Fri Aug 17 10:15:21 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip /usr/local/freesurfer-6.0/bin/recon-all -i /home/shize/JSZ/MRI/SEEG/SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all subjid SubJ01_ReoT13THip setenv SUBJECTS_DIR /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Actual FREESURFER_HOME /usr/local/freesurfer-6.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 63816 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 16352044 13053556 3298488 50424 140488 4438444 -/+ buffers/cache: 8474624 7877420 Swap: 33551356 1574156 31977200 ######################################## 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: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default 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: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default 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: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default 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: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default 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: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:21-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:22-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:22-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:22-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/17-14:15:22-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: shize Machine: dart Platform: Linux PlatformVersion: 4.4.138-59-default CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/shize/freesurfer/SubJ01_ReoT13THip mri_convert /home/shize/JSZ/MRI/SEEG/SubJ01_ReoT1.nii /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig/001.mgz mri_convert.bin /home/shize/JSZ/MRI/SEEG/SubJ01_ReoT1.nii /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/shize/JSZ/MRI/SEEG/SubJ01_ReoT1.nii... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.9995, -0.0069555, -0.0308424) j_ras = (0.0116454, 0.987909, 0.1546) k_ras = (0.0293942, -0.154881, 0.987496) writing to /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Aug 17 10:15:34 EDT 2018 Found 1 runs /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig/001.mgz /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz /home/shize/freesurfer/SubJ01_ReoT13THip mri_convert /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz --conform mri_convert.bin /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.9995, -0.0069555, -0.0308424) j_ras = (0.0116454, 0.987909, 0.1546) k_ras = (0.0293942, -0.154881, 0.987496) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz... mri_add_xform_to_header -c /home/shize/freesurfer/SubJ01_ReoT13THip/mri/transforms/talairach.xfm /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Aug 17 10:15:44 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/shize/freesurfer/SubJ01_ReoT13THip/mri /usr/local/freesurfer-6.0/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 dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) x86_64 x86_64 x86_64 GNU/Linux Fri Aug 17 10:15:44 EDT 2018 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.19351 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19351/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.19351/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, -1.86265e-09) j_ras = (-1.86265e-09, 0, -1) k_ras = (4.65661e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.19351/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Aug 17 10:15:46 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.19351/nu0.mnc ./tmp.mri_nu_correct.mni.19351/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19351/0/ -iterations 1000 -distance 50 [shize@dart:/home/shize/freesurfer/SubJ01_ReoT13THip/mri/] [2018-08-17 10:15:46] running: /usr/local/freesurfer-6.0/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.19351/0/ ./tmp.mri_nu_correct.mni.19351/nu0.mnc ./tmp.mri_nu_correct.mni.19351/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000995891 mri_convert ./tmp.mri_nu_correct.mni.19351/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.19351/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.19351/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, -1.86265e-09) j_ras = (-1.86265e-09, 0, -1) k_ras = (4.65661e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Fri Aug 17 10:16:43 EDT 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Fri Aug 17 10:16:43 EDT 2018 Ended at Fri Aug 17 10:17:11 EDT 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Aug 17 10:17:13 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7471, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer-6.0/bin/extract_talairach_avi_QA.awk /home/shize/freesurfer/SubJ01_ReoT13THip/mri/transforms/talairach_avi.log tal_QC_AZS /home/shize/freesurfer/SubJ01_ReoT13THip/mri/transforms/talairach_avi.log TalAviQA: 0.95352 z-score: -5 #-------------------------------------------- #@# Nu Intensity Correction Fri Aug 17 10:17:13 EDT 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /home/shize/freesurfer/SubJ01_ReoT13THip/mri /usr/local/freesurfer-6.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) x86_64 x86_64 x86_64 GNU/Linux Fri Aug 17 10:17:13 EDT 2018 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.20207 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20207/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.20207/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.23, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, -1.86265e-09) j_ras = (-1.86265e-09, 0, -1) k_ras = (4.65661e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20207/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Aug 17 10:17:15 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.20207/nu0.mnc ./tmp.mri_nu_correct.mni.20207/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20207/0/ -iterations 1000 -distance 50 [shize@dart:/home/shize/freesurfer/SubJ01_ReoT13THip/mri/] [2018-08-17 10:17:15] running: /usr/local/freesurfer-6.0/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.20207/0/ ./tmp.mri_nu_correct.mni.20207/nu0.mnc ./tmp.mri_nu_correct.mni.20207/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000995891 mri_binarize --i ./tmp.mri_nu_correct.mni.20207/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20207/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/shize/freesurfer/SubJ01_ReoT13THip/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.20207/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20207/ones.mgz sysname Linux hostname dart machine x86_64 user shize input ./tmp.mri_nu_correct.mni.20207/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20207/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.20207/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20207/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20207/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.20207/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20207/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20207/input.mean.dat sysname Linux hostname dart machine x86_64 user shize UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20207/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.20207/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20207/ones.mgz --i ./tmp.mri_nu_correct.mni.20207/nu1.mnc --sum ./tmp.mri_nu_correct.mni.20207/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20207/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.20207/ones.mgz --i ./tmp.mri_nu_correct.mni.20207/nu1.mnc --sum ./tmp.mri_nu_correct.mni.20207/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20207/output.mean.dat sysname Linux hostname dart machine x86_64 user shize UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20207/ones.mgz Loading ./tmp.mri_nu_correct.mni.20207/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.20207/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.20207/nu1.mnc ./tmp.mri_nu_correct.mni.20207/nu1.mnc mul 1.02825589044663975482 Saving result to './tmp.mri_nu_correct.mni.20207/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20207/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.20207/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.20207/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-10, -1.86265e-09) j_ras = (-1.86265e-09, 0, -1) k_ras = (4.65661e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (15, 89) to ( 3, 110) Fri Aug 17 10:18:37 EDT 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /home/shize/freesurfer/SubJ01_ReoT13THip/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Aug 17 10:18:38 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 1.01357 0.00229 -0.00207 -0.00175; -0.03899 1.14233 0.10911 1.61710; 0.00383 -0.07275 1.09964 -2.04822; 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 = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 83 (83), valley at 34 (34) csf peak at 42, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 22 (22) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 57 seconds. #-------------------------------------------- #@# Skull Stripping Fri Aug 17 10:20:36 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_em_register -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer-6.0/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 '/usr/local/freesurfer-6.0/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=10.0 skull bounding box = (38, 40, 36) --> (214, 230, 229) using (97, 103, 133) as brain centroid... mean wm in atlas = 108, using box (75,80,109) --> (118, 126,156) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 106 +- 6.8 after smoothing, mri peak at 106, scaling input intensities by 1.019 scaling channel 0 by 1.01887 initial log_p = -4.715 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.542486 @ (-9.091, 9.091, -27.273) max log p = -4.512799 @ (4.545, -4.545, 4.545) max log p = -4.475897 @ (2.273, -6.818, -2.273) max log p = -4.456306 @ (1.136, 3.409, 1.136) max log p = -4.456306 @ (0.000, 0.000, 0.000) max log p = -4.454743 @ (-0.284, -0.284, -1.420) Found translation: (-1.4, 0.9, -25.3): log p = -4.455 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.347, old_max_log_p =-4.455 (thresh=-4.5) 1.00000 0.00000 0.00000 -1.42046; 0.00000 1.22567 0.16136 -45.51919; 0.00000 -0.16136 1.22567 -33.21837; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.347, old_max_log_p =-4.347 (thresh=-4.3) 1.00000 0.00000 0.00000 -1.42046; 0.00000 1.22567 0.16136 -45.51919; 0.00000 -0.16136 1.22567 -33.21837; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.299, old_max_log_p =-4.347 (thresh=-4.3) 0.99900 0.04569 -0.02926 -3.38741; -0.03270 1.21899 0.20150 -47.79195; 0.03051 -0.18973 1.17416 -24.50621; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.297, old_max_log_p =-4.299 (thresh=-4.3) 1.01824 0.03888 0.00910 -10.02697; -0.03228 1.23486 0.24431 -53.88939; -0.00116 -0.23521 1.18916 -16.29381; 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=-4.287, old_max_log_p =-4.297 (thresh=-4.3) 1.01501 -0.00522 0.02116 -6.66192; 0.00104 1.24049 0.22590 -56.87231; -0.01833 -0.21533 1.19129 -17.57745; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.282, old_max_log_p =-4.287 (thresh=-4.3) 1.01381 -0.00521 0.02114 -6.50740; 0.00103 1.23904 0.22563 -56.63905; -0.01826 -0.21457 1.18711 -17.12604; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.282, old_max_log_p =-4.282 (thresh=-4.3) 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 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 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.282 (old=-4.715) transform before final EM align: 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 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 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.7 tol 0.000000 final transform: 1.01381 -0.00521 0.02114 -6.50740; 0.00104 1.24049 0.22590 -56.87203; -0.01824 -0.21432 1.18572 -16.97598; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 964.301736 mri_em_register stimesec 2.883945 mri_em_register ru_maxrss 613920 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161806 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 mri_em_register ru_oublock 40 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 26 mri_em_register ru_nivcsw 42823 registration took 16 minutes and 9 seconds. mri_watershed -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer-6.0/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=128 y=119 z=130 r=79 first estimation of the main basin volume: 2070250 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=151, y=108, z=98, Imax=255 CSF=20, 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=296209487 voxels, voxel volume =1.000 = 296209487 mmm3 = 296209.472 cm3 done. PostAnalyze...Basin Prior 4 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=122, z=128, r=8750 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=23, CSF_MAX=54 , nb = 45314 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1034521965 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1045132831 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=56 , nb = 1053035174 LEFT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=53 , nb = 1064929450 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 1077742766 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. 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 : 54, 50, 48, 73 after analyzing : 43, 50, 50, 55 RIGHT_CER before analyzing : 4, 3, 0, 23 after analyzing : 3, 17, 25, 19 LEFT_CER before analyzing : 4, 3, 0, 23 after analyzing : 3, 17, 25, 19 RIGHT_BRAIN before analyzing : 56, 34, 27, 38 after analyzing : 31, 34, 34, 35 LEFT_BRAIN before analyzing : 53, 38, 35, 43 after analyzing : 34, 38, 38, 39 OTHER before analyzing : 7, 5, 0, 23 after analyzing : 5, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...56 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 72.168, std = 5.675 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.50, sigma = 6.68 after rotation: sse = 4.50, sigma = 6.68 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.81, its var is 5.85 before Erosion-Dilatation 1.43% 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...43 iterations mri_strip_skull: done peeling brain Brain Size = 1636531 voxels, voxel volume = 1.000 mm3 = 1636531 mmm3 = 1636.531 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 18.096659 mri_watershed stimesec 0.339787 mri_watershed ru_maxrss 832328 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211571 mri_watershed ru_majflt 15 mri_watershed ru_nswap 0 mri_watershed ru_inblock 175488 mri_watershed ru_oublock 2480 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 223 mri_watershed ru_nivcsw 397 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Aug 17 10:37:04 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_em_register -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer-6.0/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 '/usr/local/freesurfer-6.0/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=28.0 skull bounding box = (56, 59, 58) --> (200, 177, 208) using (104, 98, 133) as brain centroid... mean wm in atlas = 107, using box (86,84,115) --> (121, 112,151) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 5.2 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.503 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.070477 @ (-9.091, -9.091, -27.273) max log p = -3.945037 @ (4.545, 4.545, 4.545) max log p = -3.914891 @ (2.273, 6.818, -2.273) max log p = -3.874167 @ (-1.136, -5.682, 1.136) max log p = -3.866990 @ (-0.568, -1.705, -1.705) max log p = -3.865177 @ (-0.284, 0.852, 0.284) Found translation: (-4.3, -4.3, -25.3): log p = -3.865 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.865, old_max_log_p =-3.865 (thresh=-3.9) 1.00000 0.00000 0.00000 -4.26137; 0.00000 1.00000 0.00000 -4.26137; 0.00000 0.00000 1.00000 -25.28409; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.820, old_max_log_p =-3.865 (thresh=-3.9) 0.99305 -0.05203 -0.10557 16.87921; 0.06526 0.98988 0.12601 -28.03298; 0.09795 -0.13202 0.98640 -20.02536; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.820, old_max_log_p =-3.820 (thresh=-3.8) 0.99305 -0.05203 -0.10557 16.87921; 0.06526 0.98988 0.12601 -28.03298; 0.09795 -0.13202 0.98640 -20.02536; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.796, old_max_log_p =-3.820 (thresh=-3.8) 0.99132 -0.06008 -0.10648 18.68595; 0.07319 0.98710 0.12485 -29.05379; 0.09760 -0.13156 0.98293 -20.52100; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.781, old_max_log_p =-3.796 (thresh=-3.8) 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.781, old_max_log_p =-3.781 (thresh=-3.8) 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.781 (old=-4.503) transform before final EM align: 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 679.854004 mri_em_register stimesec 2.495816 mri_em_register ru_maxrss 603240 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162514 mri_em_register ru_majflt 2 mri_em_register ru_nswap 0 mri_em_register ru_inblock 141064 mri_em_register ru_oublock 40 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 38 mri_em_register ru_nivcsw 29896 registration took 11 minutes and 23 seconds. #-------------------------------------- #@# CA Normalize Fri Aug 17 10:48:27 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer-6.0/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 '/usr/local/freesurfer-6.0/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=28.0 skull bounding box = (56, 59, 58) --> (200, 177, 208) using (104, 98, 133) as brain centroid... mean wm in atlas = 107, using box (86,84,115) --> (121, 112,151) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 5.2 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16314; 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 (122, 55, 52) --> (198, 172, 220) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 5321 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 59, 55) --> (137, 176, 222) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 3 of 4506 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 146, 77) --> (180, 187, 132) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 39 of 79 (49.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 147, 79) --> (130, 189, 137) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 0 of 27 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 135, 115) --> (151, 206, 146) Brain_Stem: limiting intensities to 103.0 --> 132.0 70 of 296 (23.6%) samples deleted using 10229 total control points for intensity normalization... bias field = 0.951 +- 0.060 106 of 10117 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (122, 55, 52) --> (198, 172, 220) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 5862 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 59, 55) --> (137, 176, 222) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 28 of 4980 (0.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 146, 77) --> (180, 187, 132) Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 10 of 132 (7.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 147, 79) --> (130, 189, 137) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 63 (11.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 135, 115) --> (151, 206, 146) Brain_Stem: limiting intensities to 88.0 --> 132.0 156 of 400 (39.0%) samples deleted using 11437 total control points for intensity normalization... bias field = 1.060 +- 0.066 85 of 11180 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (122, 55, 52) --> (198, 172, 220) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 5996 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 59, 55) --> (137, 176, 222) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 5089 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 146, 77) --> (180, 187, 132) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 79 of 214 (36.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 147, 79) --> (130, 189, 137) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 39 of 98 (39.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 135, 115) --> (151, 206, 146) Brain_Stem: limiting intensities to 88.0 --> 132.0 236 of 425 (55.5%) samples deleted using 11822 total control points for intensity normalization... bias field = 1.058 +- 0.061 63 of 11328 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 25 seconds. #-------------------------------------- #@# CA Reg Fri Aug 17 10:49:53 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_ca_register -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0/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 '/usr/local/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.99 (predicted orig area = 8.1) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.050, neg=0, invalid=762 0001: dt=362.508773, rms=0.875 (16.699%), neg=0, invalid=762 0002: dt=328.152349, rms=0.812 (7.213%), neg=0, invalid=762 0003: dt=198.603175, rms=0.792 (2.386%), neg=0, invalid=762 0004: dt=295.936000, rms=0.779 (1.632%), neg=0, invalid=762 0005: dt=168.000000, rms=0.773 (0.822%), neg=0, invalid=762 0006: dt=517.888000, rms=0.765 (1.024%), neg=0, invalid=762 0007: dt=129.900990, rms=0.761 (0.486%), neg=0, invalid=762 0008: dt=1775.616000, rms=0.751 (1.391%), neg=0, invalid=762 0009: dt=148.666667, rms=0.746 (0.597%), neg=0, invalid=762 0010: dt=295.936000, rms=0.745 (0.122%), neg=0, invalid=762 0011: dt=295.936000, rms=0.744 (0.221%), neg=0, invalid=762 0012: dt=295.936000, rms=0.742 (0.293%), neg=0, invalid=762 0013: dt=295.936000, rms=0.740 (0.205%), neg=0, invalid=762 0014: dt=295.936000, rms=0.736 (0.544%), neg=0, invalid=762 0015: dt=295.936000, rms=0.733 (0.379%), neg=0, invalid=762 0016: dt=295.936000, rms=0.731 (0.250%), neg=0, invalid=762 0017: dt=295.936000, rms=0.728 (0.436%), neg=0, invalid=762 0018: dt=295.936000, rms=0.726 (0.299%), neg=0, invalid=762 0019: dt=295.936000, rms=0.725 (0.190%), neg=0, invalid=762 0020: dt=295.936000, rms=0.723 (0.227%), neg=0, invalid=762 0021: dt=295.936000, rms=0.721 (0.282%), neg=0, invalid=762 0022: dt=295.936000, rms=0.719 (0.206%), neg=0, invalid=762 0023: dt=295.936000, rms=0.719 (0.038%), neg=0, invalid=762 0024: dt=295.936000, rms=0.718 (0.158%), neg=0, invalid=762 0025: dt=295.936000, rms=0.717 (0.170%), neg=0, invalid=762 0026: dt=295.936000, rms=0.717 (0.031%), neg=0, invalid=762 0027: dt=295.936000, rms=0.716 (0.131%), neg=0, invalid=762 0028: dt=295.936000, rms=0.714 (0.199%), neg=0, invalid=762 0029: dt=295.936000, rms=0.714 (0.060%), neg=0, invalid=762 0030: dt=295.936000, rms=0.713 (0.130%), neg=0, invalid=762 0031: dt=295.936000, rms=0.711 (0.217%), neg=0, invalid=762 0032: dt=295.936000, rms=0.711 (0.075%), neg=0, invalid=762 0033: dt=295.936000, rms=0.710 (0.148%), neg=0, invalid=762 0034: dt=295.936000, rms=0.709 (0.092%), neg=0, invalid=762 0035: dt=295.936000, rms=0.709 (0.059%), neg=0, invalid=762 0036: dt=295.936000, rms=0.708 (0.057%), neg=0, invalid=762 0037: dt=295.936000, rms=0.708 (-0.145%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=762 0038: dt=129.472000, rms=0.707 (0.285%), neg=0, invalid=762 0039: dt=110.976000, rms=0.707 (0.008%), neg=0, invalid=762 0040: dt=110.976000, rms=0.707 (0.004%), neg=0, invalid=762 0041: dt=110.976000, rms=0.707 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0042: dt=75.985019, rms=0.719 (0.508%), neg=0, invalid=762 0043: dt=242.247934, rms=0.707 (1.796%), neg=0, invalid=762 0044: dt=30.096654, rms=0.703 (0.523%), neg=0, invalid=762 0045: dt=19.200000, rms=0.703 (0.034%), neg=0, invalid=762 0046: dt=19.200000, rms=0.702 (0.035%), neg=0, invalid=762 0047: dt=19.200000, rms=0.702 (0.061%), neg=0, invalid=762 0048: dt=19.200000, rms=0.701 (0.125%), neg=0, invalid=762 0049: dt=19.200000, rms=0.699 (0.245%), neg=0, invalid=762 0050: dt=19.200000, rms=0.697 (0.371%), neg=0, invalid=762 0051: dt=19.200000, rms=0.694 (0.429%), neg=0, invalid=762 0052: dt=19.200000, rms=0.691 (0.405%), neg=0, invalid=762 0053: dt=19.200000, rms=0.689 (0.352%), neg=0, invalid=762 0054: dt=19.200000, rms=0.686 (0.297%), neg=0, invalid=762 0055: dt=19.200000, rms=0.685 (0.234%), neg=0, invalid=762 0056: dt=19.200000, rms=0.683 (0.212%), neg=0, invalid=762 0057: dt=19.200000, rms=0.682 (0.226%), neg=0, invalid=762 0058: dt=19.200000, rms=0.680 (0.248%), neg=0, invalid=762 0059: dt=19.200000, rms=0.678 (0.262%), neg=0, invalid=762 0060: dt=19.200000, rms=0.677 (0.251%), neg=0, invalid=762 0061: dt=19.200000, rms=0.675 (0.221%), neg=0, invalid=762 0062: dt=19.200000, rms=0.674 (0.197%), neg=0, invalid=762 0063: dt=19.200000, rms=0.673 (0.178%), neg=0, invalid=762 0064: dt=19.200000, rms=0.672 (0.165%), neg=0, invalid=762 0065: dt=19.200000, rms=0.670 (0.160%), neg=0, invalid=762 0066: dt=19.200000, rms=0.669 (0.165%), neg=0, invalid=762 0067: dt=19.200000, rms=0.668 (0.164%), neg=0, invalid=762 0068: dt=19.200000, rms=0.667 (0.158%), neg=0, invalid=762 0069: dt=19.200000, rms=0.666 (0.145%), neg=0, invalid=762 0070: dt=19.200000, rms=0.665 (0.130%), neg=0, invalid=762 0071: dt=19.200000, rms=0.665 (0.115%), neg=0, invalid=762 0072: dt=19.200000, rms=0.664 (0.104%), neg=0, invalid=762 0073: dt=145.152000, rms=0.664 (0.048%), neg=0, invalid=762 0074: dt=145.152000, rms=0.664 (-0.114%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0075: dt=36.288000, rms=0.662 (0.276%), neg=0, invalid=762 0076: dt=36.288000, rms=0.662 (0.031%), neg=0, invalid=762 0077: dt=36.288000, rms=0.662 (0.010%), neg=0, invalid=762 0078: dt=36.288000, rms=0.662 (0.006%), neg=0, invalid=762 0079: dt=36.288000, rms=0.662 (0.001%), neg=0, invalid=762 0080: dt=331.776000, rms=0.661 (0.150%), neg=0, invalid=762 0081: dt=20.736000, rms=0.661 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0082: dt=9.600000, rms=0.698 (0.247%), neg=0, invalid=762 0083: dt=11.200000, rms=0.698 (0.098%), neg=0, invalid=762 0084: dt=11.200000, rms=0.697 (0.104%), neg=0, invalid=762 0085: dt=11.200000, rms=0.696 (0.065%), neg=0, invalid=762 0086: dt=11.200000, rms=0.696 (-0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=762 0087: dt=2.800000, rms=0.696 (0.081%), neg=0, invalid=762 0088: dt=2.400000, rms=0.696 (0.001%), neg=0, invalid=762 0089: dt=2.400000, rms=0.696 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.773, neg=0, invalid=762 0090: dt=4.064516, rms=0.768 (0.686%), neg=0, invalid=762 0091: dt=3.627907, rms=0.767 (0.145%), neg=0, invalid=762 0092: dt=3.627907, rms=0.766 (0.034%), neg=0, invalid=762 0093: dt=3.627907, rms=0.766 (-0.169%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.767, neg=0, invalid=762 0094: dt=0.000000, rms=0.766 (0.056%), neg=0, invalid=762 0095: dt=0.000000, rms=0.766 (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=0.862, neg=0, invalid=762 0096: dt=0.256000, rms=0.861 (0.065%), neg=0, invalid=762 0097: dt=0.256000, rms=0.861 (0.011%), neg=0, invalid=762 0098: dt=0.256000, rms=0.861 (0.008%), neg=0, invalid=762 0099: dt=0.256000, rms=0.861 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.861, neg=0, invalid=762 0100: dt=0.448000, rms=0.860 (0.109%), neg=0, invalid=762 0101: dt=0.768000, rms=0.860 (0.072%), neg=0, invalid=762 0102: dt=0.768000, rms=0.859 (0.091%), neg=0, invalid=762 0103: dt=0.768000, rms=0.858 (0.048%), neg=0, invalid=762 0104: dt=0.768000, rms=0.858 (-0.088%), 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=0.740, neg=0, invalid=762 0105: dt=0.898178, rms=0.722 (2.547%), neg=0, invalid=762 0106: dt=0.096000, rms=0.720 (0.163%), neg=0, invalid=762 0107: dt=0.096000, rms=0.720 (-0.077%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.721, neg=0, invalid=762 0108: dt=0.028000, rms=0.720 (0.080%), neg=0, invalid=762 0109: dt=0.016000, rms=0.720 (0.004%), neg=0, invalid=762 0110: dt=0.016000, rms=0.720 (-0.003%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10088 (31) Left_Lateral_Ventricle (4): linear fit = 1.62 x + 0.0 (1932 voxels, overlap=0.290) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1932 voxels, peak = 32), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.20783 (27) Right_Lateral_Ventricle (43): linear fit = 1.71 x + 0.0 (1741 voxels, overlap=0.165) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1741 voxels, peak = 27), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.07506 (81) Right_Pallidum (52): linear fit = 0.86 x + 0.0 (1091 voxels, overlap=0.836) Right_Pallidum (52): linear fit = 0.86 x + 0.0 (1091 voxels, peak = 82), gca=82.1 gca peak = 0.20183 (93) mri peak = 0.09763 (84) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (1164 voxels, overlap=0.107) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (1164 voxels, peak = 82), gca=82.3 gca peak = 0.21683 (55) mri peak = 0.05816 (69) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1420 voxels, overlap=0.021) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1420 voxels, peak = 68), gca=68.5 gca peak = 0.30730 (58) mri peak = 0.07846 (72) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1470 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1470 voxels, peak = 71), gca=71.1 gca peak = 0.11430 (101) mri peak = 0.09072 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (85997 voxels, overlap=0.975) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (85997 voxels, peak = 101), gca=101.0 gca peak = 0.12076 (102) mri peak = 0.07941 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (93412 voxels, overlap=0.914) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (93412 voxels, peak = 103), gca=102.5 gca peak = 0.14995 (59) mri peak = 0.03409 (71) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (32797 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (32797 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.03453 (72) Right_Cerebral_Cortex (42): linear fit = 1.28 x + 0.0 (31677 voxels, overlap=0.002) Right_Cerebral_Cortex (42): linear fit = 1.28 x + 0.0 (31677 voxels, peak = 75), gca=74.5 gca peak = 0.14161 (67) mri peak = 0.07585 (74) Right_Caudate (50): linear fit = 1.10 x + 0.0 (870 voxels, overlap=0.203) Right_Caudate (50): linear fit = 1.10 x + 0.0 (870 voxels, peak = 73), gca=73.4 gca peak = 0.15243 (71) mri peak = 0.10699 (79) Left_Caudate (11): linear fit = 1.09 x + 0.0 (1393 voxels, overlap=0.576) Left_Caudate (11): linear fit = 1.09 x + 0.0 (1393 voxels, peak = 77), gca=77.0 gca peak = 0.13336 (57) mri peak = 0.04485 (78) Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (19731 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (19731 voxels, peak = 77), gca=76.7 gca peak = 0.13252 (56) mri peak = 0.04415 (78) Right_Cerebellum_Cortex (47): linear fit = 1.39 x + 0.0 (21766 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.39 x + 0.0 (21766 voxels, peak = 78), gca=78.1 gca peak = 0.18181 (84) mri peak = 0.03860 (83) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (11058 voxels, overlap=0.896) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (11058 voxels, peak = 83), gca=82.7 gca peak = 0.20573 (83) mri peak = 0.04653 (82) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7844 voxels, overlap=0.982) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7844 voxels, peak = 83), gca=82.6 gca peak = 0.21969 (57) mri peak = 0.11210 (75) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (612 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (612 voxels, peak = 74), gca=74.4 gca peak = 0.39313 (56) mri peak = 0.06362 (72) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (414 voxels, overlap=0.888) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (414 voxels, peak = 67), gca=67.5 gca peak = 0.14181 (85) mri peak = 0.08011 (100) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (7006 voxels, overlap=0.060) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (7006 voxels, peak = 102), gca=101.6 gca peak = 0.11978 (83) mri peak = 0.07561 (95) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (5127 voxels, overlap=0.103) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (5127 voxels, peak = 96), gca=95.9 gca peak = 0.13399 (79) mri peak = 0.08986 (84) Left_Putamen (12): linear fit = 1.05 x + 0.0 (3213 voxels, overlap=0.772) Left_Putamen (12): linear fit = 1.05 x + 0.0 (3213 voxels, peak = 83), gca=83.3 gca peak = 0.14159 (79) mri peak = 0.09742 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (3196 voxels, overlap=0.760) Right_Putamen (51): linear fit = 1.04 x + 0.0 (3196 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.08051 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9547 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9547 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.12250 (96) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1485 voxels, overlap=0.109) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1485 voxels, peak = 95), gca=95.0 gca peak = 0.12801 (89) mri peak = 0.07849 (101) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1845 voxels, overlap=0.630) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1845 voxels, peak = 100), gca=100.1 gca peak = 0.20494 (23) mri peak = 0.44444 (51) Third_Ventricle (14): linear fit = 2.17 x + 0.0 (160 voxels, overlap=0.013) Third_Ventricle (14): linear fit = 2.17 x + 0.0 (160 voxels, peak = 50), gca=50.0 gca peak = 0.15061 (21) mri peak = 0.06649 (23) Fourth_Ventricle (15): linear fit = 1.65 x + 0.0 (854 voxels, overlap=0.467) Fourth_Ventricle (15): linear fit = 1.65 x + 0.0 (854 voxels, peak = 35), gca=34.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.27 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.50 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=0.707, neg=0, invalid=762 0111: dt=147.001821, rms=0.661 (6.498%), neg=0, invalid=762 0112: dt=265.899281, rms=0.650 (1.684%), neg=0, invalid=762 0113: dt=129.472000, rms=0.647 (0.476%), neg=0, invalid=762 0114: dt=887.808000, rms=0.640 (1.075%), neg=0, invalid=762 0115: dt=129.472000, rms=0.638 (0.223%), neg=0, invalid=762 0116: dt=517.888000, rms=0.636 (0.291%), neg=0, invalid=762 0117: dt=129.472000, rms=0.635 (0.134%), neg=0, invalid=762 0118: dt=443.904000, rms=0.635 (0.086%), neg=0, invalid=762 0119: dt=129.472000, rms=0.634 (0.147%), neg=0, invalid=762 0120: dt=517.888000, rms=0.633 (0.094%), neg=0, invalid=762 0121: dt=129.472000, rms=0.633 (0.121%), neg=0, invalid=762 0122: dt=517.888000, rms=0.632 (0.090%), neg=0, invalid=762 0123: dt=129.472000, rms=0.631 (0.087%), neg=0, invalid=762 0124: dt=369.920000, rms=0.631 (0.032%), neg=0, invalid=762 0125: dt=369.920000, rms=0.631 (0.097%), neg=0, invalid=762 0126: dt=369.920000, rms=0.631 (-0.078%), neg=0, invalid=762 0127: dt=73.984000, rms=0.630 (0.060%), neg=0, invalid=762 0128: dt=110.976000, rms=0.630 (0.015%), neg=0, invalid=762 0129: dt=110.976000, rms=0.630 (0.018%), neg=0, invalid=762 0130: dt=110.976000, rms=0.630 (0.034%), neg=0, invalid=762 0131: dt=110.976000, rms=0.630 (0.056%), neg=0, invalid=762 0132: dt=110.976000, rms=0.629 (0.073%), neg=0, invalid=762 0133: dt=110.976000, rms=0.629 (0.070%), neg=0, invalid=762 0134: dt=110.976000, rms=0.628 (0.071%), neg=0, invalid=762 0135: dt=110.976000, rms=0.628 (0.077%), neg=0, invalid=762 0136: dt=110.976000, rms=0.627 (0.081%), neg=0, invalid=762 0137: dt=110.976000, rms=0.627 (0.073%), neg=0, invalid=762 0138: dt=110.976000, rms=0.626 (0.067%), neg=0, invalid=762 0139: dt=110.976000, rms=0.626 (0.058%), neg=0, invalid=762 0140: dt=110.976000, rms=0.626 (0.057%), neg=0, invalid=762 0141: dt=110.976000, rms=0.625 (0.060%), neg=0, invalid=762 0142: dt=110.976000, rms=0.625 (0.057%), neg=0, invalid=762 0143: dt=110.976000, rms=0.625 (0.058%), neg=0, invalid=762 0144: dt=110.976000, rms=0.624 (0.049%), neg=0, invalid=762 0145: dt=110.976000, rms=0.624 (0.053%), neg=0, invalid=762 0146: dt=110.976000, rms=0.624 (0.054%), neg=0, invalid=762 0147: dt=110.976000, rms=0.623 (0.056%), neg=0, invalid=762 0148: dt=110.976000, rms=0.623 (0.042%), neg=0, invalid=762 0149: dt=110.976000, rms=0.623 (0.054%), neg=0, invalid=762 0150: dt=110.976000, rms=0.622 (0.048%), neg=0, invalid=762 0151: dt=110.976000, rms=0.622 (0.044%), neg=0, invalid=762 0152: dt=110.976000, rms=0.622 (0.035%), neg=0, invalid=762 0153: dt=110.976000, rms=0.622 (0.044%), neg=0, invalid=762 0154: dt=110.976000, rms=0.621 (0.049%), neg=0, invalid=762 0155: dt=110.976000, rms=0.621 (0.052%), neg=0, invalid=762 0156: dt=110.976000, rms=0.621 (0.043%), neg=0, invalid=762 0157: dt=110.976000, rms=0.620 (0.040%), neg=0, invalid=762 0158: dt=110.976000, rms=0.620 (0.035%), neg=0, invalid=762 0159: dt=110.976000, rms=0.620 (0.044%), neg=0, invalid=762 0160: dt=110.976000, rms=0.620 (0.035%), neg=0, invalid=762 0161: dt=110.976000, rms=0.619 (0.045%), neg=0, invalid=762 0162: dt=110.976000, rms=0.619 (0.038%), neg=0, invalid=762 0163: dt=110.976000, rms=0.619 (0.033%), neg=0, invalid=762 0164: dt=110.976000, rms=0.619 (0.034%), neg=0, invalid=762 0165: dt=110.976000, rms=0.619 (0.036%), neg=0, invalid=762 0166: dt=110.976000, rms=0.618 (0.029%), neg=0, invalid=762 0167: dt=110.976000, rms=0.618 (0.036%), neg=0, invalid=762 0168: dt=110.976000, rms=0.618 (0.035%), neg=0, invalid=762 0169: dt=110.976000, rms=0.618 (0.031%), neg=0, invalid=762 0170: dt=110.976000, rms=0.618 (0.026%), neg=0, invalid=762 0171: dt=110.976000, rms=0.617 (0.026%), neg=0, invalid=762 0172: dt=110.976000, rms=0.617 (0.026%), neg=0, invalid=762 0173: dt=110.976000, rms=0.617 (0.019%), neg=0, invalid=762 0174: dt=110.976000, rms=0.617 (0.018%), neg=0, invalid=762 0175: dt=1183.744000, rms=0.617 (0.044%), neg=0, invalid=762 0176: dt=32.368000, rms=0.617 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=762 0177: dt=73.984000, rms=0.617 (0.041%), neg=0, invalid=762 0178: dt=32.368000, rms=0.617 (0.005%), neg=0, invalid=762 0179: dt=32.368000, rms=0.617 (0.003%), neg=0, invalid=762 0180: dt=32.368000, rms=0.617 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.618, neg=0, invalid=762 0181: dt=145.152000, rms=0.613 (0.808%), neg=0, invalid=762 0182: dt=183.391813, rms=0.608 (0.864%), neg=0, invalid=762 0183: dt=66.129952, rms=0.605 (0.497%), neg=0, invalid=762 0184: dt=580.608000, rms=0.596 (1.499%), neg=0, invalid=762 0185: dt=77.128205, rms=0.593 (0.447%), neg=0, invalid=762 0186: dt=103.680000, rms=0.591 (0.299%), neg=0, invalid=762 0187: dt=36.288000, rms=0.591 (0.096%), neg=0, invalid=762 0188: dt=331.776000, rms=0.589 (0.303%), neg=0, invalid=762 0189: dt=65.469729, rms=0.587 (0.364%), neg=0, invalid=762 0190: dt=82.944000, rms=0.586 (0.072%), neg=0, invalid=762 0191: dt=145.152000, rms=0.585 (0.215%), neg=0, invalid=762 0192: dt=36.288000, rms=0.585 (0.061%), neg=0, invalid=762 0193: dt=145.152000, rms=0.584 (0.120%), neg=0, invalid=762 0194: dt=103.680000, rms=0.583 (0.174%), neg=0, invalid=762 0195: dt=36.288000, rms=0.583 (0.042%), neg=0, invalid=762 0196: dt=36.288000, rms=0.582 (0.043%), neg=0, invalid=762 0197: dt=36.288000, rms=0.582 (0.061%), neg=0, invalid=762 0198: dt=36.288000, rms=0.581 (0.103%), neg=0, invalid=762 0199: dt=36.288000, rms=0.581 (0.134%), neg=0, invalid=762 0200: dt=36.288000, rms=0.580 (0.149%), neg=0, invalid=762 0201: dt=36.288000, rms=0.579 (0.153%), neg=0, invalid=762 0202: dt=36.288000, rms=0.578 (0.162%), neg=0, invalid=762 0203: dt=36.288000, rms=0.577 (0.161%), neg=0, invalid=762 0204: dt=36.288000, rms=0.576 (0.174%), neg=0, invalid=762 0205: dt=36.288000, rms=0.575 (0.184%), neg=0, invalid=762 0206: dt=36.288000, rms=0.574 (0.178%), neg=0, invalid=762 0207: dt=36.288000, rms=0.574 (0.015%), neg=0, invalid=762 0208: dt=36.288000, rms=0.574 (0.035%), neg=0, invalid=762 0209: dt=36.288000, rms=0.573 (0.056%), neg=0, invalid=762 0210: dt=36.288000, rms=0.573 (0.071%), neg=0, invalid=762 0211: dt=36.288000, rms=0.572 (0.084%), neg=0, invalid=762 0212: dt=36.288000, rms=0.572 (0.087%), neg=0, invalid=762 0213: dt=36.288000, rms=0.571 (0.088%), neg=0, invalid=762 0214: dt=36.288000, rms=0.571 (0.090%), neg=0, invalid=762 0215: dt=36.288000, rms=0.571 (0.020%), neg=0, invalid=762 0216: dt=36.288000, rms=0.571 (0.031%), neg=0, invalid=762 0217: dt=36.288000, rms=0.570 (0.036%), neg=0, invalid=762 0218: dt=36.288000, rms=0.570 (0.018%), neg=0, invalid=762 0219: dt=9.072000, rms=0.570 (0.003%), neg=0, invalid=762 0220: dt=2.268000, rms=0.570 (0.001%), neg=0, invalid=762 0221: dt=0.283500, rms=0.570 (0.000%), neg=0, invalid=762 0222: dt=0.141750, rms=0.570 (0.000%), neg=0, invalid=762 0223: dt=0.035437, rms=0.570 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.571, neg=0, invalid=762 0224: dt=0.007594, rms=0.570 (0.044%), neg=0, invalid=762 0225: dt=0.000000, rms=0.570 (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=0.578, neg=0, invalid=762 0226: dt=44.800000, rms=0.567 (1.908%), neg=0, invalid=762 0227: dt=32.000000, rms=0.562 (0.892%), neg=0, invalid=762 0228: dt=44.800000, rms=0.556 (1.028%), neg=0, invalid=762 0229: dt=44.800000, rms=0.552 (0.700%), neg=0, invalid=762 0230: dt=44.800000, rms=0.549 (0.634%), neg=0, invalid=762 0231: dt=44.800000, rms=0.547 (0.402%), neg=0, invalid=762 0232: dt=11.200000, rms=0.546 (0.202%), neg=0, invalid=762 0233: dt=2.800000, rms=0.545 (0.042%), neg=0, invalid=762 0234: dt=2.800000, rms=0.545 (0.032%), neg=0, invalid=762 0235: dt=0.350000, rms=0.545 (0.005%), neg=0, invalid=762 0236: dt=0.175000, rms=0.545 (0.002%), neg=0, invalid=762 0237: dt=0.043750, rms=0.545 (0.000%), neg=0, invalid=762 0238: dt=0.043750, rms=0.545 (0.001%), neg=0, invalid=762 0239: dt=0.021875, rms=0.545 (0.000%), neg=0, invalid=762 0240: dt=0.000684, rms=0.545 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=762 0241: dt=53.810945, rms=0.541 (0.759%), neg=0, invalid=762 0242: dt=38.400000, rms=0.539 (0.377%), neg=0, invalid=762 0243: dt=38.400000, rms=0.537 (0.313%), neg=0, invalid=762 0244: dt=38.400000, rms=0.536 (0.210%), neg=0, invalid=762 0245: dt=38.400000, rms=0.535 (0.224%), neg=0, invalid=762 0246: dt=32.000000, rms=0.534 (0.180%), neg=0, invalid=762 0247: dt=38.400000, rms=0.533 (0.178%), neg=0, invalid=762 0248: dt=32.000000, rms=0.532 (0.143%), neg=0, invalid=762 0249: dt=38.400000, rms=0.532 (0.149%), neg=0, invalid=762 0250: dt=32.000000, rms=0.531 (0.115%), neg=0, invalid=762 0251: dt=32.000000, rms=0.530 (0.119%), neg=0, invalid=762 0252: dt=32.000000, rms=0.530 (0.108%), neg=0, invalid=762 0253: dt=32.000000, rms=0.529 (0.101%), neg=0, invalid=762 0254: dt=2.400000, rms=0.529 (0.013%), neg=0, invalid=762 0255: dt=0.150000, rms=0.529 (0.004%), neg=0, invalid=762 0256: dt=0.075000, rms=0.529 (0.001%), neg=0, invalid=762 0257: dt=0.037500, rms=0.529 (0.000%), neg=0, invalid=762 0258: dt=0.010937, rms=0.529 (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=0.549, neg=0, invalid=762 0259: dt=3.333333, rms=0.548 (0.105%), neg=0, invalid=762 0260: dt=2.304000, rms=0.548 (0.021%), neg=0, invalid=762 0261: dt=2.304000, rms=0.548 (0.010%), neg=0, invalid=762 0262: dt=2.304000, rms=0.548 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0263: dt=2.285714, rms=0.548 (0.054%), neg=0, invalid=762 0264: dt=1.008000, rms=0.548 (0.004%), neg=0, invalid=762 0265: dt=1.008000, rms=0.548 (0.003%), neg=0, invalid=762 0266: dt=1.008000, rms=0.548 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0267: dt=1.280000, rms=0.578 (0.200%), neg=0, invalid=762 0268: dt=0.448000, rms=0.578 (0.014%), neg=0, invalid=762 0269: dt=0.448000, rms=0.578 (0.002%), neg=0, invalid=762 0270: dt=0.448000, rms=0.578 (-0.033%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=762 0271: dt=1.792000, rms=0.577 (0.210%), neg=0, invalid=762 0272: dt=1.280000, rms=0.577 (0.031%), neg=0, invalid=762 0273: dt=1.280000, rms=0.577 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0274: dt=0.448000, rms=0.528 (2.573%), neg=0, invalid=762 0275: dt=0.448000, rms=0.524 (0.723%), neg=0, invalid=762 0276: dt=0.448000, rms=0.522 (0.437%), neg=0, invalid=762 0277: dt=0.448000, rms=0.520 (0.270%), neg=0, invalid=762 0278: dt=0.448000, rms=0.519 (0.202%), neg=0, invalid=762 0279: dt=0.448000, rms=0.518 (0.148%), neg=0, invalid=762 0280: dt=0.448000, rms=0.518 (0.120%), neg=0, invalid=762 0281: dt=0.448000, rms=0.517 (0.093%), neg=0, invalid=762 0282: dt=0.448000, rms=0.517 (0.080%), neg=0, invalid=762 0283: dt=0.448000, rms=0.517 (0.062%), neg=0, invalid=762 0284: dt=0.448000, rms=0.516 (0.058%), neg=0, invalid=762 0285: dt=0.448000, rms=0.516 (0.044%), neg=0, invalid=762 0286: dt=0.448000, rms=0.516 (0.043%), neg=0, invalid=762 0287: dt=0.448000, rms=0.516 (0.072%), neg=0, invalid=762 0288: dt=0.448000, rms=0.515 (0.084%), neg=0, invalid=762 0289: dt=0.448000, rms=0.515 (0.087%), neg=0, invalid=762 0290: dt=0.448000, rms=0.514 (0.081%), neg=0, invalid=762 0291: dt=0.448000, rms=0.514 (0.067%), neg=0, invalid=762 0292: dt=0.448000, rms=0.514 (0.041%), neg=0, invalid=762 0293: dt=0.448000, rms=0.514 (0.026%), neg=0, invalid=762 0294: dt=0.448000, rms=0.513 (0.012%), neg=0, invalid=762 0295: dt=0.448000, rms=0.513 (-0.002%), neg=0, invalid=762 0296: dt=0.080000, rms=0.513 (0.000%), neg=0, invalid=762 0297: dt=0.007000, rms=0.513 (0.001%), neg=0, invalid=762 0298: dt=0.006000, rms=0.513 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0299: dt=0.448000, rms=0.510 (0.753%), neg=0, invalid=762 0300: dt=0.448000, rms=0.509 (0.089%), neg=0, invalid=762 0301: dt=0.448000, rms=0.509 (0.017%), neg=0, invalid=762 0302: dt=0.448000, rms=0.509 (-0.003%), 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=0.506, neg=0, invalid=762 0303: dt=23.120000, rms=0.506 (0.060%), neg=0, invalid=762 0304: dt=4.624000, rms=0.506 (0.001%), neg=0, invalid=762 0305: dt=4.624000, rms=0.506 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=762 0306: dt=55.488000, rms=0.506 (0.071%), neg=0, invalid=762 0307: dt=110.976000, rms=0.506 (0.010%), neg=0, invalid=762 0308: dt=110.976000, rms=0.506 (0.015%), neg=0, invalid=762 0309: dt=110.976000, rms=0.506 (0.019%), neg=0, invalid=762 0310: dt=110.976000, rms=0.506 (0.009%), neg=0, invalid=762 0311: dt=110.976000, rms=0.506 (0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.506, neg=0, invalid=762 0312: dt=36.288000, rms=0.505 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0313: dt=36.288000, rms=0.505 (0.030%), neg=0, invalid=762 0314: dt=36.288000, rms=0.505 (0.012%), neg=0, invalid=762 0315: dt=36.288000, rms=0.505 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0316: dt=36.288000, rms=0.505 (-0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 0317: dt=67.168317, rms=0.504 (0.361%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0318: dt=82.944000, rms=0.503 (0.147%), neg=0, invalid=762 0319: dt=82.944000, rms=0.503 (0.004%), neg=0, invalid=762 0320: dt=82.944000, rms=0.501 (0.287%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=82.944000, rms=0.501 (-0.008%), neg=0, invalid=762 0322: dt=82.944000, rms=0.501 (0.068%), neg=0, invalid=762 0323: dt=36.288000, rms=0.501 (0.045%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.501, neg=0, invalid=762 iter 0, gcam->neg = 12 after 0 iterations, nbhd size=0, neg = 0 0324: dt=36.585987, rms=0.498 (0.695%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 8 iterations, nbhd size=1, neg = 0 0325: dt=64.521739, rms=0.493 (1.011%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0326: dt=11.200000, rms=0.492 (0.265%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0327: dt=11.200000, rms=0.491 (0.107%), neg=0, invalid=762 0328: dt=11.200000, rms=0.491 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0329: dt=11.200000, rms=0.490 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0330: dt=11.200000, rms=0.489 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0331: dt=11.200000, rms=0.488 (0.231%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=0, neg = 0 0332: dt=11.200000, rms=0.487 (0.250%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0333: dt=11.200000, rms=0.486 (0.222%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0334: dt=11.200000, rms=0.485 (0.199%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0335: dt=11.200000, rms=0.484 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0336: dt=11.200000, rms=0.483 (0.113%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0337: dt=11.200000, rms=0.483 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 13 iterations, nbhd size=1, neg = 0 0338: dt=11.200000, rms=0.482 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0339: dt=102.400000, rms=0.482 (0.180%), neg=0, invalid=762 0340: dt=11.200000, rms=0.481 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0341: dt=11.200000, rms=0.481 (0.036%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0342: dt=11.200000, rms=0.481 (0.015%), neg=0, invalid=762 0343: dt=11.200000, rms=0.481 (0.021%), neg=0, invalid=762 0344: dt=11.200000, rms=0.481 (0.048%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0345: dt=11.200000, rms=0.480 (0.070%), neg=0, invalid=762 0346: dt=11.200000, rms=0.480 (0.062%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.481, neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0347: dt=44.800000, rms=0.477 (0.755%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0348: dt=25.600000, rms=0.476 (0.211%), neg=0, invalid=762 0349: dt=25.600000, rms=0.475 (0.136%), neg=0, invalid=762 0350: dt=25.600000, rms=0.475 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0351: dt=25.600000, rms=0.474 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0352: dt=25.600000, rms=0.473 (0.086%), neg=0, invalid=762 0353: dt=25.600000, rms=0.473 (0.070%), neg=0, invalid=762 0354: dt=32.000000, rms=0.473 (0.058%), neg=0, invalid=762 0355: dt=32.000000, rms=0.473 (0.037%), neg=0, invalid=762 0356: dt=32.000000, rms=0.472 (0.081%), neg=0, invalid=762 0357: dt=32.000000, rms=0.472 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0358: dt=32.000000, rms=0.472 (0.098%), neg=0, invalid=762 0359: dt=32.000000, rms=0.471 (0.075%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 0360: dt=2.000000, rms=0.479 (0.067%), neg=0, invalid=762 0361: dt=0.216000, rms=0.479 (0.003%), neg=0, invalid=762 0362: dt=0.216000, rms=0.479 (0.001%), neg=0, invalid=762 0363: dt=0.216000, rms=0.479 (0.000%), neg=0, invalid=762 0364: dt=0.216000, rms=0.479 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 0365: dt=2.880000, rms=0.479 (0.087%), neg=0, invalid=762 0366: dt=1.008000, rms=0.479 (0.008%), neg=0, invalid=762 0367: dt=1.008000, rms=0.478 (0.002%), neg=0, invalid=762 0368: dt=1.008000, rms=0.478 (0.001%), neg=0, invalid=762 0369: dt=1.008000, rms=0.478 (-0.017%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0370: dt=0.448000, rms=0.490 (0.089%), neg=0, invalid=762 0371: dt=0.256000, rms=0.490 (0.006%), neg=0, invalid=762 0372: dt=0.256000, rms=0.490 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0373: dt=1.280000, rms=0.489 (0.190%), neg=0, invalid=762 0374: dt=0.448000, rms=0.489 (0.022%), neg=0, invalid=762 0375: dt=0.448000, rms=0.489 (0.011%), neg=0, invalid=762 0376: dt=0.448000, rms=0.489 (-0.010%), 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=0.477, neg=0, invalid=762 iter 0, gcam->neg = 806 after 15 iterations, nbhd size=1, neg = 0 0377: dt=2.020267, rms=0.450 (5.796%), neg=0, invalid=762 0378: dt=0.028000, rms=0.449 (0.012%), neg=0, invalid=762 0379: dt=0.028000, rms=0.449 (0.001%), neg=0, invalid=762 0380: dt=0.028000, rms=0.449 (-0.030%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0381: dt=0.064000, rms=0.449 (0.098%), neg=0, invalid=762 0382: dt=0.000000, rms=0.449 (0.003%), neg=0, invalid=762 0383: dt=0.050000, rms=0.449 (-0.017%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0384: dt=0.000000, rms=0.436 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0385: dt=32.368000, rms=0.436 (0.003%), neg=0, invalid=762 0386: dt=27.744000, rms=0.436 (0.001%), neg=0, invalid=762 0387: dt=27.744000, rms=0.436 (-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=0.436, neg=0, invalid=762 0388: dt=0.001898, rms=0.436 (0.000%), neg=0, invalid=762 0389: dt=0.000000, rms=0.436 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0390: dt=36.288000, rms=0.436 (0.028%), neg=0, invalid=762 0391: dt=103.680000, rms=0.436 (0.030%), neg=0, invalid=762 0392: dt=145.152000, rms=0.436 (0.049%), neg=0, invalid=762 0393: dt=82.944000, rms=0.436 (0.008%), neg=0, invalid=762 0394: dt=82.944000, rms=0.435 (0.025%), neg=0, invalid=762 0395: dt=82.944000, rms=0.435 (0.030%), neg=0, invalid=762 0396: dt=82.944000, rms=0.435 (0.023%), neg=0, invalid=762 0397: dt=82.944000, rms=0.435 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0398: dt=11.200000, rms=0.435 (0.078%), neg=0, invalid=762 0399: dt=11.200000, rms=0.435 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0400: dt=11.200000, rms=0.435 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0401: dt=11.200000, rms=0.435 (-0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0402: dt=44.800000, rms=0.433 (0.577%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0403: dt=25.600000, rms=0.432 (0.226%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0404: dt=25.600000, rms=0.431 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0405: dt=25.600000, rms=0.430 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0406: dt=25.600000, rms=0.430 (0.219%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0407: dt=25.600000, rms=0.429 (0.185%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0408: dt=25.600000, rms=0.428 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0409: dt=25.600000, rms=0.427 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0410: dt=25.600000, rms=0.427 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0411: dt=25.600000, rms=0.426 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0412: dt=25.600000, rms=0.426 (0.114%), neg=0, invalid=762 0413: dt=38.400000, rms=0.425 (0.039%), neg=0, invalid=762 0414: dt=38.400000, rms=0.425 (0.002%), neg=0, invalid=762 0415: dt=38.400000, rms=0.425 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0416: dt=38.400000, rms=0.425 (0.021%), neg=0, invalid=762 0417: dt=38.400000, rms=0.425 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0418: dt=38.400000, rms=0.425 (0.014%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 0419: dt=1.008000, rms=0.430 (0.004%), neg=0, invalid=762 0420: dt=0.180000, rms=0.430 (0.000%), neg=0, invalid=762 0421: dt=0.180000, 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 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0422: dt=8.000000, rms=0.429 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0423: dt=10.594595, rms=0.429 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0424: dt=10.594595, rms=0.429 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=10.594595, rms=0.429 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 0426: dt=10.594595, rms=0.428 (0.083%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=1, neg = 0 0427: dt=10.594595, rms=0.428 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0428: dt=10.594595, rms=0.427 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0429: dt=10.594595, rms=0.426 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 3 iterations, nbhd size=0, neg = 0 0430: dt=10.594595, rms=0.426 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 2 iterations, nbhd size=0, neg = 0 0431: dt=10.594595, rms=0.425 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 5 iterations, nbhd size=0, neg = 0 0432: dt=10.594595, rms=0.425 (-0.014%), neg=0, invalid=762 0433: dt=0.002250, rms=0.425 (0.000%), neg=0, invalid=762 0434: dt=0.000000, rms=0.425 (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=0.433, neg=0, invalid=762 0435: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0436: dt=0.000000, rms=0.433 (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=0.420, neg=0, invalid=762 iter 0, gcam->neg = 554 after 13 iterations, nbhd size=1, neg = 0 0437: dt=1.280000, rms=0.411 (2.209%), neg=0, invalid=762 0438: dt=0.000023, rms=0.411 (0.000%), neg=0, invalid=762 0439: dt=0.000023, rms=0.411 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0440: dt=0.096000, rms=0.411 (0.041%), neg=0, invalid=762 0441: dt=0.028000, rms=0.411 (0.005%), neg=0, invalid=762 0442: dt=0.028000, rms=0.411 (0.003%), neg=0, invalid=762 0443: dt=0.028000, rms=0.411 (-0.004%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 54 minutes and 52 seconds. mri_ca_register utimesec 6858.957117 mri_ca_register stimesec 16.129989 mri_ca_register ru_maxrss 1359020 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5628386 mri_ca_register ru_majflt 14 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 11768 mri_ca_register ru_oublock 63216 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4009 mri_ca_register ru_nivcsw 397397 FSRUNTIME@ mri_ca_register 1.9145 hours 1 threads #-------------------------------------- #@# SubCort Seg Fri Aug 17 12:44:45 EDT 2018 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname dart machine x86_64 setenv SUBJECTS_DIR /home/shize/freesurfer cd /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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 8.10 Atlas used for the 3D morph was /usr/local/freesurfer-6.0/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 = 0.11441 (31) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (2147 voxels, overlap=0.188) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (2147 voxels, peak = 30), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.14421 (27) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (1804 voxels, overlap=0.176) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1804 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.15359 (90) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (876 voxels, overlap=0.478) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (876 voxels, peak = 89), gca=88.8 gca peak = 0.16930 (96) mri peak = 0.11512 (92) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (713 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (713 voxels, peak = 92), gca=91.7 gca peak = 0.24553 (55) mri peak = 0.16674 (69) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1108 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1108 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.11914 (70) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1339 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1339 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.08917 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52748 voxels, overlap=0.815) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52748 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.09142 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46511 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46511 voxels, peak = 103), gca=103.5 gca peak = 0.09712 (58) mri peak = 0.03845 (71) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (45039 voxels, overlap=0.052) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (45039 voxels, peak = 73), gca=73.4 gca peak = 0.11620 (58) mri peak = 0.04160 (71) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (34387 voxels, overlap=0.033) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (34387 voxels, peak = 73), gca=72.8 gca peak = 0.30970 (66) mri peak = 0.19040 (76) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1041 voxels, overlap=0.025) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1041 voxels, peak = 74), gca=74.2 gca peak = 0.15280 (69) mri peak = 0.13650 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (987 voxels, overlap=0.569) Left_Caudate (11): linear fit = 1.05 x + 0.0 (987 voxels, peak = 73), gca=72.8 gca peak = 0.13902 (56) mri peak = 0.06399 (72) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (25557 voxels, overlap=0.002) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (25557 voxels, peak = 73), gca=72.5 gca peak = 0.14777 (55) mri peak = 0.06555 (75) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (28998 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (28998 voxels, peak = 74), gca=74.0 gca peak = 0.16765 (84) mri peak = 0.04917 (100) Left_Cerebellum_White_Matter (7): linear fit = 1.17 x + 0.0 (12019 voxels, overlap=0.346) Left_Cerebellum_White_Matter (7): linear fit = 1.17 x + 0.0 (12019 voxels, peak = 99), gca=98.7 gca peak = 0.18739 (84) mri peak = 0.09280 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8986 voxels, overlap=0.039) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8986 voxels, peak = 94), gca=94.5 gca peak = 0.29869 (57) mri peak = 0.14601 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (561 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (561 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.15849 (72) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (527 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (527 voxels, peak = 72), gca=71.5 gca peak = 0.11131 (90) mri peak = 0.06706 (100) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5149 voxels, overlap=0.284) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5149 voxels, peak = 102), gca=102.2 gca peak = 0.11793 (83) mri peak = 0.09017 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5644 voxels, overlap=0.427) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5644 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.14039 (79) Left_Putamen (12): linear fit = 1.03 x + 0.0 (2030 voxels, overlap=0.757) Left_Putamen (12): linear fit = 1.03 x + 0.0 (2030 voxels, peak = 84), gca=83.8 gca peak = 0.10360 (77) mri peak = 0.14539 (79) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2366 voxels, overlap=0.697) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2366 voxels, peak = 79), gca=78.9 gca peak = 0.08424 (78) mri peak = 0.08961 (83) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12211 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12211 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.08607 (97) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1897 voxels, overlap=0.013) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1897 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.07929 (97) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1681 voxels, overlap=0.349) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1681 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.16410 (42) Third_Ventricle (14): linear fit = 1.53 x + 0.0 (152 voxels, overlap=0.043) Third_Ventricle (14): linear fit = 1.53 x + 0.0 (152 voxels, peak = 37), gca=36.8 gca peak = 0.19357 (14) mri peak = 0.13700 (23) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (850 voxels, overlap=0.302) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (850 voxels, peak = 22), gca=21.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak 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 1.25 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.11441 (31) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2147 voxels, overlap=0.779) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2147 voxels, peak = 30), gca=30.2 gca peak = 0.13981 (19) mri peak = 0.14421 (27) Right_Lateral_Ventricle (43): linear fit = 1.37 x + 0.0 (1804 voxels, overlap=0.370) Right_Lateral_Ventricle (43): linear fit = 1.37 x + 0.0 (1804 voxels, peak = 26), gca=25.9 gca peak = 0.26011 (88) mri peak = 0.15359 (90) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (876 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (876 voxels, peak = 89), gca=89.3 gca peak = 0.17294 (92) mri peak = 0.11512 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (713 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (713 voxels, peak = 92), gca=92.0 gca peak = 0.25349 (68) mri peak = 0.16674 (69) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1108 voxels, overlap=0.886) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 68), gca=68.0 gca peak = 0.28839 (69) mri peak = 0.11914 (70) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1339 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1339 voxels, peak = 68), gca=68.0 gca peak = 0.07845 (102) mri peak = 0.08917 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52748 voxels, overlap=0.801) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52748 voxels, peak = 101), gca=101.5 gca peak = 0.08069 (104) mri peak = 0.09142 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46511 voxels, overlap=0.729) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46511 voxels, peak = 103), gca=103.5 gca peak = 0.07794 (73) mri peak = 0.03845 (71) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (45039 voxels, overlap=0.966) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (45039 voxels, peak = 76), gca=75.6 gca peak = 0.09522 (73) mri peak = 0.04160 (71) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (34387 voxels, overlap=0.956) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (34387 voxels, peak = 72), gca=71.9 gca peak = 0.25483 (75) mri peak = 0.19040 (76) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1041 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1041 voxels, peak = 75), gca=75.0 gca peak = 0.15201 (72) mri peak = 0.13650 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (987 voxels, overlap=0.838) Left_Caudate (11): linear fit = 1.00 x + 0.0 (987 voxels, peak = 72), gca=72.0 gca peak = 0.11178 (72) mri peak = 0.06399 (72) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25557 voxels, overlap=0.968) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25557 voxels, peak = 72), gca=71.6 gca peak = 0.11249 (74) mri peak = 0.06555 (75) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28998 voxels, overlap=0.955) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28998 voxels, peak = 74), gca=73.6 gca peak = 0.13464 (99) mri peak = 0.04917 (100) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (12019 voxels, overlap=0.994) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (12019 voxels, peak = 99), gca=99.5 gca peak = 0.14907 (95) mri peak = 0.09280 (93) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8986 voxels, overlap=0.926) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8986 voxels, peak = 94), gca=93.6 gca peak = 0.29104 (75) mri peak = 0.14601 (75) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (561 voxels, overlap=1.011) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (561 voxels, peak = 74), gca=73.9 gca peak = 0.30615 (71) mri peak = 0.15849 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (527 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (527 voxels, peak = 71), gca=71.0 gca peak = 0.10850 (100) mri peak = 0.06706 (100) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5149 voxels, overlap=0.928) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5149 voxels, peak = 102), gca=101.5 gca peak = 0.10785 (90) mri peak = 0.09017 (94) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5644 voxels, overlap=0.958) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5644 voxels, peak = 91), gca=91.3 gca peak = 0.08285 (84) mri peak = 0.14039 (79) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2030 voxels, overlap=0.846) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2030 voxels, peak = 83), gca=82.7 gca peak = 0.10144 (79) mri peak = 0.14539 (79) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2366 voxels, overlap=0.787) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2366 voxels, peak = 79), gca=79.0 gca peak = 0.07197 (83) mri peak = 0.08961 (83) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12211 voxels, overlap=0.723) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12211 voxels, peak = 82), gca=81.8 gca peak = 0.09893 (100) mri peak = 0.08607 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1897 voxels, overlap=0.789) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1897 voxels, peak = 100), gca=100.5 gca peak = 0.15300 (97) mri peak = 0.07929 (97) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1681 voxels, overlap=0.872) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1681 voxels, peak = 96), gca=95.5 gca peak = 0.12656 (38) mri peak = 0.16410 (42) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (152 voxels, overlap=0.684) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (152 voxels, peak = 39), gca=39.3 gca peak = 0.16542 (24) mri peak = 0.13700 (23) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (850 voxels, overlap=0.749) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (850 voxels, peak = 25), gca=24.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (102) gca peak CSF = 0.15446 (55) gca peak Left_Accumbens_area = 0.59857 (66) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.20093 (28) gca peak Right_Accumbens_area = 0.35084 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (46) gca peak WM_hypointensities = 0.08480 (76) gca peak non_WM_hypointensities = 0.11534 (54) gca peak Optic_Chiasm = 0.63187 (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 1.10 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 90415 voxels changed in iteration 0 of unlikely voxel relabeling 560 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 97336 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 984 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 79636 changed. image ll: -2.137, PF=0.500 pass 2: 22014 changed. image ll: -2.136, PF=0.500 pass 3: 7175 changed. pass 4: 2834 changed. 92395 voxels changed in iteration 0 of unlikely voxel relabeling 591 voxels changed in iteration 1 of unlikely voxel relabeling 23 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8544 voxels changed in iteration 0 of unlikely voxel relabeling 123 voxels changed in iteration 1 of unlikely voxel relabeling 15 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7599 voxels changed in iteration 0 of unlikely voxel relabeling 65 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 7182 voxels changed in iteration 0 of unlikely voxel relabeling 17 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3735.938374 mri_ca_label stimesec 4.623116 mri_ca_label ru_maxrss 2113468 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 734680 mri_ca_label ru_majflt 14 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 12120 mri_ca_label ru_oublock 456 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 77 mri_ca_label ru_nivcsw 173282 auto-labeling took 62 minutes and 26 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/shize/freesurfer/SubJ01_ReoT13THip/mri/transforms/cc_up.lta SubJ01_ReoT13THip will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/shize/freesurfer/SubJ01_ReoT13THip/mri/transforms/cc_up.lta reading aseg from /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aseg.auto_noCCseg.mgz reading norm from /home/shize/freesurfer/SubJ01_ReoT13THip/mri/norm.mgz 19122 voxels in left wm, 33140 in right wm, xrange [126, 132] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 global minimum found at slice 129.0, rotations (0.24, 0.59) final transformation (x=129.0, yr=0.243, zr=0.592): 0.99994 -0.01033 0.00424 -0.47214; 0.01033 0.99995 0.00004 19.66719; -0.00424 0.00000 0.99999 -9.45147; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 107 138 eigenvectors: -0.00090 0.00190 1.00000; 0.06496 -0.99789 0.00196; 0.99789 0.06496 0.00078; error in mid anterior detected - correcting... writing aseg with callosum to /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Fri Aug 17 13:47:42 EDT 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Aug 17 13:47:42 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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... 1044 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 80 (80), valley at 47 (47) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 80 (80), valley at 45 (45) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 45 seconds. #-------------------------------------------- #@# Mask BFS Fri Aug 17 13:50:29 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1614527 voxels in mask (pct= 9.62) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Aug 17 13:50:30 EDT 2018 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 (101.0): 101.2 +- 7.3 [79.0 --> 125.0] GM (75.0) : 74.0 +- 10.7 [30.0 --> 95.0] setting bottom of white matter range to 84.6 setting top of gray matter range to 95.3 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4133 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3539 filled 131 bright non-wm voxels segmented. 2273 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.47 minutes reading wm segmentation from wm.seg.mgz... 433 voxels added to wm to prevent paths from MTL structures to cortex 3944 additional wm voxels added 0 additional wm voxels added SEG EDIT: 41699 voxels turned on, 55627 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+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 16 found - 16 modified | TOTAL: 38 pass 2 (xy-): 0 found - 16 modified | TOTAL: 38 pass 1 (yz+): 41 found - 41 modified | TOTAL: 79 pass 2 (yz+): 0 found - 41 modified | TOTAL: 79 pass 1 (yz-): 24 found - 24 modified | TOTAL: 103 pass 2 (yz-): 0 found - 24 modified | TOTAL: 103 pass 1 (xz+): 19 found - 19 modified | TOTAL: 122 pass 2 (xz+): 0 found - 19 modified | TOTAL: 122 pass 1 (xz-): 19 found - 19 modified | TOTAL: 141 pass 2 (xz-): 0 found - 19 modified | TOTAL: 141 Iteration Number : 1 pass 1 (+++): 16 found - 16 modified | TOTAL: 16 pass 2 (+++): 0 found - 16 modified | TOTAL: 16 pass 1 (+++): 2 found - 2 modified | TOTAL: 18 pass 2 (+++): 0 found - 2 modified | TOTAL: 18 pass 1 (+++): 17 found - 17 modified | TOTAL: 35 pass 2 (+++): 0 found - 17 modified | TOTAL: 35 pass 1 (+++): 14 found - 14 modified | TOTAL: 49 pass 2 (+++): 0 found - 14 modified | TOTAL: 49 Iteration Number : 1 pass 1 (++): 59 found - 59 modified | TOTAL: 59 pass 2 (++): 0 found - 59 modified | TOTAL: 59 pass 1 (+-): 62 found - 62 modified | TOTAL: 121 pass 2 (+-): 0 found - 62 modified | TOTAL: 121 pass 1 (--): 51 found - 51 modified | TOTAL: 172 pass 2 (--): 0 found - 51 modified | TOTAL: 172 pass 1 (-+): 52 found - 52 modified | TOTAL: 224 pass 2 (-+): 0 found - 52 modified | TOTAL: 224 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 7 found - 7 modified | TOTAL: 15 pass 2 (yz-): 0 found - 7 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 1 found - 1 modified | TOTAL: 18 pass 2 (xz-): 0 found - 1 modified | TOTAL: 18 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 2 found - 2 modified | TOTAL: 4 pass 2 (+-): 0 found - 2 modified | TOTAL: 4 pass 1 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 1 found - 1 modified | TOTAL: 6 pass 2 (-+): 0 found - 1 modified | TOTAL: 6 Iteration Number : 3 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-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 445 (out of 626835: 0.070992) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Aug 17 13:52:48 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16315; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.98932 -0.05900 -0.11439 19.85572; 0.07231 0.98699 0.11668 -27.84807; 0.10593 -0.12351 0.97956 -22.16315; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2434 (min = 350, max = 1400), aspect = 1.04 (min = 0.10, max = 0.75) need search nearby using seed (127, 107, 93), TAL = (1.0, -35.0, 21.0) talairach voxel to voxel transform 0.99397 0.07285 0.10739 -15.32709; -0.05923 0.99396 -0.12531 26.07864; -0.11496 0.11745 0.99345 27.57116; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 107, 93) --> (1.0, -35.0, 21.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (1.00, -35.00, 21.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -35.00, 21.00) SRC: (110.80, 114.32, 120.00) search lh wm seed point around talairach space (-17.00, -35.00, 21.00), SRC: (146.58, 112.19, 115.86) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Aug 17 13:53:24 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 2 found - 2 modified | TOTAL: 5 pass 2 (xz+): 0 found - 2 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 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 (-+): 0 found - 0 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 = 6 (out of 308156: 0.001947) 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 60: 1172 vertices, 1273 faces slice 70: 6862 vertices, 7132 faces slice 80: 15259 vertices, 15579 faces slice 90: 26105 vertices, 26505 faces slice 100: 38532 vertices, 38980 faces slice 110: 50853 vertices, 51252 faces slice 120: 64183 vertices, 64647 faces slice 130: 77550 vertices, 78061 faces slice 140: 90691 vertices, 91167 faces slice 150: 103530 vertices, 103999 faces slice 160: 114732 vertices, 115191 faces slice 170: 124666 vertices, 125086 faces slice 180: 133814 vertices, 134163 faces slice 190: 142331 vertices, 142712 faces slice 200: 148991 vertices, 149284 faces slice 210: 151338 vertices, 151450 faces slice 220: 151338 vertices, 151450 faces slice 230: 151338 vertices, 151450 faces slice 240: 151338 vertices, 151450 faces slice 250: 151338 vertices, 151450 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... 151338 voxel in cpt #1: X=-112 [v=151338,e=454350,f=302900] located at (-33.032589, 0.727127, 13.219178) For the whole surface: X=-112 [v=151338,e=454350,f=302900] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri Aug 17 13:53:28 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 299858: 0.001667) 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 60: 338 vertices, 378 faces slice 70: 3564 vertices, 3793 faces slice 80: 11421 vertices, 11702 faces slice 90: 21037 vertices, 21417 faces slice 100: 32771 vertices, 33160 faces slice 110: 45518 vertices, 45972 faces slice 120: 59631 vertices, 60164 faces slice 130: 74446 vertices, 74979 faces slice 140: 88775 vertices, 89308 faces slice 150: 101886 vertices, 102379 faces slice 160: 113857 vertices, 114318 faces slice 170: 124184 vertices, 124607 faces slice 180: 133837 vertices, 134213 faces slice 190: 142292 vertices, 142682 faces slice 200: 148979 vertices, 149292 faces slice 210: 152256 vertices, 152394 faces slice 220: 152402 vertices, 152524 faces slice 230: 152402 vertices, 152524 faces slice 240: 152402 vertices, 152524 faces slice 250: 152402 vertices, 152524 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... 152402 voxel in cpt #1: X=-122 [v=152402,e=457572,f=305048] located at (30.335245, 3.698068, 13.667518) For the whole surface: X=-122 [v=152402,e=457572,f=305048] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Aug 17 13:53:33 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 Fri Aug 17 13:53:38 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 Fri Aug 17 13:53:43 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.3 mm, total surface area = 81405 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.075 (target=0.015) step 025: RMS=0.068 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.051 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.049 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 31.021617 mris_inflate stimesec 0.111962 mris_inflate ru_maxrss 198936 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 46145 mris_inflate ru_majflt 12 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11472 mris_inflate ru_oublock 10656 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 142 mris_inflate ru_nivcsw 1589 #-------------------------------------------- #@# Inflation1 rh Fri Aug 17 13:54:15 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.8 mm, total surface area = 81216 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.083 (target=0.015) step 020: RMS=0.075 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.050 (target=0.015) step 060: RMS=0.049 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 30.542886 mris_inflate stimesec 0.071969 mris_inflate ru_maxrss 200476 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 25042 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10728 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 159 mris_inflate ru_nivcsw 1305 #-------------------------------------------- #@# QSphere lh Fri Aug 17 13:54:45 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.55 (0.00-->8.87) (max @ vno 57962 --> 57987) face area 0.03 +- 0.03 (-0.15-->0.79) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.474, avgs=0 005/300: dt: 0.9000, rms radial error=175.217, avgs=0 010/300: dt: 0.9000, rms radial error=174.665, avgs=0 015/300: dt: 0.9000, rms radial error=173.940, avgs=0 020/300: dt: 0.9000, rms radial error=173.114, avgs=0 025/300: dt: 0.9000, rms radial error=172.230, avgs=0 030/300: dt: 0.9000, rms radial error=171.315, avgs=0 035/300: dt: 0.9000, rms radial error=170.382, avgs=0 040/300: dt: 0.9000, rms radial error=169.441, avgs=0 045/300: dt: 0.9000, rms radial error=168.497, avgs=0 050/300: dt: 0.9000, rms radial error=167.554, avgs=0 055/300: dt: 0.9000, rms radial error=166.614, avgs=0 060/300: dt: 0.9000, rms radial error=165.676, avgs=0 065/300: dt: 0.9000, rms radial error=164.743, avgs=0 070/300: dt: 0.9000, rms radial error=163.814, avgs=0 075/300: dt: 0.9000, rms radial error=162.890, avgs=0 080/300: dt: 0.9000, rms radial error=161.971, avgs=0 085/300: dt: 0.9000, rms radial error=161.056, avgs=0 090/300: dt: 0.9000, rms radial error=160.147, avgs=0 095/300: dt: 0.9000, rms radial error=159.242, avgs=0 100/300: dt: 0.9000, rms radial error=158.342, avgs=0 105/300: dt: 0.9000, rms radial error=157.447, avgs=0 110/300: dt: 0.9000, rms radial error=156.556, avgs=0 115/300: dt: 0.9000, rms radial error=155.671, avgs=0 120/300: dt: 0.9000, rms radial error=154.790, avgs=0 125/300: dt: 0.9000, rms radial error=153.914, avgs=0 130/300: dt: 0.9000, rms radial error=153.043, avgs=0 135/300: dt: 0.9000, rms radial error=152.176, avgs=0 140/300: dt: 0.9000, rms radial error=151.314, avgs=0 145/300: dt: 0.9000, rms radial error=150.457, avgs=0 150/300: dt: 0.9000, rms radial error=149.605, avgs=0 155/300: dt: 0.9000, rms radial error=148.757, avgs=0 160/300: dt: 0.9000, rms radial error=147.914, avgs=0 165/300: dt: 0.9000, rms radial error=147.075, avgs=0 170/300: dt: 0.9000, rms radial error=146.241, avgs=0 175/300: dt: 0.9000, rms radial error=145.412, avgs=0 180/300: dt: 0.9000, rms radial error=144.588, avgs=0 185/300: dt: 0.9000, rms radial error=143.768, avgs=0 190/300: dt: 0.9000, rms radial error=142.952, avgs=0 195/300: dt: 0.9000, rms radial error=142.142, avgs=0 200/300: dt: 0.9000, rms radial error=141.335, avgs=0 205/300: dt: 0.9000, rms radial error=140.534, avgs=0 210/300: dt: 0.9000, rms radial error=139.736, avgs=0 215/300: dt: 0.9000, rms radial error=138.946, avgs=0 220/300: dt: 0.9000, rms radial error=138.160, avgs=0 225/300: dt: 0.9000, rms radial error=137.378, avgs=0 230/300: dt: 0.9000, rms radial error=136.602, avgs=0 235/300: dt: 0.9000, rms radial error=135.829, avgs=0 240/300: dt: 0.9000, rms radial error=135.062, avgs=0 245/300: dt: 0.9000, rms radial error=134.298, avgs=0 250/300: dt: 0.9000, rms radial error=133.540, avgs=0 255/300: dt: 0.9000, rms radial error=132.785, avgs=0 260/300: dt: 0.9000, rms radial error=132.036, avgs=0 265/300: dt: 0.9000, rms radial error=131.291, avgs=0 270/300: dt: 0.9000, rms radial error=130.551, avgs=0 275/300: dt: 0.9000, rms radial error=129.816, avgs=0 280/300: dt: 0.9000, rms radial error=129.084, avgs=0 285/300: dt: 0.9000, rms radial error=128.357, avgs=0 290/300: dt: 0.9000, rms radial error=127.634, avgs=0 295/300: dt: 0.9000, rms radial error=126.914, avgs=0 300/300: dt: 0.9000, rms radial error=126.199, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17437.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2838.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 288.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00274 epoch 4 (K=640.0), pass 1, starting sse = 30.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00550 final distance error %23.61 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 187.917994 mris_sphere stimesec 0.520083 mris_sphere ru_maxrss 199308 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 25200 mris_sphere ru_majflt 12 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11552 mris_sphere ru_oublock 10656 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 122 mris_sphere ru_nivcsw 15362 FSRUNTIME@ mris_sphere 0.0525 hours 1 threads #-------------------------------------------- #@# QSphere rh Fri Aug 17 13:57:55 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.54 (0.00-->7.35) (max @ vno 108888 --> 108889) face area 0.03 +- 0.03 (-0.17-->0.75) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.321... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.697, avgs=0 005/300: dt: 0.9000, rms radial error=175.438, avgs=0 010/300: dt: 0.9000, rms radial error=174.882, avgs=0 015/300: dt: 0.9000, rms radial error=174.152, avgs=0 020/300: dt: 0.9000, rms radial error=173.321, avgs=0 025/300: dt: 0.9000, rms radial error=172.432, avgs=0 030/300: dt: 0.9000, rms radial error=171.511, avgs=0 035/300: dt: 0.9000, rms radial error=170.573, avgs=0 040/300: dt: 0.9000, rms radial error=169.627, avgs=0 045/300: dt: 0.9000, rms radial error=168.679, avgs=0 050/300: dt: 0.9000, rms radial error=167.732, avgs=0 055/300: dt: 0.9000, rms radial error=166.787, avgs=0 060/300: dt: 0.9000, rms radial error=165.847, avgs=0 065/300: dt: 0.9000, rms radial error=164.910, avgs=0 070/300: dt: 0.9000, rms radial error=163.979, avgs=0 075/300: dt: 0.9000, rms radial error=163.052, avgs=0 080/300: dt: 0.9000, rms radial error=162.130, avgs=0 085/300: dt: 0.9000, rms radial error=161.213, avgs=0 090/300: dt: 0.9000, rms radial error=160.300, avgs=0 095/300: dt: 0.9000, rms radial error=159.393, avgs=0 100/300: dt: 0.9000, rms radial error=158.491, avgs=0 105/300: dt: 0.9000, rms radial error=157.593, avgs=0 110/300: dt: 0.9000, rms radial error=156.701, avgs=0 115/300: dt: 0.9000, rms radial error=155.814, avgs=0 120/300: dt: 0.9000, rms radial error=154.933, avgs=0 125/300: dt: 0.9000, rms radial error=154.058, avgs=0 130/300: dt: 0.9000, rms radial error=153.188, avgs=0 135/300: dt: 0.9000, rms radial error=152.323, avgs=0 140/300: dt: 0.9000, rms radial error=151.463, avgs=0 145/300: dt: 0.9000, rms radial error=150.607, avgs=0 150/300: dt: 0.9000, rms radial error=149.756, avgs=0 155/300: dt: 0.9000, rms radial error=148.911, avgs=0 160/300: dt: 0.9000, rms radial error=148.069, avgs=0 165/300: dt: 0.9000, rms radial error=147.233, avgs=0 170/300: dt: 0.9000, rms radial error=146.401, avgs=0 175/300: dt: 0.9000, rms radial error=145.574, avgs=0 180/300: dt: 0.9000, rms radial error=144.752, avgs=0 185/300: dt: 0.9000, rms radial error=143.934, avgs=0 190/300: dt: 0.9000, rms radial error=143.121, avgs=0 195/300: dt: 0.9000, rms radial error=142.312, avgs=0 200/300: dt: 0.9000, rms radial error=141.508, avgs=0 205/300: dt: 0.9000, rms radial error=140.709, avgs=0 210/300: dt: 0.9000, rms radial error=139.914, avgs=0 215/300: dt: 0.9000, rms radial error=139.123, avgs=0 220/300: dt: 0.9000, rms radial error=138.337, avgs=0 225/300: dt: 0.9000, rms radial error=137.555, avgs=0 230/300: dt: 0.9000, rms radial error=136.778, avgs=0 235/300: dt: 0.9000, rms radial error=136.005, avgs=0 240/300: dt: 0.9000, rms radial error=135.236, avgs=0 245/300: dt: 0.9000, rms radial error=134.472, avgs=0 250/300: dt: 0.9000, rms radial error=133.712, avgs=0 255/300: dt: 0.9000, rms radial error=132.956, avgs=0 260/300: dt: 0.9000, rms radial error=132.205, avgs=0 265/300: dt: 0.9000, rms radial error=131.457, avgs=0 270/300: dt: 0.9000, rms radial error=130.714, avgs=0 275/300: dt: 0.9000, rms radial error=129.976, avgs=0 280/300: dt: 0.9000, rms radial error=129.241, avgs=0 285/300: dt: 0.9000, rms radial error=128.511, avgs=0 290/300: dt: 0.9000, rms radial error=127.784, avgs=0 295/300: dt: 0.9000, rms radial error=127.062, avgs=0 300/300: dt: 0.9000, rms radial error=126.344, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17599.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2847.76 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 = 280.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00476 epoch 4 (K=640.0), pass 1, starting sse = 23.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00529 final distance error %23.60 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 187.932374 mris_sphere stimesec 0.415655 mris_sphere ru_maxrss 200888 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 25056 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10728 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 121 mris_sphere ru_nivcsw 14176 FSRUNTIME@ mris_sphere 0.0525 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Fri Aug 17 14:01:04 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri Aug 17 14:01:04 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri Aug 17 14:01:04 EDT 2018 mris_fix_topology -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 SubJ01_ReoT13THip 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=-112 (nv=151338, nf=302900, ne=454350, g=57) 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... 14652 ambiguous faces found in tessellation segmenting defects... 56 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 24 55 defects to be corrected 0 vertices coincident reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1366 (-4.5683) -vertex loglikelihood: -5.8944 (-2.9472) -normal dot loglikelihood: -3.5835 (-3.5835) -quad curv loglikelihood: -6.0944 (-3.0472) Total Loglikelihood : -24.7089 CORRECTING DEFECT 0 (vertices=58, convex hull=113, v0=552) After retessellation of defect 0 (v0=552), euler #=-50 (142775,425548,282723) : difference with theory (-52) = -2 CORRECTING DEFECT 1 (vertices=8, convex hull=26, v0=9983) After retessellation of defect 1 (v0=9983), euler #=-49 (142776,425560,282735) : difference with theory (-51) = -2 CORRECTING DEFECT 2 (vertices=36, convex hull=60, v0=12933) After retessellation of defect 2 (v0=12933), euler #=-48 (142793,425637,282796) : difference with theory (-50) = -2 CORRECTING DEFECT 3 (vertices=141, convex hull=108, v0=14142) After retessellation of defect 3 (v0=14142), euler #=-47 (142814,425749,282888) : difference with theory (-49) = -2 CORRECTING DEFECT 4 (vertices=31, convex hull=28, v0=15780) After retessellation of defect 4 (v0=15780), euler #=-46 (142816,425768,282906) : difference with theory (-48) = -2 CORRECTING DEFECT 5 (vertices=32, convex hull=64, v0=18669) After retessellation of defect 5 (v0=18669), euler #=-45 (142826,425825,282954) : difference with theory (-47) = -2 CORRECTING DEFECT 6 (vertices=27, convex hull=60, v0=22535) After retessellation of defect 6 (v0=22535), euler #=-44 (142841,425890,283005) : difference with theory (-46) = -2 CORRECTING DEFECT 7 (vertices=35, convex hull=58, v0=36402) After retessellation of defect 7 (v0=36402), euler #=-44 (142851,425947,283052) : difference with theory (-45) = -1 CORRECTING DEFECT 8 (vertices=17, convex hull=52, v0=39034) After retessellation of defect 8 (v0=39034), euler #=-43 (142860,425994,283091) : difference with theory (-44) = -1 CORRECTING DEFECT 9 (vertices=24, convex hull=62, v0=42931) After retessellation of defect 9 (v0=42931), euler #=-42 (142874,426059,283143) : difference with theory (-43) = -1 CORRECTING DEFECT 10 (vertices=156, convex hull=222, v0=43115) After retessellation of defect 10 (v0=43115), euler #=-41 (142964,426428,283423) : difference with theory (-42) = -1 CORRECTING DEFECT 11 (vertices=374, convex hull=431, v0=45513) After retessellation of defect 11 (v0=45513), euler #=-40 (143086,427001,283875) : difference with theory (-41) = -1 CORRECTING DEFECT 12 (vertices=45, convex hull=24, v0=46494) After retessellation of defect 12 (v0=46494), euler #=-39 (143089,427014,283886) : difference with theory (-40) = -1 CORRECTING DEFECT 13 (vertices=5, convex hull=14, v0=49334) After retessellation of defect 13 (v0=49334), euler #=-38 (143089,427017,283890) : difference with theory (-39) = -1 CORRECTING DEFECT 14 (vertices=200, convex hull=157, v0=51633) After retessellation of defect 14 (v0=51633), euler #=-37 (143153,427284,284094) : difference with theory (-38) = -1 CORRECTING DEFECT 15 (vertices=162, convex hull=86, v0=51664) After retessellation of defect 15 (v0=51664), euler #=-36 (143181,427404,284187) : difference with theory (-37) = -1 CORRECTING DEFECT 16 (vertices=208, convex hull=184, v0=54490) normal vector of length zero at vertex 144271 with 3 faces normal vector of length zero at vertex 144271 with 3 faces normal vector of length zero at vertex 144253 with 4 faces After retessellation of defect 16 (v0=54490), euler #=-35 (143273,427764,284456) : difference with theory (-36) = -1 CORRECTING DEFECT 17 (vertices=1369, convex hull=624, v0=55739) XL defect detected... After retessellation of defect 17 (v0=55739), euler #=-35 (143703,429378,285640) : difference with theory (-35) = 0 CORRECTING DEFECT 18 (vertices=20, convex hull=49, v0=62374) After retessellation of defect 18 (v0=62374), euler #=-34 (143712,429423,285677) : difference with theory (-34) = 0 CORRECTING DEFECT 19 (vertices=34, convex hull=21, v0=66696) After retessellation of defect 19 (v0=66696), euler #=-33 (143713,429434,285688) : difference with theory (-33) = 0 CORRECTING DEFECT 20 (vertices=91, convex hull=84, v0=68075) After retessellation of defect 20 (v0=68075), euler #=-32 (143754,429594,285808) : difference with theory (-32) = 0 CORRECTING DEFECT 21 (vertices=64, convex hull=92, v0=73264) After retessellation of defect 21 (v0=73264), euler #=-31 (143789,429742,285922) : difference with theory (-31) = 0 CORRECTING DEFECT 22 (vertices=665, convex hull=296, v0=74645) After retessellation of defect 22 (v0=74645), euler #=-30 (143859,430093,286204) : difference with theory (-30) = 0 CORRECTING DEFECT 23 (vertices=696, convex hull=319, v0=83401) After retessellation of defect 23 (v0=83401), euler #=-29 (143985,430625,286611) : difference with theory (-29) = 0 CORRECTING DEFECT 24 (vertices=604, convex hull=436, v0=83946) After retessellation of defect 24 (v0=83946), euler #=-27 (144217,431545,287301) : difference with theory (-28) = -1 CORRECTING DEFECT 25 (vertices=554, convex hull=286, v0=87969) After retessellation of defect 25 (v0=87969), euler #=-26 (144374,432169,287769) : difference with theory (-27) = -1 CORRECTING DEFECT 26 (vertices=33, convex hull=48, v0=91912) After retessellation of defect 26 (v0=91912), euler #=-25 (144388,432227,287814) : difference with theory (-26) = -1 CORRECTING DEFECT 27 (vertices=944, convex hull=251, v0=94956) After retessellation of defect 27 (v0=94956), euler #=-24 (144464,432580,288092) : difference with theory (-25) = -1 CORRECTING DEFECT 28 (vertices=28, convex hull=53, v0=96233) After retessellation of defect 28 (v0=96233), euler #=-23 (144479,432645,288143) : difference with theory (-24) = -1 CORRECTING DEFECT 29 (vertices=30, convex hull=71, v0=101053) After retessellation of defect 29 (v0=101053), euler #=-22 (144494,432716,288200) : difference with theory (-23) = -1 CORRECTING DEFECT 30 (vertices=34, convex hull=64, v0=109283) After retessellation of defect 30 (v0=109283), euler #=-21 (144511,432792,288260) : difference with theory (-22) = -1 CORRECTING DEFECT 31 (vertices=27, convex hull=79, v0=109909) After retessellation of defect 31 (v0=109909), euler #=-20 (144527,432870,288323) : difference with theory (-21) = -1 CORRECTING DEFECT 32 (vertices=52, convex hull=40, v0=110309) After retessellation of defect 32 (v0=110309), euler #=-19 (144531,432896,288346) : difference with theory (-20) = -1 CORRECTING DEFECT 33 (vertices=251, convex hull=93, v0=111399) After retessellation of defect 33 (v0=111399), euler #=-18 (144586,433100,288496) : difference with theory (-19) = -1 CORRECTING DEFECT 34 (vertices=84, convex hull=60, v0=117510) After retessellation of defect 34 (v0=117510), euler #=-17 (144604,433176,288555) : difference with theory (-18) = -1 CORRECTING DEFECT 35 (vertices=27, convex hull=66, v0=118506) After retessellation of defect 35 (v0=118506), euler #=-16 (144613,433229,288600) : difference with theory (-17) = -1 CORRECTING DEFECT 36 (vertices=27, convex hull=36, v0=119483) After retessellation of defect 36 (v0=119483), euler #=-15 (144615,433245,288615) : difference with theory (-16) = -1 CORRECTING DEFECT 37 (vertices=58, convex hull=42, v0=121616) After retessellation of defect 37 (v0=121616), euler #=-14 (144621,433280,288645) : difference with theory (-15) = -1 CORRECTING DEFECT 38 (vertices=67, convex hull=100, v0=121781) After retessellation of defect 38 (v0=121781), euler #=-13 (144650,433410,288747) : difference with theory (-14) = -1 CORRECTING DEFECT 39 (vertices=30, convex hull=71, v0=123410) After retessellation of defect 39 (v0=123410), euler #=-12 (144662,433475,288801) : difference with theory (-13) = -1 CORRECTING DEFECT 40 (vertices=154, convex hull=211, v0=124832) After retessellation of defect 40 (v0=124832), euler #=-11 (144744,433832,289077) : difference with theory (-12) = -1 CORRECTING DEFECT 41 (vertices=16, convex hull=22, v0=128620) After retessellation of defect 41 (v0=128620), euler #=-10 (144747,433846,289089) : difference with theory (-11) = -1 CORRECTING DEFECT 42 (vertices=74, convex hull=114, v0=133999) After retessellation of defect 42 (v0=133999), euler #=-9 (144790,434025,289226) : difference with theory (-10) = -1 CORRECTING DEFECT 43 (vertices=42, convex hull=25, v0=134583) After retessellation of defect 43 (v0=134583), euler #=-8 (144793,434040,289239) : difference with theory (-9) = -1 CORRECTING DEFECT 44 (vertices=165, convex hull=41, v0=134608) After retessellation of defect 44 (v0=134608), euler #=-7 (144805,434091,289279) : difference with theory (-8) = -1 CORRECTING DEFECT 45 (vertices=80, convex hull=61, v0=134621) After retessellation of defect 45 (v0=134621), euler #=-7 (144848,434248,289393) : difference with theory (-7) = 0 CORRECTING DEFECT 46 (vertices=21, convex hull=54, v0=137691) After retessellation of defect 46 (v0=137691), euler #=-6 (144857,434296,289433) : difference with theory (-6) = 0 CORRECTING DEFECT 47 (vertices=81, convex hull=87, v0=138007) After retessellation of defect 47 (v0=138007), euler #=-5 (144885,434419,289529) : difference with theory (-5) = 0 CORRECTING DEFECT 48 (vertices=105, convex hull=89, v0=139527) After retessellation of defect 48 (v0=139527), euler #=-4 (144918,434555,289633) : difference with theory (-4) = 0 CORRECTING DEFECT 49 (vertices=263, convex hull=154, v0=139796) After retessellation of defect 49 (v0=139796), euler #=-3 (144946,434711,289762) : difference with theory (-3) = 0 CORRECTING DEFECT 50 (vertices=60, convex hull=124, v0=140923) After retessellation of defect 50 (v0=140923), euler #=-2 (144984,434885,289899) : difference with theory (-2) = 0 CORRECTING DEFECT 51 (vertices=42, convex hull=80, v0=146773) After retessellation of defect 51 (v0=146773), euler #=-1 (145013,435005,289991) : difference with theory (-1) = 0 CORRECTING DEFECT 52 (vertices=68, convex hull=31, v0=147235) After retessellation of defect 52 (v0=147235), euler #=0 (145017,435027,290010) : difference with theory (0) = 0 CORRECTING DEFECT 53 (vertices=8, convex hull=29, v0=149891) After retessellation of defect 53 (v0=149891), euler #=1 (145018,435041,290024) : difference with theory (1) = 0 CORRECTING DEFECT 54 (vertices=52, convex hull=22, v0=150328) After retessellation of defect 54 (v0=150328), euler #=2 (145018,435048,290032) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.29 (0.07-->15.76) (max @ vno 75752 --> 80618) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.29 (0.07-->15.76) (max @ vno 75752 --> 80618) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 153 mutations (33.7%), 301 crossovers (66.3%), 670 vertices were eliminated building final representation... 6320 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=145018, nf=290032, ne=435048, g=0) writing corrected surface to /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 31.9 minutes 0 defective edges removing intersecting faces 000: 789 intersecting 001: 61 intersecting 002: 8 intersecting mris_fix_topology utimesec 1906.199329 mris_fix_topology stimesec 3.011310 mris_fix_topology ru_maxrss 482780 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 80303 mris_fix_topology ru_majflt 12 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 11528 mris_fix_topology ru_oublock 13752 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 167 mris_fix_topology ru_nivcsw 111795 FSRUNTIME@ mris_fix_topology lh 0.5315 hours 1 threads #@# Fix Topology rh Fri Aug 17 14:32:57 EDT 2018 mris_fix_topology -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 SubJ01_ReoT13THip 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=-122 (nv=152402, nf=305048, ne=457572, g=62) 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 10 iterations marking ambiguous vertices... 10550 ambiguous faces found in tessellation segmenting defects... 66 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 8 -merging segment 15 into 12 -merging segment 23 into 12 -merging segment 54 into 53 62 defects to be corrected 0 vertices coincident reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1040 (-4.5520) -vertex loglikelihood: -5.9358 (-2.9679) -normal dot loglikelihood: -3.5841 (-3.5841) -quad curv loglikelihood: -5.8672 (-2.9336) Total Loglikelihood : -24.4912 CORRECTING DEFECT 0 (vertices=18, convex hull=65, v0=2118) After retessellation of defect 0 (v0=2118), euler #=-62 (145809,434506,288635) : difference with theory (-59) = 3 CORRECTING DEFECT 1 (vertices=30, convex hull=77, v0=3362) After retessellation of defect 1 (v0=3362), euler #=-61 (145823,434576,288692) : difference with theory (-58) = 3 CORRECTING DEFECT 2 (vertices=56, convex hull=84, v0=7413) After retessellation of defect 2 (v0=7413), euler #=-60 (145842,434668,288766) : difference with theory (-57) = 3 CORRECTING DEFECT 3 (vertices=121, convex hull=51, v0=14700) After retessellation of defect 3 (v0=14700), euler #=-59 (145855,434726,288812) : difference with theory (-56) = 3 CORRECTING DEFECT 4 (vertices=17, convex hull=51, v0=17479) After retessellation of defect 4 (v0=17479), euler #=-58 (145864,434774,288852) : difference with theory (-55) = 3 CORRECTING DEFECT 5 (vertices=42, convex hull=82, v0=18233) After retessellation of defect 5 (v0=18233), euler #=-57 (145884,434872,288931) : difference with theory (-54) = 3 CORRECTING DEFECT 6 (vertices=9, convex hull=25, v0=23851) After retessellation of defect 6 (v0=23851), euler #=-56 (145884,434882,288942) : difference with theory (-53) = 3 CORRECTING DEFECT 7 (vertices=18, convex hull=37, v0=33124) After retessellation of defect 7 (v0=33124), euler #=-55 (145893,434922,288974) : difference with theory (-52) = 3 CORRECTING DEFECT 8 (vertices=55, convex hull=84, v0=38060) After retessellation of defect 8 (v0=38060), euler #=-53 (145927,435069,289089) : difference with theory (-51) = 2 CORRECTING DEFECT 9 (vertices=22, convex hull=56, v0=41241) After retessellation of defect 9 (v0=41241), euler #=-52 (145936,435116,289128) : difference with theory (-50) = 2 CORRECTING DEFECT 10 (vertices=38, convex hull=82, v0=42739) After retessellation of defect 10 (v0=42739), euler #=-51 (145952,435195,289192) : difference with theory (-49) = 2 CORRECTING DEFECT 11 (vertices=1023, convex hull=984, v0=43752) XL defect detected... After retessellation of defect 11 (v0=43752), euler #=-48 (146433,437125,290644) : difference with theory (-48) = 0 CORRECTING DEFECT 12 (vertices=132, convex hull=147, v0=43903) After retessellation of defect 12 (v0=43903), euler #=-47 (146458,437264,290759) : difference with theory (-47) = 0 CORRECTING DEFECT 13 (vertices=34, convex hull=77, v0=44477) After retessellation of defect 13 (v0=44477), euler #=-46 (146467,437319,290806) : difference with theory (-46) = 0 CORRECTING DEFECT 14 (vertices=536, convex hull=337, v0=48035) After retessellation of defect 14 (v0=48035), euler #=-46 (146637,438011,291328) : difference with theory (-45) = 1 CORRECTING DEFECT 15 (vertices=175, convex hull=209, v0=50269) After retessellation of defect 15 (v0=50269), euler #=-45 (146688,438262,291529) : difference with theory (-44) = 1 CORRECTING DEFECT 16 (vertices=33, convex hull=28, v0=54231) After retessellation of defect 16 (v0=54231), euler #=-44 (146693,438286,291549) : difference with theory (-43) = 1 CORRECTING DEFECT 17 (vertices=14, convex hull=45, v0=54498) After retessellation of defect 17 (v0=54498), euler #=-43 (146702,438328,291583) : difference with theory (-42) = 1 CORRECTING DEFECT 18 (vertices=207, convex hull=228, v0=55576) After retessellation of defect 18 (v0=55576), euler #=-42 (146797,438721,291882) : difference with theory (-41) = 1 CORRECTING DEFECT 19 (vertices=170, convex hull=40, v0=55879) After retessellation of defect 19 (v0=55879), euler #=-41 (146816,438790,291933) : difference with theory (-40) = 1 CORRECTING DEFECT 20 (vertices=5, convex hull=12, v0=59697) After retessellation of defect 20 (v0=59697), euler #=-40 (146816,438792,291936) : difference with theory (-39) = 1 CORRECTING DEFECT 21 (vertices=279, convex hull=255, v0=66903) After retessellation of defect 21 (v0=66903), euler #=-39 (146910,439200,292251) : difference with theory (-38) = 1 CORRECTING DEFECT 22 (vertices=95, convex hull=95, v0=67055) After retessellation of defect 22 (v0=67055), euler #=-38 (146919,439270,292313) : difference with theory (-37) = 1 CORRECTING DEFECT 23 (vertices=19, convex hull=38, v0=70514) After retessellation of defect 23 (v0=70514), euler #=-37 (146928,439311,292346) : difference with theory (-36) = 1 CORRECTING DEFECT 24 (vertices=19, convex hull=48, v0=70806) After retessellation of defect 24 (v0=70806), euler #=-36 (146937,439355,292382) : difference with theory (-35) = 1 CORRECTING DEFECT 25 (vertices=28, convex hull=44, v0=72426) After retessellation of defect 25 (v0=72426), euler #=-35 (146940,439376,292401) : difference with theory (-34) = 1 CORRECTING DEFECT 26 (vertices=24, convex hull=65, v0=80665) After retessellation of defect 26 (v0=80665), euler #=-34 (146949,439428,292445) : difference with theory (-33) = 1 CORRECTING DEFECT 27 (vertices=350, convex hull=476, v0=81067) L defect detected... After retessellation of defect 27 (v0=81067), euler #=-33 (147145,440271,293093) : difference with theory (-32) = 1 CORRECTING DEFECT 28 (vertices=63, convex hull=115, v0=81368) After retessellation of defect 28 (v0=81368), euler #=-32 (147190,440454,293232) : difference with theory (-31) = 1 CORRECTING DEFECT 29 (vertices=60, convex hull=111, v0=82296) After retessellation of defect 29 (v0=82296), euler #=-31 (147227,440610,293352) : difference with theory (-30) = 1 CORRECTING DEFECT 30 (vertices=582, convex hull=381, v0=84097) After retessellation of defect 30 (v0=84097), euler #=-30 (147379,441254,293845) : difference with theory (-29) = 1 CORRECTING DEFECT 31 (vertices=272, convex hull=142, v0=84352) After retessellation of defect 31 (v0=84352), euler #=-29 (147433,441481,294019) : difference with theory (-28) = 1 CORRECTING DEFECT 32 (vertices=31, convex hull=36, v0=85943) After retessellation of defect 32 (v0=85943), euler #=-28 (147434,441495,294033) : difference with theory (-27) = 1 CORRECTING DEFECT 33 (vertices=17, convex hull=25, v0=94891) After retessellation of defect 33 (v0=94891), euler #=-27 (147436,441506,294043) : difference with theory (-26) = 1 CORRECTING DEFECT 34 (vertices=69, convex hull=130, v0=95252) After retessellation of defect 34 (v0=95252), euler #=-26 (147487,441718,294205) : difference with theory (-25) = 1 CORRECTING DEFECT 35 (vertices=24, convex hull=36, v0=95306) After retessellation of defect 35 (v0=95306), euler #=-25 (147489,441739,294225) : difference with theory (-24) = 1 CORRECTING DEFECT 36 (vertices=58, convex hull=73, v0=96638) After retessellation of defect 36 (v0=96638), euler #=-24 (147517,441850,294309) : difference with theory (-23) = 1 CORRECTING DEFECT 37 (vertices=11, convex hull=30, v0=99831) After retessellation of defect 37 (v0=99831), euler #=-23 (147518,441863,294322) : difference with theory (-22) = 1 CORRECTING DEFECT 38 (vertices=141, convex hull=49, v0=104141) After retessellation of defect 38 (v0=104141), euler #=-22 (147527,441911,294362) : difference with theory (-21) = 1 CORRECTING DEFECT 39 (vertices=528, convex hull=207, v0=105187) After retessellation of defect 39 (v0=105187), euler #=-21 (147586,442191,294584) : difference with theory (-20) = 1 CORRECTING DEFECT 40 (vertices=10, convex hull=26, v0=108755) After retessellation of defect 40 (v0=108755), euler #=-20 (147588,442207,294599) : difference with theory (-19) = 1 CORRECTING DEFECT 41 (vertices=81, convex hull=91, v0=109134) After retessellation of defect 41 (v0=109134), euler #=-19 (147608,442303,294676) : difference with theory (-18) = 1 CORRECTING DEFECT 42 (vertices=8, convex hull=20, v0=109975) After retessellation of defect 42 (v0=109975), euler #=-18 (147610,442313,294685) : difference with theory (-17) = 1 CORRECTING DEFECT 43 (vertices=105, convex hull=87, v0=116889) After retessellation of defect 43 (v0=116889), euler #=-17 (147640,442444,294787) : difference with theory (-16) = 1 CORRECTING DEFECT 44 (vertices=67, convex hull=93, v0=123596) After retessellation of defect 44 (v0=123596), euler #=-16 (147663,442562,294883) : difference with theory (-15) = 1 CORRECTING DEFECT 45 (vertices=28, convex hull=68, v0=123834) After retessellation of defect 45 (v0=123834), euler #=-15 (147674,442622,294933) : difference with theory (-14) = 1 CORRECTING DEFECT 46 (vertices=42, convex hull=81, v0=124704) After retessellation of defect 46 (v0=124704), euler #=-14 (147697,442723,295012) : difference with theory (-13) = 1 CORRECTING DEFECT 47 (vertices=42, convex hull=86, v0=126110) After retessellation of defect 47 (v0=126110), euler #=-13 (147714,442816,295089) : difference with theory (-12) = 1 CORRECTING DEFECT 48 (vertices=30, convex hull=48, v0=131552) After retessellation of defect 48 (v0=131552), euler #=-12 (147728,442877,295137) : difference with theory (-11) = 1 CORRECTING DEFECT 49 (vertices=129, convex hull=93, v0=134670) After retessellation of defect 49 (v0=134670), euler #=-11 (147753,442993,295229) : difference with theory (-10) = 1 CORRECTING DEFECT 50 (vertices=363, convex hull=177, v0=138767) After retessellation of defect 50 (v0=138767), euler #=-9 (147810,443248,295429) : difference with theory (-9) = 0 CORRECTING DEFECT 51 (vertices=19, convex hull=52, v0=144824) After retessellation of defect 51 (v0=144824), euler #=-8 (147823,443308,295477) : difference with theory (-8) = 0 CORRECTING DEFECT 52 (vertices=20, convex hull=46, v0=145687) After retessellation of defect 52 (v0=145687), euler #=-7 (147834,443357,295516) : difference with theory (-7) = 0 CORRECTING DEFECT 53 (vertices=37, convex hull=60, v0=146232) After retessellation of defect 53 (v0=146232), euler #=-6 (147854,443445,295585) : difference with theory (-6) = 0 CORRECTING DEFECT 54 (vertices=37, convex hull=60, v0=147530) After retessellation of defect 54 (v0=147530), euler #=-5 (147871,443520,295644) : difference with theory (-5) = 0 CORRECTING DEFECT 55 (vertices=28, convex hull=56, v0=149160) After retessellation of defect 55 (v0=149160), euler #=-4 (147881,443571,295686) : difference with theory (-4) = 0 CORRECTING DEFECT 56 (vertices=27, convex hull=33, v0=149991) After retessellation of defect 56 (v0=149991), euler #=-3 (147882,443586,295701) : difference with theory (-3) = 0 CORRECTING DEFECT 57 (vertices=39, convex hull=38, v0=150381) After retessellation of defect 57 (v0=150381), euler #=-2 (147882,443601,295717) : difference with theory (-2) = 0 CORRECTING DEFECT 58 (vertices=7, convex hull=25, v0=150434) After retessellation of defect 58 (v0=150434), euler #=-1 (147883,443613,295729) : difference with theory (-1) = 0 CORRECTING DEFECT 59 (vertices=12, convex hull=27, v0=150839) After retessellation of defect 59 (v0=150839), euler #=0 (147885,443628,295743) : difference with theory (0) = 0 CORRECTING DEFECT 60 (vertices=27, convex hull=47, v0=151079) After retessellation of defect 60 (v0=151079), euler #=1 (147894,443671,295778) : difference with theory (1) = 0 CORRECTING DEFECT 61 (vertices=16, convex hull=17, v0=152290) After retessellation of defect 61 (v0=152290), euler #=2 (147894,443676,295784) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.04-->17.64) (max @ vno 79298 --> 85976) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.04-->17.64) (max @ vno 79298 --> 85976) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 231 mutations (36.0%), 410 crossovers (64.0%), 479 vertices were eliminated building final representation... 4508 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147894, nf=295784, ne=443676, g=0) writing corrected surface to /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 46.5 minutes 0 defective edges removing intersecting faces 000: 680 intersecting 001: 25 intersecting mris_fix_topology utimesec 2779.383749 mris_fix_topology stimesec 4.922299 mris_fix_topology ru_maxrss 487576 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 60081 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13976 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 126 mris_fix_topology ru_nivcsw 222344 FSRUNTIME@ mris_fix_topology rh 0.7757 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 145018 - 435048 + 290032 = 2 --> 0 holes F =2V-4: 290032 = 290036-4 (0) 2E=3F: 870096 = 870096 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 147894 - 443676 + 295784 = 2 --> 0 holes F =2V-4: 295784 = 295788-4 (0) 2E=3F: 887352 = 887352 (0) total defect index = 0 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 178 intersecting 001: 38 intersecting 002: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 133 intersecting 001: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Aug 17 15:19:40 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs SubJ01_ReoT13THip 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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/filled.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/brain.finalsurfs.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/../mri/aseg.presurf.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... 19674 bright wm thresholded. 226 bright non-wm voxels segmented. reading original surface position from /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.orig... computing class statistics... border white: 283446 voxels (1.69%) border gray 315426 voxels (1.88%) WM (98.0): 99.0 +- 6.7 [70.0 --> 110.0] GM (80.0) : 78.7 +- 10.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.6 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.2 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.24 (0.03-->8.53) (max @ vno 143867 --> 143973) face area 0.29 +- 0.17 (0.00-->18.67) mean absolute distance = 0.72 +- 0.94 4320 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=101+-5.2, GM=78+-7.0 mean inside = 95.5, mean outside = 82.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=87.2, 226 (226) missing vertices, mean dist 0.2 [0.7 (%38.9)->0.7 (%61.1))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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 0.91 +- 0.27 (0.10-->8.27) (max @ vno 143867 --> 143973) face area 0.29 +- 0.17 (0.00-->16.62) mean absolute distance = 0.47 +- 0.77 6921 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2372293.0, rms=7.904 001: dt: 0.5000, sse=1636968.8, rms=6.102 (22.794%) 002: dt: 0.5000, sse=1263735.1, rms=4.892 (19.831%) 003: dt: 0.5000, sse=1052560.4, rms=3.986 (18.525%) 004: dt: 0.5000, sse=877499.9, rms=3.168 (20.528%) 005: dt: 0.5000, sse=793775.9, rms=2.638 (16.726%) 006: dt: 0.5000, sse=762534.2, rms=2.400 (9.037%) 007: dt: 0.5000, sse=753962.7, rms=2.347 (2.178%) 008: dt: 0.5000, sse=746110.4, rms=2.290 (2.444%) rms = 2.31, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=693602.2, rms=1.754 (23.424%) 010: dt: 0.2500, sse=684487.5, rms=1.573 (10.296%) rms = 1.57, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=679557.2, rms=1.569 (0.267%) 012: dt: 0.1250, sse=666137.0, rms=1.418 (9.606%) rms = 1.38, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=662953.7, rms=1.378 (2.824%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.3, 177 (76) missing vertices, mean dist -0.3 [0.6 (%68.1)->0.3 (%31.9))] %72 local maxima, %22 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dart, 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 (0.07-->8.03) (max @ vno 143867 --> 143973) face area 0.35 +- 0.20 (0.00-->19.18) mean absolute distance = 0.38 +- 0.52 6164 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1089822.5, rms=3.590 014: dt: 0.5000, sse=922112.2, rms=2.571 (28.395%) 015: dt: 0.5000, sse=857213.6, rms=2.145 (16.552%) 016: dt: 0.5000, sse=869953.9, rms=2.085 (2.830%) 017: dt: 0.5000, sse=836197.7, rms=1.960 (5.984%) rms = 2.04, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=800445.4, rms=1.591 (18.799%) 019: dt: 0.2500, sse=795724.3, rms=1.504 (5.494%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=801764.2, rms=1.499 (0.343%) 021: dt: 0.1250, sse=782191.1, rms=1.323 (11.733%) rms = 1.27, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=777207.6, rms=1.275 (3.626%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.9, 200 (55) missing vertices, mean dist -0.2 [0.4 (%66.9)->0.3 (%33.1))] %81 local maxima, %14 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dart, 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 (0.05-->7.96) (max @ vno 143867 --> 143973) face area 0.34 +- 0.20 (0.00-->18.09) mean absolute distance = 0.32 +- 0.43 4573 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=923473.7, rms=2.765 023: dt: 0.5000, sse=844953.5, rms=2.041 (26.189%) 024: dt: 0.5000, sse=809019.2, rms=1.727 (15.411%) rms = 1.90, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=769221.1, rms=1.387 (19.678%) rms = 1.35, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=768608.1, rms=1.350 (2.678%) 027: dt: 0.1250, sse=755078.2, rms=1.192 (11.704%) rms = 1.16, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=751990.1, rms=1.156 (3.036%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=91.6, 294 (50) missing vertices, mean dist -0.1 [0.3 (%57.6)->0.3 (%42.4))] %85 local maxima, %10 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dart, 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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=777530.8, rms=1.644 rms = 1.62, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=807577.9, rms=1.620 (1.473%) 030: dt: 0.2500, sse=761132.8, rms=1.196 (26.172%) rms = 1.30, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=737506.6, rms=1.104 (7.725%) 032: dt: 0.1250, sse=728117.7, rms=0.965 (12.556%) rms = 0.96, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=729805.2, rms=0.956 (0.908%) positioning took 0.5 minutes generating cortex label... 16 non-cortical segments detected only using segment with 7980 vertices erasing segment 0 (vno[0] = 31340) erasing segment 2 (vno[0] = 55831) erasing segment 3 (vno[0] = 55846) erasing segment 4 (vno[0] = 59988) erasing segment 5 (vno[0] = 62872) erasing segment 6 (vno[0] = 69522) erasing segment 7 (vno[0] = 74613) erasing segment 8 (vno[0] = 80683) erasing segment 9 (vno[0] = 83629) erasing segment 10 (vno[0] = 86357) erasing segment 11 (vno[0] = 99428) erasing segment 12 (vno[0] = 100599) erasing segment 13 (vno[0] = 102642) erasing segment 14 (vno[0] = 102670) erasing segment 15 (vno[0] = 105645) writing cortex label to /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label... writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.area vertex spacing 0.89 +- 0.27 (0.03-->7.87) (max @ vno 143867 --> 143973) face area 0.33 +- 0.20 (0.00-->17.31) refinement took 4.6 minutes #-------------------------------------------- #@# Make White Surf rh Fri Aug 17 15:24:14 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs SubJ01_ReoT13THip 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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/filled.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/brain.finalsurfs.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/../mri/aseg.presurf.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... 19674 bright wm thresholded. 226 bright non-wm voxels segmented. reading original surface position from /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.orig... computing class statistics... border white: 283446 voxels (1.69%) border gray 315426 voxels (1.88%) WM (98.0): 99.0 +- 6.7 [70.0 --> 110.0] GM (80.0) : 78.7 +- 10.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.6 (was 70) setting MAX_BORDER_WHITE to 108.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.2 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.24 (0.02-->8.10) (max @ vno 146172 --> 146246) face area 0.28 +- 0.14 (0.00-->8.46) mean absolute distance = 0.70 +- 0.90 4704 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=102+-5.2, GM=78+-6.1 mean inside = 96.0, mean outside = 82.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.1, 104 (104) missing vertices, mean dist 0.2 [0.6 (%40.0)->0.7 (%60.0))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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 0.91 +- 0.26 (0.08-->7.76) (max @ vno 146172 --> 146246) face area 0.28 +- 0.14 (0.00-->6.87) mean absolute distance = 0.43 +- 0.71 6226 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2173387.8, rms=7.357 001: dt: 0.5000, sse=1350263.9, rms=5.127 (30.316%) 002: dt: 0.5000, sse=1004756.0, rms=3.770 (26.463%) 003: dt: 0.5000, sse=860078.8, rms=3.027 (19.701%) 004: dt: 0.5000, sse=795320.3, rms=2.622 (13.395%) 005: dt: 0.5000, sse=771959.2, rms=2.453 (6.425%) 006: dt: 0.5000, sse=756810.5, rms=2.341 (4.595%) rms = 2.31, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=754412.0, rms=2.306 (1.486%) 008: dt: 0.2500, sse=679991.6, rms=1.539 (33.250%) 009: dt: 0.2500, sse=669069.6, rms=1.402 (8.908%) rms = 1.36, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=666699.1, rms=1.365 (2.670%) rms = 1.32, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=662878.1, rms=1.321 (3.213%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=89.2, 99 (25) missing vertices, mean dist -0.3 [0.5 (%69.6)->0.3 (%30.4))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dart, 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 (0.05-->7.81) (max @ vno 146172 --> 146264) face area 0.35 +- 0.17 (0.00-->9.01) mean absolute distance = 0.33 +- 0.49 5493 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1084015.5, rms=3.453 012: dt: 0.5000, sse=889306.6, rms=2.225 (35.551%) 013: dt: 0.5000, sse=851754.5, rms=1.931 (13.253%) 014: dt: 0.5000, sse=839749.0, rms=1.834 (5.000%) rms = 1.87, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=808094.4, rms=1.483 (19.124%) 016: dt: 0.2500, sse=797555.5, rms=1.316 (11.270%) 017: dt: 0.2500, sse=793824.4, rms=1.254 (4.757%) rms = 1.22, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=792109.3, rms=1.218 (2.823%) rms = 1.17, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=787078.4, rms=1.173 (3.732%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=91.0, 81 (11) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.2 (%29.9))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dart, 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 (0.04-->7.88) (max @ vno 146172 --> 146264) face area 0.34 +- 0.17 (0.00-->9.26) mean absolute distance = 0.27 +- 0.40 3860 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=932874.5, rms=2.710 020: dt: 0.5000, sse=832731.2, rms=1.755 (35.236%) 021: dt: 0.5000, sse=814957.8, rms=1.640 (6.552%) rms = 1.64, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=822186.2, rms=1.638 (0.134%) 023: dt: 0.2500, sse=784238.8, rms=1.171 (28.538%) 024: dt: 0.2500, sse=768024.9, rms=1.091 (6.826%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=760762.9, rms=1.068 (2.031%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=91.7, 140 (7) missing vertices, mean dist -0.1 [0.3 (%57.9)->0.2 (%42.1))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dart, 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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=778901.2, rms=1.522 026: dt: 0.5000, sse=782647.7, rms=1.241 (18.443%) rms = 1.44, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=749067.9, rms=0.991 (20.140%) rms = 0.98, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=746486.2, rms=0.975 (1.618%) 029: dt: 0.1250, sse=734500.6, rms=0.892 (8.527%) rms = 0.87, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=732002.7, rms=0.869 (2.616%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 7757 vertices erasing segment 1 (vno[0] = 53250) erasing segment 2 (vno[0] = 54520) erasing segment 3 (vno[0] = 54786) erasing segment 4 (vno[0] = 90210) erasing segment 5 (vno[0] = 99275) erasing segment 6 (vno[0] = 100479) erasing segment 7 (vno[0] = 102743) erasing segment 8 (vno[0] = 125056) writing cortex label to /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label... writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.area vertex spacing 0.88 +- 0.27 (0.02-->8.09) (max @ vno 146172 --> 146264) face area 0.33 +- 0.17 (0.00-->8.73) refinement took 4.5 minutes #-------------------------------------------- #@# Smooth2 lh Fri Aug 17 15:28:44 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 Fri Aug 17 15:28:49 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 Fri Aug 17 15:28:54 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_inflate -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.4 mm, total surface area = 87207 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.034 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.028 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 28.840092 mris_inflate stimesec 0.147918 mris_inflate ru_maxrss 191396 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26492 mris_inflate ru_majflt 12 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11472 mris_inflate ru_oublock 11344 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 109 mris_inflate ru_nivcsw 4284 #-------------------------------------------- #@# Inflation2 rh Fri Aug 17 15:29:23 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_inflate -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.8 mm, total surface area = 88305 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.175 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.081 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 29.469629 mris_inflate stimesec 0.119843 mris_inflate ru_maxrss 194940 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 27405 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 648 mris_inflate ru_oublock 11568 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 174 mris_inflate ru_nivcsw 3619 #-------------------------------------------- #@# Curv .H and .K lh Fri Aug 17 15:29:53 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/surf mris_curvature -w lh.white.preaparc total integrated curvature = 21.207*4pi (266.492) --> -20 handles ICI = 201.7, FI = 1651.8, variation=27334.418 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 173 vertices thresholded to be in k1 ~ [-0.32 0.87], k2 ~ [-0.18 0.09] total integrated curvature = 0.286*4pi (3.597) --> 1 handles ICI = 1.5, FI = 9.0, variation=159.549 152 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 126 vertices thresholded to be in [-0.18 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 done. #-------------------------------------------- #@# Curv .H and .K rh Fri Aug 17 15:31:10 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/surf mris_curvature -w rh.white.preaparc total integrated curvature = 20.027*4pi (251.667) --> -19 handles ICI = 194.5, FI = 1794.9, variation=28798.330 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 196 vertices thresholded to be in k1 ~ [-0.44 0.66], k2 ~ [-0.15 0.10] total integrated curvature = 0.196*4pi (2.461) --> 1 handles ICI = 1.5, FI = 9.6, variation=171.437 136 vertices thresholded to be in [-0.02 0.04] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 143 vertices thresholded to be in [-0.22 0.26] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Fri Aug 17 15:32:28 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm SubJ01_ReoT13THip 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 [ SubJ01_ReoT13THip/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 [ 264 ] Gb_filter = 0 WARN: S lookup min: -0.712135 WARN: S explicit min: 0.000000 vertex = 530 #----------------------------------------- #@# Curvature Stats rh Fri Aug 17 15:32:31 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm SubJ01_ReoT13THip 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 [ SubJ01_ReoT13THip/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 [ 291 ] Gb_filter = 0 WARN: S lookup min: -0.022377 WARN: S explicit min: 0.000000 vertex = 302 #-------------------------------------------- #@# Sphere lh Fri Aug 17 15:32:34 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_sphere -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/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 0.306... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= dart, 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 %20.23 pass 1: epoch 2 of 3 starting distance error %20.22 unfolding complete - removing small folds... starting distance error %20.08 removing remaining folds... final distance error %20.11 MRISunfold() return, current seed 1234 -01: dt=0.0000, 331 negative triangles 216: dt=0.9900, 331 negative triangles 217: dt=0.9900, 197 negative triangles 218: dt=0.9900, 154 negative triangles 219: dt=0.9900, 112 negative triangles 220: dt=0.9900, 101 negative triangles 221: dt=0.9900, 84 negative triangles 222: dt=0.9900, 76 negative triangles 223: dt=0.9900, 68 negative triangles 224: dt=0.9900, 72 negative triangles 225: dt=0.9900, 59 negative triangles 226: dt=0.9900, 57 negative triangles 227: dt=0.9900, 57 negative triangles 228: dt=0.9900, 51 negative triangles 229: dt=0.9900, 51 negative triangles 230: dt=0.9900, 45 negative triangles 231: dt=0.9900, 38 negative triangles 232: dt=0.9900, 49 negative triangles 233: dt=0.9900, 42 negative triangles 234: dt=0.9900, 36 negative triangles 235: dt=0.9900, 32 negative triangles 236: dt=0.9900, 34 negative triangles 237: dt=0.9900, 35 negative triangles 238: dt=0.9900, 30 negative triangles 239: dt=0.9900, 36 negative triangles 240: dt=0.9900, 34 negative triangles 241: dt=0.9900, 28 negative triangles 242: dt=0.9900, 23 negative triangles 243: dt=0.9900, 28 negative triangles 244: dt=0.9900, 23 negative triangles 245: dt=0.9900, 20 negative triangles 246: dt=0.9900, 21 negative triangles 247: dt=0.9900, 18 negative triangles 248: dt=0.9900, 20 negative triangles 249: dt=0.9900, 22 negative triangles 250: dt=0.9900, 18 negative triangles 251: dt=0.9900, 17 negative triangles 252: dt=0.9900, 15 negative triangles 253: dt=0.9900, 19 negative triangles 254: dt=0.9900, 16 negative triangles 255: dt=0.9900, 16 negative triangles 256: dt=0.9900, 20 negative triangles 257: dt=0.9900, 16 negative triangles 258: dt=0.9900, 19 negative triangles 259: dt=0.9900, 16 negative triangles 260: dt=0.9900, 12 negative triangles 261: dt=0.9900, 18 negative triangles 262: dt=0.9900, 14 negative triangles 263: dt=0.9900, 14 negative triangles 264: dt=0.9900, 16 negative triangles 265: dt=0.9900, 17 negative triangles 266: dt=0.9900, 13 negative triangles 267: dt=0.9900, 13 negative triangles 268: dt=0.9900, 15 negative triangles 269: dt=0.9900, 8 negative triangles 270: dt=0.9900, 13 negative triangles 271: dt=0.9900, 12 negative triangles 272: dt=0.9900, 10 negative triangles 273: dt=0.9900, 14 negative triangles 274: dt=0.9900, 8 negative triangles 275: dt=0.9900, 7 negative triangles 276: dt=0.9900, 8 negative triangles 277: dt=0.9900, 10 negative triangles 278: dt=0.9900, 8 negative triangles 279: dt=0.9900, 9 negative triangles 280: dt=0.9900, 8 negative triangles 281: dt=0.9900, 6 negative triangles 282: dt=0.9900, 6 negative triangles 283: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.69 hours mris_sphere utimesec 2467.218818 mris_sphere stimesec 3.759102 mris_sphere ru_maxrss 261588 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49955 mris_sphere ru_majflt 13 mris_sphere ru_nswap 0 mris_sphere ru_inblock 21912 mris_sphere ru_oublock 10208 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 97 mris_sphere ru_nivcsw 163557 FSRUNTIME@ mris_sphere 0.6879 hours 1 threads #-------------------------------------------- #@# Sphere rh Fri Aug 17 16:13:51 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_sphere -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/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 0.305... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= dart, 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 %20.35 pass 1: epoch 2 of 3 starting distance error %20.32 unfolding complete - removing small folds... starting distance error %20.24 removing remaining folds... final distance error %20.27 MRISunfold() return, current seed 1234 -01: dt=0.0000, 259 negative triangles 224: dt=0.9900, 259 negative triangles 225: dt=0.9900, 137 negative triangles 226: dt=0.9900, 125 negative triangles 227: dt=0.9900, 111 negative triangles 228: dt=0.9900, 113 negative triangles 229: dt=0.9900, 108 negative triangles 230: dt=0.9900, 93 negative triangles 231: dt=0.9900, 89 negative triangles 232: dt=0.9900, 83 negative triangles 233: dt=0.9900, 80 negative triangles 234: dt=0.9900, 86 negative triangles 235: dt=0.9900, 75 negative triangles 236: dt=0.9900, 66 negative triangles 237: dt=0.9900, 67 negative triangles 238: dt=0.9900, 58 negative triangles 239: dt=0.9900, 65 negative triangles 240: dt=0.9900, 63 negative triangles 241: dt=0.9900, 63 negative triangles 242: dt=0.9900, 56 negative triangles 243: dt=0.9900, 62 negative triangles 244: dt=0.9900, 58 negative triangles 245: dt=0.9900, 53 negative triangles 246: dt=0.9900, 51 negative triangles 247: dt=0.9900, 45 negative triangles 248: dt=0.9900, 51 negative triangles 249: dt=0.9900, 48 negative triangles 250: dt=0.9900, 50 negative triangles 251: dt=0.9900, 51 negative triangles 252: dt=0.9900, 46 negative triangles 253: dt=0.9900, 44 negative triangles 254: dt=0.9900, 51 negative triangles 255: dt=0.9900, 45 negative triangles 256: dt=0.9900, 41 negative triangles 257: dt=0.9900, 45 negative triangles 258: dt=0.9900, 41 negative triangles 259: dt=0.9900, 44 negative triangles 260: dt=0.9900, 43 negative triangles 261: dt=0.9900, 39 negative triangles 262: dt=0.9900, 45 negative triangles 263: dt=0.9900, 50 negative triangles 264: dt=0.9900, 41 negative triangles 265: dt=0.9900, 42 negative triangles 266: dt=0.9900, 41 negative triangles 267: dt=0.9900, 34 negative triangles 268: dt=0.9900, 41 negative triangles 269: dt=0.9900, 45 negative triangles 270: dt=0.9900, 42 negative triangles 271: dt=0.9900, 43 negative triangles 272: dt=0.9900, 43 negative triangles 273: dt=0.9900, 35 negative triangles 274: dt=0.9900, 36 negative triangles 275: dt=0.9900, 31 negative triangles 276: dt=0.9900, 36 negative triangles 277: dt=0.9900, 34 negative triangles 278: dt=0.9900, 37 negative triangles 279: dt=0.9900, 36 negative triangles 280: dt=0.9900, 27 negative triangles 281: dt=0.9900, 32 negative triangles 282: dt=0.9900, 30 negative triangles 283: dt=0.9900, 32 negative triangles 284: dt=0.9900, 28 negative triangles 285: dt=0.9900, 27 negative triangles 286: dt=0.9900, 24 negative triangles 287: dt=0.9900, 23 negative triangles 288: dt=0.9900, 23 negative triangles 289: dt=0.9900, 25 negative triangles 290: dt=0.9900, 20 negative triangles 291: dt=0.9900, 23 negative triangles 292: dt=0.9900, 20 negative triangles 293: dt=0.9900, 21 negative triangles 294: dt=0.9900, 17 negative triangles 295: dt=0.9900, 17 negative triangles 296: dt=0.9900, 16 negative triangles 297: dt=0.9900, 13 negative triangles 298: dt=0.9900, 16 negative triangles 299: dt=0.9900, 19 negative triangles 300: dt=0.9900, 15 negative triangles 301: dt=0.9900, 12 negative triangles 302: dt=0.9900, 13 negative triangles 303: dt=0.9900, 11 negative triangles 304: dt=0.9900, 12 negative triangles 305: dt=0.9900, 11 negative triangles 306: dt=0.9900, 12 negative triangles 307: dt=0.9900, 10 negative triangles 308: dt=0.9900, 8 negative triangles 309: dt=0.9900, 5 negative triangles 310: dt=0.9900, 7 negative triangles 311: dt=0.9900, 2 negative triangles 312: dt=0.9900, 2 negative triangles 313: dt=0.9900, 2 negative triangles 314: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.76 hours mris_sphere utimesec 2728.877853 mris_sphere stimesec 1.755707 mris_sphere ru_maxrss 266580 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 42504 mris_sphere ru_majflt 2 mris_sphere ru_nswap 0 mris_sphere ru_inblock 21376 mris_sphere ru_oublock 10408 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 112 mris_sphere ru_nivcsw 74118 FSRUNTIME@ mris_sphere 0.7593 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Fri Aug 17 16:59:25 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_register -curv -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/shize/freesurfer/SubJ01_ReoT13THip/scripts cmdline mris_register -curv -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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= dart, 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= dart, 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 = 5.746 curvature mean = 0.034, std = 0.817 curvature mean = 0.023, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 372271.2, tmin=0.9151 d=32.00 min @ (0.00, -8.00, -8.00) sse = 309777.3, tmin=1.8528 d=16.00 min @ (4.00, 4.00, 0.00) sse = 306141.0, tmin=2.8059 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 298665.2, tmin=3.7786 d=4.00 min @ (0.00, 0.00, 1.00) sse = 298172.9, tmin=4.7591 d=2.00 min @ (0.00, 0.50, -0.50) sse = 298071.8, tmin=5.7415 d=1.00 min @ (0.00, -0.25, 0.25) sse = 297994.2, tmin=6.7175 d=0.50 min @ (0.00, 0.00, -0.12) sse = 297969.3, tmin=7.6944 tol=1.0e+00, sigma=0.5, host= dart, 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 7.69 min curvature mean = -0.006, std = 0.834 curvature mean = 0.006, std = 0.942 curvature mean = -0.008, std = 0.845 curvature mean = 0.002, std = 0.976 curvature mean = -0.010, std = 0.847 curvature mean = 0.000, std = 0.989 2 Reading smoothwm curvature mean = -0.038, std = 0.391 curvature mean = 0.035, std = 0.245 curvature mean = 0.052, std = 0.260 curvature mean = 0.030, std = 0.303 curvature mean = 0.036, std = 0.387 curvature mean = 0.029, std = 0.329 curvature mean = 0.022, std = 0.487 curvature mean = 0.029, std = 0.338 curvature mean = 0.009, std = 0.574 MRISregister() return, current seed 0 -01: dt=0.0000, 166 negative triangles 126: dt=0.9900, 166 negative triangles expanding nbhd size to 1 127: dt=0.9900, 202 negative triangles 128: dt=0.9900, 167 negative triangles 129: dt=0.9900, 160 negative triangles 130: dt=0.9900, 153 negative triangles 131: dt=0.9900, 141 negative triangles 132: dt=0.9900, 133 negative triangles 133: dt=0.9900, 134 negative triangles 134: dt=0.9900, 126 negative triangles 135: dt=0.9900, 121 negative triangles 136: dt=0.9900, 120 negative triangles 137: dt=0.9900, 107 negative triangles 138: dt=0.9900, 101 negative triangles 139: dt=0.9900, 91 negative triangles 140: dt=0.9900, 90 negative triangles 141: dt=0.9900, 87 negative triangles 142: dt=0.9900, 84 negative triangles 143: dt=0.9900, 85 negative triangles 144: dt=0.9900, 78 negative triangles 145: dt=0.9900, 75 negative triangles 146: dt=0.9900, 74 negative triangles 147: dt=0.9900, 68 negative triangles 148: dt=0.9900, 64 negative triangles 149: dt=0.9900, 63 negative triangles 150: dt=0.9900, 63 negative triangles 151: dt=0.9900, 62 negative triangles 152: dt=0.9900, 57 negative triangles 153: dt=0.9900, 53 negative triangles 154: dt=0.9900, 48 negative triangles 155: dt=0.9900, 46 negative triangles 156: dt=0.9900, 46 negative triangles 157: dt=0.9900, 45 negative triangles 158: dt=0.9900, 41 negative triangles 159: dt=0.9900, 44 negative triangles 160: dt=0.9900, 41 negative triangles 161: dt=0.9900, 40 negative triangles 162: dt=0.9900, 38 negative triangles 163: dt=0.9900, 39 negative triangles 164: dt=0.9900, 36 negative triangles 165: dt=0.9900, 33 negative triangles 166: dt=0.9900, 33 negative triangles 167: dt=0.9900, 27 negative triangles 168: dt=0.9900, 28 negative triangles 169: dt=0.9900, 28 negative triangles 170: dt=0.9900, 25 negative triangles 171: dt=0.9900, 23 negative triangles 172: dt=0.9900, 23 negative triangles 173: dt=0.9900, 22 negative triangles 174: dt=0.9900, 21 negative triangles 175: dt=0.9900, 22 negative triangles 176: dt=0.9900, 21 negative triangles 177: dt=0.9900, 19 negative triangles 178: dt=0.9900, 17 negative triangles 179: dt=0.9900, 18 negative triangles 180: dt=0.9900, 17 negative triangles 181: dt=0.9900, 17 negative triangles 182: dt=0.9900, 15 negative triangles 183: dt=0.9900, 14 negative triangles 184: dt=0.9900, 14 negative triangles 185: dt=0.9900, 15 negative triangles 186: dt=0.9900, 14 negative triangles 187: dt=0.9900, 14 negative triangles 188: dt=0.9900, 14 negative triangles 189: dt=0.9900, 14 negative triangles 190: dt=0.9900, 14 negative triangles 191: dt=0.9900, 14 negative triangles 192: dt=0.9900, 14 negative triangles 193: dt=0.9405, 15 negative triangles 194: dt=0.9405, 13 negative triangles 195: dt=0.9405, 13 negative triangles 196: dt=0.9405, 13 negative triangles 197: dt=0.9405, 12 negative triangles 198: dt=0.9405, 11 negative triangles 199: dt=0.9405, 11 negative triangles 200: dt=0.9405, 11 negative triangles 201: dt=0.9405, 11 negative triangles 202: dt=0.9405, 12 negative triangles 203: dt=0.9405, 11 negative triangles 204: dt=0.9405, 11 negative triangles 205: dt=0.9405, 9 negative triangles 206: dt=0.9405, 8 negative triangles 207: dt=0.9405, 8 negative triangles 208: dt=0.9405, 8 negative triangles 209: dt=0.9405, 8 negative triangles 210: dt=0.9405, 8 negative triangles 211: dt=0.9405, 9 negative triangles 212: dt=0.9405, 10 negative triangles 213: dt=0.9405, 10 negative triangles 214: dt=0.9405, 10 negative triangles 215: dt=0.9405, 8 negative triangles 216: dt=0.8935, 8 negative triangles 217: dt=0.8935, 8 negative triangles 218: dt=0.8935, 7 negative triangles 219: dt=0.8935, 7 negative triangles 220: dt=0.8935, 7 negative triangles 221: dt=0.8935, 7 negative triangles 222: dt=0.8935, 7 negative triangles 223: dt=0.8935, 7 negative triangles 224: dt=0.8935, 9 negative triangles 225: dt=0.8935, 8 negative triangles 226: dt=0.8935, 6 negative triangles 227: dt=0.8935, 3 negative triangles 228: dt=0.8935, 3 negative triangles 229: dt=0.8935, 3 negative triangles 230: dt=0.8935, 3 negative triangles 231: dt=0.8935, 3 negative triangles 232: dt=0.8935, 4 negative triangles 233: dt=0.8935, 3 negative triangles 234: dt=0.8935, 3 negative triangles 235: dt=0.8935, 2 negative triangles 236: dt=0.8935, 2 negative triangles 237: dt=0.8935, 1 negative triangles 238: dt=0.8935, 2 negative triangles 239: dt=0.8935, 1 negative triangles 240: dt=0.8935, 1 negative triangles 241: dt=0.8935, 2 negative triangles 242: dt=0.8935, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.85 hours mris_register utimesec 3050.427308 mris_register stimesec 2.267916 mris_register ru_maxrss 243956 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 35503 mris_register ru_majflt 12 mris_register ru_nswap 0 mris_register ru_inblock 28704 mris_register ru_oublock 10208 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 104 mris_register ru_nivcsw 73088 FSRUNTIME@ mris_register 0.8488 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Fri Aug 17 17:50:20 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_register -curv -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer-6.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/shize/freesurfer/SubJ01_ReoT13THip/scripts cmdline mris_register -curv -rusage /home/shize/freesurfer/SubJ01_ReoT13THip/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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= dart, 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= dart, 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 = 5.669 curvature mean = 0.020, std = 0.806 curvature mean = 0.026, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 390776.4, tmin=0.9359 d=32.00 min @ (8.00, 8.00, -8.00) sse = 334310.2, tmin=1.9008 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 317822.6, tmin=2.8819 d=4.00 min @ (1.00, 0.00, 1.00) sse = 315524.4, tmin=4.8404 d=1.00 min @ (-0.25, -0.25, -0.25) sse = 315411.9, tmin=6.8062 d=0.50 min @ (0.12, 0.12, 0.00) sse = 315387.9, tmin=7.8045 tol=1.0e+00, sigma=0.5, host= dart, 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 7.80 min curvature mean = -0.006, std = 0.813 curvature mean = 0.008, std = 0.939 curvature mean = -0.010, std = 0.821 curvature mean = 0.003, std = 0.974 curvature mean = -0.012, std = 0.823 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.034, std = 0.348 curvature mean = 0.031, std = 0.238 curvature mean = 0.058, std = 0.290 curvature mean = 0.028, std = 0.293 curvature mean = 0.033, std = 0.446 curvature mean = 0.027, std = 0.318 curvature mean = 0.020, std = 0.562 curvature mean = 0.027, std = 0.328 curvature mean = 0.008, std = 0.660 MRISregister() return, current seed 0 -01: dt=0.0000, 122 negative triangles 133: dt=0.9900, 122 negative triangles expanding nbhd size to 1 134: dt=0.9900, 152 negative triangles 135: dt=0.9900, 118 negative triangles 136: dt=0.9900, 111 negative triangles 137: dt=0.9900, 111 negative triangles 138: dt=0.9900, 100 negative triangles 139: dt=0.9900, 94 negative triangles 140: dt=0.9900, 103 negative triangles 141: dt=0.9900, 94 negative triangles 142: dt=0.9900, 86 negative triangles 143: dt=0.9900, 81 negative triangles 144: dt=0.9900, 83 negative triangles 145: dt=0.9900, 86 negative triangles 146: dt=0.9900, 87 negative triangles 147: dt=0.9900, 79 negative triangles 148: dt=0.9900, 71 negative triangles 149: dt=0.9900, 69 negative triangles 150: dt=0.9900, 69 negative triangles 151: dt=0.9900, 73 negative triangles 152: dt=0.9900, 72 negative triangles 153: dt=0.9900, 68 negative triangles 154: dt=0.9900, 65 negative triangles 155: dt=0.9900, 68 negative triangles 156: dt=0.9900, 71 negative triangles 157: dt=0.9900, 75 negative triangles 158: dt=0.9900, 65 negative triangles 159: dt=0.9900, 65 negative triangles 160: dt=0.9900, 57 negative triangles 161: dt=0.9900, 59 negative triangles 162: dt=0.9900, 56 negative triangles 163: dt=0.9900, 58 negative triangles 164: dt=0.9900, 52 negative triangles 165: dt=0.9900, 53 negative triangles 166: dt=0.9900, 50 negative triangles 167: dt=0.9900, 48 negative triangles 168: dt=0.9900, 53 negative triangles 169: dt=0.9900, 52 negative triangles 170: dt=0.9900, 49 negative triangles 171: dt=0.9900, 45 negative triangles 172: dt=0.9900, 41 negative triangles 173: dt=0.9900, 40 negative triangles 174: dt=0.9900, 37 negative triangles 175: dt=0.9900, 42 negative triangles 176: dt=0.9900, 39 negative triangles 177: dt=0.9900, 39 negative triangles 178: dt=0.9900, 36 negative triangles 179: dt=0.9900, 35 negative triangles 180: dt=0.9900, 33 negative triangles 181: dt=0.9900, 29 negative triangles 182: dt=0.9900, 30 negative triangles 183: dt=0.9900, 28 negative triangles 184: dt=0.9900, 28 negative triangles 185: dt=0.9900, 26 negative triangles 186: dt=0.9900, 29 negative triangles 187: dt=0.9900, 29 negative triangles 188: dt=0.9900, 23 negative triangles 189: dt=0.9900, 19 negative triangles 190: dt=0.9900, 21 negative triangles 191: dt=0.9900, 20 negative triangles 192: dt=0.9900, 23 negative triangles 193: dt=0.9900, 21 negative triangles 194: dt=0.9900, 15 negative triangles 195: dt=0.9900, 18 negative triangles 196: dt=0.9900, 12 negative triangles 197: dt=0.9900, 14 negative triangles 198: dt=0.9900, 12 negative triangles 199: dt=0.9900, 7 negative triangles 200: dt=0.9900, 9 negative triangles 201: dt=0.9900, 10 negative triangles 202: dt=0.9900, 9 negative triangles 203: dt=0.9900, 7 negative triangles 204: dt=0.9900, 4 negative triangles 205: dt=0.9900, 2 negative triangles 206: dt=0.9900, 2 negative triangles 207: dt=0.9900, 1 negative triangles 208: dt=0.9900, 1 negative triangles 209: dt=0.9900, 1 negative triangles 210: dt=0.9900, 1 negative triangles 211: dt=0.9900, 2 negative triangles 212: dt=0.9900, 1 negative triangles 213: dt=0.9900, 1 negative triangles 214: dt=0.9900, 1 negative triangles 215: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.96 hours mris_register utimesec 3455.498421 mris_register stimesec 2.039788 mris_register ru_maxrss 248488 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 34106 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 6752 mris_register ru_oublock 10408 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 101 mris_register ru_nivcsw 81446 FSRUNTIME@ mris_register 0.9614 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Fri Aug 17 18:48:01 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 Fri Aug 17 18:48:03 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 Fri Aug 17 18:48:05 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mrisp_paint -a 5 /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Fri Aug 17 18:48:06 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mrisp_paint -a 5 /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Aug 17 18:48:07 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SubJ01_ReoT13THip lh ../surf/lh.sphere.reg /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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... 1011 labels changed using aseg relabeling using gibbs priors... 000: 3435 changed, 145018 examined... 001: 782 changed, 14119 examined... 002: 186 changed, 4250 examined... 003: 69 changed, 1114 examined... 004: 24 changed, 417 examined... 005: 14 changed, 146 examined... 006: 9 changed, 89 examined... 007: 3 changed, 47 examined... 008: 0 changed, 19 examined... 217 labels changed using aseg 000: 121 total segments, 80 labels (214 vertices) changed 001: 43 total segments, 2 labels (2 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 14 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1805 vertices marked for relabeling... 1805 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Cortical Parc rh Fri Aug 17 18:48:18 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SubJ01_ReoT13THip rh ../surf/rh.sphere.reg /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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... 1087 labels changed using aseg relabeling using gibbs priors... 000: 3069 changed, 147894 examined... 001: 735 changed, 13093 examined... 002: 172 changed, 4068 examined... 003: 73 changed, 1050 examined... 004: 29 changed, 425 examined... 005: 10 changed, 168 examined... 006: 6 changed, 62 examined... 007: 2 changed, 36 examined... 008: 0 changed, 13 examined... 139 labels changed using aseg 000: 106 total segments, 69 labels (233 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1601 vertices marked for relabeling... 1601 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Aug 17 18:48:29 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs SubJ01_ReoT13THip 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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/filled.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/brain.finalsurfs.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/../mri/aseg.presurf.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... 19674 bright wm thresholded. 226 bright non-wm voxels segmented. reading original surface position from /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.orig... computing class statistics... border white: 283446 voxels (1.69%) border gray 315426 voxels (1.88%) WM (98.0): 99.0 +- 6.7 [70.0 --> 110.0] GM (80.0) : 78.7 +- 10.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.6 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.2 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.8 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-5.2, GM=78+-7.0 mean inside = 95.5, mean outside = 82.4 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-->7.87) (max @ vno 143867 --> 143973) face area 0.33 +- 0.20 (0.00-->17.18) mean absolute distance = 0.71 +- 0.96 4310 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 136 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 85 points - only 0.00% unknown deleting segment 6 with 16 points - only 0.00% unknown deleting segment 7 with 175 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown mean border=87.1, 269 (241) missing vertices, mean dist 0.4 [0.9 (%17.3)->0.7 (%82.7))] %62 local maxima, %33 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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 0.91 +- 0.27 (0.05-->7.72) (max @ vno 143867 --> 143973) face area 0.33 +- 0.19 (0.00-->16.53) mean absolute distance = 0.45 +- 0.72 5252 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1721514.0, rms=6.063 001: dt: 0.5000, sse=1153188.5, rms=4.056 (33.100%) 002: dt: 0.5000, sse=929924.3, rms=2.934 (27.661%) 003: dt: 0.5000, sse=872401.7, rms=2.551 (13.065%) 004: dt: 0.5000, sse=823608.3, rms=2.222 (12.874%) rms = 2.24, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=786626.4, rms=1.857 (16.443%) 006: dt: 0.2500, sse=779463.7, rms=1.722 (7.286%) rms = 1.70, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=781949.1, rms=1.701 (1.199%) 008: dt: 0.1250, sse=761421.0, rms=1.529 (10.104%) rms = 1.48, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=755706.1, rms=1.484 (2.939%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 146 points - only 0.00% unknown deleting segment 2 with 59 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 89 points - only 0.00% unknown deleting segment 5 with 103 points - only 0.00% unknown mean border=89.3, 179 (58) missing vertices, mean dist -0.3 [0.5 (%68.0)->0.3 (%32.0))] %73 local maxima, %22 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dart, 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 0.89 +- 0.27 (0.07-->7.66) (max @ vno 143867 --> 143973) face area 0.35 +- 0.20 (0.00-->17.25) mean absolute distance = 0.37 +- 0.52 6072 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1058001.8, rms=3.423 010: dt: 0.5000, sse=910502.2, rms=2.506 (26.784%) 011: dt: 0.5000, sse=852151.6, rms=2.047 (18.303%) rms = 2.02, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=854214.6, rms=2.020 (1.328%) 013: dt: 0.2500, sse=798462.1, rms=1.494 (26.064%) 014: dt: 0.2500, sse=793554.2, rms=1.436 (3.890%) rms = 1.43, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=793235.0, rms=1.429 (0.433%) 016: dt: 0.1250, sse=779107.1, rms=1.252 (12.423%) rms = 1.21, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=782629.0, rms=1.212 (3.151%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 158 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 42 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown deleting segment 4 with 197 points - only 0.00% unknown deleting segment 5 with 42 points - only 0.00% unknown mean border=90.9, 191 (25) missing vertices, mean dist -0.2 [0.4 (%66.9)->0.3 (%33.1))] %81 local maxima, %14 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dart, 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 (0.03-->7.59) (max @ vno 143867 --> 143973) face area 0.34 +- 0.20 (0.00-->16.32) mean absolute distance = 0.31 +- 0.43 4617 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=925156.9, rms=2.716 018: dt: 0.5000, sse=837504.7, rms=1.983 (26.987%) 019: dt: 0.5000, sse=799087.6, rms=1.691 (14.727%) rms = 1.87, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=769203.6, rms=1.362 (19.468%) rms = 1.35, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=772135.8, rms=1.349 (0.901%) 022: dt: 0.1250, sse=759199.2, rms=1.181 (12.461%) rms = 1.15, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=753552.9, rms=1.147 (2.907%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 157 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 35 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 195 points - only 0.00% unknown deleting segment 6 with 42 points - only 0.00% unknown mean border=91.6, 256 (17) missing vertices, mean dist -0.1 [0.3 (%57.4)->0.3 (%42.6))] %85 local maxima, %10 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dart, 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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=780123.5, rms=1.643 rms = 1.62, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=790882.7, rms=1.616 (1.634%) 025: dt: 0.2500, sse=750975.3, rms=1.210 (25.128%) rms = 1.28, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=741451.8, rms=1.123 (7.166%) 027: dt: 0.1250, sse=733712.9, rms=0.984 (12.401%) rms = 0.97, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=730684.0, rms=0.966 (1.834%) positioning took 0.5 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7982 vertices erasing segment 0 (vno[0] = 31340) erasing segment 2 (vno[0] = 55831) erasing segment 3 (vno[0] = 55846) erasing segment 4 (vno[0] = 59988) erasing segment 5 (vno[0] = 69522) erasing segment 6 (vno[0] = 73346) erasing segment 7 (vno[0] = 74613) erasing segment 8 (vno[0] = 83629) erasing segment 9 (vno[0] = 86357) erasing segment 10 (vno[0] = 100599) erasing segment 11 (vno[0] = 102642) erasing segment 12 (vno[0] = 102670) erasing segment 13 (vno[0] = 105645) writing cortex label to /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label... writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.area vertex spacing 0.89 +- 0.28 (0.03-->7.53) (max @ vno 143867 --> 143973) face area 0.33 +- 0.20 (0.00-->16.02) 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... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown deleting segment 6 with 39 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=65.8, 234 (234) missing vertices, mean dist 1.7 [1.1 (%0.0)->3.0 (%100.0))] %19 local maxima, %34 large gradients and %43 min vals, 823 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= dart, 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=20696388.0, rms=26.884 001: dt: 0.0500, sse=18814654.0, rms=25.589 (4.818%) 002: dt: 0.0500, sse=17473768.0, rms=24.624 (3.770%) 003: dt: 0.0500, sse=16438916.0, rms=23.853 (3.133%) 004: dt: 0.0500, sse=15589542.0, rms=23.200 (2.735%) 005: dt: 0.0500, sse=14863429.0, rms=22.628 (2.468%) 006: dt: 0.0500, sse=14224953.0, rms=22.112 (2.280%) 007: dt: 0.0500, sse=13651473.0, rms=21.638 (2.143%) 008: dt: 0.0500, sse=13128011.0, rms=21.196 (2.042%) 009: dt: 0.0500, sse=12645344.0, rms=20.780 (1.962%) 010: dt: 0.0500, sse=12196070.0, rms=20.386 (1.899%) positioning took 0.8 minutes mean border=65.6, 213 (135) missing vertices, mean dist 1.4 [0.2 (%0.3)->2.5 (%99.7))] %19 local maxima, %34 large gradients and %42 min vals, 786 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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=13016518.0, rms=21.094 011: dt: 0.0500, sse=12588255.0, rms=20.724 (1.755%) 012: dt: 0.0500, sse=12186425.0, rms=20.370 (1.706%) 013: dt: 0.0500, sse=11805306.0, rms=20.029 (1.674%) 014: dt: 0.0500, sse=11445001.0, rms=19.701 (1.637%) 015: dt: 0.0500, sse=11103457.0, rms=19.385 (1.604%) 016: dt: 0.0500, sse=10779612.0, rms=19.081 (1.571%) 017: dt: 0.0500, sse=10471921.0, rms=18.787 (1.541%) 018: dt: 0.0500, sse=10178321.0, rms=18.502 (1.517%) 019: dt: 0.0500, sse=9898289.0, rms=18.225 (1.492%) 020: dt: 0.0500, sse=9630397.0, rms=17.957 (1.471%) positioning took 0.8 minutes mean border=65.5, 225 (112) missing vertices, mean dist 1.2 [0.1 (%1.6)->2.1 (%98.4))] %20 local maxima, %34 large gradients and %42 min vals, 767 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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=9725730.0, rms=18.055 021: dt: 0.0500, sse=9460856.0, rms=17.788 (1.482%) 022: dt: 0.0500, sse=9210842.0, rms=17.531 (1.442%) 023: dt: 0.0500, sse=8970927.0, rms=17.282 (1.424%) 024: dt: 0.0500, sse=8741361.0, rms=17.039 (1.403%) 025: dt: 0.0500, sse=8521567.0, rms=16.804 (1.382%) 026: dt: 0.0500, sse=8310921.5, rms=16.575 (1.362%) 027: dt: 0.0500, sse=8108675.0, rms=16.352 (1.345%) 028: dt: 0.0500, sse=7913312.5, rms=16.134 (1.335%) 029: dt: 0.0500, sse=7724075.5, rms=15.919 (1.329%) 030: dt: 0.0500, sse=7540635.0, rms=15.709 (1.323%) positioning took 0.8 minutes mean border=65.4, 240 (99) missing vertices, mean dist 1.0 [0.1 (%7.1)->1.9 (%92.9))] %20 local maxima, %34 large gradients and %41 min vals, 778 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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=7630513.5, rms=15.812 031: dt: 0.5000, sse=6341216.5, rms=14.256 (9.839%) 032: dt: 0.5000, sse=5252736.0, rms=12.789 (10.288%) 033: dt: 0.5000, sse=4439252.5, rms=11.574 (9.503%) 034: dt: 0.5000, sse=3691723.5, rms=10.325 (10.786%) 035: dt: 0.5000, sse=3154792.2, rms=9.328 (9.656%) 036: dt: 0.5000, sse=2645602.8, rms=8.268 (11.370%) 037: dt: 0.5000, sse=2313294.2, rms=7.499 (9.297%) 038: dt: 0.5000, sse=1994022.0, rms=6.671 (11.037%) 039: dt: 0.5000, sse=1838492.2, rms=6.232 (6.584%) 040: dt: 0.5000, sse=1664689.2, rms=5.693 (8.657%) 041: dt: 0.5000, sse=1607137.1, rms=5.508 (3.246%) 042: dt: 0.5000, sse=1509233.6, rms=5.165 (6.219%) rms = 5.15, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1504980.0, rms=5.153 (0.232%) 044: dt: 0.2500, sse=1357542.1, rms=4.554 (11.638%) 045: dt: 0.2500, sse=1329105.8, rms=4.438 (2.530%) rms = 4.44, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=1330061.4, rms=4.437 (0.027%) 047: dt: 0.1250, sse=1279092.5, rms=4.216 (4.983%) rms = 4.17, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1268168.9, rms=4.169 (1.127%) positioning took 1.9 minutes mean border=64.8, 2747 (31) missing vertices, mean dist 0.1 [0.2 (%49.3)->0.7 (%50.7))] %29 local maxima, %28 large gradients and %37 min vals, 431 gradients ignored tol=1.0e-04, sigma=1.0, host= dart, 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=1456307.5, rms=4.402 rms = 4.54, time step reduction 1 of 3 to 0.250... 049: dt: 0.2500, sse=1362841.0, rms=3.980 (9.577%) 050: dt: 0.2500, sse=1301551.0, rms=3.675 (7.678%) rms = 3.66, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=1297385.4, rms=3.656 (0.521%) 052: dt: 0.1250, sse=1236961.8, rms=3.329 (8.936%) 053: dt: 0.1250, sse=1221281.4, rms=3.243 (2.568%) rms = 3.21, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1214370.6, rms=3.206 (1.165%) positioning took 0.9 minutes mean border=64.4, 3051 (24) missing vertices, mean dist 0.1 [0.2 (%47.1)->0.5 (%52.9))] %37 local maxima, %20 large gradients and %36 min vals, 492 gradients ignored tol=1.0e-04, sigma=0.5, host= dart, 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=1242339.8, rms=3.409 rms = 3.80, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1210159.9, rms=3.230 (5.263%) 056: dt: 0.2500, sse=1196669.4, rms=3.160 (2.172%) rms = 3.24, time step reduction 2 of 3 to 0.125... rms = 3.12, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1189862.6, rms=3.118 (1.325%) positioning took 0.6 minutes mean border=63.9, 6073 (22) missing vertices, mean dist 0.1 [0.2 (%46.4)->0.4 (%53.6))] %40 local maxima, %17 large gradients and %35 min vals, 472 gradients ignored tol=1.0e-04, sigma=0.2, host= dart, 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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1211088.8, rms=3.223 rms = 3.68, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1187471.9, rms=3.084 (4.298%) 059: dt: 0.2500, sse=1174587.1, rms=3.023 (1.976%) rms = 3.11, time step reduction 2 of 3 to 0.125... rms = 2.98, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1167342.4, rms=2.977 (1.536%) positioning took 0.6 minutes writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.area.pial vertex spacing 0.98 +- 0.44 (0.06-->7.58) (max @ vno 143867 --> 143973) face area 0.38 +- 0.32 (0.00-->18.68) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 145018 vertices processed 25000 of 145018 vertices processed 50000 of 145018 vertices processed 75000 of 145018 vertices processed 100000 of 145018 vertices processed 125000 of 145018 vertices processed 0 of 145018 vertices processed 25000 of 145018 vertices processed 50000 of 145018 vertices processed 75000 of 145018 vertices processed 100000 of 145018 vertices processed 125000 of 145018 vertices processed thickness calculation complete, 586:1384 truncations. 39343 vertices at 0 distance 102369 vertices at 1 distance 78685 vertices at 2 distance 34979 vertices at 3 distance 13524 vertices at 4 distance 4961 vertices at 5 distance 1878 vertices at 6 distance 744 vertices at 7 distance 283 vertices at 8 distance 130 vertices at 9 distance 74 vertices at 10 distance 52 vertices at 11 distance 25 vertices at 12 distance 23 vertices at 13 distance 18 vertices at 14 distance 29 vertices at 15 distance 17 vertices at 16 distance 11 vertices at 17 distance 8 vertices at 18 distance 10 vertices at 19 distance 13 vertices at 20 distance writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.thickness positioning took 12.2 minutes #-------------------------------------------- #@# Make Pial Surf rh Fri Aug 17 19:00:41 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs SubJ01_ReoT13THip 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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/filled.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/brain.finalsurfs.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/../mri/aseg.presurf.mgz... reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... 19674 bright wm thresholded. 226 bright non-wm voxels segmented. reading original surface position from /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.orig... computing class statistics... border white: 283446 voxels (1.69%) border gray 315426 voxels (1.88%) WM (98.0): 99.0 +- 6.7 [70.0 --> 110.0] GM (80.0) : 78.7 +- 10.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.6 (was 70) setting MAX_BORDER_WHITE to 108.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.2 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.8 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-5.2, GM=78+-6.1 mean inside = 96.0, mean outside = 82.2 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 0.88 +- 0.27 (0.02-->8.09) (max @ vno 146172 --> 146264) face area 0.33 +- 0.17 (0.00-->8.66) mean absolute distance = 0.67 +- 0.89 3839 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 88 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 200 points - only 0.00% unknown deleting segment 8 with 142 points - only 0.00% unknown deleting segment 9 with 22 points - only 0.00% unknown deleting segment 10 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 35 points - only 0.00% unknown deleting segment 14 with 50 points - only 0.00% unknown deleting segment 15 with 46 points - only 0.00% unknown mean border=86.9, 162 (159) missing vertices, mean dist 0.4 [0.8 (%15.4)->0.6 (%84.6))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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 0.91 +- 0.27 (0.07-->7.91) (max @ vno 146172 --> 146264) face area 0.33 +- 0.17 (0.00-->7.81) mean absolute distance = 0.42 +- 0.70 5801 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1788594.1, rms=6.173 001: dt: 0.5000, sse=1147590.6, rms=3.921 (36.480%) 002: dt: 0.5000, sse=927057.6, rms=2.820 (28.086%) 003: dt: 0.5000, sse=861430.9, rms=2.405 (14.725%) 004: dt: 0.5000, sse=831157.0, rms=2.170 (9.746%) rms = 2.13, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=826314.8, rms=2.127 (1.979%) 006: dt: 0.2500, sse=771587.2, rms=1.546 (27.302%) 007: dt: 0.2500, sse=763052.4, rms=1.431 (7.441%) rms = 1.39, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=759725.8, rms=1.388 (3.004%) rms = 1.34, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=755610.2, rms=1.342 (3.348%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 53 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 206 points - only 0.00% unknown deleting segment 5 with 148 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 32 points - only 0.00% unknown deleting segment 9 with 34 points - only 0.00% unknown deleting segment 10 with 40 points - only 0.00% unknown mean border=89.2, 106 (41) missing vertices, mean dist -0.3 [0.5 (%69.2)->0.3 (%30.8))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dart, 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 (0.04-->7.81) (max @ vno 146172 --> 146264) face area 0.35 +- 0.18 (0.00-->8.67) mean absolute distance = 0.33 +- 0.49 5293 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1079607.0, rms=3.392 010: dt: 0.5000, sse=891653.0, rms=2.187 (35.524%) 011: dt: 0.5000, sse=856893.6, rms=1.881 (13.988%) 012: dt: 0.5000, sse=854892.8, rms=1.787 (4.994%) rms = 1.82, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=815732.5, rms=1.437 (19.603%) 014: dt: 0.2500, sse=802206.1, rms=1.263 (12.095%) 015: dt: 0.2500, sse=801421.9, rms=1.195 (5.404%) rms = 1.17, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=798418.4, rms=1.170 (2.049%) rms = 1.13, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=791988.9, rms=1.127 (3.707%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 61 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 216 points - only 0.00% unknown deleting segment 5 with 146 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown deleting segment 8 with 29 points - only 0.00% unknown deleting segment 9 with 37 points - only 0.00% unknown deleting segment 10 with 43 points - only 0.00% unknown mean border=91.0, 120 (24) missing vertices, mean dist -0.2 [0.4 (%70.3)->0.2 (%29.7))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dart, 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 (0.03-->7.97) (max @ vno 146172 --> 146264) face area 0.34 +- 0.18 (0.00-->8.61) mean absolute distance = 0.27 +- 0.40 4029 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=935749.4, rms=2.699 018: dt: 0.5000, sse=835999.2, rms=1.743 (35.419%) 019: dt: 0.5000, sse=811756.2, rms=1.624 (6.828%) rms = 1.64, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=783346.2, rms=1.282 (21.036%) 021: dt: 0.2500, sse=780943.6, rms=1.114 (13.166%) rms = 1.10, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=776376.0, rms=1.101 (1.142%) rms = 1.06, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=769514.6, rms=1.057 (3.967%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 8 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 42 points - only 0.00% unknown deleting segment 4 with 227 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 145 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 36 points - only 0.00% unknown deleting segment 11 with 32 points - only 0.00% unknown deleting segment 12 with 31 points - only 0.00% unknown mean border=91.7, 160 (19) missing vertices, mean dist -0.1 [0.3 (%58.2)->0.2 (%41.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dart, 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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=788374.3, rms=1.518 024: dt: 0.5000, sse=790061.9, rms=1.185 (21.970%) rms = 1.37, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=753695.7, rms=0.969 (18.218%) rms = 0.97, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=752172.6, rms=0.965 (0.392%) 027: dt: 0.1250, sse=768178.7, rms=0.890 (7.736%) rms = 0.88, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=739009.0, rms=0.877 (1.492%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 7722 vertices erasing segment 1 (vno[0] = 53250) erasing segment 2 (vno[0] = 54520) erasing segment 3 (vno[0] = 54786) erasing segment 4 (vno[0] = 91441) erasing segment 5 (vno[0] = 99275) erasing segment 6 (vno[0] = 100479) erasing segment 7 (vno[0] = 101568) erasing segment 8 (vno[0] = 102743) writing cortex label to /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label... writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.area vertex spacing 0.88 +- 0.27 (0.02-->8.16) (max @ vno 146172 --> 146264) face area 0.33 +- 0.18 (0.00-->8.35) 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 13 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 23 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 5 with 216 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 137 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 40 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown deleting segment 17 with 151 points - only 0.00% unknown deleting segment 18 with 16 points - only 0.00% unknown deleting segment 19 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 20 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=66.0, 192 (192) missing vertices, mean dist 1.7 [1.2 (%0.1)->2.9 (%99.9))] %17 local maxima, %38 large gradients and %40 min vals, 650 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= dart, 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=20673530.0, rms=26.583 001: dt: 0.0500, sse=18666756.0, rms=25.213 (5.156%) 002: dt: 0.0500, sse=17244550.0, rms=24.194 (4.039%) 003: dt: 0.0500, sse=16152950.0, rms=23.382 (3.356%) 004: dt: 0.0500, sse=15265414.0, rms=22.701 (2.915%) 005: dt: 0.0500, sse=14513885.0, rms=22.107 (2.615%) 006: dt: 0.0500, sse=13858376.0, rms=21.576 (2.403%) 007: dt: 0.0500, sse=13274454.0, rms=21.092 (2.245%) 008: dt: 0.0500, sse=12745805.0, rms=20.643 (2.126%) 009: dt: 0.0500, sse=12260813.0, rms=20.223 (2.036%) 010: dt: 0.0500, sse=11812715.0, rms=19.827 (1.959%) positioning took 0.8 minutes mean border=65.8, 172 (123) missing vertices, mean dist 1.4 [0.4 (%0.2)->2.4 (%99.8))] %18 local maxima, %38 large gradients and %40 min vals, 589 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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=12707935.0, rms=20.606 011: dt: 0.0500, sse=12286191.0, rms=20.241 (1.774%) 012: dt: 0.0500, sse=11891755.0, rms=19.893 (1.719%) 013: dt: 0.0500, sse=11521190.0, rms=19.560 (1.672%) 014: dt: 0.0500, sse=11173085.0, rms=19.242 (1.625%) 015: dt: 0.0500, sse=10844966.0, rms=18.938 (1.582%) 016: dt: 0.0500, sse=10535591.0, rms=18.646 (1.540%) 017: dt: 0.0500, sse=10243508.0, rms=18.366 (1.500%) 018: dt: 0.0500, sse=9966880.0, rms=18.097 (1.465%) 019: dt: 0.0500, sse=9704279.0, rms=17.838 (1.432%) 020: dt: 0.0500, sse=9454885.0, rms=17.588 (1.400%) positioning took 0.8 minutes mean border=65.6, 184 (97) missing vertices, mean dist 1.2 [0.1 (%1.3)->2.0 (%98.7))] %18 local maxima, %38 large gradients and %39 min vals, 604 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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=9578744.0, rms=17.715 021: dt: 0.0500, sse=9333913.0, rms=17.468 (1.394%) 022: dt: 0.0500, sse=9102514.0, rms=17.232 (1.355%) 023: dt: 0.0500, sse=8881303.0, rms=17.002 (1.331%) 024: dt: 0.0500, sse=8670504.0, rms=16.781 (1.303%) 025: dt: 0.0500, sse=8469179.0, rms=16.566 (1.278%) 026: dt: 0.0500, sse=8276395.5, rms=16.358 (1.256%) 027: dt: 0.0500, sse=8091498.0, rms=16.156 (1.236%) 028: dt: 0.0500, sse=7912969.0, rms=15.958 (1.224%) 029: dt: 0.0500, sse=7739965.5, rms=15.764 (1.216%) 030: dt: 0.0500, sse=7571689.0, rms=15.573 (1.212%) positioning took 0.8 minutes mean border=65.6, 199 (78) missing vertices, mean dist 1.0 [0.1 (%9.1)->1.9 (%90.9))] %19 local maxima, %38 large gradients and %39 min vals, 561 gradients ignored tol=1.0e-04, sigma=2.0, host= dart, 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=7652819.0, rms=15.664 031: dt: 0.5000, sse=6414473.5, rms=14.189 (9.418%) 032: dt: 0.5000, sse=5368286.5, rms=12.804 (9.755%) 033: dt: 0.5000, sse=4506117.0, rms=11.541 (9.864%) 034: dt: 0.5000, sse=3736089.2, rms=10.278 (10.943%) 035: dt: 0.5000, sse=3143116.5, rms=9.190 (10.593%) 036: dt: 0.5000, sse=2645490.0, rms=8.161 (11.195%) 037: dt: 0.5000, sse=2295024.8, rms=7.352 (9.905%) 038: dt: 0.5000, sse=2004034.4, rms=6.602 (10.201%) 039: dt: 0.5000, sse=1817090.4, rms=6.075 (7.989%) 040: dt: 0.5000, sse=1656815.9, rms=5.579 (8.156%) 041: dt: 0.5000, sse=1577240.8, rms=5.319 (4.670%) 042: dt: 0.5000, sse=1498625.5, rms=5.044 (5.174%) 043: dt: 0.5000, sse=1473304.1, rms=4.954 (1.780%) 044: dt: 0.5000, sse=1431404.5, rms=4.797 (3.167%) rms = 4.80, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1430478.6, rms=4.795 (0.037%) 046: dt: 0.2500, sse=1312960.9, rms=4.286 (10.627%) 047: dt: 0.2500, sse=1283702.2, rms=4.162 (2.881%) rms = 4.18, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1269880.5, rms=4.099 (1.507%) 049: dt: 0.1250, sse=1252665.9, rms=4.019 (1.971%) rms = 4.00, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1248455.4, rms=3.999 (0.495%) positioning took 2.2 minutes mean border=64.7, 2272 (48) missing vertices, mean dist 0.2 [0.2 (%48.3)->0.6 (%51.7))] %29 local maxima, %30 large gradients and %35 min vals, 268 gradients ignored tol=1.0e-04, sigma=1.0, host= dart, 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=1512821.2, rms=4.429 051: dt: 0.5000, sse=1483362.1, rms=4.320 (2.457%) 052: dt: 0.5000, sse=1371795.8, rms=3.852 (10.842%) rms = 4.16, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1273084.0, rms=3.320 (13.816%) 054: dt: 0.2500, sse=1248303.8, rms=3.167 (4.606%) rms = 3.23, time step reduction 2 of 3 to 0.125... 055: dt: 0.1250, sse=1235719.6, rms=3.090 (2.422%) 056: dt: 0.1250, sse=1221007.5, rms=2.997 (3.025%) rms = 2.96, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1214463.6, rms=2.956 (1.346%) positioning took 1.1 minutes mean border=64.0, 2846 (40) missing vertices, mean dist 0.1 [0.2 (%45.9)->0.5 (%54.1))] %38 local maxima, %22 large gradients and %34 min vals, 295 gradients ignored tol=1.0e-04, sigma=0.5, host= dart, 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=1267602.5, rms=3.297 rms = 3.71, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1232519.5, rms=3.095 (6.116%) 059: dt: 0.2500, sse=1219036.0, rms=3.017 (2.521%) rms = 3.07, time step reduction 2 of 3 to 0.125... rms = 2.98, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1213266.6, rms=2.981 (1.221%) positioning took 0.6 minutes mean border=63.5, 5491 (36) missing vertices, mean dist 0.1 [0.2 (%45.7)->0.4 (%54.3))] %42 local maxima, %17 large gradients and %33 min vals, 332 gradients ignored tol=1.0e-04, sigma=0.2, host= dart, 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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1233856.5, rms=3.100 rms = 3.47, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1210550.1, rms=2.959 (4.548%) 062: dt: 0.2500, sse=1196079.1, rms=2.883 (2.555%) rms = 2.93, time step reduction 2 of 3 to 0.125... rms = 2.85, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1190421.4, rms=2.845 (1.314%) positioning took 0.6 minutes writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.area.pial vertex spacing 0.99 +- 0.44 (0.08-->6.84) (max @ vno 90744 --> 89619) face area 0.39 +- 0.32 (0.00-->8.39) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147894 vertices processed 25000 of 147894 vertices processed 50000 of 147894 vertices processed 75000 of 147894 vertices processed 100000 of 147894 vertices processed 125000 of 147894 vertices processed 0 of 147894 vertices processed 25000 of 147894 vertices processed 50000 of 147894 vertices processed 75000 of 147894 vertices processed 100000 of 147894 vertices processed 125000 of 147894 vertices processed thickness calculation complete, 685:1399 truncations. 39405 vertices at 0 distance 104076 vertices at 1 distance 81606 vertices at 2 distance 36145 vertices at 3 distance 13561 vertices at 4 distance 5024 vertices at 5 distance 1768 vertices at 6 distance 623 vertices at 7 distance 254 vertices at 8 distance 126 vertices at 9 distance 80 vertices at 10 distance 73 vertices at 11 distance 49 vertices at 12 distance 38 vertices at 13 distance 19 vertices at 14 distance 7 vertices at 15 distance 8 vertices at 16 distance 8 vertices at 17 distance 13 vertices at 18 distance 13 vertices at 19 distance 28 vertices at 20 distance writing curvature file /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.thickness positioning took 13.0 minutes #-------------------------------------------- #@# Surf Volume lh Fri Aug 17 19:13:42 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/surf /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip lh /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.volume masking with /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label Total face volume 255233 Total vertex volume 251778 (mask=0) #@# SubJ01_ReoT13THip lh 251778 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fri Aug 17 19:13:44 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/surf /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip rh /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.volume masking with /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label Total face volume 263885 Total vertex volume 260302 (mask=0) #@# SubJ01_ReoT13THip rh 260302 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fri Aug 17 19:13:47 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip SUBJECTS_DIR is /home/shize/freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 378 writing volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/ribbon.mgz mris_volmask took 8.06 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fri Aug 17 19:21:50 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 255233 Total vertex volume 251778 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1858 1348 2342 1.877 0.600 0.113 0.023 13 2.2 bankssts 927 621 2292 3.120 0.722 0.111 0.020 12 0.8 caudalanteriorcingulate 4263 2702 7456 2.776 0.689 0.113 0.028 34 5.1 caudalmiddlefrontal 2093 1416 2929 1.905 0.479 0.147 0.040 32 3.7 cuneus 795 501 2237 3.209 1.072 0.099 0.027 6 0.9 entorhinal 4546 3108 10149 2.877 0.644 0.128 0.033 61 6.1 fusiform 6719 4188 11105 2.490 0.536 0.119 0.029 79 8.3 inferiorparietal 4950 3491 10539 2.631 0.793 0.135 0.041 74 8.8 inferiortemporal 1411 910 2805 2.677 0.956 0.127 0.029 20 1.6 isthmuscingulate 7265 4455 10121 2.097 0.488 0.137 0.035 98 10.5 lateraloccipital 3741 2527 8493 2.931 0.845 0.131 0.048 63 7.3 lateralorbitofrontal 3433 2307 5624 2.244 0.602 0.130 0.035 45 4.7 lingual 2675 1818 5678 2.769 0.893 0.127 0.033 40 3.4 medialorbitofrontal 4552 3568 9308 2.415 0.799 0.142 0.038 64 7.9 middletemporal 1213 780 2515 2.784 0.635 0.079 0.015 5 0.7 parahippocampal 2010 1214 3427 2.720 0.553 0.100 0.018 15 1.5 paracentral 2657 1759 4471 2.373 0.710 0.118 0.030 28 3.5 parsopercularis 910 616 2392 2.729 0.754 0.142 0.062 17 2.1 parsorbitalis 2641 1649 5189 2.806 0.592 0.128 0.041 36 4.5 parstriangularis 1468 980 1541 1.670 0.483 0.126 0.031 15 1.8 pericalcarine 5863 3880 7823 1.938 0.647 0.106 0.023 45 5.7 postcentral 1649 1169 4047 3.107 0.732 0.131 0.026 23 1.6 posteriorcingulate 8496 5505 15166 2.747 0.758 0.113 0.028 66 10.0 precentral 6135 4209 12561 2.716 0.614 0.128 0.027 75 6.6 precuneus 1233 782 3017 3.043 1.090 0.111 0.036 14 1.8 rostralanteriorcingulate 10030 6466 17084 2.466 0.608 0.133 0.041 122 17.5 rostralmiddlefrontal 10292 6597 24137 3.238 0.717 0.120 0.040 122 17.4 superiorfrontal 9050 5656 14993 2.419 0.541 0.107 0.024 84 8.1 superiorparietal 8108 5567 13527 2.348 0.807 0.121 0.029 79 10.7 superiortemporal 9734 6228 15005 2.344 0.712 0.123 0.036 107 15.3 supramarginal 278 184 982 3.560 0.659 0.174 0.052 5 0.5 frontalpole 855 563 2558 3.344 0.714 0.118 0.043 11 1.3 temporalpole 987 690 1840 2.296 0.492 0.131 0.032 11 1.1 transversetemporal 3898 2661 8397 3.213 0.862 0.115 0.027 32 3.9 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 SubJ01_ReoT13THip lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 255233 Total vertex volume 251778 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1858 1256 2342 1.877 0.600 0.105 0.022 21 1.9 bankssts 927 871 2292 3.120 0.722 0.162 0.042 18 1.4 caudalanteriorcingulate 4263 2850 7456 2.776 0.689 0.107 0.024 51 4.8 caudalmiddlefrontal 2093 1737 2929 1.905 0.479 0.156 0.035 32 3.5 cuneus 795 928 2237 3.209 1.072 0.160 0.034 7 1.3 entorhinal 4546 3858 10149 2.877 0.644 0.146 0.035 62 7.3 fusiform 6719 4670 11105 2.490 0.536 0.122 0.027 88 7.5 inferiorparietal 4950 4294 10539 2.631 0.793 0.142 0.037 78 8.5 inferiortemporal 1411 1120 2805 2.677 0.956 0.139 0.030 26 1.7 isthmuscingulate 7265 5268 10121 2.097 0.488 0.127 0.029 85 9.7 lateraloccipital 3741 3022 8493 2.931 0.845 0.143 0.039 72 6.5 lateralorbitofrontal 3433 2819 5624 2.244 0.602 0.140 0.032 53 5.2 lingual 2675 2339 5678 2.769 0.893 0.144 0.032 32 3.9 medialorbitofrontal 4552 4207 9308 2.415 0.799 0.131 0.029 64 6.4 middletemporal 1213 1050 2515 2.784 0.635 0.116 0.024 7 1.4 parahippocampal 2010 1324 3427 2.720 0.553 0.108 0.023 39 1.9 paracentral 2657 1996 4471 2.373 0.710 0.121 0.030 29 3.4 parsopercularis 910 1023 2392 2.729 0.754 0.179 0.039 11 1.6 parsorbitalis 2641 1961 5189 2.806 0.592 0.132 0.031 48 4.0 parstriangularis 1468 893 1541 1.670 0.483 0.118 0.033 23 1.9 pericalcarine 5863 4500 7823 1.938 0.647 0.110 0.021 43 5.7 postcentral 1649 1453 4047 3.107 0.732 0.153 0.032 33 2.1 posteriorcingulate 8496 5777 15166 2.747 0.758 0.105 0.023 97 8.8 precentral 6135 4899 12561 2.716 0.614 0.143 0.031 252 8.2 precuneus 1233 1068 3017 3.043 1.090 0.156 0.037 18 2.0 rostralanteriorcingulate 10030 7425 17084 2.466 0.608 0.127 0.031 123 14.5 rostralmiddlefrontal 10292 7972 24137 3.238 0.717 0.122 0.031 121 13.5 superiorfrontal 9050 6562 14993 2.419 0.541 0.114 0.022 99 8.6 superiorparietal 8108 6031 13527 2.348 0.807 0.114 0.028 122 10.1 superiortemporal 9734 6817 15005 2.344 0.712 0.117 0.030 117 12.4 supramarginal 278 344 982 3.560 0.659 0.192 0.035 3 0.5 frontalpole 855 954 2558 3.344 0.714 0.152 0.030 6 1.2 temporalpole 987 950 1840 2.296 0.492 0.136 0.024 6 1.1 transversetemporal 3898 2283 8397 3.213 0.862 0.110 0.029 70 4.5 insula #----------------------------------------- #@# Parcellation Stats rh Fri Aug 17 19:22:49 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 263885 Total vertex volume 260302 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1518 1201 2269 2.066 0.710 0.130 0.025 12 1.9 bankssts 856 542 1817 3.019 0.772 0.109 0.016 9 0.6 caudalanteriorcingulate 3074 1974 5569 2.757 0.546 0.113 0.029 26 3.8 caudalmiddlefrontal 2640 1754 3624 1.966 0.497 0.169 0.045 47 5.0 cuneus 596 397 2321 3.845 0.712 0.124 0.055 8 1.3 entorhinal 5108 3479 11571 2.958 0.667 0.128 0.029 60 6.0 fusiform 8055 5379 13771 2.448 0.581 0.119 0.026 93 8.6 inferiorparietal 4983 3428 10259 2.590 0.858 0.142 0.039 81 8.9 inferiortemporal 1426 891 2766 2.557 1.109 0.113 0.026 18 1.2 isthmuscingulate 9090 5801 15190 2.328 0.577 0.130 0.029 111 10.6 lateraloccipital 4408 3003 9017 2.786 0.730 0.137 0.045 64 8.7 lateralorbitofrontal 4412 3035 7275 2.225 0.666 0.145 0.037 60 6.7 lingual 2824 1886 6146 2.735 0.750 0.131 0.037 42 4.4 medialorbitofrontal 5843 4081 9995 2.218 0.787 0.127 0.034 75 8.9 middletemporal 1052 659 2099 2.772 0.620 0.078 0.015 5 0.5 parahippocampal 2494 1508 4639 2.880 0.555 0.112 0.026 22 2.8 paracentral 1991 1334 3569 2.535 0.627 0.113 0.026 21 2.3 parsopercularis 1341 887 3478 2.740 0.853 0.134 0.037 20 1.9 parsorbitalis 2772 1765 5518 2.640 0.569 0.124 0.028 45 3.2 parstriangularis 1889 1326 2002 1.680 0.430 0.135 0.031 19 2.3 pericalcarine 5965 3683 7777 1.970 0.650 0.106 0.024 50 5.9 postcentral 1817 1289 4672 3.005 0.846 0.148 0.037 29 2.6 posteriorcingulate 8031 4872 13364 2.610 0.646 0.112 0.029 75 10.2 precentral 6050 4122 12145 2.810 0.530 0.133 0.029 77 7.4 precuneus 960 610 2039 2.936 0.709 0.109 0.019 10 0.8 rostralanteriorcingulate 11345 7142 19599 2.425 0.633 0.127 0.037 162 17.9 rostralmiddlefrontal 10710 6806 25572 3.233 0.703 0.116 0.031 120 13.4 superiorfrontal 10168 6442 18141 2.505 0.527 0.123 0.029 118 11.8 superiorparietal 6928 4717 12008 2.346 0.784 0.113 0.025 65 7.7 superiortemporal 6120 3945 9268 2.311 0.683 0.127 0.032 81 8.4 supramarginal 387 255 886 2.523 0.948 0.162 0.045 8 0.7 frontalpole 679 460 2390 3.357 0.720 0.124 0.038 9 1.0 temporalpole 531 342 948 2.379 0.351 0.101 0.015 6 0.3 transversetemporal 3593 2451 8498 3.560 0.681 0.115 0.026 33 3.7 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 SubJ01_ReoT13THip rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 263885 Total vertex volume 260302 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1518 1186 2269 2.066 0.710 0.125 0.032 15 2.3 bankssts 856 723 1817 3.019 0.772 0.130 0.027 10 1.2 caudalanteriorcingulate 3074 2076 5569 2.757 0.546 0.107 0.027 31 3.3 caudalmiddlefrontal 2640 2004 3624 1.966 0.497 0.145 0.034 38 4.0 cuneus 596 773 2321 3.845 0.712 0.191 0.047 8 1.4 entorhinal 5108 4275 11571 2.958 0.667 0.144 0.035 69 8.3 fusiform 8055 5799 13771 2.448 0.581 0.120 0.027 92 10.2 inferiorparietal 4983 4301 10259 2.590 0.858 0.144 0.035 64 8.3 inferiortemporal 1426 1130 2766 2.557 1.109 0.126 0.030 20 1.8 isthmuscingulate 9090 7188 15190 2.328 0.577 0.129 0.028 113 11.1 lateraloccipital 4408 3488 9017 2.786 0.730 0.139 0.037 81 7.7 lateralorbitofrontal 4412 3580 7275 2.225 0.666 0.131 0.031 60 6.2 lingual 2824 2552 6146 2.735 0.750 0.153 0.038 34 4.8 medialorbitofrontal 5843 5084 9995 2.218 0.787 0.125 0.028 57 7.8 middletemporal 1052 836 2099 2.772 0.620 0.105 0.021 6 1.0 parahippocampal 2494 1725 4639 2.880 0.555 0.111 0.024 638 2.4 paracentral 1991 1473 3569 2.535 0.627 0.119 0.025 21 2.4 parsopercularis 1341 1495 3478 2.740 0.853 0.178 0.033 19 2.0 parsorbitalis 2772 2380 5518 2.640 0.569 0.146 0.027 32 3.5 parstriangularis 1889 1173 2002 1.680 0.430 0.113 0.029 23 2.3 pericalcarine 5965 4316 7777 1.970 0.650 0.111 0.023 48 5.9 postcentral 1817 1625 4672 3.005 0.846 0.153 0.032 39 2.6 posteriorcingulate 8031 5333 13364 2.610 0.646 0.100 0.024 96 9.0 precentral 6050 4472 12145 2.810 0.530 0.130 0.030 85 8.1 precuneus 960 779 2039 2.936 0.709 0.161 0.091 49 5.7 rostralanteriorcingulate 11345 8737 19599 2.425 0.633 0.137 0.031 130 16.7 rostralmiddlefrontal 10710 8732 25572 3.233 0.703 0.132 0.031 158 15.4 superiorfrontal 10168 7984 18141 2.505 0.527 0.130 0.029 133 12.9 superiorparietal 6928 5379 12008 2.346 0.784 0.118 0.024 80 7.1 superiortemporal 6120 4231 9268 2.311 0.683 0.116 0.028 69 7.3 supramarginal 387 422 886 2.523 0.948 0.212 0.044 5 1.0 frontalpole 679 901 2390 3.357 0.720 0.193 0.038 7 1.3 temporalpole 531 450 948 2.379 0.351 0.105 0.019 3 0.4 transversetemporal 3593 2191 8498 3.560 0.681 0.114 0.028 51 4.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Aug 17 19:23:48 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SubJ01_ReoT13THip lh ../surf/lh.sphere.reg /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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... 7 labels changed using aseg relabeling using gibbs priors... 000: 9205 changed, 145018 examined... 001: 2143 changed, 35945 examined... 002: 641 changed, 11236 examined... 003: 263 changed, 3620 examined... 004: 122 changed, 1485 examined... 005: 63 changed, 697 examined... 006: 44 changed, 368 examined... 007: 18 changed, 227 examined... 008: 9 changed, 110 examined... 009: 2 changed, 56 examined... 010: 4 changed, 14 examined... 011: 3 changed, 19 examined... 012: 1 changed, 21 examined... 013: 1 changed, 5 examined... 014: 2 changed, 6 examined... 015: 0 changed, 8 examined... 0 labels changed using aseg 000: 237 total segments, 151 labels (2164 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, 30 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1112 vertices marked for relabeling... 1112 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Fri Aug 17 19:24:03 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SubJ01_ReoT13THip rh ../surf/rh.sphere.reg /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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... 16 labels changed using aseg relabeling using gibbs priors... 000: 9454 changed, 147894 examined... 001: 2227 changed, 37151 examined... 002: 644 changed, 11691 examined... 003: 244 changed, 3639 examined... 004: 125 changed, 1495 examined... 005: 81 changed, 741 examined... 006: 51 changed, 461 examined... 007: 36 changed, 252 examined... 008: 16 changed, 196 examined... 009: 8 changed, 87 examined... 010: 5 changed, 51 examined... 011: 5 changed, 32 examined... 012: 2 changed, 27 examined... 013: 1 changed, 12 examined... 014: 2 changed, 6 examined... 015: 0 changed, 10 examined... 7 labels changed using aseg 000: 290 total segments, 203 labels (3027 vertices) changed 001: 110 total segments, 23 labels (136 vertices) changed 002: 90 total segments, 3 labels (20 vertices) changed 003: 87 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... 1109 vertices marked for relabeling... 1109 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Aug 17 19:24:18 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 255233 Total vertex volume 251778 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1175 809 2427 2.671 0.789 0.160 0.054 19 2.9 G&S_frontomargin 1399 868 2207 2.258 0.582 0.135 0.031 17 1.7 G&S_occipital_inf 1634 903 2696 2.450 0.617 0.108 0.030 18 2.0 G&S_paracentral 1737 1169 2979 2.266 0.843 0.126 0.031 17 2.5 G&S_subcentral 758 511 2346 3.078 0.745 0.164 0.054 14 1.6 G&S_transv_frontopol 2062 1414 5070 3.183 0.756 0.110 0.029 18 2.4 G&S_cingul-Ant 1331 943 3031 3.096 0.584 0.116 0.022 15 1.2 G&S_cingul-Mid-Ant 1188 862 2740 3.095 0.542 0.114 0.023 12 1.0 G&S_cingul-Mid-Post 675 441 2302 3.592 0.628 0.154 0.038 13 0.9 G_cingul-Post-dorsal 245 162 611 3.302 0.693 0.148 0.036 4 0.3 G_cingul-Post-ventral 1964 1258 2937 1.935 0.555 0.152 0.044 35 3.6 G_cuneus 1308 883 2758 2.464 0.839 0.132 0.040 18 2.1 G_front_inf-Opercular 395 269 1234 3.131 0.574 0.152 0.049 8 0.6 G_front_inf-Orbital 1954 1121 3861 2.751 0.643 0.133 0.049 32 4.2 G_front_inf-Triangul 6000 3489 10608 2.490 0.727 0.137 0.046 90 12.8 G_front_middle 7033 4313 17834 3.310 0.758 0.127 0.046 94 13.7 G_front_sup 538 391 1424 3.452 0.749 0.132 0.025 6 0.4 G_Ins_lg&S_cent_ins 948 613 2779 3.351 1.058 0.123 0.036 11 1.4 G_insular_short 2243 1189 3671 2.357 0.504 0.124 0.039 33 3.4 G_occipital_middle 1452 936 2474 2.291 0.528 0.138 0.030 18 1.7 G_occipital_sup 1806 1223 4714 2.869 0.622 0.138 0.038 31 2.8 G_oc-temp_lat-fusifor 2320 1515 4250 2.334 0.582 0.144 0.043 36 4.1 G_oc-temp_med-Lingual 1494 948 3923 3.072 0.958 0.091 0.021 9 1.2 G_oc-temp_med-Parahip 2531 1635 6730 2.831 0.810 0.154 0.079 63 8.2 G_orbital 2870 1614 5505 2.574 0.663 0.123 0.042 44 4.9 G_pariet_inf-Angular 5037 3136 7338 2.134 0.771 0.135 0.045 68 9.9 G_pariet_inf-Supramar 3522 2005 6318 2.501 0.590 0.113 0.030 44 4.2 G_parietal_sup 2202 1244 2755 1.927 0.606 0.101 0.028 20 2.4 G_postcentral 3319 1859 5956 2.743 0.906 0.109 0.034 29 4.6 G_precentral 3222 2116 8016 2.829 0.616 0.140 0.035 53 4.1 G_precuneus 948 609 2375 2.712 0.887 0.153 0.046 23 1.9 G_rectus 876 585 1821 3.304 1.224 0.110 0.037 8 0.9 G_subcallosal 936 644 1761 2.318 0.518 0.141 0.036 11 1.4 G_temp_sup-G_T_transv 2828 1738 4448 2.127 0.932 0.131 0.040 30 4.9 G_temp_sup-Lateral 881 591 2181 3.052 0.824 0.079 0.017 4 0.6 G_temp_sup-Plan_polar 1439 1018 2352 2.329 0.650 0.119 0.031 11 2.2 G_temp_sup-Plan_tempo 2691 1869 6985 2.713 0.904 0.153 0.056 56 6.5 G_temporal_inf 2897 2075 5619 2.344 0.848 0.139 0.041 47 5.4 G_temporal_middle 266 195 492 2.626 0.378 0.115 0.020 2 0.2 Lat_Fis-ant-Horizont 431 299 582 2.395 0.719 0.108 0.012 2 0.3 Lat_Fis-ant-Vertical 1429 1029 2273 2.771 0.605 0.118 0.023 11 1.2 Lat_Fis-post 2104 1255 2745 1.930 0.459 0.154 0.044 38 3.8 Pole_occipital 1984 1370 5893 3.116 0.779 0.142 0.048 35 3.8 Pole_temporal 1826 1272 2157 1.875 0.691 0.120 0.027 17 2.0 S_calcarine 2715 2194 3989 2.065 0.712 0.120 0.021 18 2.3 S_central 1162 831 2023 2.635 0.427 0.095 0.013 5 0.7 S_cingul-Marginalis 539 369 891 3.046 0.528 0.090 0.013 2 0.3 S_circular_insula_ant 2487 1872 4763 2.815 0.689 0.117 0.023 25 2.5 S_circular_insula_inf 1700 1165 2556 2.794 0.488 0.107 0.019 9 1.3 S_circular_insula_sup 1068 734 2032 3.179 0.773 0.122 0.032 10 1.4 S_collat_transv_ant 409 281 433 2.033 0.366 0.130 0.027 3 0.5 S_collat_transv_post 3130 2075 4433 2.474 0.561 0.106 0.023 21 2.8 S_front_inf 1673 1186 2616 2.569 0.433 0.114 0.027 13 1.7 S_front_middle 2712 1817 4698 2.862 0.585 0.098 0.021 14 2.1 S_front_sup 637 447 855 2.511 0.399 0.115 0.021 4 0.7 S_interm_prim-Jensen 3611 2411 5376 2.411 0.483 0.102 0.018 26 2.7 S_intrapariet&P_trans 1000 671 1099 1.965 0.376 0.115 0.018 7 0.8 S_oc_middle&Lunatus 1243 857 1693 2.223 0.395 0.117 0.023 9 1.4 S_oc_sup&transversal 570 392 809 2.263 0.393 0.116 0.017 5 0.4 S_occipital_ant 865 622 1430 2.611 0.373 0.101 0.018 5 0.6 S_oc-temp_lat 2188 1482 3280 2.520 0.564 0.099 0.017 13 1.4 S_oc-temp_med&Lingual 425 310 620 2.265 0.632 0.125 0.022 3 0.5 S_orbital_lateral 533 403 974 3.004 0.888 0.121 0.020 4 0.4 S_orbital_med-olfact 1238 851 2515 2.857 0.969 0.110 0.026 12 1.2 S_orbital-H_Shaped 2119 1487 3179 2.464 0.649 0.116 0.022 15 2.0 S_parieto_occipital 1115 651 1177 2.266 0.894 0.094 0.017 12 0.6 S_pericallosal 3655 2380 5159 2.370 0.549 0.098 0.018 22 2.5 S_postcentral 2062 1431 3422 2.671 0.542 0.102 0.022 13 1.8 S_precentral-inf-part 1760 1212 3250 3.208 0.480 0.108 0.019 11 1.4 S_precentral-sup-part 833 564 1385 2.586 0.827 0.130 0.026 10 0.8 S_suborbital 1264 918 2108 2.599 0.491 0.125 0.023 14 1.3 S_subparietal 1474 1049 1925 2.322 0.471 0.113 0.020 10 1.4 S_temporal_inf 6011 4651 9209 2.200 0.573 0.120 0.023 49 6.6 S_temporal_sup 638 405 697 2.046 0.416 0.097 0.012 4 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Fri Aug 17 19:24:48 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 263885 Total vertex volume 260302 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1047 704 1739 2.096 0.684 0.154 0.049 19 2.2 G&S_frontomargin 1656 1090 3740 2.791 0.615 0.126 0.027 21 1.7 G&S_occipital_inf 1719 963 3154 2.726 0.680 0.111 0.028 16 2.0 G&S_paracentral 1831 1122 3144 2.457 0.738 0.130 0.033 22 2.8 G&S_subcentral 1098 711 2819 3.058 0.773 0.163 0.060 21 2.7 G&S_transv_frontopol 2956 2017 5964 2.863 0.674 0.109 0.021 23 2.5 G&S_cingul-Ant 1305 941 2769 3.051 0.489 0.108 0.015 9 0.8 G&S_cingul-Mid-Ant 1419 1016 3638 3.210 0.484 0.134 0.029 17 1.6 G&S_cingul-Mid-Post 596 341 2048 3.518 0.865 0.158 0.060 15 1.4 G_cingul-Post-dorsal 296 177 881 3.117 0.751 0.120 0.031 4 0.3 G_cingul-Post-ventral 2384 1574 3245 1.897 0.523 0.165 0.043 41 4.4 G_cuneus 1273 812 2892 2.802 0.658 0.125 0.032 21 1.9 G_front_inf-Opercular 605 381 1471 2.848 0.540 0.145 0.034 12 0.8 G_front_inf-Orbital 1336 746 2656 2.699 0.550 0.134 0.037 31 2.0 G_front_inf-Triangul 4825 2782 9859 2.675 0.657 0.130 0.043 79 8.6 G_front_middle 7168 4185 18965 3.390 0.703 0.119 0.036 100 10.6 G_front_sup 684 458 1799 3.701 0.728 0.120 0.031 9 0.8 G_Ins_lg&S_cent_ins 807 523 2639 3.988 0.642 0.121 0.034 11 1.1 G_insular_short 2354 1378 4418 2.437 0.563 0.132 0.039 38 3.5 G_occipital_middle 2285 1400 3888 2.332 0.542 0.129 0.032 31 3.0 G_occipital_sup 2409 1566 6202 3.096 0.683 0.140 0.034 41 3.3 G_oc-temp_lat-fusifor 2787 1906 4905 2.146 0.674 0.147 0.042 38 4.9 G_oc-temp_med-Lingual 1353 831 4099 3.417 0.819 0.100 0.035 12 1.8 G_oc-temp_med-Parahip 3071 2024 8044 2.853 0.762 0.148 0.057 62 7.4 G_orbital 3178 1973 6188 2.355 0.719 0.134 0.038 57 5.2 G_pariet_inf-Angular 2873 1787 4889 2.417 0.708 0.139 0.040 47 4.9 G_pariet_inf-Supramar 3069 1862 6261 2.634 0.499 0.131 0.034 42 4.2 G_parietal_sup 2034 1125 2750 1.955 0.545 0.103 0.028 20 2.3 G_postcentral 3257 1711 5480 2.597 0.710 0.114 0.037 36 5.3 G_precentral 2640 1718 6491 2.887 0.545 0.146 0.037 48 4.0 G_precuneus 946 621 2528 2.587 0.811 0.158 0.056 23 2.4 G_rectus 210 129 475 3.146 0.872 0.112 0.049 3 0.2 G_subcallosal 518 328 978 2.370 0.408 0.096 0.012 6 0.3 G_temp_sup-G_T_transv 2736 1833 5186 2.252 1.028 0.143 0.037 38 4.7 G_temp_sup-Lateral 1070 794 2548 3.156 0.811 0.119 0.039 8 2.1 G_temp_sup-Plan_polar 1104 707 1306 1.857 0.511 0.097 0.021 7 1.2 G_temp_sup-Plan_tempo 2811 1841 6275 2.587 0.922 0.154 0.051 64 6.6 G_temporal_inf 3332 2254 5574 2.161 0.801 0.155 0.049 61 7.7 G_temporal_middle 274 193 492 2.592 0.479 0.095 0.010 1 0.1 Lat_Fis-ant-Horizont 280 212 417 2.255 0.438 0.102 0.012 1 0.1 Lat_Fis-ant-Vertical 1486 1022 2069 2.539 0.765 0.104 0.016 10 1.0 Lat_Fis-post 3835 2472 5912 2.126 0.565 0.144 0.034 54 5.1 Pole_occipital 1780 1279 6242 3.032 0.926 0.147 0.038 26 2.8 Pole_temporal 1985 1401 2545 2.084 0.778 0.134 0.027 21 2.1 S_calcarine 2603 1788 2920 1.900 0.557 0.094 0.016 12 1.6 S_central 1209 881 2185 2.755 0.394 0.112 0.018 9 0.9 S_cingul-Marginalis 695 468 1030 2.785 0.647 0.093 0.014 3 0.4 S_circular_insula_ant 1387 938 2248 2.877 0.488 0.074 0.009 3 0.5 S_circular_insula_inf 1329 924 2485 3.341 0.433 0.112 0.021 7 1.2 S_circular_insula_sup 941 646 1658 2.803 0.808 0.103 0.019 6 0.6 S_collat_transv_ant 494 354 675 2.456 0.483 0.117 0.024 3 0.5 S_collat_transv_post 2573 1719 3804 2.376 0.464 0.091 0.016 14 1.7 S_front_inf 3298 2163 4927 2.273 0.604 0.125 0.034 41 4.9 S_front_middle 2659 1806 4406 2.663 0.549 0.103 0.022 18 2.3 S_front_sup 552 362 690 2.207 0.477 0.131 0.027 6 0.7 S_interm_prim-Jensen 4419 2940 6727 2.455 0.434 0.104 0.020 32 3.7 S_intrapariet&P_trans 1107 755 1290 2.063 0.309 0.122 0.023 9 1.1 S_oc_middle&Lunatus 2029 1337 3327 2.404 0.593 0.128 0.028 24 2.1 S_oc_sup&transversal 795 545 1143 2.331 0.421 0.099 0.016 4 0.5 S_occipital_ant 1199 840 1967 2.706 0.404 0.117 0.021 9 1.1 S_oc-temp_lat 2266 1595 3482 2.595 0.555 0.103 0.016 14 1.4 S_oc-temp_med&Lingual 692 475 1187 2.237 0.706 0.123 0.028 6 0.8 S_orbital_lateral 731 517 1182 2.772 0.701 0.105 0.017 4 0.4 S_orbital_med-olfact 1408 957 2633 2.645 0.782 0.130 0.031 18 2.0 S_orbital-H_Shaped 2456 1669 3873 2.606 0.547 0.128 0.027 24 2.7 S_parieto_occipital 1468 940 1555 2.175 1.004 0.114 0.020 18 0.9 S_pericallosal 2695 1804 3378 2.143 0.510 0.116 0.022 23 2.4 S_postcentral 1799 1304 3024 2.481 0.526 0.117 0.026 15 2.2 S_precentral-inf-part 1828 1227 2983 2.753 0.443 0.110 0.017 14 1.3 S_precentral-sup-part 267 201 534 3.131 0.488 0.152 0.034 2 0.4 S_suborbital 1244 902 2215 2.824 0.487 0.126 0.024 11 1.2 S_subparietal 1327 967 1922 2.404 0.810 0.113 0.019 9 1.1 S_temporal_inf 7227 5345 10904 2.302 0.567 0.111 0.019 53 6.1 S_temporal_sup 319 220 367 1.882 0.297 0.096 0.009 2 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Aug 17 19:25:18 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SubJ01_ReoT13THip lh ../surf/lh.sphere.reg /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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... 1330 labels changed using aseg relabeling using gibbs priors... 000: 2095 changed, 145018 examined... 001: 500 changed, 9473 examined... 002: 144 changed, 2843 examined... 003: 52 changed, 808 examined... 004: 25 changed, 309 examined... 005: 20 changed, 144 examined... 006: 12 changed, 109 examined... 007: 15 changed, 70 examined... 008: 11 changed, 69 examined... 009: 10 changed, 65 examined... 010: 6 changed, 55 examined... 011: 4 changed, 30 examined... 012: 4 changed, 24 examined... 013: 1 changed, 23 examined... 014: 2 changed, 6 examined... 015: 5 changed, 11 examined... 016: 3 changed, 21 examined... 017: 2 changed, 16 examined... 018: 3 changed, 12 examined... 019: 3 changed, 15 examined... 020: 3 changed, 14 examined... 021: 2 changed, 14 examined... 022: 0 changed, 13 examined... 265 labels changed using aseg 000: 64 total segments, 31 labels (284 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 774 vertices marked for relabeling... 774 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Fri Aug 17 19:25:30 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SubJ01_ReoT13THip rh ../surf/rh.sphere.reg /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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... 1317 labels changed using aseg relabeling using gibbs priors... 000: 2099 changed, 147894 examined... 001: 475 changed, 9594 examined... 002: 133 changed, 2719 examined... 003: 64 changed, 794 examined... 004: 39 changed, 361 examined... 005: 30 changed, 232 examined... 006: 15 changed, 149 examined... 007: 11 changed, 88 examined... 008: 7 changed, 59 examined... 009: 6 changed, 44 examined... 010: 7 changed, 37 examined... 011: 5 changed, 39 examined... 012: 4 changed, 35 examined... 013: 2 changed, 23 examined... 014: 2 changed, 12 examined... 015: 0 changed, 14 examined... 235 labels changed using aseg 000: 55 total segments, 22 labels (262 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 851 vertices marked for relabeling... 851 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Aug 17 19:25:41 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 255233 Total vertex volume 251778 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1358 936 3121 3.131 0.629 0.113 0.022 16 1.1 caudalanteriorcingulate 4611 2925 7980 2.770 0.680 0.113 0.029 37 5.5 caudalmiddlefrontal 2884 1937 4261 2.020 0.519 0.140 0.036 40 4.5 cuneus 716 446 2011 3.186 1.104 0.093 0.025 5 0.7 entorhinal 3999 2742 8433 2.848 0.622 0.124 0.030 48 4.8 fusiform 6941 4271 11588 2.515 0.551 0.116 0.029 80 8.3 inferiorparietal 5107 3569 11901 2.750 0.819 0.141 0.044 84 9.6 inferiortemporal 1407 908 2795 2.682 0.950 0.127 0.029 19 1.6 isthmuscingulate 7434 4566 10341 2.084 0.482 0.137 0.035 100 10.6 lateraloccipital 4181 2839 9723 2.957 0.923 0.141 0.056 76 9.6 lateralorbitofrontal 3526 2370 5748 2.244 0.602 0.133 0.036 47 5.0 lingual 2231 1491 4888 2.798 0.899 0.131 0.036 36 3.2 medialorbitofrontal 6171 4771 11471 2.294 0.774 0.134 0.034 76 9.7 middletemporal 1280 818 2618 2.766 0.645 0.079 0.015 5 0.7 parahippocampal 2356 1400 4230 2.776 0.557 0.097 0.019 17 1.7 paracentral 2394 1620 4040 2.373 0.720 0.119 0.030 26 3.1 parsopercularis 878 598 1961 2.726 0.615 0.124 0.040 11 1.1 parsorbitalis 3506 2196 6479 2.678 0.618 0.127 0.039 44 5.8 parstriangularis 1412 952 1482 1.667 0.469 0.124 0.031 14 1.7 pericalcarine 6870 4536 9546 2.026 0.669 0.110 0.024 55 6.9 postcentral 1800 1280 4317 3.077 0.723 0.130 0.025 24 1.7 posteriorcingulate 8376 5398 14914 2.738 0.754 0.114 0.028 67 9.9 precentral 5999 4116 12582 2.734 0.603 0.128 0.028 75 6.4 precuneus 1556 1009 3622 2.995 1.034 0.111 0.032 16 2.1 rostralanteriorcingulate 6999 4462 11764 2.469 0.624 0.129 0.038 83 11.7 rostralmiddlefrontal 11829 7646 27402 3.120 0.766 0.125 0.041 147 20.7 superiorfrontal 7411 4563 11989 2.407 0.546 0.103 0.023 66 6.6 superiorparietal 10303 7048 18122 2.423 0.843 0.118 0.029 99 13.2 superiortemporal 8931 5763 13462 2.328 0.720 0.126 0.037 100 14.6 supramarginal 998 695 1824 2.284 0.492 0.131 0.032 11 1.1 transversetemporal 3270 2237 7163 3.187 0.834 0.113 0.025 26 3.3 insula #----------------------------------------- #@# Parcellation Stats 3 rh Fri Aug 17 19:26:10 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 263885 Total vertex volume 260302 (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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 940 596 1934 2.988 0.774 0.109 0.016 9 0.6 caudalanteriorcingulate 3283 2106 5945 2.746 0.552 0.116 0.030 29 4.4 caudalmiddlefrontal 3156 2091 4429 2.026 0.514 0.162 0.042 53 5.6 cuneus 554 370 2208 3.864 0.732 0.125 0.055 7 1.2 entorhinal 4715 3200 10266 2.957 0.650 0.127 0.029 56 5.4 fusiform 7937 5202 13323 2.443 0.577 0.117 0.027 92 8.5 inferiorparietal 5481 3771 11919 2.634 0.852 0.141 0.039 87 9.6 inferiortemporal 1437 899 2748 2.558 1.108 0.112 0.026 18 1.1 isthmuscingulate 8915 5720 14818 2.309 0.579 0.129 0.029 108 10.2 lateraloccipital 4894 3316 10139 2.731 0.768 0.147 0.051 83 11.2 lateralorbitofrontal 4335 2987 7103 2.219 0.654 0.146 0.037 58 6.6 lingual 2245 1492 5257 2.750 0.766 0.140 0.042 39 3.9 medialorbitofrontal 6830 4859 11792 2.254 0.767 0.127 0.032 84 10.0 middletemporal 1160 732 2346 2.806 0.668 0.079 0.016 6 0.7 parahippocampal 2643 1600 4957 2.903 0.555 0.112 0.026 23 2.9 paracentral 2465 1596 4307 2.566 0.610 0.113 0.027 26 2.9 parsopercularis 1215 796 2552 2.587 0.728 0.125 0.035 15 1.6 parsorbitalis 2766 1796 5490 2.580 0.598 0.121 0.026 44 3.0 parstriangularis 1915 1343 2079 1.688 0.455 0.137 0.031 20 2.3 pericalcarine 6581 4111 8849 2.006 0.641 0.110 0.024 58 6.8 postcentral 1906 1341 4787 3.003 0.827 0.146 0.038 31 2.8 posteriorcingulate 7424 4487 12306 2.610 0.648 0.109 0.027 68 8.6 precentral 6213 4215 12571 2.800 0.530 0.134 0.030 81 7.7 precuneus 1297 823 3012 3.056 0.740 0.113 0.022 14 1.2 rostralanteriorcingulate 8430 5263 14949 2.439 0.647 0.123 0.034 116 11.8 rostralmiddlefrontal 13588 8719 30478 3.070 0.759 0.120 0.033 158 18.9 superiorfrontal 8763 5541 15670 2.526 0.523 0.121 0.029 99 10.1 superiorparietal 8872 6175 16383 2.406 0.855 0.116 0.026 84 10.2 superiortemporal 5936 3772 8910 2.304 0.691 0.125 0.031 75 8.0 supramarginal 551 351 980 2.369 0.351 0.100 0.015 6 0.3 transversetemporal 3251 2226 7797 3.582 0.647 0.116 0.024 30 3.2 insula #----------------------------------------- #@# WM/GM Contrast lh Fri Aug 17 19:26:40 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts pctsurfcon --s SubJ01_ReoT13THip --lh-only Log file is /home/shize/freesurfer/SubJ01_ReoT13THip/scripts/pctsurfcon.log Fri Aug 17 19:26:40 EDT 2018 setenv SUBJECTS_DIR /home/shize/freesurfer cd /home/shize/freesurfer/SubJ01_ReoT13THip/scripts /usr/local/freesurfer-6.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer-6.0 mri_vol2surf --mov /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22633/lh.wm.mgh --regheader SubJ01_ReoT13THip --cortex srcvol = /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99950 0.00696 0.03084 -0.00005; 0.02939 -0.15488 0.98750 -0.00002; -0.01165 -0.98791 -0.15460 -0.00004; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label Reading surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 = 83576 Masking with /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label Writing to /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22633/lh.wm.mgh Dim: 145018 1 1 mri_vol2surf --mov /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22633/lh.gm.mgh --projfrac 0.3 --regheader SubJ01_ReoT13THip --cortex srcvol = /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99950 0.00696 0.03084 -0.00005; 0.02939 -0.15488 0.98750 -0.00002; -0.01165 -0.98791 -0.15460 -0.00004; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label Reading surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Done reading source surface Reading thickness /home/shize/freesurfer/SubJ01_ReoT13THip/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 = 96861 Masking with /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.cortex.label Writing to /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22633/lh.gm.mgh Dim: 145018 1 1 mri_concat /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22633/lh.wm.mgh /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22633/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.w-g.pct.mgh mri_segstats --in /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.w-g.pct.mgh --annot SubJ01_ReoT13THip lh aparc --sum /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.w-g.pct.mgh --annot SubJ01_ReoT13THip lh aparc --sum /home/shize/freesurfer/SubJ01_ReoT13THip/stats/lh.w-g.pct.stats --snr sysname Linux hostname dart machine x86_64 user shize UseRobust 0 Constructing seg from annotation Reading annotation /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.w-g.pct.mgh Vertex Area is 0.659122 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 Fri Aug 17 19:26:45 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/scripts pctsurfcon --s SubJ01_ReoT13THip --rh-only Log file is /home/shize/freesurfer/SubJ01_ReoT13THip/scripts/pctsurfcon.log Fri Aug 17 19:26:45 EDT 2018 setenv SUBJECTS_DIR /home/shize/freesurfer cd /home/shize/freesurfer/SubJ01_ReoT13THip/scripts /usr/local/freesurfer-6.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer-6.0 mri_vol2surf --mov /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22687/rh.wm.mgh --regheader SubJ01_ReoT13THip --cortex srcvol = /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99950 0.00696 0.03084 -0.00005; 0.02939 -0.15488 0.98750 -0.00002; -0.01165 -0.98791 -0.15460 -0.00004; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label Reading surface /home/shize/freesurfer/SubJ01_ReoT13THip/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 = 83772 Masking with /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label Writing to /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22687/rh.wm.mgh Dim: 147894 1 1 mri_vol2surf --mov /home/shize/freesurfer/SubJ01_ReoT13THip/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22687/rh.gm.mgh --projfrac 0.3 --regheader SubJ01_ReoT13THip --cortex srcvol = /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99950 0.00696 0.03084 -0.00005; 0.02939 -0.15488 0.98750 -0.00002; -0.01165 -0.98791 -0.15460 -0.00004; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label Reading surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Done reading source surface Reading thickness /home/shize/freesurfer/SubJ01_ReoT13THip/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 = 99554 Masking with /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.cortex.label Writing to /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22687/rh.gm.mgh Dim: 147894 1 1 mri_concat /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22687/rh.wm.mgh /home/shize/freesurfer/SubJ01_ReoT13THip/surf/tmp.pctsurfcon.22687/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.w-g.pct.mgh mri_segstats --in /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.w-g.pct.mgh --annot SubJ01_ReoT13THip rh aparc --sum /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.w-g.pct.mgh --annot SubJ01_ReoT13THip rh aparc --sum /home/shize/freesurfer/SubJ01_ReoT13THip/stats/rh.w-g.pct.stats --snr sysname Linux hostname dart machine x86_64 user shize UseRobust 0 Constructing seg from annotation Reading annotation /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.w-g.pct.mgh Vertex Area is 0.655209 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 Fri Aug 17 19:26:50 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 10398 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 4097 voxels changed to hypointensity... 14307 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fri Aug 17 19:27:08 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip mri_aparc2aseg --s SubJ01_ReoT13THip --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer-6.0/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: /usr/local/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/shize/freesurfer subject SubJ01_ReoT13THip outvol /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading lh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial Loading lh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading rh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial Loading rh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 8.10 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 30 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 99 rescaling Left_Cerebellum_Cortex from 60 --> 72 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 102 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 92 rescaling Third_Ventricle from 25 --> 39 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 68 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 26 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 94 rescaling Right_Cerebellum_Cortex from 59 --> 74 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 89 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 71 rescaling Right_Accumbens_area from 65 --> 74 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 507734 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 108 changed. pass 2: 10 changed. pass 3: 5 changed. pass 4: 3 changed. pass 5: 3 changed. pass 6: 3 changed. pass 7: 3 changed. pass 8: 3 changed. pass 9: 3 changed. pass 10: 3 changed. pass 11: 3 changed. nchanged = 0 Writing output aseg to /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Fri Aug 17 19:32:19 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip mri_aparc2aseg --s SubJ01_ReoT13THip --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer-6.0/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: /usr/local/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/shize/freesurfer subject SubJ01_ReoT13THip outvol /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading lh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial Loading lh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading rh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial Loading rh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 8.10 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 30 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 99 rescaling Left_Cerebellum_Cortex from 60 --> 72 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 102 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 92 rescaling Third_Ventricle from 25 --> 39 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 68 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 26 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 94 rescaling Right_Cerebellum_Cortex from 59 --> 74 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 89 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 71 rescaling Right_Accumbens_area from 65 --> 74 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 507805 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 108 changed. pass 2: 10 changed. pass 3: 5 changed. pass 4: 3 changed. pass 5: 3 changed. pass 6: 3 changed. pass 7: 3 changed. pass 8: 3 changed. pass 9: 3 changed. pass 10: 3 changed. pass 11: 3 changed. nchanged = 0 Writing output aseg to /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fri Aug 17 19:37:35 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip mri_aparc2aseg --s SubJ01_ReoT13THip --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer-6.0/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: /usr/local/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/shize/freesurfer subject SubJ01_ReoT13THip outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading lh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial Loading lh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading rh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial Loading rh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 8.10 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 30 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 99 rescaling Left_Cerebellum_Cortex from 60 --> 72 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 102 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 92 rescaling Third_Ventricle from 25 --> 39 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 68 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 26 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 94 rescaling Right_Cerebellum_Cortex from 59 --> 74 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 89 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 71 rescaling Right_Accumbens_area from 65 --> 74 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 507805 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 108 changed. pass 2: 10 changed. pass 3: 5 changed. pass 4: 3 changed. pass 5: 3 changed. pass 6: 3 changed. pass 7: 3 changed. pass 8: 3 changed. pass 9: 3 changed. pass 10: 3 changed. pass 11: 3 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Fri Aug 17 19:42:45 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Fri Aug 17 19:42:45 EDT 2018 setenv SUBJECTS_DIR /home/shize/freesurfer cd /home/shize/freesurfer/SubJ01_ReoT13THip/mri /usr/local/freesurfer-6.0/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 dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) 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 /home/shize/freesurfer/SubJ01_ReoT13THip/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 dart machine x86_64 user shize 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 Fri Aug 17 19:42:45 EDT 2018 Ended at Fri Aug 17 19:42:50 EDT 2018 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Fri Aug 17 19:42:50 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip 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 /usr/local/freesurfer-6.0/ASegStatsLUT.txt --subject SubJ01_ReoT13THip $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 /usr/local/freesurfer-6.0/ASegStatsLUT.txt --subject SubJ01_ReoT13THip sysname Linux hostname dart machine x86_64 user shize UseRobust 0 atlas_icv (eTIV) = 1520363 mm^3 (det: 1.281342 ) Computing euler number orig.nofix lheno = -112, rheno = -122 orig.nofix lhholes = 57, rhholes = 62 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 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 Fri Aug 17 19:44:38 EDT 2018 /home/shize/freesurfer/SubJ01_ReoT13THip mri_aparc2aseg --s SubJ01_ReoT13THip --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/shize/freesurfer subject SubJ01_ReoT13THip outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aparc+aseg.mgz Reading lh white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading lh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial Loading lh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading rh pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial Loading rh annotations from /home/shize/freesurfer/SubJ01_ReoT13THip/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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/ribbon.mgz Loading filled from /home/shize/freesurfer/SubJ01_ReoT13THip/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8283 vertices from left hemi Ripped 8238 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 /home/shize/freesurfer/SubJ01_ReoT13THip/mri/aseg.mgz Loading Ctx Seg File /home/shize/freesurfer/SubJ01_ReoT13THip/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 = 1007420 Used brute-force search on 447 voxels Fixing Parahip LH WM Found 14 clusters 0 k 4.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 23.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 11 k 1.000000 12 k 1.000000 13 k 1727.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1571.000000 1 k 1.000000 2 k 1.000000 3 k 30.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 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 SubJ01_ReoT13THip --surf-wm-vol --ctab /usr/local/freesurfer-6.0/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 SubJ01_ReoT13THip --surf-wm-vol --ctab /usr/local/freesurfer-6.0/WMParcStatsLUT.txt --etiv sysname Linux hostname dart machine x86_64 user shize UseRobust 0 atlas_icv (eTIV) = 1520363 mm^3 (det: 1.281342 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 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 /home/shize/freesurfer/SubJ01_ReoT13THip/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Aug 17 19:52:46 EDT 2018 mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4376 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 832 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8741 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 179 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 387 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6370 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 502 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6286 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 235 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4305 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 1901 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15490 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 736 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4917 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 1999 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 5421 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 946 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5587 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 2095 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10209 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2263 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1421 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 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 /home/shize/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2216 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1517 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2042 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2432 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1601 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 838 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7873 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2095 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 899 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 2050 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 592 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3997 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 937 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4271 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 569 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 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 /home/shize/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/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 145018 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 481 mri_label2label: Done mris_label2annot --s SubJ01_ReoT13THip --hemi lh --ctab /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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 /home/shize/freesurfer/SubJ01_ReoT13THip/label cmdline mris_label2annot --s SubJ01_ReoT13THip --hemi lh --ctab /usr/local/freesurfer-6.0/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 dart machine x86_64 user shize subject SubJ01_ReoT13THip hemi lh SUBJECTS_DIR /home/shize/freesurfer ColorTable /usr/local/freesurfer-6.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/shize/freesurfer/SubJ01_ReoT13THip/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 102791 unhit vertices Writing annot to /home/shize/freesurfer/SubJ01_ReoT13THip/label/lh.BA_exvivo.annot mris_label2annot --s SubJ01_ReoT13THip --hemi lh --ctab /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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 /home/shize/freesurfer/SubJ01_ReoT13THip/label cmdline mris_label2annot --s SubJ01_ReoT13THip --hemi lh --ctab /usr/local/freesurfer-6.0/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 dart machine x86_64 user shize subject SubJ01_ReoT13THip hemi lh SUBJECTS_DIR /home/shize/freesurfer ColorTable /usr/local/freesurfer-6.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/shize/freesurfer/SubJ01_ReoT13THip/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 121732 unhit vertices Writing annot to /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 255233 Total vertex volume 251778 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer-6.0/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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 1115 590 1360 1.900 0.536 0.117 0.039 14 1.6 BA1_exvivo 4580 2907 6627 2.359 0.670 0.102 0.024 35 4.2 BA2_exvivo 914 786 1213 1.917 0.535 0.154 0.029 9 1.0 BA3a_exvivo 2233 1480 2600 1.652 0.664 0.112 0.024 16 2.9 BA3b_exvivo 1579 903 3041 2.928 0.546 0.099 0.022 13 1.4 BA4a_exvivo 1220 910 2253 2.662 0.595 0.116 0.025 8 1.3 BA4p_exvivo 10213 6318 20879 3.013 0.820 0.111 0.032 88 13.5 BA6_exvivo 2469 1673 4402 2.541 0.635 0.118 0.033 25 3.5 BA44_exvivo 4549 2828 7960 2.613 0.664 0.123 0.037 53 7.1 BA45_exvivo 2898 1895 3756 1.777 0.569 0.135 0.036 43 4.5 V1_exvivo 7308 4716 10262 2.077 0.520 0.145 0.038 104 11.4 V2_exvivo 1710 1088 2708 2.300 0.461 0.121 0.025 17 1.7 MT_exvivo 696 436 1866 3.002 1.059 0.084 0.022 4 0.6 perirhinal_exvivo 743 492 1883 3.272 0.687 0.092 0.021 5 0.6 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 SubJ01_ReoT13THip lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 255233 Total vertex volume 251778 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer-6.0/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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 699 339 853 1.983 0.480 0.119 0.039 8 1.0 BA1_exvivo 1524 961 2066 2.154 0.524 0.089 0.018 7 1.1 BA2_exvivo 706 559 806 1.891 0.543 0.145 0.031 7 0.7 BA3a_exvivo 1176 848 1221 1.426 0.343 0.087 0.012 5 0.7 BA3b_exvivo 1430 844 2808 2.885 0.568 0.097 0.025 11 1.5 BA4a_exvivo 981 765 1799 2.579 0.560 0.128 0.026 7 1.0 BA4p_exvivo 5492 3245 10956 3.079 0.757 0.109 0.033 49 7.9 BA6_exvivo 1456 1023 2629 2.416 0.654 0.120 0.034 15 2.1 BA44_exvivo 1957 1141 3399 2.605 0.674 0.120 0.038 24 3.1 BA45_exvivo 3045 2016 4101 1.797 0.568 0.135 0.036 45 4.8 V1_exvivo 3651 2331 5039 2.046 0.531 0.160 0.047 63 7.1 V2_exvivo 434 289 833 2.416 0.436 0.132 0.029 6 0.5 MT_exvivo 357 227 946 2.863 1.093 0.067 0.017 1 0.3 perirhinal_exvivo 378 252 1039 3.305 0.910 0.080 0.015 1 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Fri Aug 17 19:56:47 EDT 2018 mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 253 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4215 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7006 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4070 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4708 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 606 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4661 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 1676 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13932 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 1319 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8231 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 1746 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7101 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 1395 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6122 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 3163 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11179 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 661 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1169 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 825 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 942 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2762 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1730 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2252 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1548 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1519 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 1050 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8009 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 145 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1157 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 377 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 823 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4055 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 1449 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4886 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 345 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 793 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/shize/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject SubJ01_ReoT13THip --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/shize/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SubJ01_ReoT13THip 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 /home/shize/freesurfer FREESURFER_HOME /usr/local/freesurfer-6.0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/shize/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white Reading target registration /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.sphere.reg Rescaling ... original radius = 100 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 147894 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 324 mri_label2label: Done mris_label2annot --s SubJ01_ReoT13THip --hemi rh --ctab /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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 /home/shize/freesurfer/SubJ01_ReoT13THip/label cmdline mris_label2annot --s SubJ01_ReoT13THip --hemi rh --ctab /usr/local/freesurfer-6.0/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 dart machine x86_64 user shize subject SubJ01_ReoT13THip hemi rh SUBJECTS_DIR /home/shize/freesurfer ColorTable /usr/local/freesurfer-6.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/shize/freesurfer/SubJ01_ReoT13THip/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 104060 unhit vertices Writing annot to /home/shize/freesurfer/SubJ01_ReoT13THip/label/rh.BA_exvivo.annot mris_label2annot --s SubJ01_ReoT13THip --hemi rh --ctab /usr/local/freesurfer-6.0/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 /usr/local/freesurfer-6.0/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 /home/shize/freesurfer/SubJ01_ReoT13THip/label cmdline mris_label2annot --s SubJ01_ReoT13THip --hemi rh --ctab /usr/local/freesurfer-6.0/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 dart machine x86_64 user shize subject SubJ01_ReoT13THip hemi rh SUBJECTS_DIR /home/shize/freesurfer ColorTable /usr/local/freesurfer-6.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/shize/freesurfer/SubJ01_ReoT13THip/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 124013 unhit vertices Writing annot to /home/shize/freesurfer/SubJ01_ReoT13THip/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 SubJ01_ReoT13THip rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 263885 Total vertex volume 260302 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer-6.0/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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 976 502 1451 2.187 0.488 0.126 0.043 13 1.6 BA1_exvivo 3128 2027 4021 2.076 0.513 0.112 0.022 26 2.8 BA2_exvivo 996 666 977 1.964 0.552 0.119 0.025 8 0.9 BA3a_exvivo 1864 1198 2084 1.622 0.457 0.097 0.018 13 1.5 BA3b_exvivo 1691 938 2895 2.733 0.611 0.095 0.023 11 1.8 BA4a_exvivo 1093 731 1649 2.357 0.627 0.099 0.019 6 0.8 BA4p_exvivo 9254 5526 18675 2.985 0.671 0.108 0.028 81 10.9 BA6_exvivo 3804 2530 7185 2.587 0.616 0.119 0.029 45 5.2 BA44_exvivo 5366 3267 10004 2.575 0.612 0.117 0.029 74 6.2 BA45_exvivo 3644 2417 5103 1.892 0.643 0.137 0.033 44 4.8 V1_exvivo 8615 5744 12776 2.130 0.556 0.148 0.036 121 12.9 V2_exvivo 2365 1551 3865 2.398 0.537 0.111 0.022 20 2.1 MT_exvivo 646 416 2283 3.632 0.733 0.114 0.047 7 1.2 perirhinal_exvivo 392 257 1044 3.212 0.652 0.094 0.034 3 0.4 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 SubJ01_ReoT13THip rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/shize/freesurfer/SubJ01_ReoT13THip/mri/wm.mgz... reading input surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... reading input pial surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.pial... reading input white surface /home/shize/freesurfer/SubJ01_ReoT13THip/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 263885 Total vertex volume 260302 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer-6.0/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) = 1520363 mm^3 (det: 1.281342 ) lhCtxGM: 249539.003 249252.000 diff= 287.0 pctdiff= 0.115 rhCtxGM: 259259.097 258722.000 diff= 537.1 pctdiff= 0.207 lhCtxWM: 254081.145 255153.000 diff=-1071.9 pctdiff=-0.422 rhCtxWM: 246630.397 247772.000 diff=-1141.6 pctdiff=-0.463 SubCortGMVol 65681.000 SupraTentVol 1095157.642 (1092433.000) diff=2724.642 pctdiff=0.249 SupraTentVolNotVent 1079305.642 (1076581.000) diff=2724.642 pctdiff=0.252 BrainSegVol 1246312.000 (1241952.000) diff=4360.000 pctdiff=0.350 BrainSegVolNotVent 1224624.000 (1223004.642) diff=1619.358 pctdiff=0.132 BrainSegVolNotVent 1224624.000 CerebellumVol 147813.000 VentChorVol 15852.000 3rd4th5thCSF 5836.000 CSFVol 1476.000, OptChiasmVol 230.000 MaskVol 1626746.000 626 304 905 2.121 0.495 0.117 0.047 8 1.1 BA1_exvivo 1687 1070 2125 1.921 0.477 0.097 0.016 11 1.1 BA2_exvivo 872 593 801 1.930 0.488 0.125 0.023 7 0.7 BA3a_exvivo 1417 921 1389 1.480 0.305 0.077 0.011 6 0.7 BA3b_exvivo 1152 540 2040 3.077 0.562 0.094 0.026 8 1.3 BA4a_exvivo 886 623 1296 2.231 0.532 0.097 0.017 4 0.7 BA4p_exvivo 6136 3628 11901 2.940 0.665 0.109 0.030 55 7.8 BA6_exvivo 875 598 1728 2.574 0.527 0.117 0.029 11 1.2 BA44_exvivo 1356 762 2378 2.557 0.535 0.126 0.033 21 2.0 BA45_exvivo 3420 2290 4570 1.855 0.604 0.135 0.032 40 4.4 V1_exvivo 4465 2944 6521 2.047 0.618 0.160 0.042 72 7.9 V2_exvivo 318 203 603 2.301 0.543 0.134 0.033 4 0.6 MT_exvivo 408 261 1320 3.537 0.743 0.106 0.052 5 0.9 perirhinal_exvivo 263 184 868 3.757 0.660 0.117 0.034 2 0.4 entorhinal_exvivo Linux dart 4.4.138-59-default #1 SMP Mon Jun 18 13:48:42 UTC 2018 (f0b8f6b) x86_64 x86_64 x86_64 GNU/Linux recon-all -s SubJ01_ReoT13THip exited with ERRORS at Fri Aug 17 20:00:52 EDT 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting