: 13 intersecting step 11 with no progress (num=13, old_num=13) 015: 13 intersecting step 12 with no progress (num=13, old_num=13) 016: 13 intersecting step 13 with no progress (num=13, old_num=13) 017: 13 intersecting step 14 with no progress (num=13, old_num=13) 018: 13 intersecting step 15 with no progress (num=13, old_num=13) 019: 13 intersecting step 16 with no progress (num=13, old_num=13) terminating search with 13 intersecting Remeshed surface quality stats nv0 = 117225 nv = 121584 1.03718 Area 243164 0.30508 0.03419 0.065995 0.4749 Corner 729492 60.00000 8.87462 15.151449 149.0102 Edge 364746 0.84752 0.08340 0.287002 1.3090 Hinge 364746 9.94181 10.62489 0.000014 168.5767 mris_remesh done @#@FSTIME 2020:07:15:09:35:43 mris_remesh N 7 e 298.09 S 0.93 U 101.53 P 34% M 899044 F 0 R 190332 W 0 c 42530 w 112 I 0 O 0 L 14.85 14.94 15.33 @#@FSLOADPOST 2020:07:15:09:40:41 mris_remesh N 7 14.80 15.00 15.25 mris_remesh --remesh --iters 3 --input /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.premesh --output /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.712866 remeshing to edge length 0.712866 with 3 iterations avg qual before : 0.889735 after: 0.971439 Removing intersections Remeshed surface quality stats nv0 = 115913 nv = 120651 1.04088 Area 241298 0.30392 0.03362 0.083496 0.4849 Corner 723894 60.00000 8.75570 14.239817 150.2662 Edge 361947 0.84570 0.08224 0.459830 1.3036 Hinge 361947 9.92537 10.56286 0.000005 162.7806 mris_remesh done @#@FSTIME 2020:07:15:09:40:41 mris_remesh N 7 e 130.20 S 0.62 U 45.69 P 35% M 662644 F 0 R 117379 W 0 c 19688 w 42 I 0 O 0 L 14.80 15.00 15.25 @#@FSLOADPOST 2020:07:15:09:42:51 mris_remesh N 7 15.20 15.00 15.21 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.04 hours removing intersecting faces 000: 13 intersecting step 1 with no progress (num=13, old_num=13) 001: 13 intersecting step 2 with no progress (num=13, old_num=13) 002: 13 intersecting step 3 with no progress (num=13, old_num=13) 003: 13 intersecting step 4 with no progress (num=13, old_num=13) 004: 13 intersecting step 5 with no progress (num=13, old_num=13) 005: 13 intersecting step 6 with no progress (num=13, old_num=13) 006: 13 intersecting step 7 with no progress (num=13, old_num=13) 007: 13 intersecting step 8 with no progress (num=13, old_num=13) 008: 13 intersecting step 9 with no progress (num=13, old_num=13) 009: 13 intersecting step 10 with no progress (num=13, old_num=13) 010: 13 intersecting step 11 with no progress (num=13, old_num=13) 011: 13 intersecting step 12 with no progress (num=13, old_num=13) 012: 13 intersecting step 13 with no progress (num=13, old_num=13) 013: 13 intersecting step 14 with no progress (num=13, old_num=13) 014: 13 intersecting step 15 with no progress (num=13, old_num=13) 015: 13 intersecting step 16 with no progress (num=13, old_num=13) terminating search with 13 intersecting writing corrected surface to ../surf/lh.orig @#@FSTIME 2020:07:15:09:42:51 mris_remove_intersection N 2 e 145.72 S 2.01 U 42.67 P 30% M 362360 F 0 R 695836 W 0 c 18594 w 186 I 0 O 0 L 15.20 15.00 15.21 @#@FSLOADPOST 2020:07:15:09:45:17 mris_remove_intersection N 2 16.89 15.97 15.55 rm ../surf/lh.inflated /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2020:07:15:09:45:18 mris_remove_intersection N 2 e 11.10 S 0.20 U 3.63 P 34% M 310856 F 0 R 59051 W 0 c 1553 w 37 I 0 O 0 L 16.89 15.97 15.55 @#@FSLOADPOST 2020:07:15:09:45:29 mris_remove_intersection N 2 16.90 16.00 15.57 rm ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Wed Jul 15 09:45:29 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 215539 voxels (1.28%) border gray 248151 voxels (1.48%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (97.0): 97.1 +- 9.1 [70.0 --> 110.0] CCS GM (69.0) : 68.5 +- 10.9 [30.0 --> 110.0] white_mean = 97.0982 +/- 9.1407, gray_mean = 68.4735 +/- 10.8946 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=170 nbins=171 intensity peaks found at WM=103+-6.1, GM=63+-8.7 white_mode = 103, gray_mode = 63 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 52.1 (was 70.000000) setting MAX_BORDER_WHITE to 112.1 (was 105.000000) setting MIN_BORDER_WHITE to 63.0 (was 85.000000) setting MAX_CSF to 41.2 (was 40.000000) setting MAX_GRAY to 93.9 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 52.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 30.3 (was 40.000000) When placing the white surface white_border_hi = 112.141; white_border_low = 63; white_outside_low = 52.1054; white_inside_hi = 120; white_outside_hi = 112.141; When placing the pial surface pial_border_hi = 52.1054; pial_border_low = 30.3162; pial_outside_low = 10; pial_inside_hi = 93.8593; pial_outside_hi = 46.6581; #VMPC# mris_autodet_gwstats VmPeak 351532 mris_autodet_gwstats done @#@FSTIME 2020:07:15:09:45:29 mris_autodet_gwstats N 8 e 19.97 S 0.14 U 5.83 P 29% M 217228 F 0 R 31751 W 0 c 2538 w 84 I 0 O 0 L 16.90 16.00 15.57 @#@FSLOADPOST 2020:07:15:09:45:49 mris_autodet_gwstats N 8 16.72 16.02 15.58 #-------------------------------------------- #@# AutoDetGWStats rh Wed Jul 15 09:45:49 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 215539 voxels (1.28%) border gray 248151 voxels (1.48%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (97.0): 97.1 +- 9.1 [70.0 --> 110.0] CCS GM (69.0) : 68.5 +- 10.9 [30.0 --> 110.0] white_mean = 97.0982 +/- 9.1407, gray_mean = 68.4735 +/- 10.8946 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=170 nbins=171 intensity peaks found at WM=102+-6.1, GM=62+-7.8 white_mode = 102, gray_mode = 62 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 51.1 (was 70.000000) setting MAX_BORDER_WHITE to 111.1 (was 105.000000) setting MIN_BORDER_WHITE to 62.0 (was 85.000000) setting MAX_CSF to 40.2 (was 40.000000) setting MAX_GRAY to 92.9 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 51.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 29.3 (was 40.000000) When placing the white surface white_border_hi = 111.141; white_border_low = 62; white_outside_low = 51.1054; white_inside_hi = 120; white_outside_hi = 111.141; When placing the pial surface pial_border_hi = 51.1054; pial_border_low = 29.3162; pial_outside_low = 10; pial_inside_hi = 92.8593; pial_outside_hi = 45.6581; #VMPC# mris_autodet_gwstats VmPeak 349716 mris_autodet_gwstats done @#@FSTIME 2020:07:15:09:45:49 mris_autodet_gwstats N 8 e 18.52 S 0.17 U 5.34 P 29% M 215412 F 0 R 32759 W 0 c 3251 w 47 I 0 O 0 L 16.72 16.02 15.58 @#@FSLOADPOST 2020:07:15:09:46:08 mris_autodet_gwstats N 8 16.29 15.97 15.57 #-------------------------------------------- #@# WhitePreAparc lh Wed Jul 15 09:46:08 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 243164 0.26804 0.06524 0.001282 0.5788 Corner 729492 60.00000 9.72910 1.250939 176.6314 Edge 364746 0.79052 0.11821 0.027763 1.4499 Hinge 364746 6.56435 6.70407 0.000003 176.4319 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5928, nmarked2=88, nripped=5928 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60792: xyz = (-58.8021,-7.92064,-5.67842) oxyz = (-58.8021,-7.92064,-5.67842) wxzy = (-58.8021,-7.92064,-5.67842) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5928 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5928, nmarked2=88, nripped=5928 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=2 had to be increased for 382 vertices, nripped=5928 mean border=76.7, 212 (212) missing vertices, mean dist 0.3 [0.6 (%34.6)->0.8 (%65.4))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.1468 min Finding expansion regions mean absolute distance = 0.72 +- 0.90 3981 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=login, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=3476924.2, rms=12.025 001: dt: 0.5000, sse=1957007.0, rms=8.886 (26.102%) 002: dt: 0.5000, sse=1271381.0, rms=7.017 (21.040%) 003: dt: 0.5000, sse=911760.0, rms=5.814 (17.144%) 004: dt: 0.5000, sse=721233.1, rms=5.026 (13.542%) 005: dt: 0.5000, sse=610799.6, rms=4.537 (9.738%) 006: dt: 0.5000, sse=557652.9, rms=4.255 (6.216%) 007: dt: 0.5000, sse=529148.8, rms=4.095 (3.760%) 008: dt: 0.5000, sse=511661.2, rms=3.999 (2.353%) 009: dt: 0.5000, sse=502670.1, rms=3.935 (1.590%) rms = 3.8880/3.9350, sse=490895.5/502670.1, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=490895.5, rms=3.888 (1.196%) 011: dt: 0.2500, sse=300157.0, rms=2.569 (33.923%) 012: dt: 0.2500, sse=264336.3, rms=2.249 (12.465%) 013: dt: 0.2500, sse=252026.0, rms=2.149 (4.446%) 014: dt: 0.2500, sse=251589.7, rms=2.094 (2.569%) rms = 2.0593/2.0936, sse=250885.3/251589.7, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=250885.3, rms=2.059 (1.642%) 016: dt: 0.1250, sse=242574.7, rms=1.997 (3.025%) rms = 1.9797/1.9970, sse=237112.6/242574.7, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=237112.6, rms=1.980 (0.863%) maximum number of reductions reached, breaking from loop positioning took 7.8 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5928 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6364, nmarked2=157, nripped=6364 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=1 had to be increased for 233 vertices, nripped=6364 mean border=80.0, 165 (30) missing vertices, mean dist -0.2 [0.4 (%74.1)->0.3 (%25.9))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.6676 min Finding expansion regions mean absolute distance = 0.34 +- 0.59 2910 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=login, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=799813.9, rms=5.126 018: dt: 0.5000, sse=487162.2, rms=3.519 (31.357%) rms = 3.6224/3.5190, sse=503292.2/487162.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=368327.5, rms=2.709 (23.020%) 020: dt: 0.2500, sse=306206.3, rms=2.145 (20.823%) 021: dt: 0.2500, sse=295760.2, rms=1.886 (12.077%) 022: dt: 0.2500, sse=273602.5, rms=1.755 (6.916%) 023: dt: 0.2500, sse=260971.0, rms=1.674 (4.619%) rms = 1.6331/1.6743, sse=260040.5/260971.0, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=260040.5, rms=1.633 (2.460%) rms = 1.5847/1.6331, sse=254768.8/260040.5, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=254768.8, rms=1.585 (2.962%) maximum number of reductions reached, breaking from loop positioning took 3.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6364 removing 1 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6403, nmarked2=159, nripped=6403 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 230 vertices, nripped=6403 mean border=82.2, 164 (11) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.2 (%30.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.3456 min Finding expansion regions mean absolute distance = 0.25 +- 0.41 2834 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=login, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=445945.8, rms=3.307 026: dt: 0.5000, sse=409634.2, rms=2.995 (9.437%) rms = 3.3583/2.9947, sse=466227.5/409634.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=296186.9, rms=2.056 (31.341%) 028: dt: 0.2500, sse=265971.3, rms=1.647 (19.903%) 029: dt: 0.2500, sse=251253.6, rms=1.524 (7.445%) rms = 1.5060/1.5243, sse=247044.5/251253.6, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=247044.5, rms=1.506 (1.197%) rms = 1.4419/1.5060, sse=252885.9/247044.5, time step reduction 3 of 3 to 0.062 0 1 0 031: dt: 0.1250, sse=252885.9, rms=1.442 (4.261%) maximum number of reductions reached, breaking from loop positioning took 3.2 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6403 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6452, nmarked2=163, nripped=6452 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 210 vertices, nripped=6452 mean border=83.1, 210 (9) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2548 min Finding expansion regions mean absolute distance = 0.22 +- 0.34 2885 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=login, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=280889.9, rms=1.841 rms = 2.0694/1.8414, sse=299295.2/280889.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=241265.5, rms=1.416 (23.089%) 033: dt: 0.2500, sse=232365.8, rms=1.219 (13.925%) rms = 1.2093/1.2190, sse=226177.0/232365.8, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=226177.0, rms=1.209 (0.801%) rms = 1.1882/1.2093, sse=225739.9/226177.0, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=225739.9, rms=1.188 (1.744%) maximum number of reductions reached, breaking from loop positioning took 2.1 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 19.59 minutes #VMPC# mris_make_surfaces VmPeak 2268436 mris_place_surface done @#@FSTIME 2020:07:15:09:46:08 mris_place_surface N 16 e 1213.04 S 2.23 U 361.64 P 29% M 1897728 F 0 R 267270 W 0 c 166090 w 364 I 0 O 0 L 16.29 15.97 15.57 @#@FSLOADPOST 2020:07:15:10:06:22 mris_place_surface N 16 15.99 16.09 15.92 #-------------------------------------------- #@# WhitePreAparc rh Wed Jul 15 10:06:22 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface with 5 iterations Area 241298 0.26699 0.06456 0.007102 0.6288 Corner 723894 60.00000 9.65011 11.784599 141.8663 Edge 361947 0.78892 0.11695 0.104140 1.3036 Hinge 361947 6.54318 6.66458 0.000004 144.1443 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6059, nmarked2=117, nripped=6059 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60326: xyz = (6.01705,-6.86342,31.6417) oxyz = (6.01705,-6.86342,31.6417) wxzy = (6.01705,-6.86342,31.6417) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6059 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6059, nmarked2=117, nripped=6059 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=2 had to be increased for 312 vertices, nripped=6059 mean border=75.6, 145 (145) missing vertices, mean dist 0.4 [0.5 (%33.7)->0.8 (%66.3))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.0789 min Finding expansion regions mean absolute distance = 0.72 +- 0.87 4077 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=login, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=3665531.8, rms=12.421 001: dt: 0.5000, sse=2095957.2, rms=9.272 (25.357%) 002: dt: 0.5000, sse=1354492.2, rms=7.321 (21.036%) 003: dt: 0.5000, sse=949174.2, rms=5.991 (18.169%) 004: dt: 0.5000, sse=721683.4, rms=5.090 (15.035%) 005: dt: 0.5000, sse=596332.1, rms=4.503 (11.535%) 006: dt: 0.5000, sse=530020.9, rms=4.173 (7.321%) 007: dt: 0.5000, sse=494010.1, rms=3.973 (4.813%) 008: dt: 0.5000, sse=478600.8, rms=3.881 (2.313%) 009: dt: 0.5000, sse=467669.2, rms=3.814 (1.730%) rms = 3.7794/3.8135, sse=462995.1/467669.2, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=462995.1, rms=3.779 (0.896%) 011: dt: 0.2500, sse=268287.6, rms=2.379 (37.056%) 012: dt: 0.2500, sse=233601.4, rms=2.038 (14.345%) 013: dt: 0.2500, sse=225496.0, rms=1.946 (4.514%) rms = 1.8961/1.9456, sse=221585.8/225496.0, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=221585.8, rms=1.896 (2.547%) 015: dt: 0.1250, sse=215442.0, rms=1.822 (3.916%) rms = 1.8089/1.8218, sse=214660.6/215442.0, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=214660.6, rms=1.809 (0.708%) maximum number of reductions reached, breaking from loop positioning took 7.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6059 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6237, nmarked2=127, nripped=6237 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=1 had to be increased for 153 vertices, nripped=6237 mean border=78.9, 133 (27) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.3 (%26.5))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.5167 min Finding expansion regions mean absolute distance = 0.33 +- 0.56 2468 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=login, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=769020.4, rms=5.028 017: dt: 0.5000, sse=454514.9, rms=3.387 (32.637%) rms = 3.5764/3.3872, sse=492826.9/454514.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=336518.3, rms=2.522 (25.546%) 019: dt: 0.2500, sse=278828.8, rms=1.963 (22.159%) 020: dt: 0.2500, sse=257350.2, rms=1.711 (12.847%) 021: dt: 0.2500, sse=249612.5, rms=1.605 (6.179%) 022: dt: 0.2500, sse=245451.3, rms=1.540 (4.054%) rms = 1.5027/1.5401, sse=243460.7/245451.3, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=243460.7, rms=1.503 (2.425%) 024: dt: 0.1250, sse=240099.3, rms=1.443 (3.972%) rms = 1.4319/1.4430, sse=240130.2/240099.3, time step reduction 3 of 3 to 0.062 0 1 1 025: dt: 0.1250, sse=240130.2, rms=1.432 (0.769%) maximum number of reductions reached, breaking from loop positioning took 3.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6237 removing 1 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6258, nmarked2=129, nripped=6258 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 148 vertices, nripped=6258 mean border=81.3, 153 (17) missing vertices, mean dist -0.1 [0.3 (%70.4)->0.2 (%29.6))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2423 min Finding expansion regions mean absolute distance = 0.25 +- 0.39 3160 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=login, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=458944.4, rms=3.427 026: dt: 0.5000, sse=400976.1, rms=3.003 (12.368%) rms = 3.3509/3.0031, sse=446989.6/400976.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=284047.4, rms=1.993 (33.651%) 028: dt: 0.2500, sse=245300.2, rms=1.509 (24.257%) 029: dt: 0.2500, sse=235658.6, rms=1.356 (10.124%) rms = 1.3323/1.3564, sse=237407.4/235658.6, time step reduction 2 of 3 to 0.125 0 1 1 030: dt: 0.2500, sse=237407.4, rms=1.332 (1.775%) 031: dt: 0.1250, sse=228890.5, rms=1.255 (5.797%) rms = 1.2445/1.2551, sse=229090.6/228890.5, time step reduction 3 of 3 to 0.062 0 1 1 032: dt: 0.1250, sse=229090.6, rms=1.244 (0.849%) maximum number of reductions reached, breaking from loop positioning took 2.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6258 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6340, nmarked2=132, nripped=6340 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 169 vertices, nripped=6340 mean border=82.2, 197 (14) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.1989 min Finding expansion regions mean absolute distance = 0.21 +- 0.33 2576 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=login, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=256688.6, rms=1.695 rms = 1.9535/1.6949, sse=277768.8/256688.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=223117.0, rms=1.202 (29.083%) 034: dt: 0.2500, sse=213086.8, rms=0.970 (19.332%) rms = 0.9744/0.9696, sse=211636.4/213086.8, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.9644/0.9696, sse=212590.6/213086.8, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=212590.6, rms=0.964 (0.533%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 16.94 minutes #VMPC# mris_make_surfaces VmPeak 2242380 mris_place_surface done @#@FSTIME 2020:07:15:10:06:22 mris_place_surface N 16 e 1059.51 S 2.15 U 363.83 P 34% M 1871676 F 0 R 271428 W 0 c 152414 w 94 I 0 O 0 L 15.99 16.09 15.92 @#@FSLOADPOST 2020:07:15:10:24:01 mris_place_surface N 16 14.99 15.03 15.34 #-------------------------------------------- #@# CortexLabel lh Wed Jul 15 10:24:02 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 13 non-cortical segments detected only using segment with 6953 vertices erasing segment 0 (vno[0] = 28085) erasing segment 2 (vno[0] = 47776) erasing segment 3 (vno[0] = 59671) erasing segment 4 (vno[0] = 68493) erasing segment 5 (vno[0] = 68527) erasing segment 6 (vno[0] = 68537) erasing segment 7 (vno[0] = 70026) erasing segment 8 (vno[0] = 73772) erasing segment 9 (vno[0] = 75175) erasing segment 10 (vno[0] = 99377) erasing segment 11 (vno[0] = 100092) erasing segment 12 (vno[0] = 116209) @#@FSTIME 2020:07:15:10:24:02 mri_label2label N 5 e 66.70 S 0.27 U 21.01 P 31% M 337432 F 0 R 34969 W 0 c 9912 w 83 I 0 O 0 L 14.99 15.03 15.34 @#@FSLOADPOST 2020:07:15:10:25:09 mri_label2label N 5 14.92 14.98 15.30 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Wed Jul 15 10:25:09 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 12 non-cortical segments detected only using segment with 5251 vertices erasing segment 0 (vno[0] = 28085) erasing segment 2 (vno[0] = 42986) erasing segment 3 (vno[0] = 59671) erasing segment 4 (vno[0] = 65078) erasing segment 5 (vno[0] = 67719) erasing segment 6 (vno[0] = 68493) erasing segment 7 (vno[0] = 68527) erasing segment 8 (vno[0] = 70026) erasing segment 9 (vno[0] = 73772) erasing segment 10 (vno[0] = 75175) erasing segment 11 (vno[0] = 116209) @#@FSTIME 2020:07:15:10:25:09 mri_label2label N 5 e 56.37 S 0.33 U 20.41 P 36% M 333156 F 0 R 33901 W 0 c 12284 w 80 I 0 O 0 L 14.92 14.98 15.30 @#@FSLOADPOST 2020:07:15:10:26:05 mri_label2label N 5 14.65 14.89 15.25 #-------------------------------------------- #@# CortexLabel rh Wed Jul 15 10:26:05 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 10 non-cortical segments detected only using segment with 7065 vertices erasing segment 0 (vno[0] = 12690) erasing segment 1 (vno[0] = 16270) erasing segment 2 (vno[0] = 17595) erasing segment 4 (vno[0] = 31685) erasing segment 5 (vno[0] = 37963) erasing segment 6 (vno[0] = 47835) erasing segment 7 (vno[0] = 55527) erasing segment 8 (vno[0] = 75567) erasing segment 9 (vno[0] = 111761) @#@FSTIME 2020:07:15:10:26:06 mri_label2label N 5 e 66.11 S 0.26 U 21.02 P 32% M 323108 F 0 R 33373 W 0 c 9028 w 39 I 0 O 0 L 14.65 14.89 15.25 @#@FSLOADPOST 2020:07:15:10:27:12 mri_label2label N 5 15.10 15.02 15.27 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Wed Jul 15 10:27:12 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 17 non-cortical segments detected only using segment with 4742 vertices erasing segment 0 (vno[0] = 12690) erasing segment 1 (vno[0] = 16270) erasing segment 2 (vno[0] = 17595) erasing segment 4 (vno[0] = 31685) erasing segment 5 (vno[0] = 32340) erasing segment 6 (vno[0] = 33753) erasing segment 7 (vno[0] = 35537) erasing segment 8 (vno[0] = 37963) erasing segment 9 (vno[0] = 47835) erasing segment 10 (vno[0] = 54146) erasing segment 11 (vno[0] = 55527) erasing segment 12 (vno[0] = 64868) erasing segment 13 (vno[0] = 67152) erasing segment 14 (vno[0] = 75567) erasing segment 15 (vno[0] = 102073) erasing segment 16 (vno[0] = 111761) @#@FSTIME 2020:07:15:10:27:12 mri_label2label N 5 e 61.91 S 0.30 U 20.80 P 34% M 352808 F 0 R 36200 W 0 c 13073 w 42 I 0 O 0 L 15.10 15.02 15.27 @#@FSLOADPOST 2020:07:15:10:28:14 mri_label2label N 5 14.92 14.95 15.23 #-------------------------------------------- #@# Smooth2 lh Wed Jul 15 10:28:14 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts 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... @#@FSTIME 2020:07:15:10:28:14 mris_smooth N 7 e 17.87 S 0.20 U 5.06 P 29% M 186804 F 0 R 32871 W 0 c 5597 w 173 I 0 O 0 L 14.92 14.95 15.23 @#@FSLOADPOST 2020:07:15:10:28:32 mris_smooth N 7 15.31 15.04 15.25 #-------------------------------------------- #@# Smooth2 rh Wed Jul 15 10:28:32 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts 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... @#@FSTIME 2020:07:15:10:28:32 mris_smooth N 7 e 15.79 S 0.15 U 5.05 P 32% M 185348 F 0 R 31937 W 0 c 3272 w 44 I 0 O 0 L 15.31 15.04 15.25 @#@FSLOADPOST 2020:07:15:10:28:48 mris_smooth N 7 15.39 15.07 15.26 #-------------------------------------------- #@# Inflation2 lh Wed Jul 15 10:28:48 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.6 mm, total surface area = 76598 mm^2 step 000: RMS=0.176 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 2.0 minutes mris_inflate utimesec 35.241642 mris_inflate stimesec 0.404938 mris_inflate ru_maxrss 248576 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49073 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 79 mris_inflate ru_nivcsw 24291 @#@FSTIME 2020:07:15:10:28:49 mris_inflate N 2 e 118.01 S 0.42 U 35.24 P 30% M 248576 F 0 R 49075 W 0 c 24306 w 82 I 0 O 0 L 15.39 15.07 15.26 @#@FSLOADPOST 2020:07:15:10:30:47 mris_inflate N 2 15.14 15.09 15.24 #-------------------------------------------- #@# Inflation2 rh Wed Jul 15 10:30:47 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.3 mm, total surface area = 76666 mm^2 step 000: RMS=0.178 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.028 (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) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 1.7 minutes mris_inflate utimesec 34.694725 mris_inflate stimesec 0.417936 mris_inflate ru_maxrss 246652 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49551 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 124 mris_inflate ru_nivcsw 22121 @#@FSTIME 2020:07:15:10:30:47 mris_inflate N 2 e 104.36 S 0.44 U 34.69 P 33% M 246652 F 0 R 49553 W 0 c 22135 w 128 I 0 O 0 L 15.14 15.09 15.24 @#@FSLOADPOST 2020:07:15:10:32:31 mris_inflate N 2 14.93 15.02 15.20 #-------------------------------------------- #@# Curv .H and .K lh Wed Jul 15 10:32:31 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 28.422*4pi (357.157) --> -27 handles ICI = 156.7, FI = 1478.6, variation=23374.157 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2020:07:15:10:32:31 mris_curvature N 4 e 8.50 S 0.14 U 2.43 P 30% M 137828 F 0 R 24572 W 0 c 2591 w 140 I 0 O 0 L 14.93 15.02 15.20 @#@FSLOADPOST 2020:07:15:10:32:40 mris_curvature N 4 14.85 15.00 15.19 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 -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 127 vertices thresholded to be in k1 ~ [-0.63 0.70], k2 ~ [-0.14 0.35] total integrated curvature = 0.409*4pi (5.139) --> 1 handles ICI = 1.4, FI = 9.2, variation=157.379 128 vertices thresholded to be in [-0.10 0.04] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 104 vertices thresholded to be in [-0.26 0.24] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.019, std = 0.025 done. @#@FSTIME 2020:07:15:10:32:40 mris_curvature N 12 e 193.88 S 0.68 U 65.39 P 34% M 328460 F 0 R 71211 W 0 c 38163 w 89 I 0 O 0 L 14.85 15.00 15.19 @#@FSLOADPOST 2020:07:15:10:35:54 mris_curvature N 12 15.13 15.04 15.16 #-------------------------------------------- #@# Curv .H and .K rh Wed Jul 15 10:35:54 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 20.169*4pi (253.457) --> -19 handles ICI = 148.1, FI = 1440.3, variation=22763.521 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2020:07:15:10:35:54 mris_curvature N 4 e 8.38 S 0.10 U 2.56 P 31% M 136740 F 0 R 24235 W 0 c 1190 w 102 I 0 O 0 L 15.13 15.04 15.16 @#@FSLOADPOST 2020:07:15:10:36:03 mris_curvature N 4 15.33 15.09 15.18 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 -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 127 vertices thresholded to be in k1 ~ [-0.31 0.38], k2 ~ [-0.11 0.09] total integrated curvature = 0.518*4pi (6.512) --> 0 handles ICI = 1.4, FI = 8.8, variation=151.876 98 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 118 vertices thresholded to be in [-0.16 0.18] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.023 done. @#@FSTIME 2020:07:15:10:36:03 mris_curvature N 12 e 189.61 S 0.79 U 63.31 P 33% M 325892 F 0 R 71521 W 0 c 44107 w 92 I 0 O 0 L 15.33 15.09 15.18 @#@FSLOADPOST 2020:07:15:10:39:13 mris_curvature N 12 15.40 15.25 15.22 #-------------------------------------------- #@# Sphere lh Wed Jul 15 10:39:13 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.285... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=login, 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.72 pass 1: epoch 2 of 3 starting distance error %21.71 unfolding complete - removing small folds... starting distance error %21.57 removing remaining folds... final distance error %21.62 MRISunfold() return, current seed 1234 -01: dt=0.0000, 16 negative triangles 195: dt=0.9900, 16 negative triangles 196: dt=0.9900, 12 negative triangles 197: dt=0.9900, 7 negative triangles 198: dt=0.9900, 6 negative triangles 199: dt=0.9900, 5 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 4 negative triangles 202: dt=0.9900, 1 negative triangles 203: dt=0.9900, 5 negative triangles 204: dt=0.9900, 3 negative triangles 205: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere mris_sphere utimesec 1078.363063 mris_sphere stimesec 10.827353 mris_sphere ru_maxrss 2004944 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 849751 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 67 mris_sphere ru_nivcsw 722996 spherical transformation took 1.4473 hours FSRUNTIME@ mris_sphere 1.4473 hours 1 threads @#@FSTIME 2020:07:15:10:39:13 mris_sphere N 6 e 5211.20 S 11.02 U 1078.36 P 20% M 2004944 F 0 R 849754 W 0 c 723087 w 79 I 0 O 0 L 15.40 15.25 15.22 @#@FSLOADPOST 2020:07:15:12:06:04 mris_sphere N 6 22.13 22.91 23.14 #-------------------------------------------- #@# Sphere rh Wed Jul 15 12:06:05 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.283... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=login, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %43.73 pass 1: epoch 2 of 3 starting distance error %22.40 unfolding complete - removing small folds... starting distance error %22.21 removing remaining folds... final distance error %22.26 MRISunfold() return, current seed 1234 -01: dt=0.0000, 0 negative triangles writing spherical brain to ../surf/rh.sphere mris_sphere utimesec 877.764559 mris_sphere stimesec 8.751669 mris_sphere ru_maxrss 1893040 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 803747 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 256 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 848 mris_sphere ru_nivcsw 600201 spherical transformation took 1.0223 hours FSRUNTIME@ mris_sphere 1.0223 hours 1 threads @#@FSTIME 2020:07:15:12:06:05 mris_sphere N 6 e 3681.38 S 8.97 U 877.76 P 24% M 1893040 F 1 R 803836 W 0 c 600424 w 1036 I 256 O 0 L 22.13 22.91 23.14 @#@FSLOADPOST 2020:07:15:13:07:26 mris_sphere N 6 19.57 19.86 20.33 #-------------------------------------------- #@# Surf Reg lh Wed Jul 15 13:07:26 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.0 7.1.0 reading surface from ../surf/lh.sphere... reading template parameterization from /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=login, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=login, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=login, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.581 curvature mean = 0.041, std = 0.813 curvature mean = 0.008, std = 0.873 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (0.50, -6.50, 9.50) sse = 225953.2, elapsed since starting=2.3579 min MRISrigidBodyAlignGlobal() done 2.36 min curvature mean = 0.020, std = 0.838 curvature mean = 0.003, std = 0.953 curvature mean = 0.017, std = 0.850 curvature mean = 0.001, std = 0.982 curvature mean = 0.017, std = 0.853 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.023, std = 0.272 curvature mean = 0.044, std = 0.249 curvature mean = 0.052, std = 0.389 curvature mean = 0.034, std = 0.310 curvature mean = 0.036, std = 0.575 curvature mean = 0.033, std = 0.338 curvature mean = 0.019, std = 0.716 curvature mean = 0.033, std = 0.350 curvature mean = 0.006, std = 0.821 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles 106: dt=0.9900, 15 negative triangles 107: dt=0.9900, 13 negative triangles 108: dt=0.9900, 10 negative triangles 109: dt=0.9900, 10 negative triangles 110: dt=0.9900, 8 negative triangles 111: dt=0.9900, 2 negative triangles 112: dt=0.9900, 5 negative triangles 113: dt=0.9900, 4 negative triangles 114: dt=0.9900, 1 negative triangles 115: dt=0.9900, 2 negative triangles 116: dt=0.9900, 1 negative triangles 117: dt=0.9900, 3 negative triangles 118: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.87 hours #VMPC# mris_register VmPeak 1623492 FSRUNTIME@ mris_register 0.8685 hours 1 threads @#@FSTIME 2020:07:15:13:07:27 mris_register N 6 e 3127.76 S 6.15 U 746.98 P 24% M 1252580 F 3 R 498486 W 0 c 687941 w 654 I 680 O 0 L 19.57 19.86 20.33 @#@FSLOADPOST 2020:07:15:13:59:35 mris_register N 6 32.65 32.57 28.79 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Wed Jul 15 13:59:35 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.0 7.1.0 reading surface from ../surf/rh.sphere... reading template parameterization from /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=login, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=login, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=login, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.770 curvature mean = 0.062, std = 0.813 curvature mean = 0.005, std = 0.876 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.50, -11.00, 12.50) sse = 277082.9, elapsed since starting=4.1615 min MRISrigidBodyAlignGlobal() done 4.17 min curvature mean = 0.036, std = 0.834 curvature mean = 0.003, std = 0.954 curvature mean = 0.033, std = 0.845 curvature mean = 0.001, std = 0.982 curvature mean = 0.032, std = 0.848 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.020, std = 0.273 curvature mean = 0.044, std = 0.244 curvature mean = 0.051, std = 0.387 curvature mean = 0.037, std = 0.303 curvature mean = 0.033, std = 0.574 curvature mean = 0.036, std = 0.330 curvature mean = 0.016, std = 0.713 curvature mean = 0.036, std = 0.342 curvature mean = 0.004, std = 0.817 MRISregister() return, current seed 0 -01: dt=0.0000, 3 negative triangles 107: dt=0.9900, 3 negative triangles 108: dt=0.9900, 1 negative triangles 109: dt=0.9900, 2 negative triangles 110: dt=0.9900, 2 negative triangles 111: dt=0.9900, 1 negative triangles 112: dt=0.9900, 2 negative triangles 113: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 2.12 hours #VMPC# mris_register VmPeak 1614780 FSRUNTIME@ mris_register 2.1164 hours 1 threads @#@FSTIME 2020:07:15:13:59:36 mris_register N 6 e 7621.66 S 8.14 U 855.45 P 11% M 1243832 F 0 R 494959 W 0 c 736196 w 723 I 0 O 0 L 32.65 32.57 28.79 @#@FSLOADPOST 2020:07:15:16:06:38 mris_register N 6 47.44 48.76 48.99 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Wed Jul 15 16:06:38 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2020:07:15:16:06:39 mris_jacobian N 3 e 25.49 S 0.21 U 1.78 P 7% M 186444 F 0 R 36733 W 0 c 1836 w 113 I 0 O 0 L 47.44 48.76 48.99 @#@FSLOADPOST 2020:07:15:16:07:04 mris_jacobian N 3 47.37 48.65 48.95 #-------------------------------------------- #@# Jacobian white rh Wed Jul 15 16:07:05 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2020:07:15:16:07:05 mris_jacobian N 3 e 26.97 S 0.24 U 1.75 P 7% M 184988 F 0 R 34264 W 0 c 1555 w 65 I 0 O 0 L 47.58 48.67 48.95 @#@FSLOADPOST 2020:07:15:16:07:32 mris_jacobian N 3 49.13 48.95 49.04 #-------------------------------------------- #@# AvgCurv lh Wed Jul 15 16:07:32 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2020:07:15:16:07:33 mrisp_paint N 5 e 18.62 S 0.13 U 1.36 P 8% M 142968 F 0 R 23569 W 0 c 1562 w 109 I 0 O 0 L 49.13 48.95 49.04 @#@FSLOADPOST 2020:07:15:16:07:52 mrisp_paint N 5 48.29 48.75 48.97 #-------------------------------------------- #@# AvgCurv rh Wed Jul 15 16:07:52 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2020:07:15:16:07:53 mrisp_paint N 5 e 17.72 S 0.11 U 1.38 P 8% M 141884 F 0 R 25277 W 0 c 2034 w 64 I 0 O 0 L 48.29 48.75 48.97 @#@FSLOADPOST 2020:07:15:16:08:11 mrisp_paint N 5 48.59 48.78 48.97 #----------------------------------------- #@# Cortical Parc lh Wed Jul 15 16:08:11 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK lh ../surf/lh.sphere.reg /public/apps/freesurfer/7.1.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.1.0 7.1.0 reading atlas from /public/apps/freesurfer/7.1.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 934 labels changed using aseg relabeling using gibbs priors... 000: 2780 changed, 121584 examined... 001: 640 changed, 11727 examined... 002: 137 changed, 3668 examined... 003: 67 changed, 821 examined... 004: 19 changed, 378 examined... 005: 5 changed, 112 examined... 006: 2 changed, 27 examined... 007: 0 changed, 13 examined... 261 labels changed using aseg 000: 95 total segments, 52 labels (177 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2103 vertices marked for relabeling... 2103 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 3 minutes and 38 seconds. @#@FSTIME 2020:07:15:16:08:12 mris_ca_label N 11 e 218.32 S 0.97 U 16.93 P 8% M 1058256 F 0 R 168431 W 0 c 14975 w 133 I 0 O 0 L 48.59 48.78 48.97 @#@FSLOADPOST 2020:07:15:16:11:50 mris_ca_label N 11 48.77 48.59 48.84 #----------------------------------------- #@# Cortical Parc rh Wed Jul 15 16:11:51 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK rh ../surf/rh.sphere.reg /public/apps/freesurfer/7.1.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.1.0 7.1.0 reading atlas from /public/apps/freesurfer/7.1.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1069 labels changed using aseg relabeling using gibbs priors... 000: 2532 changed, 120651 examined... 001: 558 changed, 11079 examined... 002: 97 changed, 3257 examined... 003: 24 changed, 603 examined... 004: 10 changed, 161 examined... 005: 3 changed, 66 examined... 006: 3 changed, 20 examined... 007: 3 changed, 14 examined... 008: 0 changed, 13 examined... 152 labels changed using aseg 000: 78 total segments, 40 labels (181 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1631 vertices marked for relabeling... 1631 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 3 minutes and 29 seconds. @#@FSTIME 2020:07:15:16:11:51 mris_ca_label N 11 e 209.74 S 0.80 U 16.45 P 8% M 979880 F 0 R 157941 W 0 c 11395 w 51 I 0 O 0 L 48.77 48.59 48.84 @#@FSLOADPOST 2020:07:15:16:15:21 mris_ca_label N 11 47.60 48.15 48.62 #-------------------------------------------- #@# WhiteSurfs lh Wed Jul 15 16:15:21 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 243164 0.35052 0.13931 0.000742 2.7779 Corner 729492 60.00000 15.11349 0.045430 179.7944 Edge 364746 0.91335 0.22618 0.017634 4.7994 Hinge 364746 11.01831 12.74392 0.000030 179.9306 Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 596 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60792: xyz = (-58.9003,-8.02607,-5.80896) oxyz = (-58.9003,-8.02607,-5.80896) wxzy = (-58.9003,-8.02607,-5.80896) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=2 had to be increased for 240 vertices, nripped=7784 mean border=76.3, 169 (169) missing vertices, mean dist 0.3 [1.0 (%13.2)->0.5 (%86.8))] %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 3.5884 min Finding expansion regions mean absolute distance = 0.58 +- 0.85 2158 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=login, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1816108.8, rms=8.463 001: dt: 0.5000, sse=761890.1, rms=5.042 (40.428%) 002: dt: 0.5000, sse=542524.4, rms=3.906 (22.532%) 003: dt: 0.5000, sse=510930.9, rms=3.737 (4.316%) 004: dt: 0.5000, sse=477735.1, rms=3.552 (4.955%) rms = 3.6597/3.5519, sse=492807.5/477735.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=340966.9, rms=2.577 (27.455%) 006: dt: 0.2500, sse=294615.1, rms=2.130 (17.333%) 007: dt: 0.2500, sse=282812.5, rms=1.992 (6.490%) rms = 1.9671/1.9919, sse=279674.3/282812.5, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=279674.3, rms=1.967 (1.246%) rms = 1.9194/1.9671, sse=276148.4/279674.3, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=276148.4, rms=1.919 (2.423%) maximum number of reductions reached, breaking from loop positioning took 18.5 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=1 had to be increased for 276 vertices, nripped=7784 mean border=79.7, 206 (68) missing vertices, mean dist -0.2 [0.4 (%74.5)->0.3 (%25.5))] %75 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 2.5873 min Finding expansion regions mean absolute distance = 0.35 +- 0.62 2462 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=login, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=780637.4, rms=5.035 010: dt: 0.5000, sse=480954.8, rms=3.476 (30.960%) rms = 3.5866/3.4761, sse=496520.5/480954.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 011: dt: 0.2500, sse=370672.8, rms=2.715 (21.902%) 012: dt: 0.2500, sse=311422.1, rms=2.170 (20.058%) 013: dt: 0.2500, sse=287658.0, rms=1.912 (11.889%) 014: dt: 0.2500, sse=280988.2, rms=1.793 (6.259%) 015: dt: 0.2500, sse=279102.2, rms=1.725 (3.746%) rms = 1.6902/1.7254, sse=273442.7/279102.2, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=273442.7, rms=1.690 (2.036%) rms = 1.6414/1.6902, sse=271509.2/273442.7, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=271509.2, rms=1.641 (2.891%) maximum number of reductions reached, breaking from loop positioning took 14.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 218 vertices, nripped=7784 mean border=82.1, 245 (46) missing vertices, mean dist -0.1 [0.3 (%70.0)->0.2 (%30.0))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.4124 min Finding expansion regions mean absolute distance = 0.26 +- 0.43 2822 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=login, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=464447.0, rms=3.377 018: dt: 0.5000, sse=415216.3, rms=3.033 (10.200%) rms = 3.3342/3.0326, sse=453680.2/415216.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=303280.6, rms=2.105 (30.574%) 020: dt: 0.2500, sse=276947.9, rms=1.677 (20.324%) 021: dt: 0.2500, sse=255222.4, rms=1.554 (7.360%) rms = 1.5239/1.5540, sse=252445.7/255222.4, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=252445.7, rms=1.524 (1.941%) 023: dt: 0.1250, sse=246584.7, rms=1.465 (3.889%) rms = 1.4565/1.4646, sse=245848.6/246584.7, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=245848.6, rms=1.457 (0.553%) maximum number of reductions reached, breaking from loop positioning took 14.9 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 195 vertices, nripped=7784 mean border=82.9, 283 (34) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.0619 min Finding expansion regions mean absolute distance = 0.22 +- 0.34 2829 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=login, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=270942.9, rms=1.829 rms = 2.0282/1.8292, sse=299500.0/270942.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=241175.6, rms=1.409 (22.968%) 026: dt: 0.2500, sse=233158.7, rms=1.219 (13.491%) rms = 1.2137/1.2190, sse=232376.9/233158.7, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=232376.9, rms=1.214 (0.431%) rms = 1.1924/1.2137, sse=232168.5/232376.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=232168.5, rms=1.192 (1.756%) maximum number of reductions reached, breaking from loop positioning took 8.8 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 66.29 minutes #VMPC# mris_make_surfaces VmPeak 2141292 mris_place_surface done @#@FSTIME 2020:07:15:16:15:22 mris_place_surface N 23 e 4149.17 S 5.93 U 323.59 P 7% M 1768592 F 2632 R 271850 W 0 c 295899 w 3578 I 105032 O 0 L 47.60 48.15 48.62 @#@FSLOADPOST 2020:07:15:17:24:31 mris_place_surface N 23 53.61 52.78 51.81 #-------------------------------------------- #@# WhiteSurfs rh Wed Jul 15 17:24:32 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 241298 0.35396 0.14338 0.000520 2.5626 Corner 723894 60.00000 15.19336 0.179379 179.1707 Edge 361947 0.91800 0.23261 0.018004 3.7026 Hinge 361947 10.94590 12.23444 0.000008 179.8654 Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 452 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60326: xyz = (5.85365,-6.8849,31.622) oxyz = (5.85365,-6.8849,31.622) wxzy = (5.85365,-6.8849,31.622) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=2 had to be increased for 197 vertices, nripped=7736 mean border=75.0, 148 (148) missing vertices, mean dist 0.3 [0.9 (%12.5)->0.5 (%87.5))] %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 4.0024 min Finding expansion regions mean absolute distance = 0.58 +- 0.82 1979 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=login, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1939352.0, rms=8.812 001: dt: 0.5000, sse=787804.2, rms=5.175 (41.277%) 002: dt: 0.5000, sse=531802.2, rms=3.900 (24.630%) 003: dt: 0.5000, sse=489836.5, rms=3.679 (5.677%) 004: dt: 0.5000, sse=458009.6, rms=3.480 (5.394%) rms = 3.5871/3.4802, sse=475411.5/458009.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=320597.2, rms=2.444 (29.770%) 006: dt: 0.2500, sse=273653.1, rms=1.959 (19.863%) 007: dt: 0.2500, sse=261204.7, rms=1.803 (7.956%) rms = 1.7668/1.8029, sse=258120.7/261204.7, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=258120.7, rms=1.767 (2.001%) 009: dt: 0.1250, sse=254029.7, rms=1.710 (3.214%) rms = 1.7007/1.7100, sse=253070.1/254029.7, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=253070.0, rms=1.701 (0.542%) maximum number of reductions reached, breaking from loop positioning took 24.4 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=1 had to be increased for 159 vertices, nripped=7736 mean border=78.6, 138 (54) missing vertices, mean dist -0.2 [0.4 (%74.5)->0.3 (%25.5))] %76 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 3.0638 min Finding expansion regions mean absolute distance = 0.34 +- 0.58 2278 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=login, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=760242.0, rms=4.978 011: dt: 0.5000, sse=441958.4, rms=3.267 (34.363%) rms = 3.4424/3.2673, sse=466857.3/441958.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=333185.9, rms=2.424 (25.810%) 013: dt: 0.2500, sse=279080.3, rms=1.861 (23.221%) 014: dt: 0.2500, sse=265366.9, rms=1.615 (13.217%) 015: dt: 0.2500, sse=253889.9, rms=1.525 (5.593%) rms = 1.4853/1.5248, sse=251691.9/253889.9, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=251691.9, rms=1.485 (2.594%) rms = 1.4385/1.4853, sse=248710.8/251691.9, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=248710.8, rms=1.438 (3.150%) maximum number of reductions reached, breaking from loop positioning took 15.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 145 vertices, nripped=7736 mean border=81.1, 164 (35) missing vertices, mean dist -0.1 [0.3 (%70.8)->0.2 (%29.2))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.6255 min Finding expansion regions mean absolute distance = 0.26 +- 0.41 2595 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=login, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=472997.0, rms=3.503 018: dt: 0.5000, sse=412031.8, rms=3.029 (13.531%) rms = 3.3378/3.0288, sse=449040.2/412031.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=294910.4, rms=2.030 (32.986%) 020: dt: 0.2500, sse=254716.6, rms=1.542 (24.005%) 021: dt: 0.2500, sse=248713.9, rms=1.387 (10.064%) rms = 1.3599/1.3872, sse=240037.8/248713.9, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=240037.8, rms=1.360 (1.970%) 023: dt: 0.1250, sse=233839.1, rms=1.293 (4.937%) rms = 1.2875/1.2928, sse=233486.5/233839.1, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=233486.5, rms=1.288 (0.407%) maximum number of reductions reached, breaking from loop positioning took 15.3 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 138 vertices, nripped=7736 mean border=82.0, 209 (30) missing vertices, mean dist -0.0 [0.2 (%56.9)->0.2 (%43.1))] %87 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.0509 min Finding expansion regions mean absolute distance = 0.22 +- 0.33 2535 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=login, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=260555.1, rms=1.735 rms = 1.9964/1.7346, sse=287061.2/260555.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=229627.0, rms=1.252 (27.814%) 026: dt: 0.2500, sse=219146.3, rms=1.033 (17.501%) rms = 1.0314/1.0330, sse=217569.0/219146.3, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=217569.0, rms=1.031 (0.151%) rms = 1.0134/1.0314, sse=216242.6/217569.0, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=216242.6, rms=1.013 (1.748%) maximum number of reductions reached, breaking from loop positioning took 9.3 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 75.43 minutes #VMPC# mris_make_surfaces VmPeak 2129072 mris_place_surface done @#@FSTIME 2020:07:15:17:24:33 mris_place_surface N 23 e 4723.99 S 5.03 U 327.43 P 7% M 1757292 F 4 R 278451 W 0 c 305331 w 787 I 824 O 64 L 53.61 52.78 51.81 @#@FSLOADPOST 2020:07:15:18:43:17 mris_place_surface N 23 56.98 57.22 57.29 #-------------------------------------------- #@# T1PialSurf lh Wed Jul 15 18:43:17 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 243164 0.35508 0.15712 0.000874 4.4682 Corner 729492 60.00000 16.47148 0.254243 178.5570 Edge 364746 0.92106 0.24746 0.012757 4.3354 Hinge 364746 11.16895 13.05167 0.000027 179.9306 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 62.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60792: xyz = (-58.963,-8.04709,-5.8071) oxyz = (-58.963,-8.04709,-5.8071) wxzy = (-58.963,-8.04709,-5.8071) pxyz = (-58.963,-8.04709,-5.8071) n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=2 had to be increased for 320 vertices, nripped=5585 mean border=50.2, 224 (224) missing vertices, mean dist 1.7 [1.3 (%0.1)->2.8 (%99.9))] %11 local maxima, %46 large gradients and %38 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 3.9182 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=login, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=25938204.0, rms=33.349 001: dt: 0.5000, sse=17847246.0, rms=27.617 (17.188%) 002: dt: 0.5000, sse=12116156.0, rms=22.696 (17.818%) 003: dt: 0.5000, sse=8437364.0, rms=18.871 (16.852%) 004: dt: 0.5000, sse=6180912.0, rms=16.080 (14.793%) 005: dt: 0.5000, sse=4713887.0, rms=13.967 (13.138%) 006: dt: 0.5000, sse=3640777.0, rms=12.191 (12.717%) 007: dt: 0.5000, sse=2813310.2, rms=10.619 (12.896%) 008: dt: 0.5000, sse=2181212.8, rms=9.238 (13.008%) 009: dt: 0.5000, sse=1715378.0, rms=8.068 (12.660%) 010: dt: 0.5000, sse=1389966.5, rms=7.136 (11.551%) 011: dt: 0.5000, sse=1184974.5, rms=6.478 (9.222%) 012: dt: 0.5000, sse=1047280.2, rms=5.994 (7.480%) 013: dt: 0.5000, sse=967312.0, rms=5.691 (5.046%) 014: dt: 0.5000, sse=910099.2, rms=5.463 (4.011%) 015: dt: 0.5000, sse=871898.5, rms=5.304 (2.916%) 016: dt: 0.5000, sse=840485.1, rms=5.168 (2.551%) 017: dt: 0.5000, sse=821681.5, rms=5.084 (1.637%) 018: dt: 0.5000, sse=801881.8, rms=4.994 (1.764%) rms = 4.9502/4.9940, sse=792886.2/801881.8, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=792886.2, rms=4.950 (0.878%) 020: dt: 0.2500, sse=669104.8, rms=4.356 (11.998%) 021: dt: 0.2500, sse=639890.6, rms=4.206 (3.447%) rms = 4.1760/4.2061, sse=634538.9/639890.6, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=634538.9, rms=4.176 (0.717%) 023: dt: 0.1250, sse=609071.9, rms=4.038 (3.296%) rms = 4.0060/4.0383, sse=603256.6/609071.9, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=603256.6, rms=4.006 (0.800%) maximum number of reductions reached, breaking from loop positioning took 44.6 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8682 vertices, nripped=5585 mean border=48.8, 1746 (64) missing vertices, mean dist 0.2 [0.2 (%51.7)->0.7 (%48.3))] %20 local maxima, %39 large gradients and %34 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.1219 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=login, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=809096.6, rms=4.783 rms = 4.7555/4.7825, sse=802806.3/809096.5, time step reduction 1 of 3 to 0.250 0 0 1 025: dt: 0.5000, sse=802806.2, rms=4.756 (0.564%) 026: dt: 0.2500, sse=680436.2, rms=4.161 (12.506%) 027: dt: 0.2500, sse=651473.6, rms=4.007 (3.693%) rms = 4.0038/4.0072, sse=651012.7/651473.5, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=651012.7, rms=4.004 (0.084%) 029: dt: 0.1250, sse=619307.0, rms=3.825 (4.461%) rms = 3.7795/3.8252, sse=611342.5/619307.0, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=611342.5, rms=3.780 (1.193%) maximum number of reductions reached, breaking from loop positioning took 11.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9272 vertices, nripped=5585 mean border=47.9, 2092 (53) missing vertices, mean dist 0.1 [0.2 (%48.4)->0.5 (%51.6))] %32 local maxima, %27 large gradients and %34 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.6667 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=login, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=664772.2, rms=4.048 rms = 4.3106/4.0475, sse=714540.1/664772.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=632151.8, rms=3.868 (4.432%) 032: dt: 0.2500, sse=614336.4, rms=3.769 (2.561%) rms = 3.7559/3.7691, sse=611604.8/614336.4, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=611604.8, rms=3.756 (0.350%) 034: dt: 0.1250, sse=590582.2, rms=3.631 (3.323%) rms = 3.5909/3.6310, sse=583760.5/590582.3, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=583760.4, rms=3.591 (1.105%) maximum number of reductions reached, breaking from loop positioning took 10.4 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7944 vertices, nripped=5585 mean border=47.3, 3958 (46) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.4 (%50.5))] %37 local maxima, %22 large gradients and %34 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.4333 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=login, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=602589.2, rms=3.695 rms = 3.9956/3.6949, sse=653918.8/602589.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=584005.9, rms=3.585 (2.988%) 037: dt: 0.2500, sse=573074.0, rms=3.524 (1.692%) rms = 3.5299/3.5239, sse=573340.5/573074.0, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 3.4926/3.5239, sse=568073.3/573074.0, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=568073.3, rms=3.493 (0.889%) maximum number of reductions reached, breaking from loop positioning took 8.4 minutes Pinning medial wall to white surface removing intersecting faces 000: 3 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 83.92 minutes #VMPC# mris_make_surfaces VmPeak 1473616 mris_place_surface done @#@FSTIME 2020:07:15:18:43:18 mris_place_surface N 26 e 5233.99 S 6.39 U 362.66 P 7% M 1101704 F 8 R 237231 W 0 c 358545 w 578 I 1456 O 0 L 56.98 57.22 57.29 @#@FSLOADPOST 2020:07:15:20:10:33 mris_place_surface N 26 57.97 57.85 57.00 #-------------------------------------------- #@# T1PialSurf rh Wed Jul 15 20:10:33 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 241298 0.35801 0.15879 0.001113 2.7729 Corner 723894 60.00000 16.49117 0.337430 178.9545 Edge 361947 0.92452 0.25065 0.018004 3.7782 Hinge 361947 11.10815 12.73349 0.000008 179.8859 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 61.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60326: xyz = (5.74563,-6.88357,31.7087) oxyz = (5.74563,-6.88357,31.7087) wxzy = (5.74563,-6.88357,31.7087) pxyz = (5.74563,-6.88357,31.7087) n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=2 had to be increased for 297 vertices, nripped=4992 mean border=49.2, 187 (187) missing vertices, mean dist 1.7 [2.3 (%0.0)->2.7 (%100.0))] %11 local maxima, %49 large gradients and %36 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 3.9522 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=login, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=25941204.0, rms=33.393 001: dt: 0.5000, sse=17783662.0, rms=27.602 (17.344%) 002: dt: 0.5000, sse=12049190.0, rms=22.660 (17.904%) 003: dt: 0.5000, sse=8382952.0, rms=18.831 (16.897%) 004: dt: 0.5000, sse=6142514.0, rms=16.046 (14.789%) 005: dt: 0.5000, sse=4675148.5, rms=13.922 (13.239%) 006: dt: 0.5000, sse=3605052.2, rms=12.139 (12.805%) 007: dt: 0.5000, sse=2780183.5, rms=10.560 (13.009%) 008: dt: 0.5000, sse=2154788.8, rms=9.182 (13.053%) 009: dt: 0.5000, sse=1685812.0, rms=7.991 (12.965%) 010: dt: 0.5000, sse=1351264.4, rms=7.017 (12.189%) 011: dt: 0.5000, sse=1123493.8, rms=6.266 (10.705%) 012: dt: 0.5000, sse=977897.1, rms=5.732 (8.518%) 013: dt: 0.5000, sse=884450.2, rms=5.360 (6.498%) 014: dt: 0.5000, sse=825659.1, rms=5.109 (4.669%) 015: dt: 0.5000, sse=787147.9, rms=4.937 (3.370%) 016: dt: 0.5000, sse=759816.6, rms=4.810 (2.571%) 017: dt: 0.5000, sse=740951.1, rms=4.719 (1.893%) 018: dt: 0.5000, sse=726515.9, rms=4.648 (1.513%) 019: dt: 0.5000, sse=715975.2, rms=4.594 (1.151%) rms = 4.5491/4.5943, sse=707275.9/715975.2, time step reduction 1 of 3 to 0.250 0 0 1 020: dt: 0.5000, sse=707275.9, rms=4.549 (0.985%) 021: dt: 0.2500, sse=584760.2, rms=3.899 (14.284%) 022: dt: 0.2500, sse=555068.7, rms=3.728 (4.404%) rms = 3.7037/3.7276, sse=551356.3/555068.7, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=551356.3, rms=3.704 (0.641%) 024: dt: 0.1250, sse=529348.9, rms=3.569 (3.645%) rms = 3.5401/3.5687, sse=524803.8/529349.0, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=524803.8, rms=3.540 (0.800%) maximum number of reductions reached, breaking from loop positioning took 45.4 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8322 vertices, nripped=4992 mean border=47.9, 1427 (63) missing vertices, mean dist 0.1 [0.1 (%53.5)->0.6 (%46.5))] %20 local maxima, %42 large gradients and %33 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 1.0400 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=login, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=700082.9, rms=4.248 rms = 4.2881/4.2479, sse=707653.9/700082.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=638710.1, rms=3.920 (7.716%) 027: dt: 0.2500, sse=602381.1, rms=3.713 (5.294%) 028: dt: 0.2500, sse=590101.8, rms=3.642 (1.913%) rms = 3.5964/3.6416, sse=582424.8/590101.7, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=582424.8, rms=3.596 (1.241%) 030: dt: 0.1250, sse=562045.3, rms=3.468 (3.562%) rms = 3.4271/3.4683, sse=555494.0/562045.3, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=555493.9, rms=3.427 (1.187%) maximum number of reductions reached, breaking from loop positioning took 11.8 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 8817 vertices, nripped=4992 mean border=47.0, 1792 (43) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))] %34 local maxima, %28 large gradients and %33 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.6432 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=login, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=610533.0, rms=3.737 rms = 3.9764/3.7365, sse=652093.2/610533.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=575329.5, rms=3.525 (5.656%) 033: dt: 0.2500, sse=558595.2, rms=3.423 (2.894%) rms = 3.3996/3.4231, sse=554415.7/558595.3, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=554415.7, rms=3.400 (0.686%) 035: dt: 0.1250, sse=538461.6, rms=3.294 (3.098%) rms = 3.2625/3.2943, sse=533519.2/538461.6, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=533519.2, rms=3.263 (0.964%) maximum number of reductions reached, breaking from loop positioning took 9.7 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7533 vertices, nripped=4992 mean border=46.3, 3689 (38) missing vertices, mean dist 0.1 [0.2 (%49.8)->0.4 (%50.2))] %39 local maxima, %22 large gradients and %32 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.4147 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=login, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=555795.0, rms=3.398 rms = 3.6953/3.3981, sse=602513.7/555795.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=537152.0, rms=3.276 (3.578%) 038: dt: 0.2500, sse=526221.2, rms=3.209 (2.051%) rms = 3.1817/3.2092, sse=521400.9/526221.3, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=521400.9, rms=3.182 (0.860%) 040: dt: 0.1250, sse=506172.2, rms=3.075 (3.349%) rms = 3.0394/3.0751, sse=500877.1/506172.2, time step reduction 3 of 3 to 0.062 0 0 1 041: dt: 0.1250, sse=500877.1, rms=3.039 (1.162%) maximum number of reductions reached, breaking from loop positioning took 9.1 minutes Pinning medial wall to white surface removing intersecting faces 000: 11 intersecting step 1 with no progress (num=20, old_num=11) 001: 20 intersecting step 2 with no progress (num=34, old_num=20) 002: 34 intersecting step 3 with no progress (num=36, old_num=34) 003: 36 intersecting 004: 31 intersecting step 1 with no progress (num=31, old_num=31) 005: 31 intersecting step 2 with no progress (num=31, old_num=31) 006: 31 intersecting step 3 with no progress (num=31, old_num=31) 007: 31 intersecting step 4 with no progress (num=31, old_num=31) 008: 31 intersecting step 5 with no progress (num=31, old_num=31) 009: 31 intersecting step 6 with no progress (num=31, old_num=31) 010: 31 intersecting step 7 with no progress (num=31, old_num=31) 011: 31 intersecting step 8 with no progress (num=31, old_num=31) 012: 31 intersecting step 9 with no progress (num=31, old_num=31) 013: 31 intersecting step 10 with no progress (num=31, old_num=31) 014: 31 intersecting step 11 with no progress (num=31, old_num=31) 015: 31 intersecting step 12 with no progress (num=31, old_num=31) 016: 31 intersecting step 13 with no progress (num=31, old_num=31) 017: 31 intersecting step 14 with no progress (num=31, old_num=31) 018: 31 intersecting step 15 with no progress (num=31, old_num=31) 019: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 11 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 98.37 minutes #VMPC# mris_make_surfaces VmPeak 1483504 mris_place_surface done @#@FSTIME 2020:07:15:20:10:34 mris_place_surface N 26 e 6100.21 S 8.15 U 448.74 P 7% M 1111972 F 6 R 238107 W 0 c 462827 w 1017 I 1032 O 0 L 57.65 57.78 56.99 @#@FSLOADPOST 2020:07:15:21:52:14 mris_place_surface N 26 49.29 49.38 49.82 #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Jul 15 21:52:15 EDT 2020 bbregister --s 2012-646-010-KK --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz --lta /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 tmp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905 Log file is /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.log Wed Jul 15 21:52:17 EDT 2020 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts /public/apps/freesurfer/7.1.0/bin/bbregister --s 2012-646-010-KK --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz --lta /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 bbregister 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /public/apps/freesurfer/7.1.0 mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii... mri_coreg --s 2012-646-010-KK --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --regdat /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.init.dat --reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mri_coreg --s 2012-646-010-KK --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --regdat /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.init.dat --reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname loginnode2 machine x86_64 user pankumar dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii Reading in ref /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brainmask.mgz Reading in and applying refmask /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters 0.0329 -0.0267 -0.9344 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1056.8065 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0674189311 nhits = 195385 out of 16777216, Percent Overlap: 74.5 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.03286; 0.00000 1.00000 0.00000 -0.02670; 0.00000 0.00000 1.00000 -0.93436; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.99878 0.04198 -0.02611 -9.86693; 0.02250 0.08435 0.99618 -21.13648; 0.04402 -0.99554 0.08330 220.19832; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 0.03286 -0.02670 -0.93436 0.00000 0.00000 0.00000 -1.0565005 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0674189329 #@# 4 188 0.03286 -0.02670 -0.93436 0.00000 0.00000 0.00000 -1.0674189 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.067419 #@# 4 195 -0.00715 -0.02670 -0.93436 0.00000 0.00000 0.00000 -1.0674207 #@# 4 207 -0.00715 0.01230 -0.93436 0.00000 0.00000 0.00000 -1.0674248 #@# 4 211 -0.00715 0.01230 0.06564 0.00000 0.00000 0.00000 -1.0677868 #@# 4 215 -0.00715 0.01230 -0.31632 0.00000 0.00000 0.00000 -1.0681895 #@# 4 225 -0.00715 0.01230 -0.31632 0.09335 0.00000 0.00000 -1.0682040 #@# 4 226 -0.00715 0.01230 -0.31632 0.10335 0.00000 0.00000 -1.0682043 #@# 4 227 -0.00715 0.01230 -0.31632 0.11335 0.00000 0.00000 -1.0682051 #@# 4 238 -0.00715 0.01230 -0.31632 0.11335 0.01000 0.00000 -1.0682068 #@# 4 242 -0.00715 0.01230 -0.31632 0.11335 0.02000 0.00000 -1.0682083 #@# 4 249 -0.00715 0.01230 -0.31632 0.11335 0.02000 -0.18020 -1.0682358 #@# 4 250 -0.00715 0.01230 -0.31632 0.11335 0.02000 -0.19020 -1.0682368 #@# 4 252 -0.00715 0.01230 -0.31632 0.11335 0.02000 -0.22813 -1.0682371 powell nthiter 1: fret = -1.068237 #@# 4 263 -0.01789 0.01230 -0.31632 0.11335 0.02000 -0.22813 -1.0682374 #@# 4 271 -0.01789 0.04378 -0.31632 0.11335 0.02000 -0.22813 -1.0682410 #@# 4 272 -0.01789 0.05872 -0.31632 0.11335 0.02000 -0.22813 -1.0682428 #@# 4 283 -0.01789 0.05872 -0.32841 0.11335 0.02000 -0.22813 -1.0682434 #@# 4 291 -0.01789 0.05872 -0.32841 0.09233 0.02000 -0.22813 -1.0682442 #@# 4 301 -0.01789 0.05872 -0.32841 0.09233 0.00397 -0.22813 -1.0682453 Powell done niters total = 1 OptTimeSec 321.7 sec OptTimeMin 5.36 min nEvals 312 Final parameters -0.01789498 0.05871913 -0.32841101 0.09232926 0.00396726 -0.22813173 Final cost -1.068245252208528 --------------------------------- Final RefRAS-to-MovRAS 0.99999 -0.00398 0.00007 -0.01789; 0.00398 0.99999 0.00161 0.05872; -0.00008 -0.00161 1.00000 -0.32841; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.99887 0.04209 -0.02207 -10.32984; 0.01853 0.08275 0.99640 -20.37796; 0.04376 -0.99567 0.08187 221.02483; 0.00000 0.00000 0.00000 1.00000; Final parameters -0.0179 0.0587 -0.3284 0.0923 0.0040 -0.2281 nhits = 195366 out of 16777216, Percent Overlap: 74.5 mri_coreg RunTimeSec 1813.4 sec To check run: tkregisterfv --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --targ /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brainmask.mgz --reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/mri_coreg.lta --s 2012-646-010-KK --surfs mri_coreg done mri_segreg --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --init-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.init.dat --out-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 7.1.0 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_segreg --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --init-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.init.dat --out-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 sysname Linux hostname loginnode2 machine x86_64 user pankumar movvol /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii regfile /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.init.dat subject 2012-646-010-KK dof 6 outregfile /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1594909178 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99887 0.02207 0.04209 -0.08826; -0.04376 0.08187 0.99568 -0.34006; 0.01853 -0.99640 0.08275 -0.12389; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.051520 1 -25.0 -25.0 25.0 1.032998 2 -25.0 25.0 -25.0 1.024743 3 -25.0 25.0 25.0 1.013629 4 25.0 -25.0 -25.0 1.037696 5 25.0 -25.0 25.0 1.016000 6 25.0 25.0 -25.0 1.064261 7 25.0 25.0 25.0 1.060207 REL: 8 1.282380 8.301054 1.037632 rel = 1.23587 Initial costs ---------------- Number of surface hits 2276 WM Intensity 600.0881 +/- 91.1476 Ctx Intensity 549.1576 +/- 116.3532 Pct Contrast -10.2228 +/- 27.2771 Cost 1.2824 RelCost 1.2359 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0132 1.0132 0.0 17 -4.0000 -4.0000 -4.0000 0.0000 4.0000 4.0000 1.0124 1.0124 0.0 41 -4.0000 -4.0000 0.0000 0.0000 0.0000 4.0000 0.9760 0.9760 0.0 259 0.0000 -4.0000 -4.0000 0.0000 4.0000 0.0000 0.9654 0.9654 0.2 269 0.0000 -4.0000 -4.0000 4.0000 4.0000 4.0000 0.9608 0.9608 0.2 295 0.0000 -4.0000 0.0000 4.0000 4.0000 0.0000 0.9516 0.9516 0.2 Brute Force -------------------------- Min cost was 0.951626 Number of iterations 729 Search time 31.052523 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 4.000 4.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 4 4 4 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.951626 9 -0.031 -4.000 0.000 4.000 4.000 0.000 0.9513853061 11 -0.020 -4.000 0.000 4.000 4.000 0.000 0.9512764410 21 -0.020 -4.301 0.000 4.000 4.000 0.000 0.9508001136 22 -0.020 -4.273 0.000 4.000 4.000 0.000 0.9506605662 26 -0.020 -4.260 0.000 4.000 4.000 0.000 0.9504559063 29 -0.020 -4.257 0.000 4.000 4.000 0.000 0.9504317732 40 -0.020 -4.257 0.037 4.000 4.000 0.000 0.9497460111 41 -0.020 -4.257 0.041 4.000 4.000 0.000 0.9497455708 43 -0.020 -4.257 0.040 4.000 4.000 0.000 0.9497447537 53 -0.020 -4.257 0.040 3.912 4.000 0.000 0.9488219565 54 -0.020 -4.257 0.040 3.920 4.000 0.000 0.9487538181 55 -0.020 -4.257 0.040 3.934 4.000 0.000 0.9487059383 57 -0.020 -4.257 0.040 3.931 4.000 0.000 0.9487043081 73 -0.020 -4.257 0.040 3.931 3.995 0.000 0.9486723991 74 -0.020 -4.257 0.040 3.931 3.994 0.000 0.9486711588 84 -0.020 -4.257 0.040 3.931 3.994 -0.024 0.9485265850 85 -0.020 -4.257 0.040 3.931 3.994 -0.040 0.9484983838 86 -0.020 -4.257 0.040 3.931 3.994 -0.039 0.9484982496 powell nthiter 1: fret = 0.948498 100 -0.026 -4.257 0.040 3.931 3.994 -0.039 0.9484747324 102 -0.025 -4.257 0.040 3.931 3.994 -0.039 0.9484743166 115 -0.025 -4.260 0.040 3.931 3.994 -0.039 0.9484517907 116 -0.025 -4.269 0.040 3.931 3.994 -0.039 0.9484355353 117 -0.025 -4.267 0.040 3.931 3.994 -0.039 0.9484337169 128 -0.025 -4.267 0.051 3.931 3.994 -0.039 0.9482977953 129 -0.025 -4.267 0.057 3.931 3.994 -0.039 0.9482883444 130 -0.025 -4.267 0.056 3.931 3.994 -0.039 0.9482872447 142 -0.025 -4.267 0.056 3.918 3.994 -0.039 0.9482388983 143 -0.025 -4.267 0.056 3.920 3.994 -0.039 0.9482361215 155 -0.025 -4.267 0.056 3.920 3.995 -0.039 0.9482358188 166 -0.025 -4.267 0.056 3.920 3.995 -0.036 0.9482353435 167 -0.025 -4.267 0.056 3.920 3.995 -0.037 0.9482353262 169 -0.030 -4.276 0.072 3.909 3.996 -0.035 0.9481934407 177 -0.031 -4.278 0.076 3.906 3.997 -0.034 0.9481770304 178 -0.031 -4.280 0.078 3.905 3.997 -0.034 0.9481620490 179 -0.032 -4.280 0.080 3.904 3.997 -0.034 0.9481482587 187 -0.032 -4.280 0.079 3.904 3.997 -0.034 0.9481481037 powell nthiter 2: fret = 0.948148 195 -0.181 -4.280 0.079 3.904 3.997 -0.034 0.9478260997 196 -0.134 -4.280 0.079 3.904 3.997 -0.034 0.9472475879 198 -0.139 -4.280 0.079 3.904 3.997 -0.034 0.9468325953 199 -0.155 -4.280 0.079 3.904 3.997 -0.034 0.9467702681 200 -0.147 -4.280 0.079 3.904 3.997 -0.034 0.9465368696 201 -0.146 -4.280 0.079 3.904 3.997 -0.034 0.9465113010 215 -0.146 -4.277 0.079 3.904 3.997 -0.034 0.9465107048 217 -0.146 -4.278 0.079 3.904 3.997 -0.034 0.9465102166 227 -0.146 -4.278 0.079 3.904 3.997 -0.069 0.9464174557 228 -0.146 -4.278 0.079 3.904 3.997 -0.059 0.9463484279 229 -0.146 -4.278 0.079 3.904 3.997 -0.055 0.9463475018 230 -0.146 -4.278 0.079 3.904 3.997 -0.057 0.9463462945 240 -0.146 -4.278 0.079 3.907 3.997 -0.057 0.9463271005 241 -0.146 -4.278 0.079 3.918 3.997 -0.057 0.9463223777 243 -0.146 -4.278 0.079 3.913 3.997 -0.057 0.9463152594 244 -0.146 -4.278 0.079 3.914 3.997 -0.057 0.9463149664 252 -0.146 -4.278 0.079 3.914 4.034 -0.057 0.9443493675 253 -0.146 -4.278 0.079 3.914 4.148 -0.057 0.9429173591 257 -0.146 -4.278 0.079 3.914 4.135 -0.057 0.9428705545 259 -0.146 -4.278 0.079 3.914 4.137 -0.057 0.9428665749 267 -0.148 -4.282 0.086 3.910 4.138 -0.056 0.9426873682 268 -0.149 -4.284 0.089 3.907 4.138 -0.055 0.9426034677 269 -0.150 -4.285 0.092 3.905 4.138 -0.055 0.9425556741 270 -0.151 -4.286 0.093 3.904 4.138 -0.055 0.9425276092 273 -0.151 -4.287 0.094 3.904 4.138 -0.055 0.9425208682 powell nthiter 3: fret = 0.942521 287 -0.216 -4.287 0.094 3.904 4.138 -0.055 0.9407775509 290 -0.202 -4.287 0.094 3.904 4.138 -0.055 0.9405855863 291 -0.198 -4.287 0.094 3.904 4.138 -0.055 0.9405800278 305 -0.198 -4.282 0.094 3.904 4.138 -0.055 0.9405766479 306 -0.198 -4.281 0.094 3.904 4.138 -0.055 0.9405765266 315 -0.198 -4.281 0.094 3.904 4.138 -0.067 0.9405084070 316 -0.198 -4.281 0.094 3.904 4.138 -0.078 0.9404813209 317 -0.198 -4.281 0.094 3.904 4.138 -0.080 0.9404803652 373 -0.206 -4.280 0.094 3.904 4.138 -0.086 0.9404802705 374 -0.202 -4.281 0.094 3.904 4.138 -0.083 0.9404766733 powell nthiter 4: fret = 0.940477 408 -0.202 -4.283 0.094 3.904 4.138 -0.083 0.9404720090 409 -0.202 -4.285 0.094 3.904 4.138 -0.083 0.9404716031 419 -0.202 -4.285 0.094 3.904 4.138 -0.086 0.9404697752 421 -0.202 -4.285 0.094 3.904 4.138 -0.085 0.9404693629 449 -0.249 -4.280 0.094 3.904 4.138 -0.112 0.9404086444 455 -0.251 -4.280 0.094 3.904 4.138 -0.113 0.9404064103 457 -0.255 -4.279 0.094 3.904 4.138 -0.115 0.9404054505 458 -0.253 -4.279 0.094 3.904 4.138 -0.114 0.9404036770 459 -0.253 -4.279 0.094 3.904 4.138 -0.114 0.9404032598 463 -0.253 -4.279 0.094 3.904 4.138 -0.114 0.9404031262 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.003128 1 -25.0 -25.0 25.0 1.043222 2 -25.0 25.0 -25.0 1.061809 3 -25.0 25.0 25.0 1.035219 4 25.0 -25.0 -25.0 1.041234 5 25.0 -25.0 25.0 0.994572 6 25.0 25.0 -25.0 1.040369 7 25.0 25.0 25.0 1.050885 REL: 8 0.940403 8.270439 1.033805 rel = 0.909652 Number of iterations 4 Min cost was 0.940403 Number of FunctionCalls 466 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 19.304648 sec Parameters at optimum (transmm) -0.25319 -4.27930 0.09365 Parameters at optimum (rotdeg) 3.90403 4.13831 -0.11410 Final costs ---------------- Number of surface hits 2202 WM Intensity 562.8490 +/- 121.9845 Ctx Intensity 559.6511 +/- 139.8324 Pct Contrast -1.7090 +/- 38.3324 Cost 0.9404 RelCost 1.2359 Reg at min cost was 0.99729 -0.04903 0.05479 -0.35247; -0.04691 0.14962 0.98763 -4.60994; -0.05662 -0.98753 0.14692 -0.04635; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat, type = 14 Original Reg 0.99887 0.02207 0.04209 -0.08826; -0.04376 0.08187 0.99568 -0.34006; 0.01853 -0.99640 0.08275 -0.12389; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00158 0.07110 -0.01271 0.26421; 0.00315 -0.06775 0.00805 4.26988; 0.07515 -0.00887 -0.06417 -0.07754; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.085430 Computing change in rh position Surface-RMS-Diff-mm 7.065601 2.507488 13.254423 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --init-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat --out-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat.mincost --dof 6 --nmax 36 --param /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 7.1.0 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_segreg --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii --init-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat --out-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat.mincost --dof 6 --nmax 36 --param /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname loginnode2 machine x86_64 user pankumar movvol /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/template.nii regfile /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/tmp.bbregister.26905/bbr.pass1.dat subject 2012-646-010-KK dof 6 outregfile /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 1.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1595073052 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99729 -0.04903 0.05479 -0.35247; -0.04691 0.14962 0.98763 -4.60994; -0.05662 -0.98753 0.14692 -0.04635; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 1.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.028501 1 -25.0 -25.0 25.0 1.038689 2 -25.0 25.0 -25.0 1.046467 3 -25.0 25.0 25.0 1.033355 4 25.0 -25.0 -25.0 1.044855 5 25.0 -25.0 25.0 1.013750 6 25.0 25.0 -25.0 1.030627 7 25.0 25.0 25.0 1.048850 REL: 8 1.022448 8.285095 1.035637 rel = 0.987265 Initial costs ---------------- Number of surface hits 220307 WM Intensity 565.1623 +/- 125.5919 Ctx Intensity 554.1362 +/- 142.8274 Pct Contrast -3.8713 +/- 36.4262 Cost 1.0224 RelCost 0.9873 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9703 0.9703 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9678 0.9678 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.9650 0.9650 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.9616 0.9616 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.9616 0.9616 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.9576 0.9576 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.9548 0.9548 0.0 51 -0.1000 -0.1000 0.0000 0.1000 0.1000 -0.1000 0.9523 0.9523 0.0 78 -0.1000 -0.1000 0.1000 0.1000 0.1000 -0.1000 0.9521 0.9521 0.0 294 0.0000 -0.1000 0.0000 0.1000 0.1000 -0.1000 0.9513 0.9513 0.2 318 0.0000 -0.1000 0.1000 0.1000 0.0000 -0.1000 0.9502 0.9502 0.2 561 0.1000 -0.1000 0.1000 0.1000 0.0000 -0.1000 0.9484 0.9484 0.4 645 0.1000 0.0000 0.1000 0.1000 0.1000 -0.1000 0.9480 0.9480 0.4 Brute Force -------------------------- Min cost was 0.947999 Number of iterations 729 Search time 26.519215 sec Parameters at best (transmm, rotdeg) 0.100 0.000 0.100 0.100 0.100 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0 2 0.1 3 0.1 4 0.1 5 -0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.023800 3 -1.518 0.000 0.100 0.100 0.100 -0.100 1.0037883179 6 -2.518 0.000 0.100 0.100 0.100 -0.100 0.9982762968 9 -2.680 0.000 0.100 0.100 0.100 -0.100 0.9981292045 13 -2.690 0.000 0.100 0.100 0.100 -0.100 0.9980622536 14 -2.708 0.000 0.100 0.100 0.100 -0.100 0.9980619447 16 -2.699 0.000 0.100 0.100 0.100 -0.100 0.9980416576 18 -2.702 0.000 0.100 0.100 0.100 -0.100 0.9980352695 20 -2.701 0.000 0.100 0.100 0.100 -0.100 0.9980338531 23 -2.701 -1.618 0.100 0.100 0.100 -0.100 0.9913433151 24 -2.701 -1.482 0.100 0.100 0.100 -0.100 0.9912298217 30 -2.701 -1.472 0.100 0.100 0.100 -0.100 0.9911815198 32 -2.701 -1.461 0.100 0.100 0.100 -0.100 0.9911800223 33 -2.701 -1.465 0.100 0.100 0.100 -0.100 0.9911783496 34 -2.701 -1.466 0.100 0.100 0.100 -0.100 0.9911644974 36 -2.701 -1.467 0.100 0.100 0.100 -0.100 0.9911602339 41 -2.701 -1.467 -0.518 0.100 0.100 -0.100 0.9911517369 44 -2.701 -1.467 -0.664 0.100 0.100 -0.100 0.9910245043 46 -2.701 -1.467 -0.608 0.100 0.100 -0.100 0.9909041467 47 -2.701 -1.467 -0.604 0.100 0.100 -0.100 0.9908980095 52 -2.701 -1.467 -0.603 0.100 0.100 -0.100 0.9908968082 56 -2.701 -1.467 -0.603 -1.518 0.100 -0.100 0.9823540560 60 -2.701 -1.467 -0.603 -2.549 0.100 -0.100 0.9783153088 65 -2.701 -1.467 -0.603 -2.554 0.100 -0.100 0.9782954086 78 -2.701 -1.467 -0.603 -2.554 0.101 -0.100 0.9782846651 79 -2.701 -1.467 -0.603 -2.554 0.107 -0.100 0.9782782897 83 -2.701 -1.467 -0.603 -2.554 0.106 -0.100 0.9782685934 90 -2.701 -1.467 -0.603 -2.554 0.106 -0.329 0.9780839405 91 -2.701 -1.467 -0.603 -2.554 0.106 -0.305 0.9780498096 94 -2.701 -1.467 -0.603 -2.554 0.106 -0.314 0.9780488806 96 -2.701 -1.467 -0.603 -2.554 0.106 -0.310 0.9780485097 97 -2.701 -1.467 -0.603 -2.554 0.106 -0.311 0.9780342052 powell nthiter 1: fret = 0.978034 101 -1.701 -1.467 -0.603 -2.554 0.106 -0.311 0.9773476716 106 -1.838 -1.467 -0.603 -2.554 0.106 -0.311 0.9772079927 111 -1.837 -1.467 -0.603 -2.554 0.106 -0.311 0.9772066169 116 -1.837 -3.085 -0.603 -2.554 0.106 -0.311 0.9721569543 124 -1.837 -3.251 -0.603 -2.554 0.106 -0.311 0.9717691650 125 -1.837 -3.248 -0.603 -2.554 0.106 -0.311 0.9717453459 126 -1.837 -3.188 -0.603 -2.554 0.106 -0.311 0.9716482745 128 -1.837 -3.209 -0.603 -2.554 0.106 -0.311 0.9716136695 131 -1.837 -3.214 -0.603 -2.554 0.106 -0.311 0.9716093854 132 -1.837 -3.212 -0.603 -2.554 0.106 -0.311 0.9715985306 133 -1.837 -3.211 -0.603 -2.554 0.106 -0.311 0.9715930264 140 -1.837 -3.211 -0.221 -2.554 0.106 -0.311 0.9709514162 141 -1.837 -3.211 -0.147 -2.554 0.106 -0.311 0.9706870783 147 -1.837 -3.211 -0.143 -2.554 0.106 -0.311 0.9706751834 148 -1.837 -3.211 -0.141 -2.554 0.106 -0.311 0.9706725031 153 -1.837 -3.211 -0.141 -4.172 0.106 -0.311 0.9689804148 157 -1.837 -3.211 -0.141 -5.172 0.106 -0.311 0.9683225273 159 -1.837 -3.211 -0.141 -4.843 0.106 -0.311 0.9677982179 160 -1.837 -3.211 -0.141 -4.771 0.106 -0.311 0.9676949998 163 -1.837 -3.211 -0.141 -4.773 0.106 -0.311 0.9676837011 164 -1.837 -3.211 -0.141 -4.800 0.106 -0.311 0.9676778660 170 -1.837 -3.211 -0.141 -4.798 0.106 -0.311 0.9676740045 176 -1.837 -3.211 -0.141 -4.798 -0.512 -0.311 0.9671708574 180 -1.837 -3.211 -0.141 -4.798 -0.391 -0.311 0.9668879367 183 -1.837 -3.211 -0.141 -4.798 -0.390 -0.311 0.9668856672 185 -1.837 -3.211 -0.141 -4.798 -0.381 -0.311 0.9668724569 197 -1.837 -3.211 -0.141 -4.798 -0.381 -0.297 0.9668706252 198 -1.837 -3.211 -0.141 -4.798 -0.381 -0.298 0.9668701861 201 -0.972 -4.955 0.321 -7.041 -0.868 -0.285 0.9624424802 207 -1.303 -4.289 0.144 -6.184 -0.682 -0.290 0.9613091439 208 -1.266 -4.362 0.164 -6.278 -0.702 -0.289 0.9610785168 209 -1.189 -4.518 0.205 -6.479 -0.746 -0.288 0.9610384728 212 -1.185 -4.526 0.207 -6.490 -0.748 -0.288 0.9609938128 213 -1.155 -4.586 0.223 -6.568 -0.765 -0.287 0.9607065506 218 -1.154 -4.589 0.224 -6.570 -0.766 -0.287 0.9607064523 powell nthiter 2: fret = 0.960706 220 -0.154 -4.589 0.224 -6.570 -0.766 -0.287 0.9573909361 224 -0.536 -4.589 0.224 -6.570 -0.766 -0.287 0.9566502122 226 -0.377 -4.589 0.224 -6.570 -0.766 -0.287 0.9565113782 228 -0.437 -4.589 0.224 -6.570 -0.766 -0.287 0.9564160708 229 -0.439 -4.589 0.224 -6.570 -0.766 -0.287 0.9564126380 231 -0.449 -4.589 0.224 -6.570 -0.766 -0.287 0.9563890866 233 -0.450 -4.589 0.224 -6.570 -0.766 -0.287 0.9563887708 239 -0.450 -4.589 0.224 -6.570 -0.766 -0.905 0.9545219697 243 -0.450 -4.589 0.224 -6.570 -0.766 -0.876 0.9544432766 252 -0.450 -4.589 -1.394 -6.570 -0.766 -0.876 0.9525275974 253 -0.450 -4.589 -0.662 -6.570 -0.766 -0.876 0.9501929345 255 -0.450 -4.589 -0.324 -6.570 -0.766 -0.876 0.9501404240 257 -0.450 -4.589 -0.488 -6.570 -0.766 -0.876 0.9496002710 259 -0.450 -4.589 -0.452 -6.570 -0.766 -0.876 0.9495587458 263 -0.450 -4.589 -0.443 -6.570 -0.766 -0.876 0.9495289376 265 -0.450 -4.589 -0.444 -6.570 -0.766 -0.876 0.9495260230 273 -0.450 -4.589 -0.444 -6.188 -0.766 -0.876 0.9477667137 274 -0.450 -4.589 -0.444 -6.089 -0.766 -0.876 0.9476149655 276 -0.450 -4.589 -0.444 -6.110 -0.766 -0.876 0.9475751006 286 -0.450 -4.589 -0.444 -6.110 -1.384 -0.876 0.9471525165 290 -0.450 -4.589 -0.444 -6.110 -1.313 -0.876 0.9471190789 293 -0.450 -4.589 -0.444 -6.110 -1.325 -0.876 0.9471164529 294 -0.450 -4.589 -0.444 -6.110 -1.326 -0.876 0.9471095011 295 -0.450 -4.589 -0.444 -6.110 -1.331 -0.876 0.9471067542 305 -0.561 -4.364 -0.504 -5.821 -1.269 -0.878 0.9460508578 306 -0.610 -4.265 -0.530 -5.693 -1.241 -0.879 0.9453851507 308 -0.667 -4.150 -0.560 -5.546 -1.209 -0.880 0.9448371107 312 -0.666 -4.152 -0.560 -5.549 -1.210 -0.880 0.9448236820 powell nthiter 3: fret = 0.944824 316 0.334 -4.152 -0.560 -5.549 -1.210 -0.880 0.9432400440 320 -0.048 -4.152 -0.560 -5.549 -1.210 -0.880 0.9405319435 322 -0.058 -4.152 -0.560 -5.549 -1.210 -0.880 0.9404628793 324 -0.091 -4.152 -0.560 -5.549 -1.210 -0.880 0.9404457098 325 -0.076 -4.152 -0.560 -5.549 -1.210 -0.880 0.9404108829 328 -0.078 -4.152 -0.560 -5.549 -1.210 -0.880 0.9404083539 342 -0.078 -4.152 -0.560 -5.549 -1.210 -0.876 0.9404028317 343 -0.078 -4.152 -0.560 -5.549 -1.210 -0.877 0.9403974211 349 -0.078 -4.152 -1.178 -5.549 -1.210 -0.877 0.9388768933 351 -0.078 -4.152 -0.993 -5.549 -1.210 -0.877 0.9380245834 352 -0.078 -4.152 -0.944 -5.549 -1.210 -0.877 0.9379713572 355 -0.078 -4.152 -0.951 -5.549 -1.210 -0.877 0.9379478723 357 -0.078 -4.152 -0.949 -5.549 -1.210 -0.877 0.9379434731 359 -0.078 -4.152 -0.950 -5.549 -1.210 -0.877 0.9379410264 384 -0.078 -4.152 -0.950 -5.549 -1.232 -0.877 0.9379223271 385 -0.078 -4.152 -0.950 -5.549 -1.233 -0.877 0.9379162549 398 -0.030 -4.250 -0.924 -5.674 -1.260 -0.877 0.9378270800 399 -0.050 -4.208 -0.935 -5.621 -1.248 -0.877 0.9377458500 400 -0.050 -4.210 -0.935 -5.623 -1.249 -0.877 0.9377309861 401 -0.042 -4.225 -0.931 -5.642 -1.253 -0.877 0.9377252778 powell nthiter 4: fret = 0.937725 414 0.016 -4.225 -0.931 -5.642 -1.253 -0.877 0.9374820431 415 0.068 -4.225 -0.931 -5.642 -1.253 -0.877 0.9373986336 416 0.076 -4.225 -0.931 -5.642 -1.253 -0.877 0.9373752601 419 0.087 -4.225 -0.931 -5.642 -1.253 -0.877 0.9373653644 421 0.097 -4.225 -0.931 -5.642 -1.253 -0.877 0.9373599254 435 0.097 -4.225 -0.931 -5.642 -1.253 -0.878 0.9373579701 436 0.097 -4.225 -0.931 -5.642 -1.253 -0.879 0.9373570593 446 0.097 -4.225 -0.937 -5.642 -1.253 -0.879 0.9373398032 453 0.097 -4.225 -0.938 -5.642 -1.253 -0.879 0.9373327007 462 0.097 -4.225 -0.938 -5.634 -1.253 -0.879 0.9373077105 478 0.097 -4.225 -0.938 -5.634 -1.258 -0.879 0.9373033408 480 0.097 -4.225 -0.938 -5.634 -1.256 -0.879 0.9372929126 481 0.097 -4.225 -0.938 -5.634 -1.255 -0.879 0.9372885326 489 0.034 -4.096 -0.972 -5.468 -1.219 -0.880 0.9370654663 491 0.058 -4.147 -0.959 -5.533 -1.233 -0.880 0.9370117085 502 0.097 -4.117 -0.970 -5.491 -1.225 -0.881 0.9369500318 504 0.121 -4.098 -0.976 -5.465 -1.221 -0.881 0.9369077460 507 0.128 -4.092 -0.978 -5.457 -1.219 -0.881 0.9368719814 511 0.127 -4.093 -0.978 -5.458 -1.219 -0.881 0.9368624114 512 0.127 -4.093 -0.978 -5.457 -1.219 -0.881 0.9368622428 513 0.128 -4.093 -0.978 -5.457 -1.219 -0.881 0.9368622213 514 0.128 -4.093 -0.978 -5.457 -1.219 -0.881 0.9368621275 powell nthiter 5: fret = 0.936862 521 0.024 -3.883 -1.034 -5.188 -1.161 -0.883 0.9366128574 532 0.025 -3.886 -1.033 -5.191 -1.161 -0.883 0.9366061986 540 0.025 -3.886 -1.033 -5.191 -1.161 -0.889 0.9365856997 541 0.025 -3.886 -1.033 -5.191 -1.161 -1.123 0.9365831186 542 0.025 -3.886 -1.033 -5.191 -1.161 -1.007 0.9363499337 543 0.025 -3.886 -1.033 -5.191 -1.161 -1.006 0.9363447438 556 0.025 -3.886 -1.054 -5.191 -1.161 -1.006 0.9362958386 562 0.025 -3.886 -1.055 -5.191 -1.161 -1.006 0.9362938595 570 0.025 -3.886 -1.055 -5.205 -1.161 -1.006 0.9362669764 583 0.025 -3.886 -1.055 -5.205 -1.250 -1.006 0.9358071531 584 0.025 -3.886 -1.055 -5.205 -1.263 -1.006 0.9357482990 586 0.025 -3.886 -1.055 -5.205 -1.270 -1.006 0.9357442015 587 0.025 -3.886 -1.055 -5.205 -1.268 -1.006 0.9357378593 595 0.063 -3.856 -1.066 -5.163 -1.260 -1.007 0.9356669723 598 0.059 -3.859 -1.065 -5.168 -1.261 -1.007 0.9356467293 600 0.057 -3.860 -1.064 -5.170 -1.261 -1.007 0.9356391786 603 0.058 -3.860 -1.064 -5.170 -1.261 -1.007 0.9356355872 605 0.058 -3.860 -1.065 -5.169 -1.261 -1.007 0.9356344554 powell nthiter 6: fret = 0.935634 614 0.033 -3.810 -1.078 -5.106 -1.247 -1.007 0.9355645302 618 0.036 -3.817 -1.076 -5.114 -1.249 -1.007 0.9355116721 633 0.036 -3.817 -1.076 -5.114 -1.249 -1.005 0.9355096914 636 0.036 -3.817 -1.076 -5.114 -1.249 -1.006 0.9355058091 645 0.036 -3.817 -1.089 -5.114 -1.249 -1.006 0.9354686503 673 0.036 -3.817 -1.089 -5.114 -1.250 -1.006 0.9354672123 676 0.036 -3.817 -1.089 -5.114 -1.251 -1.006 0.9354665054 677 0.036 -3.817 -1.089 -5.114 -1.252 -1.006 0.9354663542 693 0.037 -3.817 -1.089 -5.114 -1.252 -1.006 0.9354656020 powell nthiter 7: fret = 0.935466 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.012148 1 -25.0 -25.0 25.0 1.026058 2 -25.0 25.0 -25.0 1.035661 3 -25.0 25.0 25.0 1.019148 4 25.0 -25.0 -25.0 1.039796 5 25.0 -25.0 25.0 1.037536 6 25.0 25.0 -25.0 1.038075 7 25.0 25.0 25.0 1.038770 REL: 8 0.935466 8.247190 1.030899 rel = 0.907427 Number of iterations 7 Min cost was 0.935466 Number of FunctionCalls 778 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 923.294131 sec Parameters at optimum (transmm) 0.03652 -3.81653 -1.08888 Parameters at optimum (rotdeg) -5.11361 -1.25210 -1.00572 Final costs ---------------- Number of surface hits 211353 WM Intensity 556.3939 +/- 129.6900 Ctx Intensity 554.1604 +/- 147.3919 Pct Contrast -2.3410 +/- 38.4881 Cost 0.9355 RelCost 0.9873 Reg at min cost was 0.99713 -0.02616 0.07100 -0.40444; -0.06928 0.06148 0.99570 -8.40522; -0.03041 -0.99777 0.05949 -0.73195; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat, type = 14 Original Reg 0.99729 -0.04903 0.05479 -0.35247; -0.04691 0.14962 0.98763 -4.60994; -0.05662 -0.98753 0.14692 -0.04635; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00016 -0.02287 -0.01620 0.05197; 0.02237 0.08815 -0.00807 3.79529; -0.02621 0.01024 0.08743 0.68560; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 4.238683 Computing change in rh position Surface-RMS-Diff-mm 4.309827 1.978297 9.665579 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.935466 556.393901 554.160404 -2.340994 tkregister2_cmdl --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz --reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat --noedit --ltaout /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz reg file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.dat LoadVol 0 ZeroCRAS 0 7.1.0 Diagnostic Level -1 ---- Input registration matrix -------- 0.99713 -0.02616 0.07100 -0.40444; -0.06928 0.06148 0.99570 -8.40522; -0.03041 -0.99777 0.05949 -0.73195; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 120.00000; 0.00000 0.00000 1.00001 -110.00097; 0.00000 -1.00000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99713 -0.02616 0.07100 -0.40444; -0.06928 0.06148 0.99570 -8.40522; -0.03041 -0.99777 0.05949 -0.73195; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = 2012-646-010-KK RegMat --------------------------- 0.99713 -0.02616 0.07100 -0.40444; -0.06928 0.06148 0.99570 -8.40522; -0.03041 -0.99777 0.05949 -0.73195; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jul 15 21:52:16 EDT 2020 Ended at Wed Jul 15 22:42:39 EDT 2020 BBR-Run-Time-Sec 3022 bbregister Done To check results, run: tkregisterfv --mov /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz --reg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.lta --surfs @#@FSTIME 2020:07:15:21:52:16 bbregister N 12 e 3023.17 S 9.91 U 234.23 P 8% M 661624 F 7 R 2001364 W 0 c 243183 w 2818 I 176 O 0 L 49.29 49.38 49.82 @#@FSLOADPOST 2020:07:15:22:42:39 bbregister N 12 47.09 47.13 47.97 cp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.auto.lta /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.lta @#@FSTIME 2020:07:15:22:42:39 cp N 2 e 0.05 S 0.00 U 0.00 P 1% M 860 F 0 R 277 W 0 c 0 w 4 I 0 O 0 L 47.09 47.13 47.97 @#@FSLOADPOST 2020:07:15:22:42:40 cp N 2 47.48 47.21 47.99 mri_convert -odt float -at /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.lta -rl /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.prenorm.mgz reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) INFO: Reading transformation from file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.lta... Reading transform with LTAreadEx() reading template info from volume /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... INFO: Applying transformation from file /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/FLAIRraw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99828 0.05056 -0.02968 -0.14015; -0.05128 0.99839 -0.02406 0.33224; 0.02842 0.02554 0.99927 8.15356; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.prenorm.mgz... @#@FSTIME 2020:07:15:22:42:40 mri_convert N 8 e 46.30 S 0.09 U 3.80 P 8% M 119100 F 0 R 2734 W 0 c 3590 w 155 I 0 O 0 L 47.48 47.21 47.99 @#@FSLOADPOST 2020:07:15:22:43:27 mri_convert N 8 47.48 47.23 47.96 mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.presurf.mgz -surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.white identity.nofile -surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.white identity.nofile /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.prenorm.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.norm.mgz setting seed for random number genererator to 1234 using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading mri_src from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.prenorm.mgz... Copying mri_dst from mri_src computing distance transform computing distance transform min_dist = 1 Erasing Border planes 4 Removing non-wm voxels 49298 non wm control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 MRIapplyBiasCorrectionSameGeometry() writing normalized volume to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.norm.mgz #VMPC# mri_normalize VmPeak 961068 mri_normalize done @#@FSTIME 2020:07:15:22:43:27 mri_normalize N 18 e 731.91 S 4.48 U 56.94 P 8% M 718140 F 0 R 170561 W 0 c 53898 w 1279 I 0 O 2120 L 47.48 47.23 47.96 @#@FSLOADPOST 2020:07:15:22:55:39 mri_normalize N 18 45.36 46.92 47.77 mri_mask -transfer 255 -keep_mask_deletion_edits /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.norm.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Writing masked volume to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.mgz...done. @#@FSTIME 2020:07:15:22:55:40 mri_mask N 6 e 44.60 S 0.18 U 4.03 P 9% M 234952 F 0 R 5643 W 0 c 3306 w 424 I 0 O 0 L 45.01 46.82 47.74 @#@FSLOADPOST 2020:07:15:22:56:25 mri_mask N 6 44.90 46.57 47.61 #-------------------------------------------- #@# MMPialSurf lh Wed Jul 15 22:56:25 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.FLAIR --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol FLAIR.mgz FLAIR 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.FLAIR --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol FLAIR.mgz FLAIR Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface Area 243164 0.43667 0.35354 0.000139 7.3411 Corner 729492 60.00000 31.74131 0.027299 179.8211 Edge 364746 1.06678 0.50880 0.003885 6.6718 Hinge 364746 20.45717 26.05839 0.000171 179.9949 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 62.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume FLAIR.mgz vertex 60792: xyz = (-60.0886,-7.91666,-8.50294) oxyz = (-58.963,-8.04709,-5.8071) wxzy = (-58.963,-8.04709,-5.8071) pxyz = (-60.0886,-7.91666,-8.50294) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (2) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.01, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=2 Creating lowres distance volumes t=0.073579 Creating white distance volumes t=18.8276 (box.dx, box.dy, box.dz) = (148, 194, 328) (region->dx, region->dy, region->dz) = (148, 194, 328) (region->dx, region->dy, region->dz) = (148, 194, 328) Creating pial distance volumes t=35.0305 (box.dx, box.dy, box.dz) = (156, 204, 336) (region->dx, region->dy, region->dz) = (156, 204, 336) (region->dx, region->dy, region->dz) = (156, 204, 336) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 54.5441 Starting loop over 121584 vertices vno = 0, t = 54.5443 vno = 20000, t = 82.2012 vno = 40000, t = 161.652 vno = 60000, t = 203.242 vno = 80000, t = 240.747 error: Numerical result out of range error: MRIhistogramLabelRegion: constant image error: Numerical result out of range error: MRIhistogramLabelRegion: constant image @#@FSTIME 2020:07:15:22:56:26 mris_place_surface N 29 e 16187.68 S 29.27 U 1379.90 P 8% M 1843800 F 1630 R 1004132 W 0 c 1180758 w 2684 I 95384 O 736 L 44.99 46.56 47.61 @#@FSLOADPOST 2020:07:16:03:26:14 mris_place_surface N 29 41.59 42.15 42.94 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012-646-010-KK exited with ERRORS at Thu Jul 16 03:26:14 EDT 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Thu Jul 16 22:29:07 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -all -noskullstrip subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 1024 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/17-02:29:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Thu Jul 16 22:29:28 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:16:22:29:28 mri_convert N 4 e 13.71 S 0.03 U 1.91 P 14% M 53380 F 1 R 1929 W 0 c 1486 w 44 I 48 O 0 L 25.54 25.46 25.24 @#@FSLOADPOST 2020:07:16:22:29:42 mri_convert N 4 25.87 25.53 25.27 #-------------------------------------------- #@# MotionCor Thu Jul 16 22:29:42 EDT 2020 Found 1 runs /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261116, -0.041979) j_ras = (-0.0224984, 0.996182, -0.0843504) k_ras = (-0.0440213, 0.0833028, 0.995551) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 3297.37 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... @#@FSTIME 2020:07:16:22:29:47 mri_convert N 3 e 51.42 S 0.02 U 7.73 P 15% M 65372 F 0 R 3506 W 0 c 2282 w 24 I 0 O 0 L 26.12 25.59 25.29 @#@FSLOADPOST 2020:07:16:22:30:38 mri_convert N 3 26.15 25.68 25.33 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:07:16:22:30:39 mri_add_xform_to_header N 4 e 4.90 S 0.01 U 0.65 P 13% M 20204 F 0 R 1686 W 0 c 169 w 31 I 0 O 0 L 26.15 25.68 25.33 @#@FSLOADPOST 2020:07:16:22:30:44 mri_add_xform_to_header N 4 26.06 25.67 25.33 #-------------------------------------------- #@# Talairach Thu Jul 16 22:30:45 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 16 22:30:45 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.1660 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.1660/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.1660/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.1660/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.1660/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Thu Jul 16 22:53:21 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:16:22:30:45 mri_nu_correct.mni N 12 e 1356.23 S 0.83 U 214.39 P 15% M 485232 F 1 R 38238 W 0 c 100133 w 213 I 16 O 0 L 26.06 25.67 25.33 @#@FSLOADPOST 2020:07:16:22:53:21 mri_nu_correct.mni N 12 25.43 25.23 25.20 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Jul 16 22:53:22 EDT 2020 Ended at Thu Jul 16 22:56:50 EDT 2020 talairach_avi done @#@FSTIME 2020:07:16:22:53:22 talairach_avi N 4 e 208.52 S 1.23 U 30.09 P 15% M 253892 F 0 R 41606 W 0 c 13277 w 804 I 0 O 32 L 25.43 25.23 25.20 @#@FSLOADPOST 2020:07:16:22:56:50 talairach_avi N 4 25.20 25.18 25.18 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 16 22:56:51 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5199, pval=0.1531 >= threshold=0.0050) @#@FSTIME 2020:07:16:22:56:51 talairach_afd N 4 e 0.28 S 0.00 U 0.00 P 1% M 2096 F 0 R 613 W 0 c 2 w 48 I 0 O 0 L 25.20 25.18 25.18 @#@FSLOADPOST 2020:07:16:22:56:51 talairach_afd N 4 25.20 25.18 25.18 awk -f /public/apps/freesurfer/7.1.0/bin/extract_talairach_avi_QA.awk /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log tal_QC_AZS /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log TalAviQA: 0.96317 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 16 22:56:52 EDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 16 22:56:53 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.25070 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz sysname Linux hostname loginnode2 machine x86_64 user pankumar input /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.25070/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 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.25070/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.25070/input.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.25070/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.25070/input.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.25070/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 /dev/shm/tmp.mri_nu_correct.mni.25070/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.25070/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.25070/output.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.25070/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.25070/output.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.25070/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.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 /dev/shm/tmp.mri_nu_correct.mni.25070/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz mul 1.15054592399081702868 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.25070/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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 56 seconds. mapping (13, 196) to ( 3, 110) Thu Jul 16 23:23:28 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:16:22:56:52 mri_nu_correct.mni N 9 e 1595.66 S 1.30 U 250.96 P 15% M 610744 F 0 R 188571 W 0 c 79032 w 420 I 0 O 0 L 25.18 25.17 25.18 @#@FSLOADPOST 2020:07:16:23:23:28 mri_nu_correct.mni N 9 25.14 25.23 25.16 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2020:07:16:23:23:28 mri_add_xform_to_header N 4 e 5.71 S 0.02 U 0.83 P 15% M 20280 F 0 R 1705 W 0 c 336 w 25 I 0 O 0 L 25.14 25.23 25.16 @#@FSLOADPOST 2020:07:16:23:23:34 mri_add_xform_to_header N 4 25.12 25.22 25.16 #-------------------------------------------- #@# Intensity Normalization Thu Jul 16 23:23:34 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 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(): error: MRIhistogramRegion: input mri nu.mgz is blank MRIsplineNormalize(): npeaks = 12 Starting OpenSpline(): npoints = 12 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 56 (56), valley at 0 (-1) csf peak at 28, setting threshold to 46 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 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 13 minutes and 22 seconds. @#@FSTIME 2020:07:16:23:23:35 mri_normalize N 7 e 807.19 S 0.65 U 127.63 P 15% M 578528 F 0 R 14847 W 0 c 64739 w 40 I 0 O 0 L 25.12 25.22 25.16 @#@FSLOADPOST 2020:07:16:23:37:02 mri_normalize N 7 25.08 25.08 25.13 #------------------------------------- #@# EM Registration Thu Jul 16 23:37:02 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 8 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, 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=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -3.918 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (-2.632, -2.632, -2.632) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) Found translation: (-2.6, -2.6, -2.6): log p = -3.811 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.811 (thresh=-3.8) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; iteration took 17 minutes and 14 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.624 (thresh=-3.6) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 16 minutes and 12 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.624 (thresh=-3.6) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; iteration took 15 minutes and 33 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 15 minutes and 40 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.505, old_max_log_p =-3.534 (thresh=-3.5) 1.03379 0.01049 0.00809 -9.19070; -0.00869 1.28704 0.00797 -40.93967; -0.00832 -0.01033 0.99642 -0.34468; 0.00000 0.00000 0.00000 1.00000; iteration took 13 minutes and 43 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.505 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; iteration took 13 minutes and 39 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.488 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.488 (old=-3.918) transform before final EM align: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 885440 FSRUNTIME@ mri_em_register 1.9645 hours 1 threads registration took 117 minutes and 52 seconds. @#@FSTIME 2020:07:16:23:37:02 mri_em_register N 7 e 7072.31 S 4.26 U 1165.92 P 16% M 612752 F 0 R 112771 W 0 c 400030 w 71 I 0 O 0 L 25.08 25.08 25.13 @#@FSLOADPOST 2020:07:17:01:34:55 mri_em_register N 7 24.41 24.28 24.20 #-------------------------------------- #@# CA Normalize Fri Jul 17 01:34:55 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.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 '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 133 of 656 (20.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 395 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 15 (0.0%) samples deleted using 1091 total control points for intensity normalization... bias field = 0.959 +- 0.058 1 of 958 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 823 (1.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 533 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 64 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 53 (3.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 27 of 79 (34.2%) samples deleted using 1552 total control points for intensity normalization... bias field = 1.009 +- 0.066 3 of 1469 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 824 (1.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 626 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 84 (53.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 77 (32.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 86 of 139 (61.9%) samples deleted using 1750 total control points for intensity normalization... bias field = 1.002 +- 0.054 1 of 1545 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 9 minutes and 43 seconds. @#@FSTIME 2020:07:17:01:34:55 mri_ca_normalize N 8 e 582.87 S 1.97 U 92.16 P 16% M 891380 F 0 R 145564 W 0 c 52061 w 72 I 0 O 0 L 24.41 24.28 24.20 @#@FSLOADPOST 2020:07:17:01:44:38 mri_ca_normalize N 8 24.55 24.48 24.33 #-------------------------------------- #@# CA Reg Fri Jul 17 01:44:39 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.935117 #FOTS# QuadFit found better minimum quadopt=(dt=246.905,rms=0.794434) vs oldopt=(dt=92.48,rms=0.845465) #GCMRL# 0 dt 246.904762 rms 0.794 15.044% neg 0 invalid 762 tFOTS 161.9230 tGradient 62.2380 tsec 236.0170 #FOTS# QuadFit found better minimum quadopt=(dt=209.836,rms=0.765228) vs oldopt=(dt=92.48,rms=0.774396) #GCMRL# 1 dt 209.836066 rms 0.765 3.676% neg 0 invalid 762 tFOTS 170.0990 tGradient 58.7530 tsec 240.9220 #FOTS# QuadFit found better minimum quadopt=(dt=229.859,rms=0.750881) vs oldopt=(dt=92.48,rms=0.755764) #GCMRL# 2 dt 229.859155 rms 0.751 1.875% neg 0 invalid 762 tFOTS 172.4340 tGradient 59.9750 tsec 245.1570 #FOTS# QuadFit found better minimum quadopt=(dt=129.506,rms=0.74519) vs oldopt=(dt=92.48,rms=0.745844) #GCMRL# 3 dt 129.505882 rms 0.745 0.758% neg 0 invalid 762 tFOTS 167.8060 tGradient 62.3690 tsec 241.4870 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.734166) vs oldopt=(dt=369.92,rms=0.736011) #GCMRL# 4 dt 517.888000 rms 0.734 1.479% neg 0 invalid 762 tFOTS 175.8390 tGradient 58.3900 tsec 246.0900 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.7319) vs oldopt=(dt=92.48,rms=0.731939) #GCMRL# 5 dt 110.976000 rms 0.732 0.309% neg 0 invalid 762 tFOTS 183.7590 tGradient 61.6650 tsec 256.8210 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.716292) vs oldopt=(dt=1479.68,rms=0.718156) #GCMRL# 6 dt 2071.552000 rms 0.716 2.132% neg 0 invalid 762 tFOTS 162.3030 tGradient 57.1000 tsec 230.4750 #GCMRL# 7 dt 92.480000 rms 0.713 0.459% neg 0 invalid 762 tFOTS 154.3810 tGradient 58.8740 tsec 225.0540 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.712379) vs oldopt=(dt=369.92,rms=0.712527) #GCMRL# 8 dt 221.952000 rms 0.712 0.000% neg 0 invalid 762 tFOTS 162.8100 tGradient 61.9480 tsec 235.7380 #GCMRL# 9 dt 221.952000 rms 0.711 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.1500 tsec 63.3020 #GCMRL# 10 dt 221.952000 rms 0.710 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.1640 tsec 64.5950 #GCMRL# 11 dt 221.952000 rms 0.710 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.1550 tsec 62.4290 #GCMRL# 12 dt 221.952000 rms 0.708 0.284% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.8400 tsec 64.1180 #GCMRL# 13 dt 221.952000 rms 0.706 0.288% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.2940 tsec 63.1170 #GCMRL# 14 dt 221.952000 rms 0.704 0.260% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.3860 tsec 65.4340 #GCMRL# 15 dt 221.952000 rms 0.702 0.307% neg 0 invalid 762 tFOTS 0.0000 tGradient 56.1870 tsec 66.2270 #GCMRL# 16 dt 221.952000 rms 0.699 0.343% neg 0 invalid 762 tFOTS 0.0000 tGradient 57.3120 tsec 68.0080 #GCMRL# 17 dt 221.952000 rms 0.697 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.8490 tsec 65.9710 #GCMRL# 18 dt 221.952000 rms 0.696 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.8260 tsec 67.0500 #GCMRL# 19 dt 221.952000 rms 0.695 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.9300 tsec 67.5530 #GCMRL# 20 dt 221.952000 rms 0.693 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.4830 tsec 63.9570 #GCMRL# 21 dt 221.952000 rms 0.693 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.3230 tsec 64.9860 #GCMRL# 22 dt 221.952000 rms 0.692 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.4070 tsec 66.3230 #GCMRL# 23 dt 221.952000 rms 0.691 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.1020 tsec 65.3560 #GCMRL# 24 dt 221.952000 rms 0.690 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 56.7690 tsec 67.7700 #GCMRL# 25 dt 221.952000 rms 0.690 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.4190 tsec 65.6370 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.689488) vs oldopt=(dt=369.92,rms=0.68951) #GCMRL# 26 dt 295.936000 rms 0.689 0.066% neg 0 invalid 762 tFOTS 160.8440 tGradient 53.6310 tsec 225.3220 #GCAMreg# pass 0 level1 5 level2 1 tsec 3761.66 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.689936 #GCMRL# 28 dt 92.480000 rms 0.689 0.112% neg 0 invalid 762 tFOTS 151.5080 tGradient 52.1070 tsec 214.7170 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.688749) vs oldopt=(dt=369.92,rms=0.688806) #GCMRL# 29 dt 295.936000 rms 0.689 0.000% neg 0 invalid 762 tFOTS 164.5000 tGradient 57.2750 tsec 233.0340 #GCMRL# 30 dt 295.936000 rms 0.688 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 50.7270 tsec 61.5610 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.706108 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704881) vs oldopt=(dt=25.92,rms=0.704889) #GCMRL# 32 dt 31.104000 rms 0.705 0.174% neg 0 invalid 762 tFOTS 150.0660 tGradient 45.0550 tsec 205.1150 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704506) vs oldopt=(dt=25.92,rms=0.704515) #GCMRL# 33 dt 31.104000 rms 0.705 0.000% neg 0 invalid 762 tFOTS 143.7490 tGradient 43.7500 tsec 198.1620 #GCMRL# 34 dt 31.104000 rms 0.704 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 42.2690 tsec 52.4430 #GCMRL# 35 dt 31.104000 rms 0.704 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 41.2460 tsec 51.7950 #GCAMreg# pass 0 level1 4 level2 1 tsec 601.312 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.704365 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.70353) vs oldopt=(dt=25.92,rms=0.703568) #GCMRL# 37 dt 36.288000 rms 0.704 0.119% neg 0 invalid 762 tFOTS 157.5810 tGradient 44.2050 tsec 212.3260 #FOTS# QuadFit found better minimum quadopt=(dt=15.552,rms=0.703504) vs oldopt=(dt=25.92,rms=0.703509) #GCMRL# 38 dt 15.552000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 161.2300 tGradient 42.1820 tsec 214.8780 #GCMRL# 39 dt 15.552000 rms 0.703 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 44.7570 tsec 55.4050 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.73685 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.735541) vs oldopt=(dt=8,rms=0.735619) #GCMRL# 41 dt 6.400000 rms 0.736 0.178% neg 0 invalid 762 tFOTS 147.8550 tGradient 35.9950 tsec 193.7290 #FOTS# QuadFit found better minimum quadopt=(dt=2.4,rms=0.735475) vs oldopt=(dt=2,rms=0.735476) #GCMRL# 42 dt 2.400000 rms 0.735 0.000% neg 0 invalid 762 tFOTS 153.3720 tGradient 36.4250 tsec 201.0040 #GCAMreg# pass 0 level1 3 level2 1 tsec 489.803 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.73596 #GCMRL# 44 dt 0.000000 rms 0.735 0.067% neg 0 invalid 762 tFOTS 142.2120 tGradient 37.5800 tsec 190.4590 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.817881 #FOTS# QuadFit found better minimum quadopt=(dt=3.31099,rms=0.806528) vs oldopt=(dt=2.88,rms=0.806715) #GCMRL# 46 dt 3.310987 rms 0.807 1.388% neg 0 invalid 762 tFOTS 140.0680 tGradient 37.4580 tsec 188.1590 #FOTS# QuadFit found better minimum quadopt=(dt=1.93269,rms=0.804898) vs oldopt=(dt=2.88,rms=0.805279) #GCMRL# 47 dt 1.932692 rms 0.805 0.000% neg 0 invalid 762 tFOTS 138.9580 tGradient 36.1220 tsec 186.7230 #GCMRL# 48 dt 1.932692 rms 0.803 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.9200 tsec 47.2640 #GCMRL# 49 dt 1.932692 rms 0.803 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.9540 tsec 44.7210 #GCMRL# 50 dt 1.932692 rms 0.803 -0.411% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.3410 tsec 56.2040 #GCAMreg# pass 0 level1 2 level2 1 tsec 769.111 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.803105 #GCMRL# 52 dt 0.000000 rms 0.803 0.068% neg 0 invalid 762 tFOTS 132.5050 tGradient 35.0060 tsec 178.5540 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.877757 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877204) vs oldopt=(dt=0.08,rms=0.877207) #GCMRL# 54 dt 0.064000 rms 0.877 0.063% neg 0 invalid 762 tFOTS 141.3180 tGradient 35.1420 tsec 187.1620 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877178) vs oldopt=(dt=0.08,rms=0.877183) #GCMRL# 55 dt 0.064000 rms 0.877 0.000% neg 0 invalid 762 tFOTS 134.7410 tGradient 32.2670 tsec 177.7740 #GCMRL# 56 dt 0.064000 rms 0.877 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.3470 tsec 42.1140 #GCMRL# 57 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.5710 tsec 40.4710 #GCMRL# 58 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.5630 tsec 45.4350 #GCMRL# 59 dt 0.064000 rms 0.877 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.5160 tsec 45.3560 #GCMRL# 60 dt 0.064000 rms 0.876 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.0970 tsec 43.7780 #GCMRL# 61 dt 0.064000 rms 0.875 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.6990 tsec 43.2780 #GCMRL# 62 dt 0.064000 rms 0.874 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.7660 tsec 45.1910 #GCMRL# 63 dt 0.064000 rms 0.872 0.191% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.5930 tsec 44.4090 #GCMRL# 64 dt 0.064000 rms 0.871 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.0410 tsec 44.2700 #GCMRL# 65 dt 0.064000 rms 0.869 0.179% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.6400 tsec 44.3080 #GCMRL# 66 dt 0.064000 rms 0.868 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.1590 tsec 46.0620 #GCMRL# 67 dt 0.064000 rms 0.867 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.7070 tsec 44.7510 #GCMRL# 68 dt 0.064000 rms 0.866 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.3320 tsec 45.3540 #GCMRL# 69 dt 0.064000 rms 0.865 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.4080 tsec 46.5640 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.862601) vs oldopt=(dt=1.28,rms=0.862653) #GCMRL# 70 dt 1.536000 rms 0.863 0.268% neg 0 invalid 762 tFOTS 141.0880 tGradient 33.9170 tsec 185.7330 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.861829) vs oldopt=(dt=0.32,rms=0.862083) #GCMRL# 71 dt 0.192000 rms 0.862 0.000% neg 0 invalid 762 tFOTS 146.0380 tGradient 33.2770 tsec 190.2820 #GCMRL# 72 dt 0.192000 rms 0.861 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.2290 tsec 44.8610 #GCMRL# 73 dt 0.192000 rms 0.860 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.9460 tsec 43.2710 #GCMRL# 74 dt 0.192000 rms 0.860 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.2300 tsec 44.0590 #GCMRL# 75 dt 0.192000 rms 0.859 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 35.1800 tsec 46.5650 #GCAMreg# pass 0 level1 1 level2 1 tsec 1761.6 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.859744 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.858997) vs oldopt=(dt=0.32,rms=0.859029) #GCMRL# 77 dt 0.192000 rms 0.859 0.087% neg 0 invalid 762 tFOTS 144.8210 tGradient 35.6810 tsec 190.9570 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.858993) vs oldopt=(dt=0.02,rms=0.858993) #GCMRL# 78 dt 0.028000 rms 0.859 0.000% neg 0 invalid 762 tFOTS 148.2200 tGradient 34.0820 tsec 194.4070 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.798691 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.792197) vs oldopt=(dt=0.32,rms=0.792517) #GCMRL# 80 dt 0.256000 rms 0.792 0.813% neg 0 invalid 762 tFOTS 142.1960 tGradient 29.1150 tsec 181.7440 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.791804) vs oldopt=(dt=0.02,rms=0.791836) #GCMRL# 81 dt 0.028000 rms 0.792 0.000% neg 0 invalid 762 tFOTS 142.2560 tGradient 26.9600 tsec 179.6930 #GCAMreg# pass 0 level1 0 level2 1 tsec 447.106 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.792455 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.791733) vs oldopt=(dt=0.02,rms=0.79174) #GCMRL# 83 dt 0.016000 rms 0.792 0.091% neg 0 invalid 762 tFOTS 147.5400 tGradient 28.0990 tsec 186.8380 GCAMregister done in 178.8 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.02912 ( 6) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, overlap=0.766) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, peak = 18), gca=18.5 gca peak = 0.17690 (16) mri peak = 0.06897 (30) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, overlap=0.426) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, peak = 23), gca=23.4 gca peak = 0.28275 (96) mri peak = 0.06787 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, overlap=0.966) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, peak = 93), gca=92.6 gca peak = 0.18948 (93) mri peak = 0.06458 (96) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, overlap=1.008) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, peak = 92), gca=91.6 gca peak = 0.20755 (55) mri peak = 0.11697 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, peak = 55), gca=55.0 gca peak = 0.31831 (58) mri peak = 0.08625 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, peak = 55), gca=54.8 gca peak = 0.11957 (102) mri peak = 0.06876 (109) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, peak = 110), gca=109.7 gca peak = 0.11429 (102) mri peak = 0.06805 (111) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, overlap=0.521) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, peak = 111), gca=110.7 gca peak = 0.14521 (59) mri peak = 0.03738 (55) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, overlap=0.966) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, peak = 54), gca=54.0 gca peak = 0.14336 (58) mri peak = 0.04502 (53) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, overlap=0.848) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, peak = 52), gca=51.9 gca peak = 0.13305 (70) mri peak = 0.08346 (76) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, overlap=0.651) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, peak = 77), gca=77.3 gca peak = 0.15761 (71) mri peak = 0.06809 (83) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, overlap=0.571) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, peak = 77), gca=77.0 gca peak = 0.13537 (57) mri peak = 0.03402 (55) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, overlap=0.918) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, peak = 55), gca=55.0 gca peak = 0.13487 (56) mri peak = 0.03585 (51) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, peak = 54), gca=54.0 gca peak = 0.19040 (84) mri peak = 0.06228 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, overlap=0.746) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, peak = 87), gca=86.9 gca peak = 0.18871 (83) mri peak = 0.08367 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, peak = 86), gca=85.9 gca peak = 0.24248 (57) mri peak = 0.13222 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, overlap=0.798) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, peak = 51), gca=51.0 gca peak = 0.35833 (56) mri peak = 0.11187 (55) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, overlap=0.978) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, peak = 54), gca=54.0 gca peak = 0.12897 (85) mri peak = 0.05445 (88) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, overlap=0.975) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, peak = 83), gca=82.9 gca peak = 0.13127 (83) mri peak = 0.05455 (82) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, overlap=0.920) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, peak = 86), gca=85.9 gca peak = 0.12974 (78) mri peak = 0.06301 (81) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, overlap=0.985) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, peak = 82), gca=81.5 gca peak = 0.17796 (79) mri peak = 0.07260 (81) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, overlap=0.934) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, peak = 82), gca=81.8 gca peak = 0.10999 (80) mri peak = 0.09164 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.05790 (86) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, overlap=0.730) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.05402 (89) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, overlap=0.853) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, peak = 97), gca=96.6 gca peak = 0.20775 (25) mri peak = 0.03183 (12) gca peak = 0.13297 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.08 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 37.3045 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.848745 #FOTS# QuadFit found better minimum quadopt=(dt=182.491,rms=0.80955) vs oldopt=(dt=92.48,rms=0.818919) #GCMRL# 85 dt 182.490818 rms 0.810 4.618% neg 0 invalid 762 tFOTS 143.8060 tGradient 77.9990 tsec 231.8750 #FOTS# QuadFit found better minimum quadopt=(dt=175.23,rms=0.798144) vs oldopt=(dt=92.48,rms=0.801288) #GCMRL# 86 dt 175.229947 rms 0.798 1.409% neg 0 invalid 762 tFOTS 155.2470 tGradient 74.9700 tsec 240.6000 #FOTS# QuadFit found better minimum quadopt=(dt=176.792,rms=0.790975) vs oldopt=(dt=92.48,rms=0.79302) #GCMRL# 87 dt 176.792079 rms 0.791 0.898% neg 0 invalid 762 tFOTS 152.6850 tGradient 78.4680 tsec 242.1830 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.787162) vs oldopt=(dt=92.48,rms=0.787957) #GCMRL# 88 dt 129.472000 rms 0.787 0.482% neg 0 invalid 762 tFOTS 141.4020 tGradient 72.7260 tsec 225.1270 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.779255) vs oldopt=(dt=369.92,rms=0.780123) #GCMRL# 89 dt 517.888000 rms 0.779 1.005% neg 0 invalid 762 tFOTS 150.7260 tGradient 73.1040 tsec 234.6380 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.775457) vs oldopt=(dt=92.48,rms=0.775669) #GCMRL# 90 dt 129.472000 rms 0.775 0.487% neg 0 invalid 762 tFOTS 153.1640 tGradient 70.3930 tsec 234.0230 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.772686) vs oldopt=(dt=369.92,rms=0.773004) #GCMRL# 91 dt 295.936000 rms 0.773 0.357% neg 0 invalid 762 tFOTS 153.6690 tGradient 73.7260 tsec 238.1170 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.770251) vs oldopt=(dt=92.48,rms=0.77046) #GCMRL# 92 dt 129.472000 rms 0.770 0.315% neg 0 invalid 762 tFOTS 157.8730 tGradient 73.3770 tsec 241.5290 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.768064) vs oldopt=(dt=369.92,rms=0.768174) #GCMRL# 93 dt 295.936000 rms 0.768 0.284% neg 0 invalid 762 tFOTS 150.7520 tGradient 75.9270 tsec 236.8540 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.766199) vs oldopt=(dt=92.48,rms=0.766423) #GCMRL# 94 dt 129.472000 rms 0.766 0.243% neg 0 invalid 762 tFOTS 149.1570 tGradient 71.6680 tsec 231.7250 #GCMRL# 95 dt 369.920000 rms 0.764 0.240% neg 0 invalid 762 tFOTS 149.0940 tGradient 73.0390 tsec 232.3670 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.762431) vs oldopt=(dt=92.48,rms=0.762576) #GCMRL# 96 dt 129.472000 rms 0.762 0.253% neg 0 invalid 762 tFOTS 163.0880 tGradient 70.9420 tsec 244.6880 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.761167) vs oldopt=(dt=369.92,rms=0.761516) #GCMRL# 97 dt 221.952000 rms 0.761 0.166% neg 0 invalid 762 tFOTS 152.3430 tGradient 73.0980 tsec 236.5000 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.760028) vs oldopt=(dt=92.48,rms=0.760234) #GCMRL# 98 dt 129.472000 rms 0.760 0.150% neg 0 invalid 762 tFOTS 158.8180 tGradient 77.0750 tsec 247.1130 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.758301) vs oldopt=(dt=369.92,rms=0.758399) #GCMRL# 99 dt 517.888000 rms 0.758 0.227% neg 0 invalid 762 tFOTS 158.6730 tGradient 70.5170 tsec 239.8990 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.75648) vs oldopt=(dt=92.48,rms=0.756592) #GCMRL# 100 dt 129.472000 rms 0.756 0.240% neg 0 invalid 762 tFOTS 171.6210 tGradient 75.1030 tsec 256.9640 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.755734) vs oldopt=(dt=92.48,rms=0.755844) #GCMRL# 101 dt 129.472000 rms 0.756 0.099% neg 0 invalid 762 tFOTS 160.9210 tGradient 72.0240 tsec 243.5430 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.753709) vs oldopt=(dt=369.92,rms=0.754086) #GCMRL# 102 dt 517.888000 rms 0.754 0.268% neg 0 invalid 762 tFOTS 154.9230 tGradient 76.3830 tsec 242.8790 #GCMRL# 103 dt 92.480000 rms 0.753 0.116% neg 0 invalid 762 tFOTS 153.1170 tGradient 76.5520 tsec 240.9840 #FOTS# QuadFit found better minimum quadopt=(dt=4734.98,rms=0.742561) vs oldopt=(dt=5918.72,rms=0.743082) #GCMRL# 104 dt 4734.976000 rms 0.743 1.365% neg 0 invalid 762 tFOTS 164.9250 tGradient 75.0960 tsec 251.4990 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.740244) vs oldopt=(dt=92.48,rms=0.740309) #GCMRL# 105 dt 73.984000 rms 0.740 0.312% neg 0 invalid 762 tFOTS 157.1320 tGradient 73.7720 tsec 242.6680 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.740078) vs oldopt=(dt=92.48,rms=0.740106) #GCMRL# 106 dt 129.472000 rms 0.740 0.000% neg 0 invalid 762 tFOTS 155.4860 tGradient 76.8020 tsec 243.2120 #GCMRL# 107 dt 129.472000 rms 0.740 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 75.1360 tsec 86.0830 #GCMRL# 108 dt 129.472000 rms 0.739 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.7210 tsec 85.3270 #GCMRL# 109 dt 129.472000 rms 0.739 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.5710 tsec 87.8340 #GCMRL# 110 dt 129.472000 rms 0.738 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 78.8770 tsec 89.6770 #GCMRL# 111 dt 129.472000 rms 0.737 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 85.0380 tsec 96.0330 #GCMRL# 112 dt 129.472000 rms 0.736 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 83.4370 tsec 95.7870 #GCMRL# 113 dt 129.472000 rms 0.735 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 90.8950 tsec 102.4770 #GCMRL# 114 dt 129.472000 rms 0.734 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.0000 tsec 84.9680 #GCMRL# 115 dt 129.472000 rms 0.733 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 73.1380 tsec 83.5970 #GCMRL# 116 dt 129.472000 rms 0.732 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 72.6450 tsec 83.7430 #GCMRL# 117 dt 129.472000 rms 0.731 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 69.2640 tsec 78.6080 #GCMRL# 118 dt 129.472000 rms 0.731 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.5800 tsec 88.0780 #GCMRL# 119 dt 129.472000 rms 0.730 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 72.3310 tsec 83.9390 #GCMRL# 120 dt 129.472000 rms 0.729 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.9880 tsec 85.8540 #GCMRL# 121 dt 129.472000 rms 0.728 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.4440 tsec 87.3580 #GCMRL# 122 dt 129.472000 rms 0.727 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.9310 tsec 85.4820 #GCMRL# 123 dt 129.472000 rms 0.726 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.9660 tsec 87.6510 #GCMRL# 124 dt 129.472000 rms 0.726 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 83.5760 tsec 94.2270 #GCMRL# 125 dt 129.472000 rms 0.725 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 73.3240 tsec 88.1000 #GCMRL# 126 dt 129.472000 rms 0.724 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 89.4290 tsec 106.6010 #GCMRL# 127 dt 129.472000 rms 0.724 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 83.9780 tsec 95.2970 #GCMRL# 128 dt 129.472000 rms 0.723 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 78.2330 tsec 90.3980 #GCMRL# 129 dt 129.472000 rms 0.723 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.8770 tsec 88.1260 #GCMRL# 130 dt 129.472000 rms 0.722 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 79.2370 tsec 90.0420 #GCMRL# 131 dt 129.472000 rms 0.721 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 83.5740 tsec 93.0040 #GCMRL# 132 dt 129.472000 rms 0.721 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 82.8260 tsec 93.3610 #GCMRL# 133 dt 129.472000 rms 0.720 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 78.6810 tsec 89.2590 #GCMRL# 134 dt 129.472000 rms 0.720 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 91.2320 tsec 102.0010 #GCMRL# 135 dt 129.472000 rms 0.719 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.8470 tsec 87.6350 #GCMRL# 136 dt 129.472000 rms 0.719 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.4250 tsec 88.3530 #GCMRL# 137 dt 129.472000 rms 0.718 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.8330 tsec 88.0450 #GCMRL# 138 dt 129.472000 rms 0.718 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.4230 tsec 89.1400 #GCMRL# 139 dt 129.472000 rms 0.718 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 89.2730 tsec 101.9850 #GCMRL# 140 dt 129.472000 rms 0.717 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 86.0120 tsec 102.4780 #GCMRL# 141 dt 129.472000 rms 0.717 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 78.3600 tsec 89.4700 #GCMRL# 142 dt 129.472000 rms 0.716 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 89.7130 tsec 102.3970 #GCMRL# 143 dt 129.472000 rms 0.716 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 80.9380 tsec 92.6720 #GCMRL# 144 dt 129.472000 rms 0.715 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 86.7650 tsec 99.1630 #GCMRL# 145 dt 129.472000 rms 0.715 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 81.6590 tsec 94.0950 #GCMRL# 146 dt 129.472000 rms 0.715 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.4450 tsec 87.5420 #GCMRL# 147 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 88.6730 tsec 101.8830 #GCMRL# 148 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 81.7770 tsec 93.1870 #GCMRL# 149 dt 129.472000 rms 0.714 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 80.1740 tsec 92.3540 #GCMRL# 150 dt 129.472000 rms 0.713 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 81.8260 tsec 92.9030 #GCMRL# 151 dt 129.472000 rms 0.713 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 79.8510 tsec 91.7320 #GCMRL# 152 dt 129.472000 rms 0.713 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 82.9370 tsec 93.6830 #GCMRL# 153 dt 129.472000 rms 0.712 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 84.7870 tsec 97.4620 #GCMRL# 154 dt 129.472000 rms 0.712 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 89.7010 tsec 101.5000 #GCMRL# 155 dt 129.472000 rms 0.712 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 88.8770 tsec 101.8240 #GCMRL# 156 dt 129.472000 rms 0.712 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 89.5590 tsec 105.3770 #GCMRL# 157 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 83.0600 tsec 95.4900 #GCMRL# 158 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 85.2200 tsec 95.6620 #GCMRL# 159 dt 129.472000 rms 0.711 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 85.7870 tsec 97.4690 #GCMRL# 160 dt 129.472000 rms 0.710 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 79.2740 tsec 91.5000 #GCMRL# 161 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 82.9210 tsec 95.9000 #GCMRL# 162 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.8580 tsec 88.5270 #GCMRL# 163 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 82.3060 tsec 94.8130 #GCMRL# 164 dt 129.472000 rms 0.710 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 86.9850 tsec 98.6840 #GCMRL# 165 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 85.1570 tsec 97.6460 #GCMRL# 166 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 81.0730 tsec 93.9290 #GCMRL# 167 dt 129.472000 rms 0.709 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 79.8160 tsec 91.0770 #GCMRL# 168 dt 129.472000 rms 0.709 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.8700 tsec 88.5300 #GCMRL# 169 dt 129.472000 rms 0.709 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 79.2660 tsec 90.8860 #GCMRL# 170 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.8530 tsec 88.3410 #GCMRL# 171 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 83.5390 tsec 97.1530 #GCMRL# 172 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 80.1380 tsec 89.5850 #GCMRL# 173 dt 129.472000 rms 0.708 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 79.6640 tsec 92.8500 #GCMRL# 174 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 78.8910 tsec 88.9660 #GCMRL# 175 dt 129.472000 rms 0.707 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 75.6160 tsec 86.7430 #GCMRL# 176 dt 129.472000 rms 0.707 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 71.9810 tsec 81.7640 #GCMRL# 177 dt 129.472000 rms 0.707 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 68.2540 tsec 77.3700 #GCMRL# 178 dt 129.472000 rms 0.707 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 66.5150 tsec 76.0900 #GCMRL# 179 dt 5918.720000 rms 0.706 0.071% neg 0 invalid 762 tFOTS 150.4280 tGradient 68.7150 tsec 229.9540 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.70616) vs oldopt=(dt=92.48,rms=0.706165) #GCMRL# 180 dt 73.984000 rms 0.706 0.000% neg 0 invalid 762 tFOTS 135.7350 tGradient 66.4690 tsec 211.3500 #GCMRL# 181 dt 73.984000 rms 0.706 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 68.6650 tsec 78.3360 #GCMRL# 182 dt 73.984000 rms 0.706 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 65.1670 tsec 74.9050 #GCAMreg# pass 0 level1 5 level2 1 tsec 12623 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.706908 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.705379) vs oldopt=(dt=92.48,rms=0.705528) #GCMRL# 184 dt 129.472000 rms 0.705 0.216% neg 0 invalid 762 tFOTS 156.5510 tGradient 74.3080 tsec 240.4540 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.704347) vs oldopt=(dt=369.92,rms=0.704522) #GCMRL# 185 dt 517.888000 rms 0.704 0.146% neg 0 invalid 762 tFOTS 156.9840 tGradient 73.4280 tsec 240.8160 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.704176) vs oldopt=(dt=92.48,rms=0.704194) #GCMRL# 186 dt 129.472000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 150.9960 tGradient 72.8260 tsec 235.2310 #GCMRL# 187 dt 129.472000 rms 0.704 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 73.0360 tsec 83.0850 #GCMRL# 188 dt 129.472000 rms 0.704 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 71.9170 tsec 82.9240 #GCMRL# 189 dt 129.472000 rms 0.704 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 72.1930 tsec 82.8380 #GCMRL# 190 dt 129.472000 rms 0.704 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.3970 tsec 86.6100 #GCMRL# 191 dt 129.472000 rms 0.703 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 67.0800 tsec 78.3240 #GCMRL# 192 dt 129.472000 rms 0.703 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 73.8230 tsec 84.3270 #GCMRL# 193 dt 129.472000 rms 0.703 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 72.6000 tsec 83.9890 #GCMRL# 194 dt 129.472000 rms 0.703 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 75.0200 tsec 86.0790 #GCMRL# 195 dt 129.472000 rms 0.703 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.9260 tsec 85.7780 #GCMRL# 196 dt 129.472000 rms 0.702 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.5100 tsec 88.0980 #GCMRL# 197 dt 129.472000 rms 0.702 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 77.5800 tsec 88.4780 #GCMRL# 198 dt 129.472000 rms 0.702 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 75.8950 tsec 85.9040 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.70213) vs oldopt=(dt=369.92,rms=0.702135) #GCMRL# 199 dt 295.936000 rms 0.702 0.000% neg 0 invalid 762 tFOTS 166.5040 tGradient 71.8920 tsec 249.0860 #GCMRL# 200 dt 295.936000 rms 0.702 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 74.8340 tsec 85.6510 #GCMRL# 201 dt 295.936000 rms 0.702 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 76.1400 tsec 87.5170 #GCMRL# 202 dt 295.936000 rms 0.702 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 75.0070 tsec 85.2540 #GCMRL# 203 dt 295.936000 rms 0.702 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 67.8920 tsec 77.1150 #GCMRL# 204 dt 295.936000 rms 0.702 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 71.0510 tsec 82.0320 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701437) vs oldopt=(dt=92.48,rms=0.701445) #GCMRL# 205 dt 129.472000 rms 0.701 0.019% neg 0 invalid 762 tFOTS 144.8240 tGradient 71.0430 tsec 224.9460 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701443) vs oldopt=(dt=92.48,rms=0.701444) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.704686 #FOTS# QuadFit found better minimum quadopt=(dt=169.475,rms=0.699018) vs oldopt=(dt=103.68,rms=0.699625) #GCMRL# 207 dt 169.474860 rms 0.699 0.804% neg 0 invalid 762 tFOTS 140.2050 tGradient 50.0200 tsec 200.5840 #FOTS# QuadFit found better minimum quadopt=(dt=192,rms=0.689646) vs oldopt=(dt=103.68,rms=0.691455) #GCMRL# 208 dt 192.000000 rms 0.690 1.341% neg 0 invalid 762 tFOTS 141.6730 tGradient 48.7310 tsec 200.8100 #FOTS# QuadFit found better minimum quadopt=(dt=67.7333,rms=0.686057) vs oldopt=(dt=25.92,rms=0.686985) #GCMRL# 209 dt 67.733333 rms 0.686 0.520% neg 0 invalid 762 tFOTS 142.9300 tGradient 48.0820 tsec 201.5010 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.678544) vs oldopt=(dt=414.72,rms=0.678631) #GCMRL# 210 dt 331.776000 rms 0.679 1.095% neg 0 invalid 762 tFOTS 129.8230 tGradient 47.8490 tsec 187.4230 #FOTS# QuadFit found better minimum quadopt=(dt=61.9221,rms=0.674719) vs oldopt=(dt=25.92,rms=0.675676) #GCMRL# 211 dt 61.922078 rms 0.675 0.564% neg 0 invalid 762 tFOTS 140.1020 tGradient 45.5320 tsec 195.1350 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.671901) vs oldopt=(dt=103.68,rms=0.672143) #GCMRL# 212 dt 145.152000 rms 0.672 0.418% neg 0 invalid 762 tFOTS 137.2540 tGradient 45.2480 tsec 191.7180 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.670285) vs oldopt=(dt=25.92,rms=0.670597) #GCMRL# 213 dt 36.288000 rms 0.670 0.241% neg 0 invalid 762 tFOTS 140.8580 tGradient 47.6600 tsec 198.6660 #GCMRL# 214 dt 414.720000 rms 0.666 0.585% neg 0 invalid 762 tFOTS 129.3780 tGradient 48.1420 tsec 186.8630 #FOTS# QuadFit found better minimum quadopt=(dt=58.022,rms=0.662064) vs oldopt=(dt=25.92,rms=0.663079) #GCMRL# 215 dt 58.021978 rms 0.662 0.646% neg 0 invalid 762 tFOTS 147.6610 tGradient 50.7640 tsec 206.4960 #FOTS# QuadFit found better minimum quadopt=(dt=68.6829,rms=0.661125) vs oldopt=(dt=103.68,rms=0.661322) #GCMRL# 216 dt 68.682927 rms 0.661 0.142% neg 0 invalid 762 tFOTS 144.8490 tGradient 47.5460 tsec 201.5580 #GCMRL# 217 dt 103.680000 rms 0.660 0.206% neg 0 invalid 762 tFOTS 145.9710 tGradient 49.3090 tsec 204.9690 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.659053) vs oldopt=(dt=25.92,rms=0.659202) #GCMRL# 218 dt 36.288000 rms 0.659 0.108% neg 0 invalid 762 tFOTS 134.9290 tGradient 45.2180 tsec 189.4630 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.654714) vs oldopt=(dt=414.72,rms=0.65545) #GCMRL# 219 dt 580.608000 rms 0.655 0.658% neg 0 invalid 762 tFOTS 149.2570 tGradient 44.9650 tsec 205.4620 #FOTS# QuadFit found better minimum quadopt=(dt=67.6364,rms=0.652369) vs oldopt=(dt=25.92,rms=0.652822) #GCMRL# 220 dt 67.636364 rms 0.652 0.358% neg 0 invalid 762 tFOTS 147.3630 tGradient 52.7530 tsec 211.8110 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.651527) vs oldopt=(dt=25.92,rms=0.651666) #GCMRL# 221 dt 36.288000 rms 0.652 0.129% neg 0 invalid 762 tFOTS 154.6930 tGradient 51.0220 tsec 215.5760 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.648123) vs oldopt=(dt=414.72,rms=0.648688) #GCMRL# 222 dt 580.608000 rms 0.648 0.522% neg 0 invalid 762 tFOTS 160.8590 tGradient 55.8630 tsec 228.4860 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.646406) vs oldopt=(dt=25.92,rms=0.646678) #GCMRL# 223 dt 36.288000 rms 0.646 0.265% neg 0 invalid 762 tFOTS 162.5350 tGradient 53.3540 tsec 226.7120 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.645724) vs oldopt=(dt=103.68,rms=0.645835) #GCMRL# 224 dt 145.152000 rms 0.646 0.105% neg 0 invalid 762 tFOTS 157.8010 tGradient 54.1540 tsec 223.0760 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.64461) vs oldopt=(dt=103.68,rms=0.644727) #GCMRL# 225 dt 145.152000 rms 0.645 0.173% neg 0 invalid 762 tFOTS 166.0120 tGradient 55.1260 tsec 231.8800 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.644212) vs oldopt=(dt=25.92,rms=0.6443) #GCMRL# 226 dt 36.288000 rms 0.644 0.062% neg 0 invalid 762 tFOTS 169.7380 tGradient 52.2210 tsec 232.8230 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.643363) vs oldopt=(dt=414.72,rms=0.643531) #GCMRL# 227 dt 248.832000 rms 0.643 0.132% neg 0 invalid 762 tFOTS 153.9050 tGradient 54.4960 tsec 219.2210 #FOTS# QuadFit found better minimum quadopt=(dt=85.3333,rms=0.642294) vs oldopt=(dt=103.68,rms=0.642346) #GCMRL# 228 dt 85.333333 rms 0.642 0.166% neg 0 invalid 762 tFOTS 167.3630 tGradient 55.9420 tsec 234.6050 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.641898) vs oldopt=(dt=103.68,rms=0.641953) #GCMRL# 229 dt 82.944000 rms 0.642 0.062% neg 0 invalid 762 tFOTS 164.4910 tGradient 51.4220 tsec 227.8920 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.641285) vs oldopt=(dt=103.68,rms=0.641286) #GCMRL# 230 dt 124.416000 rms 0.641 0.095% neg 0 invalid 762 tFOTS 166.7830 tGradient 55.0370 tsec 234.8810 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.64088) vs oldopt=(dt=25.92,rms=0.640968) #GCMRL# 231 dt 36.288000 rms 0.641 0.063% neg 0 invalid 762 tFOTS 183.4520 tGradient 56.1520 tsec 251.3860 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.639431) vs oldopt=(dt=414.72,rms=0.639473) #GCMRL# 232 dt 497.664000 rms 0.639 0.226% neg 0 invalid 762 tFOTS 163.8320 tGradient 54.0230 tsec 229.9620 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.638071) vs oldopt=(dt=25.92,rms=0.638305) #GCMRL# 233 dt 36.288000 rms 0.638 0.213% neg 0 invalid 762 tFOTS 178.9860 tGradient 61.1590 tsec 252.4260 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.637494) vs oldopt=(dt=103.68,rms=0.637549) #GCMRL# 234 dt 145.152000 rms 0.637 0.090% neg 0 invalid 762 tFOTS 164.0920 tGradient 55.6200 tsec 230.4600 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.637132) vs oldopt=(dt=25.92,rms=0.637209) #GCMRL# 235 dt 36.288000 rms 0.637 0.057% neg 0 invalid 762 tFOTS 177.3280 tGradient 49.0490 tsec 237.8000 #GCMRL# 236 dt 414.720000 rms 0.636 0.165% neg 0 invalid 762 tFOTS 169.7730 tGradient 52.3340 tsec 232.7150 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.635115) vs oldopt=(dt=25.92,rms=0.635299) #GCMRL# 237 dt 36.288000 rms 0.635 0.152% neg 0 invalid 762 tFOTS 166.0370 tGradient 53.1320 tsec 231.9370 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.634581) vs oldopt=(dt=103.68,rms=0.63463) #GCMRL# 238 dt 145.152000 rms 0.635 0.084% neg 0 invalid 762 tFOTS 158.8700 tGradient 52.4390 tsec 221.4120 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.63422) vs oldopt=(dt=103.68,rms=0.634322) #GCMRL# 239 dt 62.208000 rms 0.634 0.057% neg 0 invalid 762 tFOTS 160.6640 tGradient 50.6440 tsec 223.0410 #GCMRL# 240 dt 414.720000 rms 0.633 0.151% neg 0 invalid 762 tFOTS 165.1490 tGradient 59.7060 tsec 236.4320 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.63243) vs oldopt=(dt=25.92,rms=0.63257) #GCMRL# 241 dt 36.288000 rms 0.632 0.131% neg 0 invalid 762 tFOTS 162.4650 tGradient 48.4330 tsec 221.7270 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.632065) vs oldopt=(dt=103.68,rms=0.632075) #GCMRL# 242 dt 124.416000 rms 0.632 0.058% neg 0 invalid 762 tFOTS 164.5740 tGradient 50.0250 tsec 226.5760 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631657) vs oldopt=(dt=103.68,rms=0.631671) #GCMRL# 243 dt 82.944000 rms 0.632 0.065% neg 0 invalid 762 tFOTS 167.2440 tGradient 51.5870 tsec 231.7810 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631393) vs oldopt=(dt=103.68,rms=0.631399) #GCMRL# 244 dt 82.944000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 180.9830 tGradient 54.2090 tsec 250.7100 #GCMRL# 245 dt 82.944000 rms 0.631 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 75.5740 tsec 86.7840 #GCMRL# 246 dt 82.944000 rms 0.631 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 59.4670 tsec 71.9720 #GCMRL# 247 dt 82.944000 rms 0.630 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 60.9230 tsec 82.2510 #GCMRL# 248 dt 82.944000 rms 0.629 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 65.1580 tsec 78.6510 #GCMRL# 249 dt 82.944000 rms 0.628 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 70.7270 tsec 83.6550 #GCMRL# 250 dt 82.944000 rms 0.627 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.8300 tsec 66.5930 #GCMRL# 251 dt 82.944000 rms 0.625 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 57.1070 tsec 69.3950 #GCMRL# 252 dt 82.944000 rms 0.624 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 68.8540 tsec 80.9030 #GCMRL# 253 dt 82.944000 rms 0.623 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.0410 tsec 66.4360 #GCMRL# 254 dt 82.944000 rms 0.622 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 52.0420 tsec 63.3060 #GCMRL# 255 dt 82.944000 rms 0.621 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 56.4010 tsec 68.0890 #GCMRL# 256 dt 82.944000 rms 0.620 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.9520 tsec 64.1370 #GCMRL# 257 dt 82.944000 rms 0.619 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.2350 tsec 64.4670 #GCMRL# 258 dt 82.944000 rms 0.618 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.6280 tsec 61.4720 #GCMRL# 259 dt 82.944000 rms 0.617 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.9640 tsec 64.2350 #GCMRL# 260 dt 82.944000 rms 0.616 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.7370 tsec 63.8640 #GCMRL# 261 dt 82.944000 rms 0.615 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.8790 tsec 62.6200 #GCMRL# 262 dt 82.944000 rms 0.614 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 48.4150 tsec 58.4730 #GCMRL# 263 dt 82.944000 rms 0.614 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 57.1240 tsec 68.7910 #GCMRL# 264 dt 82.944000 rms 0.613 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 52.6580 tsec 65.7570 #GCMRL# 265 dt 82.944000 rms 0.612 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 60.3920 tsec 71.5510 #GCMRL# 266 dt 82.944000 rms 0.612 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.9150 tsec 64.2710 #GCMRL# 267 dt 82.944000 rms 0.612 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 57.4600 tsec 72.2080 #GCMRL# 268 dt 20.736000 rms 0.612 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.3740 tsec 76.2530 #GCMRL# 269 dt 5.184000 rms 0.612 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.6120 tsec 73.9330 #FOTS# QuadFit found better minimum quadopt=(dt=0.567,rms=0.611569) vs oldopt=(dt=0.405,rms=0.611569) #GCMRL# 270 dt 0.567000 rms 0.612 0.000% neg 0 invalid 762 tFOTS 112.6520 tGradient 55.6370 tsec 181.2940 #GCMRL# 271 dt 0.141750 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 60.1430 tsec 85.0440 #GCMRL# 272 dt 0.070875 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 51.9620 tsec 75.4900 #GCAMreg# pass 0 level1 4 level2 1 tsec 10546.7 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.612649 #FOTS# QuadFit found better minimum quadopt=(dt=0.0354375,rms=0.611567) vs oldopt=(dt=0.0253125,rms=0.611568) #GCMRL# 274 dt 0.035437 rms 0.612 0.176% neg 0 invalid 762 tFOTS 94.3450 tGradient 54.0740 tsec 162.1470 #FOTS# QuadFit found better minimum quadopt=(dt=0.00885937,rms=0.611567) vs oldopt=(dt=0.00632812,rms=0.611567) #GCMRL# 275 dt 0.008859 rms 0.612 0.000% neg 0 invalid 762 tFOTS 76.1650 tGradient 54.5490 tsec 143.6600 #GCMRL# 276 dt 0.002215 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 53.9590 tsec 75.7930 #GCMRL# 277 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 54.7730 tsec 72.6420 #GCMRL# 278 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 55.9770 tsec 65.5190 #GCMRL# 279 dt 0.000138 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 50.5230 tsec 76.7020 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.625485 #FOTS# QuadFit found better minimum quadopt=(dt=87.0701,rms=0.614414) vs oldopt=(dt=128,rms=0.616497) #GCMRL# 281 dt 87.070059 rms 0.614 1.770% neg 0 invalid 762 tFOTS 155.3520 tGradient 38.3400 tsec 204.4480 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.610965) vs oldopt=(dt=8,rms=0.61191) #GCMRL# 282 dt 11.200000 rms 0.611 0.561% neg 0 invalid 762 tFOTS 143.3520 tGradient 40.4960 tsec 194.6010 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.608422) vs oldopt=(dt=8,rms=0.609126) #GCMRL# 283 dt 11.200000 rms 0.608 0.416% neg 0 invalid 762 tFOTS 137.5840 tGradient 40.8610 tsec 190.8990 #GCMRL# 284 dt 32.000000 rms 0.603 0.902% neg 0 invalid 762 tFOTS 140.1680 tGradient 38.4610 tsec 189.8860 #FOTS# QuadFit found better minimum quadopt=(dt=153.6,rms=0.588486) vs oldopt=(dt=128,rms=0.590481) #GCMRL# 285 dt 153.600000 rms 0.588 2.396% neg 0 invalid 762 tFOTS 172.0660 tGradient 42.2260 tsec 225.9290 #GCMRL# 286 dt 32.000000 rms 0.586 0.367% neg 0 invalid 762 tFOTS 144.3460 tGradient 38.6290 tsec 194.1990 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.584802) vs oldopt=(dt=32,rms=0.58511) #GCMRL# 287 dt 44.800000 rms 0.585 0.260% neg 0 invalid 762 tFOTS 144.6610 tGradient 39.0250 tsec 195.0270 #GCMRL# 288 dt 32.000000 rms 0.583 0.332% neg 0 invalid 762 tFOTS 153.7470 tGradient 41.5050 tsec 206.2930 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.581944) vs oldopt=(dt=32,rms=0.581955) #GCMRL# 289 dt 38.400000 rms 0.582 0.157% neg 0 invalid 762 tFOTS 142.4820 tGradient 38.1400 tsec 190.3080 #GCMRL# 290 dt 32.000000 rms 0.580 0.313% neg 0 invalid 762 tFOTS 152.5410 tGradient 38.1850 tsec 203.2680 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.579347) vs oldopt=(dt=32,rms=0.579356) #GCMRL# 291 dt 25.600000 rms 0.579 0.133% neg 0 invalid 762 tFOTS 155.8580 tGradient 49.1920 tsec 215.6380 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.577879) vs oldopt=(dt=32,rms=0.578021) #GCMRL# 292 dt 38.400000 rms 0.578 0.253% neg 0 invalid 762 tFOTS 144.5610 tGradient 42.7260 tsec 197.3840 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.577186) vs oldopt=(dt=32,rms=0.5772) #GCMRL# 293 dt 25.600000 rms 0.577 0.120% neg 0 invalid 762 tFOTS 144.6930 tGradient 35.6180 tsec 190.1050 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.575765) vs oldopt=(dt=32,rms=0.575998) #GCMRL# 294 dt 44.800000 rms 0.576 0.246% neg 0 invalid 762 tFOTS 142.9040 tGradient 37.1170 tsec 190.3440 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.575121) vs oldopt=(dt=32,rms=0.575172) #GCMRL# 295 dt 25.600000 rms 0.575 0.112% neg 0 invalid 762 tFOTS 147.0810 tGradient 38.5450 tsec 199.3430 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.573811) vs oldopt=(dt=32,rms=0.574018) #GCMRL# 296 dt 44.800000 rms 0.574 0.228% neg 0 invalid 762 tFOTS 137.5010 tGradient 33.5820 tsec 181.4990 #FOTS# QuadFit found better minimum quadopt=(dt=24.9449,rms=0.573318) vs oldopt=(dt=32,rms=0.573419) #GCMRL# 297 dt 24.944882 rms 0.573 0.086% neg 0 invalid 762 tFOTS 137.6990 tGradient 35.6170 tsec 183.4810 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.572173) vs oldopt=(dt=32,rms=0.572327) #GCMRL# 298 dt 44.800000 rms 0.572 0.200% neg 0 invalid 762 tFOTS 135.3550 tGradient 37.6770 tsec 183.9920 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.571704) vs oldopt=(dt=32,rms=0.571867) #GCMRL# 299 dt 19.200000 rms 0.572 0.082% neg 0 invalid 762 tFOTS 145.0980 tGradient 39.3370 tsec 196.9140 #GCMRL# 300 dt 128.000000 rms 0.569 0.411% neg 0 invalid 762 tFOTS 147.6010 tGradient 33.8870 tsec 196.4080 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.56885) vs oldopt=(dt=8,rms=0.56897) #GCMRL# 301 dt 11.200000 rms 0.569 0.089% neg 0 invalid 762 tFOTS 138.8520 tGradient 38.1060 tsec 187.0770 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.568437) vs oldopt=(dt=32,rms=0.568504) #GCMRL# 302 dt 19.200000 rms 0.568 0.073% neg 0 invalid 762 tFOTS 156.8700 tGradient 39.8280 tsec 208.2800 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.566753) vs oldopt=(dt=128,rms=0.566905) #GCMRL# 303 dt 179.200000 rms 0.567 0.296% neg 0 invalid 762 tFOTS 141.3140 tGradient 45.0340 tsec 198.1780 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.565599) vs oldopt=(dt=32,rms=0.565671) #GCMRL# 304 dt 25.600000 rms 0.566 0.204% neg 0 invalid 762 tFOTS 135.3290 tGradient 43.6410 tsec 189.1610 #GCMRL# 305 dt 32.000000 rms 0.565 0.151% neg 0 invalid 762 tFOTS 121.4090 tGradient 34.9830 tsec 164.4670 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.564467) vs oldopt=(dt=32,rms=0.564525) #GCMRL# 306 dt 19.200000 rms 0.564 0.000% neg 0 invalid 762 tFOTS 122.3440 tGradient 31.0480 tsec 162.2070 #GCMRL# 307 dt 19.200000 rms 0.564 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.6800 tsec 38.6340 #GCMRL# 308 dt 19.200000 rms 0.564 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.8300 tsec 44.9890 #GCMRL# 309 dt 19.200000 rms 0.563 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 31.3730 tsec 39.9090 #GCMRL# 310 dt 19.200000 rms 0.562 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.3590 tsec 35.8050 #GCMRL# 311 dt 19.200000 rms 0.562 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.2260 tsec 36.0440 #GCMRL# 312 dt 19.200000 rms 0.561 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 34.4630 tsec 42.4530 #GCMRL# 313 dt 19.200000 rms 0.560 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.2270 tsec 36.1280 #GCMRL# 314 dt 19.200000 rms 0.559 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.2640 tsec 41.6980 #GCMRL# 315 dt 19.200000 rms 0.558 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 33.0580 tsec 43.8550 #GCMRL# 316 dt 19.200000 rms 0.558 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.9700 tsec 39.9780 #GCMRL# 317 dt 19.200000 rms 0.557 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 32.3180 tsec 39.9630 #GCMRL# 318 dt 19.200000 rms 0.557 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.2830 tsec 38.2660 #GCMRL# 319 dt 19.200000 rms 0.557 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 28.0310 tsec 35.4830 #GCMRL# 320 dt 9.600000 rms 0.557 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 27.5120 tsec 41.5850 #GCMRL# 321 dt 1.200000 rms 0.557 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 36.7160 tsec 61.0950 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.556586) vs oldopt=(dt=0.5,rms=0.556587) #GCMRL# 322 dt 0.700000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 99.4590 tGradient 29.2240 tsec 140.1580 #GCMRL# 323 dt 0.350000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 30.8020 tsec 46.5170 #GCMRL# 324 dt 0.087500 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 29.9530 tsec 47.7490 #GCAMreg# pass 0 level1 3 level2 1 tsec 5984.06 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.557587 #FOTS# QuadFit found better minimum quadopt=(dt=56.5828,rms=0.55345) vs oldopt=(dt=32,rms=0.553854) #GCMRL# 326 dt 56.582781 rms 0.553 0.742% neg 0 invalid 762 tFOTS 122.9470 tGradient 32.1690 tsec 164.2760 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.552809) vs oldopt=(dt=8,rms=0.552932) #GCMRL# 327 dt 11.200000 rms 0.553 0.116% neg 0 invalid 762 tFOTS 121.6730 tGradient 30.5620 tsec 161.1970 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.552079) vs oldopt=(dt=32,rms=0.552132) #GCMRL# 328 dt 44.800000 rms 0.552 0.132% neg 0 invalid 762 tFOTS 141.5800 tGradient 32.3010 tsec 186.0930 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.551251) vs oldopt=(dt=32,rms=0.551272) #GCMRL# 329 dt 38.400000 rms 0.551 0.150% neg 0 invalid 762 tFOTS 143.5100 tGradient 30.8780 tsec 186.5810 #New# invocation of recon-all Sat Jul 18 13:31:15 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -all -noskullstrip subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 1024 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:24-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:25-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:26-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:27-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:28-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:29-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:30-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-17:31:31-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Sat Jul 18 13:31:31 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:18:13:31:31 mri_convert N 4 e 2.06 S 0.06 U 1.85 P 92% M 53736 F 1 R 2034 W 0 c 312 w 52 I 88 O 0 L 0.30 0.09 0.02 @#@FSLOADPOST 2020:07:18:13:31:33 mri_convert N 4 0.30 0.09 0.02 #-------------------------------------------- #@# MotionCor Sat Jul 18 13:31:33 EDT 2020 Found 1 runs /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261116, -0.041979) j_ras = (-0.0224984, 0.996182, -0.0843504) k_ras = (-0.0440213, 0.0833028, 0.995551) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 3297.37 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... @#@FSTIME 2020:07:18:13:31:37 mri_convert N 3 e 4.74 S 0.03 U 4.65 P 98% M 65728 F 0 R 3612 W 0 c 263 w 31 I 0 O 0 L 0.28 0.08 0.02 @#@FSLOADPOST 2020:07:18:13:31:41 mri_convert N 3 0.33 0.10 0.02 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:07:18:13:31:41 mri_add_xform_to_header N 4 e 0.98 S 0.01 U 0.69 P 71% M 20492 F 0 R 1772 W 0 c 43 w 33 I 0 O 0 L 0.33 0.10 0.02 @#@FSLOADPOST 2020:07:18:13:31:42 mri_add_xform_to_header N 4 0.33 0.10 0.02 #-------------------------------------------- #@# Talairach Sat Jul 18 13:31:42 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Jul 18 13:31:43 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.3722 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.3722/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.3722/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.3722/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.3722/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Sat Jul 18 13:35:19 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:18:13:31:42 mri_nu_correct.mni N 12 e 216.90 S 0.74 U 214.74 P 99% M 500276 F 0 R 40367 W 0 c 8216 w 224 I 0 O 0 L 0.33 0.10 0.02 @#@FSLOADPOST 2020:07:18:13:35:19 mri_nu_correct.mni N 12 0.98 0.55 0.22 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Jul 18 13:35:19 EDT 2020 Ended at Sat Jul 18 13:35:53 EDT 2020 talairach_avi done @#@FSTIME 2020:07:18:13:35:19 talairach_avi N 4 e 33.74 S 1.09 U 25.56 P 78% M 253940 F 1 R 41912 W 0 c 3714 w 954 I 48 O 32 L 0.98 0.55 0.22 @#@FSLOADPOST 2020:07:18:13:35:53 talairach_avi N 4 0.91 0.58 0.24 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Jul 18 13:35:53 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5199, pval=0.1531 >= threshold=0.0050) @#@FSTIME 2020:07:18:13:35:53 talairach_afd N 4 e 0.26 S 0.00 U 0.00 P 2% M 2452 F 0 R 718 W 0 c 8 w 53 I 0 O 0 L 0.91 0.58 0.24 @#@FSLOADPOST 2020:07:18:13:35:54 talairach_afd N 4 0.91 0.58 0.24 awk -f /public/apps/freesurfer/7.1.0/bin/extract_talairach_avi_QA.awk /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log tal_QC_AZS /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log TalAviQA: 0.96317 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Sat Jul 18 13:35:54 EDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Jul 18 13:35:54 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.4264 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz sysname Linux hostname loginnode2 machine x86_64 user pankumar input /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.4264/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 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.4264/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4264/input.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.4264/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4264/input.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.4264/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 /dev/shm/tmp.mri_nu_correct.mni.4264/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.4264/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4264/output.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.4264/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4264/output.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.4264/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.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 /dev/shm/tmp.mri_nu_correct.mni.4264/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz mul 1.15054592399081702868 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.4264/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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 8 seconds. mapping (13, 196) to ( 3, 110) Sat Jul 18 13:40:06 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:18:13:35:54 mri_nu_correct.mni N 9 e 252.08 S 1.93 U 248.71 P 99% M 611088 F 0 R 191055 W 0 c 8820 w 431 I 0 O 0 L 0.91 0.58 0.24 @#@FSLOADPOST 2020:07:18:13:40:06 mri_nu_correct.mni N 9 1.03 0.84 0.42 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2020:07:18:13:40:06 mri_add_xform_to_header N 4 e 0.46 S 0.02 U 0.43 P 97% M 20568 F 0 R 1793 W 0 c 9 w 33 I 0 O 0 L 1.03 0.84 0.42 @#@FSLOADPOST 2020:07:18:13:40:06 mri_add_xform_to_header N 4 1.03 0.84 0.42 #-------------------------------------------- #@# Intensity Normalization Sat Jul 18 13:40:06 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 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(): error: MRIhistogramRegion: input mri nu.mgz is blank MRIsplineNormalize(): npeaks = 12 Starting OpenSpline(): npoints = 12 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 56 (56), valley at 0 (-1) csf peak at 28, setting threshold to 46 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 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 7 seconds. @#@FSTIME 2020:07:18:13:40:06 mri_normalize N 7 e 127.93 S 0.47 U 127.04 P 99% M 578872 F 0 R 13924 W 0 c 3686 w 47 I 0 O 0 L 1.03 0.84 0.42 @#@FSLOADPOST 2020:07:18:13:42:14 mri_normalize N 7 1.00 0.89 0.49 #------------------------------------- #@# EM Registration Sat Jul 18 13:42:14 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, 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=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -3.918 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (-2.632, -2.632, -2.632) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) Found translation: (-2.6, -2.6, -2.6): log p = -3.811 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.811 (thresh=-3.8) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 16 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.624 (thresh=-3.6) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 9 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.624 (thresh=-3.6) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 3 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 6 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.505, old_max_log_p =-3.534 (thresh=-3.5) 1.03379 0.01049 0.00809 -9.19070; -0.00869 1.28704 0.00797 -40.93967; -0.00832 -0.01033 0.99642 -0.34468; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 50 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.505 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 49 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.488 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.488 (old=-3.918) transform before final EM align: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 886180 FSRUNTIME@ mri_em_register 0.2656 hours 1 threads registration took 15 minutes and 56 seconds. @#@FSTIME 2020:07:18:13:42:14 mri_em_register N 7 e 956.18 S 3.41 U 949.67 P 99% M 613100 F 0 R 112869 W 0 c 22105 w 82 I 0 O 0 L 1.00 0.89 0.49 @#@FSLOADPOST 2020:07:18:13:58:10 mri_em_register N 7 1.00 1.00 0.80 #-------------------------------------- #@# CA Normalize Sat Jul 18 13:58:10 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.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 '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 133 of 656 (20.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 395 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 15 (0.0%) samples deleted using 1091 total control points for intensity normalization... bias field = 0.959 +- 0.058 1 of 958 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 823 (1.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 533 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 64 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 53 (3.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 27 of 79 (34.2%) samples deleted using 1552 total control points for intensity normalization... bias field = 1.009 +- 0.066 3 of 1469 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 824 (1.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 626 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 84 (53.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 77 (32.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 86 of 139 (61.9%) samples deleted using 1750 total control points for intensity normalization... bias field = 1.002 +- 0.054 1 of 1545 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 33 seconds. @#@FSTIME 2020:07:18:13:58:11 mri_ca_normalize N 8 e 92.85 S 1.17 U 91.28 P 99% M 927664 F 0 R 127919 W 0 c 1865 w 68 I 0 O 0 L 1.00 1.00 0.80 @#@FSLOADPOST 2020:07:18:13:59:43 mri_ca_normalize N 8 1.06 1.01 0.82 #-------------------------------------- #@# CA Reg Sat Jul 18 13:59:43 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.935117 #FOTS# QuadFit found better minimum quadopt=(dt=246.905,rms=0.794434) vs oldopt=(dt=92.48,rms=0.845465) #GCMRL# 0 dt 246.904762 rms 0.794 15.044% neg 0 invalid 762 tFOTS 22.5120 tGradient 9.2770 tsec 33.4480 #FOTS# QuadFit found better minimum quadopt=(dt=209.836,rms=0.765228) vs oldopt=(dt=92.48,rms=0.774396) #GCMRL# 1 dt 209.836066 rms 0.765 3.676% neg 0 invalid 762 tFOTS 24.2560 tGradient 8.9820 tsec 34.8070 #FOTS# QuadFit found better minimum quadopt=(dt=229.859,rms=0.750881) vs oldopt=(dt=92.48,rms=0.755764) #GCMRL# 2 dt 229.859155 rms 0.751 1.875% neg 0 invalid 762 tFOTS 24.5730 tGradient 8.9240 tsec 35.2350 #FOTS# QuadFit found better minimum quadopt=(dt=129.506,rms=0.74519) vs oldopt=(dt=92.48,rms=0.745844) #GCMRL# 3 dt 129.505882 rms 0.745 0.758% neg 0 invalid 762 tFOTS 24.5120 tGradient 9.1090 tsec 35.3290 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.734166) vs oldopt=(dt=369.92,rms=0.736011) #GCMRL# 4 dt 517.888000 rms 0.734 1.479% neg 0 invalid 762 tFOTS 24.2770 tGradient 8.7340 tsec 34.7350 #New# invocation of recon-all Sat Jul 18 14:03:37 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -all -noskullstrip subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 1024 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:03:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #New# invocation of recon-all Sat Jul 18 14:10:38 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -all -noskullstrip -no-isrunning subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 1024 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/18-18:10:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Sat Jul 18 14:10:39 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:18:14:10:39 mri_convert N 4 e 1.93 S 0.03 U 1.81 P 95% M 53736 F 0 R 1525 W 0 c 45 w 44 I 0 O 0 L 0.00 0.23 0.52 @#@FSLOADPOST 2020:07:18:14:10:41 mri_convert N 4 0.08 0.25 0.52 #-------------------------------------------- #@# MotionCor Sat Jul 18 14:10:41 EDT 2020 Found 1 runs /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261116, -0.041979) j_ras = (-0.0224984, 0.996182, -0.0843504) k_ras = (-0.0440213, 0.0833028, 0.995551) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 3297.37 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... @#@FSTIME 2020:07:18:14:10:44 mri_convert N 3 e 6.00 S 0.03 U 5.91 P 99% M 65732 F 0 R 3613 W 0 c 436 w 20 I 0 O 0 L 0.08 0.25 0.52 @#@FSLOADPOST 2020:07:18:14:10:51 mri_convert N 3 0.22 0.27 0.53 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:07:18:14:10:51 mri_add_xform_to_header N 4 e 0.42 S 0.01 U 0.39 P 97% M 20492 F 0 R 1772 W 0 c 23 w 26 I 0 O 0 L 0.22 0.27 0.53 @#@FSLOADPOST 2020:07:18:14:10:51 mri_add_xform_to_header N 4 0.22 0.27 0.53 #-------------------------------------------- #@# Talairach Sat Jul 18 14:10:51 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Jul 18 14:10:51 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.7230 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.7230/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.7230/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.7230/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.7230/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Sat Jul 18 14:14:27 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:18:14:10:51 mri_nu_correct.mni N 12 e 216.32 S 0.60 U 215.06 P 99% M 500280 F 0 R 38423 W 0 c 6284 w 188 I 0 O 0 L 0.22 0.27 0.53 @#@FSLOADPOST 2020:07:18:14:14:27 mri_nu_correct.mni N 12 0.98 0.64 0.61 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Jul 18 14:14:27 EDT 2020 Ended at Sat Jul 18 14:14:58 EDT 2020 talairach_avi done @#@FSTIME 2020:07:18:14:14:27 talairach_avi N 4 e 30.87 S 1.03 U 23.29 P 78% M 253936 F 0 R 42242 W 0 c 3716 w 883 I 0 O 32 L 0.98 0.64 0.61 @#@FSLOADPOST 2020:07:18:14:14:58 talairach_avi N 4 0.96 0.67 0.63 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Jul 18 14:14:58 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5199, pval=0.1531 >= threshold=0.0050) @#@FSTIME 2020:07:18:14:14:58 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 57% M 2448 F 0 R 716 W 0 c 3 w 29 I 0 O 0 L 0.96 0.67 0.63 @#@FSLOADPOST 2020:07:18:14:14:58 talairach_afd N 4 0.96 0.67 0.63 awk -f /public/apps/freesurfer/7.1.0/bin/extract_talairach_avi_QA.awk /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log tal_QC_AZS /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log TalAviQA: 0.96317 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Sat Jul 18 14:14:58 EDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.0 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Jul 18 14:14:58 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.7672 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz sysname Linux hostname loginnode2 machine x86_64 user pankumar input /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.7672/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 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.7672/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.7672/input.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.7672/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.7672/input.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.7672/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 /dev/shm/tmp.mri_nu_correct.mni.7672/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.7672/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.7672/output.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.7672/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.7672/output.mean.dat sysname Linux hostname loginnode2 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.7672/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.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 /dev/shm/tmp.mri_nu_correct.mni.7672/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz mul 1.15054592399081702868 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.7672/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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 9 seconds. mapping (13, 196) to ( 3, 110) Sat Jul 18 14:19:08 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:18:14:14:58 mri_nu_correct.mni N 9 e 249.80 S 1.41 U 247.41 P 99% M 611112 F 0 R 190172 W 0 c 12821 w 424 I 0 O 0 L 0.96 0.67 0.63 @#@FSLOADPOST 2020:07:18:14:19:08 mri_nu_correct.mni N 9 1.00 0.86 0.71 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2020:07:18:14:19:08 mri_add_xform_to_header N 4 e 0.41 S 0.01 U 0.38 P 98% M 20568 F 0 R 1793 W 0 c 6 w 36 I 0 O 0 L 1.00 0.86 0.71 @#@FSLOADPOST 2020:07:18:14:19:09 mri_add_xform_to_header N 4 1.00 0.86 0.71 #-------------------------------------------- #@# Intensity Normalization Sat Jul 18 14:19:09 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 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(): error: MRIhistogramRegion: input mri nu.mgz is blank MRIsplineNormalize(): npeaks = 12 Starting OpenSpline(): npoints = 12 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 56 (56), valley at 0 (-1) csf peak at 28, setting threshold to 46 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 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 4 seconds. @#@FSTIME 2020:07:18:14:19:09 mri_normalize N 7 e 124.92 S 0.38 U 124.11 P 99% M 578888 F 0 R 13417 W 0 c 5883 w 33 I 0 O 0 L 1.00 0.86 0.71 @#@FSLOADPOST 2020:07:18:14:21:14 mri_normalize N 7 1.00 0.90 0.74 #------------------------------------- #@# EM Registration Sat Jul 18 14:21:14 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, 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=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -3.918 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (-2.632, -2.632, -2.632) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) Found translation: (-2.6, -2.6, -2.6): log p = -3.811 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.811 (thresh=-3.8) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 15 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.624 (thresh=-3.6) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 18 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.624 (thresh=-3.6) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 7 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 8 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.505, old_max_log_p =-3.534 (thresh=-3.5) 1.03379 0.01049 0.00809 -9.19070; -0.00869 1.28704 0.00797 -40.93967; -0.00832 -0.01033 0.99642 -0.34468; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 49 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.505 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 49 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.488 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.488 (old=-3.918) transform before final EM align: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 886180 FSRUNTIME@ mri_em_register 0.2675 hours 1 threads registration took 16 minutes and 3 seconds. @#@FSTIME 2020:07:18:14:21:14 mri_em_register N 7 e 963.18 S 1.74 U 958.63 P 99% M 613100 F 0 R 112885 W 0 c 25304 w 70 I 0 O 0 L 1.00 0.90 0.74 @#@FSLOADPOST 2020:07:18:14:37:17 mri_em_register N 7 1.05 1.01 0.89 #-------------------------------------- #@# CA Normalize Sat Jul 18 14:37:17 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.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 '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 133 of 656 (20.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 395 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 15 (0.0%) samples deleted using 1091 total control points for intensity normalization... bias field = 0.959 +- 0.058 1 of 958 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 823 (1.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 533 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 64 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 53 (3.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 27 of 79 (34.2%) samples deleted using 1552 total control points for intensity normalization... bias field = 1.009 +- 0.066 3 of 1469 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 824 (1.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 626 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 84 (53.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 77 (32.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 86 of 139 (61.9%) samples deleted using 1750 total control points for intensity normalization... bias field = 1.002 +- 0.054 1 of 1545 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 31 seconds. @#@FSTIME 2020:07:18:14:37:17 mri_ca_normalize N 8 e 90.84 S 0.82 U 89.61 P 99% M 927660 F 0 R 129451 W 0 c 4197 w 54 I 0 O 0 L 1.05 1.01 0.89 @#@FSLOADPOST 2020:07:18:14:38:48 mri_ca_normalize N 8 1.01 1.00 0.90 #-------------------------------------- #@# CA Reg Sat Jul 18 14:38:48 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.935117 #FOTS# QuadFit found better minimum quadopt=(dt=246.905,rms=0.794434) vs oldopt=(dt=92.48,rms=0.845465) #GCMRL# 0 dt 246.904762 rms 0.794 15.044% neg 0 invalid 762 tFOTS 22.7540 tGradient 9.7800 tsec 34.3120 #FOTS# QuadFit found better minimum quadopt=(dt=209.836,rms=0.765228) vs oldopt=(dt=92.48,rms=0.774396) #GCMRL# 1 dt 209.836066 rms 0.765 3.676% neg 0 invalid 762 tFOTS 24.8710 tGradient 9.4240 tsec 35.9450 #FOTS# QuadFit found better minimum quadopt=(dt=229.859,rms=0.750881) vs oldopt=(dt=92.48,rms=0.755764) #GCMRL# 2 dt 229.859155 rms 0.751 1.875% neg 0 invalid 762 tFOTS 24.7850 tGradient 9.7470 tsec 36.1930 #FOTS# QuadFit found better minimum quadopt=(dt=129.506,rms=0.74519) vs oldopt=(dt=92.48,rms=0.745844) #GCMRL# 3 dt 129.505882 rms 0.745 0.758% neg 0 invalid 762 tFOTS 24.5880 tGradient 9.1400 tsec 35.5730 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.734166) vs oldopt=(dt=369.92,rms=0.736011) #GCMRL# 4 dt 517.888000 rms 0.734 1.479% neg 0 invalid 762 tFOTS 24.9420 tGradient 9.8800 tsec 36.7140 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.7319) vs oldopt=(dt=92.48,rms=0.731939) #GCMRL# 5 dt 110.976000 rms 0.732 0.309% neg 0 invalid 762 tFOTS 26.6990 tGradient 9.7230 tsec 38.3280 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.716292) vs oldopt=(dt=1479.68,rms=0.718156) #GCMRL# 6 dt 2071.552000 rms 0.716 2.132% neg 0 invalid 762 tFOTS 24.3180 tGradient 9.0980 tsec 35.0250 #GCMRL# 7 dt 92.480000 rms 0.713 0.459% neg 0 invalid 762 tFOTS 24.4000 tGradient 10.1570 tsec 36.0830 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.712379) vs oldopt=(dt=369.92,rms=0.712527) #GCMRL# 8 dt 221.952000 rms 0.712 0.000% neg 0 invalid 762 tFOTS 25.6550 tGradient 9.9910 tsec 37.2140 #GCMRL# 9 dt 221.952000 rms 0.711 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2300 tsec 11.0960 #GCMRL# 10 dt 221.952000 rms 0.710 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.0940 tsec 11.8370 #GCMRL# 11 dt 221.952000 rms 0.710 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7270 tsec 11.3320 #GCMRL# 12 dt 221.952000 rms 0.708 0.284% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5370 tsec 11.3590 #GCMRL# 13 dt 221.952000 rms 0.706 0.288% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.9560 tsec 11.6670 #GCMRL# 14 dt 221.952000 rms 0.704 0.260% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7320 tsec 11.3020 #GCMRL# 15 dt 221.952000 rms 0.702 0.307% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8300 tsec 11.6490 #GCMRL# 16 dt 221.952000 rms 0.699 0.343% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7280 tsec 10.4460 #GCMRL# 17 dt 221.952000 rms 0.697 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7650 tsec 10.6200 #GCMRL# 18 dt 221.952000 rms 0.696 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3160 tsec 10.8790 #GCMRL# 19 dt 221.952000 rms 0.695 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7890 tsec 10.4940 #GCMRL# 20 dt 221.952000 rms 0.693 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4010 tsec 9.9020 #GCMRL# 21 dt 221.952000 rms 0.693 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7390 tsec 11.3750 #GCMRL# 22 dt 221.952000 rms 0.692 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5310 tsec 10.0830 #GCMRL# 23 dt 221.952000 rms 0.691 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6180 tsec 10.1500 #GCMRL# 24 dt 221.952000 rms 0.690 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2910 tsec 10.7850 #GCMRL# 25 dt 221.952000 rms 0.690 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7350 tsec 11.6030 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.689488) vs oldopt=(dt=369.92,rms=0.68951) #GCMRL# 26 dt 295.936000 rms 0.689 0.066% neg 0 invalid 762 tFOTS 25.6340 tGradient 9.3740 tsec 36.8190 #GCAMreg# pass 0 level1 5 level2 1 tsec 594.921 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.689936 #GCMRL# 28 dt 92.480000 rms 0.689 0.112% neg 0 invalid 762 tFOTS 24.7390 tGradient 9.2950 tsec 35.6350 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.688749) vs oldopt=(dt=369.92,rms=0.688806) #GCMRL# 29 dt 295.936000 rms 0.689 0.000% neg 0 invalid 762 tFOTS 25.8950 tGradient 9.2800 tsec 36.8170 #GCMRL# 30 dt 295.936000 rms 0.688 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1560 tsec 10.7690 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.706108 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704881) vs oldopt=(dt=25.92,rms=0.704889) #GCMRL# 32 dt 31.104000 rms 0.705 0.174% neg 0 invalid 762 tFOTS 24.9240 tGradient 7.5240 tsec 34.3100 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704506) vs oldopt=(dt=25.92,rms=0.704515) #GCMRL# 33 dt 31.104000 rms 0.705 0.000% neg 0 invalid 762 tFOTS 22.6160 tGradient 7.5930 tsec 32.1120 #GCMRL# 34 dt 31.104000 rms 0.704 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3600 tsec 9.1560 #GCMRL# 35 dt 31.104000 rms 0.704 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1700 tsec 8.8180 #GCAMreg# pass 0 level1 4 level2 1 tsec 100.372 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.704365 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.70353) vs oldopt=(dt=25.92,rms=0.703568) #GCMRL# 37 dt 36.288000 rms 0.704 0.119% neg 0 invalid 762 tFOTS 25.8120 tGradient 7.4400 tsec 35.1140 #FOTS# QuadFit found better minimum quadopt=(dt=15.552,rms=0.703504) vs oldopt=(dt=25.92,rms=0.703509) #GCMRL# 38 dt 15.552000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 25.8590 tGradient 7.6150 tsec 35.2160 #GCMRL# 39 dt 15.552000 rms 0.703 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2600 tsec 8.9780 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.73685 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.735541) vs oldopt=(dt=8,rms=0.735619) #GCMRL# 41 dt 6.400000 rms 0.736 0.178% neg 0 invalid 762 tFOTS 25.2120 tGradient 6.6510 tsec 33.6780 #FOTS# QuadFit found better minimum quadopt=(dt=2.4,rms=0.735475) vs oldopt=(dt=2,rms=0.735476) #GCMRL# 42 dt 2.400000 rms 0.735 0.000% neg 0 invalid 762 tFOTS 24.8860 tGradient 6.5280 tsec 33.2450 #GCAMreg# pass 0 level1 3 level2 1 tsec 83.767 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.73596 #GCMRL# 44 dt 0.000000 rms 0.735 0.067% neg 0 invalid 762 tFOTS 23.3310 tGradient 6.7880 tsec 31.8440 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.817881 #FOTS# QuadFit found better minimum quadopt=(dt=3.31099,rms=0.806528) vs oldopt=(dt=2.88,rms=0.806715) #GCMRL# 46 dt 3.310987 rms 0.807 1.388% neg 0 invalid 762 tFOTS 23.7110 tGradient 6.1240 tsec 31.6410 #FOTS# QuadFit found better minimum quadopt=(dt=1.93269,rms=0.804898) vs oldopt=(dt=2.88,rms=0.805279) #GCMRL# 47 dt 1.932692 rms 0.805 0.000% neg 0 invalid 762 tFOTS 23.1250 tGradient 5.9910 tsec 30.9840 #GCMRL# 48 dt 1.932692 rms 0.803 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0540 tsec 7.6940 #GCMRL# 49 dt 1.932692 rms 0.803 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6690 tsec 7.3890 #GCMRL# 50 dt 1.932692 rms 0.803 -0.411% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0240 tsec 9.5260 #GCAMreg# pass 0 level1 2 level2 1 tsec 125.886 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.803105 #GCMRL# 52 dt 0.000000 rms 0.803 0.068% neg 0 invalid 762 tFOTS 22.4820 tGradient 6.2510 tsec 30.4990 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.877757 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877204) vs oldopt=(dt=0.08,rms=0.877207) #GCMRL# 54 dt 0.064000 rms 0.877 0.063% neg 0 invalid 762 tFOTS 23.1900 tGradient 5.4710 tsec 30.4500 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877178) vs oldopt=(dt=0.08,rms=0.877183) #GCMRL# 55 dt 0.064000 rms 0.877 0.000% neg 0 invalid 762 tFOTS 23.0440 tGradient 5.5800 tsec 30.4180 #GCMRL# 56 dt 0.064000 rms 0.877 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3780 tsec 7.1170 #GCMRL# 57 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3590 tsec 6.9570 #GCMRL# 58 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5500 tsec 7.3870 #GCMRL# 59 dt 0.064000 rms 0.877 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1380 tsec 6.8190 #GCMRL# 60 dt 0.064000 rms 0.876 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1530 tsec 6.8010 #GCMRL# 61 dt 0.064000 rms 0.875 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2250 tsec 7.0470 #GCMRL# 62 dt 0.064000 rms 0.874 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3780 tsec 7.0180 #GCMRL# 63 dt 0.064000 rms 0.872 0.191% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5620 tsec 7.2450 #GCMRL# 64 dt 0.064000 rms 0.871 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2090 tsec 6.8240 #GCMRL# 65 dt 0.064000 rms 0.869 0.179% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5910 tsec 7.2120 #GCMRL# 66 dt 0.064000 rms 0.868 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2400 tsec 6.9700 #GCMRL# 67 dt 0.064000 rms 0.867 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1900 tsec 6.9370 #GCMRL# 68 dt 0.064000 rms 0.866 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3810 tsec 6.9960 #GCMRL# 69 dt 0.064000 rms 0.865 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3640 tsec 7.2280 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.862601) vs oldopt=(dt=1.28,rms=0.862653) #GCMRL# 70 dt 1.536000 rms 0.863 0.268% neg 0 invalid 762 tFOTS 22.7620 tGradient 5.3140 tsec 29.6840 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.861829) vs oldopt=(dt=0.32,rms=0.862083) #GCMRL# 71 dt 0.192000 rms 0.862 0.000% neg 0 invalid 762 tFOTS 22.7700 tGradient 5.5690 tsec 30.0630 #GCMRL# 72 dt 0.192000 rms 0.861 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4490 tsec 7.0630 #GCMRL# 73 dt 0.192000 rms 0.860 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5770 tsec 7.1700 #GCMRL# 74 dt 0.192000 rms 0.860 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6480 tsec 7.2690 #GCMRL# 75 dt 0.192000 rms 0.859 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3670 tsec 7.0460 #GCAMreg# pass 0 level1 1 level2 1 tsec 282.894 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.859744 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.858997) vs oldopt=(dt=0.32,rms=0.859029) #GCMRL# 77 dt 0.192000 rms 0.859 0.087% neg 0 invalid 762 tFOTS 23.1290 tGradient 5.6030 tsec 30.5290 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.858993) vs oldopt=(dt=0.02,rms=0.858993) #GCMRL# 78 dt 0.028000 rms 0.859 0.000% neg 0 invalid 762 tFOTS 23.5010 tGradient 5.5930 tsec 30.9120 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.798691 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.792197) vs oldopt=(dt=0.32,rms=0.792517) #GCMRL# 80 dt 0.256000 rms 0.792 0.813% neg 0 invalid 762 tFOTS 23.0950 tGradient 4.5270 tsec 29.3310 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.791804) vs oldopt=(dt=0.02,rms=0.791836) #GCMRL# 81 dt 0.028000 rms 0.792 0.000% neg 0 invalid 762 tFOTS 23.7810 tGradient 4.6170 tsec 30.2490 #GCAMreg# pass 0 level1 0 level2 1 tsec 73.968 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.792455 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.791733) vs oldopt=(dt=0.02,rms=0.79174) #GCMRL# 83 dt 0.016000 rms 0.792 0.091% neg 0 invalid 762 tFOTS 23.4360 tGradient 4.5350 tsec 29.7500 GCAMregister done in 28.9325 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.02912 ( 6) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, overlap=0.766) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, peak = 18), gca=18.5 gca peak = 0.17690 (16) mri peak = 0.06897 (30) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, overlap=0.426) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, peak = 23), gca=23.4 gca peak = 0.28275 (96) mri peak = 0.06787 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, overlap=0.966) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, peak = 93), gca=92.6 gca peak = 0.18948 (93) mri peak = 0.06458 (96) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, overlap=1.008) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, peak = 92), gca=91.6 gca peak = 0.20755 (55) mri peak = 0.11697 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, peak = 55), gca=55.0 gca peak = 0.31831 (58) mri peak = 0.08625 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, peak = 55), gca=54.8 gca peak = 0.11957 (102) mri peak = 0.06876 (109) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, peak = 110), gca=109.7 gca peak = 0.11429 (102) mri peak = 0.06805 (111) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, overlap=0.521) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, peak = 111), gca=110.7 gca peak = 0.14521 (59) mri peak = 0.03738 (55) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, overlap=0.966) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, peak = 54), gca=54.0 gca peak = 0.14336 (58) mri peak = 0.04502 (53) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, overlap=0.848) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, peak = 52), gca=51.9 gca peak = 0.13305 (70) mri peak = 0.08346 (76) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, overlap=0.651) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, peak = 77), gca=77.3 gca peak = 0.15761 (71) mri peak = 0.06809 (83) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, overlap=0.571) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, peak = 77), gca=77.0 gca peak = 0.13537 (57) mri peak = 0.03402 (55) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, overlap=0.918) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, peak = 55), gca=55.0 gca peak = 0.13487 (56) mri peak = 0.03585 (51) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, peak = 54), gca=54.0 gca peak = 0.19040 (84) mri peak = 0.06228 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, overlap=0.746) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, peak = 87), gca=86.9 gca peak = 0.18871 (83) mri peak = 0.08367 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, peak = 86), gca=85.9 gca peak = 0.24248 (57) mri peak = 0.13222 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, overlap=0.798) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, peak = 51), gca=51.0 gca peak = 0.35833 (56) mri peak = 0.11187 (55) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, overlap=0.978) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, peak = 54), gca=54.0 gca peak = 0.12897 (85) mri peak = 0.05445 (88) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, overlap=0.975) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, peak = 83), gca=82.9 gca peak = 0.13127 (83) mri peak = 0.05455 (82) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, overlap=0.920) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, peak = 86), gca=85.9 gca peak = 0.12974 (78) mri peak = 0.06301 (81) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, overlap=0.985) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, peak = 82), gca=81.5 gca peak = 0.17796 (79) mri peak = 0.07260 (81) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, overlap=0.934) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, peak = 82), gca=81.8 gca peak = 0.10999 (80) mri peak = 0.09164 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.05790 (86) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, overlap=0.730) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.05402 (89) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, overlap=0.853) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, peak = 97), gca=96.6 gca peak = 0.20775 (25) mri peak = 0.03183 (12) gca peak = 0.13297 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.08 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 6.2134 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.848745 #FOTS# QuadFit found better minimum quadopt=(dt=182.491,rms=0.80955) vs oldopt=(dt=92.48,rms=0.818919) #GCMRL# 85 dt 182.490818 rms 0.810 4.618% neg 0 invalid 762 tFOTS 23.6900 tGradient 10.1540 tsec 35.6940 #FOTS# QuadFit found better minimum quadopt=(dt=175.23,rms=0.798144) vs oldopt=(dt=92.48,rms=0.801288) #GCMRL# 86 dt 175.229947 rms 0.798 1.409% neg 0 invalid 762 tFOTS 24.8830 tGradient 10.1490 tsec 36.7860 #FOTS# QuadFit found better minimum quadopt=(dt=176.792,rms=0.790975) vs oldopt=(dt=92.48,rms=0.79302) #GCMRL# 87 dt 176.792079 rms 0.791 0.898% neg 0 invalid 762 tFOTS 24.7150 tGradient 10.5940 tsec 37.0450 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.787162) vs oldopt=(dt=92.48,rms=0.787957) #GCMRL# 88 dt 129.472000 rms 0.787 0.482% neg 0 invalid 762 tFOTS 23.6800 tGradient 10.2590 tsec 35.7290 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.779255) vs oldopt=(dt=369.92,rms=0.780123) #GCMRL# 89 dt 517.888000 rms 0.779 1.005% neg 0 invalid 762 tFOTS 25.6300 tGradient 10.6710 tsec 38.1250 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.775457) vs oldopt=(dt=92.48,rms=0.775669) #GCMRL# 90 dt 129.472000 rms 0.775 0.487% neg 0 invalid 762 tFOTS 24.8500 tGradient 10.2670 tsec 36.8620 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.772686) vs oldopt=(dt=369.92,rms=0.773004) #GCMRL# 91 dt 295.936000 rms 0.773 0.357% neg 0 invalid 762 tFOTS 24.6460 tGradient 10.1640 tsec 36.4070 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.770251) vs oldopt=(dt=92.48,rms=0.77046) #GCMRL# 92 dt 129.472000 rms 0.770 0.315% neg 0 invalid 762 tFOTS 26.4150 tGradient 10.0720 tsec 38.1550 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.768064) vs oldopt=(dt=369.92,rms=0.768174) #GCMRL# 93 dt 295.936000 rms 0.768 0.284% neg 0 invalid 762 tFOTS 25.4130 tGradient 10.0130 tsec 37.2310 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.766199) vs oldopt=(dt=92.48,rms=0.766423) #GCMRL# 94 dt 129.472000 rms 0.766 0.243% neg 0 invalid 762 tFOTS 24.4810 tGradient 10.4680 tsec 36.6910 #GCMRL# 95 dt 369.920000 rms 0.764 0.240% neg 0 invalid 762 tFOTS 24.8890 tGradient 10.1820 tsec 36.8230 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.762431) vs oldopt=(dt=92.48,rms=0.762576) #GCMRL# 96 dt 129.472000 rms 0.762 0.253% neg 0 invalid 762 tFOTS 25.9430 tGradient 10.0780 tsec 37.8980 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.761167) vs oldopt=(dt=369.92,rms=0.761516) #GCMRL# 97 dt 221.952000 rms 0.761 0.166% neg 0 invalid 762 tFOTS 25.4400 tGradient 10.3480 tsec 37.4530 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.760028) vs oldopt=(dt=92.48,rms=0.760234) #GCMRL# 98 dt 129.472000 rms 0.760 0.150% neg 0 invalid 762 tFOTS 24.4380 tGradient 10.4980 tsec 36.6230 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.758301) vs oldopt=(dt=369.92,rms=0.758399) #GCMRL# 99 dt 517.888000 rms 0.758 0.227% neg 0 invalid 762 tFOTS 23.7530 tGradient 9.8360 tsec 35.1500 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.75648) vs oldopt=(dt=92.48,rms=0.756592) #GCMRL# 100 dt 129.472000 rms 0.756 0.240% neg 0 invalid 762 tFOTS 25.5260 tGradient 9.3550 tsec 36.5460 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.755734) vs oldopt=(dt=92.48,rms=0.755844) #GCMRL# 101 dt 129.472000 rms 0.756 0.099% neg 0 invalid 762 tFOTS 24.6110 tGradient 10.2400 tsec 36.5700 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.753709) vs oldopt=(dt=369.92,rms=0.754086) #GCMRL# 102 dt 517.888000 rms 0.754 0.268% neg 0 invalid 762 tFOTS 24.4070 tGradient 9.7640 tsec 35.8270 #GCMRL# 103 dt 92.480000 rms 0.753 0.116% neg 0 invalid 762 tFOTS 23.6000 tGradient 9.3600 tsec 34.5520 #FOTS# QuadFit found better minimum quadopt=(dt=4734.98,rms=0.742561) vs oldopt=(dt=5918.72,rms=0.743082) #GCMRL# 104 dt 4734.976000 rms 0.743 1.365% neg 0 invalid 762 tFOTS 24.8210 tGradient 9.3650 tsec 35.8070 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.740244) vs oldopt=(dt=92.48,rms=0.740309) #GCMRL# 105 dt 73.984000 rms 0.740 0.312% neg 0 invalid 762 tFOTS 23.2060 tGradient 8.9000 tsec 33.8030 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.740078) vs oldopt=(dt=92.48,rms=0.740106) #GCMRL# 106 dt 129.472000 rms 0.740 0.000% neg 0 invalid 762 tFOTS 22.8740 tGradient 9.0520 tsec 33.5820 #GCMRL# 107 dt 129.472000 rms 0.740 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0510 tsec 10.6840 #GCMRL# 108 dt 129.472000 rms 0.739 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1010 tsec 10.6890 #GCMRL# 109 dt 129.472000 rms 0.739 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1680 tsec 10.7360 #GCMRL# 110 dt 129.472000 rms 0.738 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0490 tsec 10.6810 #GCMRL# 111 dt 129.472000 rms 0.737 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1830 tsec 10.7340 #GCMRL# 112 dt 129.472000 rms 0.736 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1850 tsec 10.7150 #GCMRL# 113 dt 129.472000 rms 0.735 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1080 tsec 10.6310 #GCMRL# 114 dt 129.472000 rms 0.734 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1950 tsec 10.7880 #GCMRL# 115 dt 129.472000 rms 0.733 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5970 tsec 11.1250 #GCMRL# 116 dt 129.472000 rms 0.732 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1610 tsec 10.6950 #GCMRL# 117 dt 129.472000 rms 0.731 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2120 tsec 10.7360 #GCMRL# 118 dt 129.472000 rms 0.731 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3400 tsec 10.9100 #GCMRL# 119 dt 129.472000 rms 0.730 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9550 tsec 10.5210 #GCMRL# 120 dt 129.472000 rms 0.729 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2560 tsec 10.7690 #GCMRL# 121 dt 129.472000 rms 0.728 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5580 tsec 11.1110 #GCMRL# 122 dt 129.472000 rms 0.727 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1640 tsec 10.6780 #GCMRL# 123 dt 129.472000 rms 0.726 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3910 tsec 10.8650 #GCMRL# 124 dt 129.472000 rms 0.726 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3730 tsec 10.9650 #GCMRL# 125 dt 129.472000 rms 0.725 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2980 tsec 10.8950 #GCMRL# 126 dt 129.472000 rms 0.724 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1210 tsec 10.6620 #GCMRL# 127 dt 129.472000 rms 0.724 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8600 tsec 10.3860 #GCMRL# 128 dt 129.472000 rms 0.723 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0940 tsec 10.6420 #GCMRL# 129 dt 129.472000 rms 0.723 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1160 tsec 10.6050 #GCMRL# 130 dt 129.472000 rms 0.722 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7630 tsec 10.2670 #GCMRL# 131 dt 129.472000 rms 0.721 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1690 tsec 10.6630 #GCMRL# 132 dt 129.472000 rms 0.721 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0200 tsec 10.5270 #GCMRL# 133 dt 129.472000 rms 0.720 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8840 tsec 10.4680 #GCMRL# 134 dt 129.472000 rms 0.720 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1130 tsec 10.5900 #GCMRL# 135 dt 129.472000 rms 0.719 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0340 tsec 10.5060 #GCMRL# 136 dt 129.472000 rms 0.719 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2480 tsec 10.8110 #GCMRL# 137 dt 129.472000 rms 0.718 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0820 tsec 10.5730 #GCMRL# 138 dt 129.472000 rms 0.718 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0880 tsec 10.5890 #GCMRL# 139 dt 129.472000 rms 0.718 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9100 tsec 10.4060 #GCMRL# 140 dt 129.472000 rms 0.717 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9480 tsec 10.5020 #GCMRL# 141 dt 129.472000 rms 0.717 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1330 tsec 10.7410 #GCMRL# 142 dt 129.472000 rms 0.716 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1940 tsec 10.7740 #GCMRL# 143 dt 129.472000 rms 0.716 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2010 tsec 10.7150 #GCMRL# 144 dt 129.472000 rms 0.715 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0020 tsec 10.5980 #GCMRL# 145 dt 129.472000 rms 0.715 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8400 tsec 10.4010 #GCMRL# 146 dt 129.472000 rms 0.715 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1720 tsec 10.6860 #GCMRL# 147 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0530 tsec 10.6010 #GCMRL# 148 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2480 tsec 10.9140 #GCMRL# 149 dt 129.472000 rms 0.714 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7630 tsec 11.3580 #GCMRL# 150 dt 129.472000 rms 0.713 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1740 tsec 10.6970 #GCMRL# 151 dt 129.472000 rms 0.713 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7780 tsec 11.3440 #GCMRL# 152 dt 129.472000 rms 0.713 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3130 tsec 10.8370 #GCMRL# 153 dt 129.472000 rms 0.712 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2870 tsec 10.8380 #GCMRL# 154 dt 129.472000 rms 0.712 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3140 tsec 10.7590 #GCMRL# 155 dt 129.472000 rms 0.712 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1650 tsec 10.7170 #GCMRL# 156 dt 129.472000 rms 0.712 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3950 tsec 10.9760 #GCMRL# 157 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1940 tsec 10.7350 #GCMRL# 158 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0580 tsec 10.6390 #GCMRL# 159 dt 129.472000 rms 0.711 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9510 tsec 10.5030 #GCMRL# 160 dt 129.472000 rms 0.710 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1660 tsec 10.7940 #GCMRL# 161 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0850 tsec 10.6220 #GCMRL# 162 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0330 tsec 10.5890 #GCMRL# 163 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0450 tsec 10.6400 #GCMRL# 164 dt 129.472000 rms 0.710 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0950 tsec 10.6900 #GCMRL# 165 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1950 tsec 10.6990 #GCMRL# 166 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1300 tsec 10.6970 #GCMRL# 167 dt 129.472000 rms 0.709 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1030 tsec 10.6650 #GCMRL# 168 dt 129.472000 rms 0.709 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0650 tsec 10.6460 #GCMRL# 169 dt 129.472000 rms 0.709 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9330 tsec 10.4350 #GCMRL# 170 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1270 tsec 10.7220 #GCMRL# 171 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4140 tsec 11.0290 #GCMRL# 172 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5730 tsec 11.1940 #GCMRL# 173 dt 129.472000 rms 0.708 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1500 tsec 10.6600 #GCMRL# 174 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0880 tsec 10.6270 #GCMRL# 175 dt 129.472000 rms 0.707 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1330 tsec 10.6910 #GCMRL# 176 dt 129.472000 rms 0.707 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.6930 tsec 11.3780 #GCMRL# 177 dt 129.472000 rms 0.707 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3850 tsec 10.9120 #GCMRL# 178 dt 129.472000 rms 0.707 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2690 tsec 10.8230 #GCMRL# 179 dt 5918.720000 rms 0.706 0.071% neg 0 invalid 762 tFOTS 22.9260 tGradient 9.2320 tsec 33.7060 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.70616) vs oldopt=(dt=92.48,rms=0.706165) #GCMRL# 180 dt 73.984000 rms 0.706 0.000% neg 0 invalid 762 tFOTS 22.2140 tGradient 9.1650 tsec 33.0090 #GCMRL# 181 dt 73.984000 rms 0.706 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2030 tsec 10.7460 #GCMRL# 182 dt 73.984000 rms 0.706 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0430 tsec 10.6330 #GCAMreg# pass 0 level1 5 level2 1 tsec 1678.16 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.706908 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.705379) vs oldopt=(dt=92.48,rms=0.705528) #GCMRL# 184 dt 129.472000 rms 0.705 0.216% neg 0 invalid 762 tFOTS 21.8030 tGradient 9.2750 tsec 32.5820 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.704347) vs oldopt=(dt=369.92,rms=0.704522) #GCMRL# 185 dt 517.888000 rms 0.704 0.146% neg 0 invalid 762 tFOTS 21.7890 tGradient 9.1370 tsec 32.4030 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.704176) vs oldopt=(dt=92.48,rms=0.704194) #GCMRL# 186 dt 129.472000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 22.2960 tGradient 9.2320 tsec 33.1630 #GCMRL# 187 dt 129.472000 rms 0.704 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3210 tsec 10.8640 #GCMRL# 188 dt 129.472000 rms 0.704 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3170 tsec 10.8490 #GCMRL# 189 dt 129.472000 rms 0.704 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3430 tsec 10.9180 #GCMRL# 190 dt 129.472000 rms 0.704 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3750 tsec 10.9650 #GCMRL# 191 dt 129.472000 rms 0.703 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5320 tsec 11.0790 #GCMRL# 192 dt 129.472000 rms 0.703 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4990 tsec 11.0430 #GCMRL# 193 dt 129.472000 rms 0.703 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.9300 tsec 11.5080 #GCMRL# 194 dt 129.472000 rms 0.703 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2410 tsec 10.7190 #GCMRL# 195 dt 129.472000 rms 0.703 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5960 tsec 11.0990 #GCMRL# 196 dt 129.472000 rms 0.702 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.6950 tsec 11.1840 #GCMRL# 197 dt 129.472000 rms 0.702 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5390 tsec 11.0880 #GCMRL# 198 dt 129.472000 rms 0.702 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3240 tsec 11.0260 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.70213) vs oldopt=(dt=369.92,rms=0.702135) #GCMRL# 199 dt 295.936000 rms 0.702 0.000% neg 0 invalid 762 tFOTS 23.4090 tGradient 9.4600 tsec 34.4660 #GCMRL# 200 dt 295.936000 rms 0.702 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4050 tsec 10.9460 #GCMRL# 201 dt 295.936000 rms 0.702 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9600 tsec 10.4360 #GCMRL# 202 dt 295.936000 rms 0.702 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4280 tsec 10.9130 #GCMRL# 203 dt 295.936000 rms 0.702 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1490 tsec 10.6680 #GCMRL# 204 dt 295.936000 rms 0.702 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3250 tsec 10.9510 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701437) vs oldopt=(dt=92.48,rms=0.701445) #GCMRL# 205 dt 129.472000 rms 0.701 0.019% neg 0 invalid 762 tFOTS 21.8630 tGradient 9.3830 tsec 32.8300 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701443) vs oldopt=(dt=92.48,rms=0.701444) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.704686 #FOTS# QuadFit found better minimum quadopt=(dt=169.475,rms=0.699018) vs oldopt=(dt=103.68,rms=0.699625) #GCMRL# 207 dt 169.474860 rms 0.699 0.804% neg 0 invalid 762 tFOTS 21.7850 tGradient 7.0450 tsec 30.3880 #FOTS# QuadFit found better minimum quadopt=(dt=192,rms=0.689646) vs oldopt=(dt=103.68,rms=0.691455) #GCMRL# 208 dt 192.000000 rms 0.690 1.341% neg 0 invalid 762 tFOTS 22.0470 tGradient 7.2650 tsec 30.8440 #FOTS# QuadFit found better minimum quadopt=(dt=67.7333,rms=0.686057) vs oldopt=(dt=25.92,rms=0.686985) #GCMRL# 209 dt 67.733333 rms 0.686 0.520% neg 0 invalid 762 tFOTS 21.6590 tGradient 6.8940 tsec 30.0540 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.678544) vs oldopt=(dt=414.72,rms=0.678631) #GCMRL# 210 dt 331.776000 rms 0.679 1.095% neg 0 invalid 762 tFOTS 20.5000 tGradient 7.0980 tsec 29.1940 #FOTS# QuadFit found better minimum quadopt=(dt=61.9221,rms=0.674719) vs oldopt=(dt=25.92,rms=0.675676) #GCMRL# 211 dt 61.922078 rms 0.675 0.564% neg 0 invalid 762 tFOTS 21.6160 tGradient 7.0250 tsec 30.2450 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.671901) vs oldopt=(dt=103.68,rms=0.672143) #GCMRL# 212 dt 145.152000 rms 0.672 0.418% neg 0 invalid 762 tFOTS 21.0750 tGradient 7.2040 tsec 29.8260 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.670285) vs oldopt=(dt=25.92,rms=0.670597) #GCMRL# 213 dt 36.288000 rms 0.670 0.241% neg 0 invalid 762 tFOTS 22.4070 tGradient 6.9630 tsec 30.9370 #GCMRL# 214 dt 414.720000 rms 0.666 0.585% neg 0 invalid 762 tFOTS 20.9550 tGradient 7.1300 tsec 29.5860 #FOTS# QuadFit found better minimum quadopt=(dt=58.022,rms=0.662064) vs oldopt=(dt=25.92,rms=0.663079) #GCMRL# 215 dt 58.021978 rms 0.662 0.646% neg 0 invalid 762 tFOTS 21.8170 tGradient 7.0130 tsec 30.3310 #FOTS# QuadFit found better minimum quadopt=(dt=68.6829,rms=0.661125) vs oldopt=(dt=103.68,rms=0.661322) #GCMRL# 216 dt 68.682927 rms 0.661 0.142% neg 0 invalid 762 tFOTS 21.9300 tGradient 7.1100 tsec 30.5320 #GCMRL# 217 dt 103.680000 rms 0.660 0.206% neg 0 invalid 762 tFOTS 22.1150 tGradient 7.1620 tsec 30.7850 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.659053) vs oldopt=(dt=25.92,rms=0.659202) #GCMRL# 218 dt 36.288000 rms 0.659 0.108% neg 0 invalid 762 tFOTS 20.7120 tGradient 7.0100 tsec 29.2370 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.654714) vs oldopt=(dt=414.72,rms=0.65545) #GCMRL# 219 dt 580.608000 rms 0.655 0.658% neg 0 invalid 762 tFOTS 21.5480 tGradient 7.1180 tsec 30.2250 #FOTS# QuadFit found better minimum quadopt=(dt=67.6364,rms=0.652369) vs oldopt=(dt=25.92,rms=0.652822) #GCMRL# 220 dt 67.636364 rms 0.652 0.358% neg 0 invalid 762 tFOTS 21.5170 tGradient 7.1720 tsec 30.1590 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.651527) vs oldopt=(dt=25.92,rms=0.651666) #GCMRL# 221 dt 36.288000 rms 0.652 0.129% neg 0 invalid 762 tFOTS 20.3110 tGradient 6.9450 tsec 28.7370 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.648123) vs oldopt=(dt=414.72,rms=0.648688) #GCMRL# 222 dt 580.608000 rms 0.648 0.522% neg 0 invalid 762 tFOTS 21.6520 tGradient 7.3350 tsec 30.5490 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.646406) vs oldopt=(dt=25.92,rms=0.646678) #GCMRL# 223 dt 36.288000 rms 0.646 0.265% neg 0 invalid 762 tFOTS 21.8220 tGradient 6.9330 tsec 30.2970 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.645724) vs oldopt=(dt=103.68,rms=0.645835) #GCMRL# 224 dt 145.152000 rms 0.646 0.105% neg 0 invalid 762 tFOTS 21.4390 tGradient 6.9180 tsec 29.8630 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.64461) vs oldopt=(dt=103.68,rms=0.644727) #GCMRL# 225 dt 145.152000 rms 0.645 0.173% neg 0 invalid 762 tFOTS 22.4190 tGradient 7.0500 tsec 31.0200 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.644212) vs oldopt=(dt=25.92,rms=0.6443) #GCMRL# 226 dt 36.288000 rms 0.644 0.062% neg 0 invalid 762 tFOTS 21.5640 tGradient 6.9830 tsec 30.0700 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.643363) vs oldopt=(dt=414.72,rms=0.643531) #GCMRL# 227 dt 248.832000 rms 0.643 0.132% neg 0 invalid 762 tFOTS 21.8370 tGradient 6.9230 tsec 30.3720 #FOTS# QuadFit found better minimum quadopt=(dt=85.3333,rms=0.642294) vs oldopt=(dt=103.68,rms=0.642346) #GCMRL# 228 dt 85.333333 rms 0.642 0.166% neg 0 invalid 762 tFOTS 21.7920 tGradient 7.0720 tsec 30.4020 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.641898) vs oldopt=(dt=103.68,rms=0.641953) #GCMRL# 229 dt 82.944000 rms 0.642 0.062% neg 0 invalid 762 tFOTS 21.5350 tGradient 7.2360 tsec 30.3220 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.641285) vs oldopt=(dt=103.68,rms=0.641286) #GCMRL# 230 dt 124.416000 rms 0.641 0.095% neg 0 invalid 762 tFOTS 21.7260 tGradient 6.9810 tsec 30.2620 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.64088) vs oldopt=(dt=25.92,rms=0.640968) #GCMRL# 231 dt 36.288000 rms 0.641 0.063% neg 0 invalid 762 tFOTS 23.2880 tGradient 7.1790 tsec 31.9800 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.639431) vs oldopt=(dt=414.72,rms=0.639473) #GCMRL# 232 dt 497.664000 rms 0.639 0.226% neg 0 invalid 762 tFOTS 21.3920 tGradient 6.9420 tsec 29.8310 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.638071) vs oldopt=(dt=25.92,rms=0.638305) #GCMRL# 233 dt 36.288000 rms 0.638 0.213% neg 0 invalid 762 tFOTS 22.1990 tGradient 6.9510 tsec 30.5660 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.637494) vs oldopt=(dt=103.68,rms=0.637549) #GCMRL# 234 dt 145.152000 rms 0.637 0.090% neg 0 invalid 762 tFOTS 21.6860 tGradient 6.9090 tsec 30.1250 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.637132) vs oldopt=(dt=25.92,rms=0.637209) #GCMRL# 235 dt 36.288000 rms 0.637 0.057% neg 0 invalid 762 tFOTS 22.8590 tGradient 6.9580 tsec 31.3530 #GCMRL# 236 dt 414.720000 rms 0.636 0.165% neg 0 invalid 762 tFOTS 21.5520 tGradient 7.2020 tsec 30.2960 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.635115) vs oldopt=(dt=25.92,rms=0.635299) #GCMRL# 237 dt 36.288000 rms 0.635 0.152% neg 0 invalid 762 tFOTS 20.4590 tGradient 7.2880 tsec 29.2680 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.634581) vs oldopt=(dt=103.68,rms=0.63463) #GCMRL# 238 dt 145.152000 rms 0.635 0.084% neg 0 invalid 762 tFOTS 21.6810 tGradient 6.9450 tsec 30.1720 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.63422) vs oldopt=(dt=103.68,rms=0.634322) #GCMRL# 239 dt 62.208000 rms 0.634 0.057% neg 0 invalid 762 tFOTS 21.7780 tGradient 7.1680 tsec 30.4290 #GCMRL# 240 dt 414.720000 rms 0.633 0.151% neg 0 invalid 762 tFOTS 21.4840 tGradient 7.2670 tsec 30.2080 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.63243) vs oldopt=(dt=25.92,rms=0.63257) #GCMRL# 241 dt 36.288000 rms 0.632 0.131% neg 0 invalid 762 tFOTS 21.8040 tGradient 7.2700 tsec 30.5760 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.632065) vs oldopt=(dt=103.68,rms=0.632075) #GCMRL# 242 dt 124.416000 rms 0.632 0.058% neg 0 invalid 762 tFOTS 21.5510 tGradient 7.0910 tsec 30.1240 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631657) vs oldopt=(dt=103.68,rms=0.631671) #GCMRL# 243 dt 82.944000 rms 0.632 0.065% neg 0 invalid 762 tFOTS 21.8970 tGradient 7.0420 tsec 30.4020 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631393) vs oldopt=(dt=103.68,rms=0.631399) #GCMRL# 244 dt 82.944000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 21.6850 tGradient 6.9690 tsec 30.1490 #GCMRL# 245 dt 82.944000 rms 0.631 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9890 tsec 8.4490 #GCMRL# 246 dt 82.944000 rms 0.631 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2210 tsec 8.7740 #GCMRL# 247 dt 82.944000 rms 0.630 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1390 tsec 8.7360 #GCMRL# 248 dt 82.944000 rms 0.629 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2290 tsec 8.7180 #GCMRL# 249 dt 82.944000 rms 0.628 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1240 tsec 8.6470 #GCMRL# 250 dt 82.944000 rms 0.627 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0370 tsec 8.5960 #GCMRL# 251 dt 82.944000 rms 0.625 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9940 tsec 8.5040 #GCMRL# 252 dt 82.944000 rms 0.624 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9430 tsec 8.4260 #GCMRL# 253 dt 82.944000 rms 0.623 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0280 tsec 8.5560 #GCMRL# 254 dt 82.944000 rms 0.622 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0700 tsec 8.5770 #GCMRL# 255 dt 82.944000 rms 0.621 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1000 tsec 8.6360 #GCMRL# 256 dt 82.944000 rms 0.620 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2920 tsec 8.9070 #GCMRL# 257 dt 82.944000 rms 0.619 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0540 tsec 8.5470 #GCMRL# 258 dt 82.944000 rms 0.618 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9700 tsec 8.4920 #GCMRL# 259 dt 82.944000 rms 0.617 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1880 tsec 8.7680 #GCMRL# 260 dt 82.944000 rms 0.616 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3440 tsec 8.8900 #GCMRL# 261 dt 82.944000 rms 0.615 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0490 tsec 8.5080 #GCMRL# 262 dt 82.944000 rms 0.614 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9130 tsec 8.4000 #GCMRL# 263 dt 82.944000 rms 0.614 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.8440 tsec 8.3250 #GCMRL# 264 dt 82.944000 rms 0.613 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0660 tsec 8.5470 #GCMRL# 265 dt 82.944000 rms 0.612 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0640 tsec 8.5710 #GCMRL# 266 dt 82.944000 rms 0.612 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0240 tsec 8.5090 #GCMRL# 267 dt 82.944000 rms 0.612 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1130 tsec 9.2390 #GCMRL# 268 dt 20.736000 rms 0.612 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0740 tsec 10.2550 #GCMRL# 269 dt 5.184000 rms 0.612 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9950 tsec 10.2620 #FOTS# QuadFit found better minimum quadopt=(dt=0.567,rms=0.611569) vs oldopt=(dt=0.405,rms=0.611569) #GCMRL# 270 dt 0.567000 rms 0.612 0.000% neg 0 invalid 762 tFOTS 15.1550 tGradient 7.1320 tsec 23.7870 #GCMRL# 271 dt 0.141750 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9670 tsec 10.0460 #GCMRL# 272 dt 0.070875 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0320 tsec 9.6400 #GCAMreg# pass 0 level1 4 level2 1 tsec 1428.43 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.612649 #FOTS# QuadFit found better minimum quadopt=(dt=0.0354375,rms=0.611567) vs oldopt=(dt=0.0253125,rms=0.611568) #GCMRL# 274 dt 0.035437 rms 0.612 0.176% neg 0 invalid 762 tFOTS 12.5110 tGradient 7.1420 tsec 21.1330 #FOTS# QuadFit found better minimum quadopt=(dt=0.00885937,rms=0.611567) vs oldopt=(dt=0.00632812,rms=0.611567) #GCMRL# 275 dt 0.008859 rms 0.612 0.000% neg 0 invalid 762 tFOTS 11.5000 tGradient 7.0460 tsec 20.0730 #GCMRL# 276 dt 0.002215 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9670 tsec 10.0800 #GCMRL# 277 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0510 tsec 9.6720 #GCMRL# 278 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1050 tsec 8.6080 #GCMRL# 279 dt 0.000138 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3220 tsec 11.1410 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.625485 #FOTS# QuadFit found better minimum quadopt=(dt=87.0701,rms=0.614414) vs oldopt=(dt=128,rms=0.616497) #GCMRL# 281 dt 87.070059 rms 0.614 1.770% neg 0 invalid 762 tFOTS 21.5280 tGradient 5.7740 tsec 28.8620 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.610965) vs oldopt=(dt=8,rms=0.61191) #GCMRL# 282 dt 11.200000 rms 0.611 0.561% neg 0 invalid 762 tFOTS 18.9580 tGradient 5.7510 tsec 26.2660 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.608422) vs oldopt=(dt=8,rms=0.609126) #GCMRL# 283 dt 11.200000 rms 0.608 0.416% neg 0 invalid 762 tFOTS 20.4350 tGradient 6.0280 tsec 27.9720 #GCMRL# 284 dt 32.000000 rms 0.603 0.902% neg 0 invalid 762 tFOTS 20.4970 tGradient 5.7380 tsec 27.7540 #FOTS# QuadFit found better minimum quadopt=(dt=153.6,rms=0.588486) vs oldopt=(dt=128,rms=0.590481) #GCMRL# 285 dt 153.600000 rms 0.588 2.396% neg 0 invalid 762 tFOTS 21.5140 tGradient 5.8250 tsec 28.8160 #GCMRL# 286 dt 32.000000 rms 0.586 0.367% neg 0 invalid 762 tFOTS 20.3960 tGradient 5.9640 tsec 27.8920 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.584802) vs oldopt=(dt=32,rms=0.58511) #GCMRL# 287 dt 44.800000 rms 0.585 0.260% neg 0 invalid 762 tFOTS 20.1610 tGradient 5.9440 tsec 27.6450 #GCMRL# 288 dt 32.000000 rms 0.583 0.332% neg 0 invalid 762 tFOTS 20.2830 tGradient 5.9900 tsec 27.8210 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.581944) vs oldopt=(dt=32,rms=0.581955) #GCMRL# 289 dt 38.400000 rms 0.582 0.157% neg 0 invalid 762 tFOTS 20.3610 tGradient 6.1260 tsec 27.9920 #GCMRL# 290 dt 32.000000 rms 0.580 0.313% neg 0 invalid 762 tFOTS 20.1970 tGradient 5.9310 tsec 27.6690 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.579347) vs oldopt=(dt=32,rms=0.579356) #GCMRL# 291 dt 25.600000 rms 0.579 0.133% neg 0 invalid 762 tFOTS 20.9500 tGradient 5.7820 tsec 28.2590 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.577879) vs oldopt=(dt=32,rms=0.578021) #GCMRL# 292 dt 38.400000 rms 0.578 0.253% neg 0 invalid 762 tFOTS 20.4930 tGradient 6.0660 tsec 28.0720 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.577186) vs oldopt=(dt=32,rms=0.5772) #GCMRL# 293 dt 25.600000 rms 0.577 0.120% neg 0 invalid 762 tFOTS 20.2820 tGradient 6.0000 tsec 27.7810 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.575765) vs oldopt=(dt=32,rms=0.575998) #GCMRL# 294 dt 44.800000 rms 0.576 0.246% neg 0 invalid 762 tFOTS 20.3370 tGradient 6.0230 tsec 27.8900 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.575121) vs oldopt=(dt=32,rms=0.575172) #GCMRL# 295 dt 25.600000 rms 0.575 0.112% neg 0 invalid 762 tFOTS 20.2610 tGradient 5.8730 tsec 27.7040 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.573811) vs oldopt=(dt=32,rms=0.574018) #GCMRL# 296 dt 44.800000 rms 0.574 0.228% neg 0 invalid 762 tFOTS 20.4680 tGradient 5.8770 tsec 27.8370 #FOTS# QuadFit found better minimum quadopt=(dt=24.9449,rms=0.573318) vs oldopt=(dt=32,rms=0.573419) #GCMRL# 297 dt 24.944882 rms 0.573 0.086% neg 0 invalid 762 tFOTS 20.7270 tGradient 5.8400 tsec 28.0750 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.572173) vs oldopt=(dt=32,rms=0.572327) #GCMRL# 298 dt 44.800000 rms 0.572 0.200% neg 0 invalid 762 tFOTS 20.6910 tGradient 5.9930 tsec 28.1500 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.571704) vs oldopt=(dt=32,rms=0.571867) #GCMRL# 299 dt 19.200000 rms 0.572 0.082% neg 0 invalid 762 tFOTS 20.6890 tGradient 5.7890 tsec 27.9600 #GCMRL# 300 dt 128.000000 rms 0.569 0.411% neg 0 invalid 762 tFOTS 20.5760 tGradient 5.6880 tsec 27.7510 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.56885) vs oldopt=(dt=8,rms=0.56897) #GCMRL# 301 dt 11.200000 rms 0.569 0.089% neg 0 invalid 762 tFOTS 20.4070 tGradient 5.9080 tsec 27.8390 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.568437) vs oldopt=(dt=32,rms=0.568504) #GCMRL# 302 dt 19.200000 rms 0.568 0.073% neg 0 invalid 762 tFOTS 20.2500 tGradient 5.7570 tsec 27.4630 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.566753) vs oldopt=(dt=128,rms=0.566905) #GCMRL# 303 dt 179.200000 rms 0.567 0.296% neg 0 invalid 762 tFOTS 20.2690 tGradient 5.6710 tsec 27.4080 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.565599) vs oldopt=(dt=32,rms=0.565671) #GCMRL# 304 dt 25.600000 rms 0.566 0.204% neg 0 invalid 762 tFOTS 21.7460 tGradient 6.6560 tsec 29.9130 #GCMRL# 305 dt 32.000000 rms 0.565 0.151% neg 0 invalid 762 tFOTS 20.3770 tGradient 6.0500 tsec 27.9100 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.564467) vs oldopt=(dt=32,rms=0.564525) #GCMRL# 306 dt 19.200000 rms 0.564 0.000% neg 0 invalid 762 tFOTS 21.5480 tGradient 5.7330 tsec 28.8650 #GCMRL# 307 dt 19.200000 rms 0.564 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8840 tsec 7.4400 #GCMRL# 308 dt 19.200000 rms 0.564 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6980 tsec 7.1500 #GCMRL# 309 dt 19.200000 rms 0.563 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8460 tsec 7.3950 #GCMRL# 310 dt 19.200000 rms 0.562 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7270 tsec 7.2400 #GCMRL# 311 dt 19.200000 rms 0.562 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6540 tsec 7.1580 #GCMRL# 312 dt 19.200000 rms 0.561 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7760 tsec 7.3310 #GCMRL# 313 dt 19.200000 rms 0.560 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8400 tsec 7.4640 #GCMRL# 314 dt 19.200000 rms 0.559 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7090 tsec 7.2350 #GCMRL# 315 dt 19.200000 rms 0.558 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8620 tsec 7.3920 #GCMRL# 316 dt 19.200000 rms 0.558 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7670 tsec 8.0310 #GCMRL# 317 dt 19.200000 rms 0.557 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6880 tsec 7.1680 #GCMRL# 318 dt 19.200000 rms 0.557 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8030 tsec 7.2870 #GCMRL# 319 dt 19.200000 rms 0.557 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7120 tsec 7.2100 #GCMRL# 320 dt 9.600000 rms 0.557 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7860 tsec 8.3760 #GCMRL# 321 dt 1.200000 rms 0.557 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7670 tsec 9.5630 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.556586) vs oldopt=(dt=0.5,rms=0.556587) #GCMRL# 322 dt 0.700000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 16.8100 tGradient 5.7530 tsec 24.1030 #GCMRL# 323 dt 0.350000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8280 tsec 8.5690 #GCMRL# 324 dt 0.087500 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7580 tsec 8.9600 #GCAMreg# pass 0 level1 3 level2 1 tsec 897.403 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.557587 #FOTS# QuadFit found better minimum quadopt=(dt=56.5828,rms=0.55345) vs oldopt=(dt=32,rms=0.553854) #GCMRL# 326 dt 56.582781 rms 0.553 0.742% neg 0 invalid 762 tFOTS 20.6790 tGradient 5.6670 tsec 27.8140 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.552809) vs oldopt=(dt=8,rms=0.552932) #GCMRL# 327 dt 11.200000 rms 0.553 0.116% neg 0 invalid 762 tFOTS 20.4710 tGradient 5.7990 tsec 27.7920 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.552079) vs oldopt=(dt=32,rms=0.552132) #GCMRL# 328 dt 44.800000 rms 0.552 0.132% neg 0 invalid 762 tFOTS 20.2570 tGradient 5.8620 tsec 27.6580 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.551251) vs oldopt=(dt=32,rms=0.551272) #GCMRL# 329 dt 38.400000 rms 0.551 0.150% neg 0 invalid 762 tFOTS 20.2590 tGradient 5.9470 tsec 27.7520 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.551016) vs oldopt=(dt=8,rms=0.551061) #GCMRL# 330 dt 11.200000 rms 0.551 0.000% neg 0 invalid 762 tFOTS 20.2550 tGradient 5.7830 tsec 27.6240 #GCMRL# 331 dt 11.200000 rms 0.551 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8470 tsec 7.3280 #GCMRL# 332 dt 11.200000 rms 0.551 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7890 tsec 7.3220 #GCMRL# 333 dt 11.200000 rms 0.550 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7540 tsec 7.2410 #GCMRL# 334 dt 11.200000 rms 0.550 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7590 tsec 7.2830 #GCMRL# 335 dt 11.200000 rms 0.549 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8700 tsec 7.3480 #GCMRL# 336 dt 11.200000 rms 0.549 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8520 tsec 7.3590 #GCMRL# 337 dt 11.200000 rms 0.549 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6960 tsec 7.2280 #GCMRL# 338 dt 11.200000 rms 0.548 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8120 tsec 7.3990 #GCMRL# 339 dt 11.200000 rms 0.548 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6800 tsec 7.1810 #GCMRL# 340 dt 11.200000 rms 0.547 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8160 tsec 7.2700 #GCMRL# 341 dt 11.200000 rms 0.547 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7920 tsec 7.2620 #GCMRL# 342 dt 11.200000 rms 0.546 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7810 tsec 7.3140 #GCMRL# 343 dt 11.200000 rms 0.546 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6020 tsec 7.1480 #GCMRL# 344 dt 11.200000 rms 0.545 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6670 tsec 7.2000 #GCMRL# 345 dt 11.200000 rms 0.545 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5840 tsec 7.1360 #GCMRL# 346 dt 11.200000 rms 0.545 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7850 tsec 7.3290 #GCMRL# 347 dt 11.200000 rms 0.544 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8810 tsec 7.3420 #GCMRL# 348 dt 11.200000 rms 0.544 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7970 tsec 7.5190 #GCMRL# 349 dt 11.200000 rms 0.543 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7570 tsec 7.3170 #GCMRL# 350 dt 11.200000 rms 0.543 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5850 tsec 7.1040 #GCMRL# 351 dt 11.200000 rms 0.542 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8540 tsec 7.4170 #GCMRL# 352 dt 11.200000 rms 0.542 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6460 tsec 7.1980 #GCMRL# 353 dt 11.200000 rms 0.542 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7050 tsec 7.2360 #GCMRL# 354 dt 11.200000 rms 0.541 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8760 tsec 7.3550 #GCMRL# 355 dt 11.200000 rms 0.541 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7800 tsec 7.2940 #GCMRL# 356 dt 11.200000 rms 0.541 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8380 tsec 7.3950 #GCMRL# 357 dt 11.200000 rms 0.540 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7520 tsec 7.2960 #GCMRL# 358 dt 11.200000 rms 0.540 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6010 tsec 7.1140 #GCMRL# 359 dt 11.200000 rms 0.540 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9090 tsec 7.3980 #GCMRL# 360 dt 11.200000 rms 0.539 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7540 tsec 7.2510 #GCMRL# 361 dt 11.200000 rms 0.539 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6490 tsec 7.1300 #GCMRL# 362 dt 11.200000 rms 0.539 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8190 tsec 7.3460 #GCMRL# 363 dt 11.200000 rms 0.539 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8810 tsec 7.3790 #GCMRL# 364 dt 11.200000 rms 0.538 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7420 tsec 7.2270 #GCMRL# 365 dt 11.200000 rms 0.538 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7670 tsec 7.2610 #GCMRL# 366 dt 11.200000 rms 0.538 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6960 tsec 7.1550 #GCMRL# 367 dt 11.200000 rms 0.538 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6430 tsec 7.1510 #GCMRL# 368 dt 11.200000 rms 0.537 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8700 tsec 7.3780 #GCMRL# 369 dt 11.200000 rms 0.537 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7870 tsec 7.3220 #GCMRL# 370 dt 11.200000 rms 0.537 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6920 tsec 7.2460 #GCMRL# 371 dt 11.200000 rms 0.537 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7630 tsec 7.2990 #GCMRL# 372 dt 11.200000 rms 0.537 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7140 tsec 7.2860 #GCMRL# 373 dt 11.200000 rms 0.536 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9690 tsec 7.4910 #GCMRL# 374 dt 11.200000 rms 0.536 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9690 tsec 7.5520 #GCMRL# 375 dt 11.200000 rms 0.536 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7680 tsec 7.3250 #GCMRL# 376 dt 11.200000 rms 0.536 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8430 tsec 7.4530 #GCMRL# 377 dt 11.200000 rms 0.536 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8670 tsec 7.4260 #GCMRL# 378 dt 11.200000 rms 0.536 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9040 tsec 7.3550 #GCMRL# 379 dt 11.200000 rms 0.535 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6460 tsec 7.1400 #GCMRL# 380 dt 11.200000 rms 0.535 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6420 tsec 7.0870 #GCMRL# 381 dt 11.200000 rms 0.535 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7030 tsec 7.2520 #GCMRL# 382 dt 11.200000 rms 0.535 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9280 tsec 7.5020 #GCMRL# 383 dt 11.200000 rms 0.535 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7500 tsec 7.3000 #GCMRL# 384 dt 11.200000 rms 0.535 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6450 tsec 7.1180 #GCMRL# 385 dt 11.200000 rms 0.534 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5840 tsec 7.1280 #GCMRL# 386 dt 11.200000 rms 0.534 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6330 tsec 7.1990 #GCMRL# 387 dt 11.200000 rms 0.534 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7320 tsec 7.2500 #GCMRL# 388 dt 11.200000 rms 0.534 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7680 tsec 7.2970 #GCMRL# 389 dt 11.200000 rms 0.534 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8330 tsec 7.4140 #GCMRL# 390 dt 11.200000 rms 0.534 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7290 tsec 7.2910 #GCMRL# 391 dt 11.200000 rms 0.534 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6910 tsec 7.2530 #GCMRL# 392 dt 11.200000 rms 0.534 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7790 tsec 7.3390 #FOTS# QuadFit found better minimum quadopt=(dt=76.8,rms=0.533466) vs oldopt=(dt=128,rms=0.533478) #GCMRL# 393 dt 76.800000 rms 0.533 0.000% neg 0 invalid 762 tFOTS 20.1700 tGradient 5.7660 tsec 27.4940 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.564323 #GCMRL# 395 dt 0.000000 rms 0.563 0.169% neg 0 invalid 762 tFOTS 19.7720 tGradient 5.3450 tsec 26.6370 #GCMRL# 396 dt 0.150000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 20.4740 tGradient 5.5260 tsec 28.9690 #GCAMreg# pass 0 level1 2 level2 1 tsec 69.898 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.564323 #GCMRL# 398 dt 0.000000 rms 0.563 0.169% neg 0 invalid 762 tFOTS 20.8760 tGradient 5.2980 tsec 27.7060 #GCMRL# 399 dt 0.150000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 20.8160 tGradient 5.3500 tsec 29.1650 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.623015 #FOTS# QuadFit found better minimum quadopt=(dt=0.850794,rms=0.620011) vs oldopt=(dt=1.28,rms=0.620289) #GCMRL# 401 dt 0.850794 rms 0.620 0.482% neg 0 invalid 762 tFOTS 19.5310 tGradient 4.8210 tsec 25.9140 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.619967) vs oldopt=(dt=0.08,rms=0.619976) #GCMRL# 402 dt 0.112000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 20.9340 tGradient 5.0250 tsec 27.5290 #GCMRL# 403 dt 0.112000 rms 0.620 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9700 tsec 6.6060 #GCAMreg# pass 0 level1 1 level2 1 tsec 73.836 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.620798 #GCMRL# 405 dt 0.320000 rms 0.620 0.163% neg 0 invalid 762 tFOTS 20.6760 tGradient 4.7640 tsec 27.0020 #FOTS# QuadFit found better minimum quadopt=(dt=0.048,rms=0.619772) vs oldopt=(dt=0.08,rms=0.619772) #GCMRL# 406 dt 0.048000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 20.6930 tGradient 4.8070 tsec 27.0560 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.538626 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.521641) vs oldopt=(dt=0.32,rms=0.526028) #GCMRL# 408 dt 0.448000 rms 0.522 3.153% neg 0 invalid 762 tFOTS 19.9100 tGradient 4.0300 tsec 25.5280 #GCMRL# 409 dt 0.320000 rms 0.519 0.500% neg 0 invalid 762 tFOTS 20.0070 tGradient 3.9730 tsec 25.4170 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.516828) vs oldopt=(dt=0.32,rms=0.517189) #GCMRL# 410 dt 0.384000 rms 0.517 0.425% neg 0 invalid 762 tFOTS 19.7170 tGradient 4.1670 tsec 25.4140 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.515466) vs oldopt=(dt=0.32,rms=0.515684) #GCMRL# 411 dt 0.384000 rms 0.515 0.264% neg 0 invalid 762 tFOTS 19.4540 tGradient 4.3770 tsec 25.3110 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.514442) vs oldopt=(dt=0.32,rms=0.514602) #GCMRL# 412 dt 0.384000 rms 0.514 0.199% neg 0 invalid 762 tFOTS 19.7080 tGradient 3.9230 tsec 25.1530 #FOTS# QuadFit found better minimum quadopt=(dt=0.395833,rms=0.513723) vs oldopt=(dt=0.32,rms=0.513848) #GCMRL# 413 dt 0.395833 rms 0.514 0.140% neg 0 invalid 762 tFOTS 19.1850 tGradient 4.0090 tsec 24.7730 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.513152) vs oldopt=(dt=0.32,rms=0.513241) #GCMRL# 414 dt 0.384000 rms 0.513 0.111% neg 0 invalid 762 tFOTS 19.1010 tGradient 4.0220 tsec 24.6460 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.5127) vs oldopt=(dt=0.32,rms=0.512757) #GCMRL# 415 dt 0.384000 rms 0.513 0.088% neg 0 invalid 762 tFOTS 19.1160 tGradient 4.0340 tsec 24.6200 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.512332) vs oldopt=(dt=0.32,rms=0.512386) #GCMRL# 416 dt 0.384000 rms 0.512 0.072% neg 0 invalid 762 tFOTS 18.9060 tGradient 4.1190 tsec 24.4900 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.512026) vs oldopt=(dt=0.32,rms=0.512057) #GCMRL# 417 dt 0.384000 rms 0.512 0.060% neg 0 invalid 762 tFOTS 18.9720 tGradient 3.9470 tsec 24.4110 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.511776) vs oldopt=(dt=0.32,rms=0.511811) #GCMRL# 418 dt 0.384000 rms 0.512 0.000% neg 0 invalid 762 tFOTS 18.9700 tGradient 3.9790 tsec 24.4820 #GCMRL# 419 dt 0.384000 rms 0.512 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9910 tsec 5.4700 #GCMRL# 420 dt 0.384000 rms 0.511 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0230 tsec 5.4890 #GCMRL# 421 dt 0.384000 rms 0.511 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8950 tsec 5.9260 #GCMRL# 422 dt 0.384000 rms 0.511 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9310 tsec 5.9900 #GCMRL# 423 dt 0.384000 rms 0.511 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9430 tsec 5.4300 #GCMRL# 424 dt 0.192000 rms 0.511 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9480 tsec 6.5970 #GCMRL# 425 dt 0.192000 rms 0.510 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9750 tsec 5.5260 #GCMRL# 426 dt 0.192000 rms 0.510 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0210 tsec 5.4720 #GCMRL# 427 dt 0.192000 rms 0.510 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9500 tsec 6.0820 #GCMRL# 428 dt 0.192000 rms 0.510 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9720 tsec 5.4270 #GCMRL# 429 dt 0.192000 rms 0.510 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9080 tsec 5.3490 #GCMRL# 430 dt 0.192000 rms 0.510 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9470 tsec 5.4610 #GCMRL# 431 dt 0.192000 rms 0.510 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9150 tsec 5.3880 #GCMRL# 432 dt 0.192000 rms 0.510 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9060 tsec 5.4340 #GCMRL# 433 dt 0.192000 rms 0.510 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9180 tsec 5.4210 #GCMRL# 434 dt 0.192000 rms 0.509 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8780 tsec 5.4150 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.509489) vs oldopt=(dt=0.08,rms=0.50949) #GCMRL# 435 dt 0.112000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 19.7450 tGradient 3.7750 tsec 25.1200 #GCMRL# 436 dt 0.112000 rms 0.509 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1070 tsec 5.6700 #GCMRL# 437 dt 0.112000 rms 0.509 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1110 tsec 5.6880 #GCMRL# 438 dt 0.112000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9760 tsec 5.5130 #GCMRL# 439 dt 0.112000 rms 0.509 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8720 tsec 5.4100 #GCAMreg# pass 0 level1 0 level2 1 tsec 424.433 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.510508 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.508267) vs oldopt=(dt=0.08,rms=0.508608) #GCMRL# 441 dt 0.112000 rms 0.508 0.439% neg 0 invalid 762 tFOTS 18.0100 tGradient 4.1340 tsec 23.6660 #FOTS# QuadFit found better minimum quadopt=(dt=0.177083,rms=0.506797) vs oldopt=(dt=0.08,rms=0.507584) #GCMRL# 442 dt 0.177083 rms 0.507 0.289% neg 0 invalid 762 tFOTS 18.0010 tGradient 4.0280 tsec 23.5910 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.506224) vs oldopt=(dt=0.08,rms=0.506389) #GCMRL# 443 dt 0.112000 rms 0.506 0.113% neg 0 invalid 762 tFOTS 18.3420 tGradient 4.1160 tsec 23.9910 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505762) vs oldopt=(dt=0.08,rms=0.50589) #GCMRL# 444 dt 0.112000 rms 0.506 0.091% neg 0 invalid 762 tFOTS 18.1390 tGradient 4.1180 tsec 23.7950 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505406) vs oldopt=(dt=0.08,rms=0.505506) #GCMRL# 445 dt 0.112000 rms 0.505 0.070% neg 0 invalid 762 tFOTS 17.9300 tGradient 3.8890 tsec 23.3840 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505143) vs oldopt=(dt=0.08,rms=0.50522) #GCMRL# 446 dt 0.112000 rms 0.505 0.052% neg 0 invalid 762 tFOTS 17.9580 tGradient 3.8550 tsec 23.3950 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.504924) vs oldopt=(dt=0.08,rms=0.504985) #GCMRL# 447 dt 0.112000 rms 0.505 0.000% neg 0 invalid 762 tFOTS 18.0010 tGradient 4.0570 tsec 23.6500 #GCMRL# 448 dt 0.112000 rms 0.505 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9720 tsec 5.5260 #GCMRL# 449 dt 0.112000 rms 0.504 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0580 tsec 5.5730 #GCMRL# 450 dt 0.112000 rms 0.504 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9080 tsec 5.4430 #GCMRL# 451 dt 0.112000 rms 0.504 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9350 tsec 5.4490 #GCMRL# 452 dt 0.112000 rms 0.504 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8840 tsec 5.4400 #GCMRL# 453 dt 0.112000 rms 0.504 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0290 tsec 5.5890 #GCMRL# 454 dt 0.112000 rms 0.504 -0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0230 tsec 6.9580 GCAMregister done in 101.192 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.502289 #GCMRL# 456 dt 0.000000 rms 0.501 0.212% neg 0 invalid 762 tFOTS 22.7880 tGradient 9.2780 tsec 33.5910 #GCAMreg# pass 0 level1 5 level2 1 tsec 74.328 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.502289 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.500834) vs oldopt=(dt=92.48,rms=0.500897) #GCMRL# 458 dt 129.472000 rms 0.501 0.290% neg 0 invalid 762 tFOTS 23.1090 tGradient 9.5220 tsec 34.1550 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.500631) vs oldopt=(dt=92.48,rms=0.500667) #GCMRL# 459 dt 129.472000 rms 0.501 0.000% neg 0 invalid 762 tFOTS 22.8610 tGradient 9.3400 tsec 33.7700 #GCMRL# 460 dt 129.472000 rms 0.501 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3770 tsec 10.9050 #GCMRL# 461 dt 129.472000 rms 0.500 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5220 tsec 11.0050 #GCMRL# 462 dt 129.472000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3160 tsec 10.8740 #GCMRL# 463 dt 129.472000 rms 0.500 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4070 tsec 10.9220 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.500115) vs oldopt=(dt=23.12,rms=0.500116) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.5012 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.500138) vs oldopt=(dt=1.62,rms=0.500139) #GCMRL# 465 dt 2.268000 rms 0.500 0.212% neg 0 invalid 762 tFOTS 24.5940 tGradient 6.8060 tsec 32.9230 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.500136) vs oldopt=(dt=1.62,rms=0.500136) #GCMRL# 466 dt 2.268000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 24.1450 tGradient 6.8310 tsec 32.5120 #GCMRL# 467 dt 2.268000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1390 tsec 8.6540 #GCAMreg# pass 0 level1 4 level2 1 tsec 89.994 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.501191 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.498188) vs oldopt=(dt=103.68,rms=0.498518) #GCMRL# 469 dt 145.152000 rms 0.498 0.599% neg 0 invalid 762 tFOTS 23.2850 tGradient 7.0680 tsec 31.9160 #GCMRL# 470 dt 25.920000 rms 0.498 0.000% neg 0 invalid 762 tFOTS 24.4940 tGradient 6.9920 tsec 33.1760 #GCMRL# 471 dt 25.920000 rms 0.498 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.8230 tsec 8.4610 #GCMRL# 472 dt 25.920000 rms 0.498 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0410 tsec 8.5930 #GCMRL# 473 dt 25.920000 rms 0.497 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.8680 tsec 8.4180 #GCMRL# 474 dt 25.920000 rms 0.497 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0000 tsec 8.5990 #GCMRL# 475 dt 25.920000 rms 0.496 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9340 tsec 8.5600 #GCMRL# 476 dt 25.920000 rms 0.496 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1000 tsec 8.6080 #GCMRL# 477 dt 25.920000 rms 0.496 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.8600 tsec 8.4130 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.495277) vs oldopt=(dt=414.72,rms=0.495335) setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.496637 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.49411) vs oldopt=(dt=32,rms=0.494205) #GCMRL# 479 dt 25.600000 rms 0.494 0.509% neg 0 invalid 762 tFOTS 24.7300 tGradient 5.7680 tsec 32.0380 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49218) vs oldopt=(dt=32,rms=0.492438) #GCMRL# 480 dt 44.800000 rms 0.492 0.391% neg 0 invalid 762 tFOTS 24.6140 tGradient 5.8160 tsec 32.0000 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.49171) vs oldopt=(dt=8,rms=0.49179) #GCMRL# 481 dt 11.200000 rms 0.492 0.000% neg 0 invalid 762 tFOTS 24.2220 tGradient 5.7450 tsec 31.5350 #GCMRL# 482 dt 11.200000 rms 0.491 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8760 tsec 7.3750 #GCMRL# 483 dt 11.200000 rms 0.491 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9470 tsec 7.4510 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 484 dt 11.200000 rms 0.490 0.156% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8890 tsec 10.9530 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 485 dt 11.200000 rms 0.489 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6890 tsec 10.6690 #GCMRL# 486 dt 11.200000 rms 0.489 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6470 tsec 7.1620 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 487 dt 11.200000 rms 0.488 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6650 tsec 13.5160 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 488 dt 11.200000 rms 0.488 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6840 tsec 10.8090 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 489 dt 11.200000 rms 0.487 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7870 tsec 12.1000 #GCMRL# 490 dt 128.000000 rms 0.486 0.247% neg 0 invalid 762 tFOTS 22.6700 tGradient 5.6110 tsec 29.8040 #FOTS# QuadFit found better minimum quadopt=(dt=23.6883,rms=0.485417) vs oldopt=(dt=32,rms=0.485554) #GCMRL# 491 dt 23.688312 rms 0.485 0.000% neg 0 invalid 762 tFOTS 24.0150 tGradient 5.8400 tsec 31.3840 #GCMRL# 492 dt 23.688312 rms 0.485 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7340 tsec 7.2010 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 493 dt 23.688312 rms 0.485 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4880 tsec 8.7520 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 268.954 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.485738 #FOTS# QuadFit found better minimum quadopt=(dt=44.2483,rms=0.480719) vs oldopt=(dt=32,rms=0.48093) #GCMRL# 495 dt 44.248276 rms 0.481 1.033% neg 0 invalid 762 tFOTS 23.9630 tGradient 5.8200 tsec 31.3150 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.479586) vs oldopt=(dt=8,rms=0.479781) #GCMRL# 496 dt 11.200000 rms 0.480 0.000% neg 0 invalid 762 tFOTS 24.1990 tGradient 5.7910 tsec 31.4870 #GCMRL# 497 dt 11.200000 rms 0.479 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6300 tsec 7.0800 #GCMRL# 498 dt 11.200000 rms 0.479 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6370 tsec 7.1340 #GCMRL# 499 dt 11.200000 rms 0.478 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8060 tsec 7.3170 #GCMRL# 500 dt 11.200000 rms 0.477 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6660 tsec 7.2030 #GCMRL# 501 dt 11.200000 rms 0.476 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5460 tsec 7.0220 #GCMRL# 502 dt 11.200000 rms 0.476 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7180 tsec 7.2370 #GCMRL# 503 dt 11.200000 rms 0.475 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7830 tsec 7.2370 #GCMRL# 504 dt 11.200000 rms 0.475 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6140 tsec 7.1850 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.474794) vs oldopt=(dt=32,rms=0.474809) #GCMRL# 505 dt 25.600000 rms 0.475 0.000% neg 0 invalid 762 tFOTS 24.0030 tGradient 5.7140 tsec 31.2410 #GCMRL# 506 dt 25.600000 rms 0.475 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6320 tsec 7.1410 #GCMRL# 507 dt 25.600000 rms 0.474 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6830 tsec 7.1410 #GCMRL# 508 dt 25.600000 rms 0.474 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8130 tsec 7.3220 #GCMRL# 509 dt 25.600000 rms 0.474 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9400 tsec 7.4610 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.478517 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.47742) vs oldopt=(dt=0.72,rms=0.477423) #GCMRL# 511 dt 1.008000 rms 0.477 0.229% neg 0 invalid 762 tFOTS 23.1750 tGradient 5.3350 tsec 30.0020 #FOTS# QuadFit found better minimum quadopt=(dt=0.864,rms=0.477412) vs oldopt=(dt=0.72,rms=0.477412) #GCMRL# 512 dt 0.864000 rms 0.477 0.000% neg 0 invalid 762 tFOTS 23.0200 tGradient 5.2770 tsec 29.8590 #GCMRL# 513 dt 0.864000 rms 0.477 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1960 tsec 6.6620 #GCAMreg# pass 0 level1 2 level2 1 tsec 80.548 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.478505 #FOTS# QuadFit found better minimum quadopt=(dt=8.44444,rms=0.476945) vs oldopt=(dt=2.88,rms=0.477088) #GCMRL# 515 dt 8.444444 rms 0.477 0.326% neg 0 invalid 762 tFOTS 24.5050 tGradient 5.2660 tsec 31.3110 #FOTS# QuadFit found better minimum quadopt=(dt=21.8182,rms=0.475445) vs oldopt=(dt=11.52,rms=0.475763) iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 516 dt 21.818182 rms 0.476 0.288% neg 0 invalid 762 tFOTS 24.1360 tGradient 5.2490 tsec 37.8910 #FOTS# QuadFit found better minimum quadopt=(dt=15.3287,rms=0.473825) vs oldopt=(dt=11.52,rms=0.473933) iter 0, gcam->neg = 130 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 517 dt 15.328671 rms 0.474 0.307% neg 0 invalid 762 tFOTS 23.9250 tGradient 5.2600 tsec 42.3610 #FOTS# QuadFit found better minimum quadopt=(dt=11.0983,rms=0.472941) vs oldopt=(dt=11.52,rms=0.472943) iter 0, gcam->neg = 18 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 518 dt 11.098266 rms 0.473 0.000% neg 0 invalid 762 tFOTS 24.0350 tGradient 5.1480 tsec 39.9590 iter 0, gcam->neg = 16 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 519 dt 11.098266 rms 0.472 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2170 tsec 21.2080 iter 0, gcam->neg = 41 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 520 dt 11.098266 rms 0.471 0.285% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2860 tsec 18.1500 iter 0, gcam->neg = 53 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 521 dt 11.098266 rms 0.469 0.314% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0240 tsec 20.2310 iter 0, gcam->neg = 76 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 522 dt 11.098266 rms 0.468 0.373% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1700 tsec 18.6860 iter 0, gcam->neg = 138 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 523 dt 11.098266 rms 0.466 0.269% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1790 tsec 19.9550 iter 0, gcam->neg = 157 after 23 iterations, nbhd size=1, neg = 0 #GCMRL# 524 dt 11.098266 rms 0.466 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3210 tsec 24.8630 iter 0, gcam->neg = 85 after 21 iterations, nbhd size=1, neg = 0 #GCMRL# 525 dt 11.098266 rms 0.465 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3150 tsec 23.6000 iter 0, gcam->neg = 125 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 526 dt 11.098266 rms 0.464 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1380 tsec 18.6130 iter 0, gcam->neg = 113 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 527 dt 11.098266 rms 0.464 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1430 tsec 20.8150 #FOTS# QuadFit found better minimum quadopt=(dt=8.26144,rms=0.463143) vs oldopt=(dt=11.52,rms=0.46324) iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 528 dt 8.261438 rms 0.463 0.133% neg 0 invalid 762 tFOTS 23.9610 tGradient 4.9890 tsec 38.5930 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.463098) vs oldopt=(dt=2.88,rms=0.463104) iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 529 dt 4.032000 rms 0.463 0.000% neg 0 invalid 762 tFOTS 24.1070 tGradient 5.1330 tsec 34.0920 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 530 dt 4.032000 rms 0.463 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1860 tsec 9.2830 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=0, neg = 0 #GCMRL# 531 dt 4.032000 rms 0.463 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0060 tsec 14.2070 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.469979 #GCMRL# 533 dt 0.000000 rms 0.469 0.240% neg 0 invalid 762 tFOTS 22.5370 tGradient 4.7970 tsec 28.8060 #GCAMreg# pass 0 level1 1 level2 1 tsec 64.77 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.469979 #GCMRL# 535 dt 0.000000 rms 0.469 0.240% neg 0 invalid 762 tFOTS 22.8010 tGradient 4.8150 tsec 29.1180 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.460177 #FOTS# QuadFit found better minimum quadopt=(dt=1.7452,rms=0.43232) vs oldopt=(dt=1.28,rms=0.434429) iter 0, gcam->neg = 1479 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 537 dt 1.745196 rms 0.434 5.614% neg 0 invalid 762 tFOTS 24.3370 tGradient 4.0670 tsec 44.0710 #GCMRL# 538 dt 0.000013 rms 0.434 0.000% neg 0 invalid 762 tFOTS 30.7980 tGradient 3.9660 tsec 36.3660 #GCAMreg# pass 0 level1 0 level2 1 tsec 93.48 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.435572 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.434228) vs oldopt=(dt=0.02,rms=0.434236) #GCMRL# 540 dt 0.028000 rms 0.434 0.309% neg 0 invalid 762 tFOTS 24.3190 tGradient 3.9430 tsec 29.8400 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.434227) vs oldopt=(dt=0.005,rms=0.434227) #GCMRL# 541 dt 0.007000 rms 0.434 0.000% neg 0 invalid 762 tFOTS 24.1190 tGradient 4.0920 tsec 29.7000 label assignment complete, 0 changed (0.00%) GCAMregister done in 29.3551 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.422819 #GCAMreg# pass 0 level1 5 level2 1 tsec 39.321 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.422819 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.422814) vs oldopt=(dt=5.78,rms=0.422815) #GCMRL# 544 dt 8.092000 rms 0.423 0.001% neg 0 invalid 762 tFOTS 23.6140 tGradient 8.3950 tsec 33.4620 #FOTS# QuadFit found better minimum quadopt=(dt=4.624,rms=0.422814) vs oldopt=(dt=5.78,rms=0.422814) #GCMRL# 545 dt 4.624000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 23.8330 tGradient 7.8980 tsec 33.2800 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.422963 #GCAMreg# pass 0 level1 4 level2 1 tsec 36.949 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.422963 #GCMRL# 548 dt 25.920000 rms 0.423 0.016% neg 0 invalid 762 tFOTS 22.4200 tGradient 5.9810 tsec 29.9220 #GCMRL# 549 dt 25.920000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 23.5900 tGradient 5.9110 tsec 31.0230 #GCMRL# 550 dt 25.920000 rms 0.423 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0590 tsec 7.5650 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.42343 #GCMRL# 552 dt 8.000000 rms 0.423 0.044% neg 0 invalid 762 tFOTS 23.7390 tGradient 4.9220 tsec 30.1730 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.423222) vs oldopt=(dt=2,rms=0.423226) #GCMRL# 553 dt 2.800000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 23.9500 tGradient 5.2100 tsec 30.7180 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 554 dt 2.800000 rms 0.423 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1130 tsec 8.8900 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 86.736 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.423218 #FOTS# QuadFit found better minimum quadopt=(dt=65.1852,rms=0.421087) vs oldopt=(dt=32,rms=0.421436) iter 0, gcam->neg = 34 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 556 dt 65.185185 rms 0.421 0.466% neg 0 invalid 762 tFOTS 23.4290 tGradient 5.1380 tsec 40.6320 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.42064) vs oldopt=(dt=8,rms=0.420762) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 557 dt 11.200000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 23.6440 tGradient 4.9380 tsec 32.6420 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 558 dt 11.200000 rms 0.420 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7930 tsec 7.9310 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 559 dt 11.200000 rms 0.420 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9990 tsec 10.1310 iter 0, gcam->neg = 18 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 560 dt 11.200000 rms 0.420 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0060 tsec 10.7400 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.419479) vs oldopt=(dt=32,rms=0.419552) iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 561 dt 44.800000 rms 0.419 0.143% neg 0 invalid 762 tFOTS 23.5400 tGradient 4.9730 tsec 32.1480 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.419289) vs oldopt=(dt=32,rms=0.419343) iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.421623 #FOTS# QuadFit found better minimum quadopt=(dt=8.47059,rms=0.420838) vs oldopt=(dt=11.52,rms=0.420927) iter 0, gcam->neg = 25 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 563 dt 8.470588 rms 0.421 0.098% neg 0 invalid 762 tFOTS 24.0960 tGradient 4.3110 tsec 43.0980 #FOTS# QuadFit found better minimum quadopt=(dt=9.62963,rms=0.420905) vs oldopt=(dt=11.52,rms=0.420919) iter 0, gcam->neg = 35 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 564 dt 9.629630 rms 0.421 0.000% neg 0 invalid 762 tFOTS 23.7190 tGradient 4.4180 tsec 40.1540 iter 0, gcam->neg = 31 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 565 dt 9.629630 rms 0.421 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3210 tsec 16.9190 iter 0, gcam->neg = 55 after 19 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 128.724 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.421004 #FOTS# QuadFit found better minimum quadopt=(dt=16.6667,rms=0.41788) vs oldopt=(dt=11.52,rms=0.418174) iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 567 dt 16.666667 rms 0.418 0.664% neg 0 invalid 762 tFOTS 23.7000 tGradient 4.4350 tsec 44.2000 #FOTS# QuadFit found better minimum quadopt=(dt=12.2051,rms=0.417036) vs oldopt=(dt=11.52,rms=0.417039) iter 0, gcam->neg = 47 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 568 dt 12.205128 rms 0.417 0.000% neg 0 invalid 762 tFOTS 23.7220 tGradient 4.3730 tsec 41.6820 iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 569 dt 12.205128 rms 0.417 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2970 tsec 20.1630 iter 0, gcam->neg = 75 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 570 dt 12.205128 rms 0.416 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3930 tsec 13.0420 iter 0, gcam->neg = 88 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 571 dt 12.205128 rms 0.415 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3010 tsec 21.1140 iter 0, gcam->neg = 85 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 572 dt 12.205128 rms 0.415 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4170 tsec 20.1580 #FOTS# QuadFit found better minimum quadopt=(dt=9.43284,rms=0.414861) vs oldopt=(dt=11.52,rms=0.414875) iter 0, gcam->neg = 30 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 573 dt 9.432836 rms 0.415 0.000% neg 0 invalid 762 tFOTS 23.7940 tGradient 4.3710 tsec 45.7600 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 574 dt 9.432836 rms 0.415 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2630 tsec 10.3150 iter 0, gcam->neg = 17 after 16 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.420351 #FOTS# QuadFit found better minimum quadopt=(dt=6e-05,rms=0.420351) vs oldopt=(dt=5e-05,rms=0.420351) #GCMRL# 576 dt 0.000060 rms 0.420 0.000% neg 0 invalid 762 tFOTS 29.9560 tGradient 3.9390 tsec 35.3540 #GCAMreg# pass 0 level1 1 level2 1 tsec 70.417 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.420351 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.410936 #FOTS# QuadFit found better minimum quadopt=(dt=0.815789,rms=0.403298) vs oldopt=(dt=1.28,rms=0.406458) iter 0, gcam->neg = 715 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 579 dt 0.815789 rms 0.406 1.277% neg 0 invalid 762 tFOTS 23.8670 tGradient 3.2990 tsec 45.6350 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.405599) vs oldopt=(dt=0.08,rms=0.405599) #GCMRL# 580 dt 0.064000 rms 0.406 0.000% neg 0 invalid 762 tFOTS 23.6510 tGradient 3.1830 tsec 28.3620 #GCMRL# 581 dt 0.064000 rms 0.406 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3150 tsec 4.7810 #GCAMreg# pass 0 level1 0 level2 1 tsec 90.402 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.405564 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.403535) vs oldopt=(dt=0.32,rms=0.403796) iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 583 dt 0.448000 rms 0.404 0.500% neg 0 invalid 762 tFOTS 24.0380 tGradient 3.2280 tsec 30.5360 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.402674) vs oldopt=(dt=0.32,rms=0.402728) iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 584 dt 0.448000 rms 0.403 0.000% neg 0 invalid 762 tFOTS 24.0750 tGradient 3.0780 tsec 38.3600 iter 0, gcam->neg = 28 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 585 dt 0.448000 rms 0.402 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0980 tsec 15.1540 iter 0, gcam->neg = 63 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 586 dt 0.448000 rms 0.402 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1210 tsec 15.7550 iter 0, gcam->neg = 99 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 587 dt 0.448000 rms 0.402 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2280 tsec 13.5970 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 588 dt 0.320000 rms 0.401 0.157% neg 0 invalid 762 tFOTS 23.7580 tGradient 3.2770 tsec 35.0400 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 GCAMregister done in 20.8865 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4656 tmin = 26.1995 Calls to gcamLabelEnergy 4069 tmin = 2.05917 Calls to gcamJacobianEnergy 4656 tmin = 25.7454 Calls to gcamSmoothnessEnergy 4656 tmin = 19.7748 Calls to gcamLogLikelihoodTerm 590 tmin = 7.50735 Calls to gcamLabelTerm 543 tmin = 8.3443 Calls to gcamJacobianTerm 590 tmin = 15.9664 Calls to gcamSmoothnessTerm 590 tmin = 4.7148 Calls to gcamComputeGradient 590 tmin = 65.6912 Calls to gcamComputeMetricProperties 6842 tmin = 23.404 mri_ca_register took 3 hours, 7 minutes and 1 seconds. #VMPC# mri_ca_register VmPeak 2076540 FSRUNTIME@ mri_ca_register 3.1168 hours 1 threads @#@FSTIME 2020:07:18:14:38:48 mri_ca_register N 9 e 11220.63 S 6.64 U 11180.89 P 99% M 1325924 F 0 R 395264 W 0 c 292971 w 127 I 0 O 0 L 1.01 1.00 0.90 @#@FSLOADPOST 2020:07:18:17:45:48 mri_ca_register N 9 1.07 1.03 1.00 #-------------------------------------- #@# SubCort Seg Sat Jul 18 17:45:49 EDT 2020 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname loginnode2 machine x86_64 user pankumar Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname loginnode2 machine x86_64 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz 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 == Number of threads available to for OpenMP = 1 == reading 1 input volumes reading classifier array from /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.06 Atlas used for the 3D morph was /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.08824 (13) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (130 voxels, overlap=0.461) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (130 voxels, peak = 12), gca=12.3 gca peak = 0.20380 (13) mri peak = 0.06250 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.67 x + 0.0 (143 voxels, overlap=0.597) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (143 voxels, peak = 22), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.09236 (95) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (535 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (535 voxels, peak = 95), gca=94.6 gca peak = 0.15814 (97) mri peak = 0.07971 (99) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (550 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (550 voxels, peak = 103), gca=103.3 gca peak = 0.27624 (56) mri peak = 0.09660 (58) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (699 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (699 voxels, peak = 55), gca=55.2 gca peak = 0.28723 (59) mri peak = 0.09704 (57) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (717 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (717 voxels, peak = 58), gca=58.1 gca peak = 0.07623 (103) mri peak = 0.07976 (109) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (23014 voxels, overlap=0.569) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (23014 voxels, peak = 110), gca=109.7 gca peak = 0.07837 (105) mri peak = 0.08482 (111) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (26382 voxels, overlap=0.474) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (26382 voxels, peak = 112), gca=111.8 gca peak = 0.10165 (58) mri peak = 0.04337 (53) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (21952 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (21952 voxels, peak = 53), gca=53.1 gca peak = 0.11113 (58) mri peak = 0.04690 (51) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (21548 voxels, overlap=0.903) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (21548 voxels, peak = 53), gca=53.1 gca peak = 0.27796 (67) mri peak = 0.11552 (78) Right_Caudate (50): linear fit = 1.12 x + 0.0 (831 voxels, overlap=0.429) Right_Caudate (50): linear fit = 1.12 x + 0.0 (831 voxels, peak = 75), gca=75.4 gca peak = 0.14473 (69) mri peak = 0.12928 (78) Left_Caudate (11): linear fit = 1.07 x + 0.0 (772 voxels, overlap=0.625) Left_Caudate (11): linear fit = 1.07 x + 0.0 (772 voxels, peak = 73), gca=73.5 gca peak = 0.14301 (56) mri peak = 0.04642 (53) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (28473 voxels, overlap=0.984) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (28473 voxels, peak = 53), gca=52.9 gca peak = 0.14610 (55) mri peak = 0.04243 (51) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (27216 voxels, overlap=0.902) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (27216 voxels, peak = 52), gca=52.0 gca peak = 0.16309 (85) mri peak = 0.10011 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5967 voxels, overlap=0.880) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5967 voxels, peak = 87), gca=87.1 gca peak = 0.15172 (84) mri peak = 0.09966 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5693 voxels, overlap=0.876) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5693 voxels, peak = 87), gca=86.9 gca peak = 0.30461 (58) mri peak = 0.17597 (51) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (498 voxels, overlap=0.546) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (498 voxels, peak = 51), gca=50.8 gca peak = 0.32293 (57) mri peak = 0.11029 (50) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (486 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (486 voxels, peak = 55), gca=55.0 gca peak = 0.11083 (90) mri peak = 0.06853 (89) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3692 voxels, overlap=0.995) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3692 voxels, peak = 88), gca=87.8 gca peak = 0.11393 (83) mri peak = 0.06793 (90) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3349 voxels, overlap=0.979) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3349 voxels, peak = 86), gca=85.9 gca peak = 0.08575 (81) mri peak = 0.08485 (80) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1816 voxels, overlap=0.880) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1816 voxels, peak = 82), gca=82.2 gca peak = 0.08618 (78) mri peak = 0.08421 (81) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1709 voxels, overlap=0.865) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1709 voxels, peak = 80), gca=79.9 gca peak = 0.08005 (78) mri peak = 0.09874 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11215 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11215 voxels, peak = 82), gca=82.3 gca peak = 0.12854 (88) mri peak = 0.05677 (86) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1128 voxels, overlap=0.809) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1128 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.05943 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1283 voxels, overlap=0.898) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1283 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.09795 (15) gca peak = 0.17113 (14) mri peak = 0.14773 ( 8) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, overlap=0.489) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, peak = 7), gca=6.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 1.06 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.22482 (13) mri peak = 0.08824 (13) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (130 voxels, overlap=0.673) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (130 voxels, peak = 14), gca=14.5 gca peak = 0.16078 (19) mri peak = 0.06250 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (143 voxels, overlap=0.355) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (143 voxels, peak = 20), gca=20.4 gca peak = 0.21116 (94) mri peak = 0.09236 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (535 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (535 voxels, peak = 95), gca=95.4 gca peak = 0.16875 (102) mri peak = 0.07971 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (550 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (550 voxels, peak = 103), gca=102.5 gca peak = 0.30937 (55) mri peak = 0.09660 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (699 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (699 voxels, peak = 55), gca=55.0 gca peak = 0.28941 (58) mri peak = 0.09704 (57) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (717 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (717 voxels, peak = 58), gca=58.0 gca peak = 0.07344 (110) mri peak = 0.07976 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (23014 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (23014 voxels, peak = 110), gca=110.0 gca peak = 0.07460 (112) mri peak = 0.08482 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26382 voxels, overlap=0.762) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26382 voxels, peak = 112), gca=112.0 gca peak = 0.10919 (53) mri peak = 0.04337 (53) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (21952 voxels, overlap=1.000) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (21952 voxels, peak = 55), gca=55.4 gca peak = 0.12331 (53) mri peak = 0.04690 (51) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (21548 voxels, overlap=0.990) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (21548 voxels, peak = 52), gca=52.2 gca peak = 0.22309 (75) mri peak = 0.11552 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (831 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (831 voxels, peak = 75), gca=75.0 gca peak = 0.12384 (73) mri peak = 0.12928 (78) Left_Caudate (11): linear fit = 1.01 x + 0.0 (772 voxels, overlap=0.956) Left_Caudate (11): linear fit = 1.01 x + 0.0 (772 voxels, peak = 74), gca=74.1 gca peak = 0.14626 (52) mri peak = 0.04642 (53) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28473 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28473 voxels, peak = 52), gca=52.0 gca peak = 0.15405 (52) mri peak = 0.04243 (51) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27216 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27216 voxels, peak = 51), gca=51.2 gca peak = 0.15741 (87) mri peak = 0.10011 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5967 voxels, overlap=0.950) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5967 voxels, peak = 87), gca=87.0 gca peak = 0.14534 (87) mri peak = 0.09966 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5693 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5693 voxels, peak = 87), gca=86.6 gca peak = 0.26052 (51) mri peak = 0.17597 (51) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (498 voxels, overlap=0.960) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (498 voxels, peak = 51), gca=51.0 gca peak = 0.35771 (55) mri peak = 0.11029 (50) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (486 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (486 voxels, peak = 55), gca=55.0 gca peak = 0.11203 (86) mri peak = 0.06853 (89) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3692 voxels, overlap=0.991) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3692 voxels, peak = 86), gca=85.6 gca peak = 0.11103 (86) mri peak = 0.06793 (90) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3349 voxels, overlap=0.994) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3349 voxels, peak = 86), gca=85.6 gca peak = 0.08210 (82) mri peak = 0.08485 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1816 voxels, overlap=0.900) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1816 voxels, peak = 82), gca=82.0 gca peak = 0.08445 (82) mri peak = 0.08421 (81) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1709 voxels, overlap=0.918) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1709 voxels, peak = 82), gca=82.0 gca peak = 0.08443 (83) mri peak = 0.09874 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11215 voxels, overlap=0.678) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11215 voxels, peak = 83), gca=82.6 gca peak = 0.11072 (97) mri peak = 0.05677 (86) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1128 voxels, overlap=0.936) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1128 voxels, peak = 97), gca=97.5 gca peak = 0.14298 (96) mri peak = 0.05943 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1283 voxels, overlap=0.928) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1283 voxels, peak = 96), gca=96.5 gca peak = 0.20054 (28) mri peak = 0.09795 (15) gca peak = 0.16806 (17) mri peak = 0.14773 ( 8) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, overlap=0.315) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, peak = 8), gca=7.9 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19362 (27) gca peak Third_Ventricle = 0.20054 (28) gca peak Fourth_Ventricle = 0.16806 (17) gca peak CSF = 0.20346 (38) gca peak Left_Accumbens_area = 0.65277 (66) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.85300 (53) gca peak Left_choroid_plexus = 0.11687 (35) gca peak Right_Inf_Lat_Vent = 0.25588 (23) gca peak Right_Accumbens_area = 0.29156 (73) gca peak Right_vessel = 0.77367 (52) gca peak Right_choroid_plexus = 0.13288 (38) gca peak Fifth_Ventricle = 0.60973 (35) gca peak WM_hypointensities = 0.10282 (82) gca peak non_WM_hypointensities = 0.13942 (43) gca peak Optic_Chiasm = 0.60484 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt #New# invocation of recon-all Mon Jul 27 13:17:06 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -all -noskullstrip subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux n523 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 52428800 kbytes descriptors 102400 memorylocked unlimited maxproc 63708 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:07-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:07-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:07-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:07-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:08-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:09-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:10-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:11-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:12-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:13-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:14-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:15-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:16-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:17-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:18-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:19-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:20-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:21-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:22-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/27-17:17:23-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n523 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Mon Jul 27 13:17:25 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:27:13:17:26 mri_convert N 4 e 1.98 S 0.01 U 1.85 P 94% M 53388 F 0 R 1934 W 0 c 5 w 44 I 0 O 0 L 9.04 7.89 10.74 @#@FSLOADPOST 2020:07:27:13:17:28 mri_convert N 4 9.04 7.89 10.74 #-------------------------------------------- #@# MotionCor Mon Jul 27 13:17:29 EDT 2020 Found 1 runs /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/001.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform mri_convert /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz --conform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261116, -0.041979) j_ras = (-0.0224984, 0.996182, -0.0843504) k_ras = (-0.0440213, 0.0833028, 0.995551) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 3297.37 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz... @#@FSTIME 2020:07:27:13:17:35 mri_convert N 3 e 2.96 S 0.03 U 2.92 P 99% M 65376 F 0 R 3510 W 0 c 4 w 30 I 0 O 0 L 9.44 7.99 10.76 @#@FSLOADPOST 2020:07:27:13:17:38 mri_convert N 3 9.88 8.10 10.78 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:07:27:13:17:40 mri_add_xform_to_header N 4 e 0.62 S 0.01 U 0.41 P 67% M 20204 F 0 R 1687 W 0 c 3 w 36 I 0 O 0 L 9.88 8.10 10.78 @#@FSLOADPOST 2020:07:27:13:17:41 mri_add_xform_to_header N 4 9.88 8.10 10.78 #-------------------------------------------- #@# Talairach Mon Jul 27 13:17:41 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.0 Linux n523 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Jul 27 13:17:44 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.800758 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.800758/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.800758/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.800758/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.800758/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Mon Jul 27 13:20:51 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:27:13:17:42 mri_nu_correct.mni N 12 e 189.00 S 0.40 U 184.98 P 98% M 485228 F 0 R 39323 W 0 c 398 w 1727 I 0 O 0 L 10.37 8.23 10.81 @#@FSLOADPOST 2020:07:27:13:20:51 mri_nu_correct.mni N 12 16.84 12.44 11.99 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Jul 27 13:20:53 EDT 2020 Ended at Mon Jul 27 13:21:23 EDT 2020 talairach_avi done @#@FSTIME 2020:07:27:13:20:53 talairach_avi N 4 e 30.27 S 0.98 U 18.07 P 62% M 253896 F 0 R 33373 W 0 c 178 w 2699 I 0 O 32 L 16.84 12.44 11.99 @#@FSLOADPOST 2020:07:27:13:21:23 talairach_avi N 4 16.90 12.88 12.14 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jul 27 13:21:24 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5199, pval=0.1531 >= threshold=0.0050) @#@FSTIME 2020:07:27:13:21:26 talairach_afd N 4 e 0.27 S 0.00 U 0.00 P 2% M 2108 F 0 R 618 W 0 c 1 w 41 I 0 O 0 L 16.90 12.88 12.14 @#@FSLOADPOST 2020:07:27:13:21:26 talairach_afd N 4 16.99 12.96 12.17 awk -f /public/apps/freesurfer/7.1.0/bin/extract_talairach_avi_QA.awk /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log tal_QC_AZS /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach_avi.log TalAviQA: 0.96317 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Mon Jul 27 13:21:28 EDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri /public/apps/freesurfer/7.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.0 Linux n523 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Jul 27 13:21:31 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.811646 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz sysname Linux hostname n523 machine x86_64 user pankumar input /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.811646/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 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811646/input.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811646/input.mean.dat sysname Linux hostname n523 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.811646/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 /dev/shm/tmp.mri_nu_correct.mni.811646/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811646/output.mean.dat 7.1.0 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811646/output.mean.dat sysname Linux hostname n523 machine x86_64 user pankumar whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.811646/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.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 /dev/shm/tmp.mri_nu_correct.mni.811646/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz mul 1.15054592399081702868 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.811646/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-09, 3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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 6 seconds. mapping (13, 196) to ( 3, 110) Mon Jul 27 13:25:03 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:27:13:21:29 mri_nu_correct.mni N 9 e 214.58 S 1.11 U 208.69 P 97% M 610744 F 0 R 189431 W 0 c 363 w 2573 I 0 O 0 L 16.99 12.96 12.17 @#@FSLOADPOST 2020:07:27:13:25:04 mri_nu_correct.mni N 9 16.81 14.99 13.15 mri_add_xform_to_header -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2020:07:27:13:25:05 mri_add_xform_to_header N 4 e 0.50 S 0.01 U 0.45 P 92% M 20284 F 0 R 1708 W 0 c 2 w 26 I 0 O 0 L 16.81 14.99 13.15 @#@FSLOADPOST 2020:07:27:13:25:05 mri_add_xform_to_header N 4 16.81 14.99 13.15 #-------------------------------------------- #@# Intensity Normalization Mon Jul 27 13:25:06 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.13371 0.00341 0.01983 3.03738; 0.08150 1.21293 -0.03176 -14.91861; -0.05244 -0.17526 1.52897 -41.57074; 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(): error: MRIhistogramRegion: input mri nu.mgz is blank MRIsplineNormalize(): npeaks = 12 Starting OpenSpline(): npoints = 12 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 56 (56), valley at 0 (-1) csf peak at 28, setting threshold to 46 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 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 46 seconds. @#@FSTIME 2020:07:27:13:25:07 mri_normalize N 7 e 106.11 S 0.23 U 105.83 P 99% M 578544 F 0 R 12294 W 0 c 341 w 43 I 0 O 0 L 16.66 14.99 13.16 @#@FSLOADPOST 2020:07:27:13:26:54 mri_normalize N 7 16.11 15.29 13.46 #------------------------------------- #@# EM Registration Mon Jul 27 13:26:54 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, 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=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -3.918 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.928391 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (-2.632, -2.632, -2.632) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) max log p = -3.811092 @ (0.000, 0.000, 0.000) Found translation: (-2.6, -2.6, -2.6): log p = -3.811 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.811 (thresh=-3.8) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 36 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.624, old_max_log_p =-3.624 (thresh=-3.6) 1.00000 0.00000 0.00000 -2.63158; 0.00000 1.23625 0.00000 -38.93562; 0.00000 0.00000 1.00000 -2.63158; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 35 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.624 (thresh=-3.6) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 32 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 1.03694 0.00000 0.03272 -10.94883; 0.00000 1.28261 0.00000 -41.11910; -0.03395 0.00000 0.99946 1.82004; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 32 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.505, old_max_log_p =-3.534 (thresh=-3.5) 1.03379 0.01049 0.00809 -9.19070; -0.00869 1.28704 0.00797 -40.93967; -0.00832 -0.01033 0.99642 -0.34468; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 30 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.505 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 29 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.488 (thresh=-3.5) 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.488 (old=-3.918) transform before final EM align: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 885440 FSRUNTIME@ mri_em_register 0.2033 hours 1 threads registration took 12 minutes and 12 seconds. @#@FSTIME 2020:07:27:13:26:55 mri_em_register N 7 e 731.76 S 0.62 U 731.23 P 100% M 613592 F 0 R 112486 W 0 c 1820 w 91 I 0 O 0 L 16.11 15.29 13.46 @#@FSLOADPOST 2020:07:27:13:39:07 mri_em_register N 7 10.07 11.73 12.73 #-------------------------------------- #@# CA Normalize Mon Jul 27 13:39:08 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.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 '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (58, 73, 27) --> (196, 170, 189) finding center of left hemi white matter using (104, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (87,93,88) --> (120, 116,127) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 5.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.03016 0.01046 0.00806 -8.71297; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22073; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 133 of 656 (20.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 395 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 15 (0.0%) samples deleted using 1091 total control points for intensity normalization... bias field = 0.959 +- 0.058 1 of 958 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 823 (1.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 533 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 64 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 53 (3.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 27 of 79 (34.2%) samples deleted using 1552 total control points for intensity normalization... bias field = 1.009 +- 0.066 3 of 1469 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 72, 29) --> (193, 164, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 824 (1.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 72, 29) --> (131, 165, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 626 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (131, 136, 51) --> (177, 172, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 84 (53.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 136, 49) --> (129, 172, 107) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 77 (32.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 133, 87) --> (146, 186, 118) Brain_Stem: limiting intensities to 88.0 --> 132.0 86 of 139 (61.9%) samples deleted using 1750 total control points for intensity normalization... bias field = 1.002 +- 0.054 1 of 1545 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 19 seconds. @#@FSTIME 2020:07:27:13:39:09 mri_ca_normalize N 8 e 79.12 S 0.42 U 78.69 P 99% M 928988 F 0 R 125578 W 0 c 89 w 60 I 0 O 0 L 10.07 11.73 12.73 @#@FSLOADPOST 2020:07:27:13:40:28 mri_ca_normalize N 8 10.02 11.32 12.50 #-------------------------------------- #@# CA Reg Mon Jul 27 13:40:29 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.935117 #FOTS# QuadFit found better minimum quadopt=(dt=246.905,rms=0.794434) vs oldopt=(dt=92.48,rms=0.845465) #GCMRL# 0 dt 246.904762 rms 0.794 15.044% neg 0 invalid 762 tFOTS 15.6710 tGradient 6.8840 tsec 23.6900 #FOTS# QuadFit found better minimum quadopt=(dt=209.836,rms=0.765228) vs oldopt=(dt=92.48,rms=0.774396) #GCMRL# 1 dt 209.836066 rms 0.765 3.676% neg 0 invalid 762 tFOTS 16.7230 tGradient 6.6720 tsec 24.5300 #FOTS# QuadFit found better minimum quadopt=(dt=229.859,rms=0.750881) vs oldopt=(dt=92.48,rms=0.755764) #GCMRL# 2 dt 229.859155 rms 0.751 1.875% neg 0 invalid 762 tFOTS 16.6820 tGradient 6.7780 tsec 24.5960 #FOTS# QuadFit found better minimum quadopt=(dt=129.506,rms=0.74519) vs oldopt=(dt=92.48,rms=0.745844) #GCMRL# 3 dt 129.505882 rms 0.745 0.758% neg 0 invalid 762 tFOTS 16.6860 tGradient 6.7870 tsec 24.6090 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.734166) vs oldopt=(dt=369.92,rms=0.736011) #GCMRL# 4 dt 517.888000 rms 0.734 1.479% neg 0 invalid 762 tFOTS 16.7160 tGradient 6.7490 tsec 24.6020 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.7319) vs oldopt=(dt=92.48,rms=0.731939) #GCMRL# 5 dt 110.976000 rms 0.732 0.309% neg 0 invalid 762 tFOTS 17.6880 tGradient 6.7860 tsec 25.6120 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.716292) vs oldopt=(dt=1479.68,rms=0.718156) #GCMRL# 6 dt 2071.552000 rms 0.716 2.132% neg 0 invalid 762 tFOTS 16.6960 tGradient 6.7790 tsec 24.6140 #GCMRL# 7 dt 92.480000 rms 0.713 0.459% neg 0 invalid 762 tFOTS 16.6940 tGradient 7.0070 tsec 24.8360 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.712379) vs oldopt=(dt=369.92,rms=0.712527) #GCMRL# 8 dt 221.952000 rms 0.712 0.000% neg 0 invalid 762 tFOTS 16.7060 tGradient 6.6870 tsec 24.5560 #GCMRL# 9 dt 221.952000 rms 0.711 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7350 tsec 7.8740 #GCMRL# 10 dt 221.952000 rms 0.710 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6610 tsec 7.7980 #GCMRL# 11 dt 221.952000 rms 0.710 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6690 tsec 7.8090 #GCMRL# 12 dt 221.952000 rms 0.708 0.284% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6960 tsec 7.8110 #GCMRL# 13 dt 221.952000 rms 0.706 0.288% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5390 tsec 7.6570 #GCMRL# 14 dt 221.952000 rms 0.704 0.260% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6030 tsec 7.7190 #GCMRL# 15 dt 221.952000 rms 0.702 0.307% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5560 tsec 7.6740 #GCMRL# 16 dt 221.952000 rms 0.699 0.343% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6010 tsec 7.7350 #GCMRL# 17 dt 221.952000 rms 0.697 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5830 tsec 7.7140 #GCMRL# 18 dt 221.952000 rms 0.696 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6480 tsec 7.7790 #GCMRL# 19 dt 221.952000 rms 0.695 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5840 tsec 7.7140 #GCMRL# 20 dt 221.952000 rms 0.693 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5820 tsec 7.7100 #GCMRL# 21 dt 221.952000 rms 0.693 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4960 tsec 7.6120 #GCMRL# 22 dt 221.952000 rms 0.692 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4980 tsec 7.6160 #GCMRL# 23 dt 221.952000 rms 0.691 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5320 tsec 7.6480 #GCMRL# 24 dt 221.952000 rms 0.690 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4980 tsec 7.6160 #GCMRL# 25 dt 221.952000 rms 0.690 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5010 tsec 7.6450 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.689488) vs oldopt=(dt=369.92,rms=0.68951) #GCMRL# 26 dt 295.936000 rms 0.689 0.066% neg 0 invalid 762 tFOTS 17.3270 tGradient 6.4940 tsec 24.9360 #GCAMreg# pass 0 level1 5 level2 1 tsec 408.195 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.689936 #GCMRL# 28 dt 92.480000 rms 0.689 0.112% neg 0 invalid 762 tFOTS 16.3820 tGradient 6.4960 tsec 23.9920 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.688749) vs oldopt=(dt=369.92,rms=0.688806) #GCMRL# 29 dt 295.936000 rms 0.689 0.000% neg 0 invalid 762 tFOTS 17.3590 tGradient 6.5260 tsec 25.0290 #GCMRL# 30 dt 295.936000 rms 0.688 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4950 tsec 7.6470 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.706108 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704881) vs oldopt=(dt=25.92,rms=0.704889) #GCMRL# 32 dt 31.104000 rms 0.705 0.174% neg 0 invalid 762 tFOTS 16.3500 tGradient 5.1010 tsec 22.5650 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.704506) vs oldopt=(dt=25.92,rms=0.704515) #GCMRL# 33 dt 31.104000 rms 0.705 0.000% neg 0 invalid 762 tFOTS 15.3990 tGradient 5.1310 tsec 21.6860 #GCMRL# 34 dt 31.104000 rms 0.704 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1580 tsec 6.2740 #GCMRL# 35 dt 31.104000 rms 0.704 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1300 tsec 6.2460 #GCAMreg# pass 0 level1 4 level2 1 tsec 67.528 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.704365 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.70353) vs oldopt=(dt=25.92,rms=0.703568) #GCMRL# 37 dt 36.288000 rms 0.704 0.119% neg 0 invalid 762 tFOTS 17.3310 tGradient 5.1060 tsec 23.5520 #FOTS# QuadFit found better minimum quadopt=(dt=15.552,rms=0.703504) vs oldopt=(dt=25.92,rms=0.703509) #GCMRL# 38 dt 15.552000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 17.3100 tGradient 5.1290 tsec 23.5840 #GCMRL# 39 dt 15.552000 rms 0.703 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1480 tsec 6.2690 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.73685 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.735541) vs oldopt=(dt=8,rms=0.735619) #GCMRL# 41 dt 6.400000 rms 0.736 0.178% neg 0 invalid 762 tFOTS 16.3680 tGradient 4.3270 tsec 21.8090 #FOTS# QuadFit found better minimum quadopt=(dt=2.4,rms=0.735475) vs oldopt=(dt=2,rms=0.735476) #GCMRL# 42 dt 2.400000 rms 0.735 0.000% neg 0 invalid 762 tFOTS 16.6820 tGradient 4.3870 tsec 22.2390 #GCAMreg# pass 0 level1 3 level2 1 tsec 55.229 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.73596 #GCMRL# 44 dt 0.000000 rms 0.735 0.067% neg 0 invalid 762 tFOTS 15.7130 tGradient 4.5200 tsec 21.3760 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.817881 #FOTS# QuadFit found better minimum quadopt=(dt=3.31099,rms=0.806528) vs oldopt=(dt=2.88,rms=0.806715) #GCMRL# 46 dt 3.310987 rms 0.807 1.388% neg 0 invalid 762 tFOTS 15.7070 tGradient 4.1680 tsec 21.0140 #FOTS# QuadFit found better minimum quadopt=(dt=1.93269,rms=0.804898) vs oldopt=(dt=2.88,rms=0.805279) #GCMRL# 47 dt 1.932692 rms 0.805 0.000% neg 0 invalid 762 tFOTS 15.6930 tGradient 4.1670 tsec 21.0240 #GCMRL# 48 dt 1.932692 rms 0.803 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1980 tsec 5.3430 #GCMRL# 49 dt 1.932692 rms 0.803 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1330 tsec 5.2700 #GCMRL# 50 dt 1.932692 rms 0.803 -0.411% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0750 tsec 6.2930 #GCAMreg# pass 0 level1 2 level2 1 tsec 85.466 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.803105 #GCMRL# 52 dt 0.000000 rms 0.803 0.068% neg 0 invalid 762 tFOTS 14.7190 tGradient 4.0740 tsec 19.9290 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.877757 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877204) vs oldopt=(dt=0.08,rms=0.877207) #GCMRL# 54 dt 0.064000 rms 0.877 0.063% neg 0 invalid 762 tFOTS 15.7080 tGradient 3.8400 tsec 20.6840 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.877178) vs oldopt=(dt=0.08,rms=0.877183) #GCMRL# 55 dt 0.064000 rms 0.877 0.000% neg 0 invalid 762 tFOTS 15.6990 tGradient 3.8400 tsec 20.7010 #GCMRL# 56 dt 0.064000 rms 0.877 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8390 tsec 4.9820 #GCMRL# 57 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8440 tsec 4.9810 #GCMRL# 58 dt 0.064000 rms 0.877 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8400 tsec 4.9810 #GCMRL# 59 dt 0.064000 rms 0.877 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7440 tsec 4.8810 #GCMRL# 60 dt 0.064000 rms 0.876 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7490 tsec 4.8870 #GCMRL# 61 dt 0.064000 rms 0.875 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8080 tsec 4.9460 #GCMRL# 62 dt 0.064000 rms 0.874 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8380 tsec 4.9820 #GCMRL# 63 dt 0.064000 rms 0.872 0.191% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8430 tsec 4.9800 #GCMRL# 64 dt 0.064000 rms 0.871 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8400 tsec 4.9790 #GCMRL# 65 dt 0.064000 rms 0.869 0.179% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8360 tsec 4.9730 #GCMRL# 66 dt 0.064000 rms 0.868 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8380 tsec 4.9790 #GCMRL# 67 dt 0.064000 rms 0.867 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8350 tsec 4.9730 #GCMRL# 68 dt 0.064000 rms 0.866 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8390 tsec 4.9780 #GCMRL# 69 dt 0.064000 rms 0.865 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8370 tsec 5.0050 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.862601) vs oldopt=(dt=1.28,rms=0.862653) #GCMRL# 70 dt 1.536000 rms 0.863 0.268% neg 0 invalid 762 tFOTS 15.7200 tGradient 3.8390 tsec 20.6980 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.861829) vs oldopt=(dt=0.32,rms=0.862083) #GCMRL# 71 dt 0.192000 rms 0.862 0.000% neg 0 invalid 762 tFOTS 15.7230 tGradient 3.8680 tsec 20.7580 #GCMRL# 72 dt 0.192000 rms 0.861 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9650 tsec 5.1030 #GCMRL# 73 dt 0.192000 rms 0.860 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9350 tsec 5.0730 #GCMRL# 74 dt 0.192000 rms 0.860 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9310 tsec 5.0700 #GCMRL# 75 dt 0.192000 rms 0.859 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9000 tsec 5.0690 #GCAMreg# pass 0 level1 1 level2 1 tsec 197.033 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.859744 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.858997) vs oldopt=(dt=0.32,rms=0.859029) #GCMRL# 77 dt 0.192000 rms 0.859 0.087% neg 0 invalid 762 tFOTS 15.7000 tGradient 3.9340 tsec 20.7700 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.858993) vs oldopt=(dt=0.02,rms=0.858993) #GCMRL# 78 dt 0.028000 rms 0.859 0.000% neg 0 invalid 762 tFOTS 15.6910 tGradient 3.9010 tsec 20.7600 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.798691 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.792197) vs oldopt=(dt=0.32,rms=0.792517) #GCMRL# 80 dt 0.256000 rms 0.792 0.813% neg 0 invalid 762 tFOTS 15.7100 tGradient 3.2820 tsec 20.1300 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.791804) vs oldopt=(dt=0.02,rms=0.791836) #GCMRL# 81 dt 0.028000 rms 0.792 0.000% neg 0 invalid 762 tFOTS 15.7660 tGradient 3.2850 tsec 20.2170 #GCAMreg# pass 0 level1 0 level2 1 tsec 50.3 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.792455 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.791733) vs oldopt=(dt=0.02,rms=0.79174) #GCMRL# 83 dt 0.016000 rms 0.792 0.091% neg 0 invalid 762 tFOTS 15.7280 tGradient 3.2020 tsec 20.0700 GCAMregister done in 19.7358 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.02912 ( 6) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, overlap=0.766) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (589 voxels, peak = 18), gca=18.5 gca peak = 0.17690 (16) mri peak = 0.06897 (30) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, overlap=0.426) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (282 voxels, peak = 23), gca=23.4 gca peak = 0.28275 (96) mri peak = 0.06787 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, overlap=0.966) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (581 voxels, peak = 93), gca=92.6 gca peak = 0.18948 (93) mri peak = 0.06458 (96) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, overlap=1.008) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (637 voxels, peak = 92), gca=91.6 gca peak = 0.20755 (55) mri peak = 0.11697 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (829 voxels, peak = 55), gca=55.0 gca peak = 0.31831 (58) mri peak = 0.08625 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (694 voxels, peak = 55), gca=54.8 gca peak = 0.11957 (102) mri peak = 0.06876 (109) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (47040 voxels, peak = 110), gca=109.7 gca peak = 0.11429 (102) mri peak = 0.06805 (111) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, overlap=0.521) Left_Cerebral_White_Matter (2): linear fit = 1.09 x + 0.0 (46759 voxels, peak = 111), gca=110.7 gca peak = 0.14521 (59) mri peak = 0.03738 (55) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, overlap=0.966) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16350 voxels, peak = 54), gca=54.0 gca peak = 0.14336 (58) mri peak = 0.04502 (53) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, overlap=0.848) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (17402 voxels, peak = 52), gca=51.9 gca peak = 0.13305 (70) mri peak = 0.08346 (76) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, overlap=0.651) Right_Caudate (50): linear fit = 1.11 x + 0.0 (786 voxels, peak = 77), gca=77.3 gca peak = 0.15761 (71) mri peak = 0.06809 (83) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, overlap=0.571) Left_Caudate (11): linear fit = 1.09 x + 0.0 (741 voxels, peak = 77), gca=77.0 gca peak = 0.13537 (57) mri peak = 0.03402 (55) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, overlap=0.918) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24516 voxels, peak = 55), gca=55.0 gca peak = 0.13487 (56) mri peak = 0.03585 (51) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23738 voxels, peak = 54), gca=54.0 gca peak = 0.19040 (84) mri peak = 0.06228 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, overlap=0.746) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7587 voxels, peak = 87), gca=86.9 gca peak = 0.18871 (83) mri peak = 0.08367 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6439 voxels, peak = 86), gca=85.9 gca peak = 0.24248 (57) mri peak = 0.13222 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, overlap=0.798) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (401 voxels, peak = 51), gca=51.0 gca peak = 0.35833 (56) mri peak = 0.11187 (55) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, overlap=0.978) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (403 voxels, peak = 54), gca=54.0 gca peak = 0.12897 (85) mri peak = 0.05445 (88) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, overlap=0.975) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (4850 voxels, peak = 83), gca=82.9 gca peak = 0.13127 (83) mri peak = 0.05455 (82) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, overlap=0.920) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3673 voxels, peak = 86), gca=85.9 gca peak = 0.12974 (78) mri peak = 0.06301 (81) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, overlap=0.985) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1963 voxels, peak = 82), gca=81.5 gca peak = 0.17796 (79) mri peak = 0.07260 (81) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, overlap=0.934) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1897 voxels, peak = 82), gca=81.8 gca peak = 0.10999 (80) mri peak = 0.09164 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9273 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.05790 (86) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, overlap=0.730) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (639 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.05402 (89) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, overlap=0.853) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (986 voxels, peak = 97), gca=96.6 gca peak = 0.20775 (25) mri peak = 0.03183 (12) gca peak = 0.13297 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.08 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 3.85122 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.848745 #FOTS# QuadFit found better minimum quadopt=(dt=182.491,rms=0.80955) vs oldopt=(dt=92.48,rms=0.818919) #GCMRL# 85 dt 182.490818 rms 0.810 4.618% neg 0 invalid 762 tFOTS 18.6440 tGradient 6.6730 tsec 26.6690 #FOTS# QuadFit found better minimum quadopt=(dt=175.23,rms=0.798144) vs oldopt=(dt=92.48,rms=0.801288) #GCMRL# 86 dt 175.229947 rms 0.798 1.409% neg 0 invalid 762 tFOTS 19.5730 tGradient 7.1540 tsec 28.0940 #FOTS# QuadFit found better minimum quadopt=(dt=176.792,rms=0.790975) vs oldopt=(dt=92.48,rms=0.79302) #GCMRL# 87 dt 176.792079 rms 0.791 0.898% neg 0 invalid 762 tFOTS 19.4560 tGradient 7.2010 tsec 28.0230 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.787162) vs oldopt=(dt=92.48,rms=0.787957) #GCMRL# 88 dt 129.472000 rms 0.787 0.482% neg 0 invalid 762 tFOTS 18.2960 tGradient 7.0320 tsec 26.6940 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.779255) vs oldopt=(dt=369.92,rms=0.780123) #GCMRL# 89 dt 517.888000 rms 0.779 1.005% neg 0 invalid 762 tFOTS 19.3440 tGradient 7.2060 tsec 27.9090 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.775457) vs oldopt=(dt=92.48,rms=0.775669) #GCMRL# 90 dt 129.472000 rms 0.775 0.487% neg 0 invalid 762 tFOTS 19.3180 tGradient 7.0260 tsec 27.8270 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.772686) vs oldopt=(dt=369.92,rms=0.773004) #GCMRL# 91 dt 295.936000 rms 0.773 0.357% neg 0 invalid 762 tFOTS 17.1140 tGradient 7.4320 tsec 25.6620 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.770251) vs oldopt=(dt=92.48,rms=0.77046) #GCMRL# 92 dt 129.472000 rms 0.770 0.315% neg 0 invalid 762 tFOTS 17.3220 tGradient 6.3200 tsec 24.7710 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.768064) vs oldopt=(dt=369.92,rms=0.768174) #GCMRL# 93 dt 295.936000 rms 0.768 0.284% neg 0 invalid 762 tFOTS 16.4730 tGradient 6.5250 tsec 24.1240 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.766199) vs oldopt=(dt=92.48,rms=0.766423) #GCMRL# 94 dt 129.472000 rms 0.766 0.243% neg 0 invalid 762 tFOTS 16.4830 tGradient 6.5330 tsec 24.1550 #GCMRL# 95 dt 369.920000 rms 0.764 0.240% neg 0 invalid 762 tFOTS 19.9160 tGradient 6.9790 tsec 28.2570 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.762431) vs oldopt=(dt=92.48,rms=0.762576) #GCMRL# 96 dt 129.472000 rms 0.762 0.253% neg 0 invalid 762 tFOTS 19.2700 tGradient 7.1490 tsec 27.5880 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.761167) vs oldopt=(dt=369.92,rms=0.761516) #GCMRL# 97 dt 221.952000 rms 0.761 0.166% neg 0 invalid 762 tFOTS 16.7470 tGradient 6.6070 tsec 24.4830 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.760028) vs oldopt=(dt=92.48,rms=0.760234) #GCMRL# 98 dt 129.472000 rms 0.760 0.150% neg 0 invalid 762 tFOTS 16.5720 tGradient 6.5540 tsec 24.2560 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.758301) vs oldopt=(dt=369.92,rms=0.758399) #GCMRL# 99 dt 517.888000 rms 0.758 0.227% neg 0 invalid 762 tFOTS 16.5300 tGradient 6.5200 tsec 24.1760 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.75648) vs oldopt=(dt=92.48,rms=0.756592) #GCMRL# 100 dt 129.472000 rms 0.756 0.240% neg 0 invalid 762 tFOTS 17.4980 tGradient 6.5150 tsec 25.1430 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.755734) vs oldopt=(dt=92.48,rms=0.755844) #GCMRL# 101 dt 129.472000 rms 0.756 0.099% neg 0 invalid 762 tFOTS 16.4770 tGradient 6.5160 tsec 24.1160 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.753709) vs oldopt=(dt=369.92,rms=0.754086) #GCMRL# 102 dt 517.888000 rms 0.754 0.268% neg 0 invalid 762 tFOTS 16.4530 tGradient 6.5410 tsec 24.1240 #GCMRL# 103 dt 92.480000 rms 0.753 0.116% neg 0 invalid 762 tFOTS 16.4400 tGradient 6.5040 tsec 24.0640 #FOTS# QuadFit found better minimum quadopt=(dt=4734.98,rms=0.742561) vs oldopt=(dt=5918.72,rms=0.743082) #GCMRL# 104 dt 4734.976000 rms 0.743 1.365% neg 0 invalid 762 tFOTS 17.4090 tGradient 6.6040 tsec 25.1310 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.740244) vs oldopt=(dt=92.48,rms=0.740309) #GCMRL# 105 dt 73.984000 rms 0.740 0.312% neg 0 invalid 762 tFOTS 16.4010 tGradient 6.4630 tsec 23.9810 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.740078) vs oldopt=(dt=92.48,rms=0.740106) #GCMRL# 106 dt 129.472000 rms 0.740 0.000% neg 0 invalid 762 tFOTS 16.3650 tGradient 6.5920 tsec 24.1000 #GCMRL# 107 dt 129.472000 rms 0.740 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4920 tsec 7.6070 #GCMRL# 108 dt 129.472000 rms 0.739 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4980 tsec 7.6180 #GCMRL# 109 dt 129.472000 rms 0.739 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5240 tsec 7.6830 #GCMRL# 110 dt 129.472000 rms 0.738 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5500 tsec 7.7080 #GCMRL# 111 dt 129.472000 rms 0.737 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0080 tsec 8.2550 #GCMRL# 112 dt 129.472000 rms 0.736 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1150 tsec 8.3310 #GCMRL# 113 dt 129.472000 rms 0.735 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5150 tsec 7.6300 #GCMRL# 114 dt 129.472000 rms 0.734 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5450 tsec 7.6630 #GCMRL# 115 dt 129.472000 rms 0.733 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5710 tsec 7.6840 #GCMRL# 116 dt 129.472000 rms 0.732 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5420 tsec 7.6540 #GCMRL# 117 dt 129.472000 rms 0.731 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4810 tsec 7.5890 #GCMRL# 118 dt 129.472000 rms 0.731 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6790 tsec 7.7890 #GCMRL# 119 dt 129.472000 rms 0.730 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5460 tsec 7.6700 #GCMRL# 120 dt 129.472000 rms 0.729 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1930 tsec 8.3490 #GCMRL# 121 dt 129.472000 rms 0.728 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9170 tsec 8.1260 #GCMRL# 122 dt 129.472000 rms 0.727 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7130 tsec 8.9340 #GCMRL# 123 dt 129.472000 rms 0.726 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7150 tsec 7.8620 #GCMRL# 124 dt 129.472000 rms 0.726 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1850 tsec 8.3940 #GCMRL# 125 dt 129.472000 rms 0.725 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.2250 tsec 11.7950 #GCMRL# 126 dt 129.472000 rms 0.724 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1610 tsec 9.8410 #GCMRL# 127 dt 129.472000 rms 0.724 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3150 tsec 8.4770 #GCMRL# 128 dt 129.472000 rms 0.723 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9240 tsec 10.6830 #GCMRL# 129 dt 129.472000 rms 0.723 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.2270 tsec 11.9770 #GCMRL# 130 dt 129.472000 rms 0.722 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.6700 tsec 12.6340 #GCMRL# 131 dt 129.472000 rms 0.721 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1950 tsec 14.1470 #GCMRL# 132 dt 129.472000 rms 0.721 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0270 tsec 13.9580 #GCMRL# 133 dt 129.472000 rms 0.720 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1280 tsec 14.0620 #GCMRL# 134 dt 129.472000 rms 0.720 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1660 tsec 14.1060 #GCMRL# 135 dt 129.472000 rms 0.719 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0940 tsec 14.0570 #GCMRL# 136 dt 129.472000 rms 0.719 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1470 tsec 14.0830 #GCMRL# 137 dt 129.472000 rms 0.718 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0450 tsec 13.9650 #GCMRL# 138 dt 129.472000 rms 0.718 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.1760 tsec 11.9250 #GCMRL# 139 dt 129.472000 rms 0.718 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0200 tsec 13.9600 #GCMRL# 140 dt 129.472000 rms 0.717 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0040 tsec 13.9340 #GCMRL# 141 dt 129.472000 rms 0.717 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.4200 tsec 13.2950 #GCMRL# 142 dt 129.472000 rms 0.716 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0310 tsec 13.9610 #GCMRL# 143 dt 129.472000 rms 0.716 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0230 tsec 13.9520 #GCMRL# 144 dt 129.472000 rms 0.715 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0790 tsec 14.0140 #GCMRL# 145 dt 129.472000 rms 0.715 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0680 tsec 14.0150 #GCMRL# 146 dt 129.472000 rms 0.715 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1410 tsec 14.0720 #GCMRL# 147 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8890 tsec 11.6140 #GCMRL# 148 dt 129.472000 rms 0.714 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8170 tsec 11.2350 #GCMRL# 149 dt 129.472000 rms 0.714 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.4580 tsec 12.0370 #GCMRL# 150 dt 129.472000 rms 0.713 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.8200 tsec 12.7540 #GCMRL# 151 dt 129.472000 rms 0.713 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8070 tsec 11.1950 #GCMRL# 152 dt 129.472000 rms 0.713 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8990 tsec 11.7240 #GCMRL# 153 dt 129.472000 rms 0.712 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3020 tsec 12.0420 #GCMRL# 154 dt 129.472000 rms 0.712 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.0320 tsec 12.9320 #GCMRL# 155 dt 129.472000 rms 0.712 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.9650 tsec 13.8730 #GCMRL# 156 dt 129.472000 rms 0.712 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.8330 tsec 13.7750 #GCMRL# 157 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1280 tsec 14.0590 #GCMRL# 158 dt 129.472000 rms 0.711 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0820 tsec 14.0220 #GCMRL# 159 dt 129.472000 rms 0.711 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.5390 tsec 13.3900 #GCMRL# 160 dt 129.472000 rms 0.710 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.1030 tsec 12.9480 #GCMRL# 161 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.8320 tsec 13.7950 #GCMRL# 162 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1180 tsec 14.0810 #GCMRL# 163 dt 129.472000 rms 0.710 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.2590 tsec 13.2310 #GCMRL# 164 dt 129.472000 rms 0.710 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.2320 tsec 14.1860 #GCMRL# 165 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1390 tsec 14.0960 #GCMRL# 166 dt 129.472000 rms 0.709 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.9140 tsec 13.7510 #GCMRL# 167 dt 129.472000 rms 0.709 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.6070 tsec 13.4470 #GCMRL# 168 dt 129.472000 rms 0.709 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.6000 tsec 13.4370 #GCMRL# 169 dt 129.472000 rms 0.709 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.7750 tsec 13.6370 #GCMRL# 170 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.8320 tsec 13.7000 #GCMRL# 171 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.7010 tsec 13.5930 #GCMRL# 172 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1870 tsec 14.1610 #GCMRL# 173 dt 129.472000 rms 0.708 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1970 tsec 14.1460 #GCMRL# 174 dt 129.472000 rms 0.708 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.5600 tsec 13.4280 #GCMRL# 175 dt 129.472000 rms 0.707 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.0960 tsec 12.9740 #GCMRL# 176 dt 129.472000 rms 0.707 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.2020 tsec 13.0910 #GCMRL# 177 dt 129.472000 rms 0.707 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.2120 tsec 13.0660 #GCMRL# 178 dt 129.472000 rms 0.707 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.1610 tsec 12.9420 #GCMRL# 179 dt 5918.720000 rms 0.706 0.071% neg 0 invalid 762 tFOTS 29.7850 tGradient 12.0780 tsec 43.8240 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.70616) vs oldopt=(dt=92.48,rms=0.706165) #GCMRL# 180 dt 73.984000 rms 0.706 0.000% neg 0 invalid 762 tFOTS 28.6610 tGradient 12.1160 tsec 42.7930 #GCMRL# 181 dt 73.984000 rms 0.706 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0090 tsec 13.9570 #GCMRL# 182 dt 73.984000 rms 0.706 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.7320 tsec 12.5700 #GCAMreg# pass 0 level1 5 level2 1 tsec 1546.76 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.706908 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.705379) vs oldopt=(dt=92.48,rms=0.705528) #GCMRL# 184 dt 129.472000 rms 0.705 0.216% neg 0 invalid 762 tFOTS 25.1050 tGradient 9.0870 tsec 36.0650 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.704347) vs oldopt=(dt=369.92,rms=0.704522) #GCMRL# 185 dt 517.888000 rms 0.704 0.146% neg 0 invalid 762 tFOTS 24.9830 tGradient 9.3960 tsec 36.2770 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.704176) vs oldopt=(dt=92.48,rms=0.704194) #GCMRL# 186 dt 129.472000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 22.2950 tGradient 11.8610 tsec 36.0270 #GCMRL# 187 dt 129.472000 rms 0.704 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.0670 tsec 11.8370 #GCMRL# 188 dt 129.472000 rms 0.704 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.9710 tsec 12.6550 #GCMRL# 189 dt 129.472000 rms 0.704 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4500 tsec 10.0880 #GCMRL# 190 dt 129.472000 rms 0.704 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3980 tsec 9.7580 #GCMRL# 191 dt 129.472000 rms 0.703 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.6390 tsec 11.1270 #GCMRL# 192 dt 129.472000 rms 0.703 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.9170 tsec 13.7850 #GCMRL# 193 dt 129.472000 rms 0.703 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.6880 tsec 11.5130 #GCMRL# 194 dt 129.472000 rms 0.703 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.9500 tsec 12.2570 #GCMRL# 195 dt 129.472000 rms 0.703 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.8010 tsec 13.4480 #GCMRL# 196 dt 129.472000 rms 0.702 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3260 tsec 10.5230 #GCMRL# 197 dt 129.472000 rms 0.702 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1390 tsec 9.3630 #GCMRL# 198 dt 129.472000 rms 0.702 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0620 tsec 10.3790 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.70213) vs oldopt=(dt=369.92,rms=0.702135) #GCMRL# 199 dt 295.936000 rms 0.702 0.000% neg 0 invalid 762 tFOTS 24.9740 tGradient 9.5180 tsec 35.8470 #GCMRL# 200 dt 295.936000 rms 0.702 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.2600 tsec 10.0360 #GCMRL# 201 dt 295.936000 rms 0.702 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.2740 tsec 11.5830 #GCMRL# 202 dt 295.936000 rms 0.702 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4170 tsec 10.6160 #GCMRL# 203 dt 295.936000 rms 0.702 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.1530 tsec 12.0490 #GCMRL# 204 dt 295.936000 rms 0.702 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.5280 tsec 11.4590 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701437) vs oldopt=(dt=92.48,rms=0.701445) #GCMRL# 205 dt 129.472000 rms 0.701 0.019% neg 0 invalid 762 tFOTS 25.0060 tGradient 9.3330 tsec 36.1910 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.701443) vs oldopt=(dt=92.48,rms=0.701444) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.704686 #FOTS# QuadFit found better minimum quadopt=(dt=169.475,rms=0.699018) vs oldopt=(dt=103.68,rms=0.699625) #GCMRL# 207 dt 169.474860 rms 0.699 0.804% neg 0 invalid 762 tFOTS 25.7540 tGradient 8.4590 tsec 36.0430 #FOTS# QuadFit found better minimum quadopt=(dt=192,rms=0.689646) vs oldopt=(dt=103.68,rms=0.691455) #GCMRL# 208 dt 192.000000 rms 0.690 1.341% neg 0 invalid 762 tFOTS 26.2390 tGradient 7.0280 tsec 35.1800 #FOTS# QuadFit found better minimum quadopt=(dt=67.7333,rms=0.686057) vs oldopt=(dt=25.92,rms=0.686985) #GCMRL# 209 dt 67.733333 rms 0.686 0.520% neg 0 invalid 762 tFOTS 22.2870 tGradient 8.0060 tsec 31.9880 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.678544) vs oldopt=(dt=414.72,rms=0.678631) #GCMRL# 210 dt 331.776000 rms 0.679 1.095% neg 0 invalid 762 tFOTS 21.8360 tGradient 7.8160 tsec 31.5200 #FOTS# QuadFit found better minimum quadopt=(dt=61.9221,rms=0.674719) vs oldopt=(dt=25.92,rms=0.675676) #GCMRL# 211 dt 61.922078 rms 0.675 0.564% neg 0 invalid 762 tFOTS 24.2310 tGradient 8.9400 tsec 35.0280 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.671901) vs oldopt=(dt=103.68,rms=0.672143) #GCMRL# 212 dt 145.152000 rms 0.672 0.418% neg 0 invalid 762 tFOTS 21.4560 tGradient 7.3920 tsec 30.4580 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.670285) vs oldopt=(dt=25.92,rms=0.670597) #GCMRL# 213 dt 36.288000 rms 0.670 0.241% neg 0 invalid 762 tFOTS 21.3680 tGradient 5.7640 tsec 28.7790 #GCMRL# 214 dt 414.720000 rms 0.666 0.585% neg 0 invalid 762 tFOTS 18.2300 tGradient 6.5030 tsec 26.0710 #FOTS# QuadFit found better minimum quadopt=(dt=58.022,rms=0.662064) vs oldopt=(dt=25.92,rms=0.663079) #GCMRL# 215 dt 58.021978 rms 0.662 0.646% neg 0 invalid 762 tFOTS 21.2720 tGradient 5.4610 tsec 28.2280 #FOTS# QuadFit found better minimum quadopt=(dt=68.6829,rms=0.661125) vs oldopt=(dt=103.68,rms=0.661322) #GCMRL# 216 dt 68.682927 rms 0.661 0.142% neg 0 invalid 762 tFOTS 23.7750 tGradient 5.5020 tsec 30.4850 #GCMRL# 217 dt 103.680000 rms 0.660 0.206% neg 0 invalid 762 tFOTS 23.3480 tGradient 6.7040 tsec 31.5370 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.659053) vs oldopt=(dt=25.92,rms=0.659202) #GCMRL# 218 dt 36.288000 rms 0.659 0.108% neg 0 invalid 762 tFOTS 16.5300 tGradient 5.4700 tsec 23.2230 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.654714) vs oldopt=(dt=414.72,rms=0.65545) #GCMRL# 219 dt 580.608000 rms 0.655 0.658% neg 0 invalid 762 tFOTS 18.3530 tGradient 7.3510 tsec 27.0600 #FOTS# QuadFit found better minimum quadopt=(dt=67.6364,rms=0.652369) vs oldopt=(dt=25.92,rms=0.652822) #GCMRL# 220 dt 67.636364 rms 0.652 0.358% neg 0 invalid 762 tFOTS 18.2530 tGradient 5.6430 tsec 25.5860 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.651527) vs oldopt=(dt=25.92,rms=0.651666) #GCMRL# 221 dt 36.288000 rms 0.652 0.129% neg 0 invalid 762 tFOTS 16.3410 tGradient 6.0300 tsec 23.5470 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.648123) vs oldopt=(dt=414.72,rms=0.648688) #GCMRL# 222 dt 580.608000 rms 0.648 0.522% neg 0 invalid 762 tFOTS 16.8700 tGradient 5.3690 tsec 23.3760 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.646406) vs oldopt=(dt=25.92,rms=0.646678) #GCMRL# 223 dt 36.288000 rms 0.646 0.265% neg 0 invalid 762 tFOTS 19.2570 tGradient 5.3100 tsec 25.7380 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.645724) vs oldopt=(dt=103.68,rms=0.645835) #GCMRL# 224 dt 145.152000 rms 0.646 0.105% neg 0 invalid 762 tFOTS 17.8680 tGradient 5.8300 tsec 24.8640 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.64461) vs oldopt=(dt=103.68,rms=0.644727) #GCMRL# 225 dt 145.152000 rms 0.645 0.173% neg 0 invalid 762 tFOTS 16.4390 tGradient 5.4070 tsec 22.9800 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.644212) vs oldopt=(dt=25.92,rms=0.6443) #GCMRL# 226 dt 36.288000 rms 0.644 0.062% neg 0 invalid 762 tFOTS 16.6590 tGradient 5.6190 tsec 23.4470 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.643363) vs oldopt=(dt=414.72,rms=0.643531) #GCMRL# 227 dt 248.832000 rms 0.643 0.132% neg 0 invalid 762 tFOTS 16.6140 tGradient 5.2240 tsec 22.9320 #FOTS# QuadFit found better minimum quadopt=(dt=85.3333,rms=0.642294) vs oldopt=(dt=103.68,rms=0.642346) #GCMRL# 228 dt 85.333333 rms 0.642 0.166% neg 0 invalid 762 tFOTS 16.0280 tGradient 5.0750 tsec 22.1950 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.641898) vs oldopt=(dt=103.68,rms=0.641953) #GCMRL# 229 dt 82.944000 rms 0.642 0.062% neg 0 invalid 762 tFOTS 16.0210 tGradient 5.0670 tsec 22.1770 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.641285) vs oldopt=(dt=103.68,rms=0.641286) #GCMRL# 230 dt 124.416000 rms 0.641 0.095% neg 0 invalid 762 tFOTS 16.0160 tGradient 5.0000 tsec 22.1070 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.64088) vs oldopt=(dt=25.92,rms=0.640968) #GCMRL# 231 dt 36.288000 rms 0.641 0.063% neg 0 invalid 762 tFOTS 16.9050 tGradient 5.0370 tsec 23.0150 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.639431) vs oldopt=(dt=414.72,rms=0.639473) #GCMRL# 232 dt 497.664000 rms 0.639 0.226% neg 0 invalid 762 tFOTS 15.7040 tGradient 4.9140 tsec 21.6900 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.638071) vs oldopt=(dt=25.92,rms=0.638305) #GCMRL# 233 dt 36.288000 rms 0.638 0.213% neg 0 invalid 762 tFOTS 15.8190 tGradient 4.9070 tsec 21.8100 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.637494) vs oldopt=(dt=103.68,rms=0.637549) #GCMRL# 234 dt 145.152000 rms 0.637 0.090% neg 0 invalid 762 tFOTS 15.8380 tGradient 4.9580 tsec 21.8720 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.637132) vs oldopt=(dt=25.92,rms=0.637209) #GCMRL# 235 dt 36.288000 rms 0.637 0.057% neg 0 invalid 762 tFOTS 16.7250 tGradient 4.9200 tsec 22.7160 #GCMRL# 236 dt 414.720000 rms 0.636 0.165% neg 0 invalid 762 tFOTS 15.7290 tGradient 4.9370 tsec 21.7370 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.635115) vs oldopt=(dt=25.92,rms=0.635299) #GCMRL# 237 dt 36.288000 rms 0.635 0.152% neg 0 invalid 762 tFOTS 14.8740 tGradient 4.9720 tsec 20.9290 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.634581) vs oldopt=(dt=103.68,rms=0.63463) #GCMRL# 238 dt 145.152000 rms 0.635 0.084% neg 0 invalid 762 tFOTS 15.7590 tGradient 4.9790 tsec 21.8230 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.63422) vs oldopt=(dt=103.68,rms=0.634322) #GCMRL# 239 dt 62.208000 rms 0.634 0.057% neg 0 invalid 762 tFOTS 15.8880 tGradient 5.0710 tsec 22.0440 #GCMRL# 240 dt 414.720000 rms 0.633 0.151% neg 0 invalid 762 tFOTS 15.8790 tGradient 5.0710 tsec 22.0320 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.63243) vs oldopt=(dt=25.92,rms=0.63257) #GCMRL# 241 dt 36.288000 rms 0.632 0.131% neg 0 invalid 762 tFOTS 15.8800 tGradient 5.0710 tsec 22.0340 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.632065) vs oldopt=(dt=103.68,rms=0.632075) #GCMRL# 242 dt 124.416000 rms 0.632 0.058% neg 0 invalid 762 tFOTS 15.8880 tGradient 5.0540 tsec 22.0290 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631657) vs oldopt=(dt=103.68,rms=0.631671) #GCMRL# 243 dt 82.944000 rms 0.632 0.065% neg 0 invalid 762 tFOTS 15.8680 tGradient 5.0240 tsec 21.9750 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.631393) vs oldopt=(dt=103.68,rms=0.631399) #GCMRL# 244 dt 82.944000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 16.1210 tGradient 4.9950 tsec 22.4910 #GCMRL# 245 dt 82.944000 rms 0.631 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9980 tsec 6.1000 #GCMRL# 246 dt 82.944000 rms 0.631 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0270 tsec 6.1130 #GCMRL# 247 dt 82.944000 rms 0.630 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9080 tsec 5.9810 #GCMRL# 248 dt 82.944000 rms 0.629 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9230 tsec 6.0070 #GCMRL# 249 dt 82.944000 rms 0.628 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9030 tsec 5.9940 #GCMRL# 250 dt 82.944000 rms 0.627 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8770 tsec 5.9480 #GCMRL# 251 dt 82.944000 rms 0.625 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9190 tsec 5.9970 #GCMRL# 252 dt 82.944000 rms 0.624 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9440 tsec 6.0210 #GCMRL# 253 dt 82.944000 rms 0.623 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9650 tsec 6.0440 #GCMRL# 254 dt 82.944000 rms 0.622 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9490 tsec 6.0310 #GCMRL# 255 dt 82.944000 rms 0.621 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9700 tsec 6.0540 #GCMRL# 256 dt 82.944000 rms 0.620 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0000 tsec 6.0910 #GCMRL# 257 dt 82.944000 rms 0.619 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9390 tsec 6.0140 #GCMRL# 258 dt 82.944000 rms 0.618 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9230 tsec 5.9970 #GCMRL# 259 dt 82.944000 rms 0.617 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9360 tsec 6.0070 #GCMRL# 260 dt 82.944000 rms 0.616 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9350 tsec 6.0060 #GCMRL# 261 dt 82.944000 rms 0.615 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9390 tsec 6.0100 #GCMRL# 262 dt 82.944000 rms 0.614 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9360 tsec 6.0070 #GCMRL# 263 dt 82.944000 rms 0.614 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9320 tsec 6.0130 #GCMRL# 264 dt 82.944000 rms 0.613 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9330 tsec 6.0160 #GCMRL# 265 dt 82.944000 rms 0.612 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9690 tsec 6.0400 #GCMRL# 266 dt 82.944000 rms 0.612 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9090 tsec 5.9790 #GCMRL# 267 dt 82.944000 rms 0.612 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9150 tsec 6.3740 #GCMRL# 268 dt 20.736000 rms 0.612 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9650 tsec 7.1490 #GCMRL# 269 dt 5.184000 rms 0.612 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9150 tsec 7.1280 #FOTS# QuadFit found better minimum quadopt=(dt=0.567,rms=0.611569) vs oldopt=(dt=0.405,rms=0.611569) #GCMRL# 270 dt 0.567000 rms 0.612 0.000% neg 0 invalid 762 tFOTS 11.2330 tGradient 4.9670 tsec 17.3100 #GCMRL# 271 dt 0.141750 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9660 tsec 7.1810 #GCMRL# 272 dt 0.070875 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9640 tsec 6.8040 #GCAMreg# pass 0 level1 4 level2 1 tsec 1162 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.612649 #FOTS# QuadFit found better minimum quadopt=(dt=0.0354375,rms=0.611567) vs oldopt=(dt=0.0253125,rms=0.611568) #GCMRL# 274 dt 0.035437 rms 0.612 0.176% neg 0 invalid 762 tFOTS 9.3820 tGradient 4.9760 tsec 15.4420 #FOTS# QuadFit found better minimum quadopt=(dt=0.00885937,rms=0.611567) vs oldopt=(dt=0.00632812,rms=0.611567) #GCMRL# 275 dt 0.008859 rms 0.612 0.000% neg 0 invalid 762 tFOTS 8.4240 tGradient 4.9660 tsec 14.5000 #GCMRL# 276 dt 0.002215 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9680 tsec 7.1740 #GCMRL# 277 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9940 tsec 6.8440 #GCMRL# 278 dt 0.001107 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1340 tsec 6.2880 #GCMRL# 279 dt 0.000138 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7500 tsec 9.1060 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.625485 #FOTS# QuadFit found better minimum quadopt=(dt=87.0701,rms=0.614414) vs oldopt=(dt=128,rms=0.616497) #GCMRL# 281 dt 87.070059 rms 0.614 1.770% neg 0 invalid 762 tFOTS 18.2850 tGradient 4.9230 tsec 24.3500 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.610965) vs oldopt=(dt=8,rms=0.61191) #GCMRL# 282 dt 11.200000 rms 0.611 0.561% neg 0 invalid 762 tFOTS 14.3670 tGradient 4.3070 tsec 19.7820 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.608422) vs oldopt=(dt=8,rms=0.609126) #GCMRL# 283 dt 11.200000 rms 0.608 0.416% neg 0 invalid 762 tFOTS 14.3760 tGradient 4.3060 tsec 19.7930 #GCMRL# 284 dt 32.000000 rms 0.603 0.902% neg 0 invalid 762 tFOTS 15.3160 tGradient 4.3050 tsec 20.7290 #FOTS# QuadFit found better minimum quadopt=(dt=153.6,rms=0.588486) vs oldopt=(dt=128,rms=0.590481) #GCMRL# 285 dt 153.600000 rms 0.588 2.396% neg 0 invalid 762 tFOTS 16.2750 tGradient 4.3040 tsec 21.6870 #GCMRL# 286 dt 32.000000 rms 0.586 0.367% neg 0 invalid 762 tFOTS 15.3100 tGradient 4.3060 tsec 20.7240 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.584802) vs oldopt=(dt=32,rms=0.58511) #GCMRL# 287 dt 44.800000 rms 0.585 0.260% neg 0 invalid 762 tFOTS 15.3400 tGradient 4.2720 tsec 20.7180 #GCMRL# 288 dt 32.000000 rms 0.583 0.332% neg 0 invalid 762 tFOTS 15.3210 tGradient 4.3300 tsec 20.7580 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.581944) vs oldopt=(dt=32,rms=0.581955) #GCMRL# 289 dt 38.400000 rms 0.582 0.157% neg 0 invalid 762 tFOTS 15.3340 tGradient 4.4150 tsec 20.8580 #GCMRL# 290 dt 32.000000 rms 0.580 0.313% neg 0 invalid 762 tFOTS 15.2990 tGradient 4.3310 tsec 20.7410 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.579347) vs oldopt=(dt=32,rms=0.579356) #GCMRL# 291 dt 25.600000 rms 0.579 0.133% neg 0 invalid 762 tFOTS 15.3080 tGradient 4.2370 tsec 20.6530 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.577879) vs oldopt=(dt=32,rms=0.578021) #GCMRL# 292 dt 38.400000 rms 0.578 0.253% neg 0 invalid 762 tFOTS 15.3090 tGradient 4.3290 tsec 20.7520 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.577186) vs oldopt=(dt=32,rms=0.5772) #GCMRL# 293 dt 25.600000 rms 0.577 0.120% neg 0 invalid 762 tFOTS 15.3170 tGradient 4.3000 tsec 20.7240 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.575765) vs oldopt=(dt=32,rms=0.575998) #GCMRL# 294 dt 44.800000 rms 0.576 0.246% neg 0 invalid 762 tFOTS 15.3050 tGradient 4.3300 tsec 20.7450 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.575121) vs oldopt=(dt=32,rms=0.575172) #GCMRL# 295 dt 25.600000 rms 0.575 0.112% neg 0 invalid 762 tFOTS 15.3010 tGradient 4.2990 tsec 20.7080 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.573811) vs oldopt=(dt=32,rms=0.574018) #GCMRL# 296 dt 44.800000 rms 0.574 0.228% neg 0 invalid 762 tFOTS 15.3090 tGradient 4.3680 tsec 20.7880 #FOTS# QuadFit found better minimum quadopt=(dt=24.9449,rms=0.573318) vs oldopt=(dt=32,rms=0.573419) #GCMRL# 297 dt 24.944882 rms 0.573 0.086% neg 0 invalid 762 tFOTS 15.3000 tGradient 4.2370 tsec 20.6450 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.572173) vs oldopt=(dt=32,rms=0.572327) #GCMRL# 298 dt 44.800000 rms 0.572 0.200% neg 0 invalid 762 tFOTS 15.3530 tGradient 4.3280 tsec 20.7930 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.571704) vs oldopt=(dt=32,rms=0.571867) #GCMRL# 299 dt 19.200000 rms 0.572 0.082% neg 0 invalid 762 tFOTS 15.3150 tGradient 4.2700 tsec 20.6940 #GCMRL# 300 dt 128.000000 rms 0.569 0.411% neg 0 invalid 762 tFOTS 15.3100 tGradient 4.2350 tsec 20.6560 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.56885) vs oldopt=(dt=8,rms=0.56897) #GCMRL# 301 dt 11.200000 rms 0.569 0.089% neg 0 invalid 762 tFOTS 15.3260 tGradient 4.2480 tsec 20.6820 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.568437) vs oldopt=(dt=32,rms=0.568504) #GCMRL# 302 dt 19.200000 rms 0.568 0.073% neg 0 invalid 762 tFOTS 15.2980 tGradient 4.2420 tsec 20.6480 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.566753) vs oldopt=(dt=128,rms=0.566905) #GCMRL# 303 dt 179.200000 rms 0.567 0.296% neg 0 invalid 762 tFOTS 15.3400 tGradient 4.2050 tsec 20.6540 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.565599) vs oldopt=(dt=32,rms=0.565671) #GCMRL# 304 dt 25.600000 rms 0.566 0.204% neg 0 invalid 762 tFOTS 16.2680 tGradient 4.7830 tsec 22.1640 #GCMRL# 305 dt 32.000000 rms 0.565 0.151% neg 0 invalid 762 tFOTS 15.3030 tGradient 4.3360 tsec 20.7480 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.564467) vs oldopt=(dt=32,rms=0.564525) #GCMRL# 306 dt 19.200000 rms 0.564 0.000% neg 0 invalid 762 tFOTS 16.2650 tGradient 4.2640 tsec 21.6640 #GCMRL# 307 dt 19.200000 rms 0.564 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2700 tsec 5.3780 #GCMRL# 308 dt 19.200000 rms 0.564 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2040 tsec 5.3160 #GCMRL# 309 dt 19.200000 rms 0.563 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2020 tsec 5.3120 #GCMRL# 310 dt 19.200000 rms 0.562 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2020 tsec 5.3140 #GCMRL# 311 dt 19.200000 rms 0.562 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2060 tsec 5.3140 #GCMRL# 312 dt 19.200000 rms 0.561 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2020 tsec 5.3140 #GCMRL# 313 dt 19.200000 rms 0.560 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2050 tsec 5.3130 #GCMRL# 314 dt 19.200000 rms 0.559 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2420 tsec 5.3500 #GCMRL# 315 dt 19.200000 rms 0.558 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2660 tsec 5.3740 #GCMRL# 316 dt 19.200000 rms 0.558 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2040 tsec 5.7100 #GCMRL# 317 dt 19.200000 rms 0.557 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2340 tsec 5.3440 #GCMRL# 318 dt 19.200000 rms 0.557 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2040 tsec 5.3120 #GCMRL# 319 dt 19.200000 rms 0.557 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2090 tsec 5.3190 #GCMRL# 320 dt 9.600000 rms 0.557 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2380 tsec 6.1060 #GCMRL# 321 dt 1.200000 rms 0.557 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2050 tsec 6.8390 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.556586) vs oldopt=(dt=0.5,rms=0.556587) #GCMRL# 322 dt 0.700000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 12.4490 tGradient 4.2040 tsec 17.7890 #GCMRL# 323 dt 0.350000 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2060 tsec 6.0730 #GCMRL# 324 dt 0.087500 rms 0.557 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1090 tsec 6.3150 #GCAMreg# pass 0 level1 3 level2 1 tsec 667.8 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.557587 #FOTS# QuadFit found better minimum quadopt=(dt=56.5828,rms=0.55345) vs oldopt=(dt=32,rms=0.553854) #GCMRL# 326 dt 56.582781 rms 0.553 0.742% neg 0 invalid 762 tFOTS 14.9780 tGradient 4.1150 tsec 20.1820 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.552809) vs oldopt=(dt=8,rms=0.552932) #GCMRL# 327 dt 11.200000 rms 0.553 0.116% neg 0 invalid 762 tFOTS 17.8060 tGradient 4.2420 tsec 23.3340 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.552079) vs oldopt=(dt=32,rms=0.552132) #GCMRL# 328 dt 44.800000 rms 0.552 0.132% neg 0 invalid 762 tFOTS 17.7750 tGradient 4.6530 tsec 23.7650 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.551251) vs oldopt=(dt=32,rms=0.551272) #GCMRL# 329 dt 38.400000 rms 0.551 0.150% neg 0 invalid 762 tFOTS 17.7430 tGradient 4.6480 tsec 23.7330 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.551016) vs oldopt=(dt=8,rms=0.551061) #GCMRL# 330 dt 11.200000 rms 0.551 0.000% neg 0 invalid 762 tFOTS 17.7220 tGradient 4.5970 tsec 23.7050 #GCMRL# 331 dt 11.200000 rms 0.551 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6660 tsec 6.0050 #GCMRL# 332 dt 11.200000 rms 0.551 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5870 tsec 5.9220 #GCMRL# 333 dt 11.200000 rms 0.550 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6180 tsec 5.9590 #GCMRL# 334 dt 11.200000 rms 0.550 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5810 tsec 5.9050 #GCMRL# 335 dt 11.200000 rms 0.549 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6150 tsec 5.9600 #GCMRL# 336 dt 11.200000 rms 0.549 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6170 tsec 5.9590 #GCMRL# 337 dt 11.200000 rms 0.549 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6390 tsec 5.9630 #GCMRL# 338 dt 11.200000 rms 0.548 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6200 tsec 5.9600 #GCMRL# 339 dt 11.200000 rms 0.548 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6120 tsec 5.9390 #GCMRL# 340 dt 11.200000 rms 0.547 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6190 tsec 5.9580 #GCMRL# 341 dt 11.200000 rms 0.547 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6250 tsec 5.9620 #GCMRL# 342 dt 11.200000 rms 0.546 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6890 tsec 6.0510 #GCMRL# 343 dt 11.200000 rms 0.546 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6970 tsec 6.0510 #GCMRL# 344 dt 11.200000 rms 0.545 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6720 tsec 6.0130 #GCMRL# 345 dt 11.200000 rms 0.545 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6760 tsec 6.0190 #GCMRL# 346 dt 11.200000 rms 0.545 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6720 tsec 6.0150 #GCMRL# 347 dt 11.200000 rms 0.544 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6760 tsec 6.0170 #GCMRL# 348 dt 11.200000 rms 0.544 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6370 tsec 5.9670 #GCMRL# 349 dt 11.200000 rms 0.543 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6180 tsec 5.9550 #GCMRL# 350 dt 11.200000 rms 0.543 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6340 tsec 5.9740 #GCMRL# 351 dt 11.200000 rms 0.542 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6820 tsec 6.0160 #GCMRL# 352 dt 11.200000 rms 0.542 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7280 tsec 6.0680 #GCMRL# 353 dt 11.200000 rms 0.542 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6200 tsec 5.9600 #GCMRL# 354 dt 11.200000 rms 0.541 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6900 tsec 6.0670 #GCMRL# 355 dt 11.200000 rms 0.541 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9140 tsec 6.3110 #GCMRL# 356 dt 11.200000 rms 0.541 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9930 tsec 6.4200 #GCMRL# 357 dt 11.200000 rms 0.540 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9230 tsec 6.3540 #GCMRL# 358 dt 11.200000 rms 0.540 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0410 tsec 6.4710 #GCMRL# 359 dt 11.200000 rms 0.540 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9910 tsec 6.4280 #GCMRL# 360 dt 11.200000 rms 0.539 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0390 tsec 6.4770 #GCMRL# 361 dt 11.200000 rms 0.539 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0450 tsec 6.4810 #GCMRL# 362 dt 11.200000 rms 0.539 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0130 tsec 6.4410 #GCMRL# 363 dt 11.200000 rms 0.539 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0020 tsec 6.4370 #GCMRL# 364 dt 11.200000 rms 0.538 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0040 tsec 6.4300 #GCMRL# 365 dt 11.200000 rms 0.538 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0070 tsec 6.4390 #GCMRL# 366 dt 11.200000 rms 0.538 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9960 tsec 6.4130 #GCMRL# 367 dt 11.200000 rms 0.538 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9640 tsec 6.3730 #GCMRL# 368 dt 11.200000 rms 0.537 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9640 tsec 6.3540 #GCMRL# 369 dt 11.200000 rms 0.537 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8030 tsec 6.1680 #GCMRL# 370 dt 11.200000 rms 0.537 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7870 tsec 6.1480 #GCMRL# 371 dt 11.200000 rms 0.537 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7440 tsec 6.0900 #GCMRL# 372 dt 11.200000 rms 0.537 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7580 tsec 6.1120 #GCMRL# 373 dt 11.200000 rms 0.536 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6780 tsec 6.0260 #GCMRL# 374 dt 11.200000 rms 0.536 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6840 tsec 6.0250 #GCMRL# 375 dt 11.200000 rms 0.536 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6830 tsec 6.0280 #GCMRL# 376 dt 11.200000 rms 0.536 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6890 tsec 6.0400 #GCMRL# 377 dt 11.200000 rms 0.536 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6780 tsec 6.0240 #GCMRL# 378 dt 11.200000 rms 0.536 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6830 tsec 6.0300 #GCMRL# 379 dt 11.200000 rms 0.535 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6930 tsec 6.0370 #GCMRL# 380 dt 11.200000 rms 0.535 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6890 tsec 6.0380 #GCMRL# 381 dt 11.200000 rms 0.535 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6800 tsec 6.0220 #GCMRL# 382 dt 11.200000 rms 0.535 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6730 tsec 6.0230 #GCMRL# 383 dt 11.200000 rms 0.535 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6820 tsec 6.0260 #GCMRL# 384 dt 11.200000 rms 0.535 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6850 tsec 6.0300 #GCMRL# 385 dt 11.200000 rms 0.534 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6930 tsec 6.0370 #GCMRL# 386 dt 11.200000 rms 0.534 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6790 tsec 6.0230 #GCMRL# 387 dt 11.200000 rms 0.534 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6840 tsec 6.0310 #GCMRL# 388 dt 11.200000 rms 0.534 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6820 tsec 6.0280 #GCMRL# 389 dt 11.200000 rms 0.534 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6820 tsec 6.0260 #GCMRL# 390 dt 11.200000 rms 0.534 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6820 tsec 6.0240 #GCMRL# 391 dt 11.200000 rms 0.534 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6940 tsec 6.0360 #GCMRL# 392 dt 11.200000 rms 0.534 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6790 tsec 6.0680 #FOTS# QuadFit found better minimum quadopt=(dt=76.8,rms=0.533466) vs oldopt=(dt=128,rms=0.533478) #GCMRL# 393 dt 76.800000 rms 0.533 0.000% neg 0 invalid 762 tFOTS 17.9480 tGradient 4.6790 tsec 24.0240 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.564323 #GCMRL# 395 dt 0.000000 rms 0.563 0.169% neg 0 invalid 762 tFOTS 16.8130 tGradient 4.3420 tsec 22.4920 #GCMRL# 396 dt 0.150000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 16.6760 tGradient 4.3360 tsec 23.5790 #GCAMreg# pass 0 level1 2 level2 1 tsec 57.971 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.564323 #GCMRL# 398 dt 0.000000 rms 0.563 0.169% neg 0 invalid 762 tFOTS 15.0580 tGradient 3.7940 tsec 19.9400 #GCMRL# 399 dt 0.150000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 15.2110 tGradient 3.7950 tsec 21.1600 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.623015 #FOTS# QuadFit found better minimum quadopt=(dt=0.850794,rms=0.620011) vs oldopt=(dt=1.28,rms=0.620289) #GCMRL# 401 dt 0.850794 rms 0.620 0.482% neg 0 invalid 762 tFOTS 16.3070 tGradient 3.6480 tsec 21.2820 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.619967) vs oldopt=(dt=0.08,rms=0.619976) #GCMRL# 402 dt 0.112000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 16.6030 tGradient 4.2230 tsec 22.0000 #GCMRL# 403 dt 0.112000 rms 0.620 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6860 tsec 4.7940 #GCAMreg# pass 0 level1 1 level2 1 tsec 58.33 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.620798 #GCMRL# 405 dt 0.320000 rms 0.620 0.163% neg 0 invalid 762 tFOTS 15.3190 tGradient 3.6340 tsec 20.0600 #FOTS# QuadFit found better minimum quadopt=(dt=0.048,rms=0.619772) vs oldopt=(dt=0.08,rms=0.619772) #GCMRL# 406 dt 0.048000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 15.3130 tGradient 3.6300 tsec 20.0770 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.538626 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.521641) vs oldopt=(dt=0.32,rms=0.526028) #GCMRL# 408 dt 0.448000 rms 0.522 3.153% neg 0 invalid 762 tFOTS 14.1910 tGradient 3.0030 tsec 18.2880 #GCMRL# 409 dt 0.320000 rms 0.519 0.500% neg 0 invalid 762 tFOTS 14.0890 tGradient 2.9640 tsec 18.1410 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.516828) vs oldopt=(dt=0.32,rms=0.517189) #GCMRL# 410 dt 0.384000 rms 0.517 0.425% neg 0 invalid 762 tFOTS 14.1240 tGradient 2.9580 tsec 18.1850 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.515466) vs oldopt=(dt=0.32,rms=0.515684) #GCMRL# 411 dt 0.384000 rms 0.515 0.264% neg 0 invalid 762 tFOTS 14.2350 tGradient 2.9630 tsec 18.2980 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.514442) vs oldopt=(dt=0.32,rms=0.514602) #GCMRL# 412 dt 0.384000 rms 0.514 0.199% neg 0 invalid 762 tFOTS 14.3280 tGradient 2.9640 tsec 18.3960 #FOTS# QuadFit found better minimum quadopt=(dt=0.395833,rms=0.513723) vs oldopt=(dt=0.32,rms=0.513848) #GCMRL# 413 dt 0.395833 rms 0.514 0.140% neg 0 invalid 762 tFOTS 14.3300 tGradient 3.0010 tsec 18.4340 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.513152) vs oldopt=(dt=0.32,rms=0.513241) #GCMRL# 414 dt 0.384000 rms 0.513 0.111% neg 0 invalid 762 tFOTS 14.3300 tGradient 3.0010 tsec 18.4380 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.5127) vs oldopt=(dt=0.32,rms=0.512757) #GCMRL# 415 dt 0.384000 rms 0.513 0.088% neg 0 invalid 762 tFOTS 14.3260 tGradient 3.0290 tsec 18.4590 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.512332) vs oldopt=(dt=0.32,rms=0.512386) #GCMRL# 416 dt 0.384000 rms 0.512 0.072% neg 0 invalid 762 tFOTS 14.3020 tGradient 2.9980 tsec 18.4070 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.512026) vs oldopt=(dt=0.32,rms=0.512057) #GCMRL# 417 dt 0.384000 rms 0.512 0.060% neg 0 invalid 762 tFOTS 14.3340 tGradient 2.9970 tsec 18.4470 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.511776) vs oldopt=(dt=0.32,rms=0.511811) #GCMRL# 418 dt 0.384000 rms 0.512 0.000% neg 0 invalid 762 tFOTS 14.3560 tGradient 3.0080 tsec 18.4950 #GCMRL# 419 dt 0.384000 rms 0.512 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9960 tsec 4.1090 #GCMRL# 420 dt 0.384000 rms 0.511 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 4.1120 #GCMRL# 421 dt 0.384000 rms 0.511 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0020 tsec 4.5140 #GCMRL# 422 dt 0.384000 rms 0.511 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9980 tsec 4.5020 #GCMRL# 423 dt 0.384000 rms 0.511 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9970 tsec 4.1050 #GCMRL# 424 dt 0.192000 rms 0.511 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9980 tsec 4.8660 #GCMRL# 425 dt 0.192000 rms 0.510 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9980 tsec 4.1060 #GCMRL# 426 dt 0.192000 rms 0.510 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 4.1080 #GCMRL# 427 dt 0.192000 rms 0.510 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 4.5070 #GCMRL# 428 dt 0.192000 rms 0.510 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0080 tsec 4.1230 #GCMRL# 429 dt 0.192000 rms 0.510 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 4.1240 #GCMRL# 430 dt 0.192000 rms 0.510 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0100 tsec 4.1230 #GCMRL# 431 dt 0.192000 rms 0.510 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0130 tsec 4.1240 #GCMRL# 432 dt 0.192000 rms 0.510 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 4.1260 #GCMRL# 433 dt 0.192000 rms 0.510 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 4.1220 #GCMRL# 434 dt 0.192000 rms 0.509 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0100 tsec 4.1490 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.509489) vs oldopt=(dt=0.08,rms=0.50949) #GCMRL# 435 dt 0.112000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 14.3790 tGradient 3.0110 tsec 18.5240 #GCMRL# 436 dt 0.112000 rms 0.509 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0160 tsec 4.1270 #GCMRL# 437 dt 0.112000 rms 0.509 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 4.1200 #GCMRL# 438 dt 0.112000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0120 tsec 4.1290 #GCMRL# 439 dt 0.112000 rms 0.509 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 4.1230 #GCAMreg# pass 0 level1 0 level2 1 tsec 314.431 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.510508 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.508267) vs oldopt=(dt=0.08,rms=0.508608) #GCMRL# 441 dt 0.112000 rms 0.508 0.439% neg 0 invalid 762 tFOTS 13.4090 tGradient 3.0100 tsec 17.5270 #FOTS# QuadFit found better minimum quadopt=(dt=0.177083,rms=0.506797) vs oldopt=(dt=0.08,rms=0.507584) #GCMRL# 442 dt 0.177083 rms 0.507 0.289% neg 0 invalid 762 tFOTS 13.4120 tGradient 3.0150 tsec 17.5350 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.506224) vs oldopt=(dt=0.08,rms=0.506389) #GCMRL# 443 dt 0.112000 rms 0.506 0.113% neg 0 invalid 762 tFOTS 13.4180 tGradient 3.0030 tsec 17.5290 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505762) vs oldopt=(dt=0.08,rms=0.50589) #GCMRL# 444 dt 0.112000 rms 0.506 0.091% neg 0 invalid 762 tFOTS 13.4200 tGradient 3.0100 tsec 17.5430 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505406) vs oldopt=(dt=0.08,rms=0.505506) #GCMRL# 445 dt 0.112000 rms 0.505 0.070% neg 0 invalid 762 tFOTS 13.3650 tGradient 2.9970 tsec 17.4660 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.505143) vs oldopt=(dt=0.08,rms=0.50522) #GCMRL# 446 dt 0.112000 rms 0.505 0.052% neg 0 invalid 762 tFOTS 13.3560 tGradient 2.9960 tsec 17.4610 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.504924) vs oldopt=(dt=0.08,rms=0.504985) #GCMRL# 447 dt 0.112000 rms 0.505 0.000% neg 0 invalid 762 tFOTS 13.3610 tGradient 2.9950 tsec 17.4850 #GCMRL# 448 dt 0.112000 rms 0.505 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9960 tsec 4.1090 #GCMRL# 449 dt 0.112000 rms 0.504 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0070 tsec 4.1150 #GCMRL# 450 dt 0.112000 rms 0.504 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9950 tsec 4.1050 #GCMRL# 451 dt 0.112000 rms 0.504 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9950 tsec 4.1050 #GCMRL# 452 dt 0.112000 rms 0.504 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9960 tsec 4.1020 #GCMRL# 453 dt 0.112000 rms 0.504 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9960 tsec 4.1030 #GCMRL# 454 dt 0.112000 rms 0.504 -0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9940 tsec 5.1420 GCAMregister done in 85.0688 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.502289 #GCMRL# 456 dt 0.000000 rms 0.501 0.212% neg 0 invalid 762 tFOTS 17.1980 tGradient 6.3080 tsec 24.6120 #GCAMreg# pass 0 level1 5 level2 1 tsec 54.678 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.502289 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.500834) vs oldopt=(dt=92.48,rms=0.500897) #GCMRL# 458 dt 129.472000 rms 0.501 0.290% neg 0 invalid 762 tFOTS 17.2380 tGradient 6.3060 tsec 24.6560 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.500631) vs oldopt=(dt=92.48,rms=0.500667) #GCMRL# 459 dt 129.472000 rms 0.501 0.000% neg 0 invalid 762 tFOTS 17.2570 tGradient 6.3380 tsec 24.7350 #GCMRL# 460 dt 129.472000 rms 0.501 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3320 tsec 7.4410 #GCMRL# 461 dt 129.472000 rms 0.500 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3410 tsec 7.4490 #GCMRL# 462 dt 129.472000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3090 tsec 7.4140 #GCMRL# 463 dt 129.472000 rms 0.500 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3130 tsec 7.4460 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.500115) vs oldopt=(dt=23.12,rms=0.500116) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.5012 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.500138) vs oldopt=(dt=1.62,rms=0.500139) #GCMRL# 465 dt 2.268000 rms 0.500 0.212% neg 0 invalid 762 tFOTS 18.1620 tGradient 4.9640 tsec 24.2330 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.500136) vs oldopt=(dt=1.62,rms=0.500136) #GCMRL# 466 dt 2.268000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 18.1600 tGradient 4.9690 tsec 24.2600 #GCMRL# 467 dt 2.268000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9690 tsec 6.0750 #GCAMreg# pass 0 level1 4 level2 1 tsec 66.091 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.501191 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.498188) vs oldopt=(dt=103.68,rms=0.498518) #GCMRL# 469 dt 145.152000 rms 0.498 0.599% neg 0 invalid 762 tFOTS 17.1850 tGradient 4.9790 tsec 23.2670 #GCMRL# 470 dt 25.920000 rms 0.498 0.000% neg 0 invalid 762 tFOTS 18.1400 tGradient 4.9690 tsec 24.2400 #GCMRL# 471 dt 25.920000 rms 0.498 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9640 tsec 6.0690 #GCMRL# 472 dt 25.920000 rms 0.498 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9730 tsec 6.0790 #GCMRL# 473 dt 25.920000 rms 0.497 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9660 tsec 6.0710 #GCMRL# 474 dt 25.920000 rms 0.497 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9730 tsec 6.0760 #GCMRL# 475 dt 25.920000 rms 0.496 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9680 tsec 6.0730 #GCMRL# 476 dt 25.920000 rms 0.496 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9680 tsec 6.0800 #GCMRL# 477 dt 25.920000 rms 0.496 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9690 tsec 6.1020 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.495277) vs oldopt=(dt=414.72,rms=0.495335) setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.496637 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.49411) vs oldopt=(dt=32,rms=0.494205) #GCMRL# 479 dt 25.600000 rms 0.494 0.509% neg 0 invalid 762 tFOTS 18.1660 tGradient 4.2110 tsec 23.4800 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49218) vs oldopt=(dt=32,rms=0.492438) #GCMRL# 480 dt 44.800000 rms 0.492 0.391% neg 0 invalid 762 tFOTS 18.1620 tGradient 4.2100 tsec 23.4770 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.49171) vs oldopt=(dt=8,rms=0.49179) #GCMRL# 481 dt 11.200000 rms 0.492 0.000% neg 0 invalid 762 tFOTS 18.1810 tGradient 4.2130 tsec 23.5240 #GCMRL# 482 dt 11.200000 rms 0.491 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2110 tsec 5.3140 #GCMRL# 483 dt 11.200000 rms 0.491 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2100 tsec 5.3150 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 484 dt 11.200000 rms 0.490 0.156% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2090 tsec 7.5110 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 485 dt 11.200000 rms 0.489 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2090 tsec 7.5030 #GCMRL# 486 dt 11.200000 rms 0.489 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2140 tsec 5.3180 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 487 dt 11.200000 rms 0.488 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2070 tsec 9.4360 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 488 dt 11.200000 rms 0.488 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2150 tsec 7.5110 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 489 dt 11.200000 rms 0.487 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2110 tsec 8.4970 #GCMRL# 490 dt 128.000000 rms 0.486 0.247% neg 0 invalid 762 tFOTS 17.1880 tGradient 4.2220 tsec 22.5130 #FOTS# QuadFit found better minimum quadopt=(dt=23.6883,rms=0.485417) vs oldopt=(dt=32,rms=0.485554) #GCMRL# 491 dt 23.688312 rms 0.485 0.000% neg 0 invalid 762 tFOTS 18.1270 tGradient 4.2100 tsec 23.4660 #GCMRL# 492 dt 23.688312 rms 0.485 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2120 tsec 5.3200 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 493 dt 23.688312 rms 0.485 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1420 tsec 6.4500 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 196.581 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.485738 #FOTS# QuadFit found better minimum quadopt=(dt=44.2483,rms=0.480719) vs oldopt=(dt=32,rms=0.48093) #GCMRL# 495 dt 44.248276 rms 0.481 1.033% neg 0 invalid 762 tFOTS 18.1650 tGradient 4.2110 tsec 23.4800 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.479586) vs oldopt=(dt=8,rms=0.479781) #GCMRL# 496 dt 11.200000 rms 0.480 0.000% neg 0 invalid 762 tFOTS 18.1430 tGradient 4.2080 tsec 23.4820 #GCMRL# 497 dt 11.200000 rms 0.479 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2060 tsec 5.3150 #GCMRL# 498 dt 11.200000 rms 0.479 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2120 tsec 5.3170 #GCMRL# 499 dt 11.200000 rms 0.478 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2060 tsec 5.3120 #GCMRL# 500 dt 11.200000 rms 0.477 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2130 tsec 5.3180 #GCMRL# 501 dt 11.200000 rms 0.476 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2050 tsec 5.3100 #GCMRL# 502 dt 11.200000 rms 0.476 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2090 tsec 5.3180 #GCMRL# 503 dt 11.200000 rms 0.475 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2060 tsec 5.3120 #GCMRL# 504 dt 11.200000 rms 0.475 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2110 tsec 5.3440 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.474794) vs oldopt=(dt=32,rms=0.474809) #GCMRL# 505 dt 25.600000 rms 0.475 0.000% neg 0 invalid 762 tFOTS 18.2080 tGradient 4.2080 tsec 23.5530 #GCMRL# 506 dt 25.600000 rms 0.475 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2080 tsec 5.3160 #GCMRL# 507 dt 25.600000 rms 0.474 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2180 tsec 5.3290 #GCMRL# 508 dt 25.600000 rms 0.474 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2240 tsec 5.3360 #GCMRL# 509 dt 25.600000 rms 0.474 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2240 tsec 5.3420 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.478517 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.47742) vs oldopt=(dt=0.72,rms=0.477423) #GCMRL# 511 dt 1.008000 rms 0.477 0.229% neg 0 invalid 762 tFOTS 17.3870 tGradient 3.8680 tsec 22.3640 #FOTS# QuadFit found better minimum quadopt=(dt=0.864,rms=0.477412) vs oldopt=(dt=0.72,rms=0.477412) #GCMRL# 512 dt 0.864000 rms 0.477 0.000% neg 0 invalid 762 tFOTS 17.3810 tGradient 3.8760 tsec 22.3970 #GCMRL# 513 dt 0.864000 rms 0.477 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8730 tsec 4.9850 #GCAMreg# pass 0 level1 2 level2 1 tsec 60.241 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.478505 #FOTS# QuadFit found better minimum quadopt=(dt=8.44444,rms=0.476945) vs oldopt=(dt=2.88,rms=0.477088) #GCMRL# 515 dt 8.444444 rms 0.477 0.326% neg 0 invalid 762 tFOTS 18.3250 tGradient 3.8790 tsec 23.3140 #FOTS# QuadFit found better minimum quadopt=(dt=21.8182,rms=0.475445) vs oldopt=(dt=11.52,rms=0.475763) iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 516 dt 21.818182 rms 0.476 0.288% neg 0 invalid 762 tFOTS 18.2960 tGradient 3.8730 tsec 27.8550 #FOTS# QuadFit found better minimum quadopt=(dt=15.3287,rms=0.473825) vs oldopt=(dt=11.52,rms=0.473933) iter 0, gcam->neg = 130 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 517 dt 15.328671 rms 0.474 0.307% neg 0 invalid 762 tFOTS 18.2840 tGradient 3.9360 tsec 30.8450 #FOTS# QuadFit found better minimum quadopt=(dt=11.0983,rms=0.472941) vs oldopt=(dt=11.52,rms=0.472943) iter 0, gcam->neg = 18 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 518 dt 11.098266 rms 0.473 0.000% neg 0 invalid 762 tFOTS 18.2890 tGradient 3.9080 tsec 29.3740 iter 0, gcam->neg = 16 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 519 dt 11.098266 rms 0.472 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9070 tsec 14.5120 iter 0, gcam->neg = 41 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 520 dt 11.098266 rms 0.471 0.285% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8690 tsec 12.4800 iter 0, gcam->neg = 53 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 521 dt 11.098266 rms 0.469 0.314% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8700 tsec 13.9190 iter 0, gcam->neg = 76 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 522 dt 11.098266 rms 0.468 0.373% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8730 tsec 12.9640 iter 0, gcam->neg = 138 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 523 dt 11.098266 rms 0.466 0.269% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9000 tsec 14.0330 iter 0, gcam->neg = 157 after 23 iterations, nbhd size=1, neg = 0 #GCMRL# 524 dt 11.098266 rms 0.466 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8840 tsec 17.3320 iter 0, gcam->neg = 85 after 21 iterations, nbhd size=1, neg = 0 #GCMRL# 525 dt 11.098266 rms 0.465 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9010 tsec 16.4880 iter 0, gcam->neg = 125 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 526 dt 11.098266 rms 0.464 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9030 tsec 12.9950 iter 0, gcam->neg = 113 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 527 dt 11.098266 rms 0.464 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8720 tsec 14.5290 #FOTS# QuadFit found better minimum quadopt=(dt=8.26144,rms=0.463143) vs oldopt=(dt=11.52,rms=0.46324) iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 528 dt 8.261438 rms 0.463 0.133% neg 0 invalid 762 tFOTS 18.2720 tGradient 3.8650 tsec 28.8020 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.463098) vs oldopt=(dt=2.88,rms=0.463104) iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 529 dt 4.032000 rms 0.463 0.000% neg 0 invalid 762 tFOTS 18.2600 tGradient 3.8710 tsec 25.4240 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 530 dt 4.032000 rms 0.463 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8730 tsec 6.6530 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=0, neg = 0 #GCMRL# 531 dt 4.032000 rms 0.463 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8680 tsec 10.0360 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.469979 #GCMRL# 533 dt 0.000000 rms 0.469 0.240% neg 0 invalid 762 tFOTS 17.3290 tGradient 3.6290 tsec 22.0660 #GCAMreg# pass 0 level1 1 level2 1 tsec 49.606 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.469979 #GCMRL# 535 dt 0.000000 rms 0.469 0.240% neg 0 invalid 762 tFOTS 17.3320 tGradient 3.6300 tsec 22.0690 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.460177 #FOTS# QuadFit found better minimum quadopt=(dt=1.7452,rms=0.43232) vs oldopt=(dt=1.28,rms=0.434429) iter 0, gcam->neg = 1479 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 537 dt 1.745196 rms 0.434 5.614% neg 0 invalid 762 tFOTS 18.2830 tGradient 2.9890 tsec 31.4190 #GCMRL# 538 dt 0.000013 rms 0.434 0.000% neg 0 invalid 762 tFOTS 23.0630 tGradient 2.9910 tsec 27.1900 #GCAMreg# pass 0 level1 0 level2 1 tsec 68.18 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.435572 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.434228) vs oldopt=(dt=0.02,rms=0.434236) #GCMRL# 540 dt 0.028000 rms 0.434 0.309% neg 0 invalid 762 tFOTS 18.3200 tGradient 3.0000 tsec 22.4260 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.434227) vs oldopt=(dt=0.005,rms=0.434227) #GCMRL# 541 dt 0.007000 rms 0.434 0.000% neg 0 invalid 762 tFOTS 18.3530 tGradient 3.0010 tsec 22.4960 label assignment complete, 0 changed (0.00%) GCAMregister done in 21.4868 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.422819 #GCAMreg# pass 0 level1 5 level2 1 tsec 29.163 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.422819 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.422814) vs oldopt=(dt=5.78,rms=0.422815) #GCMRL# 544 dt 8.092000 rms 0.423 0.001% neg 0 invalid 762 tFOTS 17.9150 tGradient 5.7690 tsec 24.7760 #FOTS# QuadFit found better minimum quadopt=(dt=4.624,rms=0.422814) vs oldopt=(dt=5.78,rms=0.422814) #GCMRL# 545 dt 4.624000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 17.9180 tGradient 5.7760 tsec 24.8130 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.422963 #GCAMreg# pass 0 level1 4 level2 1 tsec 27.892 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.422963 #GCMRL# 548 dt 25.920000 rms 0.423 0.016% neg 0 invalid 762 tFOTS 16.9880 tGradient 4.4100 tsec 22.4890 #GCMRL# 549 dt 25.920000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 17.9150 tGradient 4.4050 tsec 23.4420 #GCMRL# 550 dt 25.920000 rms 0.423 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3890 tsec 5.4800 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.42343 #GCMRL# 552 dt 8.000000 rms 0.423 0.044% neg 0 invalid 762 tFOTS 17.8730 tGradient 3.6300 tsec 22.5940 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.423222) vs oldopt=(dt=2,rms=0.423226) #GCMRL# 553 dt 2.800000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 17.8780 tGradient 3.6320 tsec 22.6280 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 554 dt 2.800000 rms 0.423 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6490 tsec 5.9300 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 62.967 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.423218 #FOTS# QuadFit found better minimum quadopt=(dt=65.1852,rms=0.421087) vs oldopt=(dt=32,rms=0.421436) iter 0, gcam->neg = 34 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 556 dt 65.185185 rms 0.421 0.466% neg 0 invalid 762 tFOTS 17.9290 tGradient 3.6450 tsec 29.6990 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.42064) vs oldopt=(dt=8,rms=0.420762) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 557 dt 11.200000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 17.9270 tGradient 3.6440 tsec 24.3660 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 558 dt 11.200000 rms 0.420 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6420 tsec 5.9250 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 559 dt 11.200000 rms 0.420 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6430 tsec 6.8920 iter 0, gcam->neg = 18 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 560 dt 11.200000 rms 0.420 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6420 tsec 7.4100 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.419479) vs oldopt=(dt=32,rms=0.419552) iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 561 dt 44.800000 rms 0.419 0.143% neg 0 invalid 762 tFOTS 17.9060 tGradient 3.6500 tsec 23.8430 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.419289) vs oldopt=(dt=32,rms=0.419343) iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.421623 #FOTS# QuadFit found better minimum quadopt=(dt=8.47059,rms=0.420838) vs oldopt=(dt=11.52,rms=0.420927) iter 0, gcam->neg = 25 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 563 dt 8.470588 rms 0.421 0.098% neg 0 invalid 762 tFOTS 17.9470 tGradient 3.2870 tsec 31.2950 #FOTS# QuadFit found better minimum quadopt=(dt=9.62963,rms=0.420905) vs oldopt=(dt=11.52,rms=0.420919) iter 0, gcam->neg = 35 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 564 dt 9.629630 rms 0.421 0.000% neg 0 invalid 762 tFOTS 17.9370 tGradient 3.2830 tsec 29.3790 iter 0, gcam->neg = 31 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 565 dt 9.629630 rms 0.421 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2900 tsec 11.9090 iter 0, gcam->neg = 55 after 19 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 92.843 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.421004 #FOTS# QuadFit found better minimum quadopt=(dt=16.6667,rms=0.41788) vs oldopt=(dt=11.52,rms=0.418174) iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 567 dt 16.666667 rms 0.418 0.664% neg 0 invalid 762 tFOTS 17.8790 tGradient 3.2770 tsec 31.6880 #FOTS# QuadFit found better minimum quadopt=(dt=12.2051,rms=0.417036) vs oldopt=(dt=11.52,rms=0.417039) iter 0, gcam->neg = 47 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 568 dt 12.205128 rms 0.417 0.000% neg 0 invalid 762 tFOTS 17.8590 tGradient 3.2760 tsec 30.2310 iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 569 dt 12.205128 rms 0.417 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2680 tsec 13.7740 iter 0, gcam->neg = 75 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 570 dt 12.205128 rms 0.416 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2760 tsec 8.9360 iter 0, gcam->neg = 88 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 571 dt 12.205128 rms 0.415 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2680 tsec 14.2660 iter 0, gcam->neg = 85 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 572 dt 12.205128 rms 0.415 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2680 tsec 13.8110 #FOTS# QuadFit found better minimum quadopt=(dt=9.43284,rms=0.414861) vs oldopt=(dt=11.52,rms=0.414875) iter 0, gcam->neg = 30 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 573 dt 9.432836 rms 0.415 0.000% neg 0 invalid 762 tFOTS 17.8410 tGradient 3.2750 tsec 32.6210 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 574 dt 9.432836 rms 0.415 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2710 tsec 7.4960 iter 0, gcam->neg = 17 after 16 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.420351 #FOTS# QuadFit found better minimum quadopt=(dt=6e-05,rms=0.420351) vs oldopt=(dt=5e-05,rms=0.420351) #GCMRL# 576 dt 0.000060 rms 0.420 0.000% neg 0 invalid 762 tFOTS 22.5790 tGradient 3.0480 tsec 26.7140 #GCAMreg# pass 0 level1 1 level2 1 tsec 53.201 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.420351 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.410936 #FOTS# QuadFit found better minimum quadopt=(dt=0.815789,rms=0.403298) vs oldopt=(dt=1.28,rms=0.406458) iter 0, gcam->neg = 715 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 579 dt 0.815789 rms 0.406 1.277% neg 0 invalid 762 tFOTS 17.9150 tGradient 2.4080 tsec 32.3690 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.405599) vs oldopt=(dt=0.08,rms=0.405599) #GCMRL# 580 dt 0.064000 rms 0.406 0.000% neg 0 invalid 762 tFOTS 17.9170 tGradient 2.4200 tsec 21.4570 #GCMRL# 581 dt 0.064000 rms 0.406 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4200 tsec 3.5140 #GCAMreg# pass 0 level1 0 level2 1 tsec 66.232 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.405564 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.403535) vs oldopt=(dt=0.32,rms=0.403796) iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 583 dt 0.448000 rms 0.404 0.500% neg 0 invalid 762 tFOTS 17.9140 tGradient 2.4190 tsec 22.6100 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.402674) vs oldopt=(dt=0.32,rms=0.402728) iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 584 dt 0.448000 rms 0.403 0.000% neg 0 invalid 762 tFOTS 17.8860 tGradient 2.4210 tsec 27.4460 iter 0, gcam->neg = 28 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 585 dt 0.448000 rms 0.402 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4190 tsec 10.0290 iter 0, gcam->neg = 63 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 586 dt 0.448000 rms 0.402 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4200 tsec 10.5070 iter 0, gcam->neg = 99 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 587 dt 0.448000 rms 0.402 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4220 tsec 9.5820 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 588 dt 0.320000 rms 0.401 0.157% neg 0 invalid 762 tFOTS 17.8650 tGradient 2.4190 tsec 25.4590 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 GCAMregister done in 15.2046 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4656 tmin = 17.245 Calls to gcamLabelEnergy 4069 tmin = 1.46783 Calls to gcamJacobianEnergy 4656 tmin = 23.2194 Calls to gcamSmoothnessEnergy 4656 tmin = 16.8319 Calls to gcamLogLikelihoodTerm 590 tmin = 5.37645 Calls to gcamLabelTerm 543 tmin = 6.79682 Calls to gcamJacobianTerm 590 tmin = 14.53 Calls to gcamSmoothnessTerm 590 tmin = 4.25342 Calls to gcamComputeGradient 590 tmin = 54.1106 Calls to gcamComputeMetricProperties 6842 tmin = 16.7375 mri_ca_register took 2 hours, 25 minutes and 39 seconds. #VMPC# mri_ca_register VmPeak 2075796 FSRUNTIME@ mri_ca_register 2.4275 hours 1 threads @#@FSTIME 2020:07:27:13:40:30 mri_ca_register N 9 e 8738.96 S 1.44 U 8740.66 P 100% M 1329672 F 0 R 420269 W 0 c 22611 w 123 I 0 O 0 L 10.02 11.32 12.50 @#@FSLOADPOST 2020:07:27:16:06:09 mri_ca_register N 9 9.05 9.28 9.76 #-------------------------------------- #@# SubCort Seg Mon Jul 27 16:06:10 EDT 2020 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname n523 machine x86_64 user pankumar Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname n523 machine x86_64 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz 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 == Number of threads available to for OpenMP = 1 == reading 1 input volumes reading classifier array from /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.06 Atlas used for the 3D morph was /public/apps/freesurfer/7.1.0/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.08824 (13) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (130 voxels, overlap=0.461) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (130 voxels, peak = 12), gca=12.3 gca peak = 0.20380 (13) mri peak = 0.06250 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.67 x + 0.0 (143 voxels, overlap=0.597) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (143 voxels, peak = 22), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.09236 (95) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (535 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (535 voxels, peak = 95), gca=94.6 gca peak = 0.15814 (97) mri peak = 0.07971 (99) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (550 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (550 voxels, peak = 103), gca=103.3 gca peak = 0.27624 (56) mri peak = 0.09660 (58) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (699 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (699 voxels, peak = 55), gca=55.2 gca peak = 0.28723 (59) mri peak = 0.09704 (57) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (717 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (717 voxels, peak = 58), gca=58.1 gca peak = 0.07623 (103) mri peak = 0.07976 (109) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (23014 voxels, overlap=0.569) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (23014 voxels, peak = 110), gca=109.7 gca peak = 0.07837 (105) mri peak = 0.08482 (111) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (26382 voxels, overlap=0.474) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (26382 voxels, peak = 112), gca=111.8 gca peak = 0.10165 (58) mri peak = 0.04337 (53) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (21952 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (21952 voxels, peak = 53), gca=53.1 gca peak = 0.11113 (58) mri peak = 0.04690 (51) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (21548 voxels, overlap=0.903) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (21548 voxels, peak = 53), gca=53.1 gca peak = 0.27796 (67) mri peak = 0.11552 (78) Right_Caudate (50): linear fit = 1.12 x + 0.0 (831 voxels, overlap=0.429) Right_Caudate (50): linear fit = 1.12 x + 0.0 (831 voxels, peak = 75), gca=75.4 gca peak = 0.14473 (69) mri peak = 0.12928 (78) Left_Caudate (11): linear fit = 1.07 x + 0.0 (772 voxels, overlap=0.625) Left_Caudate (11): linear fit = 1.07 x + 0.0 (772 voxels, peak = 73), gca=73.5 gca peak = 0.14301 (56) mri peak = 0.04642 (53) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (28473 voxels, overlap=0.984) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (28473 voxels, peak = 53), gca=52.9 gca peak = 0.14610 (55) mri peak = 0.04243 (51) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (27216 voxels, overlap=0.902) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (27216 voxels, peak = 52), gca=52.0 gca peak = 0.16309 (85) mri peak = 0.10011 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5967 voxels, overlap=0.880) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5967 voxels, peak = 87), gca=87.1 gca peak = 0.15172 (84) mri peak = 0.09966 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5693 voxels, overlap=0.876) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5693 voxels, peak = 87), gca=86.9 gca peak = 0.30461 (58) mri peak = 0.17597 (51) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (498 voxels, overlap=0.546) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (498 voxels, peak = 51), gca=50.8 gca peak = 0.32293 (57) mri peak = 0.11029 (50) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (486 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (486 voxels, peak = 55), gca=55.0 gca peak = 0.11083 (90) mri peak = 0.06853 (89) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3692 voxels, overlap=0.995) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3692 voxels, peak = 88), gca=87.8 gca peak = 0.11393 (83) mri peak = 0.06793 (90) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3349 voxels, overlap=0.979) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3349 voxels, peak = 86), gca=85.9 gca peak = 0.08575 (81) mri peak = 0.08485 (80) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1816 voxels, overlap=0.880) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1816 voxels, peak = 82), gca=82.2 gca peak = 0.08618 (78) mri peak = 0.08421 (81) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1709 voxels, overlap=0.865) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1709 voxels, peak = 80), gca=79.9 gca peak = 0.08005 (78) mri peak = 0.09874 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11215 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11215 voxels, peak = 82), gca=82.3 gca peak = 0.12854 (88) mri peak = 0.05677 (86) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1128 voxels, overlap=0.809) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1128 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.05943 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1283 voxels, overlap=0.898) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1283 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.09795 (15) gca peak = 0.17113 (14) mri peak = 0.14773 ( 8) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, overlap=0.489) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, peak = 7), gca=6.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 1.06 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.22482 (13) mri peak = 0.08824 (13) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (130 voxels, overlap=0.673) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (130 voxels, peak = 14), gca=14.5 gca peak = 0.16078 (19) mri peak = 0.06250 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (143 voxels, overlap=0.355) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (143 voxels, peak = 20), gca=20.4 gca peak = 0.21116 (94) mri peak = 0.09236 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (535 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (535 voxels, peak = 95), gca=95.4 gca peak = 0.16875 (102) mri peak = 0.07971 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (550 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (550 voxels, peak = 103), gca=102.5 gca peak = 0.30937 (55) mri peak = 0.09660 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (699 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (699 voxels, peak = 55), gca=55.0 gca peak = 0.28941 (58) mri peak = 0.09704 (57) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (717 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (717 voxels, peak = 58), gca=58.0 gca peak = 0.07344 (110) mri peak = 0.07976 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (23014 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (23014 voxels, peak = 110), gca=110.0 gca peak = 0.07460 (112) mri peak = 0.08482 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26382 voxels, overlap=0.762) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26382 voxels, peak = 112), gca=112.0 gca peak = 0.10919 (53) mri peak = 0.04337 (53) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (21952 voxels, overlap=1.000) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (21952 voxels, peak = 55), gca=55.4 gca peak = 0.12331 (53) mri peak = 0.04690 (51) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (21548 voxels, overlap=0.990) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (21548 voxels, peak = 52), gca=52.2 gca peak = 0.22309 (75) mri peak = 0.11552 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (831 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (831 voxels, peak = 75), gca=75.0 gca peak = 0.12384 (73) mri peak = 0.12928 (78) Left_Caudate (11): linear fit = 1.01 x + 0.0 (772 voxels, overlap=0.956) Left_Caudate (11): linear fit = 1.01 x + 0.0 (772 voxels, peak = 74), gca=74.1 gca peak = 0.14626 (52) mri peak = 0.04642 (53) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28473 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28473 voxels, peak = 52), gca=52.0 gca peak = 0.15405 (52) mri peak = 0.04243 (51) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27216 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27216 voxels, peak = 51), gca=51.2 gca peak = 0.15741 (87) mri peak = 0.10011 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5967 voxels, overlap=0.950) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5967 voxels, peak = 87), gca=87.0 gca peak = 0.14534 (87) mri peak = 0.09966 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5693 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5693 voxels, peak = 87), gca=86.6 gca peak = 0.26052 (51) mri peak = 0.17597 (51) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (498 voxels, overlap=0.960) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (498 voxels, peak = 51), gca=51.0 gca peak = 0.35771 (55) mri peak = 0.11029 (50) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (486 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (486 voxels, peak = 55), gca=55.0 gca peak = 0.11203 (86) mri peak = 0.06853 (89) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3692 voxels, overlap=0.991) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3692 voxels, peak = 86), gca=85.6 gca peak = 0.11103 (86) mri peak = 0.06793 (90) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3349 voxels, overlap=0.994) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3349 voxels, peak = 86), gca=85.6 gca peak = 0.08210 (82) mri peak = 0.08485 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1816 voxels, overlap=0.900) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1816 voxels, peak = 82), gca=82.0 gca peak = 0.08445 (82) mri peak = 0.08421 (81) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1709 voxels, overlap=0.918) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1709 voxels, peak = 82), gca=82.0 gca peak = 0.08443 (83) mri peak = 0.09874 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11215 voxels, overlap=0.678) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11215 voxels, peak = 83), gca=82.6 gca peak = 0.11072 (97) mri peak = 0.05677 (86) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1128 voxels, overlap=0.936) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1128 voxels, peak = 97), gca=97.5 gca peak = 0.14298 (96) mri peak = 0.05943 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1283 voxels, overlap=0.928) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1283 voxels, peak = 96), gca=96.5 gca peak = 0.20054 (28) mri peak = 0.09795 (15) gca peak = 0.16806 (17) mri peak = 0.14773 ( 8) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, overlap=0.315) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (88 voxels, peak = 8), gca=7.9 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19362 (27) gca peak Third_Ventricle = 0.20054 (28) gca peak Fourth_Ventricle = 0.16806 (17) gca peak CSF = 0.20346 (38) gca peak Left_Accumbens_area = 0.65277 (66) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.85300 (53) gca peak Left_choroid_plexus = 0.11687 (35) gca peak Right_Inf_Lat_Vent = 0.25588 (23) gca peak Right_Accumbens_area = 0.29156 (73) gca peak Right_vessel = 0.77367 (52) gca peak Right_choroid_plexus = 0.13288 (38) gca peak Fifth_Ventricle = 0.60973 (35) gca peak WM_hypointensities = 0.10282 (82) gca peak non_WM_hypointensities = 0.13942 (43) gca peak Optic_Chiasm = 0.60484 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 51140 voxels changed in iteration 0 of unlikely voxel relabeling 189 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 24401 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 324 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 59768 changed. image ll: -2.087, PF=0.500 pass 2: 16880 changed. image ll: -2.086, PF=0.500 pass 3: 5473 changed. pass 4: 2005 changed. 30539 voxels changed in iteration 0 of unlikely voxel relabeling 123 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4831 voxels changed in iteration 0 of unlikely voxel relabeling 84 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 4989 voxels changed in iteration 0 of unlikely voxel relabeling 67 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4003 voxels changed in iteration 0 of unlikely voxel relabeling 11 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 2 with volume 5926 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 264 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 6676 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 7 with volume 131 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2577.120218 mri_ca_label stimesec 1.248810 mri_ca_label ru_maxrss 2176060 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 423944 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 153 mri_ca_label ru_nivcsw 12990 auto-labeling took 42 minutes and 58 seconds. @#@FSTIME 2020:07:27:16:06:14 mri_ca_label N 10 e 2578.06 S 1.25 U 2577.12 P 100% M 2176060 F 0 R 423945 W 0 c 12990 w 158 I 0 O 0 L 9.05 9.27 9.75 @#@FSLOADPOST 2020:07:27:16:49:13 mri_ca_label N 10 9.68 9.29 11.07 #-------------------------------------- #@# CC Seg Mon Jul 27 16:49:13 EDT 2020 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/cc_up.lta 2012-646-010-KK will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/transforms/cc_up.lta reading aseg from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.auto_noCCseg.mgz reading norm from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/norm.mgz 9626 voxels in left wm, 39757 in right wm, xrange [123, 130] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 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 128.0, rotations (-0.50, -0.20) final transformation (x=128.0, yr=-0.503, zr=-0.200): 0.99996 0.00349 -0.00878 0.58606; -0.00349 0.99999 0.00003 15.44415; 0.00878 0.00000 0.99996 15.88011; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 113 111 eigenvectors: 0.01165 0.00725 0.99991; 0.05494 -0.99847 0.00660; 0.99842 0.05486 -0.01203; error in mid anterior detected - correcting... writing aseg with callosum to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes @#@FSTIME 2020:07:27:16:49:14 mri_cc N 7 e 37.35 S 0.23 U 36.85 P 99% M 418060 F 0 R 14187 W 0 c 41 w 68 I 0 O 0 L 10.18 9.40 11.10 @#@FSLOADPOST 2020:07:27:16:49:52 mri_cc N 7 11.87 9.91 11.21 #-------------------------------------- #@# Merge ASeg Mon Jul 27 16:49:52 EDT 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Jul 27 16:49:53 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 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 mri_src from norm.mgz... MRImask(): AllowDiffGeom = 1 Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 840 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 57 (57), valley at 0 (-1) csf peak at 28, setting threshold to 47 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 61 (61), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 39 seconds. @#@FSTIME 2020:07:27:16:49:54 mri_normalize N 9 e 161.46 S 0.76 U 160.49 P 99% M 1259696 F 0 R 216499 W 0 c 179 w 77 I 0 O 0 L 11.96 9.96 11.22 @#@FSLOADPOST 2020:07:27:16:52:36 mri_normalize N 9 13.87 11.64 11.65 #-------------------------------------------- #@# Mask BFS Mon Jul 27 16:52:36 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1304683 voxels in mask (pct= 7.78) MRImask(): AllowDiffGeom = 1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2020:07:27:16:52:37 mri_mask N 5 e 1.50 S 0.02 U 1.20 P 81% M 71080 F 0 R 3807 W 0 c 5 w 58 I 0 O 0 L 13.87 11.64 11.65 @#@FSLOADPOST 2020:07:27:16:52:39 mri_mask N 5 13.88 11.68 11.67 #-------------------------------------------- #@# WM Segmentation Mon Jul 27 16:52:39 EDT 2020 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname n523 machine x86_64 user pankumar input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 7.1.0 cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname n523 machine x86_64 user pankumar input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: -1 deletes, -1 fills cp wm.mgz wm.seg.mgz AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2020:07:27:16:52:49 AntsDenoiseImageFs N 4 e 37.84 S 0.08 U 37.46 P 99% M 347444 F 0 R 3981 W 0 c 79 w 74 I 0 O 0 L 13.82 11.74 11.69 @#@FSLOADPOST 2020:07:27:16:53:27 AntsDenoiseImageFs N 4 13.90 11.99 11.77 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz preserving editing changes in output volume... wsizemm = 13, voxres = 1, wsize = 13 WHITE_MATTER_MEAN 110 wsize 13 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm_low 79 wm_hi 125 gray_low 30 gray_hi 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (103.0): 103.7 +- 4.5 [79.0 --> 125.0] CCS GM (71.0) : 70.3 +- 9.1 [30.0 --> 95.0] white_mean 103.672 white_sigma 4.53265 gray_mean 70.2502 gray_sigma 9.09654 setting bottom of white matter range wm_low to 79.3 setting top of gray matter range gray_hi to 88.4 wm_low 79.3468 wm_hi 125 gray_low 30 gray_hi 88.4433 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 79.3468 wm_hi 125 gray_low 30 gray_hi 88.4433 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 88.4433, wm_low = 79.3468 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=88.4433, wmlow=79.3468 95483 voxels processed (0.57%) 44684 voxels white (0.27%) 50799 voxels non-white (0.30%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=74.3468, gray_hi=88.4433, wsize=13 162977 voxels tested (0.97%) 37597 voxels changed (0.22%) 39830 multi-scale searches (0.24%) Recovering bright white MRIrecoverBrightWhite() wm_low 79.3468 wm_hi 125 slack 4.53265 pct_thresh 0.33 intensity_thresh 129.533 nvox_thresh 8.58 14 voxels tested (0.00%) 14 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=74.3468, hithr=88.4433 smoothing input volume with sigma = 0.250 61941 voxels tested (0.37%) 12936 voxels changed (0.08%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1885 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1260 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3978 filled MRIfindBrightNonWM(): 2 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... @#@FSTIME 2020:07:27:16:53:28 mri_segment N 6 e 69.45 S 0.21 U 68.99 P 99% M 154680 F 0 R 42492 W 0 c 237 w 68 I 0 O 0 L 13.90 11.99 11.77 @#@FSLOADPOST 2020:07:27:16:54:38 mri_segment N 6 12.97 12.18 11.85 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 0.56 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 3894 additional wm voxels added 0 additional wm voxels added SEG EDIT: 47157 voxels turned on, 32990 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 103 new 103 115,126,128 old 103 new 103 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2020:07:27:16:54:39 mri_edit_wm_with_aseg N 5 e 33.95 S 0.22 U 33.44 P 99% M 473428 F 0 R 18719 W 0 c 39 w 86 I 0 O 0 L 12.82 12.16 11.85 @#@FSLOADPOST 2020:07:27:16:55:14 mri_edit_wm_with_aseg N 5 12.01 12.03 11.81 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 24 found - 24 modified | TOTAL: 40 pass 2 (xy-): 0 found - 24 modified | TOTAL: 40 pass 1 (yz+): 24 found - 24 modified | TOTAL: 64 pass 2 (yz+): 0 found - 24 modified | TOTAL: 64 pass 1 (yz-): 11 found - 11 modified | TOTAL: 75 pass 2 (yz-): 0 found - 11 modified | TOTAL: 75 pass 1 (xz+): 11 found - 11 modified | TOTAL: 86 pass 2 (xz+): 0 found - 11 modified | TOTAL: 86 pass 1 (xz-): 12 found - 12 modified | TOTAL: 98 pass 2 (xz-): 0 found - 12 modified | TOTAL: 98 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 4 found - 4 modified | TOTAL: 14 pass 2 (+++): 0 found - 4 modified | TOTAL: 14 pass 1 (+++): 4 found - 4 modified | TOTAL: 18 pass 2 (+++): 0 found - 4 modified | TOTAL: 18 Iteration Number : 1 pass 1 (++): 62 found - 62 modified | TOTAL: 62 pass 2 (++): 0 found - 62 modified | TOTAL: 62 pass 1 (+-): 102 found - 102 modified | TOTAL: 164 pass 2 (+-): 0 found - 102 modified | TOTAL: 164 pass 1 (--): 59 found - 59 modified | TOTAL: 223 pass 2 (--): 0 found - 59 modified | TOTAL: 223 pass 1 (-+): 94 found - 94 modified | TOTAL: 317 pass 2 (-+): 0 found - 94 modified | TOTAL: 317 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 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 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 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 Total Number of Modified Voxels = 448 (out of 441090: 0.101567) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done @#@FSTIME 2020:07:27:16:55:15 mri_pretess N 5 e 3.65 S 0.03 U 3.30 P 91% M 53776 F 0 R 3623 W 0 c 5 w 72 I 0 O 0 L 12.01 12.03 11.81 @#@FSLOADPOST 2020:07:27:16:55:19 mri_pretess N 5 11.85 11.99 11.80 #-------------------------------------------- #@# Fill Mon Jul 27 16:55:19 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.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.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03016 0.01046 0.00806 -8.71298; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22072; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03016 0.01046 0.00806 -8.71298; -0.00869 1.28704 0.00797 -40.93967; -0.00831 -0.01032 0.99525 -0.22072; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1005 (min = 350, max = 1400), aspect = 0.42 (min = 0.10, max = 0.75) no need to search using seed (126, 121, 149), TAL = (2.0, 21.0, 7.0) talairach voxel to voxel transform 0.97060 -0.00795 -0.00779 8.12970; 0.00651 0.77688 -0.00627 31.86034; 0.00817 0.00799 1.00464 0.62001; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 121, 149) --> (2.0, 21.0, 7.0) done. writing output to filled.mgz... filling took 1.2 minutes talairach cc position changed to (2.00, 21.00, 7.00) Erasing brainstem...done. MRImask(): AllowDiffGeom = 1 seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 7.00) SRC: (110.83, 125.63, 152.16) search lh wm seed point around talairach space (-16.00, 21.00, 7.00), SRC: (145.77, 125.86, 152.45) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... @#@FSTIME 2020:07:27:16:55:20 mri_fill N 8 e 71.23 S 0.81 U 70.18 P 99% M 966408 F 0 R 291552 W 0 c 98 w 62 I 0 O 0 L 11.85 11.99 11.80 @#@FSLOADPOST 2020:07:27:16:56:32 mri_fill N 8 9.94 11.39 11.61 #-------------------------------------------- #@# Tessellate lh Mon Jul 27 16:56:32 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 2 found - 2 modified | TOTAL: 6 pass 2 (xy-): 0 found - 2 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 4 found - 4 modified | TOTAL: 13 pass 2 (yz-): 0 found - 4 modified | TOTAL: 13 pass 1 (xz+): 0 found - 0 modified | TOTAL: 13 pass 1 (xz-): 4 found - 4 modified | TOTAL: 17 pass 2 (xz-): 0 found - 4 modified | TOTAL: 17 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (-+): 2 found - 2 modified | TOTAL: 2 pass 2 (-+): 0 found - 2 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 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 Total Number of Modified Voxels = 26 (out of 216539: 0.012007) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:27:16:56:33 mri_pretess N 4 e 2.34 S 0.01 U 2.32 P 99% M 36944 F 0 R 2291 W 0 c 5 w 39 I 0 O 0 L 9.94 11.39 11.61 @#@FSLOADPOST 2020:07:27:16:56:36 mri_pretess N 4 9.94 11.37 11.60 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.1.0 7.1.0 slice 30: 318 vertices, 370 faces slice 40: 3905 vertices, 4066 faces slice 50: 9065 vertices, 9233 faces slice 60: 14611 vertices, 14834 faces slice 70: 21758 vertices, 22050 faces slice 80: 29683 vertices, 29997 faces slice 90: 38691 vertices, 39033 faces slice 100: 49124 vertices, 49481 faces slice 110: 60299 vertices, 60684 faces slice 120: 70412 vertices, 70774 faces slice 130: 80568 vertices, 80933 faces slice 140: 89583 vertices, 89910 faces slice 150: 97628 vertices, 97926 faces slice 160: 105102 vertices, 105425 faces slice 170: 112115 vertices, 112359 faces slice 180: 117690 vertices, 117885 faces slice 190: 120067 vertices, 120116 faces slice 200: 120086 vertices, 120126 faces slice 210: 120086 vertices, 120126 faces slice 220: 120086 vertices, 120126 faces slice 230: 120086 vertices, 120126 faces slice 240: 120086 vertices, 120126 faces slice 250: 120086 vertices, 120126 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; @#@FSTIME 2020:07:27:16:56:37 mri_tessellate N 3 e 1.82 S 0.00 U 1.64 P 90% M 44828 F 0 R 1610 W 0 c 3 w 40 I 0 O 0 L 9.94 11.37 11.60 @#@FSLOADPOST 2020:07:27:16:56:39 mri_tessellate N 3 9.87 11.33 11.58 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 120086 voxel in cpt #1: X=-40 [v=120086,e=360378,f=240252] located at (-28.104359, -18.978382, 7.232117) For the whole surface: X=-40 [v=120086,e=360378,f=240252] One single component has been found nothing to do done @#@FSTIME 2020:07:27:16:56:41 mris_extract_main_component N 2 e 1.05 S 0.10 U 0.72 P 77% M 237756 F 0 R 25448 W 0 c 2 w 43 I 0 O 0 L 9.87 11.33 11.58 @#@FSLOADPOST 2020:07:27:16:56:42 mris_extract_main_component N 2 9.87 11.33 11.58 #-------------------------------------------- #@# Tessellate rh Mon Jul 27 16:56:42 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 0 found - 3 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 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 = 10 (out of 205883: 0.004857) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:27:16:56:43 mri_pretess N 4 e 1.72 S 0.01 U 1.71 P 99% M 36936 F 0 R 2289 W 0 c 3 w 42 I 0 O 0 L 9.87 11.33 11.58 @#@FSLOADPOST 2020:07:27:16:56:45 mri_pretess N 4 9.72 11.27 11.57 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.1.0 7.1.0 slice 30: 112 vertices, 142 faces slice 40: 2951 vertices, 3088 faces slice 50: 8335 vertices, 8560 faces slice 60: 15032 vertices, 15253 faces slice 70: 22425 vertices, 22730 faces slice 80: 31421 vertices, 31745 faces slice 90: 40636 vertices, 40953 faces slice 100: 50877 vertices, 51245 faces slice 110: 61610 vertices, 61967 faces slice 120: 71232 vertices, 71594 faces slice 130: 80664 vertices, 81021 faces slice 140: 89956 vertices, 90260 faces slice 150: 96668 vertices, 96933 faces slice 160: 103953 vertices, 104204 faces slice 170: 110088 vertices, 110310 faces slice 180: 115690 vertices, 115884 faces slice 190: 118150 vertices, 118186 faces slice 200: 118150 vertices, 118186 faces slice 210: 118150 vertices, 118186 faces slice 220: 118150 vertices, 118186 faces slice 230: 118150 vertices, 118186 faces slice 240: 118150 vertices, 118186 faces slice 250: 118150 vertices, 118186 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; @#@FSTIME 2020:07:27:16:56:47 mri_tessellate N 3 e 1.65 S 0.01 U 1.62 P 99% M 44672 F 0 R 1588 W 0 c 4 w 28 I 0 O 0 L 9.72 11.27 11.57 @#@FSLOADPOST 2020:07:27:16:56:48 mri_tessellate N 3 9.58 11.22 11.55 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 118150 voxel in cpt #1: X=-36 [v=118150,e=354558,f=236372] located at (27.710352, -20.338045, 9.246179) For the whole surface: X=-36 [v=118150,e=354558,f=236372] One single component has been found nothing to do done @#@FSTIME 2020:07:27:16:56:50 mris_extract_main_component N 2 e 0.84 S 0.10 U 0.71 P 97% M 233932 F 0 R 24376 W 0 c 3 w 28 I 0 O 0 L 9.58 11.22 11.55 @#@FSLOADPOST 2020:07:27:16:56:51 mris_extract_main_component N 2 9.58 11.22 11.55 #-------------------------------------------- #@# Smooth1 lh Mon Jul 27 16:56:51 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2020:07:27:16:56:53 mris_smooth N 5 e 3.32 S 0.08 U 2.99 P 92% M 189736 F 0 R 31966 W 0 c 4 w 50 I 0 O 0 L 9.58 11.22 11.55 @#@FSLOADPOST 2020:07:27:16:56:56 mris_smooth N 5 9.53 11.18 11.53 #-------------------------------------------- #@# Smooth1 rh Mon Jul 27 16:56:57 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2020:07:27:16:56:58 mris_smooth N 5 e 3.04 S 0.09 U 2.94 P 99% M 186712 F 0 R 32116 W 0 c 5 w 29 I 0 O 0 L 9.53 11.18 11.53 @#@FSLOADPOST 2020:07:27:16:57:01 mris_smooth N 5 9.57 11.16 11.52 #-------------------------------------------- #@# Inflation1 lh Mon Jul 27 16:57:01 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.8 mm, total surface area = 64331 mm^2 step 000: RMS=0.153 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 18.619169 mris_inflate stimesec 0.109983 mris_inflate ru_maxrss 250912 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 45719 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 61 mris_inflate ru_nivcsw 29 @#@FSTIME 2020:07:27:16:57:03 mris_inflate N 3 e 18.94 S 0.12 U 18.61 P 98% M 250912 F 0 R 45720 W 0 c 29 w 63 I 0 O 0 L 9.57 11.16 11.52 @#@FSLOADPOST 2020:07:27:16:57:22 mris_inflate N 3 9.41 11.02 11.47 #-------------------------------------------- #@# Inflation1 rh Mon Jul 27 16:57:22 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.3 mm, total surface area = 63328 mm^2 step 000: RMS=0.152 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 17.988265 mris_inflate stimesec 0.096985 mris_inflate ru_maxrss 246948 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 46153 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 28 mris_inflate ru_nivcsw 25 @#@FSTIME 2020:07:27:16:57:23 mris_inflate N 3 e 18.10 S 0.10 U 17.98 P 99% M 246948 F 0 R 46154 W 0 c 25 w 29 I 0 O 0 L 9.41 11.02 11.47 @#@FSLOADPOST 2020:07:27:16:57:42 mris_inflate N 3 9.42 10.92 11.43 #-------------------------------------------- #@# QSphere lh Mon Jul 27 16:57:42 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.314... inflating... Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.549, avgs=0 005/300: dt: 0.9000, rms radial error=177.288, avgs=0 010/300: dt: 0.9000, rms radial error=176.730, avgs=0 015/300: dt: 0.9000, rms radial error=175.997, avgs=0 020/300: dt: 0.9000, rms radial error=175.162, avgs=0 025/300: dt: 0.9000, rms radial error=174.271, avgs=0 030/300: dt: 0.9000, rms radial error=173.347, avgs=0 035/300: dt: 0.9000, rms radial error=172.406, avgs=0 040/300: dt: 0.9000, rms radial error=171.457, avgs=0 045/300: dt: 0.9000, rms radial error=170.505, avgs=0 050/300: dt: 0.9000, rms radial error=169.554, avgs=0 055/300: dt: 0.9000, rms radial error=168.605, avgs=0 060/300: dt: 0.9000, rms radial error=167.659, avgs=0 065/300: dt: 0.9000, rms radial error=166.717, avgs=0 070/300: dt: 0.9000, rms radial error=165.780, avgs=0 075/300: dt: 0.9000, rms radial error=164.848, avgs=0 080/300: dt: 0.9000, rms radial error=163.920, avgs=0 085/300: dt: 0.9000, rms radial error=162.998, avgs=0 090/300: dt: 0.9000, rms radial error=162.080, avgs=0 095/300: dt: 0.9000, rms radial error=161.167, avgs=0 100/300: dt: 0.9000, rms radial error=160.258, avgs=0 105/300: dt: 0.9000, rms radial error=159.355, avgs=0 110/300: dt: 0.9000, rms radial error=158.457, avgs=0 115/300: dt: 0.9000, rms radial error=157.563, avgs=0 120/300: dt: 0.9000, rms radial error=156.675, avgs=0 125/300: dt: 0.9000, rms radial error=155.793, avgs=0 130/300: dt: 0.9000, rms radial error=154.915, avgs=0 135/300: dt: 0.9000, rms radial error=154.041, avgs=0 140/300: dt: 0.9000, rms radial error=153.173, avgs=0 145/300: dt: 0.9000, rms radial error=152.309, avgs=0 150/300: dt: 0.9000, rms radial error=151.450, avgs=0 155/300: dt: 0.9000, rms radial error=150.596, avgs=0 160/300: dt: 0.9000, rms radial error=149.746, avgs=0 165/300: dt: 0.9000, rms radial error=148.901, avgs=0 170/300: dt: 0.9000, rms radial error=148.061, avgs=0 175/300: dt: 0.9000, rms radial error=147.226, avgs=0 180/300: dt: 0.9000, rms radial error=146.395, avgs=0 185/300: dt: 0.9000, rms radial error=145.568, avgs=0 190/300: dt: 0.9000, rms radial error=144.747, avgs=0 195/300: dt: 0.9000, rms radial error=143.929, avgs=0 200/300: dt: 0.9000, rms radial error=143.117, avgs=0 205/300: dt: 0.9000, rms radial error=142.309, avgs=0 210/300: dt: 0.9000, rms radial error=141.505, avgs=0 215/300: dt: 0.9000, rms radial error=140.706, avgs=0 220/300: dt: 0.9000, rms radial error=139.911, avgs=0 225/300: dt: 0.9000, rms radial error=139.121, avgs=0 230/300: dt: 0.9000, rms radial error=138.335, avgs=0 235/300: dt: 0.9000, rms radial error=137.554, avgs=0 240/300: dt: 0.9000, rms radial error=136.777, avgs=0 245/300: dt: 0.9000, rms radial error=136.005, avgs=0 250/300: dt: 0.9000, rms radial error=135.236, avgs=0 255/300: dt: 0.9000, rms radial error=134.473, avgs=0 260/300: dt: 0.9000, rms radial error=133.713, avgs=0 265/300: dt: 0.9000, rms radial error=132.958, avgs=0 270/300: dt: 0.9000, rms radial error=132.207, avgs=0 275/300: dt: 0.9000, rms radial error=131.460, avgs=0 280/300: dt: 0.9000, rms radial error=130.717, avgs=0 285/300: dt: 0.9000, rms radial error=129.979, avgs=0 290/300: dt: 0.9000, rms radial error=129.245, avgs=0 295/300: dt: 0.9000, rms radial error=128.514, avgs=0 300/300: dt: 0.9000, rms radial error=127.788, avgs=0 spherical inflation complete. projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.05 +- 0.61 (0.00-->7.39) (max @ vno 83129 --> 83130) face area 0.03 +- 0.03 (-0.09-->0.60) epoch 1 (K=10.0), pass 1, starting sse = 13959.20 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00036 epoch 2 (K=40.0), pass 1, starting sse = 2262.17 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00036 epoch 3 (K=160.0), pass 1, starting sse = 237.19 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00733 epoch 4 (K=640.0), pass 1, starting sse = 18.37 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/22 = 0.00520 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix mris_sphere utimesec 165.670814 mris_sphere stimesec 0.535918 mris_sphere ru_maxrss 946044 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 314472 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 52 mris_sphere ru_nivcsw 208 spherical transformation took 0.0461 hours FSRUNTIME@ mris_sphere 0.0461 hours 1 threads @#@FSTIME 2020:07:27:16:57:43 mris_sphere N 9 e 166.47 S 0.59 U 165.67 P 99% M 946044 F 0 R 314473 W 0 c 208 w 55 I 0 O 0 L 9.42 10.92 11.43 @#@FSLOADPOST 2020:07:27:17:00:30 mris_sphere N 9 9.13 10.13 11.03 #-------------------------------------------- #@# QSphere rh Mon Jul 27 17:00:30 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.315... inflating... Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.552, avgs=0 005/300: dt: 0.9000, rms radial error=177.293, avgs=0 010/300: dt: 0.9000, rms radial error=176.737, avgs=0 015/300: dt: 0.9000, rms radial error=176.006, avgs=0 020/300: dt: 0.9000, rms radial error=175.174, avgs=0 025/300: dt: 0.9000, rms radial error=174.285, avgs=0 030/300: dt: 0.9000, rms radial error=173.362, avgs=0 035/300: dt: 0.9000, rms radial error=172.422, avgs=0 040/300: dt: 0.9000, rms radial error=171.475, avgs=0 045/300: dt: 0.9000, rms radial error=170.524, avgs=0 050/300: dt: 0.9000, rms radial error=169.574, avgs=0 055/300: dt: 0.9000, rms radial error=168.626, avgs=0 060/300: dt: 0.9000, rms radial error=167.682, avgs=0 065/300: dt: 0.9000, rms radial error=166.741, avgs=0 070/300: dt: 0.9000, rms radial error=165.805, avgs=0 075/300: dt: 0.9000, rms radial error=164.874, avgs=0 080/300: dt: 0.9000, rms radial error=163.947, avgs=0 085/300: dt: 0.9000, rms radial error=163.025, avgs=0 090/300: dt: 0.9000, rms radial error=162.107, avgs=0 095/300: dt: 0.9000, rms radial error=161.195, avgs=0 100/300: dt: 0.9000, rms radial error=160.287, avgs=0 105/300: dt: 0.9000, rms radial error=159.384, avgs=0 110/300: dt: 0.9000, rms radial error=158.486, avgs=0 115/300: dt: 0.9000, rms radial error=157.592, avgs=0 120/300: dt: 0.9000, rms radial error=156.704, avgs=0 125/300: dt: 0.9000, rms radial error=155.820, avgs=0 130/300: dt: 0.9000, rms radial error=154.941, avgs=0 135/300: dt: 0.9000, rms radial error=154.067, avgs=0 140/300: dt: 0.9000, rms radial error=153.197, avgs=0 145/300: dt: 0.9000, rms radial error=152.333, avgs=0 150/300: dt: 0.9000, rms radial error=151.473, avgs=0 155/300: dt: 0.9000, rms radial error=150.617, avgs=0 160/300: dt: 0.9000, rms radial error=149.767, avgs=0 165/300: dt: 0.9000, rms radial error=148.921, avgs=0 170/300: dt: 0.9000, rms radial error=148.080, avgs=0 175/300: dt: 0.9000, rms radial error=147.243, avgs=0 180/300: dt: 0.9000, rms radial error=146.411, avgs=0 185/300: dt: 0.9000, rms radial error=145.584, avgs=0 190/300: dt: 0.9000, rms radial error=144.761, avgs=0 195/300: dt: 0.9000, rms radial error=143.943, avgs=0 200/300: dt: 0.9000, rms radial error=143.129, avgs=0 205/300: dt: 0.9000, rms radial error=142.320, avgs=0 210/300: dt: 0.9000, rms radial error=141.515, avgs=0 215/300: dt: 0.9000, rms radial error=140.715, avgs=0 220/300: dt: 0.9000, rms radial error=139.919, avgs=0 225/300: dt: 0.9000, rms radial error=139.128, avgs=0 230/300: dt: 0.9000, rms radial error=138.341, avgs=0 235/300: dt: 0.9000, rms radial error=137.559, avgs=0 240/300: dt: 0.9000, rms radial error=136.781, avgs=0 245/300: dt: 0.9000, rms radial error=136.007, avgs=0 250/300: dt: 0.9000, rms radial error=135.238, avgs=0 255/300: dt: 0.9000, rms radial error=134.473, avgs=0 260/300: dt: 0.9000, rms radial error=133.712, avgs=0 265/300: dt: 0.9000, rms radial error=132.956, avgs=0 270/300: dt: 0.9000, rms radial error=132.204, avgs=0 275/300: dt: 0.9000, rms radial error=131.456, avgs=0 280/300: dt: 0.9000, rms radial error=130.712, avgs=0 285/300: dt: 0.9000, rms radial error=129.972, avgs=0 290/300: dt: 0.9000, rms radial error=129.237, avgs=0 295/300: dt: 0.9000, rms radial error=128.506, avgs=0 300/300: dt: 0.9000, rms radial error=127.779, avgs=0 spherical inflation complete. projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.61 (0.00-->6.76) (max @ vno 36866 --> 37701) face area 0.03 +- 0.03 (-0.09-->0.84) epoch 1 (K=10.0), pass 1, starting sse = 13706.98 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00027 epoch 2 (K=40.0), pass 1, starting sse = 2219.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00031 epoch 3 (K=160.0), pass 1, starting sse = 230.30 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/15 = 0.00683 epoch 4 (K=640.0), pass 1, starting sse = 17.33 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/20 = 0.00587 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix mris_sphere utimesec 137.329122 mris_sphere stimesec 0.502923 mris_sphere ru_maxrss 910560 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 299229 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 29 mris_sphere ru_nivcsw 172 spherical transformation took 0.0383 hours FSRUNTIME@ mris_sphere 0.0383 hours 1 threads @#@FSTIME 2020:07:27:17:00:32 mris_sphere N 9 e 137.82 S 0.54 U 137.32 P 100% M 910560 F 0 R 299230 W 0 c 172 w 30 I 0 O 0 L 9.13 10.13 11.03 @#@FSLOADPOST 2020:07:27:17:02:50 mris_sphere N 9 9.02 9.71 10.75 #@# Fix Topology lh Mon Jul 27 17:02:50 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 2012-646-010-KK lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.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 writing corrected surface to 'orig.premesh' 7.1.0 7.1.0 before topology correction, eno=-40 (nv=120086, nf=240252, ne=360378, g=21) 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 8 iterations marking ambiguous vertices... 6439 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 24 into 19 31 defects to be corrected 0 vertices coincident reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.4713 (-4.7356) -vertex loglikelihood: -6.6616 (-3.3308) -normal dot loglikelihood: -3.6454 (-3.6454) -quad curv loglikelihood: -5.9739 (-2.9870) Total Loglikelihood : -25.7522 CORRECTING DEFECT 0 (vertices=37, convex hull=88, v0=516) After retessellation of defect 0 (v0=516), euler #=-29 (116190,347100,230881) : difference with theory (-28) = 1 CORRECTING DEFECT 1 (vertices=33, convex hull=73, v0=1547) After retessellation of defect 1 (v0=1547), euler #=-28 (116208,347182,230946) : difference with theory (-27) = 1 CORRECTING DEFECT 2 (vertices=690, convex hull=375, v0=31979) After retessellation of defect 2 (v0=31979), euler #=-27 (116392,347920,231501) : difference with theory (-26) = 1 CORRECTING DEFECT 3 (vertices=26, convex hull=59, v0=44483) After retessellation of defect 3 (v0=44483), euler #=-26 (116407,347990,231557) : difference with theory (-25) = 1 CORRECTING DEFECT 4 (vertices=176, convex hull=178, v0=53367) After retessellation of defect 4 (v0=53367), euler #=-25 (116486,348316,231805) : difference with theory (-24) = 1 CORRECTING DEFECT 5 (vertices=17, convex hull=26, v0=60276) After retessellation of defect 5 (v0=60276), euler #=-24 (116489,348334,231821) : difference with theory (-23) = 1 CORRECTING DEFECT 6 (vertices=23, convex hull=47, v0=61852) After retessellation of defect 6 (v0=61852), euler #=-23 (116501,348384,231860) : difference with theory (-22) = 1 CORRECTING DEFECT 7 (vertices=65, convex hull=48, v0=69483) After retessellation of defect 7 (v0=69483), euler #=-22 (116517,348453,231914) : difference with theory (-21) = 1 CORRECTING DEFECT 8 (vertices=6, convex hull=31, v0=70345) After retessellation of defect 8 (v0=70345), euler #=-21 (116519,348467,231927) : difference with theory (-20) = 1 CORRECTING DEFECT 9 (vertices=53, convex hull=85, v0=78195) After retessellation of defect 9 (v0=78195), euler #=-20 (116538,348565,232007) : difference with theory (-19) = 1 CORRECTING DEFECT 10 (vertices=273, convex hull=209, v0=81313) After retessellation of defect 10 (v0=81313), euler #=-19 (116632,348947,232296) : difference with theory (-18) = 1 CORRECTING DEFECT 11 (vertices=277, convex hull=221, v0=82011) After retessellation of defect 11 (v0=82011), euler #=-18 (116641,349080,232421) : difference with theory (-17) = 1 CORRECTING DEFECT 12 (vertices=15, convex hull=35, v0=83113) After retessellation of defect 12 (v0=83113), euler #=-17 (116644,349101,232440) : difference with theory (-16) = 1 CORRECTING DEFECT 13 (vertices=13, convex hull=30, v0=84100) After retessellation of defect 13 (v0=84100), euler #=-16 (116647,349120,232457) : difference with theory (-15) = 1 CORRECTING DEFECT 14 (vertices=24, convex hull=32, v0=84822) After retessellation of defect 14 (v0=84822), euler #=-15 (116652,349143,232476) : difference with theory (-14) = 1 CORRECTING DEFECT 15 (vertices=55, convex hull=40, v0=86091) After retessellation of defect 15 (v0=86091), euler #=-14 (116661,349186,232511) : difference with theory (-13) = 1 CORRECTING DEFECT 16 (vertices=23, convex hull=27, v0=87683) After retessellation of defect 16 (v0=87683), euler #=-13 (116663,349199,232523) : difference with theory (-12) = 1 CORRECTING DEFECT 17 (vertices=108, convex hull=51, v0=87910) After retessellation of defect 17 (v0=87910), euler #=-12 (116671,349245,232562) : difference with theory (-11) = 1 CORRECTING DEFECT 18 (vertices=119, convex hull=74, v0=91823) After retessellation of defect 18 (v0=91823), euler #=-11 (116694,349351,232646) : difference with theory (-10) = 1 CORRECTING DEFECT 19 (vertices=1407, convex hull=922, v0=92999) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 19 (v0=92999), euler #=-9 (117122,351130,233999) : difference with theory (-9) = 0 CORRECTING DEFECT 20 (vertices=25, convex hull=66, v0=93365) After retessellation of defect 20 (v0=93365), euler #=-8 (117136,351197,234053) : difference with theory (-8) = 0 CORRECTING DEFECT 21 (vertices=124, convex hull=47, v0=93414) After retessellation of defect 21 (v0=93414), euler #=-7 (117151,351262,234104) : difference with theory (-7) = 0 CORRECTING DEFECT 22 (vertices=19, convex hull=32, v0=99854) After retessellation of defect 22 (v0=99854), euler #=-6 (117155,351286,234125) : difference with theory (-6) = 0 CORRECTING DEFECT 23 (vertices=49, convex hull=45, v0=101069) After retessellation of defect 23 (v0=101069), euler #=-5 (117164,351326,234157) : difference with theory (-5) = 0 CORRECTING DEFECT 24 (vertices=42, convex hull=35, v0=104253) After retessellation of defect 24 (v0=104253), euler #=-4 (117169,351354,234181) : difference with theory (-4) = 0 CORRECTING DEFECT 25 (vertices=48, convex hull=97, v0=107524) After retessellation of defect 25 (v0=107524), euler #=-3 (117186,351447,234258) : difference with theory (-3) = 0 CORRECTING DEFECT 26 (vertices=47, convex hull=101, v0=114830) After retessellation of defect 26 (v0=114830), euler #=-2 (117204,351544,234338) : difference with theory (-2) = 0 CORRECTING DEFECT 27 (vertices=46, convex hull=39, v0=116853) After retessellation of defect 27 (v0=116853), euler #=-1 (117210,351577,234366) : difference with theory (-1) = 0 CORRECTING DEFECT 28 (vertices=29, convex hull=31, v0=117813) After retessellation of defect 28 (v0=117813), euler #=0 (117214,351601,234387) : difference with theory (0) = 0 CORRECTING DEFECT 29 (vertices=17, convex hull=63, v0=118829) After retessellation of defect 29 (v0=118829), euler #=1 (117222,351648,234427) : difference with theory (1) = 0 CORRECTING DEFECT 30 (vertices=24, convex hull=39, v0=118959) After retessellation of defect 30 (v0=118959), euler #=2 (117225,351669,234446) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.04-->16.01) (max @ vno 91251 --> 98337) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.04-->16.01) (max @ vno 91251 --> 98337) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 119 mutations (35.7%), 214 crossovers (64.3%), 299 vertices were eliminated building final representation... 2861 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=117225, nf=234446, ne=351669, g=0) writing corrected surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 630 intersecting 001: 120 intersecting 002: 54 intersecting 003: 48 intersecting 004: 47 intersecting step 1 with no progress (num=47, old_num=47) 005: 47 intersecting step 2 with no progress (num=47, old_num=47) 006: 47 intersecting step 3 with no progress (num=47, old_num=47) 007: 47 intersecting step 4 with no progress (num=47, old_num=47) 008: 47 intersecting step 5 with no progress (num=47, old_num=47) 009: 47 intersecting step 6 with no progress (num=47, old_num=47) 010: 47 intersecting step 7 with no progress (num=47, old_num=47) 011: 47 intersecting step 8 with no progress (num=47, old_num=47) 012: 47 intersecting step 9 with no progress (num=47, old_num=47) 013: 47 intersecting step 10 with no progress (num=47, old_num=47) 014: 47 intersecting step 11 with no progress (num=47, old_num=47) 015: 47 intersecting step 12 with no progress (num=47, old_num=47) 016: 47 intersecting step 13 with no progress (num=47, old_num=47) 017: 47 intersecting step 14 with no progress (num=47, old_num=47) 018: 47 intersecting step 15 with no progress (num=47, old_num=47) 019: 47 intersecting step 16 with no progress (num=47, old_num=47) terminating search with 47 intersecting topology fixing took 3.6 minutes FSRUNTIME@ mris_fix_topology lh 0.0606 hours 1 threads #VMPC# mris_fix_topology VmPeak 856444 @#@FSTIME 2020:07:27:17:02:51 mris_fix_topology N 14 e 218.35 S 0.33 U 217.80 P 99% M 720996 F 0 R 161077 W 0 c 253 w 118 I 0 O 0 L 9.02 9.71 10.75 @#@FSLOADPOST 2020:07:27:17:06:30 mris_fix_topology N 14 9.02 9.35 10.37 #@# Fix Topology rh Mon Jul 27 17:06:30 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 2012-646-010-KK rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.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 writing corrected surface to 'orig.premesh' 7.1.0 7.1.0 before topology correction, eno=-36 (nv=118150, nf=236372, ne=354558, 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 11 iterations marking ambiguous vertices... 5187 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 21 into 17 -merging segment 26 into 24 24 defects to be corrected 0 vertices coincident reading input surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.6047 (-4.8023) -vertex loglikelihood: -6.6422 (-3.3211) -normal dot loglikelihood: -3.6567 (-3.6567) -quad curv loglikelihood: -6.2019 (-3.1009) Total Loglikelihood : -26.1054 CORRECTING DEFECT 0 (vertices=546, convex hull=388, v0=2225) After retessellation of defect 0 (v0=2225), euler #=-23 (115002,343819,228794) : difference with theory (-21) = 2 CORRECTING DEFECT 1 (vertices=760, convex hull=714, v0=2449) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 1 (v0=2449), euler #=-22 (115299,345062,229741) : difference with theory (-20) = 2 CORRECTING DEFECT 2 (vertices=102, convex hull=85, v0=17419) After retessellation of defect 2 (v0=17419), euler #=-21 (115325,345175,229829) : difference with theory (-19) = 2 CORRECTING DEFECT 3 (vertices=42, convex hull=64, v0=17693) After retessellation of defect 3 (v0=17693), euler #=-20 (115351,345281,229910) : difference with theory (-18) = 2 CORRECTING DEFECT 4 (vertices=13, convex hull=29, v0=20516) After retessellation of defect 4 (v0=20516), euler #=-19 (115354,345299,229926) : difference with theory (-17) = 2 CORRECTING DEFECT 5 (vertices=8, convex hull=20, v0=22931) After retessellation of defect 5 (v0=22931), euler #=-18 (115355,345307,229934) : difference with theory (-16) = 2 CORRECTING DEFECT 6 (vertices=23, convex hull=77, v0=27007) After retessellation of defect 6 (v0=27007), euler #=-17 (115370,345385,229998) : difference with theory (-15) = 2 CORRECTING DEFECT 7 (vertices=234, convex hull=199, v0=32457) After retessellation of defect 7 (v0=32457), euler #=-16 (115422,345640,230202) : difference with theory (-14) = 2 CORRECTING DEFECT 8 (vertices=55, convex hull=96, v0=42095) After retessellation of defect 8 (v0=42095), euler #=-15 (115450,345768,230303) : difference with theory (-13) = 2 CORRECTING DEFECT 9 (vertices=19, convex hull=22, v0=45786) After retessellation of defect 9 (v0=45786), euler #=-14 (115454,345790,230322) : difference with theory (-12) = 2 CORRECTING DEFECT 10 (vertices=17, convex hull=33, v0=50666) After retessellation of defect 10 (v0=50666), euler #=-13 (115459,345816,230344) : difference with theory (-11) = 2 CORRECTING DEFECT 11 (vertices=133, convex hull=138, v0=51920) After retessellation of defect 11 (v0=51920), euler #=-12 (115533,346101,230556) : difference with theory (-10) = 2 CORRECTING DEFECT 12 (vertices=56, convex hull=43, v0=52817) After retessellation of defect 12 (v0=52817), euler #=-11 (115545,346155,230599) : difference with theory (-9) = 2 CORRECTING DEFECT 13 (vertices=23, convex hull=44, v0=67426) After retessellation of defect 13 (v0=67426), euler #=-10 (115550,346186,230626) : difference with theory (-8) = 2 CORRECTING DEFECT 14 (vertices=6, convex hull=16, v0=75300) After retessellation of defect 14 (v0=75300), euler #=-9 (115551,346192,230632) : difference with theory (-7) = 2 CORRECTING DEFECT 15 (vertices=41, convex hull=40, v0=76865) After retessellation of defect 15 (v0=76865), euler #=-8 (115562,346239,230669) : difference with theory (-6) = 2 CORRECTING DEFECT 16 (vertices=635, convex hull=444, v0=80419) After retessellation of defect 16 (v0=80419), euler #=-6 (115752,347032,231274) : difference with theory (-5) = 1 CORRECTING DEFECT 17 (vertices=118, convex hull=66, v0=81382) After retessellation of defect 17 (v0=81382), euler #=-5 (115778,347138,231355) : difference with theory (-4) = 1 CORRECTING DEFECT 18 (vertices=9, convex hull=19, v0=83124) After retessellation of defect 18 (v0=83124), euler #=-4 (115781,347153,231368) : difference with theory (-3) = 1 CORRECTING DEFECT 19 (vertices=204, convex hull=201, v0=88314) After retessellation of defect 19 (v0=88314), euler #=-3 (115874,347531,231654) : difference with theory (-2) = 1 CORRECTING DEFECT 20 (vertices=27, convex hull=41, v0=103947) After retessellation of defect 20 (v0=103947), euler #=-2 (115878,347558,231678) : difference with theory (-1) = 1 CORRECTING DEFECT 21 (vertices=49, convex hull=55, v0=111278) After retessellation of defect 21 (v0=111278), euler #=-1 (115886,347605,231718) : difference with theory (0) = 1 CORRECTING DEFECT 22 (vertices=107, convex hull=68, v0=116433) After retessellation of defect 22 (v0=116433), euler #=1 (115907,347697,231791) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=19, convex hull=50, v0=117508) After retessellation of defect 23 (v0=117508), euler #=2 (115913,347733,231822) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.02-->9.15) (max @ vno 17829 --> 25251) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.02-->9.15) (max @ vno 17829 --> 25251) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 83 mutations (37.4%), 139 crossovers (62.6%), 284 vertices were eliminated building final representation... 2237 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=115913, nf=231822, ne=347733, g=0) writing corrected surface to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 425 intersecting 001: 51 intersecting 002: 12 intersecting 003: 4 intersecting step 1 with no progress (num=4, old_num=4) 004: 4 intersecting step 2 with no progress (num=4, old_num=4) 005: 4 intersecting step 3 with no progress (num=4, old_num=4) 006: 4 intersecting step 4 with no progress (num=4, old_num=4) 007: 4 intersecting step 5 with no progress (num=4, old_num=4) 008: 4 intersecting step 6 with no progress (num=4, old_num=4) 009: 4 intersecting step 7 with no progress (num=4, old_num=4) 010: 4 intersecting step 8 with no progress (num=4, old_num=4) 011: 4 intersecting step 9 with no progress (num=4, old_num=4) 012: 4 intersecting step 10 with no progress (num=4, old_num=4) 013: 4 intersecting step 11 with no progress (num=4, old_num=4) 014: 4 intersecting step 12 with no progress (num=4, old_num=4) 015: 4 intersecting step 13 with no progress (num=4, old_num=4) 016: 4 intersecting step 14 with no progress (num=4, old_num=4) 017: 4 intersecting step 15 with no progress (num=4, old_num=4) 018: 4 intersecting step 16 with no progress (num=4, old_num=4) terminating search with 4 intersecting topology fixing took 3.2 minutes FSRUNTIME@ mris_fix_topology rh 0.0536 hours 1 threads #VMPC# mris_fix_topology VmPeak 854088 @#@FSTIME 2020:07:27:17:06:31 mris_fix_topology N 14 e 193.01 S 0.31 U 192.70 P 99% M 718660 F 0 R 161618 W 0 c 474 w 94 I 0 O 0 L 9.02 9.35 10.37 @#@FSLOADPOST 2020:07:27:17:09:44 mris_fix_topology N 14 12.22 10.22 10.48 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 117225 - 351669 + 234446 = 2 --> 0 holes F =2V-4: 234446 = 234450-4 (0) 2E=3F: 703338 = 703338 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 115913 - 347733 + 231822 = 2 --> 0 holes F =2V-4: 231822 = 231826-4 (0) 2E=3F: 695466 = 695466 (0) total defect index = 0 Mon Jul 27 17:09:50 EDT 2020 setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts /public/apps/freesurfer/7.1.0/bin/defect2seg --s 2012-646-010-KK freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b defect2seg 7.1.0 Linux n523 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pid 635315 mri_label2vol --defects /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.nofix /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defect_labels /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig.mgz 1000 0 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mris_defects_pointset -s /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.nofix -d /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defect_labels -o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defects.pointset Reading in surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.nofix Reading in defect segmentation /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.defect_labels #VMPC# mris_defects_pointset 177992 mris_defects_pointset done mri_label2vol --defects /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.nofix /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defect_labels /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz 2000 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 Writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/surface.defects.mgz mris_defects_pointset -s /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.nofix -d /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defect_labels -o /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defects.pointset Reading in surface /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.nofix Reading in defect segmentation /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.defect_labels #VMPC# mris_defects_pointset 175752 mris_defects_pointset done Started at Mon Jul 27 17:09:49 EDT 2020 Ended at Mon Jul 27 17:10:00 EDT 2020 Defect2seg-Run-Time-Sec 10 Defect2seg-Run-Time-Min 0.20 Defect2seg-Run-Time-Hours 0.00 tkmeditfv 2012-646-010-KK orig.mgz -defect -c /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/?h.defects.pointset defect2seg Done @#@FSTIME 2020:07:27:17:09:48 defect2seg N 2 e 13.18 S 0.76 U 5.96 P 51% M 223320 F 1 R 107159 W 0 c 76 w 2955 I 96 O 0 L 12.22 10.22 10.48 @#@FSLOADPOST 2020:07:27:17:10:01 defect2seg N 2 12.40 10.36 10.52 mris_remesh --remesh --iters 3 --input /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig.premesh --output /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.714404 remeshing to edge length 0.714404 with 3 iterations avg qual before : 0.885761 after: 0.970733 Removing intersections removing intersecting faces 000: 33 intersecting 001: 23 intersecting 002: 15 intersecting 003: 14 intersecting 004: 13 intersecting step 1 with no progress (num=13, old_num=13) 005: 13 intersecting step 2 with no progress (num=13, old_num=13) 006: 13 intersecting step 3 with no progress (num=13, old_num=13) 007: 13 intersecting step 4 with no progress (num=13, old_num=13) 008: 13 intersecting step 5 with no progress (num=13, old_num=13) 009: 13 intersecting step 6 with no progress (num=13, old_num=13) 010: 13 intersecting step 7 with no progress (num=13, old_num=13) 011: 13 intersecting step 8 with no progress (num=13, old_num=13) 012: 13 intersecting step 9 with no progress (num=13, old_num=13) 013: 13 intersecting step 10 with no progress (num=13, old_num=13) 014: 13 intersecting step 11 with no progress (num=13, old_num=13) 015: 13 intersecting step 12 with no progress (num=13, old_num=13) 016: 13 intersecting step 13 with no progress (num=13, old_num=13) 017: 13 intersecting step 14 with no progress (num=13, old_num=13) 018: 13 intersecting step 15 with no progress (num=13, old_num=13) 019: 13 intersecting step 16 with no progress (num=13, old_num=13) terminating search with 13 intersecting Remeshed surface quality stats nv0 = 117225 nv = 121584 1.03718 Area 243164 0.30508 0.03419 0.065995 0.4749 Corner 729492 60.00000 8.87462 15.151449 149.0102 Edge 364746 0.84752 0.08340 0.287002 1.3090 Hinge 364746 9.94181 10.62489 0.000014 168.5767 mris_remesh done @#@FSTIME 2020:07:27:17:10:02 mris_remesh N 7 e 57.76 S 0.50 U 56.98 P 99% M 899240 F 0 R 183968 W 0 c 64 w 55 I 0 O 0 L 12.40 10.36 10.52 @#@FSLOADPOST 2020:07:27:17:11:00 mris_remesh N 7 10.85 10.31 10.49 mris_remesh --remesh --iters 3 --input /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig.premesh --output /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.712866 remeshing to edge length 0.712866 with 3 iterations avg qual before : 0.889735 after: 0.971439 Removing intersections Remeshed surface quality stats nv0 = 115913 nv = 120651 1.04088 Area 241298 0.30392 0.03362 0.083496 0.4849 Corner 723894 60.00000 8.75570 14.239817 150.2662 Edge 361947 0.84570 0.08224 0.459830 1.3036 Hinge 361947 9.92537 10.56286 0.000005 162.7806 mris_remesh done @#@FSTIME 2020:07:27:17:11:01 mris_remesh N 7 e 23.97 S 0.29 U 23.68 P 100% M 663648 F 0 R 110500 W 0 c 30 w 28 I 0 O 0 L 10.85 10.31 10.49 @#@FSLOADPOST 2020:07:27:17:11:26 mris_remesh N 7 10.36 10.24 10.46 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 13 intersecting step 1 with no progress (num=13, old_num=13) 001: 13 intersecting step 2 with no progress (num=13, old_num=13) 002: 13 intersecting step 3 with no progress (num=13, old_num=13) 003: 13 intersecting step 4 with no progress (num=13, old_num=13) 004: 13 intersecting step 5 with no progress (num=13, old_num=13) 005: 13 intersecting step 6 with no progress (num=13, old_num=13) 006: 13 intersecting step 7 with no progress (num=13, old_num=13) 007: 13 intersecting step 8 with no progress (num=13, old_num=13) 008: 13 intersecting step 9 with no progress (num=13, old_num=13) 009: 13 intersecting step 10 with no progress (num=13, old_num=13) 010: 13 intersecting step 11 with no progress (num=13, old_num=13) 011: 13 intersecting step 12 with no progress (num=13, old_num=13) 012: 13 intersecting step 13 with no progress (num=13, old_num=13) 013: 13 intersecting step 14 with no progress (num=13, old_num=13) 014: 13 intersecting step 15 with no progress (num=13, old_num=13) 015: 13 intersecting step 16 with no progress (num=13, old_num=13) terminating search with 13 intersecting writing corrected surface to ../surf/lh.orig @#@FSTIME 2020:07:27:17:11:27 mris_remove_intersection N 2 e 23.69 S 1.27 U 22.15 P 98% M 362052 F 0 R 693766 W 0 c 27 w 51 I 0 O 0 L 10.36 10.24 10.46 @#@FSLOADPOST 2020:07:27:17:11:51 mris_remove_intersection N 2 10.10 10.19 10.44 rm ../surf/lh.inflated /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2020:07:27:17:11:52 mris_remove_intersection N 2 e 2.22 S 0.13 U 2.08 P 99% M 310472 F 0 R 56887 W 0 c 4 w 30 I 0 O 0 L 10.10 10.19 10.44 @#@FSLOADPOST 2020:07:27:17:11:55 mris_remove_intersection N 2 10.01 10.17 10.43 rm ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Mon Jul 27 17:11:56 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 215539 voxels (1.28%) border gray 248151 voxels (1.48%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (97.0): 97.1 +- 9.1 [70.0 --> 110.0] CCS GM (69.0) : 68.5 +- 10.9 [30.0 --> 110.0] white_mean = 97.0982 +/- 9.1407, gray_mean = 68.4735 +/- 10.8946 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=170 nbins=171 intensity peaks found at WM=103+-6.1, GM=63+-8.7 white_mode = 103, gray_mode = 63 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 52.1 (was 70.000000) setting MAX_BORDER_WHITE to 112.1 (was 105.000000) setting MIN_BORDER_WHITE to 63.0 (was 85.000000) setting MAX_CSF to 41.2 (was 40.000000) setting MAX_GRAY to 93.9 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 52.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 30.3 (was 40.000000) When placing the white surface white_border_hi = 112.141; white_border_low = 63; white_outside_low = 52.1054; white_inside_hi = 120; white_outside_hi = 112.141; When placing the pial surface pial_border_hi = 52.1054; pial_border_low = 30.3162; pial_outside_low = 10; pial_inside_hi = 93.8593; pial_outside_hi = 46.6581; #VMPC# mris_autodet_gwstats VmPeak 350788 mris_autodet_gwstats done @#@FSTIME 2020:07:27:17:11:57 mris_autodet_gwstats N 8 e 4.11 S 0.08 U 3.87 P 96% M 216876 F 0 R 29096 W 0 c 5 w 66 I 0 O 0 L 10.01 10.17 10.43 @#@FSLOADPOST 2020:07:27:17:12:01 mris_autodet_gwstats N 8 10.01 10.16 10.43 #-------------------------------------------- #@# AutoDetGWStats rh Mon Jul 27 17:12:02 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 215539 voxels (1.28%) border gray 248151 voxels (1.48%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (97.0): 97.1 +- 9.1 [70.0 --> 110.0] CCS GM (69.0) : 68.5 +- 10.9 [30.0 --> 110.0] white_mean = 97.0982 +/- 9.1407, gray_mean = 68.4735 +/- 10.8946 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=170 nbins=171 intensity peaks found at WM=102+-6.1, GM=62+-7.8 white_mode = 102, gray_mode = 62 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 51.1 (was 70.000000) setting MAX_BORDER_WHITE to 111.1 (was 105.000000) setting MIN_BORDER_WHITE to 62.0 (was 85.000000) setting MAX_CSF to 40.2 (was 40.000000) setting MAX_GRAY to 92.9 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 51.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 29.3 (was 40.000000) When placing the white surface white_border_hi = 111.141; white_border_low = 62; white_outside_low = 51.1054; white_inside_hi = 120; white_outside_hi = 111.141; When placing the pial surface pial_border_hi = 51.1054; pial_border_low = 29.3162; pial_outside_low = 10; pial_inside_hi = 92.8593; pial_outside_hi = 45.6581; #VMPC# mris_autodet_gwstats VmPeak 348972 mris_autodet_gwstats done @#@FSTIME 2020:07:27:17:12:03 mris_autodet_gwstats N 8 e 3.97 S 0.08 U 3.88 P 99% M 215060 F 0 R 29591 W 0 c 7 w 43 I 0 O 0 L 10.01 10.16 10.43 @#@FSLOADPOST 2020:07:27:17:12:07 mris_autodet_gwstats N 8 9.93 10.14 10.42 #-------------------------------------------- #@# WhitePreAparc lh Mon Jul 27 17:12:08 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 243164 0.26804 0.06524 0.001282 0.5788 Corner 729492 60.00000 9.72910 1.250939 176.6314 Edge 364746 0.79052 0.11821 0.027763 1.4499 Hinge 364746 6.56435 6.70407 0.000003 176.4319 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5928, nmarked2=88, nripped=5928 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60792: xyz = (-58.8021,-7.92064,-5.67842) oxyz = (-58.8021,-7.92064,-5.67842) wxzy = (-58.8021,-7.92064,-5.67842) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5928 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5928, nmarked2=88, nripped=5928 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=2 had to be increased for 382 vertices, nripped=5928 mean border=76.7, 212 (212) missing vertices, mean dist 0.3 [0.6 (%34.6)->0.8 (%65.4))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2666 min Finding expansion regions mean absolute distance = 0.72 +- 0.90 3981 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= n523, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=3476924.2, rms=12.025 001: dt: 0.5000, sse=1957007.0, rms=8.886 (26.102%) 002: dt: 0.5000, sse=1271381.0, rms=7.017 (21.040%) 003: dt: 0.5000, sse=911760.0, rms=5.814 (17.144%) 004: dt: 0.5000, sse=721233.1, rms=5.026 (13.542%) 005: dt: 0.5000, sse=610799.6, rms=4.537 (9.738%) 006: dt: 0.5000, sse=557652.9, rms=4.255 (6.216%) 007: dt: 0.5000, sse=529148.8, rms=4.095 (3.760%) 008: dt: 0.5000, sse=511661.2, rms=3.999 (2.353%) 009: dt: 0.5000, sse=502670.1, rms=3.935 (1.590%) rms = 3.8880/3.9350, sse=490895.5/502670.1, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=490895.5, rms=3.888 (1.196%) 011: dt: 0.2500, sse=300157.0, rms=2.569 (33.923%) 012: dt: 0.2500, sse=264336.3, rms=2.249 (12.465%) 013: dt: 0.2500, sse=252026.0, rms=2.149 (4.446%) 014: dt: 0.2500, sse=251589.7, rms=2.094 (2.569%) rms = 2.0593/2.0936, sse=250885.3/251589.7, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=250885.3, rms=2.059 (1.642%) 016: dt: 0.1250, sse=242574.7, rms=1.997 (3.025%) rms = 1.9797/1.9970, sse=237112.6/242574.7, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=237112.6, rms=1.980 (0.863%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5928 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6364, nmarked2=157, nripped=6364 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=1 had to be increased for 233 vertices, nripped=6364 mean border=80.0, 165 (30) missing vertices, mean dist -0.2 [0.4 (%74.1)->0.3 (%25.9))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.1810 min Finding expansion regions mean absolute distance = 0.34 +- 0.59 2910 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= n523, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=799813.9, rms=5.126 018: dt: 0.5000, sse=487162.2, rms=3.519 (31.357%) rms = 3.6224/3.5190, sse=503292.2/487162.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=368327.5, rms=2.709 (23.020%) 020: dt: 0.2500, sse=306206.3, rms=2.145 (20.823%) 021: dt: 0.2500, sse=295760.2, rms=1.886 (12.077%) 022: dt: 0.2500, sse=273602.5, rms=1.755 (6.916%) 023: dt: 0.2500, sse=260971.0, rms=1.674 (4.619%) rms = 1.6331/1.6743, sse=260040.5/260971.0, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=260040.5, rms=1.633 (2.460%) rms = 1.5847/1.6331, sse=254768.8/260040.5, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=254768.8, rms=1.585 (2.962%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6364 removing 1 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6403, nmarked2=159, nripped=6403 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 230 vertices, nripped=6403 mean border=82.2, 164 (11) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.2 (%30.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0974 min Finding expansion regions mean absolute distance = 0.25 +- 0.41 2834 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= n523, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=445945.8, rms=3.307 026: dt: 0.5000, sse=409634.2, rms=2.995 (9.437%) rms = 3.3583/2.9947, sse=466227.5/409634.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=296186.9, rms=2.056 (31.341%) 028: dt: 0.2500, sse=265971.3, rms=1.647 (19.903%) 029: dt: 0.2500, sse=251253.6, rms=1.524 (7.445%) rms = 1.5060/1.5243, sse=247044.5/251253.6, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=247044.5, rms=1.506 (1.197%) rms = 1.4419/1.5060, sse=252885.9/247044.5, time step reduction 3 of 3 to 0.062 0 1 0 031: dt: 0.1250, sse=252885.9, rms=1.442 (4.261%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6403 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6452, nmarked2=163, nripped=6452 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 210 vertices, nripped=6452 mean border=83.1, 210 (9) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0629 min Finding expansion regions mean absolute distance = 0.22 +- 0.34 2885 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= n523, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=280889.9, rms=1.841 rms = 2.0694/1.8414, sse=299295.2/280889.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=241265.5, rms=1.416 (23.089%) 033: dt: 0.2500, sse=232365.8, rms=1.219 (13.925%) rms = 1.2093/1.2190, sse=226177.0/232365.8, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=226177.0, rms=1.209 (0.801%) rms = 1.1882/1.2093, sse=225739.9/226177.0, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=225739.9, rms=1.188 (1.744%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 4.09 minutes #VMPC# mris_make_surfaces VmPeak 2233592 mris_place_surface done @#@FSTIME 2020:07:27:17:12:09 mris_place_surface N 16 e 253.73 S 0.70 U 252.73 P 99% M 1862912 F 0 R 258304 W 0 c 841 w 87 I 0 O 0 L 9.93 10.14 10.42 @#@FSLOADPOST 2020:07:27:17:16:23 mris_place_surface N 16 15.94 11.60 10.82 #-------------------------------------------- #@# WhitePreAparc rh Mon Jul 27 17:16:24 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface with 5 iterations Area 241298 0.26699 0.06456 0.007102 0.6288 Corner 723894 60.00000 9.65011 11.784599 141.8663 Edge 361947 0.78892 0.11695 0.104140 1.3036 Hinge 361947 6.54318 6.66458 0.000004 144.1443 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6059, nmarked2=117, nripped=6059 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60326: xyz = (6.01705,-6.86342,31.6417) oxyz = (6.01705,-6.86342,31.6417) wxzy = (6.01705,-6.86342,31.6417) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6059 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6059, nmarked2=117, nripped=6059 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=2 had to be increased for 312 vertices, nripped=6059 mean border=75.6, 145 (145) missing vertices, mean dist 0.4 [0.5 (%33.7)->0.8 (%66.3))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2691 min Finding expansion regions mean absolute distance = 0.72 +- 0.87 4077 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= n523, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=3665531.8, rms=12.421 001: dt: 0.5000, sse=2095957.2, rms=9.272 (25.357%) 002: dt: 0.5000, sse=1354492.2, rms=7.321 (21.036%) 003: dt: 0.5000, sse=949174.2, rms=5.991 (18.169%) 004: dt: 0.5000, sse=721683.4, rms=5.090 (15.035%) 005: dt: 0.5000, sse=596332.1, rms=4.503 (11.535%) 006: dt: 0.5000, sse=530020.9, rms=4.173 (7.321%) 007: dt: 0.5000, sse=494010.1, rms=3.973 (4.813%) 008: dt: 0.5000, sse=478600.8, rms=3.881 (2.313%) 009: dt: 0.5000, sse=467669.2, rms=3.814 (1.730%) rms = 3.7794/3.8135, sse=462995.1/467669.2, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=462995.1, rms=3.779 (0.896%) 011: dt: 0.2500, sse=268287.6, rms=2.379 (37.056%) 012: dt: 0.2500, sse=233601.4, rms=2.038 (14.345%) 013: dt: 0.2500, sse=225496.0, rms=1.946 (4.514%) rms = 1.8961/1.9456, sse=221585.8/225496.0, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=221585.8, rms=1.896 (2.547%) 015: dt: 0.1250, sse=215442.0, rms=1.822 (3.916%) rms = 1.8089/1.8218, sse=214660.6/215442.0, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=214660.6, rms=1.809 (0.708%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6059 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6237, nmarked2=127, nripped=6237 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=1 had to be increased for 153 vertices, nripped=6237 mean border=78.9, 133 (27) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.3 (%26.5))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.1859 min Finding expansion regions mean absolute distance = 0.33 +- 0.56 2468 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= n523, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=769020.4, rms=5.028 017: dt: 0.5000, sse=454514.9, rms=3.387 (32.637%) rms = 3.5764/3.3872, sse=492826.9/454514.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=336518.3, rms=2.522 (25.546%) 019: dt: 0.2500, sse=278828.8, rms=1.963 (22.159%) 020: dt: 0.2500, sse=257350.2, rms=1.711 (12.847%) 021: dt: 0.2500, sse=249612.5, rms=1.605 (6.179%) 022: dt: 0.2500, sse=245451.3, rms=1.540 (4.054%) rms = 1.5027/1.5401, sse=243460.7/245451.3, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=243460.7, rms=1.503 (2.425%) 024: dt: 0.1250, sse=240099.3, rms=1.443 (3.972%) rms = 1.4319/1.4430, sse=240130.2/240099.3, time step reduction 3 of 3 to 0.062 0 1 1 025: dt: 0.1250, sse=240130.2, rms=1.432 (0.769%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6237 removing 1 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6258, nmarked2=129, nripped=6258 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 148 vertices, nripped=6258 mean border=81.3, 153 (17) missing vertices, mean dist -0.1 [0.3 (%70.4)->0.2 (%29.6))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0983 min Finding expansion regions mean absolute distance = 0.25 +- 0.39 3160 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= n523, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=458944.4, rms=3.427 026: dt: 0.5000, sse=400976.1, rms=3.003 (12.368%) rms = 3.3509/3.0031, sse=446989.6/400976.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=284047.4, rms=1.993 (33.651%) 028: dt: 0.2500, sse=245300.2, rms=1.509 (24.257%) 029: dt: 0.2500, sse=235658.6, rms=1.356 (10.124%) rms = 1.3323/1.3564, sse=237407.4/235658.6, time step reduction 2 of 3 to 0.125 0 1 1 030: dt: 0.2500, sse=237407.4, rms=1.332 (1.775%) 031: dt: 0.1250, sse=228890.5, rms=1.255 (5.797%) rms = 1.2445/1.2551, sse=229090.6/228890.5, time step reduction 3 of 3 to 0.062 0 1 1 032: dt: 0.1250, sse=229090.6, rms=1.244 (0.849%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6258 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6340, nmarked2=132, nripped=6340 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 169 vertices, nripped=6340 mean border=82.2, 197 (14) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0617 min Finding expansion regions mean absolute distance = 0.21 +- 0.33 2576 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= n523, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=256688.6, rms=1.695 rms = 1.9535/1.6949, sse=277768.8/256688.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=223117.0, rms=1.202 (29.083%) 034: dt: 0.2500, sse=213086.8, rms=0.970 (19.332%) rms = 0.9744/0.9696, sse=211636.4/213086.8, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.9644/0.9696, sse=212590.6/213086.8, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=212590.6, rms=0.964 (0.533%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 4.28 minutes #VMPC# mris_make_surfaces VmPeak 2241636 mris_place_surface done @#@FSTIME 2020:07:27:17:16:25 mris_place_surface N 16 e 265.49 S 0.60 U 264.80 P 99% M 1870960 F 0 R 257473 W 0 c 344 w 76 I 0 O 0 L 16.34 11.75 10.87 @#@FSLOADPOST 2020:07:27:17:20:51 mris_place_surface N 16 21.47 17.51 13.52 #-------------------------------------------- #@# CortexLabel lh Mon Jul 27 17:20:51 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 13 non-cortical segments detected only using segment with 6953 vertices erasing segment 0 (vno[0] = 28085) erasing segment 2 (vno[0] = 47776) erasing segment 3 (vno[0] = 59671) erasing segment 4 (vno[0] = 68493) erasing segment 5 (vno[0] = 68527) erasing segment 6 (vno[0] = 68537) erasing segment 7 (vno[0] = 70026) erasing segment 8 (vno[0] = 73772) erasing segment 9 (vno[0] = 75175) erasing segment 10 (vno[0] = 99377) erasing segment 11 (vno[0] = 100092) erasing segment 12 (vno[0] = 116209) @#@FSTIME 2020:07:27:17:20:52 mri_label2label N 5 e 26.25 S 0.13 U 25.81 P 98% M 337076 F 0 R 32680 W 0 c 706 w 79 I 0 O 0 L 21.47 17.51 13.52 @#@FSLOADPOST 2020:07:27:17:21:19 mri_label2label N 5 21.54 17.91 13.77 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Mon Jul 27 17:21:19 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 12 non-cortical segments detected only using segment with 5251 vertices erasing segment 0 (vno[0] = 28085) erasing segment 2 (vno[0] = 42986) erasing segment 3 (vno[0] = 59671) erasing segment 4 (vno[0] = 65078) erasing segment 5 (vno[0] = 67719) erasing segment 6 (vno[0] = 68493) erasing segment 7 (vno[0] = 68527) erasing segment 8 (vno[0] = 70026) erasing segment 9 (vno[0] = 73772) erasing segment 10 (vno[0] = 75175) erasing segment 11 (vno[0] = 116209) @#@FSTIME 2020:07:27:17:21:21 mri_label2label N 5 e 20.03 S 0.11 U 19.91 P 99% M 332804 F 0 R 31556 W 0 c 694 w 36 I 0 O 0 L 21.54 17.91 13.77 @#@FSLOADPOST 2020:07:27:17:21:41 mri_label2label N 5 21.53 18.14 13.94 #-------------------------------------------- #@# CortexLabel rh Mon Jul 27 17:21:41 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 10 non-cortical segments detected only using segment with 7065 vertices erasing segment 0 (vno[0] = 12690) erasing segment 1 (vno[0] = 16270) erasing segment 2 (vno[0] = 17595) erasing segment 4 (vno[0] = 31685) erasing segment 5 (vno[0] = 37963) erasing segment 6 (vno[0] = 47835) erasing segment 7 (vno[0] = 55527) erasing segment 8 (vno[0] = 75567) erasing segment 9 (vno[0] = 111761) @#@FSTIME 2020:07:27:17:21:43 mri_label2label N 5 e 26.81 S 0.12 U 26.63 P 99% M 322756 F 0 R 29696 W 0 c 1156 w 42 I 0 O 0 L 21.53 18.14 13.94 @#@FSLOADPOST 2020:07:27:17:22:10 mri_label2label N 5 21.53 18.46 14.18 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Mon Jul 27 17:22:10 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 17 non-cortical segments detected only using segment with 4742 vertices erasing segment 0 (vno[0] = 12690) erasing segment 1 (vno[0] = 16270) erasing segment 2 (vno[0] = 17595) erasing segment 4 (vno[0] = 31685) erasing segment 5 (vno[0] = 32340) erasing segment 6 (vno[0] = 33753) erasing segment 7 (vno[0] = 35537) erasing segment 8 (vno[0] = 37963) erasing segment 9 (vno[0] = 47835) erasing segment 10 (vno[0] = 54146) erasing segment 11 (vno[0] = 55527) erasing segment 12 (vno[0] = 64868) erasing segment 13 (vno[0] = 67152) erasing segment 14 (vno[0] = 75567) erasing segment 15 (vno[0] = 102073) erasing segment 16 (vno[0] = 111761) @#@FSTIME 2020:07:27:17:22:11 mri_label2label N 5 e 16.11 S 0.10 U 16.01 P 100% M 352460 F 0 R 33874 W 0 c 22 w 39 I 0 O 0 L 21.53 18.46 14.18 @#@FSLOADPOST 2020:07:27:17:22:28 mri_label2label N 5 21.48 18.60 14.29 #-------------------------------------------- #@# Smooth2 lh Mon Jul 27 17:22:28 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts 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... @#@FSTIME 2020:07:27:17:22:29 mris_smooth N 7 e 3.75 S 0.07 U 3.48 P 94% M 186456 F 0 R 29706 W 0 c 19 w 61 I 0 O 0 L 21.44 18.64 14.33 @#@FSLOADPOST 2020:07:27:17:22:33 mris_smooth N 7 21.44 18.64 14.33 #-------------------------------------------- #@# Smooth2 rh Mon Jul 27 17:22:34 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts 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... @#@FSTIME 2020:07:27:17:22:35 mris_smooth N 7 e 3.48 S 0.07 U 3.38 P 99% M 184996 F 0 R 29791 W 0 c 15 w 32 I 0 O 0 L 21.33 18.66 14.36 @#@FSLOADPOST 2020:07:27:17:22:39 mris_smooth N 7 21.33 18.66 14.36 #-------------------------------------------- #@# Inflation2 lh Mon Jul 27 17:22:39 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.6 mm, total surface area = 76598 mm^2 step 000: RMS=0.176 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 22.589565 mris_inflate stimesec 0.097985 mris_inflate ru_maxrss 248188 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 45313 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 72 mris_inflate ru_nivcsw 97 @#@FSTIME 2020:07:27:17:22:40 mris_inflate N 2 e 22.82 S 0.10 U 22.59 P 99% M 248188 F 0 R 45314 W 0 c 97 w 75 I 0 O 0 L 21.30 18.70 14.39 @#@FSLOADPOST 2020:07:27:17:23:03 mris_inflate N 2 21.36 18.88 14.54 #-------------------------------------------- #@# Inflation2 rh Mon Jul 27 17:23:04 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.3 mm, total surface area = 76666 mm^2 step 000: RMS=0.178 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.028 (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) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.5 minutes mris_inflate utimesec 31.068276 mris_inflate stimesec 0.114982 mris_inflate ru_maxrss 246264 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 46296 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 65 mris_inflate ru_nivcsw 2157 @#@FSTIME 2020:07:27:17:23:05 mris_inflate N 2 e 31.25 S 0.13 U 31.06 P 99% M 246264 F 0 R 46297 W 0 c 2160 w 65 I 0 O 0 L 21.17 18.88 14.57 @#@FSLOADPOST 2020:07:27:17:23:36 mris_inflate N 2 20.96 19.05 14.76 #-------------------------------------------- #@# Curv .H and .K lh Mon Jul 27 17:23:37 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 28.422*4pi (357.157) --> -27 handles ICI = 156.7, FI = 1478.6, variation=23374.157 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2020:07:27:17:23:38 mris_curvature N 4 e 2.12 S 0.05 U 1.73 P 84% M 137440 F 0 R 21588 W 0 c 36 w 128 I 0 O 0 L 20.96 19.05 14.76 @#@FSLOADPOST 2020:07:27:17:23:40 mris_curvature N 4 20.96 19.08 14.79 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 -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 127 vertices thresholded to be in k1 ~ [-0.63 0.70], k2 ~ [-0.14 0.35] total integrated curvature = 0.409*4pi (5.139) --> 1 handles ICI = 1.4, FI = 9.2, variation=157.379 128 vertices thresholded to be in [-0.10 0.04] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 104 vertices thresholded to be in [-0.26 0.24] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.019, std = 0.025 done. @#@FSTIME 2020:07:27:17:23:43 mris_curvature N 12 e 54.80 S 0.17 U 54.53 P 99% M 328076 F 0 R 68900 W 0 c 171 w 92 I 0 O 0 L 20.96 19.08 14.79 @#@FSLOADPOST 2020:07:27:17:24:38 mris_curvature N 12 20.71 19.33 15.12 #-------------------------------------------- #@# Curv .H and .K rh Mon Jul 27 17:24:38 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 20.169*4pi (253.457) --> -19 handles ICI = 148.1, FI = 1440.3, variation=22763.521 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2020:07:27:17:24:39 mris_curvature N 4 e 1.81 S 0.07 U 1.69 P 97% M 136348 F 0 R 20891 W 0 c 10 w 89 I 0 O 0 L 20.65 19.34 15.15 @#@FSLOADPOST 2020:07:27:17:24:41 mris_curvature N 4 20.65 19.34 15.15 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 -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 127 vertices thresholded to be in k1 ~ [-0.31 0.38], k2 ~ [-0.11 0.09] total integrated curvature = 0.518*4pi (6.512) --> 0 handles ICI = 1.4, FI = 8.8, variation=151.876 98 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 118 vertices thresholded to be in [-0.16 0.18] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.023 done. @#@FSTIME 2020:07:27:17:24:44 mris_curvature N 12 e 67.56 S 0.20 U 67.24 P 99% M 325496 F 0 R 67951 W 0 c 4126 w 86 I 0 O 0 L 20.65 19.34 15.15 @#@FSLOADPOST 2020:07:27:17:25:51 mris_curvature N 12 20.42 19.54 15.52 #-------------------------------------------- #@# Sphere lh Mon Jul 27 17:25:52 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.285... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n523, 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.72 pass 1: epoch 2 of 3 starting distance error %21.71 unfolding complete - removing small folds... starting distance error %21.57 removing remaining folds... final distance error %21.62 MRISunfold() return, current seed 1234 -01: dt=0.0000, 16 negative triangles 195: dt=0.9900, 16 negative triangles 196: dt=0.9900, 12 negative triangles 197: dt=0.9900, 7 negative triangles 198: dt=0.9900, 6 negative triangles 199: dt=0.9900, 5 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 4 negative triangles 202: dt=0.9900, 1 negative triangles 203: dt=0.9900, 5 negative triangles 204: dt=0.9900, 3 negative triangles 205: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere mris_sphere utimesec 730.883888 mris_sphere stimesec 1.233812 mris_sphere ru_maxrss 2004592 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 846580 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 34 mris_sphere ru_nivcsw 1210 spherical transformation took 0.2033 hours FSRUNTIME@ mris_sphere 0.2033 hours 1 threads @#@FSTIME 2020:07:27:17:25:53 mris_sphere N 6 e 732.01 S 1.34 U 730.88 P 100% M 2004592 F 0 R 846582 W 0 c 1210 w 40 I 0 O 0 L 20.42 19.54 15.52 @#@FSLOADPOST 2020:07:27:17:38:05 mris_sphere N 6 20.03 21.46 18.67 #-------------------------------------------- #@# Sphere rh Mon Jul 27 17:38:06 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.283... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n523, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %43.73 pass 1: epoch 2 of 3 starting distance error %22.40 unfolding complete - removing small folds... starting distance error %22.21 removing remaining folds... final distance error %22.26 MRISunfold() return, current seed 1234 -01: dt=0.0000, 0 negative triangles writing spherical brain to ../surf/rh.sphere mris_sphere utimesec 678.063918 mris_sphere stimesec 1.216815 mris_sphere ru_maxrss 1894428 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 800487 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 46 mris_sphere ru_nivcsw 748 spherical transformation took 0.1886 hours FSRUNTIME@ mris_sphere 0.1886 hours 1 threads @#@FSTIME 2020:07:27:17:38:07 mris_sphere N 6 e 679.27 S 1.34 U 678.06 P 100% M 1894428 F 0 R 800489 W 0 c 748 w 50 I 0 O 0 L 20.03 21.46 18.67 @#@FSLOADPOST 2020:07:27:17:49:26 mris_sphere N 6 16.04 16.87 17.57 #-------------------------------------------- #@# Surf Reg lh Mon Jul 27 17:49:27 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.0 7.1.0 reading surface from ../surf/lh.sphere... reading template parameterization from /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n523, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n523, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host= n523, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.581 curvature mean = 0.041, std = 0.813 curvature mean = 0.008, std = 0.873 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (0.50, -6.50, 9.50) sse = 225953.2, elapsed since starting=0.5003 min MRISrigidBodyAlignGlobal() done 0.50 min curvature mean = 0.020, std = 0.838 curvature mean = 0.003, std = 0.953 curvature mean = 0.017, std = 0.850 curvature mean = 0.001, std = 0.982 curvature mean = 0.017, std = 0.853 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.023, std = 0.272 curvature mean = 0.044, std = 0.249 curvature mean = 0.052, std = 0.389 curvature mean = 0.034, std = 0.310 curvature mean = 0.036, std = 0.575 curvature mean = 0.033, std = 0.338 curvature mean = 0.019, std = 0.716 curvature mean = 0.033, std = 0.350 curvature mean = 0.006, std = 0.821 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles 106: dt=0.9900, 15 negative triangles 107: dt=0.9900, 13 negative triangles 108: dt=0.9900, 10 negative triangles 109: dt=0.9900, 10 negative triangles 110: dt=0.9900, 8 negative triangles 111: dt=0.9900, 2 negative triangles 112: dt=0.9900, 5 negative triangles 113: dt=0.9900, 4 negative triangles 114: dt=0.9900, 1 negative triangles 115: dt=0.9900, 2 negative triangles 116: dt=0.9900, 1 negative triangles 117: dt=0.9900, 3 negative triangles 118: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.13 hours #VMPC# mris_register VmPeak 1622748 FSRUNTIME@ mris_register 0.1329 hours 1 threads @#@FSTIME 2020:07:27:17:49:28 mris_register N 6 e 478.83 S 0.86 U 477.58 P 99% M 1252236 F 0 R 495844 W 0 c 651 w 101 I 0 O 0 L 16.04 16.87 17.57 @#@FSLOADPOST 2020:07:27:17:57:27 mris_register N 6 5.15 8.25 13.26 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Mon Jul 27 17:57:28 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.0 7.1.0 reading surface from ../surf/rh.sphere... reading template parameterization from /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n523, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n523, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host= n523, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.770 curvature mean = 0.062, std = 0.813 curvature mean = 0.005, std = 0.876 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.50, -11.00, 12.50) sse = 277082.9, elapsed since starting=0.5073 min MRISrigidBodyAlignGlobal() done 0.51 min curvature mean = 0.036, std = 0.834 curvature mean = 0.003, std = 0.954 curvature mean = 0.033, std = 0.845 curvature mean = 0.001, std = 0.982 curvature mean = 0.032, std = 0.848 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.020, std = 0.273 curvature mean = 0.044, std = 0.244 curvature mean = 0.051, std = 0.387 curvature mean = 0.037, std = 0.303 curvature mean = 0.033, std = 0.574 curvature mean = 0.036, std = 0.330 curvature mean = 0.016, std = 0.713 curvature mean = 0.036, std = 0.342 curvature mean = 0.004, std = 0.817 MRISregister() return, current seed 0 -01: dt=0.0000, 3 negative triangles 107: dt=0.9900, 3 negative triangles 108: dt=0.9900, 1 negative triangles 109: dt=0.9900, 2 negative triangles 110: dt=0.9900, 2 negative triangles 111: dt=0.9900, 1 negative triangles 112: dt=0.9900, 2 negative triangles 113: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.15 hours #VMPC# mris_register VmPeak 1615240 FSRUNTIME@ mris_register 0.1464 hours 1 threads @#@FSTIME 2020:07:27:17:57:29 mris_register N 6 e 527.02 S 0.84 U 526.12 P 99% M 1244732 F 0 R 488088 W 0 c 908 w 60 I 0 O 0 L 5.15 8.25 13.26 @#@FSLOADPOST 2020:07:27:18:06:16 mris_register N 6 12.11 10.37 12.14 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Mon Jul 27 18:06:17 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2020:07:27:18:06:18 mris_jacobian N 3 e 1.79 S 0.10 U 1.29 P 77% M 186064 F 0 R 31314 W 0 c 13 w 86 I 0 O 0 L 12.11 10.37 12.14 @#@FSLOADPOST 2020:07:27:18:06:20 mris_jacobian N 3 12.58 10.50 12.18 #-------------------------------------------- #@# Jacobian white rh Mon Jul 27 18:06:21 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2020:07:27:18:06:22 mris_jacobian N 3 e 1.37 S 0.08 U 1.17 P 91% M 184600 F 0 R 30498 W 0 c 3 w 59 I 0 O 0 L 12.58 10.50 12.18 @#@FSLOADPOST 2020:07:27:18:06:24 mris_jacobian N 3 12.58 10.50 12.18 #-------------------------------------------- #@# AvgCurv lh Mon Jul 27 18:06:24 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2020:07:27:18:06:25 mrisp_paint N 5 e 1.52 S 0.07 U 1.06 P 74% M 142588 F 0 R 20320 W 0 c 5 w 93 I 0 O 0 L 13.01 10.62 12.21 @#@FSLOADPOST 2020:07:27:18:06:27 mrisp_paint N 5 13.01 10.62 12.21 #-------------------------------------------- #@# AvgCurv rh Mon Jul 27 18:06:27 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2020:07:27:18:06:29 mrisp_paint N 5 e 1.02 S 0.07 U 0.90 P 95% M 141496 F 0 R 21506 W 0 c 3 w 56 I 0 O 0 L 13.01 10.62 12.21 @#@FSLOADPOST 2020:07:27:18:06:30 mrisp_paint N 5 13.33 10.73 12.23 #----------------------------------------- #@# Cortical Parc lh Mon Jul 27 18:06:30 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK lh ../surf/lh.sphere.reg /public/apps/freesurfer/7.1.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.1.0 7.1.0 reading atlas from /public/apps/freesurfer/7.1.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 934 labels changed using aseg relabeling using gibbs priors... 000: 2780 changed, 121584 examined... 001: 640 changed, 11727 examined... 002: 137 changed, 3668 examined... 003: 67 changed, 821 examined... 004: 19 changed, 378 examined... 005: 5 changed, 112 examined... 006: 2 changed, 27 examined... 007: 0 changed, 13 examined... 261 labels changed using aseg 000: 95 total segments, 52 labels (177 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2103 vertices marked for relabeling... 2103 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 11 seconds. @#@FSTIME 2020:07:27:18:06:31 mris_ca_label N 11 e 11.42 S 0.43 U 10.35 P 94% M 1057280 F 0 R 165618 W 0 c 14 w 91 I 0 O 0 L 13.33 10.73 12.23 @#@FSLOADPOST 2020:07:27:18:06:43 mris_ca_label N 11 13.89 10.94 12.28 #----------------------------------------- #@# Cortical Parc rh Mon Jul 27 18:06:44 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK rh ../surf/rh.sphere.reg /public/apps/freesurfer/7.1.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.1.0 7.1.0 reading atlas from /public/apps/freesurfer/7.1.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1069 labels changed using aseg relabeling using gibbs priors... 000: 2532 changed, 120651 examined... 001: 558 changed, 11079 examined... 002: 97 changed, 3257 examined... 003: 24 changed, 603 examined... 004: 10 changed, 161 examined... 005: 3 changed, 66 examined... 006: 3 changed, 20 examined... 007: 3 changed, 14 examined... 008: 0 changed, 13 examined... 152 labels changed using aseg 000: 78 total segments, 40 labels (181 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1631 vertices marked for relabeling... 1631 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. @#@FSTIME 2020:07:27:18:06:45 mris_ca_label N 11 e 10.64 S 0.38 U 10.06 P 98% M 979500 F 0 R 154777 W 0 c 16 w 46 I 0 O 0 L 14.14 11.04 12.31 @#@FSLOADPOST 2020:07:27:18:06:56 mris_ca_label N 11 14.58 11.23 12.36 #-------------------------------------------- #@# WhiteSurfs lh Mon Jul 27 18:06:56 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 243164 0.35052 0.13931 0.000742 2.7779 Corner 729492 60.00000 15.11349 0.045430 179.7944 Edge 364746 0.91335 0.22618 0.017634 4.7994 Hinge 364746 11.01831 12.74392 0.000030 179.9306 Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 596 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60792: xyz = (-58.9003,-8.02607,-5.80896) oxyz = (-58.9003,-8.02607,-5.80896) wxzy = (-58.9003,-8.02607,-5.80896) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=2 had to be increased for 240 vertices, nripped=7784 mean border=76.3, 169 (169) missing vertices, mean dist 0.3 [1.0 (%13.2)->0.5 (%86.8))] %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2480 min Finding expansion regions mean absolute distance = 0.58 +- 0.85 2158 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= n523, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1816108.8, rms=8.463 001: dt: 0.5000, sse=761890.1, rms=5.042 (40.428%) 002: dt: 0.5000, sse=542524.4, rms=3.906 (22.532%) 003: dt: 0.5000, sse=510930.9, rms=3.737 (4.316%) 004: dt: 0.5000, sse=477735.1, rms=3.552 (4.955%) rms = 3.6597/3.5519, sse=492807.5/477735.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=340966.9, rms=2.577 (27.455%) 006: dt: 0.2500, sse=294615.1, rms=2.130 (17.333%) 007: dt: 0.2500, sse=282812.5, rms=1.992 (6.490%) rms = 1.9671/1.9919, sse=279674.3/282812.5, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=279674.3, rms=1.967 (1.246%) rms = 1.9194/1.9671, sse=276148.4/279674.3, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=276148.4, rms=1.919 (2.423%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=1 had to be increased for 276 vertices, nripped=7784 mean border=79.7, 206 (68) missing vertices, mean dist -0.2 [0.4 (%74.5)->0.3 (%25.5))] %75 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.1853 min Finding expansion regions mean absolute distance = 0.35 +- 0.62 2462 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= n523, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=780637.4, rms=5.035 010: dt: 0.5000, sse=480954.8, rms=3.476 (30.960%) rms = 3.5866/3.4761, sse=496520.5/480954.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 011: dt: 0.2500, sse=370672.8, rms=2.715 (21.902%) 012: dt: 0.2500, sse=311422.1, rms=2.170 (20.058%) 013: dt: 0.2500, sse=287658.0, rms=1.912 (11.889%) 014: dt: 0.2500, sse=280988.2, rms=1.793 (6.259%) 015: dt: 0.2500, sse=279102.2, rms=1.725 (3.746%) rms = 1.6902/1.7254, sse=273442.7/279102.2, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=273442.7, rms=1.690 (2.036%) rms = 1.6414/1.6902, sse=271509.2/273442.7, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=271509.2, rms=1.641 (2.891%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 218 vertices, nripped=7784 mean border=82.1, 245 (46) missing vertices, mean dist -0.1 [0.3 (%70.0)->0.2 (%30.0))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0980 min Finding expansion regions mean absolute distance = 0.26 +- 0.43 2822 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= n523, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=464447.0, rms=3.377 018: dt: 0.5000, sse=415216.3, rms=3.033 (10.200%) rms = 3.3342/3.0326, sse=453680.2/415216.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=303280.6, rms=2.105 (30.574%) 020: dt: 0.2500, sse=276947.9, rms=1.677 (20.324%) 021: dt: 0.2500, sse=255222.4, rms=1.554 (7.360%) rms = 1.5239/1.5540, sse=252445.7/255222.4, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=252445.7, rms=1.524 (1.941%) 023: dt: 0.1250, sse=246584.7, rms=1.465 (3.889%) rms = 1.4565/1.4646, sse=245848.6/246584.7, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=245848.6, rms=1.457 (0.553%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.1407010; border_low = 63.0000000; outside_low = 52.1054080; outside_hi = 112.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 195 vertices, nripped=7784 mean border=82.9, 283 (34) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0603 min Finding expansion regions mean absolute distance = 0.22 +- 0.34 2829 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= n523, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=270942.9, rms=1.829 rms = 2.0282/1.8292, sse=299500.0/270942.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=241175.6, rms=1.409 (22.968%) 026: dt: 0.2500, sse=233158.7, rms=1.219 (13.491%) rms = 1.2137/1.2190, sse=232376.9/233158.7, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=232376.9, rms=1.214 (0.431%) rms = 1.1924/1.2137, sse=232168.5/232376.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=232168.5, rms=1.192 (1.756%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 3.50 minutes #VMPC# mris_make_surfaces VmPeak 2143368 mris_place_surface done @#@FSTIME 2020:07:27:18:06:57 mris_place_surface N 23 e 219.06 S 0.65 U 217.97 P 99% M 1772648 F 0 R 247070 W 0 c 271 w 89 I 0 O 0 L 14.58 11.23 12.36 @#@FSLOADPOST 2020:07:27:18:10:37 mris_place_surface N 23 17.09 14.33 13.37 #-------------------------------------------- #@# WhiteSurfs rh Mon Jul 27 18:10:37 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 241298 0.35396 0.14338 0.000520 2.5626 Corner 723894 60.00000 15.19336 0.179379 179.1707 Edge 361947 0.91800 0.23261 0.018004 3.7026 Hinge 361947 10.94590 12.23444 0.000008 179.8654 Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 452 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60326: xyz = (5.85365,-6.8849,31.622) oxyz = (5.85365,-6.8849,31.622) wxzy = (5.85365,-6.8849,31.622) pxyz = (0,0,0) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=2 had to be increased for 197 vertices, nripped=7736 mean border=75.0, 148 (148) missing vertices, mean dist 0.3 [0.9 (%12.5)->0.5 (%87.5))] %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2438 min Finding expansion regions mean absolute distance = 0.58 +- 0.82 1979 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= n523, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1939352.0, rms=8.812 001: dt: 0.5000, sse=787804.2, rms=5.175 (41.277%) 002: dt: 0.5000, sse=531802.2, rms=3.900 (24.630%) 003: dt: 0.5000, sse=489836.5, rms=3.679 (5.677%) 004: dt: 0.5000, sse=458009.6, rms=3.480 (5.394%) rms = 3.5871/3.4802, sse=475411.5/458009.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=320597.2, rms=2.444 (29.770%) 006: dt: 0.2500, sse=273653.1, rms=1.959 (19.863%) 007: dt: 0.2500, sse=261204.7, rms=1.803 (7.956%) rms = 1.7668/1.8029, sse=258120.7/261204.7, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=258120.7, rms=1.767 (2.001%) 009: dt: 0.1250, sse=254029.7, rms=1.710 (3.214%) rms = 1.7007/1.7100, sse=253070.1/254029.7, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=253070.0, rms=1.701 (0.542%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=1 had to be increased for 159 vertices, nripped=7736 mean border=78.6, 138 (54) missing vertices, mean dist -0.2 [0.4 (%74.5)->0.3 (%25.5))] %76 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.1774 min Finding expansion regions mean absolute distance = 0.34 +- 0.58 2278 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= n523, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=760242.0, rms=4.978 011: dt: 0.5000, sse=441958.4, rms=3.267 (34.363%) rms = 3.4424/3.2673, sse=466857.3/441958.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=333185.9, rms=2.424 (25.810%) 013: dt: 0.2500, sse=279080.3, rms=1.861 (23.221%) 014: dt: 0.2500, sse=265366.9, rms=1.615 (13.217%) 015: dt: 0.2500, sse=253889.9, rms=1.525 (5.593%) rms = 1.4853/1.5248, sse=251691.9/253889.9, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=251691.9, rms=1.485 (2.594%) rms = 1.4385/1.4853, sse=248710.8/251691.9, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=248710.8, rms=1.438 (3.150%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 145 vertices, nripped=7736 mean border=81.1, 164 (35) missing vertices, mean dist -0.1 [0.3 (%70.8)->0.2 (%29.2))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0952 min Finding expansion regions mean absolute distance = 0.26 +- 0.41 2595 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= n523, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=472997.0, rms=3.503 018: dt: 0.5000, sse=412031.8, rms=3.029 (13.531%) rms = 3.3378/3.0288, sse=449040.2/412031.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=294910.4, rms=2.030 (32.986%) 020: dt: 0.2500, sse=254716.6, rms=1.542 (24.005%) 021: dt: 0.2500, sse=248713.9, rms=1.387 (10.064%) rms = 1.3599/1.3872, sse=240037.8/248713.9, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=240037.8, rms=1.360 (1.970%) 023: dt: 0.1250, sse=233839.1, rms=1.293 (4.937%) rms = 1.2875/1.2928, sse=233486.5/233839.1, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=233486.5, rms=1.288 (0.407%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.1407010; border_low = 62.0000000; outside_low = 51.1054080; outside_hi = 111.1407010; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 138 vertices, nripped=7736 mean border=82.0, 209 (30) missing vertices, mean dist -0.0 [0.2 (%56.9)->0.2 (%43.1))] %87 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0592 min Finding expansion regions mean absolute distance = 0.22 +- 0.33 2535 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= n523, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=260555.1, rms=1.735 rms = 1.9964/1.7346, sse=287061.2/260555.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=229627.0, rms=1.252 (27.814%) 026: dt: 0.2500, sse=219146.3, rms=1.033 (17.501%) rms = 1.0314/1.0330, sse=217569.0/219146.3, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=217569.0, rms=1.031 (0.151%) rms = 1.0134/1.0314, sse=216242.6/217569.0, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=216242.6, rms=1.013 (1.748%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 3.42 minutes #VMPC# mris_make_surfaces VmPeak 2154960 mris_place_surface done @#@FSTIME 2020:07:27:18:10:38 mris_place_surface N 23 e 214.08 S 0.64 U 213.36 P 99% M 1784364 F 0 R 246212 W 0 c 241 w 77 I 0 O 0 L 17.09 14.33 13.37 @#@FSLOADPOST 2020:07:27:18:14:13 mris_place_surface N 23 16.86 15.70 14.12 #-------------------------------------------- #@# T1PialSurf lh Mon Jul 27 18:14:13 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 243164 0.35508 0.15712 0.000874 4.4682 Corner 729492 60.00000 16.47148 0.254243 178.5570 Edge 364746 0.92106 0.24746 0.012757 4.3354 Hinge 364746 11.16895 13.05167 0.000027 179.9306 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 62.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60792: xyz = (-58.963,-8.04709,-5.8071) oxyz = (-58.963,-8.04709,-5.8071) wxzy = (-58.963,-8.04709,-5.8071) pxyz = (-58.963,-8.04709,-5.8071) n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=2 had to be increased for 320 vertices, nripped=5585 mean border=50.2, 224 (224) missing vertices, mean dist 1.7 [1.3 (%0.1)->2.8 (%99.9))] %11 local maxima, %46 large gradients and %38 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2206 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= n523, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=25938204.0, rms=33.349 001: dt: 0.5000, sse=17847246.0, rms=27.617 (17.188%) 002: dt: 0.5000, sse=12116156.0, rms=22.696 (17.818%) 003: dt: 0.5000, sse=8437364.0, rms=18.871 (16.852%) 004: dt: 0.5000, sse=6180912.0, rms=16.080 (14.793%) 005: dt: 0.5000, sse=4713887.0, rms=13.967 (13.138%) 006: dt: 0.5000, sse=3640777.0, rms=12.191 (12.717%) 007: dt: 0.5000, sse=2813310.2, rms=10.619 (12.896%) 008: dt: 0.5000, sse=2181212.8, rms=9.238 (13.008%) 009: dt: 0.5000, sse=1715378.0, rms=8.068 (12.660%) 010: dt: 0.5000, sse=1389966.5, rms=7.136 (11.551%) 011: dt: 0.5000, sse=1184974.5, rms=6.478 (9.222%) 012: dt: 0.5000, sse=1047280.2, rms=5.994 (7.480%) 013: dt: 0.5000, sse=967312.0, rms=5.691 (5.046%) 014: dt: 0.5000, sse=910099.2, rms=5.463 (4.011%) 015: dt: 0.5000, sse=871898.5, rms=5.304 (2.916%) 016: dt: 0.5000, sse=840485.1, rms=5.168 (2.551%) 017: dt: 0.5000, sse=821681.5, rms=5.084 (1.637%) 018: dt: 0.5000, sse=801881.8, rms=4.994 (1.764%) rms = 4.9502/4.9940, sse=792886.2/801881.8, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=792886.2, rms=4.950 (0.878%) 020: dt: 0.2500, sse=669104.8, rms=4.356 (11.998%) 021: dt: 0.2500, sse=639890.6, rms=4.206 (3.447%) rms = 4.1760/4.2061, sse=634538.9/639890.6, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=634538.9, rms=4.176 (0.717%) 023: dt: 0.1250, sse=609071.9, rms=4.038 (3.296%) rms = 4.0060/4.0383, sse=603256.6/609071.9, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=603256.6, rms=4.006 (0.800%) maximum number of reductions reached, breaking from loop positioning took 2.1 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8682 vertices, nripped=5585 mean border=48.8, 1746 (64) missing vertices, mean dist 0.2 [0.2 (%51.7)->0.7 (%48.3))] %20 local maxima, %39 large gradients and %34 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0656 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= n523, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=809096.6, rms=4.783 rms = 4.7555/4.7825, sse=802806.3/809096.5, time step reduction 1 of 3 to 0.250 0 0 1 025: dt: 0.5000, sse=802806.2, rms=4.756 (0.564%) 026: dt: 0.2500, sse=680436.2, rms=4.161 (12.506%) 027: dt: 0.2500, sse=651473.6, rms=4.007 (3.693%) rms = 4.0038/4.0072, sse=651012.7/651473.5, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=651012.7, rms=4.004 (0.084%) 029: dt: 0.1250, sse=619307.0, rms=3.825 (4.461%) rms = 3.7795/3.8252, sse=611342.5/619307.0, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=611342.5, rms=3.780 (1.193%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9272 vertices, nripped=5585 mean border=47.9, 2092 (53) missing vertices, mean dist 0.1 [0.2 (%48.4)->0.5 (%51.6))] %32 local maxima, %27 large gradients and %34 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0365 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= n523, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=664772.2, rms=4.048 rms = 4.3106/4.0475, sse=714540.1/664772.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=632151.8, rms=3.868 (4.432%) 032: dt: 0.2500, sse=614336.4, rms=3.769 (2.561%) rms = 3.7559/3.7691, sse=611604.8/614336.4, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=611604.8, rms=3.756 (0.350%) 034: dt: 0.1250, sse=590582.2, rms=3.631 (3.323%) rms = 3.5909/3.6310, sse=583760.5/590582.3, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=583760.4, rms=3.591 (1.105%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 93.8592990; border_hi = 52.1054080; border_low = 30.3162190; outside_low = 10.0000000; outside_hi = 46.6581120; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=121584 Gdiag_no=-1 vno start=0, stop=121584 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7944 vertices, nripped=5585 mean border=47.3, 3958 (46) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.4 (%50.5))] %37 local maxima, %22 large gradients and %34 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0231 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= n523, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=602589.2, rms=3.695 rms = 3.9956/3.6949, sse=653918.8/602589.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=584005.9, rms=3.585 (2.988%) 037: dt: 0.2500, sse=573074.0, rms=3.524 (1.692%) rms = 3.5299/3.5239, sse=573340.5/573074.0, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 3.4926/3.5239, sse=568073.3/573074.0, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=568073.3, rms=3.493 (0.889%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Pinning medial wall to white surface removing intersecting faces 000: 3 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 3.96 minutes #VMPC# mris_make_surfaces VmPeak 1473588 mris_place_surface done @#@FSTIME 2020:07:27:18:14:15 mris_place_surface N 26 e 245.88 S 0.47 U 245.39 P 99% M 1103056 F 0 R 195904 W 0 c 301 w 69 I 0 O 0 L 16.79 15.70 14.12 @#@FSLOADPOST 2020:07:27:18:18:21 mris_place_surface N 26 16.30 16.02 14.61 #-------------------------------------------- #@# T1PialSurf rh Mon Jul 27 18:18:21 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 241298 0.35801 0.15879 0.001113 2.7729 Corner 723894 60.00000 16.49117 0.337430 178.9545 Edge 361947 0.92452 0.25065 0.018004 3.7782 Hinge 361947 11.10815 12.73349 0.000008 179.8859 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 61.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 60326: xyz = (5.74563,-6.88357,31.7087) oxyz = (5.74563,-6.88357,31.7087) wxzy = (5.74563,-6.88357,31.7087) pxyz = (5.74563,-6.88357,31.7087) n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=2 had to be increased for 297 vertices, nripped=4992 mean border=49.2, 187 (187) missing vertices, mean dist 1.7 [2.3 (%0.0)->2.7 (%100.0))] %11 local maxima, %49 large gradients and %36 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.2284 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= n523, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, 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 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=25941204.0, rms=33.393 001: dt: 0.5000, sse=17783662.0, rms=27.602 (17.344%) 002: dt: 0.5000, sse=12049190.0, rms=22.660 (17.904%) 003: dt: 0.5000, sse=8382952.0, rms=18.831 (16.897%) 004: dt: 0.5000, sse=6142514.0, rms=16.046 (14.789%) 005: dt: 0.5000, sse=4675148.5, rms=13.922 (13.239%) 006: dt: 0.5000, sse=3605052.2, rms=12.139 (12.805%) 007: dt: 0.5000, sse=2780183.5, rms=10.560 (13.009%) 008: dt: 0.5000, sse=2154788.8, rms=9.182 (13.053%) 009: dt: 0.5000, sse=1685812.0, rms=7.991 (12.965%) 010: dt: 0.5000, sse=1351264.4, rms=7.017 (12.189%) 011: dt: 0.5000, sse=1123493.8, rms=6.266 (10.705%) 012: dt: 0.5000, sse=977897.1, rms=5.732 (8.518%) 013: dt: 0.5000, sse=884450.2, rms=5.360 (6.498%) 014: dt: 0.5000, sse=825659.1, rms=5.109 (4.669%) 015: dt: 0.5000, sse=787147.9, rms=4.937 (3.370%) 016: dt: 0.5000, sse=759816.6, rms=4.810 (2.571%) 017: dt: 0.5000, sse=740951.1, rms=4.719 (1.893%) 018: dt: 0.5000, sse=726515.9, rms=4.648 (1.513%) 019: dt: 0.5000, sse=715975.2, rms=4.594 (1.151%) rms = 4.5491/4.5943, sse=707275.9/715975.2, time step reduction 1 of 3 to 0.250 0 0 1 020: dt: 0.5000, sse=707275.9, rms=4.549 (0.985%) 021: dt: 0.2500, sse=584760.2, rms=3.899 (14.284%) 022: dt: 0.2500, sse=555068.7, rms=3.728 (4.404%) rms = 3.7037/3.7276, sse=551356.3/555068.7, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=551356.3, rms=3.704 (0.641%) 024: dt: 0.1250, sse=529348.9, rms=3.569 (3.645%) rms = 3.5401/3.5687, sse=524803.8/529349.0, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=524803.8, rms=3.540 (0.800%) maximum number of reductions reached, breaking from loop positioning took 2.2 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8322 vertices, nripped=4992 mean border=47.9, 1427 (63) missing vertices, mean dist 0.1 [0.1 (%53.5)->0.6 (%46.5))] %20 local maxima, %42 large gradients and %33 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0668 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= n523, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=700082.9, rms=4.248 rms = 4.2881/4.2479, sse=707653.9/700082.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=638710.1, rms=3.920 (7.716%) 027: dt: 0.2500, sse=602381.1, rms=3.713 (5.294%) 028: dt: 0.2500, sse=590101.8, rms=3.642 (1.913%) rms = 3.5964/3.6416, sse=582424.8/590101.7, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=582424.8, rms=3.596 (1.241%) 030: dt: 0.1250, sse=562045.3, rms=3.468 (3.562%) rms = 3.4271/3.4683, sse=555494.0/562045.3, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=555493.9, rms=3.427 (1.187%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 8817 vertices, nripped=4992 mean border=47.0, 1792 (43) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))] %34 local maxima, %28 large gradients and %33 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0373 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= n523, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=610533.0, rms=3.737 rms = 3.9764/3.7365, sse=652093.2/610533.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=575329.5, rms=3.525 (5.656%) 033: dt: 0.2500, sse=558595.2, rms=3.423 (2.894%) rms = 3.3996/3.4231, sse=554415.7/558595.3, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=554415.7, rms=3.400 (0.686%) 035: dt: 0.1250, sse=538461.6, rms=3.294 (3.098%) rms = 3.2625/3.2943, sse=533519.2/538461.6, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=533519.2, rms=3.263 (0.964%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 92.8592990; border_hi = 51.1054080; border_low = 29.3162190; outside_low = 10.0000000; outside_hi = 45.6581120; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 BorderValsHiRes=0 nvertices=120651 Gdiag_no=-1 vno start=0, stop=120651 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7533 vertices, nripped=4992 mean border=46.3, 3689 (38) missing vertices, mean dist 0.1 [0.2 (%49.8)->0.4 (%50.2))] %39 local maxima, %22 large gradients and %32 min vals, 0 gradients ignored MRIScomputeBorderValues_new() finished in 0.0230 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= n523, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=555795.0, rms=3.398 rms = 3.6953/3.3981, sse=602513.7/555795.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=537152.0, rms=3.276 (3.578%) 038: dt: 0.2500, sse=526221.2, rms=3.209 (2.051%) rms = 3.1817/3.2092, sse=521400.9/526221.3, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=521400.9, rms=3.182 (0.860%) 040: dt: 0.1250, sse=506172.2, rms=3.075 (3.349%) rms = 3.0394/3.0751, sse=500877.1/506172.2, time step reduction 3 of 3 to 0.062 0 0 1 041: dt: 0.1250, sse=500877.1, rms=3.039 (1.162%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Pinning medial wall to white surface removing intersecting faces 000: 11 intersecting step 1 with no progress (num=20, old_num=11) 001: 20 intersecting step 2 with no progress (num=34, old_num=20) 002: 34 intersecting step 3 with no progress (num=36, old_num=34) 003: 36 intersecting 004: 31 intersecting step 1 with no progress (num=31, old_num=31) 005: 31 intersecting step 2 with no progress (num=31, old_num=31) 006: 31 intersecting step 3 with no progress (num=31, old_num=31) 007: 31 intersecting step 4 with no progress (num=31, old_num=31) 008: 31 intersecting step 5 with no progress (num=31, old_num=31) 009: 31 intersecting step 6 with no progress (num=31, old_num=31) 010: 31 intersecting step 7 with no progress (num=31, old_num=31) 011: 31 intersecting step 8 with no progress (num=31, old_num=31) 012: 31 intersecting step 9 with no progress (num=31, old_num=31) 013: 31 intersecting step 10 with no progress (num=31, old_num=31) 014: 31 intersecting step 11 with no progress (num=31, old_num=31) 015: 31 intersecting step 12 with no progress (num=31, old_num=31) 016: 31 intersecting step 13 with no progress (num=31, old_num=31) 017: 31 intersecting step 14 with no progress (num=31, old_num=31) 018: 31 intersecting step 15 with no progress (num=31, old_num=31) 019: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 11 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 4.84 minutes #VMPC# mris_make_surfaces VmPeak 1481816 mris_place_surface done @#@FSTIME 2020:07:27:18:18:22 mris_place_surface N 26 e 298.54 S 0.48 U 298.11 P 100% M 1110812 F 0 R 211902 W 0 c 355 w 72 I 0 O 0 L 16.30 16.02 14.61 @#@FSLOADPOST 2020:07:27:18:23:21 mris_place_surface N 26 15.45 15.80 14.91 #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon Jul 27 18:23:22 EDT 2020 mri_mask -transfer 255 -keep_mask_deletion_edits /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.norm.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Writing masked volume to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.mgz...done. @#@FSTIME 2020:07:27:18:23:23 mri_mask N 6 e 3.10 S 0.05 U 2.96 P 97% M 234608 F 0 R 4012 W 0 c 5 w 46 I 0 O 0 L 15.45 15.80 14.91 @#@FSLOADPOST 2020:07:27:18:23:26 mri_mask N 6 15.42 15.79 14.91 #-------------------------------------------- #@# MMPialSurf lh Mon Jul 27 18:23:27 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.FLAIR --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol FLAIR.mgz FLAIR 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.FLAIR --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol FLAIR.mgz FLAIR Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface Area 243164 0.43667 0.35354 0.000139 7.3411 Corner 729492 60.00000 31.74131 0.027299 179.8211 Edge 364746 1.06678 0.50880 0.003885 6.6718 Hinge 364746 20.45717 26.05839 0.000171 179.9949 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 62.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume FLAIR.mgz vertex 60792: xyz = (-60.0886,-7.91666,-8.50294) oxyz = (-58.963,-8.04709,-5.8071) wxzy = (-58.963,-8.04709,-5.8071) pxyz = (-60.0886,-7.91666,-8.50294) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (2) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.01, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=2 Creating lowres distance volumes t=0.000368022 Creating white distance volumes t=0.488055 (box.dx, box.dy, box.dz) = (148, 194, 328) (region->dx, region->dy, region->dz) = (148, 194, 328) (region->dx, region->dy, region->dz) = (148, 194, 328) Creating pial distance volumes t=0.935228 (box.dx, box.dy, box.dz) = (156, 204, 336) (region->dx, region->dy, region->dz) = (156, 204, 336) (region->dx, region->dy, region->dz) = (156, 204, 336) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.472 Starting loop over 121584 vertices vno = 0, t = 1.472 vno = 20000, t = 3.5469 vno = 40000, t = 8.53104 vno = 60000, t = 11.3979 vno = 80000, t = 14.011 error: Numerical result out of range error: MRIhistogramLabelRegion: constant image error: Numerical result out of range error: MRIhistogramLabelRegion: constant image @#@FSTIME 2020:07:27:18:23:28 mris_place_surface N 29 e 958.39 S 2.93 U 955.63 P 100% M 1866020 F 0 R 850851 W 0 c 1044 w 4172 I 0 O 0 L 15.42 15.79 14.91 @#@FSLOADPOST 2020:07:27:18:39:26 mris_place_surface N 29 14.94 14.69 14.67 Linux n523 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012-646-010-KK exited with ERRORS at Mon Jul 27 18:39:27 EDT 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Wed Jul 29 12:05:47 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -s /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK -skullstrip #-------------------------------------------- #@# Skull Stripping Wed Jul 29 12:05:47 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /public/apps/freesurfer/7.1.0/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.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=129 y=125 z=112 r=56 first estimation of the main basin volume: 743002 voxels Looking for seedpoints 2 found in the cerebellum 12 found in the rest of the brain global maximum in x=110, y=108, z=86, Imax=255 CSF=12, 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=6750930062 voxels, voxel volume =1.000 = 6750930062 mmm3 = 6750929.920 cm3 done. PostAnalyze...Basin Prior 38 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=128,y=126, z=106, r=8762 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 46062 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 3708 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 3834 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 19080 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 19296 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 144 Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 4, 32, 50 after analyzing : 3, 22, 32, 29 RIGHT_CER before analyzing : 3, 4, 33, 58 after analyzing : 3, 23, 33, 31 LEFT_CER before analyzing : 3, 4, 35, 54 after analyzing : 3, 24, 35, 31 RIGHT_BRAIN before analyzing : 3, 4, 32, 50 after analyzing : 3, 22, 32, 29 LEFT_BRAIN before analyzing : 3, 4, 31, 53 after analyzing : 3, 22, 31, 29 OTHER before analyzing : 3, 3, 18, 54 after analyzing : 3, 17, 25, 26 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 67.379, std = 9.914 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.35, sigma = 7.29 after rotation: sse = 5.35, sigma = 7.29 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.49, its var is 8.56 before Erosion-Dilatation 3.29% 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...32 iterations mri_strip_skull: done peeling brain Brain Size = 1462424 voxels, voxel volume = 1.000 mm3 = 1462424 mmm3 = 1462.424 cm3 MRImask(): AllowDiffGeom = 1 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done mri_watershed utimesec 18.183235 mri_watershed stimesec 0.416936 mri_watershed ru_maxrss 823560 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 185687 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 192 mri_watershed ru_nivcsw 179 mri_watershed done @#@FSTIME 2020:07:29:12:05:47 mri_watershed N 10 e 19.46 S 0.44 U 18.18 P 95% M 823560 F 0 R 185689 W 0 c 180 w 201 I 0 O 0 L 0.02 0.01 0.00 @#@FSLOADPOST 2020:07:29:12:06:07 mri_watershed N 10 0.36 0.09 0.03 INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #@# white curv lh Wed Jul 29 12:06:07 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2020:07:29:12:06:07 mris_place_surface N 5 e 2.71 S 0.09 U 2.24 P 85% M 168344 F 0 R 29399 W 0 c 20 w 91 I 0 O 0 L 0.36 0.09 0.03 @#@FSLOADPOST 2020:07:29:12:06:09 mris_place_surface N 5 0.41 0.10 0.03 #@# white area lh Wed Jul 29 12:06:09 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2020:07:29:12:06:10 mris_place_surface N 3 e 1.33 S 0.11 U 1.18 P 97% M 168076 F 0 R 29842 W 0 c 184 w 63 I 0 O 0 L 0.41 0.10 0.03 @#@FSLOADPOST 2020:07:29:12:06:11 mris_place_surface N 3 0.41 0.10 0.03 #@# pial curv lh Wed Jul 29 12:06:11 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Wed Jul 29 12:06:11 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Wed Jul 29 12:06:11 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness error: No such file or directory error: mrisReadTriangleFile opened ../surf/lh.pial okay but surface doesn't match ../surf/lh.white. nvertices:131581 != mris->nvertices:121584 || nfaces:263158 != mris->nfaces:243164 error: No such file or directory error: mrisReadTriangleFile failed. @#@FSTIME 2020:07:29:12:06:11 mris_place_surface N 6 e 0.96 S 0.07 U 0.85 P 97% M 168008 F 0 R 28296 W 0 c 17 w 34 I 0 O 0 L 0.41 0.10 0.03 @#@FSLOADPOST 2020:07:29:12:06:12 mris_place_surface N 6 0.41 0.10 0.03 Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012-646-010-KK exited with ERRORS at Wed Jul 29 12:06:12 EDT 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Wed Jul 29 12:54:38 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -autorecon3 subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 1024 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:50-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:50-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:50-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:50-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:50-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:51-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:51-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:51-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:51-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:52-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:52-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:52-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:52-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:52-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:53-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:53-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:53-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:53-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:54-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:54-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:54-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-16:54:54-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: loginnode2 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Wed Jul 29 12:54:54 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:29:12:54:54 mri_convert N 4 e 1.89 S 0.02 U 1.71 P 91% M 53736 F 0 R 2036 W 0 c 317 w 47 I 0 O 0 L 0.35 0.50 0.72 @#@FSLOADPOST 2020:07:29:12:54:56 mri_convert N 4 0.35 0.50 0.72 #-------------------------------------------- #@# Sphere lh Wed Jul 29 12:54:56 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.285... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=login, 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 singular matrix in quadratic form #New# invocation of recon-all Wed Jul 29 13:08:31 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK /public/apps/freesurfer/7.1.0/bin/recon-all -subject 2012-646-010-KK -FLAIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz -FLAIRpial -autorecon3 subjid 2012-646-010-KK setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING FREESURFER_HOME /public/apps/freesurfer/7.1.0 Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/7.1.0 build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Linux n415 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 52428800 kbytes descriptors 102400 memorylocked unlimited maxproc 63708 ######################################## program versions used 7.1.0 (freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b) 7.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:32-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:32-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:33-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:34-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:35-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:36-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:37-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:38-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:39-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:40-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:41-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:42-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:43-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:44-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:45-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:46-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:47-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:48-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.0 TimeStamp: 2020/07/29-17:08:49-GMT BuildTime: May 11 2020 13:48:51 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b User: pankumar Machine: n415 Platform: Linux PlatformVersion: 2.6.32-696.6.3.el6.694g0000.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 ####################################### GCADIR /public/apps/freesurfer/7.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /public/apps/freesurfer/7.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Wed Jul 29 13:08:51 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform reading from /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/VISIT_0/RAW/registeredWarped.nii.gz... niiRead(): detected input as 64 bit double, reading in as 32 bit float TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998777, -0.0261115, -0.0419769) j_ras = (-0.0224985, 0.996182, -0.0843503) k_ras = (-0.0440192, 0.0833028, 0.995552) writing to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/orig/FLAIRraw.mgz... @#@FSTIME 2020:07:29:13:08:53 mri_convert N 4 e 1.99 S 0.03 U 1.79 P 91% M 53500 F 0 R 1989 W 0 c 3 w 48 I 0 O 0 L 0.33 0.08 0.05 @#@FSLOADPOST 2020:07:29:13:08:55 mri_convert N 4 0.39 0.09 0.05 #-------------------------------------------- #@# Sphere lh Wed Jul 29 13:08:55 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.285... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n415, 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.72 pass 1: epoch 2 of 3 starting distance error %21.71 unfolding complete - removing small folds... starting distance error %21.57 removing remaining folds... final distance error %21.62 MRISunfold() return, current seed 1234 -01: dt=0.0000, 16 negative triangles 195: dt=0.9900, 16 negative triangles 196: dt=0.9900, 12 negative triangles 197: dt=0.9900, 7 negative triangles 198: dt=0.9900, 6 negative triangles 199: dt=0.9900, 5 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 4 negative triangles 202: dt=0.9900, 1 negative triangles 203: dt=0.9900, 5 negative triangles 204: dt=0.9900, 3 negative triangles 205: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere mris_sphere utimesec 799.917394 mris_sphere stimesec 1.318799 mris_sphere ru_maxrss 2004708 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 849189 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 59 mris_sphere ru_nivcsw 1597 spherical transformation took 0.2225 hours FSRUNTIME@ mris_sphere 0.2225 hours 1 threads @#@FSTIME 2020:07:29:13:08:57 mris_sphere N 6 e 801.01 S 1.41 U 799.91 P 100% M 2004708 F 0 R 849191 W 0 c 1597 w 70 I 0 O 0 L 0.39 0.09 0.05 @#@FSLOADPOST 2020:07:29:13:22:18 mris_sphere N 6 1.01 0.93 0.58 #-------------------------------------------- #@# Sphere rh Wed Jul 29 13:22:18 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_sphere -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 1 == reading original vertex positions... scaling brain by 0.283... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n415, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %43.73 pass 1: epoch 2 of 3 starting distance error %22.40 unfolding complete - removing small folds... starting distance error %22.21 removing remaining folds... final distance error %22.26 MRISunfold() return, current seed 1234 -01: dt=0.0000, 0 negative triangles writing spherical brain to ../surf/rh.sphere mris_sphere utimesec 519.008098 mris_sphere stimesec 1.285804 mris_sphere ru_maxrss 1894532 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 800340 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 130 mris_sphere ru_nivcsw 904 spherical transformation took 0.1445 hours FSRUNTIME@ mris_sphere 0.1445 hours 1 threads @#@FSTIME 2020:07:29:13:22:19 mris_sphere N 6 e 520.27 S 1.35 U 519.00 P 100% M 1894532 F 0 R 800342 W 0 c 904 w 134 I 0 O 0 L 0.93 0.92 0.57 @#@FSLOADPOST 2020:07:29:13:31:00 mris_sphere N 6 1.00 0.97 0.74 #-------------------------------------------- #@# Surf Reg lh Wed Jul 29 13:31:01 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.0 7.1.0 reading surface from ../surf/lh.sphere... reading template parameterization from /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n415, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n415, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host= n415, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.581 curvature mean = 0.041, std = 0.813 curvature mean = 0.008, std = 0.873 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (0.50, -6.50, 9.50) sse = 225953.2, elapsed since starting=0.4576 min MRISrigidBodyAlignGlobal() done 0.46 min curvature mean = 0.020, std = 0.838 curvature mean = 0.003, std = 0.953 curvature mean = 0.017, std = 0.850 curvature mean = 0.001, std = 0.982 curvature mean = 0.017, std = 0.853 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.023, std = 0.272 curvature mean = 0.044, std = 0.249 curvature mean = 0.052, std = 0.389 curvature mean = 0.034, std = 0.310 curvature mean = 0.036, std = 0.575 curvature mean = 0.033, std = 0.338 curvature mean = 0.019, std = 0.716 curvature mean = 0.033, std = 0.350 curvature mean = 0.006, std = 0.821 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles 106: dt=0.9900, 15 negative triangles 107: dt=0.9900, 13 negative triangles 108: dt=0.9900, 10 negative triangles 109: dt=0.9900, 10 negative triangles 110: dt=0.9900, 8 negative triangles 111: dt=0.9900, 2 negative triangles 112: dt=0.9900, 5 negative triangles 113: dt=0.9900, 4 negative triangles 114: dt=0.9900, 1 negative triangles 115: dt=0.9900, 2 negative triangles 116: dt=0.9900, 1 negative triangles 117: dt=0.9900, 3 negative triangles 118: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.13 hours #VMPC# mris_register VmPeak 1628820 FSRUNTIME@ mris_register 0.1270 hours 1 threads @#@FSTIME 2020:07:29:13:31:02 mris_register N 6 e 457.27 S 0.77 U 456.57 P 100% M 1252348 F 0 R 495886 W 0 c 527 w 74 I 0 O 0 L 1.00 0.97 0.74 @#@FSLOADPOST 2020:07:29:13:38:39 mris_register N 6 1.00 0.97 0.82 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Wed Jul 29 13:38:40 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts cmdline mris_register -curv -rusage /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.0 7.1.0 reading surface from ../surf/rh.sphere... reading template parameterization from /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= n415, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 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 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= n415, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host= n415, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.770 curvature mean = 0.062, std = 0.813 curvature mean = 0.005, std = 0.876 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.50, -11.00, 12.50) sse = 277082.9, elapsed since starting=0.4686 min MRISrigidBodyAlignGlobal() done 0.47 min curvature mean = 0.036, std = 0.834 curvature mean = 0.003, std = 0.954 curvature mean = 0.033, std = 0.845 curvature mean = 0.001, std = 0.982 curvature mean = 0.032, std = 0.848 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.020, std = 0.273 curvature mean = 0.044, std = 0.244 curvature mean = 0.051, std = 0.387 curvature mean = 0.037, std = 0.303 curvature mean = 0.033, std = 0.574 curvature mean = 0.036, std = 0.330 curvature mean = 0.016, std = 0.713 curvature mean = 0.036, std = 0.342 curvature mean = 0.004, std = 0.817 MRISregister() return, current seed 0 -01: dt=0.0000, 3 negative triangles 107: dt=0.9900, 3 negative triangles 108: dt=0.9900, 1 negative triangles 109: dt=0.9900, 2 negative triangles 110: dt=0.9900, 2 negative triangles 111: dt=0.9900, 1 negative triangles 112: dt=0.9900, 2 negative triangles 113: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.14 hours #VMPC# mris_register VmPeak 1621312 FSRUNTIME@ mris_register 0.1397 hours 1 threads @#@FSTIME 2020:07:29:13:38:41 mris_register N 6 e 502.97 S 0.86 U 502.13 P 100% M 1244844 F 0 R 488614 W 0 c 3547 w 65 I 0 O 0 L 1.00 0.97 0.82 @#@FSLOADPOST 2020:07:29:13:47:05 mris_register N 6 1.07 1.00 0.88 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Wed Jul 29 13:47:05 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2020:07:29:13:47:07 mris_jacobian N 3 e 1.35 S 0.11 U 1.05 P 86% M 186060 F 0 R 31953 W 0 c 3 w 72 I 0 O 0 L 1.07 1.00 0.88 @#@FSLOADPOST 2020:07:29:13:47:08 mris_jacobian N 3 1.07 1.00 0.88 #-------------------------------------------- #@# Jacobian white rh Wed Jul 29 13:47:09 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2020:07:29:13:47:10 mris_jacobian N 3 e 1.48 S 0.11 U 1.15 P 85% M 184596 F 0 R 31520 W 0 c 3 w 67 I 0 O 0 L 0.98 0.98 0.88 @#@FSLOADPOST 2020:07:29:13:47:12 mris_jacobian N 3 0.98 0.98 0.88 #-------------------------------------------- #@# AvgCurv lh Wed Jul 29 13:47:12 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /public/apps/freesurfer/7.1.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2020:07:29:13:47:14 mrisp_paint N 5 e 1.01 S 0.09 U 0.84 P 92% M 142588 F 0 R 20832 W 0 c 3 w 76 I 0 O 0 L 0.98 0.98 0.88 @#@FSLOADPOST 2020:07:29:13:47:15 mrisp_paint N 5 0.98 0.98 0.88 #-------------------------------------------- #@# AvgCurv rh Wed Jul 29 13:47:15 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mrisp_paint -a 5 /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /public/apps/freesurfer/7.1.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2020:07:29:13:47:17 mrisp_paint N 5 e 0.97 S 0.09 U 0.84 P 95% M 141496 F 0 R 20947 W 0 c 3 w 55 I 0 O 0 L 0.98 0.98 0.88 @#@FSLOADPOST 2020:07:29:13:47:18 mrisp_paint N 5 0.98 0.98 0.88 #----------------------------------------- #@# Cortical Parc lh Wed Jul 29 13:47:18 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK lh ../surf/lh.sphere.reg /public/apps/freesurfer/7.1.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.1.0 7.1.0 reading atlas from /public/apps/freesurfer/7.1.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 934 labels changed using aseg relabeling using gibbs priors... 000: 2780 changed, 121584 examined... 001: 640 changed, 11727 examined... 002: 137 changed, 3668 examined... 003: 67 changed, 821 examined... 004: 19 changed, 378 examined... 005: 5 changed, 112 examined... 006: 2 changed, 27 examined... 007: 0 changed, 13 examined... 261 labels changed using aseg 000: 95 total segments, 52 labels (177 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2103 vertices marked for relabeling... 2103 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 12 seconds. @#@FSTIME 2020:07:29:13:47:19 mris_ca_label N 11 e 12.23 S 0.49 U 11.33 P 96% M 1057272 F 0 R 167149 W 0 c 22 w 81 I 0 O 0 L 0.90 0.97 0.87 @#@FSLOADPOST 2020:07:29:13:47:32 mris_ca_label N 11 0.92 0.97 0.88 #----------------------------------------- #@# Cortical Parc rh Wed Jul 29 13:47:32 EDT 2020 /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 2012-646-010-KK rh ../surf/rh.sphere.reg /public/apps/freesurfer/7.1.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.1.0 7.1.0 reading atlas from /public/apps/freesurfer/7.1.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1069 labels changed using aseg relabeling using gibbs priors... 000: 2532 changed, 120651 examined... 001: 558 changed, 11079 examined... 002: 97 changed, 3257 examined... 003: 24 changed, 603 examined... 004: 10 changed, 161 examined... 005: 3 changed, 66 examined... 006: 3 changed, 20 examined... 007: 3 changed, 14 examined... 008: 0 changed, 13 examined... 152 labels changed using aseg 000: 78 total segments, 40 labels (181 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1631 vertices marked for relabeling... 1631 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 10 seconds. @#@FSTIME 2020:07:29:13:47:34 mris_ca_label N 11 e 10.26 S 0.41 U 9.67 P 98% M 979504 F 0 R 153758 W 0 c 14 w 60 I 0 O 0 L 0.92 0.97 0.88 @#@FSLOADPOST 2020:07:29:13:47:44 mris_ca_label N 11 0.87 0.95 0.87 #-------------------------------------------- #@# WhiteSurfs lh Wed Jul 29 13:47:45 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Update not needed #-------------------------------------------- #@# WhiteSurfs rh Wed Jul 29 13:47:47 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Update not needed #-------------------------------------------- #@# T1PialSurf lh Wed Jul 29 13:47:48 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Update not needed #-------------------------------------------- #@# T1PialSurf rh Wed Jul 29 13:47:50 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Update not needed #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Jul 29 13:47:52 EDT 2020 mri_mask -transfer 255 -keep_mask_deletion_edits /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.norm.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/brain.finalsurfs.mgz /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Writing masked volume to /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri/FLAIR.mgz...done. @#@FSTIME 2020:07:29:13:47:53 mri_mask N 6 e 3.78 S 0.07 U 3.45 P 93% M 234612 F 0 R 4523 W 0 c 6 w 53 I 0 O 0 L 1.04 0.99 0.88 @#@FSLOADPOST 2020:07:29:13:47:57 mri_mask N 6 1.03 0.99 0.88 #-------------------------------------------- #@# MMPialSurf lh Wed Jul 29 13:47:58 EDT 2020 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.FLAIR --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol FLAIR.mgz FLAIR 7.1.0 7.1.0 cd /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING/2012-646-010-KK/mri setenv SUBJECTS_DIR /gs/gsfs0/users/mrrc-all/MRE_LAB/MRE3_PROCESSING mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.FLAIR --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol FLAIR.mgz FLAIR Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface Area 243164 0.43667 0.35354 0.000139 7.3411 Corner 729492 60.00000 31.74131 0.027299 179.8211 Edge 364746 1.06678 0.50880 0.003885 6.6718 Hinge 364746 20.45717 26.05839 0.000171 179.9949 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17322, wmmin=5, clip=110 MRIfindBrightNonWM(): 60 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 62.0878 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume FLAIR.mgz vertex 60792: xyz = (-60.0886,-7.91666,-8.50294) oxyz = (-58.963,-8.04709,-5.8071) wxzy = (-58.963,-8.04709,-5.8071) pxyz = (-60.0886,-7.91666,-8.50294) n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (2) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.01, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=2 Creating lowres distance volumes t=0.000389031 Creating white distance volumes t=0.405976 (box.dx, box.dy, box.dz) = (148, 194, 328) (region->dx, region->dy, region->dz) = (148, 194, 328) (region->dx, region->dy, region->dz) = (148, 194, 328) Creating pial distance volumes t=0.771787 (box.dx, box.dy, box.dz) = (156, 204, 336) (region->dx, region->dy, region->dz) = (156, 204, 336) (region->dx, region->dy, region->dz) = (156, 204, 336) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.21632 Starting loop over 121584 vertices vno = 0, t = 1.21632 vno = 20000, t = 3.38757 vno = 40000, t = 8.77043 vno = 60000, t = 11.8685 vno = 80000, t = 14.6273 error: Numerical result out of range error: MRIhistogramLabelRegion: constant image error: Numerical result out of range error: MRIhistogramLabelRegion: constant image @#@FSTIME 2020:07:29:13:47:59 mris_place_surface N 29 e 1002.13 S 3.56 U 998.66 P 100% M 1867080 F 0 R 850478 W 0 c 1132 w 3960 I 0 O 0 L 0.95 0.97 0.88 @#@FSLOADPOST 2020:07:29:14:04:41 mris_place_surface N 29 1.00 1.00 0.94 Linux n415 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012-646-010-KK exited with ERRORS at Wed Jul 29 14:04:42 EDT 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting